#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
CFAP74	85452	hgsc.bcm.edu	37	1	1887022	1887022	+	IGR	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:1887022A>G								TMEM52 (36310 upstream) : C1orf222 (32540 downstream)																							AAGGCCTAGGAAAATTCTCTA	0.537																																					p.S762P		Atlas-SNP	.											.	KIAA1751	92	.	0			c.T2284C						.						74.0	79.0	78.0					1																	1887022		1887	4091	5978	SO:0001628	intergenic_variant	85452	exon18			CCTAGGAAAATTC																													chr1.hg19:g.1887022A>G		95.0	0.0		179.0	8.0	NM_001080484		Missense_Mutation	SNP		hg19		.	.	.	.	.	.	.	.	.	.	A	9.318	1.057357	0.19907	.	.	ENSG00000142609	ENST00000270720	.	.	.	1.45	-1.37	0.09056	.	0.228496	0.26556	N	0.023701	T	0.15565	0.0375	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08452	-1.0721	9	0.87932	D	0	.	6.1345	0.20223	0.7187:0.0:0.2813:0.0	.	762	Q9C0B2	K1751_HUMAN	P	762	.	ENSP00000270720:S762P	S	-	1	0	C1orf222	1876882	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.572000	0.05881	-1.085000	0.03088	-1.489000	0.00976	TCC	.	.	0	0.537								
DDI2	84301	hgsc.bcm.edu	37	1	15959967	15959967	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:15959967A>G	ENST00000480945.1	+	4	710	c.539A>G	c.(538-540)cAg>cGg	p.Q180R		NM_032341.4	NP_115717.3	Q5TDH0	DDI2_HUMAN	DNA-damage inducible 1 homolog 2 (S. cerevisiae)	180							aspartic-type endopeptidase activity (GO:0004190)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|stomach(1)	17		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00327)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.03e-07)|COAD - Colon adenocarcinoma(227;4.48e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		GAGCAGCAGCAGGACCGAGCC	0.398																																					p.Q180R		Atlas-SNP	.											.	DDI2	38	.	0			c.A539G						.						171.0	205.0	194.0					1																	15959967		2203	4300	6503	SO:0001583	missense	84301	exon4			AGCAGCAGGACCG		CCDS30607.1	1p36.13	2010-05-04	2010-05-04		ENSG00000197312	ENSG00000197312			24578	protein-coding gene	gene with protein product			"""DDI1, DNA-damage inducible 1, homolog 2 (S. cerevisiae)"""				Standard	NM_032341		Approved	MGC14844	uc001awx.2	Q5TDH0	OTTHUMG00000002381	ENST00000480945.1:c.539A>G	chr1.hg19:g.15959967A>G	ENSP00000417748:p.Gln180Arg	67.0	0.0		118.0	5.0	NM_032341	A8KAE1|Q7RTZ0|Q9BRT1	Missense_Mutation	SNP	ENST00000480945.1	hg19	CCDS30607.1	.	.	.	.	.	.	.	.	.	.	A	11.20	1.568994	0.28003	.	.	ENSG00000197312	ENST00000480945	T	0.23348	1.91	5.64	5.64	0.86602	.	0.000000	0.85682	U	0.000000	T	0.16685	0.0401	N	0.21324	0.655	0.58432	D	0.999997	B	0.06786	0.001	B	0.10450	0.005	T	0.05402	-1.0887	10	0.05721	T	0.95	-10.7207	15.5299	0.75952	1.0:0.0:0.0:0.0	.	180	Q5TDH0	DDI2_HUMAN	R	180	ENSP00000417748:Q180R	ENSP00000449475:Q65R	Q	+	2	0	DDI2	15832554	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.890000	0.92477	2.147000	0.66899	0.533000	0.62120	CAG	.	.		0.398	DDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006826.1	NM_032341	
CELA3B	23436	hgsc.bcm.edu	37	1	22310726	22310726	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:22310726G>C	ENST00000337107.6	+	6	563	c.544G>C	c.(544-546)Gtg>Ctg	p.V182L		NM_007352.2	NP_031378.1	P08861	CEL3B_HUMAN	chymotrypsin-like elastase family, member 3B	182	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.V182M(1)		breast(2)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						CCTGCTGCCGGTGGTGGACTA	0.627																																					p.V182L		Atlas-SNP	.											CELA3B,NS,carcinoma,0,1	CELA3B	24	.	1	Substitution - Missense(1)	kidney(1)	c.G544C						.						82.0	79.0	80.0					1																	22310726		2203	4300	6503	SO:0001583	missense	23436	exon6			CTGCCGGTGGTGG	M18692	CCDS219.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000219073	ENSG00000219073	3.4.21.70		15945	protein-coding gene	gene with protein product	"""proteinase E"", ""elastase 1"", ""cholesterol-binding pancreatic protease"", ""pancreatic endopeptidase E"""		"""elastase 3B, pancreatic"""	ELA3B		2826474, 2460440	Standard	NM_007352		Approved	CBPP	uc001bfk.3	P08861	OTTHUMG00000002758	ENST00000337107.6:c.544G>C	chr1.hg19:g.22310726G>C	ENSP00000338369:p.Val182Leu	184.0	1.0		282.0	0.0	NM_007352	B2RE44|P11423|Q5VU28|Q5VU29|Q5VU30	Missense_Mutation	SNP	ENST00000337107.6	hg19	CCDS219.1	.	.	.	.	.	.	.	.	.	.	G	19.22	3.784915	0.70222	.	.	ENSG00000219073	ENST00000337107;ENST00000400277	D;D	0.89050	-2.46;-2.46	4.53	4.53	0.55603	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.88232	0.6381	N	0.11255	0.115	0.58432	D	0.999991	P	0.35363	0.497	P	0.55824	0.785	D	0.89830	0.3995	10	0.66056	D	0.02	-19.876	15.0932	0.72211	0.0:0.0:1.0:0.0	.	182	P08861	CEL3B_HUMAN	L	182;85	ENSP00000338369:V182L;ENSP00000383135:V85L	ENSP00000338369:V182L	V	+	1	0	CELA3B	22183313	1.000000	0.71417	0.976000	0.42696	0.313000	0.28021	5.358000	0.66064	2.232000	0.73038	0.650000	0.86243	GTG	.	.		0.627	CELA3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007797.1	NM_007352	
RPL11	6135	hgsc.bcm.edu	37	1	24022333	24022333	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:24022333A>G	ENST00000374550.3	+	5	487	c.442A>G	c.(442-444)Aca>Gca	p.T148A	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	148					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)|protein localization to nucleus (GO:0034504)|protein targeting (GO:0006605)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|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)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		GAAGCGCAGGACAGGCTGCAT	0.527																																					p.T148A		Atlas-SNP	.											.	RPL11	21	.	0			c.A442G						.						73.0	62.0	66.0					1																	24022333		2202	4299	6501	SO:0001583	missense	6135	exon5			CGCAGGACAGGCT	L05092	CCDS238.1	1p36.1-p35	2011-04-06			ENSG00000142676	ENSG00000142676		"""L ribosomal proteins"""	10301	protein-coding gene	gene with protein product		604175				9582194, 10343117	Standard	NM_000975		Approved	L11	uc001bhk.3	P62913	OTTHUMG00000002926	ENST00000374550.3:c.442A>G	chr1.hg19:g.24022333A>G	ENSP00000363676:p.Thr148Ala	88.0	0.0		165.0	7.0	NM_000975	P25121|P39026|Q8TDH2|Q9Y674	Missense_Mutation	SNP	ENST00000374550.3	hg19	CCDS238.1	.	.	.	.	.	.	.	.	.	.	A	16.93	3.257612	0.59321	.	.	ENSG00000142676	ENST00000374550;ENST00000458455	T;T	0.74632	-0.86;-0.86	5.7	5.7	0.88788	Ribosomal protein L5 domain (2);	0.102168	0.64402	D	0.000003	T	0.71065	0.3296	L	0.52823	1.66	0.50467	D	0.999872	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.66567	-0.5891	10	0.41790	T	0.15	-12.3044	15.9514	0.79843	1.0:0.0:0.0:0.0	.	147;148	P62913-2;P62913	.;RL11_HUMAN	A	148;146	ENSP00000363676:T148A;ENSP00000398888:T146A	ENSP00000363676:T148A	T	+	1	0	RPL11	23894920	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.779000	0.68948	2.171000	0.68590	0.482000	0.46254	ACA	.	.		0.527	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975	
YTHDF2	51441	hgsc.bcm.edu	37	1	29069727	29069727	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:29069727A>G	ENST00000373812.3	+	4	1307	c.945A>G	c.(943-945)ccA>ccG	p.P315P	YTHDF2_ENST00000542507.1_Silent_p.P315P|YTHDF2_ENST00000541996.1_Silent_p.P265P|YTHDF2_ENST00000478283.1_3'UTR	NM_016258.2	NP_057342.2	Q9Y5A9	YTHD2_HUMAN	YTH domain family, member 2	315	Localization to mRNA processing bodies (P-bodies).				humoral immune response (GO:0006959)|regulation of mRNA stability (GO:0043488)	cytoplasmic mRNA processing body (GO:0000932)	N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		ACAATAGCCCACCAGTGGCTC	0.577																																					p.P315P		Atlas-SNP	.											.	YTHDF2	47	.	0			c.A945G						.						47.0	48.0	47.0					1																	29069727		1985	4151	6136	SO:0001819	synonymous_variant	51441	exon4			TAGCCCACCAGTG	AF155095	CCDS41296.1, CCDS53287.1	1p35	2008-02-05	2004-11-16		ENSG00000198492	ENSG00000198492			31675	protein-coding gene	gene with protein product		610640	"""YTH domain family 2"""			10508479	Standard	NM_016258		Approved	HGRG8, NY-REN-2	uc021okf.1	Q9Y5A9	OTTHUMG00000003648	ENST00000373812.3:c.945A>G	chr1.hg19:g.29069727A>G		196.0	0.0		373.0	48.0	NM_016258	A6NKG4|A8K966|B4E1G7|D3DPM8|Q5VSZ9|Q8TDH0|Q9BUJ5	Silent	SNP	ENST00000373812.3	hg19	CCDS41296.1																																																																																			.	.		0.577	YTHDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010335.1	NM_016258	
PUM1	9698	hgsc.bcm.edu	37	1	31441332	31441332	+	Missense_Mutation	SNP	C	C	T	rs551662997		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:31441332C>T	ENST00000257075.5	-	11	1607	c.1514G>A	c.(1513-1515)cGt>cAt	p.R505H	PUM1_ENST00000423018.2_Missense_Mutation_p.R409H|PUM1_ENST00000424085.2_Missense_Mutation_p.R263H|PUM1_ENST00000373741.4_Missense_Mutation_p.R541H|PUM1_ENST00000373742.2_Missense_Mutation_p.R446H|PUM1_ENST00000426105.2_Missense_Mutation_p.R505H|SNORD85_ENST00000363311.1_RNA|PUM1_ENST00000440538.2_Missense_Mutation_p.R506H|PUM1_ENST00000490546.1_5'UTR|PUM1_ENST00000373747.3_Missense_Mutation_p.R506H	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	505	Ala-rich.|Gln-rich.				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)		GGCTCCTCCACGGAGAACCTG	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		19035	0.0		0.0	False		,,,				2504	0.001				p.R505H		Atlas-SNP	.											.	PUM1	107	.	0			c.G1514A						.						89.0	83.0	85.0					1																	31441332		2203	4300	6503	SO:0001583	missense	9698	exon11			CCTCCACGGAGAA	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.1514G>A	chr1.hg19:g.31441332C>T	ENSP00000257075:p.Arg505His	87.0	0.0		180.0	22.0	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	hg19	CCDS338.1	.	.	.	.	.	.	.	.	.	.	C	36	5.706510	0.96821	.	.	ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742	T;T;T;T;T;T;T;T	0.25579	1.94;1.92;2.04;2.04;1.99;2.02;2.24;1.79	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.52158	0.1717	M	0.61703	1.905	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;0.998;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.83275	0.996;0.976;0.996;0.989;0.996;0.996;0.996;0.996	T	0.47623	-0.9103	10	0.72032	D	0.01	-7.3314	20.3627	0.98863	0.0:1.0:0.0:0.0	.	446;409;541;506;505;505;506;505	B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5	.;.;.;.;PUM1_HUMAN;.;.;.	H	263;505;506;243;505;506;541;409;446	ENSP00000400141:R263H;ENSP00000257075:R505H;ENSP00000362852:R506H;ENSP00000391723:R505H;ENSP00000401777:R506H;ENSP00000362846:R541H;ENSP00000399440:R409H;ENSP00000362847:R446H	ENSP00000257075:R505H	R	-	2	0	PUM1	31213919	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.701000	0.84566	2.885000	0.99019	0.655000	0.94253	CGT	.	.		0.493	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1		
C1orf94	84970	hgsc.bcm.edu	37	1	34643426	34643426	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:34643426T>C	ENST00000488417.1	+	1	156	c.36T>C	c.(34-36)ggT>ggC	p.G12G	C1orf94_ENST00000373374.3_Intron|AC115286.1_ENST00000408126.1_RNA	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	12										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				TAGCCCTGGGTGGACAGAGGG	0.622																																					p.G12G		Atlas-SNP	.											.	C1orf94	156	.	0			c.T36C						.						9.0	11.0	10.0					1																	34643426		692	1587	2279	SO:0001819	synonymous_variant	84970	exon1			CCTGGGTGGACAG	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.36T>C	chr1.hg19:g.34643426T>C		80.0	0.0		119.0	5.0	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Silent	SNP	ENST00000488417.1	hg19	CCDS44108.1																																																																																			.	.		0.622	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	
MTF1	4520	hgsc.bcm.edu	37	1	38288327	38288327	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:38288327T>C	ENST00000373036.4	-	9	1373	c.1233A>G	c.(1231-1233)acA>acG	p.T411T		NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	411					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CTGAATTTCCTGTGGATGGCG	0.478																																					p.T411T		Atlas-SNP	.											.	MTF1	67	.	0			c.A1233G						.						71.0	79.0	76.0					1																	38288327		2203	4300	6503	SO:0001819	synonymous_variant	4520	exon9			ATTTCCTGTGGAT	BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786			7428	protein-coding gene	gene with protein product		600172				8065932	Standard	NM_005955		Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.1233A>G	chr1.hg19:g.38288327T>C		32.0	0.0		63.0	4.0	NM_005955	B2RAK6|Q96CB1	Silent	SNP	ENST00000373036.4	hg19	CCDS30676.1																																																																																			.	.		0.478	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012984.2	NM_005955	
MACF1	23499	hgsc.bcm.edu	37	1	39908507	39908507	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:39908507C>A	ENST00000372915.3	+	77	19010	c.18923C>A	c.(18922-18924)gCc>gAc	p.A6308D	MACF1_ENST00000539005.1_Missense_Mutation_p.A4220D|MACF1_ENST00000361689.2_Missense_Mutation_p.A4350D|MACF1_ENST00000564288.1_Missense_Mutation_p.A6409D|MACF1_ENST00000317713.7_Missense_Mutation_p.A4350D|MACF1_ENST00000289893.4_Missense_Mutation_p.A4852D|MACF1_ENST00000567887.1_Missense_Mutation_p.A6446D|MACF1_ENST00000545844.1_Missense_Mutation_p.A4350D			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6308			A -> T (in dbSNP:rs587404).		ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CGTTTGGAAGCCATGAACCAA	0.498																																					p.A4350D		Atlas-SNP	.											MACF1_ENST00000361689,NS,carcinoid-endocrine_tumour,0,2	MACF1	909	.	0			c.C13049A						.						63.0	54.0	57.0					1																	39908507		2203	4300	6503	SO:0001583	missense	23499	exon75			TGGAAGCCATGAA	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.18923C>A	chr1.hg19:g.39908507C>A	ENSP00000362006:p.Ala6308Asp	108.0	1.0		186.0	0.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.747|8.747	0.920321|0.920321	0.17982|0.17982	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.49432|.	1.41;0.78;1.41;1.41;1.41;0.78|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	0.195229|.	0.36066|.	N|.	0.002819|.	T|T	0.42086|0.42086	0.1187|0.1187	N|N	0.14661|0.14661	0.345|0.345	0.45183|0.45183	D|D	0.998192|0.998192	B;B|.	0.21821|.	0.061;0.061|.	B;B|.	0.28011|.	0.039;0.085|.	T|T	0.28902|0.28902	-1.0029|-1.0029	10|5	0.17369|.	T|.	0.5|.	.|.	12.8167|12.8167	0.57669|0.57669	0.1283:0.748:0.1237:0.0|0.1283:0.748:0.1237:0.0	.|.	6308;4350|.	Q9UPN3;F8W8Q1|.	MACF1_HUMAN;.|.	D|R	4350;6308;4350;4350;4220;4852|3353	ENSP00000439537:A4350D;ENSP00000362006:A6308D;ENSP00000354573:A4350D;ENSP00000313438:A4350D;ENSP00000444364:A4220D;ENSP00000289893:A4852D|.	ENSP00000289893:A4852D|.	A|S	+|+	2|3	0|2	MACF1|MACF1	39681094|39681094	0.999000|0.999000	0.42202|0.42202	0.996000|0.996000	0.52242|0.52242	0.979000|0.979000	0.70002|0.70002	3.775000|3.775000	0.55349|0.55349	2.752000|2.752000	0.94435|0.94435	0.655000|0.655000	0.94253|0.94253	GCC|AGC	.	.		0.498	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
MPL	4352	hgsc.bcm.edu	37	1	43812586	43812586	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:43812586A>G	ENST00000372470.3	+	8	1331	c.1289A>G	c.(1288-1290)gAa>gGa	p.E430G	MPL_ENST00000413998.2_Missense_Mutation_p.E430G	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	430	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	TACACAGGAGAAGGCCATCAG	0.562			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														p.E430G	NSCLC(52;534 1204 10016 41452 44427)	Atlas-SNP	.	yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	"""myeloproliferative leukemia virus oncogene, thrombopoietin receptor"""	yes	L	.	MPL	651	.	0			c.A1289G						.						51.0	47.0	48.0					1																	43812586		2203	4300	6503	SO:0001583	missense	4352	exon8			CAGGAGAAGGCCA	M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"""CD molecules"", ""Fibronectin type III domain containing"""	7217	protein-coding gene	gene with protein product		159530	"""myeloproliferative leukemia virus oncogene"""			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.1289A>G	chr1.hg19:g.43812586A>G	ENSP00000361548:p.Glu430Gly	39.0	0.0		85.0	4.0	NM_005373	Q5JUZ0	Missense_Mutation	SNP	ENST00000372470.3	hg19	CCDS483.1	.	.	.	.	.	.	.	.	.	.	a	19.68	3.872859	0.72180	.	.	ENSG00000117400	ENST00000372468;ENST00000372470;ENST00000413998	D;D	0.86627	-2.15;-2.15	5.3	5.3	0.74995	Fibronectin, type III (4);Long hematopoietin receptor, single chain, conserved site (1);Immunoglobulin-like fold (1);	1.167460	0.06230	N	0.688550	D	0.92410	0.7591	L	0.54323	1.7	0.30547	N	0.765804	D;D;D	0.89917	1.0;0.987;0.999	D;D;D	0.87578	0.998;0.912;0.979	T	0.82977	-0.0189	10	0.72032	D	0.01	-5.739	11.6301	0.51168	1.0:0.0:0.0:0.0	.	423;430;430	Q308M1;P40238;Q5JUY5	.;TPOR_HUMAN;.	G	430	ENSP00000361548:E430G;ENSP00000414004:E430G	ENSP00000361546:E430G	E	+	2	0	MPL	43585173	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.671000	0.61590	1.993000	0.58246	0.454000	0.30748	GAA	.	.		0.562	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373	
CDCP2	200008	hgsc.bcm.edu	37	1	54605317	54605317	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:54605317A>T	ENST00000371330.1	-	4	2073	c.1226T>A	c.(1225-1227)aTg>aAg	p.M409K	RP11-446E24.4_ENST00000525949.1_5'Flank|CDCP2_ENST00000530059.1_Intron	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	409						extracellular region (GO:0005576)				kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						AAGACCATTCATGGGGGGGGC	0.597																																					p.M409K		Atlas-SNP	.											.	CDCP2	52	.	0			c.T1226A						.						52.0	54.0	53.0					1																	54605317		2203	4300	6503	SO:0001583	missense	200008	exon4			CCATTCATGGGGG		CCDS588.2	1p32.3	2011-02-10			ENSG00000157211	ENSG00000157211			27297	protein-coding gene	gene with protein product		612320				12477932	Standard	NM_201546		Approved		uc001cwv.2	Q5VXM1	OTTHUMG00000155307	ENST00000371330.1:c.1226T>A	chr1.hg19:g.54605317A>T	ENSP00000360381:p.Met409Lys	104.0	0.0		137.0	6.0	NM_201546	Q6ZWJ3	Missense_Mutation	SNP	ENST00000371330.1	hg19	CCDS588.2	.	.	.	.	.	.	.	.	.	.	A	8.959	0.970117	0.18659	.	.	ENSG00000157211	ENST00000371330	T	0.26810	1.71	1.84	-3.68	0.04463	.	4.591200	0.01848	U	0.035750	T	0.12817	0.0311	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.16424	-1.0403	10	0.07644	T	0.81	0.2877	3.6798	0.08306	0.3471:0.3485:0.3044:0.0	.	409	Q5VXM1	CDCP2_HUMAN	K	409	ENSP00000360381:M409K	ENSP00000360381:M409K	M	-	2	0	CDCP2	54377905	0.000000	0.05858	0.001000	0.08648	0.097000	0.18754	-1.482000	0.02320	-1.230000	0.02561	-0.648000	0.03929	ATG	.	.		0.597	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546	
SRSF11	9295	hgsc.bcm.edu	37	1	70687464	70687464	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:70687464A>G	ENST00000370950.3	+	2	227	c.145A>G	c.(145-147)Atg>Gtg	p.M49V	SRSF11_ENST00000370951.1_Missense_Mutation_p.M49V|SRSF11_ENST00000436161.2_Missense_Mutation_p.M49V|SRSF11_ENST00000405432.1_Missense_Mutation_p.M49V|RP4-677H15.4_ENST00000422107.1_RNA|SRSF11_ENST00000454435.2_Missense_Mutation_p.M49V			Q05519	SRS11_HUMAN	serine/arginine-rich splicing factor 11	49	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|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)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(3)|ovary(2)|skin(1)	6						CTCTGAGCAGATGCGGACTCT	0.647																																					p.M49V		Atlas-SNP	.											.	SRSF11	68	.	0			c.A145G						.						80.0	81.0	81.0					1																	70687464		2203	4300	6503	SO:0001583	missense	9295	exon2			GAGCAGATGCGGA	M74002	CCDS647.1, CCDS53332.1	1p31.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000116754	ENSG00000116754		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10782	protein-coding gene	gene with protein product	"""SR splicing factor 11"""	602010	"""splicing factor, arginine/serine-rich 11"""	SFRS11		1896467, 20516191	Standard	NM_004768		Approved	p54, NET2	uc001des.3	Q05519	OTTHUMG00000009342	ENST00000370950.3:c.145A>G	chr1.hg19:g.70687464A>G	ENSP00000359988:p.Met49Val	52.0	0.0		80.0	4.0	NM_001190987	Q5T758|Q8IWE6	Missense_Mutation	SNP	ENST00000370950.3	hg19	CCDS647.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.919128	0.73098	.	.	ENSG00000116754	ENST00000370951;ENST00000370950;ENST00000405432;ENST00000454435;ENST00000395136;ENST00000436161	T;T;T;T;T;T	0.14893	2.47;2.47;2.47;2.47;2.47;2.47	5.29	5.29	0.74685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.25568	0.0622	L	0.47016	1.485	0.80722	D	1	P;P;P;P;P;P	0.44776	0.726;0.677;0.843;0.843;0.843;0.843	P;B;P;D;D;D	0.64506	0.762;0.322;0.893;0.926;0.926;0.926	T	0.01305	-1.1390	10	0.87932	D	0	.	14.8872	0.70579	1.0:0.0:0.0:0.0	.	49;49;49;49;49;49	B4DTC1;B4DWT1;Q05BU6;Q6PJB9;Q8IWE6;Q05519	.;.;.;.;.;SRS11_HUMAN	V	49	ENSP00000359989:M49V;ENSP00000359988:M49V;ENSP00000384357:M49V;ENSP00000411159:M49V;ENSP00000378568:M49V;ENSP00000405120:M49V	ENSP00000359988:M49V	M	+	1	0	SRSF11	70460052	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.573000	0.90759	1.995000	0.58328	0.379000	0.24179	ATG	.	.		0.647	SRSF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025889.1	NM_004768	
ODF2L	57489	hgsc.bcm.edu	37	1	86850466	86850466	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:86850466T>C	ENST00000359242.3	-	4	546	c.265A>G	c.(265-267)Aat>Gat	p.N89D	ODF2L_ENST00000317336.7_Missense_Mutation_p.N89D|ODF2L_ENST00000394731.1_5'UTR|ODF2L_ENST00000370566.3_Missense_Mutation_p.N89D|ODF2L_ENST00000370567.1_Missense_Mutation_p.N89D|ODF2L_ENST00000294678.2_Missense_Mutation_p.N89D	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	89						centrosome (GO:0005813)		p.N89H(1)		endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		ATCTTCAAATTCAATGCAGAA	0.279																																					p.N89D		Atlas-SNP	.											ODF2L,colon,carcinoma,0,1	ODF2L	53	.	1	Substitution - Missense(1)	large_intestine(1)	c.A265G						.						54.0	53.0	53.0					1																	86850466		2202	4284	6486	SO:0001583	missense	57489	exon4			TCAAATTCAATGC		CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.265A>G	chr1.hg19:g.86850466T>C	ENSP00000359600:p.Asn89Asp	47.0	0.0		63.0	3.0	NM_001184766	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Missense_Mutation	SNP	ENST00000359242.3	hg19	CCDS41354.2	.	.	.	.	.	.	.	.	.	.	T	0.634	-0.815961	0.02776	.	.	ENSG00000122417	ENST00000441121;ENST00000370566;ENST00000359242;ENST00000317336;ENST00000370567;ENST00000294678;ENST00000465959	T;T;T;T;T	0.22336	1.97;1.98;1.98;1.96;1.97	5.17	1.43	0.22495	.	2.459430	0.01409	N	0.013911	T	0.03390	0.0098	N	0.24115	0.695	0.09310	N	0.999998	B;B;B;P;P	0.43352	0.001;0.024;0.003;0.634;0.804	B;B;B;B;B	0.36719	0.003;0.012;0.005;0.085;0.231	T	0.19321	-1.0309	10	0.12103	T	0.63	-1.0E-4	4.0073	0.09607	0.3218:0.0891:0.0:0.5892	.	89;89;89;89;89	B4E037;Q9ULJ1-2;Q9ULJ1-4;Q9ULJ1-3;Q9ULJ1	.;.;.;.;ODF2L_HUMAN	D	89	ENSP00000359597:N89D;ENSP00000359600:N89D;ENSP00000320165:N89D;ENSP00000359598:N89D;ENSP00000294678:N89D	ENSP00000294678:N89D	N	-	1	0	ODF2L	86623054	0.001000	0.12720	0.022000	0.16811	0.364000	0.29643	0.762000	0.26503	0.048000	0.15891	0.451000	0.29950	AAT	.	.		0.279	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2		
CLCA2	9635	hgsc.bcm.edu	37	1	86900229	86900229	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:86900229A>G	ENST00000370565.4	+	6	935	c.773A>G	c.(772-774)cAc>cGc	p.H258R		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	258					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		GCAAGTACCCACAACCAAGAA	0.428																																					p.H258R	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.A773G						.						121.0	112.0	115.0					1																	86900229		2203	4300	6503	SO:0001583	missense	9635	exon6			GTACCCACAACCA		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.773A>G	chr1.hg19:g.86900229A>G	ENSP00000359596:p.His258Arg	75.0	0.0		122.0	5.0	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	hg19	CCDS708.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.558641	0.86231	.	.	ENSG00000137975	ENST00000370565	T	0.19938	2.11	6.17	6.17	0.99709	Chloride channel calcium-activated (1);	0.000000	0.85682	D	0.000000	T	0.48660	0.1512	M	0.91196	3.185	0.49687	D	0.999819	D	0.76494	0.999	D	0.71656	0.974	T	0.61143	-0.7122	10	0.87932	D	0	-9.4266	16.4837	0.84171	1.0:0.0:0.0:0.0	.	258	Q9UQC9	CLCA2_HUMAN	R	258	ENSP00000359596:H258R	ENSP00000359596:H258R	H	+	2	0	CLCA2	86672817	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.997000	0.76270	2.371000	0.80710	0.533000	0.62120	CAC	.	.		0.428	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
CLCA2	9635	hgsc.bcm.edu	37	1	86920818	86920818	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:86920818G>A	ENST00000370565.4	+	14	2602	c.2440G>A	c.(2440-2442)Gac>Aac	p.D814N		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	814					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TATCCAAGATGACTTTAACAA	0.318																																					p.D814N	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.G2440A						.						42.0	42.0	42.0					1																	86920818		2203	4300	6503	SO:0001583	missense	9635	exon14			CAAGATGACTTTA		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2440G>A	chr1.hg19:g.86920818G>A	ENSP00000359596:p.Asp814Asn	72.0	0.0		100.0	4.0	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	hg19	CCDS708.1	.	.	.	.	.	.	.	.	.	.	G	9.007	0.981460	0.18812	.	.	ENSG00000137975	ENST00000370565	T	0.02472	4.28	5.78	3.9	0.45041	.	0.266861	0.33854	N	0.004492	T	0.00906	0.0030	L	0.34521	1.04	0.33416	D	0.579243	P	0.49090	0.919	P	0.47015	0.534	T	0.26087	-1.0113	10	0.02654	T	1	-17.7009	5.6904	0.17827	0.3612:0.0:0.6388:0.0	.	814	Q9UQC9	CLCA2_HUMAN	N	814	ENSP00000359596:D814N	ENSP00000359596:D814N	D	+	1	0	CLCA2	86693406	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.061000	0.49963	1.444000	0.47605	0.585000	0.79938	GAC	.	.		0.318	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
LRRC8D	55144	hgsc.bcm.edu	37	1	90399470	90399470	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:90399470A>G	ENST00000337338.5	+	3	1250	c.843A>G	c.(841-843)ggA>ggG	p.G281G	LRRC8D_ENST00000394593.3_Silent_p.G281G	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	281					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		AAAAGGATGGAGAGCAGGCCA	0.428																																					p.G281G		Atlas-SNP	.											.	LRRC8D	78	.	0			c.A843G						.						40.0	40.0	40.0					1																	90399470		2203	4300	6503	SO:0001819	synonymous_variant	55144	exon3			GGATGGAGAGCAG	AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"""leucine rich repeat containing 5"""	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.843A>G	chr1.hg19:g.90399470A>G		68.0	0.0		111.0	5.0	NM_018103	D3DT29|Q6UWB2|Q9NVW3	Silent	SNP	ENST00000337338.5	hg19	CCDS726.1																																																																																			.	.		0.428	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103	
FNDC7	163479	hgsc.bcm.edu	37	1	109260509	109260509	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:109260509G>T	ENST00000370017.3	+	3	470	c.193G>T	c.(193-195)Ggg>Tgg	p.G65W	FNDC7_ENST00000271311.2_Missense_Mutation_p.G66W	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	65	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		GGCTGAAGACGGGGACACAGT	0.522																																					p.G65W		Atlas-SNP	.											FNDC7_ENST00000370017,colon,carcinoma,0,1	FNDC7	113	.	0			c.G193T						.						106.0	85.0	92.0					1																	109260509		692	1591	2283	SO:0001583	missense	163479	exon3			GAAGACGGGGACA		CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"""Fibronectin type III domain containing"""	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.193G>T	chr1.hg19:g.109260509G>T	ENSP00000359034:p.Gly65Trp	147.0	0.0		221.0	0.0	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	hg19	CCDS44185.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.186653	0.57909	.	.	ENSG00000143107	ENST00000370017;ENST00000271311	T;T	0.57273	0.41;0.41	5.78	5.78	0.91487	.	.	.	.	.	T	0.67767	0.2928	M	0.63428	1.95	0.44780	D	0.997789	D	0.89917	1.0	D	0.97110	1.0	T	0.69113	-0.5231	9	0.87932	D	0	.	20.0065	0.97435	0.0:0.0:1.0:0.0	.	65	E9PAZ5	.	W	65;66	ENSP00000359034:G65W;ENSP00000271311:G66W	ENSP00000271311:G66W	G	+	1	0	FNDC7	109062032	1.000000	0.71417	0.875000	0.34327	0.303000	0.27691	4.733000	0.62036	2.731000	0.93534	0.655000	0.94253	GGG	.	.		0.522	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
RPRD2	23248	hgsc.bcm.edu	37	1	150429791	150429791	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:150429791A>G	ENST00000369068.4	+	8	902	c.898A>G	c.(898-900)Aac>Gac	p.N300D	RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000401000.4_Missense_Mutation_p.N274D|RPRD2_ENST00000539519.1_Missense_Mutation_p.N274D	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	300						DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TAACCGAGTAAACAATTTAAA	0.408																																					p.N300D		Atlas-SNP	.											.	RPRD2	189	.	0			c.A898G						.						84.0	80.0	82.0					1																	150429791		1851	4098	5949	SO:0001583	missense	23248	exon8			CGAGTAAACAATT	BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"""KIAA0460"""	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.898A>G	chr1.hg19:g.150429791A>G	ENSP00000358064:p.Asn300Asp	68.0	0.0		83.0	4.0	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	hg19	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.802671	0.50315	.	.	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369068	T;T;T	0.45668	0.89;0.9;0.9	5.18	5.18	0.71444	.	0.247869	0.47852	D	0.000201	T	0.16514	0.0397	L	0.29908	0.895	0.28767	N	0.900554	B;P;P	0.36535	0.255;0.495;0.557	B;B;B	0.30716	0.053;0.119;0.116	T	0.08086	-1.0739	10	0.42905	T	0.14	-14.3218	15.4834	0.75545	1.0:0.0:0.0:0.0	.	274;300;274	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	D	274;274;300	ENSP00000383785:N274D;ENSP00000445482:N274D;ENSP00000358064:N300D	ENSP00000358064:N300D	N	+	1	0	RPRD2	148696415	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.933000	0.56545	2.291000	0.77112	0.519000	0.50382	AAC	.	.		0.408	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203	
BNIPL	149428	hgsc.bcm.edu	37	1	151019162	151019162	+	Nonstop_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:151019162A>G	ENST00000368931.3	+	10	1229	c.1073A>G	c.(1072-1074)tAg>tGg	p.*358W	C1orf56_ENST00000368926.5_5'Flank|BNIPL_ENST00000295294.7_Nonstop_Mutation_p.*276W	NM_138278.3	NP_612122.2	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein like	0					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|regulation of growth rate (GO:0040009)	cytosol (GO:0005829)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|endometrium(3)|large_intestine(1)|lung(4)|skin(1)	10	Lung SC(34;0.00471)|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)			GGAGGGACATAGCACAGGACT	0.498																																					p.X358W		Atlas-SNP	.											.	BNIPL	45	.	0			c.A1073G						.						125.0	109.0	115.0					1																	151019162		2203	4300	6503	SO:0001578	stop_lost	149428	exon10			GGACATAGCACAG	AF193056	CCDS978.2, CCDS53362.1	1q21.2	2008-02-05			ENSG00000163141	ENSG00000163141			16976	protein-coding gene	gene with protein product		611275				12681488, 11741952	Standard	NM_138278		Approved	BNIPl-1, BNIPL-2, PP753	uc001ewl.2	Q7Z465	OTTHUMG00000035157	ENST00000368931.3:c.1073A>G	chr1.hg19:g.151019162A>G	ENSP00000357927:p.*358Trpext*5	90.0	0.0		122.0	5.0	NM_138278	Q6DK43|Q8TCY7|Q8WYG2	Missense_Mutation	SNP	ENST00000368931.3	hg19	CCDS978.2	.	.	.	.	.	.	.	.	.	.	A	21.0	4.082695	0.76528	.	.	ENSG00000163141	ENST00000368931;ENST00000361277;ENST00000295294	.	.	.	5.85	0.493	0.16878	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.5308	0.04703	0.6024:0.1253:0.0785:0.1939	.	.	.	.	W	358;356;276	.	.	X	+	2	0	BNIPL	149285786	0.718000	0.27976	0.003000	0.11579	0.671000	0.39405	1.073000	0.30691	-0.150000	0.11195	0.533000	0.62120	TAG	.	.		0.498	BNIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085092.1	NM_138279	
SPRR2G	6706	hgsc.bcm.edu	37	1	153122487	153122487	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:153122487C>T	ENST00000368748.4	-	2	138	c.100G>A	c.(100-102)Gag>Aag	p.E34K		NM_001014291.3	NP_001014313.1	Q9BYE4	SPR2G_HUMAN	small proline-rich protein 2G	34	3 X 9 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)				endometrium(1)|lung(1)|skin(1)	3	all_lung(78;1.78e-30)|Lung NSC(65;7.29e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGGTAAGGCTCAGGGCACTTC	0.612																																					p.E34K		Atlas-SNP	.											.	SPRR2G	20	.	0			c.G100A						.						151.0	115.0	127.0					1																	153122487		2203	4300	6503	SO:0001583	missense	6706	exon2			AAGGCTCAGGGCA	AF333957	CCDS30868.1	1q21-q22	2008-02-05			ENSG00000159516	ENSG00000159516			11267	protein-coding gene	gene with protein product						8325635, 11279051	Standard	NM_001014291		Approved		uc009wod.2	Q9BYE4	OTTHUMG00000014399	ENST00000368748.4:c.100G>A	chr1.hg19:g.153122487C>T	ENSP00000357737:p.Glu34Lys	66.0	0.0		141.0	75.0	NM_001014291		Missense_Mutation	SNP	ENST00000368748.4	hg19	CCDS30868.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687891	0.29962	.	.	ENSG00000159516	ENST00000368748	T	0.43688	0.94	4.64	3.68	0.42216	.	.	.	.	.	T	0.40372	0.1114	.	.	.	0.09310	N	1	P	0.52061	0.95	P	0.55391	0.775	T	0.11446	-1.0587	8	0.87932	D	0	-15.1488	10.7082	0.45966	0.0:0.8074:0.1925:0.0	.	34	Q9BYE4	SPR2G_HUMAN	K	34	ENSP00000357737:E34K	ENSP00000357737:E34K	E	-	1	0	SPRR2G	151389111	0.000000	0.05858	0.055000	0.19348	0.062000	0.15995	-0.303000	0.08210	2.414000	0.81942	0.609000	0.83330	GAG	.	.		0.612	SPRR2G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040057.1		
SCAMP3	10067	hgsc.bcm.edu	37	1	155227359	155227359	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:155227359T>C	ENST00000302631.3	-	6	714	c.607A>G	c.(607-609)Atc>Gtc	p.I203V	SCAMP3_ENST00000355379.3_Missense_Mutation_p.I177V|FAM189B_ENST00000472550.1_5'Flank|FAM189B_ENST00000368368.3_5'Flank|FAM189B_ENST00000361361.2_5'Flank|SCAMP3_ENST00000472397.1_5'UTR|FAM189B_ENST00000350210.2_5'Flank	NM_005698.3	NP_005689.2	O14828	SCAM3_HUMAN	secretory carrier membrane protein 3	203					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|response to retinoic acid (GO:0032526)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|large_intestine(3)|lung(7)|ovary(4)|urinary_tract(1)	19	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			ACCCAGAGGATAGAAAGCCCA	0.562																																					p.I203V		Atlas-SNP	.											.	SCAMP3	33	.	0			c.A607G						.						73.0	74.0	74.0					1																	155227359		2203	4300	6503	SO:0001583	missense	10067	exon6			AGAGGATAGAAAG	AF005039	CCDS1105.1, CCDS1106.1	1q21	2013-02-21			ENSG00000116521	ENSG00000116521		"""Secretory carrier membrane proteins"""	10565	protein-coding gene	gene with protein product	"""Propin 1"""	606913		C1orf3		9331372, 9658162	Standard	NM_005698		Approved		uc001fjs.3	O14828	OTTHUMG00000035874	ENST00000302631.3:c.607A>G	chr1.hg19:g.155227359T>C	ENSP00000307275:p.Ile203Val	125.0	0.0		283.0	176.0	NM_005698	A9Z1W6|B1AVS6|O15128|Q96FR8|Q9BPY0	Missense_Mutation	SNP	ENST00000302631.3	hg19	CCDS1105.1	.	.	.	.	.	.	.	.	.	.	.	14.96	2.692259	0.48202	.	.	ENSG00000116521	ENST00000302631;ENST00000355379	T;T	0.20200	2.09;2.09	4.92	1.05	0.20165	.	0.167506	0.50627	D	0.000115	T	0.18635	0.0447	M	0.71036	2.16	0.46874	D	0.999233	P;B;B	0.39352	0.669;0.099;0.23	P;B;B	0.46320	0.512;0.3;0.149	T	0.04413	-1.0953	10	0.62326	D	0.03	-10.7064	12.6247	0.56623	0.0:0.0:0.315:0.685	.	203;177;203	Q6FHJ5;O14828-2;O14828	.;.;SCAM3_HUMAN	V	203;177	ENSP00000307275:I203V;ENSP00000347540:I177V	ENSP00000307275:I203V	I	-	1	0	SCAMP3	153493983	1.000000	0.71417	0.983000	0.44433	0.889000	0.51656	4.098000	0.57748	0.003000	0.14656	-0.396000	0.06452	ATC	.	.		0.562	SCAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087399.1	NM_005698	
SPTA1	6708	hgsc.bcm.edu	37	1	158641962	158641962	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:158641962T>C	ENST00000368147.4	-	11	1555	c.1375A>G	c.(1375-1377)Act>Gct	p.T459A		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	459					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AGCAGGGCAGTCCAGTTGTTG	0.378																																					p.T459A		Atlas-SNP	.											.	SPTA1	720	.	0			c.A1375G						.						97.0	90.0	92.0					1																	158641962		1902	4136	6038	SO:0001583	missense	6708	exon11			GGGCAGTCCAGTT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.1375A>G	chr1.hg19:g.158641962T>C	ENSP00000357129:p.Thr459Ala	69.0	0.0		97.0	4.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	0.117	-1.130297	0.01756	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.33654	1.4;1.4	5.0	-0.203	0.13204	.	0.554250	0.13585	N	0.377056	T	0.02119	0.0066	N	0.01081	-1.03	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45101	-0.9284	10	0.05620	T	0.96	.	5.6186	0.17446	0.2081:0.5034:0.0:0.2886	.	459	P02549	SPTA1_HUMAN	A	459	ENSP00000357130:T459A;ENSP00000357129:T459A	ENSP00000357129:T459A	T	-	1	0	SPTA1	156908586	0.000000	0.05858	0.039000	0.18376	0.012000	0.07955	-0.788000	0.04614	-0.158000	0.11040	-0.716000	0.03619	ACT	.	.		0.378	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
USP21	27005	hgsc.bcm.edu	37	1	161130443	161130443	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:161130443T>C	ENST00000289865.8	+	2	234	c.13T>C	c.(13-15)Tct>Cct	p.S5P	USP21_ENST00000368001.1_Missense_Mutation_p.S5P|RP11-297K8.2_ENST00000420498.1_RNA|USP21_ENST00000368002.3_Missense_Mutation_p.S5P	NM_012475.4	NP_036607.3	Q9UK80	UBP21_HUMAN	ubiquitin specific peptidase 21	5					histone deubiquitination (GO:0016578)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cysteine-type peptidase activity (GO:0008234)|metal ion binding (GO:0046872)|NEDD8-specific protease activity (GO:0019784)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|prostate(3)	29	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			GCCCCAGGCCTCTGAGCACCG	0.607																																					p.S5P		Atlas-SNP	.											.	USP21	63	.	0			c.T13C						.						47.0	50.0	49.0					1																	161130443		2203	4300	6503	SO:0001583	missense	27005	exon2			CAGGCCTCTGAGC	AF177758	CCDS30920.1	1q22	2008-04-11	2005-08-08		ENSG00000143258	ENSG00000143258		"""Ubiquitin-specific peptidases"""	12620	protein-coding gene	gene with protein product		604729	"""ubiquitin specific protease 21"""	USP23		12838346, 10799498	Standard	XM_006711273		Approved	USP16	uc010pkd.2	Q9UK80	OTTHUMG00000033154	ENST00000289865.8:c.13T>C	chr1.hg19:g.161130443T>C	ENSP00000289865:p.Ser5Pro	54.0	0.0		91.0	4.0	NM_012475	Q59H60|Q5BKT5|Q5VTW9|Q5VTX0|Q9BTV1|Q9HBS2|Q9NYN4	Missense_Mutation	SNP	ENST00000289865.8	hg19	CCDS30920.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.020729	0.54576	.	.	ENSG00000143258	ENST00000368002;ENST00000289865;ENST00000368001	T;T;T	0.21191	2.19;2.19;2.02	5.14	5.14	0.70334	.	0.474172	0.19882	N	0.103944	T	0.12902	0.0313	N	0.14661	0.345	0.33985	D	0.64838	D	0.65815	0.995	P	0.53185	0.72	T	0.05209	-1.0899	10	0.87932	D	0	.	14.0799	0.64914	0.0:0.0:0.0:1.0	.	5	Q9UK80	UBP21_HUMAN	P	5	ENSP00000356981:S5P;ENSP00000289865:S5P;ENSP00000356980:S5P	ENSP00000289865:S5P	S	+	1	0	USP21	159397067	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.621000	0.61233	2.155000	0.67459	0.459000	0.35465	TCT	.	.		0.607	USP21-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080801.1		
FMO4	2329	hgsc.bcm.edu	37	1	171310877	171310877	+	Missense_Mutation	SNP	T	T	C	rs569945058		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:171310877T>C	ENST00000367749.3	+	10	1906	c.1576T>C	c.(1576-1578)Tct>Cct	p.S526P		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	526					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					CCTACTTGCCTCTCTTCTACT	0.423																																					p.S526P	Pancreas(24;816 862 7754 7993 32832)	Atlas-SNP	.											.	FMO4	64	.	0			c.T1576C						.						48.0	47.0	47.0					1																	171310877		2203	4300	6503	SO:0001583	missense	2329	exon10			CTTGCCTCTCTTC	BC002780	CCDS1295.1	1q24.3	2011-08-04			ENSG00000076258	ENSG00000076258	1.14.13.8		3772	protein-coding gene	gene with protein product		136131		FMO2		8311461	Standard	NM_002022		Approved		uc001gho.3	P31512	OTTHUMG00000035506	ENST00000367749.3:c.1576T>C	chr1.hg19:g.171310877T>C	ENSP00000356723:p.Ser526Pro	79.0	0.0		150.0	6.0	NM_002022	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	hg19	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	T	18.73	3.686586	0.68157	.	.	ENSG00000076258	ENST00000367749	T	0.55760	0.5	5.76	3.44	0.39384	.	0.537430	0.18577	N	0.137151	T	0.38108	0.1028	L	0.45137	1.4	0.33823	D	0.629235	P	0.52463	0.953	P	0.53266	0.722	T	0.41016	-0.9532	10	0.62326	D	0.03	-11.6813	5.9074	0.19008	0.1346:0.0:0.3172:0.5482	.	526	P31512	FMO4_HUMAN	P	526	ENSP00000356723:S526P	ENSP00000356723:S526P	S	+	1	0	FMO4	169577501	0.298000	0.24417	0.840000	0.33206	0.839000	0.47603	0.296000	0.19083	0.961000	0.38030	0.533000	0.62120	TCT	.	.		0.423	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022	
LAMC1	3915	hgsc.bcm.edu	37	1	183109548	183109548	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:183109548G>A	ENST00000258341.4	+	27	4740	c.4483G>A	c.(4483-4485)Gct>Act	p.A1495T	RP11-181K3.4_ENST00000457852.3_RNA	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1495	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|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-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						GGCTTCACAGGCTGCTCAAGA	0.423																																					p.A1495T		Atlas-SNP	.											.	LAMC1	176	.	0			c.G4483A						.						52.0	54.0	53.0					1																	183109548		2203	4300	6503	SO:0001583	missense	3915	exon27			TCACAGGCTGCTC	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.4483G>A	chr1.hg19:g.183109548G>A	ENSP00000258341:p.Ala1495Thr	58.0	0.0		81.0	4.0	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	hg19	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.094192	0.56075	.	.	ENSG00000135862	ENST00000258341	T	0.78481	-1.18	5.31	5.31	0.75309	.	0.106561	0.64402	D	0.000006	T	0.64659	0.2618	N	0.24115	0.695	0.46901	D	0.999249	P	0.39282	0.666	B	0.33339	0.162	T	0.65899	-0.6056	10	0.31617	T	0.26	.	17.1486	0.86772	0.0:0.0:1.0:0.0	.	1495	P11047	LAMC1_HUMAN	T	1495	ENSP00000258341:A1495T	ENSP00000258341:A1495T	A	+	1	0	LAMC1	181376171	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.654000	0.74387	2.484000	0.83849	0.655000	0.94253	GCT	.	.		0.423	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
TPR	7175	hgsc.bcm.edu	37	1	186319458	186319458	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:186319458T>G	ENST00000367478.4	-	21	2969	c.2673A>C	c.(2671-2673)aaA>aaC	p.K891N	TPR_ENST00000474852.1_5'Flank	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	891					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|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)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TTAATAGTTCTTTTGTGTTAA	0.323			T	NTRK1	papillary thyroid																																p.K891N		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.A2673C						.						186.0	170.0	175.0					1																	186319458		1821	4081	5902	SO:0001583	missense	7175	exon21			TAGTTCTTTTGTG	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.2673A>C	chr1.hg19:g.186319458T>G	ENSP00000356448:p.Lys891Asn	138.0	0.0		234.0	108.0	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	hg19	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	T	18.66	3.671956	0.67928	.	.	ENSG00000047410	ENST00000367478	T	0.28454	1.61	5.88	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.47173	0.1431	M	0.65498	2.005	0.58432	D	0.999995	D	0.89917	1.0	D	0.69307	0.963	T	0.42616	-0.9441	10	0.46703	T	0.11	.	6.3881	0.21572	0.0:0.3132:0.0:0.6868	.	891	P12270	TPR_HUMAN	N	891	ENSP00000356448:K891N	ENSP00000356448:K891N	K	-	3	2	TPR	184586081	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	2.793000	0.47845	1.015000	0.39444	-0.366000	0.07423	AAA	.	.		0.323	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
C4BPA	722	hgsc.bcm.edu	37	1	207317164	207317164	+	Splice_Site	SNP	T	T	C	rs562681258		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:207317164T>C	ENST00000367070.3	+	11	1640	c.1446T>C	c.(1444-1446)gcT>gcC	p.A482A		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	482	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						CCATTACAGCTCTGTGTCGGA	0.363																																					p.A482A		Atlas-SNP	.											.	C4BPA	70	.	0			c.T1446C						.						144.0	133.0	136.0					1																	207317164		2203	4300	6503	SO:0001630	splice_region_variant	722	exon11			TACAGCTCTGTGT	M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"""complement component 4-binding protein, alpha"""	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.1445-1T>C	chr1.hg19:g.207317164T>C		94.0	0.0		126.0	6.0	NM_000715	Q5VVQ8	Silent	SNP	ENST00000367070.3	hg19	CCDS1477.1																																																																																			.	.		0.363	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3		Silent
MARK1	4139	hgsc.bcm.edu	37	1	220792019	220792019	+	Silent	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:220792019C>T	ENST00000366917.4	+	9	1097	c.831C>T	c.(829-831)ccC>ccT	p.P277P	MARK1_ENST00000366918.4_Silent_p.P255P|MARK1_ENST00000402574.1_Silent_p.P142P					MAP/microtubule affinity-regulating kinase 1											central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		ACCGTATTCCCTTCTATATGT	0.368																																					p.P277P		Atlas-SNP	.											.	MARK1	161	.	0			c.C831T						.						98.0	99.0	99.0					1																	220792019		2203	4300	6503	SO:0001819	synonymous_variant	4139	exon9			TATTCCCTTCTAT	AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.831C>T	chr1.hg19:g.220792019C>T		62.0	0.0		87.0	4.0	NM_018650		Silent	SNP	ENST00000366917.4	hg19	CCDS31029.2																																																																																			.	.		0.368	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1		
DISP1	84976	hgsc.bcm.edu	37	1	223177971	223177971	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:223177971C>A	ENST00000284476.6	+	8	3396	c.3232C>A	c.(3232-3234)Cgc>Agc	p.R1078S		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	1078					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		CTCTCTGAGTCGCGTGGGCTC	0.592																																					p.R1078S		Atlas-SNP	.											.	DISP1	145	.	0			c.C3232A						.						73.0	70.0	71.0					1																	223177971		2203	4300	6503	SO:0001583	missense	84976	exon10			CTGAGTCGCGTGG	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.3232C>A	chr1.hg19:g.223177971C>A	ENSP00000284476:p.Arg1078Ser	131.0	0.0		237.0	23.0	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	hg19	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.752065	0.89753	.	.	ENSG00000154309	ENST00000284476	T	0.15256	2.44	5.95	5.95	0.96441	.	0.190252	0.56097	D	0.000039	T	0.34366	0.0895	L	0.44542	1.39	0.80722	D	1	D	0.65815	0.995	D	0.66497	0.944	T	0.00400	-1.1763	10	0.23302	T	0.38	-38.7962	20.3719	0.98893	0.0:1.0:0.0:0.0	.	1078	Q96F81	DISP1_HUMAN	S	1078	ENSP00000284476:R1078S	ENSP00000284476:R1078S	R	+	1	0	DISP1	221244594	1.000000	0.71417	0.971000	0.41717	0.927000	0.56198	5.829000	0.69316	2.826000	0.97356	0.491000	0.48974	CGC	.	.		0.592	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
ZNF678	339500	hgsc.bcm.edu	37	1	227843072	227843072	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:227843072A>G	ENST00000343776.5	+	4	1466	c.1121A>G	c.(1120-1122)gAg>gGg	p.E374G	ZNF678_ENST00000608949.1_Intron|ZNF678_ENST00000397097.3_Missense_Mutation_p.E429G	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	374					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				CATACTGGAGAGAAACCCTAC	0.383																																					p.E429G		Atlas-SNP	.											.	ZNF678	137	.	0			c.A1286G						.						34.0	38.0	37.0					1																	227843072		2198	4294	6492	SO:0001583	missense	339500	exon4			CTGGAGAGAAACC	BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"""Zinc fingers, C2H2-type"", ""-"""	28652	protein-coding gene	gene with protein product	"""hypothetical protein MGC42493"""					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.1121A>G	chr1.hg19:g.227843072A>G	ENSP00000344828:p.Glu374Gly	45.0	0.0		81.0	4.0	NM_178549	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	hg19		.	.	.	.	.	.	.	.	.	.	A	14.94	2.685045	0.47991	.	.	ENSG00000181450	ENST00000343776;ENST00000397097	T;T	0.27557	1.66;1.66	1.5	1.5	0.22942	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40546	0.1121	L	0.56124	1.755	0.34319	D	0.686384	P	0.46656	0.882	P	0.56916	0.809	T	0.53158	-0.8478	9	0.72032	D	0.01	.	6.9712	0.24650	1.0:0.0:0.0:0.0	.	374	Q5SXM1	ZN678_HUMAN	G	374;429	ENSP00000344828:E374G;ENSP00000440403:E429G	ENSP00000344828:E374G	E	+	2	0	ZNF678	225909695	1.000000	0.71417	0.017000	0.16124	0.009000	0.06853	3.033000	0.49743	0.591000	0.29711	0.418000	0.28097	GAG	.	.		0.383	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549	
OBSCN	84033	hgsc.bcm.edu	37	1	228434396	228434396	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:228434396G>C	ENST00000422127.1	+	13	3969	c.3925G>C	c.(3925-3927)Gcg>Ccg	p.A1309P	OBSCN_ENST00000284548.11_Missense_Mutation_p.A1309P|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.A1401P	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1309	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)			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)				CATAGAGGCTGCGGGCTGCAT	0.637																																					p.A1401P		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,-2,2	OBSCN	2142	.	0			c.G4201C						.						78.0	83.0	81.0					1																	228434396		2055	4204	6259	SO:0001583	missense	84033	exon14			GAGGCTGCGGGCT	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.3925G>C	chr1.hg19:g.228434396G>C	ENSP00000409493:p.Ala1309Pro	189.0	0.0		366.0	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	.	.	.	.	.	.	.	.	.	.	.	2.050	-0.417834	0.04766	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.67523	-0.27;-0.27	5.01	-10.0	0.00425	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.320640	0.05001	N	0.469196	T	0.51346	0.1669	L	0.41415	1.275	0.09310	N	0.999999	P;P	0.40266	0.584;0.71	B;B	0.43623	0.425;0.18	T	0.54200	-0.8329	10	0.32370	T	0.25	.	2.8128	0.05446	0.1971:0.2173:0.3853:0.2003	.	1309;1309	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	P	1309	ENSP00000284548:A1309P;ENSP00000409493:A1309P	ENSP00000284548:A1309P	A	+	1	0	OBSCN	226501019	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.133000	0.15912	-3.413000	0.00168	-2.284000	0.00269	GCG	.	.		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
OBSCN	84033	hgsc.bcm.edu	37	1	228434468	228434468	+	Missense_Mutation	SNP	G	G	C	rs372487722		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:228434468G>C	ENST00000422127.1	+	13	4041	c.3997G>C	c.(3997-3999)Ggg>Cgg	p.G1333R	OBSCN_ENST00000284548.11_Missense_Mutation_p.G1333R|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.G1425R	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	158.0	0.0		293.0	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	
RYR2	6262	hgsc.bcm.edu	37	1	237711798	237711798	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:237711798C>G	ENST00000366574.2	+	26	3291	c.2974C>G	c.(2974-2976)Caa>Gaa	p.Q992E	RYR2_ENST00000360064.6_Missense_Mutation_p.Q990E|RYR2_ENST00000542537.1_Missense_Mutation_p.Q976E	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	992	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CACCCCATCACAAGAAGCAAT	0.473																																					p.Q992E		Atlas-SNP	.											RYR2,NS,carcinoma,0,1	RYR2	1273	.	0			c.C2974G						.						62.0	58.0	59.0					1																	237711798		1919	4129	6048	SO:0001583	missense	6262	exon26			CCATCACAAGAAG	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.2974C>G	chr1.hg19:g.237711798C>G	ENSP00000355533:p.Gln992Glu	142.0	0.0		248.0	0.0	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.320888	0.81469	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.91237	-2.81;-2.81;-2.81	5.51	5.51	0.81932	Ryanodine receptor Ryr (1);	0.000000	0.64402	D	0.000009	D	0.91845	0.7419	M	0.66939	2.045	0.80722	D	1	P	0.42827	0.791	P	0.44673	0.457	D	0.92329	0.5872	10	0.66056	D	0.02	.	19.7837	0.96428	0.0:1.0:0.0:0.0	.	992	Q92736	RYR2_HUMAN	E	992;990;976	ENSP00000355533:Q992E;ENSP00000353174:Q990E;ENSP00000443798:Q976E	ENSP00000353174:Q990E	Q	+	1	0	RYR2	235778421	1.000000	0.71417	0.964000	0.40570	0.548000	0.35241	7.645000	0.83430	2.738000	0.93877	0.655000	0.94253	CAA	.	.		0.473	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
ZNF670	93474	hgsc.bcm.edu	37	1	247200789	247200789	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:247200789T>G	ENST00000366503.2	-	4	1290	c.1132A>C	c.(1132-1134)Agt>Cgt	p.S378R		NM_001204220.1|NM_033213.4	NP_001191149.1|NP_149990.1	Q9BS34	ZN670_HUMAN	zinc finger protein 670	378					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00427)			CGAAGGGAACTGGAACAACTG	0.388																																					p.S378R		Atlas-SNP	.											.	ZNF670	52	.	0			c.A1132C						.						77.0	75.0	76.0					1																	247200789		2203	4300	6503	SO:0001583	missense	93474	exon4			GGGAACTGGAACA		CCDS31087.1	1q44	2013-01-08			ENSG00000135747	ENSG00000135747		"""Zinc fingers, C2H2-type"", ""-"""	28167	protein-coding gene	gene with protein product						12477932	Standard	NM_033213		Approved	MGC12466	uc001icd.2	Q9BS34	OTTHUMG00000040868	ENST00000366503.2:c.1132A>C	chr1.hg19:g.247200789T>G	ENSP00000355459:p.Ser378Arg	58.0	0.0		100.0	5.0	NM_033213		Missense_Mutation	SNP	ENST00000366503.2	hg19	CCDS31087.1	.	.	.	.	.	.	.	.	.	.	T	15.31	2.795187	0.50208	.	.	ENSG00000135747	ENST00000366503	T	0.01145	5.27	0.641	0.641	0.17759	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01661	0.0053	M	0.72118	2.19	0.09310	N	1	P	0.38020	0.615	B	0.34385	0.181	T	0.42137	-0.9469	9	0.54805	T	0.06	.	5.5163	0.16908	0.0:1.0E-4:0.0:0.9999	.	378	Q9BS34	ZN670_HUMAN	R	378	ENSP00000355459:S378R	ENSP00000355459:S378R	S	-	1	0	ZNF670	245267412	0.000000	0.05858	0.692000	0.30179	0.816000	0.46133	-1.011000	0.03652	0.508000	0.28173	0.383000	0.25322	AGT	.	.		0.388	ZNF670-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098183.3	NM_033213	
KIDINS220	57498	hgsc.bcm.edu	37	2	8872078	8872078	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:8872078A>G	ENST00000256707.3	-	30	4269	c.4088T>C	c.(4087-4089)cTc>cCc	p.L1363P	KIDINS220_ENST00000418530.1_Missense_Mutation_p.L1264P|KIDINS220_ENST00000473731.1_Missense_Mutation_p.L1344P|KIDINS220_ENST00000427284.1_Missense_Mutation_p.L1344P	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	1363					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CTGGGAATTGAGACTCGAAAG	0.373																																					p.L1363P		Atlas-SNP	.											.	KIDINS220	136	.	0			c.T4088C						.						80.0	76.0	78.0					2																	8872078		1824	4097	5921	SO:0001583	missense	57498	exon30			GAATTGAGACTCG	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"""Ankyrin repeat domain containing"""	29508	protein-coding gene	gene with protein product	"""ankyrin repeat-rich membrane-spanning protein"""	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.4088T>C	chr2.hg19:g.8872078A>G	ENSP00000256707:p.Leu1363Pro	80.0	0.0		109.0	5.0	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	hg19	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.254122	0.80135	.	.	ENSG00000134313	ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731	T;T;T;T	0.78595	-1.18;-1.19;-1.18;-1.19	5.86	5.86	0.93980	.	0.059447	0.64402	D	0.000002	D	0.82756	0.5106	L	0.34521	1.04	0.80722	D	1	D;D;D	0.76494	0.997;0.997;0.999	D;D;D	0.74023	0.979;0.954;0.982	D	0.84849	0.0812	10	0.87932	D	0	.	16.2644	0.82568	1.0:0.0:0.0:0.0	.	1264;1363;217	Q9ULH0-2;Q9ULH0;B4DG84	.;KDIS_HUMAN;.	P	1363;1344;1264;1344	ENSP00000256707:L1363P;ENSP00000411849:L1344P;ENSP00000414923:L1264P;ENSP00000418974:L1344P	ENSP00000256707:L1363P	L	-	2	0	KIDINS220	8789529	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.730000	0.91510	2.244000	0.73946	0.528000	0.53228	CTC	.	.		0.373	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738	
ASAP2	8853	hgsc.bcm.edu	37	2	9515031	9515031	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:9515031T>C	ENST00000281419.3	+	17	2044	c.1704T>C	c.(1702-1704)gaT>gaC	p.D568D	ASAP2_ENST00000315273.4_Silent_p.D568D	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	568					positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						CTTATGCTGATGGTGTGGATC	0.483																																					p.D568D		Atlas-SNP	.											.	ASAP2	91	.	0			c.T1704C						.						96.0	97.0	96.0					2																	9515031		2203	4300	6503	SO:0001819	synonymous_variant	8853	exon17			TGCTGATGGTGTG	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	2721	protein-coding gene	gene with protein product	"""centaurin, beta 3"""	603817	"""development and differentiation enhancing factor 2"""	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.1704T>C	chr2.hg19:g.9515031T>C		61.0	0.0		69.0	4.0	NM_001135191	D6W4Y8	Silent	SNP	ENST00000281419.3	hg19	CCDS1661.1																																																																																			.	.		0.483	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887	
ATP6V1C2	245973	hgsc.bcm.edu	37	2	10894153	10894153	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:10894153T>C	ENST00000272238.4	+	4	353	c.244T>C	c.(244-246)Tca>Cca	p.S82P	ATP6V1C2_ENST00000381661.3_Missense_Mutation_p.S82P	NM_001039362.1	NP_001034451.1	Q8NEY4	VATC2_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2	82					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of Wnt signaling pathway (GO:0030177)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|protein dimerization activity (GO:0046983)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)		CATGGAGGACTCAAAGGGGAA	0.547																																					p.S82P	NSCLC(188;1042 2136 10807 16813 47705)	Atlas-SNP	.											.	ATP6V1C2	73	.	0			c.T244C						.						73.0	52.0	59.0					2																	10894153		2203	4299	6502	SO:0001583	missense	245973	exon4			GAGGACTCAAAGG	AY039759	CCDS1674.1, CCDS42653.1	2p25.1	2010-04-21	2006-01-13		ENSG00000143882	ENSG00000143882		"""ATPases / V-type"""	18264	protein-coding gene	gene with protein product			"""ATPase, H+ transporting, lysosomal 42kD, V1 subunit C isoform 2"", ""ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C isoform 2"""			12384298	Standard	XR_426949		Approved	VMA5, ATP6C2	uc002ras.3	Q8NEY4	OTTHUMG00000090459	ENST00000272238.4:c.244T>C	chr2.hg19:g.10894153T>C	ENSP00000272238:p.Ser82Pro	99.0	0.0		106.0	6.0	NM_001039362	Q96EL8	Missense_Mutation	SNP	ENST00000272238.4	hg19	CCDS42653.1	.	.	.	.	.	.	.	.	.	.	T	12.07	1.826934	0.32329	.	.	ENSG00000143882	ENST00000272238;ENST00000381661	T;T	0.44881	0.91;0.91	5.72	1.45	0.22620	.	0.442738	0.25065	N	0.033416	T	0.36524	0.0970	L	0.49350	1.555	0.19300	N	0.99998	B;B	0.16802	0.002;0.019	B;B	0.25759	0.008;0.063	T	0.31943	-0.9925	10	0.48119	T	0.1	-4.0E-4	10.5921	0.45316	0.079:0.0:0.1955:0.7255	.	82;82	Q8NEY4-2;Q8NEY4	.;VATC2_HUMAN	P	82	ENSP00000272238:S82P;ENSP00000371077:S82P	ENSP00000272238:S82P	S	+	1	0	ATP6V1C2	10811604	0.013000	0.17824	0.015000	0.15790	0.836000	0.47400	0.354000	0.20146	-0.030000	0.13804	0.482000	0.46254	TCA	.	.		0.547	ATP6V1C2-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323555.1	NM_144583	
ATAD2B	54454	hgsc.bcm.edu	37	2	24033288	24033288	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:24033288A>G	ENST00000238789.5	-	18	2695	c.2352T>C	c.(2350-2352)gcT>gcC	p.A784A	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	784						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)					AAAGTGCTGGAGCAAGGTGAG	0.463																																					p.A784A		Atlas-SNP	.											.	ATAD2B	110	.	0			c.T2352C						.						89.0	91.0	91.0					2																	24033288		1964	4158	6122	SO:0001819	synonymous_variant	54454	exon18			TGCTGGAGCAAGG	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.2352T>C	chr2.hg19:g.24033288A>G		120.0	0.0		118.0	5.0	NM_001242338	B9ZVQ5|Q6ZNA6|Q8N9E7	Silent	SNP	ENST00000238789.5	hg19	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	A	11.06	1.529099	0.27387	.	.	ENSG00000119778	ENST00000381024	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	T	0.72003	0.3407	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71244	-0.4650	4	.	.	.	.	15.9297	0.79648	1.0:0.0:0.0:0.0	.	.	.	.	P	65	.	.	L	-	2	0	ATAD2B	23886792	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.887000	0.39698	2.219000	0.72066	0.533000	0.62120	CTC	.	.		0.463	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552	
EFR3B	22979	hgsc.bcm.edu	37	2	25354341	25354341	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:25354341A>G	ENST00000403714.3	+	9	1137	c.954A>G	c.(952-954)gaA>gaG	p.E318E	EFR3B_ENST00000402191.1_Silent_p.E283E|EFR3B_ENST00000401432.3_Silent_p.E318E|EFR3B_ENST00000405108.1_Silent_p.E170E	NM_014971.1	NP_055786.1	Q9Y2G0	EFR3B_HUMAN	EFR3 homolog B (S. cerevisiae)	318										endometrium(1)	1						TCTTGTCGGAAGCCGCGGTCA	0.692																																					p.E318E		Atlas-SNP	.											.	EFR3B	29	.	0			c.A954G						.						13.0	17.0	16.0					2																	25354341		692	1591	2283	SO:0001819	synonymous_variant	22979	exon9			GTCGGAAGCCGCG	AB023170	CCDS46231.1	2p24.1	2008-02-05	2007-11-14	2007-11-14	ENSG00000084710	ENSG00000084710			29155	protein-coding gene	gene with protein product			"""KIAA0953"""	KIAA0953		10231032	Standard	NM_014971		Approved	FLJ37871	uc010eyh.3	Q9Y2G0	OTTHUMG00000151988	ENST00000403714.3:c.954A>G	chr2.hg19:g.25354341A>G		46.0	0.0		76.0	4.0	NM_014971	B7WPL8|Q86XU6	Silent	SNP	ENST00000403714.3	hg19	CCDS46231.1																																																																																			.	.		0.692	EFR3B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324808.1	NM_014971	
ASXL2	55252	hgsc.bcm.edu	37	2	25966582	25966582	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:25966582T>C	ENST00000435504.4	-	13	2917	c.2624A>G	c.(2623-2625)gAt>gGt	p.D875G	ASXL2_ENST00000404843.1_Intron|ASXL2_ENST00000336112.4_Missense_Mutation_p.D847G|ASXL2_ENST00000272341.4_Intron			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	875					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)					CACACTAGCATCTGTCTTTGA	0.478																																					p.D875G		Atlas-SNP	.											.	ASXL2	217	.	0			c.A2624G						.						110.0	112.0	112.0					2																	25966582		2041	4181	6222	SO:0001583	missense	55252	exon12			CTAGCATCTGTCT			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.2624A>G	chr2.hg19:g.25966582T>C	ENSP00000391447:p.Asp875Gly	66.0	0.0		72.0	4.0	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	hg19		.	.	.	.	.	.	.	.	.	.	T	5.275	0.236102	0.10023	.	.	ENSG00000143970	ENST00000435504;ENST00000336112	T;T	0.21932	1.98;1.98	5.57	-2.32	0.06745	.	1.214150	0.05505	N	0.559175	T	0.09992	0.0245	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32693	-0.9897	10	0.87932	D	0	0.9626	3.481	0.07602	0.0847:0.4337:0.3188:0.1628	.	875	Q76L83	ASXL2_HUMAN	G	875;847	ENSP00000391447:D875G;ENSP00000337250:D847G	ENSP00000337250:D847G	D	-	2	0	ASXL2	25820086	0.000000	0.05858	0.045000	0.18777	0.321000	0.28281	-0.452000	0.06787	-0.876000	0.04017	0.460000	0.39030	GAT	.	.		0.478	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263	
CENPA	1058	hgsc.bcm.edu	37	2	27016084	27016084	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:27016084T>C	ENST00000335756.4	+	4	560	c.360T>C	c.(358-360)acT>acC	p.T120T	CENPA_ENST00000233505.8_Silent_p.T94T|CENPA_ENST00000475662.1_3'UTR	NM_001809.3	NP_001800.1	P49450	CENPA_HUMAN	centromere protein A	120	H3-like.				CENP-A containing nucleosome assembly (GO:0034080)|establishment of mitotic spindle orientation (GO:0000132)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|protein localization to chromosome, centromeric region (GO:0071459)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|condensed chromosome inner kinetochore (GO:0000939)|condensed nuclear chromosome kinetochore (GO:0000778)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(3)|lung(3)|urinary_tract(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCGAGTTACTCTCTTCCCAA	0.537																																					p.T120T	Pancreas(28;769 878 30250 30578 41330)	Atlas-SNP	.											.	CENPA	13	.	0			c.T360C						.						174.0	180.0	178.0					2																	27016084		2203	4300	6503	SO:0001819	synonymous_variant	1058	exon4			AGTTACTCTCTTC	U14518	CCDS1729.1, CCDS42662.1	2p23.3	2013-11-05	2006-06-16		ENSG00000115163	ENSG00000115163			1851	protein-coding gene	gene with protein product	"""centromere-specific histone"", ""histone H3-like centromeric protein A"""	117139	"""centromere protein A (17kD)"", ""centromere protein A, 17kDa"""				Standard	NM_001042426		Approved	CENP-A, CenH3	uc002rhr.3	P49450	OTTHUMG00000097073	ENST00000335756.4:c.360T>C	chr2.hg19:g.27016084T>C		82.0	0.0		97.0	5.0	NM_001809	D6W544|Q53T74|Q9BVW2	Silent	SNP	ENST00000335756.4	hg19	CCDS1729.1																																																																																			.	.		0.537	CENPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214190.2	NM_001809	
BRE	9577	hgsc.bcm.edu	37	2	28210936	28210936	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:28210936A>G	ENST00000342045.2	+	5	423	c.282A>G	c.(280-282)ccA>ccG	p.P94P	BRE_ENST00000379624.1_Silent_p.P94P|BRE_ENST00000379632.2_Silent_p.P94P|BRE_ENST00000361704.2_Silent_p.P94P|BRE_ENST00000603461.1_3'UTR|BRE_ENST00000344773.2_Silent_p.P94P	NM_199194.2	NP_954664.1			brain and reproductive organ-expressed (TNFRSF1A modulator)											NS(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(2)	23	Acute lymphoblastic leukemia(172;0.155)					AATTCCTGCCAGACCCCTCAG	0.413																																					p.P94P		Atlas-SNP	.											.	BRE	164	.	0			c.A282G						.						247.0	269.0	262.0					2																	28210936		2203	4300	6503	SO:0001819	synonymous_variant	9577	exon4			CCTGCCAGACCCC	AF015767	CCDS1763.1, CCDS1764.1, CCDS1765.1	2p23	2008-02-05			ENSG00000158019	ENSG00000158019			1106	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 4"""	610497				9737713, 7826398	Standard	NM_004899		Approved	BRCC45, BRCC4	uc002rls.3	Q9NXR7	OTTHUMG00000097831	ENST00000342045.2:c.282A>G	chr2.hg19:g.28210936A>G		45.0	0.0		60.0	4.0	NM_199191		Silent	SNP	ENST00000342045.2	hg19	CCDS1763.1																																																																																			.	.		0.413	BRE-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215114.1		
XDH	7498	hgsc.bcm.edu	37	2	31587070	31587070	+	Missense_Mutation	SNP	A	A	G	rs371816841		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:31587070A>G	ENST00000379416.3	-	24	2633	c.2585T>C	c.(2584-2586)gTg>gCg	p.V862A		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	862					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)	GAAGTGGTCCACCTCAAGAGC	0.542																																					p.V862A	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.T2585C						.						158.0	142.0	148.0					2																	31587070		2203	4300	6503	SO:0001583	missense	7498	exon24			TGGTCCACCTCAA	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.2585T>C	chr2.hg19:g.31587070A>G	ENSP00000368727:p.Val862Ala	93.0	0.0		90.0	4.0	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	hg19	CCDS1775.1	.	.	.	.	.	.	.	.	.	.	A	32	5.144226	0.94603	.	.	ENSG00000158125	ENST00000379416	T	0.39592	1.07	6.17	6.17	0.99709	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.000000	0.85682	D	0.000000	T	0.50888	0.1642	L	0.38953	1.18	0.80722	D	1	D	0.55800	0.973	P	0.57152	0.814	T	0.48636	-0.9018	10	0.52906	T	0.07	.	16.4957	0.84242	1.0:0.0:0.0:0.0	.	862	P47989	XDH_HUMAN	A	862	ENSP00000368727:V862A	ENSP00000368727:V862A	V	-	2	0	XDH	31440574	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	8.964000	0.93389	2.371000	0.80710	0.533000	0.62120	GTG	.	.		0.542	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
HEATR5B	54497	hgsc.bcm.edu	37	2	37217794	37217794	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:37217794T>C	ENST00000233099.5	-	34	5789	c.5694A>G	c.(5692-5694)ccA>ccG	p.P1898P	HEATR5B_ENST00000354531.2_Silent_p.P1809P	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1898						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				AACTTACCCATGGGTCGCATG	0.343																																					p.P1898P		Atlas-SNP	.											.	HEATR5B	185	.	0			c.A5694G						.						107.0	99.0	102.0					2																	37217794		2203	4300	6503	SO:0001819	synonymous_variant	54497	exon34			TACCCATGGGTCG	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.5694A>G	chr2.hg19:g.37217794T>C		98.0	0.0		96.0	4.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	hg19	CCDS33181.1																																																																																			.	.		0.343	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
CLHC1	130162	hgsc.bcm.edu	37	2	55445059	55445059	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:55445059T>C	ENST00000401408.1	-	4	598	c.253A>G	c.(253-255)Ata>Gta	p.I85V	CLHC1_ENST00000494539.1_Intron|AC012358.7_ENST00000366153.2_RNA|CLHC1_ENST00000407122.1_Missense_Mutation_p.I85V|CLHC1_ENST00000406437.2_Intron|CLHC1_ENST00000406076.1_5'UTR	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	85																	TCTTTCTTTATTGTCTCAATA	0.333																																					p.I85V		Atlas-SNP	.											.	.	.	.	0			c.A253G						.						105.0	103.0	104.0					2																	55445059		2203	4299	6502	SO:0001583	missense	130162	exon4			TCTTTATTGTCTC		CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 63"""	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.253A>G	chr2.hg19:g.55445059T>C	ENSP00000384869:p.Ile85Val	95.0	0.0		78.0	4.0	NM_152385	B2RDV1|Q53R93|Q8N403	Missense_Mutation	SNP	ENST00000401408.1	hg19	CCDS33201.1	.	.	.	.	.	.	.	.	.	.	T	9.958	1.221918	0.22457	.	.	ENSG00000162994	ENST00000407122;ENST00000401408	T;T	0.22336	1.96;1.96	5.96	-8.28	0.01013	.	0.862446	0.10359	N	0.684170	T	0.13670	0.0331	L	0.47716	1.5	0.48571	D	0.999674	B	0.06786	0.001	B	0.09377	0.004	T	0.09079	-1.0691	10	0.45353	T	0.12	-1.8293	7.3007	0.26418	0.0878:0.1115:0.5389:0.2618	.	85	Q8NHS4	CB063_HUMAN	V	85	ENSP00000385778:I85V;ENSP00000384869:I85V	ENSP00000384869:I85V	I	-	1	0	C2orf63	55298563	0.002000	0.14202	0.336000	0.25522	0.538000	0.34931	-0.372000	0.07504	-1.243000	0.02519	-1.139000	0.01908	ATA	.	.		0.333	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385	
TMEM17	200728	hgsc.bcm.edu	37	2	62729911	62729911	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:62729911C>T	ENST00000335390.5	-	2	330	c.119G>A	c.(118-120)aGt>aAt	p.S40N		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	40					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			CAGTGCCAAACTGGAGACCAT	0.358																																					p.S40N		Atlas-SNP	.											.	TMEM17	19	.	0			c.G119A						.						75.0	77.0	76.0					2																	62729911		2203	4300	6503	SO:0001583	missense	200728	exon2			GCCAAACTGGAGA		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.119G>A	chr2.hg19:g.62729911C>T	ENSP00000335094:p.Ser40Asn	207.0	0.0		199.0	9.0	NM_198276	Q53QP7|Q53R98	Missense_Mutation	SNP	ENST00000335390.5	hg19	CCDS1871.1	.	.	.	.	.	.	.	.	.	.	C	19.74	3.883387	0.72410	.	.	ENSG00000186889	ENST00000335390	T	0.54866	0.55	6.07	5.2	0.72013	.	0.190536	0.64402	N	0.000003	T	0.39733	0.1089	N	0.19112	0.55	0.54753	D	0.999985	B	0.16396	0.017	B	0.15052	0.012	T	0.15206	-1.0445	10	0.38643	T	0.18	-9.5686	15.2691	0.73686	0.0:0.933:0.0:0.067	.	40	Q86X19	TMM17_HUMAN	N	40	ENSP00000335094:S40N	ENSP00000335094:S40N	S	-	2	0	TMEM17	62583415	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.586000	0.60984	1.567000	0.49668	0.655000	0.94253	AGT	.	.		0.358	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276	
NAGK	55577	hgsc.bcm.edu	37	2	71302707	71302707	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:71302707T>C	ENST00000244204.6	+	7	664	c.602T>C	c.(601-603)cTc>cCc	p.L201P	NAGK_ENST00000443872.2_Missense_Mutation_p.L53P|NAGK_ENST00000455662.2_Missense_Mutation_p.L247P|NAGK_ENST00000443938.2_Missense_Mutation_p.L201P|NAGK_ENST00000418807.3_Missense_Mutation_p.L150P			Q9UJ70	NAGK_HUMAN	N-acetylglucosamine kinase	201					carbohydrate phosphorylation (GO:0046835)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|N-acetylglucosamine kinase activity (GO:0045127)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|urinary_tract(1)	18					N-Acetyl-D-glucosamine(DB00141)	CTAGGGATACTCACTCACCTG	0.498																																					p.L247P		Atlas-SNP	.											.	NAGK	34	.	0			c.T740C						.						94.0	90.0	91.0					2																	71302707		2203	4300	6503	SO:0001583	missense	55577	exon7			GGATACTCACTCA	AJ242910	CCDS33220.1, CCDS33220.2	2p24.3-p24.1	2008-02-05			ENSG00000124357	ENSG00000124357	2.7.1.59		17174	protein-coding gene	gene with protein product		606828				10824116	Standard	NM_017567		Approved	GNK	uc002shp.4	Q9UJ70	OTTHUMG00000153239	ENST00000244204.6:c.602T>C	chr2.hg19:g.71302707T>C	ENSP00000244204:p.Leu201Pro	118.0	0.0		96.0	4.0	NM_017567	B4DLZ5|Q53HD5|Q6IA84|Q9BS29|Q9BVP0|Q9NV37	Missense_Mutation	SNP	ENST00000244204.6	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.3|23.3	4.399084|4.399084	0.83120|0.83120	.|.	.|.	ENSG00000124357|ENSG00000124357	ENST00000244204;ENST00000455662;ENST00000531934;ENST00000418807;ENST00000529236|ENST00000443938	T;T;T|.	0.56444|.	1.09;1.05;0.46|.	5.35|5.35	5.35|5.35	0.76521|0.76521	ATPase, BadF/BadG/BcrA/BcrD type (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79644|0.79644	0.4481|0.4481	M|M	0.88310|0.88310	2.945|2.945	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.83031|0.83031	-0.0162|-0.0162	10|5	0.66056|.	D|.	0.02|.	-18.7632|-18.7632	13.5719|13.5719	0.61851|0.61851	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	201|.	Q9UJ70|.	NAGK_HUMAN|.	P|P	201;247;53;150;95|223	ENSP00000244204:L201P;ENSP00000389087:L247P;ENSP00000396070:L150P|.	ENSP00000244204:L201P|.	L|S	+|+	2|1	0|0	NAGK|NAGK	71156215|71156215	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.976000|0.976000	0.68499|0.68499	7.037000|7.037000	0.76531|0.76531	2.155000|2.155000	0.67459|0.67459	0.533000|0.533000	0.62120|0.62120	CTC|TCA	.	.		0.498	NAGK-032	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471889.1		
DYSF	8291	hgsc.bcm.edu	37	2	71801370	71801370	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:71801370T>C	ENST00000258104.3	+	30	3494	c.3217T>C	c.(3217-3219)Tct>Cct	p.S1073P	DYSF_ENST00000409744.1_Missense_Mutation_p.S1060P|DYSF_ENST00000394120.2_Missense_Mutation_p.S1074P|DYSF_ENST00000409582.3_Missense_Mutation_p.S1090P|DYSF_ENST00000409651.1_Missense_Mutation_p.S1105P|DYSF_ENST00000410020.3_Missense_Mutation_p.S1091P|DYSF_ENST00000429174.2_Missense_Mutation_p.S1073P|DYSF_ENST00000410041.1_Missense_Mutation_p.S1091P|DYSF_ENST00000413539.2_Missense_Mutation_p.S1104P|DYSF_ENST00000409366.1_Missense_Mutation_p.S1074P|DYSF_ENST00000409762.1_Missense_Mutation_p.S1090P	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1073	Arg-rich.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GGAGTACGCCTCTCTTTTTGG	0.667																																					p.S1105P		Atlas-SNP	.											.	DYSF	536	.	0			c.T3313C						.						68.0	80.0	76.0					2																	71801370		2203	4300	6503	SO:0001583	missense	8291	exon31			TACGCCTCTCTTT	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.3217T>C	chr2.hg19:g.71801370T>C	ENSP00000258104:p.Ser1073Pro	66.0	0.0		97.0	4.0	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.398940	0.83120	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.83837	-1.76;-1.77;-1.77;-1.77;-1.77;-1.76;-1.77;-1.77;-1.77;-1.77;-1.77	5.6	4.41	0.53225	Ferlin/Peroxisome membrane (1);	0.062797	0.64402	D	0.000003	D	0.86322	0.5905	L	0.48642	1.525	0.41765	D	0.989734	D;D;D;D;D;D;D;P;D;B;B;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.746;1.0;0.017;0.313;0.999;1.0;1.0	D;D;D;D;D;D;D;P;D;B;B;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.994;0.991;0.994;0.535;0.999;0.054;0.261;0.999;0.999;0.998	D	0.83801	0.0236	10	0.33141	T	0.24	-14.8294	10.1355	0.42704	0.1498:0.0:0.0:0.8502	.	1105;1091;1074;1060;1091;1060;1090;1059;1104;1090;1073;1059;1074;1073	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	P	1104;1090;1090;1073;1073;1105;1074;1060;1074;1091;1091	ENSP00000407046:S1104P;ENSP00000387137:S1090P;ENSP00000386547:S1090P;ENSP00000398305:S1073P;ENSP00000258104:S1073P;ENSP00000386683:S1105P;ENSP00000377678:S1074P;ENSP00000386285:S1060P;ENSP00000386512:S1074P;ENSP00000386881:S1091P;ENSP00000386617:S1091P	ENSP00000258104:S1073P	S	+	1	0	DYSF	71654878	1.000000	0.71417	0.997000	0.53966	0.972000	0.66771	7.661000	0.83786	0.907000	0.36646	0.528000	0.53228	TCT	.	.		0.667	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
WDR54	84058	hgsc.bcm.edu	37	2	74652051	74652051	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:74652051T>C	ENST00000348227.4	+	7	672	c.584T>C	c.(583-585)gTc>gCc	p.V195A	WDR54_ENST00000461531.1_3'UTR|WDR54_ENST00000409791.1_Missense_Mutation_p.V143A	NM_032118.2	NP_115494.1	Q9H977	WDR54_HUMAN	WD repeat domain 54	195										breast(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9						TTGCTGTGTGTCTGGCGGTCA	0.537																																					p.V195A		Atlas-SNP	.											.	WDR54	17	.	0			c.T584C						.						236.0	186.0	203.0					2																	74652051		2203	4300	6503	SO:0001583	missense	84058	exon7			TGTGTGTCTGGCG	AK023015	CCDS1940.1	2p13.1	2013-01-09			ENSG00000005448	ENSG00000005448		"""WD repeat domain containing"""	25770	protein-coding gene	gene with protein product						12477932	Standard	NM_032118		Approved	FLJ12953	uc002slb.3	Q9H977	OTTHUMG00000129951	ENST00000348227.4:c.584T>C	chr2.hg19:g.74652051T>C	ENSP00000006526:p.Val195Ala	186.0	0.0		204.0	11.0	NM_032118	D6W5I3|Q53H85|Q86V45	Missense_Mutation	SNP	ENST00000348227.4	hg19	CCDS1940.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.433301	0.83776	.	.	ENSG00000005448	ENST00000409791;ENST00000348227	T;T	0.56776	0.44;0.44	5.13	5.13	0.70059	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.070433	0.56097	D	0.000025	T	0.58323	0.2114	L	0.47716	1.5	0.42214	D	0.991828	D	0.60575	0.988	P	0.54759	0.76	T	0.62863	-0.6764	10	0.72032	D	0.01	-20.9254	12.5647	0.56304	0.0:0.0:0.0:1.0	.	195	Q9H977	WDR54_HUMAN	A	143;195	ENSP00000387236:V143A;ENSP00000006526:V195A	ENSP00000006526:V195A	V	+	2	0	WDR54	74505559	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.196000	0.72094	2.158000	0.67659	0.459000	0.35465	GTC	.	.		0.537	WDR54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252213.1	NM_032118	
DNAH6	1768	hgsc.bcm.edu	37	2	84954804	84954804	+	Silent	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:84954804C>T	ENST00000237449.6	+	60	9992	c.9984C>T	c.(9982-9984)acC>acT	p.T3328T	DNAH6_ENST00000389394.3_Silent_p.T3328T			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	3328					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TGTTCAATACCACCATTGAAA	0.393																																					p.T3328T		Atlas-SNP	.											.	DNAH6	194	.	0			c.C9984T						.						103.0	84.0	90.0					2																	84954804		692	1591	2283	SO:0001819	synonymous_variant	1768	exon61			CAATACCACCATT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.9984C>T	chr2.hg19:g.84954804C>T		222.0	0.0		192.0	65.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.393	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
RETSAT	54884	hgsc.bcm.edu	37	2	85578072	85578072	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:85578072T>C	ENST00000295802.4	-	3	540	c.428A>G	c.(427-429)cAg>cGg	p.Q143R	RETSAT_ENST00000263854.6_Missense_Mutation_p.Q143R|RETSAT_ENST00000457495.2_Missense_Mutation_p.Q82R	NM_017750.3	NP_060220.3	Q6NUM9	RETST_HUMAN	retinol saturase (all-trans-retinol 13,14-reductase)	143					oxidation-reduction process (GO:0055114)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	all-trans-retinol 13,14-reductase activity (GO:0051786)|oxidoreductase activity (GO:0016491)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	30					Vitamin A(DB00162)	CCAGTCCAGCTGCCCTTCAGT	0.517																																					p.Q143R		Atlas-SNP	.											.	RETSAT	56	.	0			c.A428G						.						70.0	68.0	69.0					2																	85578072		2203	4300	6503	SO:0001583	missense	54884	exon3			TCCAGCTGCCCTT	AK075261	CCDS1972.1	2p11.2	2008-02-05			ENSG00000042445	ENSG00000042445	1.3.99.23		25991	protein-coding gene	gene with protein product						12975309, 15358783	Standard	NM_017750		Approved	FLJ20296	uc002spd.3	Q6NUM9	OTTHUMG00000154611	ENST00000295802.4:c.428A>G	chr2.hg19:g.85578072T>C	ENSP00000295802:p.Gln143Arg	191.0	0.0		158.0	7.0	NM_017750	A6NIK3|Q53R95|Q53SA9|Q6UX05|Q8N2H5|Q96FA4|Q9NXE5	Missense_Mutation	SNP	ENST00000295802.4	hg19	CCDS1972.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	33|33	5.205535|5.205535	0.95033|0.95033	.|.	.|.	ENSG00000042445|ENSG00000042445	ENST00000295802;ENST00000263854;ENST00000457495|ENST00000409984	T;T|.	0.58358|.	2.0;0.34|.	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77658|0.77658	0.4163|0.4163	M|M	0.83384|0.83384	2.64|2.64	0.58432|0.58432	D|D	0.999999|0.999999	P;P|.	0.46784|.	0.537;0.884|.	B;B|.	0.43155|.	0.236;0.41|.	T|T	0.79460|0.79460	-0.1794|-0.1794	9|5	.|.	.|.	.|.	-25.9613|-25.9613	14.4967|14.4967	0.67694|0.67694	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	82;143|.	G5E9N3;Q6NUM9|.	.;RETST_HUMAN|.	R|G	143;143;82|82	ENSP00000295802:Q143R;ENSP00000405040:Q82R|.	.|.	Q|S	-|-	2|1	0|0	RETSAT|RETSAT	85431583|85431583	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.914000|7.914000	0.87478|0.87478	2.311000|2.311000	0.77944|0.77944	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.		0.517	RETSAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252489.1	NM_017750	
MRPS5	64969	hgsc.bcm.edu	37	2	95767468	95767468	+	Splice_Site	SNP	C	C	A	rs199914429		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:95767468C>A	ENST00000272418.2	-	8	972	c.764G>T	c.(763-765)gGt>gTt	p.G255V		NM_031902.3	NP_114108.1	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	255	S5 DRBM. {ECO:0000255|PROSITE- ProRule:PRU00268}.				translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						AATAGAAAAACCTTTAAACAA	0.323																																					p.G255V		Atlas-SNP	.											.	MRPS5	52	.	0			c.G764T						.						36.0	34.0	35.0					2																	95767468		2202	4299	6501	SO:0001630	splice_region_variant	64969	exon8			GAAAAACCTTTAA	AB049940	CCDS2010.1	2p11.2-q11.2	2012-09-13			ENSG00000144029	ENSG00000144029		"""Mitochondrial ribosomal proteins / small subunits"""	14498	protein-coding gene	gene with protein product	"""mitochondrial 28S ribosomal protein S5"""	611972					Standard	NM_031902		Approved	MRP-S5, S5mt	uc002sub.3	P82675	OTTHUMG00000130394	ENST00000272418.2:c.764-1G>T	chr2.hg19:g.95767468C>A		91.0	0.0		110.0	23.0	NM_031902	Q4ZFY5|Q96LJ6|Q9BWI4|Q9BYC4	Missense_Mutation	SNP	ENST00000272418.2	hg19	CCDS2010.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.319758	0.60524	.	.	ENSG00000144029	ENST00000272418	.	.	.	5.32	5.32	0.75619	Ribosomal protein S5, N-terminal, conserved site (1);Ribosomal protein S5, N-terminal (2);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.88347	0.6412	H	0.98027	4.13	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92102	0.5689	9	0.87932	D	0	.	14.8467	0.70264	0.0:1.0:0.0:0.0	.	255	P82675	RT05_HUMAN	V	255	.	ENSP00000272418:G255V	G	-	2	0	MRPS5	95131195	1.000000	0.71417	1.000000	0.80357	0.342000	0.28953	5.298000	0.65710	2.634000	0.89283	0.591000	0.81541	GGT	.	C|1.000;G|0.000		0.323	MRPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252772.1	NM_031902	Missense_Mutation
IL18RAP	8807	hgsc.bcm.edu	37	2	103067460	103067460	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:103067460A>G	ENST00000264260.2	+	11	1952	c.1363A>G	c.(1363-1365)Aga>Gga	p.R455G	IL18RAP_ENST00000409369.1_Missense_Mutation_p.R313G	NM_003853.2	NP_003844.1	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	455	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(4)	37						TTTGCTTGAAAGAGATGTGGC	0.423																																					p.R455G		Atlas-SNP	.											.	IL18RAP	102	.	0			c.A1363G						.						84.0	85.0	85.0					2																	103067460		2203	4300	6503	SO:0001583	missense	8807	exon11			CTTGAAAGAGATG	AF077346	CCDS2061.1	2q12.1	2013-01-11			ENSG00000115607	ENSG00000115607		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5989	protein-coding gene	gene with protein product		604509				9792649	Standard	XM_005264034		Approved	AcPL, CD218b	uc002tbx.3	O95256	OTTHUMG00000130777	ENST00000264260.2:c.1363A>G	chr2.hg19:g.103067460A>G	ENSP00000264260:p.Arg455Gly	59.0	0.0		77.0	4.0	NM_003853	B2RPJ3|Q3KPE7|Q3KPE8|Q53TT4|Q53TU5	Missense_Mutation	SNP	ENST00000264260.2	hg19	CCDS2061.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.008323	0.75046	.	.	ENSG00000115607	ENST00000264260;ENST00000409369	T;T	0.12147	2.71;2.71	5.66	3.2	0.36748	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.000000	0.64402	D	0.000002	T	0.43344	0.1243	M	0.89904	3.07	0.46078	D	0.99885	D	0.89917	1.0	D	0.91635	0.999	T	0.50259	-0.8849	10	0.87932	D	0	.	12.928	0.58270	0.7721:0.2279:0.0:0.0	.	455	O95256	I18RA_HUMAN	G	455;313	ENSP00000264260:R455G;ENSP00000387201:R313G	ENSP00000264260:R455G	R	+	1	2	IL18RAP	102433892	1.000000	0.71417	0.975000	0.42487	0.958000	0.62258	5.769000	0.68865	0.383000	0.24910	0.528000	0.53228	AGA	.	.		0.423	IL18RAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253291.2	NM_003853	
GCC2	9648	hgsc.bcm.edu	37	2	109086500	109086500	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:109086500G>A	ENST00000309863.6	+	6	1429	c.715G>A	c.(715-717)Gaa>Aaa	p.E239K	GCC2_ENST00000485546.1_3'UTR	NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	239					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						TAGTTTGCAGGAAGAGCTTTT	0.363																																					p.E239K		Atlas-SNP	.											.	GCC2	129	.	0			c.G715A						.						82.0	93.0	89.0					2																	109086500		2200	4300	6500	SO:0001583	missense	9648	exon6			TTGCAGGAAGAGC	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"""GRIP and coiled-coil domain-containing 2"""			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.715G>A	chr2.hg19:g.109086500G>A	ENSP00000307939:p.Glu239Lys	86.0	0.0		93.0	4.0	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Missense_Mutation	SNP	ENST00000309863.6	hg19	CCDS33268.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195700	0.38806	.	.	ENSG00000135968	ENST00000435553;ENST00000309863;ENST00000409821;ENST00000409896	T	0.52526	0.66	4.93	4.93	0.64822	.	0.206931	0.39834	N	0.001260	T	0.37945	0.1022	L	0.32530	0.975	0.33117	D	0.54135	P	0.37781	0.608	B	0.32980	0.156	T	0.50717	-0.8795	10	0.32370	T	0.25	.	18.5148	0.90931	0.0:0.0:1.0:0.0	.	239	Q8IWJ2	GCC2_HUMAN	K	239;239;242;202	ENSP00000307939:E239K	ENSP00000307939:E239K	E	+	1	0	GCC2	108452932	1.000000	0.71417	0.928000	0.36995	0.276000	0.26787	4.873000	0.63057	2.432000	0.82394	0.460000	0.39030	GAA	.	.		0.363	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635	
SAP130	79595	hgsc.bcm.edu	37	2	128712861	128712861	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:128712861C>A	ENST00000259235.3	-	15	2223	c.2094G>T	c.(2092-2094)atG>atT	p.M698I	SAP130_ENST00000357702.5_Missense_Mutation_p.M733I|SAP130_ENST00000259234.6_Missense_Mutation_p.M706I	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	698					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)	p.M733I(1)|p.M698I(1)		NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		ATACAGTCTCCATGGACACAG	0.468																																					p.M733I		Atlas-SNP	.											SAP130_ENST00000357702,NS,carcinoma,0,2	SAP130	169	.	2	Substitution - Missense(2)	lung(2)	c.G2199T						.						97.0	105.0	102.0					2																	128712861		2203	4300	6503	SO:0001583	missense	79595	exon16			AGTCTCCATGGAC	BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"""sin3A-associated protein, 130kDa"""			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.2094G>T	chr2.hg19:g.128712861C>A	ENSP00000259235:p.Met698Ile	188.0	0.0		190.0	60.0	NM_001145928	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Missense_Mutation	SNP	ENST00000259235.3	hg19	CCDS2153.1	.	.	.	.	.	.	.	.	.	.	C	7.865	0.726937	0.15439	.	.	ENSG00000136715	ENST00000357702;ENST00000259235;ENST00000259234	.	.	.	5.33	4.44	0.53790	.	0.593501	0.18602	N	0.136411	T	0.24275	0.0588	N	0.08118	0	0.28868	N	0.895108	B;B;B;B;B	0.18166	0.013;0.001;0.001;0.026;0.0	B;B;B;B;B	0.17979	0.006;0.001;0.001;0.02;0.0	T	0.07424	-1.0773	9	0.24483	T	0.36	-0.3078	14.3007	0.66346	0.0:0.9271:0.0:0.0729	.	733;706;698;263;335	B7ZLM3;Q96DP1;Q9H0E3;Q9H0E3-2;B3KRT9	.;.;SP130_HUMAN;.;.	I	733;698;706	.	ENSP00000259234:M706I	M	-	3	0	SAP130	128429331	1.000000	0.71417	0.998000	0.56505	0.242000	0.25591	1.559000	0.36320	2.502000	0.84385	0.632000	0.83419	ATG	.	.		0.468	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545	
ACMSD	130013	hgsc.bcm.edu	37	2	135621155	135621155	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:135621155T>C	ENST00000356140.5	+	5	576	c.440T>C	c.(439-441)gTc>gCc	p.V147A	ACMSD_ENST00000283054.4_Missense_Mutation_p.V89A|AC016725.4_ENST00000392929.2_RNA|ACMSD_ENST00000392928.1_Missense_Mutation_p.V89A	NM_138326.2	NP_612199.2	Q8TDX5	ACMSD_HUMAN	aminocarboxymuconate semialdehyde decarboxylase	147					cellular nitrogen compound metabolic process (GO:0034641)|quinolinate metabolic process (GO:0046874)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminocarboxymuconate-semialdehyde decarboxylase activity (GO:0001760)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(4)|lung(6)|skin(1)	14				BRCA - Breast invasive adenocarcinoma(221;0.115)		GGCACCCACGTCAACGAGTGG	0.657																																					p.V147A		Atlas-SNP	.											.	ACMSD	43	.	0			c.T440C						.						66.0	53.0	58.0					2																	135621155		2203	4300	6503	SO:0001583	missense	130013	exon5			CCCACGTCAACGA	AB071418	CCDS2173.2	2q21.3	2008-03-11			ENSG00000153086	ENSG00000153086	4.1.1.45		19288	protein-coding gene	gene with protein product		608889				12140278	Standard	NM_138326		Approved		uc002ttz.3	Q8TDX5	OTTHUMG00000131711	ENST00000356140.5:c.440T>C	chr2.hg19:g.135621155T>C	ENSP00000348459:p.Val147Ala	94.0	0.0		91.0	5.0	NM_138326	Q3B7X3|Q53SR5|Q96KY2	Missense_Mutation	SNP	ENST00000356140.5	hg19	CCDS2173.2	.	.	.	.	.	.	.	.	.	.	T	32	5.172638	0.94807	.	.	ENSG00000153086	ENST00000356140;ENST00000283054;ENST00000392928	.	.	.	5.74	5.74	0.90152	.	0.226724	0.51477	D	0.000099	T	0.74450	0.3718	M	0.67517	2.055	0.45899	D	0.998745	B;P	0.38922	0.131;0.651	B;P	0.55260	0.336;0.772	T	0.70439	-0.4871	9	0.25751	T	0.34	-7.4584	16.042	0.80691	0.0:0.0:0.0:1.0	.	89;147	Q53SR5;Q8TDX5	.;ACMSD_HUMAN	A	147;89;89	.	ENSP00000283054:V89A	V	+	2	0	ACMSD	135337625	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.691000	0.84191	2.188000	0.69820	0.459000	0.35465	GTC	.	.		0.657	ACMSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254627.1		
LRP1B	53353	hgsc.bcm.edu	37	2	141806696	141806696	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:141806696T>C	ENST00000389484.3	-	11	2619	c.1648A>G	c.(1648-1650)Atc>Gtc	p.I550V		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	550					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TCTATGGGGATCATGTATTCA	0.433										TSP Lung(27;0.18)																											p.I550V	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A1648G						.						183.0	179.0	180.0					2																	141806696		2203	4300	6503	SO:0001583	missense	53353	exon11			TGGGGATCATGTA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1648A>G	chr2.hg19:g.141806696T>C	ENSP00000374135:p.Ile550Val	270.0	0.0		186.0	8.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	3.098	-0.185487	0.06340	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.90676	-2.71	5.49	5.49	0.81192	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.257041	0.31257	U	0.007966	T	0.81259	0.4785	N	0.17082	0.46	0.28702	N	0.904	B	0.14438	0.01	B	0.10450	0.005	T	0.67377	-0.5686	10	0.13108	T	0.6	.	11.5754	0.50858	0.0:0.0:0.1491:0.8509	.	550	Q9NZR2	LRP1B_HUMAN	V	550;488	ENSP00000374135:I550V	ENSP00000374135:I550V	I	-	1	0	LRP1B	141523166	1.000000	0.71417	1.000000	0.80357	0.412000	0.31113	3.163000	0.50763	2.074000	0.62210	0.460000	0.39030	ATC	.	.		0.433	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
LRP1B	53353	hgsc.bcm.edu	37	2	141812812	141812812	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:141812812A>G	ENST00000389484.3	-	10	2396	c.1425T>C	c.(1423-1425)tgT>tgC	p.C475C		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	475	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.C475C(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GATCGACTTCACATGCATGGC	0.413										TSP Lung(27;0.18)																											p.C475C	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,carcinoma,0,1	LRP1B	1315	.	1	Substitution - coding silent(1)	endometrium(1)	c.T1425C						.						93.0	83.0	86.0					2																	141812812		2203	4300	6503	SO:0001819	synonymous_variant	53353	exon10			GACTTCACATGCA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1425T>C	chr2.hg19:g.141812812A>G		110.0	1.0		89.0	4.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	.		0.413	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
GALNT13	114805	hgsc.bcm.edu	37	2	155252538	155252538	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:155252538A>G	ENST00000392825.3	+	10	1759	c.1192A>G	c.(1192-1194)Aga>Gga	p.R398G	GALNT13_ENST00000487047.1_3'UTR|GALNT13_ENST00000409237.1_Missense_Mutation_p.R398G	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	398					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)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						TGTGTCAGTCAGAAAAACACT	0.373																																					p.R398G		Atlas-SNP	.											.	GALNT13	170	.	0			c.A1192G						.						88.0	84.0	85.0					2																	155252538		2203	4300	6503	SO:0001583	missense	114805	exon10			TCAGTCAGAAAAA	AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	23242	protein-coding gene	gene with protein product	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13"", ""polypeptide GalNAc transferase 13"""	608369	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"""			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.1192A>G	chr2.hg19:g.155252538A>G	ENSP00000376570:p.Arg398Gly	80.0	0.0		104.0	5.0	NM_052917	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Missense_Mutation	SNP	ENST00000392825.3	hg19	CCDS2199.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.1|21.1	4.103010|4.103010	0.76983|0.76983	.|.	.|.	ENSG00000144278|ENSG00000144278	ENST00000450838|ENST00000392825;ENST00000409237	.|T;T	.|0.58652	.|0.32;0.32	5.02|5.02	5.02|5.02	0.67125|0.67125	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.83202|0.83202	0.5203|0.5203	H|H	0.96996|0.96996	3.92|3.92	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.76494	.|0.999;0.998;0.997;0.998	.|D;D;D;D	.|0.78314	.|0.991;0.967;0.937;0.967	D|D	0.88786|0.88786	0.3274|0.3274	5|10	.|0.87932	.|D	.|0	.|.	13.8582|13.8582	0.63542|0.63542	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|398;398;398;398	.|Q8IUC8-2;B3KY85;Q08ER7;Q8IUC8	.|.;.;.;GLT13_HUMAN	R|G	16|398	.|ENSP00000376570:R398G;ENSP00000387239:R398G	.|ENSP00000376570:R398G	Q|R	+|+	2|1	0|2	GALNT13|GALNT13	154960784|154960784	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.223000|5.223000	0.65283|0.65283	2.016000|2.016000	0.59253|0.59253	0.528000|0.528000	0.53228|0.53228	CAG|AGA	.	.		0.373	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917	
GALNT13	114805	hgsc.bcm.edu	37	2	155295237	155295237	+	Splice_Site	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:155295237A>G	ENST00000392825.3	+	12	2096	c.1529A>G	c.(1528-1530)gAg>gGg	p.E510G	GALNT13_ENST00000409237.1_Splice_Site_p.E510G|AC009227.2_ENST00000434635.1_RNA	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	510	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)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						TATGATGCTGAGGTATAGTAT	0.313																																					p.E510G		Atlas-SNP	.											.	GALNT13	170	.	0			c.A1529G						.						104.0	109.0	107.0					2																	155295237		2203	4300	6503	SO:0001630	splice_region_variant	114805	exon12			ATGCTGAGGTATA	AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	23242	protein-coding gene	gene with protein product	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13"", ""polypeptide GalNAc transferase 13"""	608369	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"""			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.1530+1A>G	chr2.hg19:g.155295237A>G		63.0	0.0		72.0	4.0	NM_052917	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Missense_Mutation	SNP	ENST00000392825.3	hg19	CCDS2199.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.10|18.10	3.547727|3.547727	0.65311|0.65311	.|.	.|.	ENSG00000144278|ENSG00000144278	ENST00000392825;ENST00000409237;ENST00000453715|ENST00000450838	T;T|.	0.76448|.	-1.02;1.99|.	5.76|5.76	5.76|5.76	0.90799|0.90799	Ricin B-related lectin (1);Ricin B lectin (3);|.	0.693058|.	0.15449|.	N|.	0.261796|.	T|.	0.45438|.	0.1342|.	L|L	0.41710|0.41710	1.295|1.295	0.32964|0.32964	D|D	0.521388|0.521388	P;P|.	0.37731|.	0.607;0.464|.	P;B|.	0.45913|.	0.497;0.395|.	T|.	0.57289|.	-0.7837|.	10|.	0.38643|.	T|.	0.18|.	.|.	9.3359|9.3359	0.38049|0.38049	0.8402:0.0:0.0:0.1598|0.8402:0.0:0.0:0.1598	.|.	510;510|.	Q08ER7;Q8IUC8|.	.;GLT13_HUMAN|.	G|W	510;510;45|95	ENSP00000376570:E510G;ENSP00000387239:E510G|.	ENSP00000376570:E510G|.	E|X	+|+	2|3	0|0	GALNT13|GALNT13	155003483|155003483	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	7.210000|7.210000	0.77924|0.77924	2.197000|2.197000	0.70478|0.70478	0.533000|0.533000	0.62120|0.62120	GAG|TGA	.	.		0.313	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917	Missense_Mutation
BAZ2B	29994	hgsc.bcm.edu	37	2	160229687	160229687	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:160229687T>C	ENST00000392783.2	-	27	4577	c.4082A>G	c.(4081-4083)tAc>tGc	p.Y1361C	BAZ2B_ENST00000392782.1_Missense_Mutation_p.Y1325C|BAZ2B_ENST00000343439.5_Missense_Mutation_p.Y1261C|BAZ2B_ENST00000355831.2_Missense_Mutation_p.Y1327C	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1361					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)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						CTTCCTTCTGTACTGACTCTG	0.383																																					p.Y1361C		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A4082G						.						89.0	82.0	84.0					2																	160229687		1871	4112	5983	SO:0001583	missense	29994	exon27			CTTCTGTACTGAC	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"""Zinc fingers, PHD-type"""	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.4082A>G	chr2.hg19:g.160229687T>C	ENSP00000376534:p.Tyr1361Cys	83.0	0.0		99.0	4.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	T	10.83	1.459757	0.26248	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	T;T;T;T	0.31769	1.48;1.48;1.48;4.31	5.48	5.48	0.80851	.	0.000000	0.33834	U	0.004501	T	0.45538	0.1347	L	0.39898	1.24	0.42852	D	0.994088	D;D	0.76494	0.999;0.999	D;P	0.64595	0.927;0.894	T	0.41574	-0.9501	10	0.56958	D	0.05	-5.9942	15.5721	0.76349	0.0:0.0:0.0:1.0	.	1325;1361	Q9UIF8-5;Q9UIF8	.;BAZ2B_HUMAN	C	1325;1361;1327;1261	ENSP00000376533:Y1325C;ENSP00000376534:Y1361C;ENSP00000348087:Y1327C;ENSP00000339670:Y1261C	ENSP00000339670:Y1261C	Y	-	2	0	BAZ2B	159937933	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.091000	0.57700	2.081000	0.62600	0.383000	0.25322	TAC	.	.		0.383	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
LY75	4065	hgsc.bcm.edu	37	2	160732083	160732083	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:160732083T>C	ENST00000263636.4	-	12	1873	c.1846A>G	c.(1846-1848)Agc>Ggc	p.S616G	LY75-CD302_ENST00000505052.1_Missense_Mutation_p.S616G|LY75_ENST00000553424.1_Missense_Mutation_p.S616G|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.S616G|LY75_ENST00000554112.1_Missense_Mutation_p.S616G	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	616	C-type lectin 3. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		GCTTTGAAGCTTCTGCAGTCC	0.517																																					p.S616G		Atlas-SNP	.											.	LY75	151	.	0			c.A1846G						.						129.0	137.0	134.0					2																	160732083		2203	4300	6503	SO:0001583	missense	4065	exon12			TGAAGCTTCTGCA	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.1846A>G	chr2.hg19:g.160732083T>C	ENSP00000263636:p.Ser616Gly	83.0	0.0		105.0	5.0	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	T	16.69	3.193623	0.58017	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.20463	2.07;2.07;2.07;2.07;2.07	5.07	5.07	0.68467	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.352983	0.20491	N	0.091293	T	0.28400	0.0702	M	0.64404	1.975	0.37230	D	0.905635	B;P;P;B	0.36483	0.27;0.499;0.555;0.264	B;B;B;B	0.40982	0.232;0.234;0.345;0.085	T	0.19128	-1.0315	10	0.41790	T	0.15	-0.6067	14.1143	0.65142	0.0:0.0:0.0:1.0	.	234;616;616;616	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	G	616	ENSP00000451511:S616G;ENSP00000451446:S616G;ENSP00000263636:S616G;ENSP00000423463:S616G;ENSP00000421035:S616G	ENSP00000423463:S616G	S	-	1	0	LY75;LY75-CD302	160440329	0.634000	0.27190	0.644000	0.29465	0.982000	0.71751	2.598000	0.46223	2.029000	0.59856	0.460000	0.39030	AGC	.	.		0.517	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
DPP4	1803	hgsc.bcm.edu	37	2	162875361	162875361	+	Splice_Site	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:162875361C>T	ENST00000360534.3	-	16	1859		c.e16-1		DPP4_ENST00000491591.1_5'Flank	NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4						cell adhesion (GO:0007155)|endothelial cell migration (GO:0043542)|negative regulation of extracellular matrix disassembly (GO:0010716)|positive regulation of cell proliferation (GO:0008284)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to hypoxia (GO:0001666)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|invadopodium membrane (GO:0071438)|lamellipodium (GO:0030027)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	48					Alogliptin(DB06203)|Atorvastatin(DB01076)|Linagliptin(DB08882)|Liraglutide(DB06655)|Saxagliptin(DB06335)|Sitagliptin(DB01261)|Vildagliptin(DB04876)	AAGTTGGATTCTGTAAAACCA	0.403																																					.		Atlas-SNP	.											DPP4,NS,carcinoma,0,1	DPP4	90	.	0			c.1299-1G>A						.						116.0	108.0	111.0					2																	162875361		2203	4300	6503	SO:0001630	splice_region_variant	1803	exon17			TGGATTCTGTAAA	M74777	CCDS2216.1	2q24.2	2013-09-19	2008-08-01		ENSG00000197635	ENSG00000197635	3.4.14.5	"""CD molecules"""	3009	protein-coding gene	gene with protein product		102720	"""dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2)"", ""adenosine deaminase complexing protein 2"""	CD26, ADCP2		8101391	Standard	NM_001935		Approved	DPPIV	uc002ubz.3	P27487	OTTHUMG00000132056	ENST00000360534.3:c.1299-1G>A	chr2.hg19:g.162875361C>T		94.0	0.0		107.0	5.0	NM_001935	Q53TN1	Splice_Site	SNP	ENST00000360534.3	hg19	CCDS2216.1	.	.	.	.	.	.	.	.	.	.	C	19.60	3.857580	0.71834	.	.	ENSG00000197635	ENST00000360534	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7997	0.92011	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DPP4	162583607	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	5.486000	0.66856	2.756000	0.94617	0.563000	0.77884	.	.	.		0.403	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255079.2		Intron
OSBPL6	114880	hgsc.bcm.edu	37	2	179226415	179226415	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:179226415C>G	ENST00000190611.4	+	13	1536	c.1160C>G	c.(1159-1161)tCt>tGt	p.S387C	OSBPL6_ENST00000409045.3_Missense_Mutation_p.S356C|OSBPL6_ENST00000357080.4_Missense_Mutation_p.S356C|OSBPL6_ENST00000359685.3_Missense_Mutation_p.S387C|OSBPL6_ENST00000409631.1_Missense_Mutation_p.S387C|OSBPL6_ENST00000315022.2_Missense_Mutation_p.S391C|OSBPL6_ENST00000392505.2_Missense_Mutation_p.S412C	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	387					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			CCAGTGCATTCTCTTTTGAAG	0.413																																					p.S412C		Atlas-SNP	.											.	OSBPL6	178	.	0			c.C1235G						.						101.0	97.0	98.0					2																	179226415		2203	4300	6503	SO:0001583	missense	114880	exon14			TGCATTCTCTTTT	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"""Oxysterol binding proteins"""	16388	protein-coding gene	gene with protein product	"""OSBP-related protein 6"""	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.1160C>G	chr2.hg19:g.179226415C>G	ENSP00000190611:p.Ser387Cys	258.0	0.0		234.0	92.0	NM_001201480	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	hg19	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.087567	0.76642	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000357080;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T;T	0.14391	2.6;2.62;2.51;2.63;2.62;2.62;2.6	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.37210	0.0995	L	0.59436	1.845	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;1.0;0.999;1.0;0.999;1.0	D;D;D;D;D;D	0.91635	0.96;0.999;0.987;0.999;0.993;0.997	T	0.01468	-1.1347	10	0.59425	D	0.04	-12.2188	19.6657	0.95891	0.0:1.0:0.0:0.0	.	356;391;387;412;387;356	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3;Q86V84	.;.;.;.;OSBL6_HUMAN;.	C	412;387;356;356;387;387;391	ENSP00000376293:S412C;ENSP00000352713:S387C;ENSP00000349591:S356C;ENSP00000387248:S356C;ENSP00000190611:S387C;ENSP00000386885:S387C;ENSP00000318723:S391C	ENSP00000190611:S387C	S	+	2	0	OSBPL6	178934661	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.262000	0.72514	2.744000	0.94065	0.655000	0.94253	TCT	.	.		0.413	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523	
TTN	7273	hgsc.bcm.edu	37	2	179427959	179427959	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:179427959T>C	ENST00000591111.1	-	276	78201	c.77977A>G	c.(77977-77979)Acc>Gcc	p.T25993A	TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T18694A|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T18569A|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T27634A|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T18761A|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T25066A|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25993	Fibronectin type-III 89. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)			TTAAGCTTGGTCACTGTGAAC	0.448																																					p.T27634A		Atlas-SNP	.											.	TTN	18412	.	0			c.A82900G						.						123.0	124.0	123.0					2																	179427959		2011	4186	6197	SO:0001583	missense	7273	exon326			GCTTGGTCACTGT	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.77977A>G	chr2.hg19:g.179427959T>C	ENSP00000465570:p.Thr25993Ala	304.0	0.0		321.0	111.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	18.10	3.548853	0.65311	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.59364	0.27;0.27;0.27;0.27	5.65	5.65	0.86999	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.59348	0.2187	L	0.50993	1.605	0.49582	D	0.999803	P;P;P;P	0.44090	0.826;0.826;0.826;0.826	P;P;P;P	0.45195	0.473;0.473;0.473;0.473	T	0.64402	-0.6416	9	0.87932	D	0	.	15.861	0.79021	0.0:0.0:0.0:1.0	.	18569;18694;18761;25993	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	25066;18569;18761;18694;18567	ENSP00000343764:T25066A;ENSP00000434586:T18569A;ENSP00000340554:T18761A;ENSP00000352154:T18694A	ENSP00000340554:T18761A	T	-	1	0	TTN	179136205	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.991000	0.88244	2.152000	0.67230	0.379000	0.24179	ACC	.	.		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179500233	179500233	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:179500233C>T	ENST00000591111.1	-	177	37119	c.36895G>A	c.(36895-36897)Gaa>Aaa	p.E12299K	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E5000K|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E4875K|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E13940K|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E5067K|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E11372K|TTN-AS1_ENST00000418062.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12299	Ig-like 82.				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)			GCAATATCTTCTGGCATAGCA	0.353																																					p.E13940K		Atlas-SNP	.											.	TTN	18412	.	0			c.G41818A						.						91.0	79.0	83.0					2																	179500233		1849	4088	5937	SO:0001583	missense	7273	exon227			TATCTTCTGGCAT	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.36895G>A	chr2.hg19:g.179500233C>T	ENSP00000465570:p.Glu12299Lys	153.0	0.0		165.0	50.0	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		.	.	.	.	.	.	.	.	.	.	C	18.12	3.552617	0.65425	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.48522	0.81;0.81;0.81;0.81	5.94	5.94	0.96194	Immunoglobulin subtype (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46268	0.1384	L	0.50333	1.59	0.48830	D	0.999713	P;P;P;P	0.38922	0.651;0.651;0.651;0.651	B;B;B;B	0.33521	0.165;0.165;0.165;0.165	T	0.50591	-0.8810	9	0.87932	D	0	.	20.3658	0.98878	0.0:1.0:0.0:0.0	.	4875;5000;5067;12299	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	11372;4875;5067;5000;4875	ENSP00000343764:E11372K;ENSP00000434586:E4875K;ENSP00000340554:E5067K;ENSP00000352154:E5000K	ENSP00000340554:E5067K	E	-	1	0	TTN	179208478	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.866000	0.63005	2.820000	0.97059	0.650000	0.86243	GAA	.	.		0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PDE1A	5136	hgsc.bcm.edu	37	2	183387041	183387041	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:183387041T>C	ENST00000410103.1	-	2	146	c.63A>G	c.(61-63)ggA>ggG	p.G21G	PDE1A_ENST00000435564.1_Silent_p.G21G|PDE1A_ENST00000456212.1_Silent_p.G21G|PDE1A_ENST00000331935.6_Silent_p.G21G|PDE1A_ENST00000536095.1_5'UTR|PDE1A_ENST00000358139.2_Silent_p.G21G	NM_001003683.2	NP_001003683.1	P54750	PDE1A_HUMAN	phosphodiesterase 1A, calmodulin-dependent	21					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of smooth muscle cell apoptotic process (GO:0034391)|regulation of smooth muscle cell proliferation (GO:0048660)|signal transduction (GO:0007165)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(2)	35			OV - Ovarian serous cystadenocarcinoma(117;0.061)		Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	CAGTCTGTTCTCCTGTAAGAT	0.393																																					p.G25G		Atlas-SNP	.											.	PDE1A	184	.	0			c.A75G						.						146.0	147.0	146.0					2																	183387041		2202	4300	6502	SO:0001819	synonymous_variant	5136	exon2			CTGTTCTCCTGTA		CCDS2285.1, CCDS33344.1, CCDS58741.1, CCDS74612.1	2q32.1	2008-03-18			ENSG00000115252	ENSG00000115252	3.1.4.17	"""Phosphodiesterases"""	8774	protein-coding gene	gene with protein product		171890				8557689, 11342109	Standard	NM_005019		Approved		uc010zfq.2	P54750	OTTHUMG00000132596	ENST00000410103.1:c.63A>G	chr2.hg19:g.183387041T>C		78.0	0.0		82.0	4.0	NM_001258312	D3DPG5|Q86VZ0|Q9C0K8|Q9C0K9|Q9C0L0|Q9C0L1|Q9C0L2|Q9C0L3|Q9C0L4|Q9UFX3	Silent	SNP	ENST00000410103.1	hg19	CCDS33344.1																																																																																			.	.		0.393	PDE1A-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334356.1		
COL5A2	1290	hgsc.bcm.edu	37	2	189904144	189904144	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:189904144T>C	ENST00000374866.3	-	51	4053	c.3779A>G	c.(3778-3780)gAc>gGc	p.D1260G		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1260					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			TTTGTTTTTGTCATCAGGAGC	0.522																																					p.D1260G		Atlas-SNP	.											.	COL5A2	230	.	0			c.A3779G						.						85.0	76.0	79.0					2																	189904144		2203	4300	6503	SO:0001583	missense	1290	exon51			TTTTTGTCATCAG	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"""Collagens"""	2210	protein-coding gene	gene with protein product	"""AB collagen"""	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.3779A>G	chr2.hg19:g.189904144T>C	ENSP00000364000:p.Asp1260Gly	119.0	0.0		137.0	8.0	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	hg19	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	T	12.12	1.841703	0.32513	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	D	0.83506	-1.73	5.28	5.28	0.74379	.	0.000000	0.50627	D	0.000106	T	0.68815	0.3042	N	0.16602	0.42	0.43122	D	0.994847	B;P	0.38767	0.243;0.646	B;B	0.31442	0.079;0.13	T	0.70403	-0.4881	10	0.28530	T	0.3	.	15.1969	0.73100	0.0:0.0:0.0:1.0	.	900;1260	Q5PR22;P05997	.;CO5A2_HUMAN	G	1260;900	ENSP00000364000:D1260G	ENSP00000364000:D1260G	D	-	2	0	COL5A2	189612389	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	2.733000	0.47360	1.983000	0.57843	0.533000	0.62120	GAC	.	.		0.522	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393	
ANKAR	150709	hgsc.bcm.edu	37	2	190569759	190569759	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:190569759T>C	ENST00000520309.1	+	8	1807	c.1719T>C	c.(1717-1719)ccT>ccC	p.P573P	ANKAR_ENST00000281412.6_Silent_p.P337P|ANKAR_ENST00000438402.2_Silent_p.P573P|ANKAR_ENST00000313581.4_Silent_p.P573P|ANKAR_ENST00000431575.2_Silent_p.P502P	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	573						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)			GTCCAACACCTCTACACCTTG	0.428																																					p.P573P		Atlas-SNP	.											.	ANKAR	184	.	0			c.T1719C						.						146.0	120.0	129.0					2																	190569759		2203	4300	6503	SO:0001819	synonymous_variant	150709	exon8			AACACCTCTACAC	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.1719T>C	chr2.hg19:g.190569759T>C		83.0	0.0		85.0	4.0	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Silent	SNP	ENST00000520309.1	hg19	CCDS33351.2																																																																																			.	.		0.428	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708	
GLS	2744	hgsc.bcm.edu	37	2	191765310	191765310	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:191765310T>C	ENST00000320717.3	+	4	884	c.626T>C	c.(625-627)gTt>gCt	p.V209A	GLS_ENST00000338435.4_Missense_Mutation_p.V209A	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	209					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)	AGCAACATTGTTTTGTTGACA	0.308																																					p.V209A		Atlas-SNP	.											.	GLS	47	.	0			c.T626C						.						113.0	106.0	108.0					2																	191765310		2203	4298	6501	SO:0001583	missense	2744	exon4			ACATTGTTTTGTT	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.626T>C	chr2.hg19:g.191765310T>C	ENSP00000317379:p.Val209Ala	63.0	0.0		55.0	4.0	NM_014905	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Missense_Mutation	SNP	ENST00000320717.3	hg19	CCDS2308.1	.	.	.	.	.	.	.	.	.	.	T	16.93	3.256801	0.59321	.	.	ENSG00000115419	ENST00000320717;ENST00000338435	T;T	0.46819	0.98;0.86	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.52208	0.1720	M	0.79475	2.455	0.80722	D	1	B;B	0.21821	0.008;0.061	B;B	0.25140	0.01;0.058	T	0.50338	-0.8840	10	0.32370	T	0.25	-18.3999	15.9423	0.79768	0.0:0.0:0.0:1.0	.	209;209	O94925;O94925-3	GLSK_HUMAN;.	A	209	ENSP00000317379:V209A;ENSP00000340689:V209A	ENSP00000317379:V209A	V	+	2	0	GLS	191473555	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.980000	0.88113	2.223000	0.72356	0.455000	0.32223	GTT	.	.		0.308	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2		
STAT1	6772	hgsc.bcm.edu	37	2	191835434	191835434	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:191835434C>T	ENST00000361099.3	-	25	2635	c.2248G>A	c.(2248-2250)Gta>Ata	p.V750I	STAT1_ENST00000540176.1_3'UTR|STAT1_ENST00000409465.1_Missense_Mutation_p.V750I	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	750					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)			ATGCTCTATACTGTGTTCATC	0.368																																					p.V750I		Atlas-SNP	.											.	STAT1	93	.	0			c.G2248A						.						133.0	122.0	125.0					2																	191835434		2203	4300	6503	SO:0001583	missense	6772	exon25			TCTATACTGTGTT		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.2248G>A	chr2.hg19:g.191835434C>T	ENSP00000354394:p.Val750Ile	63.0	0.0		65.0	5.0	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	hg19	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.284187	0.40394	.	.	ENSG00000115415	ENST00000361099;ENST00000409465	D;D	0.88046	-2.33;-2.33	4.84	3.88	0.44766	.	2.274050	0.01934	N	0.041451	D	0.83266	0.5217	L	0.36672	1.1	0.32343	N	0.55943	B	0.14012	0.009	B	0.17098	0.017	T	0.71672	-0.4522	10	0.54805	T	0.06	.	7.2042	0.25897	0.0:0.8776:0.0:0.1224	.	750	P42224	STAT1_HUMAN	I	750	ENSP00000354394:V750I;ENSP00000386244:V750I	ENSP00000354394:V750I	V	-	1	0	STAT1	191543679	0.760000	0.28428	0.524000	0.27887	0.848000	0.48234	1.920000	0.40025	2.483000	0.83821	0.655000	0.94253	GTA	.	.		0.368	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315	
SF3B1	23451	hgsc.bcm.edu	37	2	198281517	198281517	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:198281517T>C	ENST00000335508.6	-	6	705	c.614A>G	c.(613-615)gAt>gGt	p.D205G		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	205	U2AF homology region; mediates interaction with RMB39.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			AGGAGTCTGATCAGCTGTTTG	0.413			Mis		myelodysplastic syndrome																																p.D205G		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	.	SF3B1	1038	.	0			c.A614G						.						171.0	169.0	170.0					2																	198281517		2203	4300	6503	SO:0001583	missense	23451	exon6			GTCTGATCAGCTG	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.614A>G	chr2.hg19:g.198281517T>C	ENSP00000335321:p.Asp205Gly	147.0	0.0		157.0	7.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	15.58	2.875995	0.51695	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.55016	0.1894	L	0.48642	1.525	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.50516	-0.8819	9	0.22109	T	0.4	.	15.3288	0.74190	0.0:0.0:0.0:1.0	.	205	O75533	SF3B1_HUMAN	G	205	.	ENSP00000335321:D205G	D	-	2	0	SF3B1	197989762	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	7.776000	0.85560	2.209000	0.71365	0.472000	0.43445	GAT	.	.		0.413	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
ORC2	4999	hgsc.bcm.edu	37	2	201778021	201778021	+	Silent	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:201778021C>T	ENST00000234296.2	-	17	1893	c.1644G>A	c.(1642-1644)aaG>aaA	p.K548K		NM_006190.4	NP_006181.1	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2	548					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	condensed chromosome inner kinetochore (GO:0000939)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	DNA replication origin binding (GO:0003688)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	20						GTCTTACCTTCTTTGTTCTTA	0.408																																					p.K548K		Atlas-SNP	.											.	ORC2	48	.	0			c.G1644A						.						115.0	105.0	109.0					2																	201778021		2203	4300	6503	SO:0001819	synonymous_variant	4999	exon17			TACCTTCTTTGTT		CCDS2334.1	2q33	2010-10-12	2010-10-12	2010-10-12	ENSG00000115942	ENSG00000115942			8488	protein-coding gene	gene with protein product		601182	"""origin recognition complex, subunit 2 (yeast homolog)-like"", ""origin recognition complex, subunit 2-like (yeast)"", ""origin recognition complex, subunit 2 homolog (yeast)"""	ORC2L		8808289	Standard	NM_006190		Approved		uc002uwr.3	Q13416	OTTHUMG00000132783	ENST00000234296.2:c.1644G>A	chr2.hg19:g.201778021C>T		70.0	0.0		77.0	4.0	NM_006190	Q13204|Q53TX5	Silent	SNP	ENST00000234296.2	hg19	CCDS2334.1																																																																																			.	.		0.408	ORC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256191.2	NM_006190	
NBEAL1	65065	hgsc.bcm.edu	37	2	204045127	204045127	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:204045127T>C	ENST00000449802.1	+	42	6733	c.6400T>C	c.(6400-6402)Ttc>Ctc	p.F2134L		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2134	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.									NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						AGATCGACAGTTCCATTCTAT	0.338																																					p.F2134L		Atlas-SNP	.											.	NBEAL1	266	.	0			c.T6400C						.						127.0	120.0	122.0					2																	204045127		1842	4098	5940	SO:0001583	missense	65065	exon42			CGACAGTTCCATT	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.6400T>C	chr2.hg19:g.204045127T>C	ENSP00000399903:p.Phe2134Leu	83.0	0.0		89.0	4.0	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.911492	0.92178	.	.	ENSG00000144426	ENST00000449802;ENST00000340268;ENST00000414576	D;D	0.83419	-1.72;-1.72	5.85	5.85	0.93711	BEACH domain (4);	0.000000	0.85682	D	0.000000	D	0.94255	0.8155	H	0.96833	3.89	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.995;0.996	D	0.95931	0.8938	10	0.72032	D	0.01	.	15.9036	0.79403	0.0:0.0:0.0:1.0	.	2134;2123	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	L	2134;2134;149	ENSP00000399903:F2134L;ENSP00000388466:F149L	ENSP00000344985:F2134L	F	+	1	0	NBEAL1	203753372	1.000000	0.71417	0.996000	0.52242	0.773000	0.43773	7.841000	0.86834	2.234000	0.73211	0.533000	0.62120	TTC	.	.		0.338	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
UNC80	285175	hgsc.bcm.edu	37	2	210809878	210809878	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:210809878A>G	ENST00000439458.1	+	45	7036	c.6956A>G	c.(6955-6957)gAg>gGg	p.E2319G	UNC80_ENST00000272845.6_Missense_Mutation_p.E2314G	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	2319					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						GACATCTTAGAGCTGGTCAAA	0.428																																					p.E2319G		Atlas-SNP	.											.	UNC80	280	.	0			c.A6956G						.						68.0	61.0	63.0					2																	210809878		692	1591	2283	SO:0001583	missense	285175	exon45			TCTTAGAGCTGGT	AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406			26582	protein-coding gene	gene with protein product		612636	"""chromosome 2 open reading frame 21"""	C2orf21		19092807	Standard	NM_032504		Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000439458.1:c.6956A>G	chr2.hg19:g.210809878A>G	ENSP00000391088:p.Glu2319Gly	97.0	0.0		97.0	6.0	NM_032504	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Missense_Mutation	SNP	ENST00000439458.1	hg19	CCDS46504.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.284413	0.80803	.	.	ENSG00000144406	ENST00000439458;ENST00000272845	T;T	0.37058	1.22;1.22	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.47192	0.1432	N	0.26042	0.785	0.80722	D	1	D	0.61080	0.989	D	0.72982	0.979	T	0.38436	-0.9661	10	0.35671	T	0.21	-22.4997	16.1299	0.81422	1.0:0.0:0.0:0.0	.	2319	Q8N2C7	UNC80_HUMAN	G	2319;2314	ENSP00000391088:E2319G;ENSP00000272845:E2314G	ENSP00000272845:E2314G	E	+	2	0	UNC80	210518123	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.527000	0.90594	2.215000	0.71742	0.528000	0.53228	GAG	.	.		0.428	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
ABCB6	10058	hgsc.bcm.edu	37	2	220075719	220075719	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:220075719C>A	ENST00000265316.3	-	15	2396	c.2080G>T	c.(2080-2082)Gat>Tat	p.D694Y	ABCB6_ENST00000439002.2_Missense_Mutation_p.D648Y	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	694	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCCACCTCATCATTCCCAGCT	0.547																																					p.D694Y		Atlas-SNP	.											.	ABCB6	76	.	0			c.G2080T						.						86.0	76.0	79.0					2																	220075719		2203	4300	6503	SO:0001583	missense	10058	exon15			CCTCATCATTCCC	AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"""ATP binding cassette transporters / subfamily B"""	47	protein-coding gene	gene with protein product	"""ATP-binding cassette half-transporter"""	605452	"""ATP-binding cassette, sub-family B (MDR/TAP), member 6"""			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.2080G>T	chr2.hg19:g.220075719C>A	ENSP00000265316:p.Asp694Tyr	115.0	0.0		149.0	42.0	NM_005689	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Missense_Mutation	SNP	ENST00000265316.3	hg19	CCDS2436.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.411|6.411	0.444004|0.444004	0.12164|0.12164	.|.	.|.	ENSG00000115657|ENSG00000115657	ENST00000265316;ENST00000439002|ENST00000295750	D;D|.	0.91068|.	-2.78;-2.78|.	4.7|4.7	-1.52|-1.52	0.08637|0.08637	ATPase, AAA+ type, core (1);ABC transporter-like (2);|.	0.915309|.	0.09535|.	N|.	0.789071|.	T|T	0.47192|0.47192	0.1432|0.1432	M|M	0.83852|0.83852	2.665|2.665	0.09310|0.09310	N|N	0.999999|0.999999	B;P|.	0.34892|.	0.297;0.474|.	B;B|.	0.40506|.	0.105;0.331|.	T|T	0.48175|0.48175	-0.9058|-0.9058	10|5	0.87932|.	D|.	0|.	0.686|0.686	2.4059|2.4059	0.04413|0.04413	0.1079:0.4165:0.2131:0.2625|0.1079:0.4165:0.2131:0.2625	.|.	648;694|.	Q9NP58-4;Q9NP58|.	.;ABCB6_HUMAN|.	Y|I	694;648|541	ENSP00000265316:D694Y;ENSP00000394333:D648Y|.	ENSP00000265316:D694Y|.	D|M	-|-	1|3	0|0	ABCB6|ABCB6	219783963|219783963	0.010000|0.010000	0.17322|0.17322	0.000000|0.000000	0.03702|0.03702	0.022000|0.022000	0.10575|0.10575	0.588000|0.588000	0.23924|0.23924	-0.096000|-0.096000	0.12329|0.12329	-0.903000|-0.903000	0.02851|0.02851	GAT|ATG	.	.		0.547	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689	
ECEL1	9427	hgsc.bcm.edu	37	2	233350834	233350834	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:233350834T>C	ENST00000304546.1	-	2	740	c.530A>G	c.(529-531)cAg>cGg	p.Q177R	ECEL1_ENST00000409941.1_Missense_Mutation_p.Q177R	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	177					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		CACCTTGCGCTgggccgcgcc	0.716																																					p.Q177R		Atlas-SNP	.											.	ECEL1	73	.	0			c.A530G						.						4.0	5.0	5.0					2																	233350834		1993	3987	5980	SO:0001583	missense	9427	exon2			TTGCGCTGGGCCG	Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"""damage induced neuronal endopeptidase"""	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.530A>G	chr2.hg19:g.233350834T>C	ENSP00000302051:p.Gln177Arg	9.0	0.0		9.0	5.0	NM_004826	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Missense_Mutation	SNP	ENST00000304546.1	hg19	CCDS2493.1	.	.	.	.	.	.	.	.	.	.	T	17.49	3.403395	0.62288	.	.	ENSG00000171551	ENST00000304546;ENST00000409941	T;T	0.73897	-0.79;-0.79	5.33	4.13	0.48395	Peptidase M13 (1);	0.135808	0.47455	D	0.000230	T	0.56247	0.1972	N	0.11255	0.115	0.35224	D	0.776337	B;B	0.31153	0.31;0.025	B;B	0.29862	0.108;0.016	T	0.64980	-0.6279	10	0.87932	D	0	-17.2238	12.0726	0.53626	0.0:0.0:0.1442:0.8557	.	177;177	O95672-2;O95672	.;ECEL1_HUMAN	R	177	ENSP00000302051:Q177R;ENSP00000386333:Q177R	ENSP00000302051:Q177R	Q	-	2	0	ECEL1	233059078	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	5.682000	0.68182	0.822000	0.34565	0.528000	0.53228	CAG	.	.		0.716	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826	
CHRNG	1146	hgsc.bcm.edu	37	2	233408309	233408309	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:233408309T>C	ENST00000389494.3	+	9	956	c.935T>C	c.(934-936)cTc>cCc	p.L312P	CHRNG_ENST00000389492.3_Missense_Mutation_p.L260P	NM_005199.4	NP_005190.4	P07510	ACHG_HUMAN	cholinergic receptor, nicotinic, gamma (muscle)	312					muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)			breast(2)|endometrium(3)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)	Galantamine(DB00674)	CTGACCTTCCTCCTGGTGGTG	0.622																																					p.L312P		Atlas-SNP	.											.	CHRNG	54	.	0			c.T935C						.						174.0	129.0	144.0					2																	233408309		2203	4300	6503	SO:0001583	missense	1146	exon9			CCTTCCTCCTGGT	X01715	CCDS33400.1	2q37.1	2012-10-02	2012-02-07		ENSG00000196811	ENSG00000196811		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1967	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, gamma (muscle)"""	100730	"""cholinergic receptor, nicotinic, gamma"""	ACHRG			Standard	NM_005199		Approved		uc002vsx.1	P07510	OTTHUMG00000153327	ENST00000389494.3:c.935T>C	chr2.hg19:g.233408309T>C	ENSP00000374145:p.Leu312Pro	129.0	0.0		169.0	7.0	NM_005199	B3KWM8|Q14DU4|Q53RG2	Missense_Mutation	SNP	ENST00000389494.3	hg19	CCDS33400.1	.	.	.	.	.	.	.	.	.	.	T	16.84	3.234536	0.58886	.	.	ENSG00000196811	ENST00000389494;ENST00000541596;ENST00000389492	D;D	0.84944	-1.92;-1.92	5.22	5.22	0.72569	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.077174	0.51477	D	0.000087	D	0.91229	0.7236	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.85130	0.997;0.974	D	0.92169	0.5742	10	0.72032	D	0.01	.	15.0989	0.72256	0.0:0.0:0.0:1.0	.	260;312	Q14DU4;P07510	.;ACHG_HUMAN	P	312;312;260	ENSP00000374145:L312P;ENSP00000374143:L260P	ENSP00000374143:L260P	L	+	2	0	CHRNG	233116553	1.000000	0.71417	1.000000	0.80357	0.697000	0.40408	5.540000	0.67205	1.973000	0.57446	0.260000	0.18958	CTC	.	.		0.622	CHRNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330743.1	NM_005199	
EIF4E2	9470	hgsc.bcm.edu	37	2	233421124	233421124	+	Splice_Site	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:233421124A>G	ENST00000258416.3	+	2	693		c.e2-1		EIF4E2_ENST00000409167.3_Splice_Site|EIF4E2_ENST00000409394.1_Splice_Site|EIF4E2_ENST00000409322.1_Splice_Site|EIF4E2_ENST00000409098.1_Splice_Site|EIF4E2_ENST00000479834.1_Splice_Site|EIF4E2_ENST00000409514.1_Splice_Site|EIF4E2_ENST00000409495.1_Splice_Site	NM_004846.2	NP_004837.1	O60573	IF4E2_HUMAN	eukaryotic translation initiation factor 4E family member 2						cytokine-mediated signaling pathway (GO:0019221)|in utero embryonic development (GO:0001701)|negative regulation of translation (GO:0017148)	cytosol (GO:0005829)|mRNA cap binding complex (GO:0005845)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	8		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;2.3e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000912)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		CTTTCCATTCAGTTTGAAAGA	0.413																																					.		Atlas-SNP	.											.	EIF4E2	23	.	0			c.21-2A>G						.						135.0	116.0	122.0					2																	233421124		2203	4300	6503	SO:0001630	splice_region_variant	9470	exon2			CCATTCAGTTTGA	AF038957	CCDS2496.1, CCDS63158.1, CCDS63159.1, CCDS74671.1	2q37.1	2008-02-05	2006-11-13	2004-10-30	ENSG00000135930	ENSG00000135930			3293	protein-coding gene	gene with protein product		605895	"""eukaryotic translation initiation factor 4E-like 3"""	EIF4EL3		9653160, 9582349	Standard	XM_005246975		Approved	IF4e, 4EHP	uc002vta.3	O60573	OTTHUMG00000133256	ENST00000258416.3:c.21-1A>G	chr2.hg19:g.233421124A>G		107.0	0.0		99.0	4.0	NM_004846	B8ZZJ9|O75349	Splice_Site	SNP	ENST00000258416.3	hg19	CCDS2496.1	.	.	.	.	.	.	.	.	.	.	A	15.92	2.976699	0.53720	.	.	ENSG00000135930	ENST00000258416;ENST00000409514;ENST00000409098;ENST00000409495;ENST00000409167;ENST00000409322;ENST00000409394;ENST00000454501	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0662	0.64831	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EIF4E2	233129368	1.000000	0.71417	0.916000	0.36221	0.505000	0.33919	8.714000	0.91412	2.214000	0.71695	0.528000	0.53228	.	.	.		0.413	EIF4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257033.2	NM_004846	Intron
HDAC4	9759	hgsc.bcm.edu	37	2	240111545	240111545	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:240111545A>G	ENST00000345617.3	-	4	1114	c.323T>C	c.(322-324)cTc>cCc	p.L108P	HDAC4_ENST00000541256.1_Missense_Mutation_p.L77P	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	108					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|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)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|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)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		GTGCTCGTGGAGCTGCGCCTC	0.682																																					p.L108P		Atlas-SNP	.											.	HDAC4	127	.	0			c.T323C						.						26.0	24.0	24.0					2																	240111545		2203	4300	6503	SO:0001583	missense	9759	exon4			TCGTGGAGCTGCG	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.323T>C	chr2.hg19:g.240111545A>G	ENSP00000264606:p.Leu108Pro	74.0	0.0		87.0	4.0	NM_006037	Q9UND6	Missense_Mutation	SNP	ENST00000345617.3	hg19	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.702272	0.68501	.	.	ENSG00000068024	ENST00000345617;ENST00000541256;ENST00000454542;ENST00000446876	T;T;T;T	0.66995	0.99;0.99;-0.24;-0.18	4.29	4.29	0.51040	Histone deacetylase, glutamine rich N-terminal domain (1);	0.000000	0.64402	D	0.000007	T	0.79598	0.4473	M	0.71206	2.165	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.995;0.999	D;D;D;D;D	0.91635	0.999;0.977;0.987;0.929;0.977	T	0.80542	-0.1336	9	.	.	.	.	13.7561	0.62937	1.0:0.0:0.0:0.0	.	103;77;77;76;108	B7Z8G5;F5H5W4;B7Z8I2;Q53SM2;P56524	.;.;.;.;HDAC4_HUMAN	P	108;77;77;81	ENSP00000264606:L108P;ENSP00000443057:L77P;ENSP00000405226:L77P;ENSP00000392912:L81P	.	L	-	2	0	HDAC4	239776482	1.000000	0.71417	0.958000	0.39756	0.665000	0.39181	8.779000	0.91792	1.736000	0.51660	0.460000	0.39030	CTC	.	.		0.682	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
SNED1	25992	hgsc.bcm.edu	37	2	241988110	241988110	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:241988110A>G	ENST00000310397.8	+	10	1431	c.1431A>G	c.(1429-1431)ggA>ggG	p.G477G	AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000342631.6_Silent_p.G477G|SNED1_ENST00000401884.1_Silent_p.G477G|SNED1_ENST00000405547.3_Silent_p.G477G|SNED1_ENST00000469006.1_3'UTR	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	477	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GCCGCAACGGAGGCAGATGCC	0.632																																					p.G477G		Atlas-SNP	.											.	SNED1	76	.	0			c.A1431G						.						50.0	62.0	58.0					2																	241988110		2062	4198	6260	SO:0001819	synonymous_variant	25992	exon10			CAACGGAGGCAGA	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.1431A>G	chr2.hg19:g.241988110A>G		111.0	0.0		121.0	5.0	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	hg19	CCDS46562.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.043|5.043	0.193556|0.193556	0.09599|0.09599	.|.	.|.	ENSG00000162804|ENSG00000162804	ENST00000431690|ENST00000401644	.|.	.|.	.|.	4.81|4.81	-4.89|-4.89	0.03103|0.03103	.|.	.|.	.|.	.|.	.|.	T|T	0.48554|0.48554	0.1506|0.1506	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.48399|0.48399	-0.9039|-0.9039	4|4	.|.	.|.	.|.	.|.	7.2522|7.2522	0.26156|0.26156	0.4664:0.0:0.4121:0.1215|0.4664:0.0:0.4121:0.1215	.|.	.|.	.|.	.|.	G|G	135|174	.|.	.|.	E|R	+|+	2|1	0|2	SNED1|SNED1	241636783|241636783	0.192000|0.192000	0.23301|0.23301	0.831000|0.831000	0.32960|0.32960	0.338000|0.338000	0.28826|0.28826	-0.758000|-0.758000	0.04766|0.04766	-0.784000|-0.784000	0.04528|0.04528	-0.376000|-0.376000	0.06991|0.06991	GAG|AGG	.	.		0.632	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
MTERF4	130916	hgsc.bcm.edu	37	2	242039228	242039228	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:242039228T>C	ENST00000391980.2	-	2	161	c.103A>G	c.(103-105)Acg>Gcg	p.T35A	MTERFD2_ENST00000495694.1_Missense_Mutation_p.T35A|MTERFD2_ENST00000407095.3_Missense_Mutation_p.T35A|MTERFD2_ENST00000406593.1_Intron|MTERFD2_ENST00000464344.2_Intron	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		35					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	rRNA binding (GO:0019843)			endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3)	20		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		GAAGCTGTCGTCCTTCTCTGT	0.507																																					p.T35A		Atlas-SNP	.											.	MTERFD2	33	.	0			c.A103G						.						50.0	51.0	51.0					2																	242039228		2203	4300	6503	SO:0001583	missense	130916	exon2			CTGTCGTCCTTCT																												ENST00000391980.2:c.103A>G	chr2.hg19:g.242039228T>C	ENSP00000375840:p.Thr35Ala	103.0	0.0		103.0	5.0	NM_182501	A8K6K0|Q9P0E0	Missense_Mutation	SNP	ENST00000391980.2	hg19	CCDS2544.1	.	.	.	.	.	.	.	.	.	.	T	10.72	1.428513	0.25726	.	.	ENSG00000122085	ENST00000495694;ENST00000401626;ENST00000391980;ENST00000424798;ENST00000407095;ENST00000434791	T;T;T;T;T;T	0.48201	0.82;0.88;2.7;1.47;1.49;0.92	4.39	0.138	0.14793	.	0.949254	0.08630	N	0.917139	T	0.29749	0.0743	L	0.29908	0.895	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.22487	-1.0215	10	0.32370	T	0.25	0.8672	2.2603	0.04065	0.2226:0.2928:0.0:0.4845	.	35;35	B4DKD5;Q7Z6M4	.;MTER2_HUMAN	A	35;35;35;28;35;14	ENSP00000419315:T35A;ENSP00000385183:T35A;ENSP00000375840:T35A;ENSP00000409023:T28A;ENSP00000385630:T35A;ENSP00000393063:T14A	ENSP00000241527:T35A	T	-	1	0	MTERFD2	241687901	0.008000	0.16893	0.001000	0.08648	0.025000	0.11179	0.979000	0.29500	0.175000	0.19841	0.482000	0.46254	ACG	.	.		0.507	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4		
CNTN6	27255	hgsc.bcm.edu	37	3	1367497	1367497	+	Splice_Site	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:1367497A>G	ENST00000446702.2	+	9	1573		c.e9-1		CNTN6_ENST00000350110.2_Splice_Site|CNTN6_ENST00000539053.1_Splice_Site			Q9UQ52	CNTN6_HUMAN	contactin 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)		TTTTTGAAACAGCTCCTCCAG	0.428																																					.		Atlas-SNP	.											.	CNTN6	245	.	0			c.947-2A>G						.						99.0	93.0	95.0					3																	1367497		2203	4300	6503	SO:0001630	splice_region_variant	27255	exon9			TGAAACAGCTCCT	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.947-1A>G	chr3.hg19:g.1367497A>G		42.0	0.0		66.0	5.0	NM_014461	Q2KHM2	Splice_Site	SNP	ENST00000446702.2	hg19	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.249872	0.80024	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7897	0.63133	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CNTN6	1342497	1.000000	0.71417	0.998000	0.56505	0.955000	0.61496	5.614000	0.67695	1.997000	0.58415	0.533000	0.62120	.	.	.		0.428	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	Intron
FANCD2	2177	hgsc.bcm.edu	37	3	10108949	10108949	+	Silent	SNP	T	T	C	rs201487858		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:10108949T>C	ENST00000419585.1	+	26	2603	c.2442T>C	c.(2440-2442)acT>acC	p.T814T	FANCD2_ENST00000287647.3_Silent_p.T814T|FANCD2_ENST00000383806.1_Silent_p.T814T|FANCD2_ENST00000383807.1_Silent_p.T814T			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	814					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		AGGTGCTCACTCGGTTAAAGC	0.413			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.T814T		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	.	FANCD2	253	.	0			c.T2442C						.						96.0	83.0	87.0					3																	10108949		2203	4300	6503	SO:0001819	synonymous_variant	2177	exon26	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GCTCACTCGGTTA	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.2442T>C	chr3.hg19:g.10108949T>C		61.0	0.0		115.0	7.0	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	hg19	CCDS33696.1																																																																																			.	T|0.998;C|0.002		0.413	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1		
GALNT15	117248	hgsc.bcm.edu	37	3	16268877	16268877	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:16268877A>G	ENST00000339732.5	+	10	2293	c.1790A>G	c.(1789-1791)cAc>cGc	p.H597R	GALNT15_ENST00000437509.1_Intron	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	597	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)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										ATGATTGTCCACATTCTTTCT	0.398																																					p.H597R		Atlas-SNP	.											.	.	.	.	0			c.A1790G						.						102.0	104.0	103.0					3																	16268877		2203	4300	6503	SO:0001583	missense	117248	exon10			TTGTCCACATTCT	AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	21531	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 15"""	615131	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"""	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.1790A>G	chr3.hg19:g.16268877A>G	ENSP00000344260:p.His597Arg	57.0	0.0		87.0	4.0	NM_054110	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Missense_Mutation	SNP	ENST00000339732.5	hg19	CCDS33711.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.949686	0.73787	.	.	ENSG00000131386	ENST00000339732;ENST00000543679	T	0.29917	1.55	5.62	5.62	0.85841	Ricin B-related lectin (1);Ricin B lectin (3);	0.000000	0.85682	D	0.000000	T	0.58380	0.2118	M	0.85041	2.73	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.64960	-0.6284	10	0.87932	D	0	.	12.4983	0.55942	1.0:0.0:0.0:0.0	.	597	Q8N3T1	GLTL2_HUMAN	R	597;127	ENSP00000344260:H597R	ENSP00000344260:H597R	H	+	2	0	GALNTL2	16243881	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.013000	0.64023	2.266000	0.75297	0.533000	0.62120	CAC	.	.		0.398	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110	
SATB1	6304	hgsc.bcm.edu	37	3	18427925	18427925	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:18427925G>T	ENST00000338745.6	-	8	3119	c.1385C>A	c.(1384-1386)cCc>cAc	p.P462H	TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000417717.2_Missense_Mutation_p.P462H|SATB1_ENST00000454909.2_Missense_Mutation_p.P462H	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	462					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						GCTGATGAGGGGGGCAGGACC	0.512																																					p.P462H		Atlas-SNP	.											.	SATB1	96	.	0			c.C1385A						.						161.0	172.0	168.0					3																	18427925		2203	4300	6503	SO:0001583	missense	6304	exon8			ATGAGGGGGGCAG		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"""Homeoboxes / CUT class"""	10541	protein-coding gene	gene with protein product		602075	"""special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"""			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.1385C>A	chr3.hg19:g.18427925G>T	ENSP00000341024:p.Pro462His	131.0	0.0		191.0	9.0	NM_002971	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	hg19	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	G	11.98	1.801329	0.31869	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717	T;T;T	0.48522	0.81;0.81;0.81	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.57592	0.2064	N	0.19112	0.55	0.80722	D	1	D;B	0.71674	0.998;0.059	D;B	0.69824	0.966;0.038	T	0.58901	-0.7554	10	0.59425	D	0.04	-0.8987	20.8794	0.99867	0.0:0.0:1.0:0.0	.	462;462	Q01826-2;Q01826	.;SATB1_HUMAN	H	462	ENSP00000341024:P462H;ENSP00000399708:P462H;ENSP00000399518:P462H	ENSP00000341024:P462H	P	-	2	0	SATB1	18402929	1.000000	0.71417	0.996000	0.52242	0.229000	0.25112	7.876000	0.87215	2.941000	0.99782	0.655000	0.94253	CCC	.	.		0.512	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010	
KCNH8	131096	hgsc.bcm.edu	37	3	19559532	19559532	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:19559532A>G	ENST00000328405.2	+	15	2851	c.2585A>G	c.(2584-2586)gAg>gGg	p.E862G		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	862					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						AAAGCAGAGGAGACCAAGCAG	0.408																																					p.E862G	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.A2585G						.						114.0	113.0	113.0					3																	19559532		2203	4300	6503	SO:0001583	missense	131096	exon15			CAGAGGAGACCAA	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.2585A>G	chr3.hg19:g.19559532A>G	ENSP00000328813:p.Glu862Gly	96.0	0.0		131.0	7.0	NM_144633	B7Z2I7|Q59GQ6	Missense_Mutation	SNP	ENST00000328405.2	hg19	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	A	17.67	3.447487	0.63178	.	.	ENSG00000183960	ENST00000328405	D	0.99105	-5.43	5.66	5.66	0.87406	.	0.000000	0.31976	U	0.006779	D	0.97558	0.9200	L	0.54323	1.7	0.80722	D	1	B	0.21606	0.058	B	0.23852	0.049	D	0.96921	0.9674	9	.	.	.	.	14.7558	0.69564	1.0:0.0:0.0:0.0	.	862	Q96L42	KCNH8_HUMAN	G	862	ENSP00000328813:E862G	.	E	+	2	0	KCNH8	19534536	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.652000	0.67959	2.277000	0.76020	0.528000	0.53228	GAG	.	.		0.408	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633	
NEK10	152110	hgsc.bcm.edu	37	3	27335088	27335088	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:27335088A>G	ENST00000429845.2	-	17	1726	c.1364T>C	c.(1363-1365)cTc>cCc	p.L455P	NEK10_ENST00000357467.2_5'Flank|NEK10_ENST00000341435.5_Missense_Mutation_p.L455P			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	455					positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CCTTTTAAAGAGTGGTCTGTT	0.348																																					p.L455P		Atlas-SNP	.											.	NEK10	271	.	0			c.T1364C						.						77.0	67.0	70.0					3																	27335088		1568	3582	5150	SO:0001583	missense	152110	exon17			TTAAAGAGTGGTC	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)- related kinase 10"""			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.1364T>C	chr3.hg19:g.27335088A>G	ENSP00000395849:p.Leu455Pro	59.0	0.0		101.0	5.0	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Missense_Mutation	SNP	ENST00000429845.2	hg19		.	.	.	.	.	.	.	.	.	.	A	18.11	3.551171	0.65311	.	.	ENSG00000163491	ENST00000341435;ENST00000396636	T	0.52526	0.66	5.44	5.44	0.79542	Armadillo-like helical (1);	0.305868	0.31335	N	0.007823	T	0.59459	0.2195	L	0.43152	1.355	0.80722	D	1	D	0.69078	0.997	P	0.62649	0.905	T	0.63056	-0.6722	10	0.87932	D	0	.	15.4989	0.75680	1.0:0.0:0.0:0.0	.	455	Q6ZWH5	NEK10_HUMAN	P	455	ENSP00000343847:L455P	ENSP00000343847:L455P	L	-	2	0	NEK10	27310092	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.591000	0.74090	2.052000	0.61016	0.528000	0.53228	CTC	.	.		0.348	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534	
OSBPL10	114884	hgsc.bcm.edu	37	3	31712394	31712394	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:31712394G>T	ENST00000396556.2	-	9	1930	c.1808C>A	c.(1807-1809)cCg>cAg	p.P603Q	OSBPL10_ENST00000438237.2_Missense_Mutation_p.P539Q	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	603					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)	p.P603L(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		CTCCACCCACGGGATGGTGAG	0.567																																					p.P603Q		Atlas-SNP	.											OSBPL10_ENST00000396556,extremity,malignant_melanoma,0,6	OSBPL10	160	.	2	Substitution - Missense(2)	skin(2)	c.C1808A						.						131.0	115.0	120.0					3																	31712394		2203	4300	6503	SO:0001583	missense	114884	exon9			ACCCACGGGATGG	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.1808C>A	chr3.hg19:g.31712394G>T	ENSP00000379804:p.Pro603Gln	140.0	0.0		197.0	0.0	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	hg19	CCDS2651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.72|17.72	3.458058|3.458058	0.63401|0.63401	.|.	.|.	ENSG00000144645|ENSG00000144645	ENST00000396556;ENST00000438237|ENST00000429492	T;T|.	0.32753|.	1.44;1.44|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87565|0.87565	0.6209|0.6209	H|H	0.95004|0.95004	3.61|3.61	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;1.0|.	D|D	0.90774|0.90774	0.4674|0.4674	10|5	0.72032|.	D|.	0.01|.	-18.8515|-18.8515	19.3207|19.3207	0.94237|0.94237	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	539;603;371|.	B4E212;Q9BXB5;Q59ED9|.	.;OSB10_HUMAN;.|.	Q|S	603;539|372	ENSP00000379804:P603Q;ENSP00000406124:P539Q|.	ENSP00000379804:P603Q|.	P|R	-|-	2|1	0|0	OSBPL10|OSBPL10	31687398|31687398	1.000000|1.000000	0.71417|0.71417	0.841000|0.841000	0.33234|0.33234	0.009000|0.009000	0.06853|0.06853	9.869000|9.869000	0.99810|0.99810	2.550000|2.550000	0.86006|0.86006	0.557000|0.557000	0.71058|0.71058	CCG|CGT	.	.		0.567	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2		
OXSR1	9943	hgsc.bcm.edu	37	3	38207429	38207429	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:38207429A>G	ENST00000446845.1	+	1	434	c.62A>G	c.(61-63)gAg>gGg	p.E21G	OXSR1_ENST00000311806.3_Missense_Mutation_p.E21G|OXSR1_ENST00000492714.1_Intron					oxidative stress responsive 1											skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		GAGCTGCAGGAGGTGATCGGT	0.716																																					p.E21G		Atlas-SNP	.											.	OXSR1	74	.	0			c.A62G						.						22.0	23.0	22.0					3																	38207429		2202	4298	6500	SO:0001583	missense	9943	exon1			TGCAGGAGGTGAT	AB017642	CCDS2675.1	3p22.2	2013-05-17	2013-05-17	2004-11-26	ENSG00000172939	ENSG00000172939			8508	protein-coding gene	gene with protein product		604046	"""oxidative-stress responsive 1"""	OSR1		10083736	Standard	XM_005265638		Approved	KIAA1101	uc003chy.3	O95747	OTTHUMG00000131084	ENST00000446845.1:c.62A>G	chr3.hg19:g.38207429A>G	ENSP00000415851:p.Glu21Gly	130.0	0.0		189.0	8.0	NM_005109		Missense_Mutation	SNP	ENST00000446845.1	hg19		.	.	.	.	.	.	.	.	.	.	A	21.6	4.172832	0.78452	.	.	ENSG00000172939	ENST00000446845;ENST00000311806	T;T	0.23754	1.89;1.89	3.89	2.72	0.32119	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.051096	0.85682	N	0.000000	T	0.28699	0.0711	L	0.59436	1.845	0.80722	D	1	P	0.41498	0.752	P	0.45119	0.47	T	0.03840	-1.0999	10	0.87932	D	0	-5.6688	7.5008	0.27516	0.8933:0.0:0.1067:0.0	.	21	O95747	OXSR1_HUMAN	G	21	ENSP00000415851:E21G;ENSP00000311713:E21G	ENSP00000311713:E21G	E	+	2	0	OXSR1	38182433	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.387000	0.73191	0.674000	0.31244	0.454000	0.30748	GAG	.	.		0.716	OXSR1-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000342708.1	NM_005109	
KIF15	56992	hgsc.bcm.edu	37	3	44835775	44835775	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:44835775T>C	ENST00000326047.4	+	8	855	c.706T>C	c.(706-708)Tct>Cct	p.S236P	AC098649.1_ENST00000459037.1_RNA	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	236	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)		ATCGTCTAGGTCTCATGCCGT	0.403																																					p.S236P		Atlas-SNP	.											.	KIF15	103	.	0			c.T706C						.						158.0	139.0	145.0					3																	44835775		2203	4300	6503	SO:0001583	missense	56992	exon8			TCTAGGTCTCATG	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.706T>C	chr3.hg19:g.44835775T>C	ENSP00000324020:p.Ser236Pro	114.0	0.0		165.0	7.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Missense_Mutation	SNP	ENST00000326047.4	hg19	CCDS33744.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.436083	0.83885	.	.	ENSG00000163808	ENST00000326047;ENST00000481166;ENST00000396031	D;D	0.87966	-2.32;-2.32	5.1	5.1	0.69264	Kinesin, motor domain (5);	0.000000	0.51477	D	0.000094	D	0.96163	0.8749	H	0.98646	4.29	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97817	1.0254	10	0.87932	D	0	.	14.882	0.70540	0.0:0.0:0.0:1.0	.	236	Q9NS87	KIF15_HUMAN	P	236;8;235	ENSP00000324020:S236P;ENSP00000425499:S8P	ENSP00000324020:S236P	S	+	1	0	KIF15	44810779	1.000000	0.71417	0.937000	0.37676	0.738000	0.42128	7.698000	0.84413	1.926000	0.55796	0.533000	0.62120	TCT	.	.		0.403	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2		
PFKFB4	5210	hgsc.bcm.edu	37	3	48561220	48561220	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:48561220T>C	ENST00000232375.3	-	11	1248	c.1136A>G	c.(1135-1137)gAg>gGg	p.E379G	PFKFB4_ENST00000536104.1_Missense_Mutation_p.E368G|PFKFB4_ENST00000383734.2_Missense_Mutation_p.E344G|PFKFB4_ENST00000490115.1_5'UTR|PFKFB4_ENST00000416568.1_Missense_Mutation_p.E372G|PFKFB4_ENST00000541519.1_Missense_Mutation_p.E345G	NM_004567.2	NP_004558.1	Q16877	F264_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	379	Fructose-2,6-bisphosphatase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(193;0.0003)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)		CCTCTCCAGCTCCATGATGAC	0.627																																					p.E379G		Atlas-SNP	.											.	PFKFB4	39	.	0			c.A1136G						.						116.0	98.0	104.0					3																	48561220		2203	4300	6503	SO:0001583	missense	5210	exon11			TCCAGCTCCATGA	BC010269	CCDS2771.1	3p22-p21	2004-03-02			ENSG00000114268	ENSG00000114268			8875	protein-coding gene	gene with protein product		605320				8830046, 10095107	Standard	NM_004567		Approved		uc003ctv.3	Q16877	OTTHUMG00000133528	ENST00000232375.3:c.1136A>G	chr3.hg19:g.48561220T>C	ENSP00000232375:p.Glu379Gly	143.0	0.0		198.0	8.0	NM_004567	Q5S3G5|Q5XLC2|Q64EX5	Missense_Mutation	SNP	ENST00000232375.3	hg19	CCDS2771.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.686400	0.88639	.	.	ENSG00000114268	ENST00000232375;ENST00000536104;ENST00000416568;ENST00000383734;ENST00000541519	T;T;T;T	0.74421	-0.84;-0.84;-0.84;-0.84	4.71	4.71	0.59529	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.85682	D	0.000000	D	0.88001	0.6320	M	0.91768	3.24	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.87578	0.998;0.986;0.998;0.992	D	0.90273	0.4309	10	0.87932	D	0	-1.8298	12.1756	0.54184	0.0:0.0:0.0:1.0	.	368;344;372;379	B7Z5C3;Q5XLC2;Q66S35;Q16877	.;.;.;F264_HUMAN	G	379;368;372;344;345	ENSP00000232375:E379G;ENSP00000438908:E368G;ENSP00000388394:E372G;ENSP00000437446:E345G	ENSP00000232375:E379G	E	-	2	0	PFKFB4	48536224	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.825000	0.86693	1.961000	0.56991	0.460000	0.39030	GAG	.	.		0.627	PFKFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257503.2	NM_004567	
APEH	327	hgsc.bcm.edu	37	3	49722913	49722913	+	IGR	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	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		262.0	0.0		552.0	46.0	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		
CDHR4	389118	hgsc.bcm.edu	37	3	49836290	49836290	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:49836290A>G	ENST00000412678.2	-	4	472	c.464T>C	c.(463-465)cTc>cCc	p.L155P	CDHR4_ENST00000343366.4_Silent_p.A180A|CDHR4_ENST00000487256.1_Missense_Mutation_p.L155P	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	155					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						GCCTGGGAGGAGCAGAGTGTA	0.597																																					p.L155P		Atlas-SNP	.											.	CDHR4	37	.	0			c.T464C						.						36.0	41.0	39.0					3																	49836290		2024	4179	6203	SO:0001583	missense	389118	exon4			GGGAGGAGCAGAG		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"""Cadherins / Cadherin-related"""	34527	protein-coding gene	gene with protein product			"""cadherin-like 29"""	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.464T>C	chr3.hg19:g.49836290A>G	ENSP00000391409:p.Leu155Pro	115.0	0.0		142.0	7.0	NM_001007540	Q6UXT0	Missense_Mutation	SNP	ENST00000412678.2	hg19	CCDS46829.1	.	.	.	.	.	.	.	.	.	.	A	14.27	2.484399	0.44147	.	.	ENSG00000187492	ENST00000412678;ENST00000487256	T;T	0.57907	0.37;0.58	4.81	4.81	0.61882	.	.	.	.	.	T	0.59004	0.2162	L	0.32530	0.975	0.54753	D	0.999982	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.54715	-0.8252	9	0.25751	T	0.34	-7.2563	12.0308	0.53396	1.0:0.0:0.0:0.0	.	155;155	E9PFE8;A6H8M9	.;CDHR4_HUMAN	P	155	ENSP00000391409:L155P;ENSP00000420677:L155P	ENSP00000391409:L155P	L	-	2	0	CDHR4	49811294	0.985000	0.35326	1.000000	0.80357	0.162000	0.22319	4.665000	0.61547	1.932000	0.55993	0.482000	0.46254	CTC	.	.		0.597	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540	
RBM6	10180	hgsc.bcm.edu	37	3	50095987	50095987	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:50095987T>C	ENST00000266022.4	+	10	2381	c.2122T>C	c.(2122-2124)Tcc>Ccc	p.S708P	RBM6_ENST00000441115.1_3'UTR|RBM6_ENST00000539992.1_Missense_Mutation_p.S50P|RBM6_ENST00000442092.1_Missense_Mutation_p.S186P|RBM6_ENST00000443081.1_Missense_Mutation_p.S576P|RBM6_ENST00000422955.1_Missense_Mutation_p.S186P	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	708					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		TGACCTCGACTCCCATGCGGT	0.542																																					p.S708P		Atlas-SNP	.											.	RBM6	85	.	0			c.T2122C						.						156.0	139.0	145.0					3																	50095987		2203	4300	6503	SO:0001583	missense	10180	exon10			CTCGACTCCCATG	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.2122T>C	chr3.hg19:g.50095987T>C	ENSP00000266022:p.Ser708Pro	51.0	0.0		86.0	4.0	NM_005777	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	hg19	CCDS2809.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.824828	0.90955	.	.	ENSG00000004534	ENST00000442092;ENST00000266022;ENST00000443081;ENST00000539992;ENST00000422955	T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75	5.71	5.71	0.89125	Nucleotide-binding, alpha-beta plait (1);	0.982328	0.08318	N	0.964376	T	0.31827	0.0809	L	0.55990	1.75	0.48830	D	0.999712	D;D	0.76494	0.999;0.995	D;P	0.70487	0.969;0.874	T	0.00080	-1.2110	9	.	.	.	-1.9563	16.0336	0.80603	0.0:0.0:0.0:1.0	.	576;708	E9PGM9;P78332	.;RBM6_HUMAN	P	186;708;576;50;186	ENSP00000393530:S186P;ENSP00000266022:S708P;ENSP00000396466:S576P;ENSP00000443165:S50P;ENSP00000392939:S186P	.	S	+	1	0	RBM6	50070991	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.086000	0.57664	2.189000	0.69895	0.529000	0.55759	TCC	.	.		0.542	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777	
DOCK3	1795	hgsc.bcm.edu	37	3	51198017	51198017	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:51198017T>C	ENST00000266037.9	+	12	944	c.921T>C	c.(919-921)ggT>ggC	p.G307G		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	307					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		CAAAGAAAGGTCCTCCTCACC	0.493																																					p.G307G		Atlas-SNP	.											.	DOCK3	397	.	0			c.T921C						.						66.0	67.0	66.0					3																	51198017		2054	4192	6246	SO:0001819	synonymous_variant	1795	exon12			GAAAGGTCCTCCT	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"""dedicator of cyto-kinesis 3"""			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.921T>C	chr3.hg19:g.51198017T>C		72.0	0.0		127.0	6.0	NM_004947	O15017	Silent	SNP	ENST00000266037.9	hg19	CCDS46835.1																																																																																			.	.		0.493	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947	
DENND6A	201627	hgsc.bcm.edu	37	3	57644895	57644895	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:57644895T>C	ENST00000311128.5	-	8	782	c.712A>G	c.(712-714)Aca>Gca	p.T238A		NM_152678.2	NP_689891.1	Q8IWF6	DEN6A_HUMAN	DENN/MADD domain containing 6A	238					positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)|recycling endosome (GO:0055037)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										TCATGACATGTGGGAATCCGT	0.393																																					p.T238A		Atlas-SNP	.											.	.	.	.	0			c.A712G						.						173.0	163.0	166.0					3																	57644895		2203	4300	6503	SO:0001583	missense	201627	exon8			GACATGTGGGAAT	AK074156	CCDS33773.1	3p14.3	2013-10-11	2012-10-03	2012-10-03	ENSG00000174839	ENSG00000174839		"""DENN/MADD domain containing"""	26635	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member A"""	FAM116A		21330364	Standard	NM_152678		Approved	FLJ34969, AFI1A	uc003dja.3	Q8IWF6	OTTHUMG00000158639	ENST00000311128.5:c.712A>G	chr3.hg19:g.57644895T>C	ENSP00000311401:p.Thr238Ala	67.0	0.0		94.0	4.0	NM_152678	Q7Z5T4|Q8N235|Q8TEG8	Missense_Mutation	SNP	ENST00000311128.5	hg19	CCDS33773.1	.	.	.	.	.	.	.	.	.	.	T	18.17	3.564656	0.65651	.	.	ENSG00000174839	ENST00000311128	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.43964	0.1271	N	0.25647	0.755	0.58432	D	0.999995	B	0.17038	0.02	B	0.20955	0.032	T	0.37267	-0.9713	9	0.07813	T	0.8	-15.4435	16.0684	0.80907	0.0:0.0:0.0:1.0	.	238	Q8IWF6	F116A_HUMAN	A	238	.	ENSP00000311401:T238A	T	-	1	0	FAM116A	57619935	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.985000	0.70556	2.272000	0.75746	0.460000	0.39030	ACA	.	.		0.393	DENND6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351594.1	NM_152678	
ROBO1	6091	hgsc.bcm.edu	37	3	78719381	78719381	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:78719381A>G	ENST00000464233.1	-	11	1526	c.1413T>C	c.(1411-1413)acT>acC	p.T471T	ROBO1_ENST00000467549.1_Silent_p.T435T|ROBO1_ENST00000495273.1_Silent_p.T435T|ROBO1_ENST00000436010.2_Silent_p.T432T	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	471	Ig-like C2-type 5.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TGAGGACGAAAGTGCCATCCA	0.507																																					p.T471T		Atlas-SNP	.											.	ROBO1	833	.	0			c.T1413C						.						45.0	44.0	44.0					3																	78719381		1963	4173	6136	SO:0001819	synonymous_variant	6091	exon11			GACGAAAGTGCCA	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10249	protein-coding gene	gene with protein product		602430	"""roundabout (axon guidance receptor, Drosophila) homolog 1"""			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.1413T>C	chr3.hg19:g.78719381A>G		48.0	0.0		95.0	4.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	hg19	CCDS54611.1																																																																																			.	.		0.507	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941	
EPHA3	2042	hgsc.bcm.edu	37	3	89480505	89480505	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:89480505C>G	ENST00000336596.2	+	13	2567	c.2342C>G	c.(2341-2343)aCa>aGa	p.T781R	EPHA3_ENST00000494014.1_Missense_Mutation_p.T781R	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	781	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		GCTTATACAACAAGAGTGAGT	0.388										TSP Lung(6;0.00050)																											p.T781R		Atlas-SNP	.											.	EPHA3	501	.	0			c.C2342G						.						94.0	90.0	92.0					3																	89480505		2203	4300	6503	SO:0001583	missense	2042	exon13			ATACAACAAGAGT	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2342C>G	chr3.hg19:g.89480505C>G	ENSP00000337451:p.Thr781Arg	121.0	0.0		141.0	83.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.279726	0.80692	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	D;D	0.82081	-1.57;-1.57	5.33	5.33	0.75918	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.88702	0.6508	L	0.48362	1.52	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87033	0.2136	9	.	.	.	.	19.3726	0.94495	0.0:1.0:0.0:0.0	.	781	P29320	EPHA3_HUMAN	R	781	ENSP00000337451:T781R;ENSP00000419190:T781R	.	T	+	2	0	EPHA3	89563195	1.000000	0.71417	1.000000	0.80357	0.730000	0.41778	7.776000	0.85560	2.648000	0.89879	0.585000	0.79938	ACA	.	.		0.388	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
SLC9C1	285335	hgsc.bcm.edu	37	3	111888153	111888153	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:111888153T>C	ENST00000305815.5	-	24	3194	c.2942A>G	c.(2941-2943)cAc>cGc	p.H981R	SLC9C1_ENST00000487372.1_Missense_Mutation_p.H933R	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	981					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										ATCATACAAGTGAGTTTTGGG	0.318																																					p.H981R		Atlas-SNP	.											.	.	.	.	0			c.A2942G						.						88.0	87.0	87.0					3																	111888153		2203	4300	6503	SO:0001583	missense	285335	exon24			TACAAGTGAGTTT	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2942A>G	chr3.hg19:g.111888153T>C	ENSP00000306627:p.His981Arg	74.0	0.0		84.0	4.0	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	hg19	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	T	13.95	2.389764	0.42410	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	D;D	0.92348	-3.02;-3.02	5.83	4.65	0.58169	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.499344	0.19936	N	0.102757	D	0.90655	0.7069	L	0.52364	1.645	0.09310	N	1	P;D	0.54397	0.713;0.966	P;P	0.52109	0.596;0.69	T	0.81206	-0.1038	10	0.15066	T	0.55	-0.562	9.0919	0.36617	0.1632:0.0:0.0:0.8368	.	933;981	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	R	981;933	ENSP00000306627:H981R;ENSP00000420688:H933R	ENSP00000306627:H981R	H	-	2	0	SLC9A10	113370843	0.981000	0.34729	0.003000	0.11579	0.008000	0.06430	2.740000	0.47418	0.993000	0.38866	0.491000	0.48974	CAC	.	.		0.318	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
SLC15A2	6565	hgsc.bcm.edu	37	3	121613348	121613348	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:121613348T>C	ENST00000489711.1	+	1	413	c.25T>C	c.(25-27)Tcc>Ccc	p.S9P	SLC15A2_ENST00000295605.2_Missense_Mutation_p.S9P	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	9					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	GAAAAATGAGTCCAAGGAAAC	0.483																																					p.S9P		Atlas-SNP	.											.	SLC15A2	92	.	0			c.T25C						.						167.0	179.0	175.0					3																	121613348		2203	4300	6503	SO:0001583	missense	6565	exon1			AATGAGTCCAAGG	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"""Solute carriers"""	10921	protein-coding gene	gene with protein product		602339	"""solute carrier family 15 (H+/peptide transporter), member 2"""			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.25T>C	chr3.hg19:g.121613348T>C	ENSP00000417085:p.Ser9Pro	68.0	0.0		93.0	4.0	NM_001145998	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	hg19	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.003908	0.74932	.	.	ENSG00000163406	ENST00000489711;ENST00000295605	T;T	0.03553	4.3;3.89	5.1	5.1	0.69264	Major facilitator superfamily domain, general substrate transporter (1);	0.102776	0.43919	D	0.000505	T	0.11410	0.0278	L	0.42245	1.32	0.35790	D	0.82235	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.06391	-1.0829	10	0.66056	D	0.02	-4.6463	11.2128	0.48808	0.0:0.0:0.0:1.0	.	9;9	B4E2A7;Q16348	.;S15A2_HUMAN	P	9	ENSP00000417085:S9P;ENSP00000295605:S9P	ENSP00000295605:S9P	S	+	1	0	SLC15A2	123096038	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.163000	0.58183	2.141000	0.66446	0.455000	0.32223	TCC	.	.		0.483	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082	
MYLK	4638	hgsc.bcm.edu	37	3	123419119	123419119	+	Missense_Mutation	SNP	C	C	G	rs372794395|rs72491150|rs75967604	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:123419119C>G	ENST00000475616.1	-	15	3195	c.3196G>C	c.(3196-3198)Gaa>Caa	p.E1066Q	MYLK_ENST00000359169.1_Missense_Mutation_p.E1066Q|MYLK_ENST00000360772.3_Missense_Mutation_p.E1066Q|MYLK_ENST00000360304.3_Missense_Mutation_p.E1066Q|MYLK_ENST00000346322.5_Missense_Mutation_p.E997Q|MYLK_ENST00000510775.1_5'Flank			Q15746	MYLK_HUMAN	myosin light chain kinase	1066	Actin-binding (calcium/calmodulin- insensitive). {ECO:0000250}.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)	p.E1066K(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		TTCTTGAGTTCTTCTTTGCTA	0.527																																					p.E1066Q		Atlas-SNP	.											MYLK,bladder,carcinoma,0,1	MYLK	224	.	1	Substitution - Missense(1)	urinary_tract(1)	c.G3196C						.						262.0	266.0	265.0					3																	123419119		2203	4300	6503	SO:0001583	missense	4638	exon18			TGAGTTCTTCTTT	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.3196G>C	chr3.hg19:g.123419119C>G	ENSP00000418335:p.Glu1066Gln	133.0	2.0		163.0	9.0	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	hg19	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	C	11.12	1.544986	0.27652	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.67523	-0.27;-0.22;-0.27;-0.2;-0.22	5.69	5.69	0.88448	.	.	.	.	.	T	0.69726	0.3143	M	0.68952	2.095	0.80722	D	1	B;B;P;P;P;B	0.47106	0.404;0.008;0.89;0.709;0.89;0.282	B;B;B;B;B;B	0.44224	0.353;0.014;0.444;0.353;0.444;0.192	T	0.71451	-0.4589	9	0.44086	T	0.13	.	17.998	0.89189	0.0:1.0:0.0:0.0	.	1066;144;997;1066;997;1066	Q15746-6;Q15746-7;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;.;MYLK_HUMAN	Q	1066;1066;1066;997;1066	ENSP00000354004:E1066Q;ENSP00000353452:E1066Q;ENSP00000352088:E1066Q;ENSP00000320622:E997Q;ENSP00000418335:E1066Q	ENSP00000320622:E997Q	E	-	1	0	MYLK	124901809	0.997000	0.39634	1.000000	0.80357	0.169000	0.22640	1.326000	0.33735	2.692000	0.91855	0.505000	0.49811	GAA	.	.		0.527	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
PLXND1	23129	hgsc.bcm.edu	37	3	129277345	129277345	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:129277345T>C	ENST00000324093.4	-	33	5549	c.5371A>G	c.(5371-5373)Atc>Gtc	p.I1791V	PLXND1_ENST00000393239.1_3'UTR|PLXND1_ENST00000504689.1_5'Flank	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1791					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						CAGGCGTCGATGTGGTCTGTC	0.577																																					p.I1791V	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.A5371G						.						81.0	74.0	77.0					3																	129277345		2203	4300	6503	SO:0001583	missense	23129	exon33			CGTCGATGTGGTC	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.5371A>G	chr3.hg19:g.129277345T>C	ENSP00000317128:p.Ile1791Val	70.0	0.0		130.0	6.0	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	5.814|5.814	0.334382|0.334382	0.11013|0.11013	.|.	.|.	ENSG00000004399|ENSG00000004399	ENST00000506979|ENST00000324093	T|T	0.11277|0.10477	2.79|2.87	4.68|4.68	4.68|4.68	0.58851|0.58851	.|Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	.|0.110120	.|0.64402	.|D	.|0.000010	T|T	0.03959|0.03959	0.0111|0.0111	N|N	0.01015|0.01015	-1.05|-1.05	0.80722|0.80722	D|D	1|1	.|B;P	.|0.35551	.|0.018;0.509	.|B;B	.|0.35607	.|0.018;0.206	T|T	0.54938|0.54938	-0.8218|-0.8218	7|10	0.44086|0.23891	T|T	0.13|0.37	.|.	13.3343|13.3343	0.60507|0.60507	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|387;1791	.|B4DRU3;Q9Y4D7	.|.;PLXD1_HUMAN	R|V	134|1791	ENSP00000427696:H134R|ENSP00000317128:I1791V	ENSP00000427696:H134R|ENSP00000317128:I1791V	H|I	-|-	2|1	0|0	PLXND1|PLXND1	130760035|130760035	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	4.010000|4.010000	0.57117|0.57117	1.737000|1.737000	0.51674|0.51674	0.459000|0.459000	0.35465|0.35465	CAT|ATC	.	.		0.577	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
COL6A6	131873	hgsc.bcm.edu	37	3	130300684	130300684	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:130300684T>C	ENST00000358511.6	+	8	3858	c.3827T>C	c.(3826-3828)cTc>cCc	p.L1276P	COL6A6_ENST00000453409.2_Missense_Mutation_p.L1276P	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1276	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						CCATCTCTTCTCAATGCAAAC	0.363																																					p.L1276P		Atlas-SNP	.											.	COL6A6	497	.	0			c.T3827C						.						173.0	167.0	169.0					3																	130300684		1873	4094	5967	SO:0001583	missense	131873	exon8			CTCTTCTCAATGC	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.3827T>C	chr3.hg19:g.130300684T>C	ENSP00000351310:p.Leu1276Pro	88.0	0.0		149.0	6.0	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.32|13.32	2.201236|2.201236	0.38905|0.38905	.|.	.|.	ENSG00000206384|ENSG00000206384	ENST00000358511;ENST00000453409|ENST00000511332	T;T|.	0.38560|.	1.13;1.13|.	6.06|6.06	6.06|6.06	0.98353|0.98353	von Willebrand factor, type A (2);|.	.|.	.|.	.|.	.|.	T|T	0.75302|0.75302	0.3831|0.3831	M|M	0.76170|0.76170	2.325|2.325	0.58432|0.58432	D|D	0.999999|0.999999	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	T|T	0.75499|0.75499	-0.3296|-0.3296	9|5	0.46703|.	T|.	0.11|.	.|.	15.5919|15.5919	0.76537|0.76537	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1276|.	A6NMZ7|.	CO6A6_HUMAN|.	P|P	1276|34	ENSP00000351310:L1276P;ENSP00000399236:L1276P|.	ENSP00000351310:L1276P|.	L|S	+|+	2|1	0|0	COL6A6|COL6A6	131783374|131783374	0.994000|0.994000	0.37717|0.37717	0.394000|0.394000	0.26270|0.26270	0.009000|0.009000	0.06853|0.06853	5.297000|5.297000	0.65704|0.65704	2.324000|2.324000	0.78689|0.78689	0.533000|0.533000	0.62120|0.62120	CTC|TCA	.	.		0.363	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
MRPS22	56945	hgsc.bcm.edu	37	3	139074572	139074572	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:139074572A>G	ENST00000495075.1	+	9	1359	c.927A>G	c.(925-927)ccA>ccG	p.P309P	MRPS22_ENST00000310776.4_Silent_p.P309P|MRPS22_ENST00000465056.1_Silent_p.P308P|MRPS22_ENST00000478464.1_Silent_p.P268P			P82650	RT22_HUMAN	mitochondrial ribosomal protein S22	309						mitochondrial ribosome (GO:0005761)|mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	12						TGCTCCATCCAGATGGCCAGT	0.418																																					p.P309P		Atlas-SNP	.											.	MRPS22	40	.	0			c.A927G						.						76.0	75.0	75.0					3																	139074572		2203	4300	6503	SO:0001819	synonymous_variant	56945	exon7			CCATCCAGATGGC	AF226045	CCDS3107.1	3q23	2012-09-13			ENSG00000175110	ENSG00000175110		"""Mitochondrial ribosomal proteins / small subunits"""	14508	protein-coding gene	gene with protein product		605810				11175783	Standard	NM_020191		Approved	MRP-S22, GK002, C3orf5, GIBT	uc003etb.3	P82650	OTTHUMG00000159910	ENST00000495075.1:c.927A>G	chr3.hg19:g.139074572A>G		154.0	0.0		243.0	10.0	NM_020191	Q9H3I1	Silent	SNP	ENST00000495075.1	hg19	CCDS3107.1																																																																																			.	.		0.418	MRPS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358120.1	NM_020191	
CHST2	9435	hgsc.bcm.edu	37	3	142840446	142840446	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:142840446T>C	ENST00000309575.3	+	2	2172	c.788T>C	c.(787-789)cTc>cCc	p.L263P		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	263					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						TCGTCACCACTCTGCCCCGCC	0.677																																					p.L263P		Atlas-SNP	.											.	CHST2	67	.	0			c.T788C						.						20.0	24.0	23.0					3																	142840446		2201	4299	6500	SO:0001583	missense	9435	exon2			CACCACTCTGCCC	BC042160	CCDS3129.1	3q24	2007-03-14			ENSG00000175040	ENSG00000175040		"""Sulfotransferases, membrane-bound"""	1970	protein-coding gene	gene with protein product		603798				10049591	Standard	NM_004267		Approved	C6ST	uc003evm.3	Q9Y4C5	OTTHUMG00000159351	ENST00000309575.3:c.788T>C	chr3.hg19:g.142840446T>C	ENSP00000307911:p.Leu263Pro	90.0	0.0		120.0	5.0	NM_004267	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	hg19	CCDS3129.1	.	.	.	.	.	.	.	.	.	.	T	14.86	2.660842	0.47572	.	.	ENSG00000175040	ENST00000309575	D	0.96856	-4.15	4.17	4.17	0.49024	Sulfotransferase domain (1);	0.000000	0.56097	U	0.000026	D	0.97467	0.9171	M	0.70275	2.135	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	D	0.97825	1.0259	10	0.62326	D	0.03	-16.2734	13.3769	0.60743	0.0:0.0:0.0:1.0	.	263	Q9Y4C5	CHST2_HUMAN	P	263	ENSP00000307911:L263P	ENSP00000307911:L263P	L	+	2	0	CHST2	144323136	1.000000	0.71417	0.795000	0.32087	0.439000	0.31926	5.778000	0.68940	1.747000	0.51819	0.334000	0.21626	CTC	.	.		0.677	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267	
AADAC	13	hgsc.bcm.edu	37	3	151542580	151542580	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:151542580A>G	ENST00000232892.7	+	4	687	c.561A>G	c.(559-561)ggA>ggG	p.G187G	RP11-454C18.2_ENST00000483843.2_RNA|AADAC_ENST00000488869.1_Silent_p.G187G|RP11-454C18.2_ENST00000475855.1_RNA	NM_001086.2	NP_001077.2	P22760	AAAD_HUMAN	arylacetamide deacetylase	187					positive regulation of triglyceride catabolic process (GO:0010898)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|deacetylase activity (GO:0019213)|lipase activity (GO:0016298)|serine hydrolase activity (GO:0017171)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(5)|skin(2)	19		Myeloproliferative disorder(1037;0.0255)|all_neural(597;0.112)	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			GTATTTCTGGAGATAGTGCAG	0.353																																					p.G187G	Ovarian(30;839 841 2699 32801 46334)	Atlas-SNP	.											.	AADAC	49	.	0			c.A561G						.						84.0	82.0	83.0					3																	151542580		2203	4300	6503	SO:0001819	synonymous_variant	13	exon4			TTCTGGAGATAGT	L32179	CCDS33877.1	3q25.1	2014-03-18	2012-07-13		ENSG00000114771	ENSG00000114771	3.1.1.3		17	protein-coding gene	gene with protein product		600338	"""arylacetamide deacetylase (esterase)"""			8063807	Standard	XM_005247103		Approved	DAC, CES5A1	uc003eze.3	P22760	OTTHUMG00000159876	ENST00000232892.7:c.561A>G	chr3.hg19:g.151542580A>G		105.0	0.0		164.0	7.0	NM_001086	A8K3L3|D3DNJ6|Q8N1A9	Silent	SNP	ENST00000232892.7	hg19	CCDS33877.1																																																																																			.	.		0.353	AADAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357883.2	NM_001086	
ARHGEF26	26084	hgsc.bcm.edu	37	3	153839867	153839867	+	Missense_Mutation	SNP	T	T	C	rs200926651	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:153839867T>C	ENST00000356448.4	+	2	370	c.86T>C	c.(85-87)gTt>gCt	p.V29A	ARHGEF26_ENST00000465817.1_Missense_Mutation_p.V29A|ARHGEF26-AS1_ENST00000467912.1_RNA|ARHGEF26-AS1_ENST00000479270.1_RNA|ARHGEF26-AS1_ENST00000491862.1_RNA|ARHGEF26-AS1_ENST00000480639.1_RNA|ARHGEF26_ENST00000465093.1_Missense_Mutation_p.V29A	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	29			V -> L (in dbSNP:rs12493885). {ECO:0000269|PubMed:12697679, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15133129, ECO:0000269|PubMed:15221005, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21406692}.		endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						CCCCACCAGGTTCTGGGCCGG	0.627																																					p.V29A	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.T86C						.						19.0	22.0	21.0					3																	153839867		1948	4153	6101	SO:0001583	missense	26084	exon2			ACCAGGTTCTGGG	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24490	protein-coding gene	gene with protein product	"""Src homology 3 domain-containing guanine nucleotide exchange factor"""					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.86T>C	chr3.hg19:g.153839867T>C	ENSP00000348828:p.Val29Ala	146.0	0.0		231.0	11.0	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	hg19	CCDS46938.1	.	.	.	.	.	.	.	.	.	.	T	12.15	1.851263	0.32699	.	.	ENSG00000114790	ENST00000356448;ENST00000465093;ENST00000465817	T;T;T	0.55234	0.53;0.53;2.31	4.49	0.538	0.17150	.	1.110460	0.06940	N	0.812561	T	0.30230	0.0758	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	0.24297	-1.0164	10	0.51188	T	0.08	-4.6961	5.2467	0.15500	0.0:0.196:0.2513:0.5526	.	29;29	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	A	29	ENSP00000348828:V29A;ENSP00000423418:V29A;ENSP00000423295:V29A	ENSP00000348828:V29A	V	+	2	0	ARHGEF26	155322557	0.088000	0.21588	0.872000	0.34217	0.713000	0.41058	0.303000	0.19210	0.555000	0.29079	0.459000	0.35465	GTT	.	.		0.627	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595	
SI	6476	hgsc.bcm.edu	37	3	164758754	164758754	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:164758754T>C	ENST00000264382.3	-	18	2195	c.2133A>G	c.(2131-2133)gaA>gaG	p.E711E		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	711	Isomaltase.				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)	TTGCTACTGTTTCTCCAAACA	0.328										HNSCC(35;0.089)																											p.E711E		Atlas-SNP	.											.	SI	500	.	0			c.A2133G						.						138.0	137.0	138.0					3																	164758754		2203	4300	6503	SO:0001819	synonymous_variant	6476	exon18			TACTGTTTCTCCA	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.2133A>G	chr3.hg19:g.164758754T>C		89.0	0.0		83.0	4.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	hg19	CCDS3196.1																																																																																			.	.		0.328	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
MECOM	2122	hgsc.bcm.edu	37	3	169099249	169099249	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:169099249C>T	ENST00000494292.1	-	2	198	c.101G>A	c.(100-102)gGa>gAa	p.G34E	MECOM_ENST00000485957.1_5'UTR	NM_004991.3	NP_004982.2	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	34					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						GCTGGCTACTCCATCTGCATC	0.448																																					p.G34E		Atlas-SNP	.											.	MECOM	216	.	0			c.G101A						.						58.0	59.0	58.0					3																	169099249		1929	4136	6065	SO:0001583	missense	2122	exon2			GCTACTCCATCTG	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000494292.1:c.101G>A	chr3.hg19:g.169099249C>T	ENSP00000417899:p.Gly34Glu	92.0	0.0		151.0	51.0	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000494292.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.78	3.218032	0.58560	.	.	ENSG00000085276	ENST00000494292;ENST00000486748	T	0.06687	3.27	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000012	T	0.28732	0.0712	M	0.63428	1.95	0.80722	D	1	D;P	0.76494	0.999;0.72	D;B	0.71656	0.974;0.346	T	0.00068	-1.2139	10	0.54805	T	0.06	.	20.1184	0.97949	0.0:1.0:0.0:0.0	.	34;34	Q13465;Q03112-3	MDS1_HUMAN;.	E	34;58	ENSP00000417899:G34E	ENSP00000419537:G58E	G	-	2	0	MECOM	170581943	1.000000	0.71417	0.982000	0.44146	0.033000	0.12548	5.030000	0.64128	2.775000	0.95449	0.650000	0.86243	GGA	.	.		0.448	MECOM-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000351517.3	NM_005241, NM_004991	
LRRIQ4	344657	hgsc.bcm.edu	37	3	169540116	169540116	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:169540116T>C	ENST00000340806.6	+	1	407	c.407T>C	c.(406-408)gTc>gCc	p.V136A		NM_001080460.1	NP_001073929.1	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	136										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30						ATTCCCGTCGTCATCTTTAAA	0.552																																					p.V136A		Atlas-SNP	.											.	LRRIQ4	68	.	0			c.T407C						.						56.0	60.0	59.0					3																	169540116		2049	4194	6243	SO:0001583	missense	344657	exon1			CCGTCGTCATCTT		CCDS46951.1	3q26.2	2008-08-08	2008-06-12	2008-06-12	ENSG00000188306	ENSG00000188306			34298	protein-coding gene	gene with protein product	"""leucine rich repeat containing 64"""						Standard	NM_001080460		Approved	LRRC64	uc003fgb.3	A6NIV6	OTTHUMG00000164420	ENST00000340806.6:c.407T>C	chr3.hg19:g.169540116T>C	ENSP00000342188:p.Val136Ala	65.0	0.0		94.0	4.0	NM_001080460		Missense_Mutation	SNP	ENST00000340806.6	hg19	CCDS46951.1	.	.	.	.	.	.	.	.	.	.	T	7.594	0.671289	0.14776	.	.	ENSG00000188306	ENST00000340806	T	0.55760	0.5	5.56	-10.7	0.00240	.	1.401490	0.04370	N	0.358914	T	0.16557	0.0398	N	0.03016	-0.435	0.09310	N	1	B	0.17268	0.021	B	0.13407	0.009	T	0.09335	-1.0679	10	0.09843	T	0.71	.	1.5474	0.02568	0.3988:0.2921:0.1674:0.1417	.	136	A6NIV6	LRIQ4_HUMAN	A	136	ENSP00000342188:V136A	ENSP00000342188:V136A	V	+	2	0	LRRIQ4	171022810	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.539000	0.06113	-1.422000	0.02004	-0.609000	0.04063	GTC	.	.		0.552	LRRIQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378698.1	NM_001080460	
DCUN1D1	54165	hgsc.bcm.edu	37	3	182665124	182665124	+	Splice_Site	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:182665124T>C	ENST00000292782.4	-	6	757		c.e6-2		DCUN1D1_ENST00000469954.1_Splice_Site	NM_020640.2	NP_065691.2	Q96GG9	DCNL1_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 1							ubiquitin ligase complex (GO:0000151)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;2.54e-44)|Epithelial(37;4.71e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			ATGATGTTCCTATTTAAAAAA	0.294																																					.		Atlas-SNP	.											.	DCUN1D1	27	.	0			c.604-2A>G						.						103.0	98.0	99.0					3																	182665124		2199	4298	6497	SO:0001630	splice_region_variant	54165	exon7			TGTTCCTATTTAA	AF292100, AK056335	CCDS3240.1	3q26.3	2013-06-10	2013-06-10		ENSG00000043093	ENSG00000043093			18184	protein-coding gene	gene with protein product	"""squamous cell carcinoma related oncogene"""	605905	"""DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)"""			10777668, 15988528	Standard	NM_020640		Approved	RP42, SCRO, DCUN1L1, Tes3, SCCRO	uc003fld.1	Q96GG9	OTTHUMG00000158314	ENST00000292782.4:c.604-2A>G	chr3.hg19:g.182665124T>C		36.0	0.0		63.0	4.0	NM_020640	B2RB37|Q7L3G9|Q8TEX7|Q9H6M1|Q9HCT3	Splice_Site	SNP	ENST00000292782.4	hg19	CCDS3240.1	.	.	.	.	.	.	.	.	.	.	T	19.59	3.855373	0.71719	.	.	ENSG00000043093	ENST00000292782;ENST00000458486;ENST00000469954	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4861	0.75569	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DCUN1D1	184147818	1.000000	0.71417	0.995000	0.50966	0.840000	0.47671	7.671000	0.83941	2.048000	0.60808	0.460000	0.39030	.	.	.		0.294	DCUN1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350658.1	NM_020640	Intron
MCCC1	56922	hgsc.bcm.edu	37	3	182751818	182751818	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:182751818A>G	ENST00000265594.4	-	14	1788	c.1642T>C	c.(1642-1644)Tcg>Ccg	p.S548P	MCCC1_ENST00000539926.1_Missense_Mutation_p.S413P|MCCC1_ENST00000489909.1_5'UTR|MCCC1_ENST00000492597.1_Missense_Mutation_p.S439P	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	548					biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	CTGGTATACGAGATATTCAGT	0.299																																					p.S548P		Atlas-SNP	.											.	MCCC1	87	.	0			c.T1642C						.						96.0	98.0	97.0					3																	182751818		2203	4300	6503	SO:0001583	missense	56922	exon14			TATACGAGATATT	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"""methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"""			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.1642T>C	chr3.hg19:g.182751818A>G	ENSP00000265594:p.Ser548Pro	67.0	0.0		110.0	5.0	NM_020166	Q59ES4|Q9H959|Q9NS97	Missense_Mutation	SNP	ENST00000265594.4	hg19	CCDS3241.1	.	.	.	.	.	.	.	.	.	.	A	1.508	-0.550372	0.03996	.	.	ENSG00000078070	ENST00000265594;ENST00000492597;ENST00000392616;ENST00000539926;ENST00000476176	D;D;D;D	0.95588	-3.75;-3.7;-3.55;-3.48	5.39	-1.99	0.07457	.	1.075510	0.07135	U	0.846277	D	0.89132	0.6628	L	0.34521	1.04	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.75909	-0.3151	10	0.27082	T	0.32	.	2.1764	0.03863	0.3659:0.2321:0.0654:0.3366	.	501;439;548	E9PG35;E9PHF7;Q96RQ3	.;.;MCCA_HUMAN	P	548;439;398;413;501	ENSP00000265594:S548P;ENSP00000419898:S439P;ENSP00000441253:S413P;ENSP00000420433:S501P	ENSP00000265594:S548P	S	-	1	0	MCCC1	184234512	0.413000	0.25400	0.001000	0.08648	0.776000	0.43924	1.453000	0.35167	-0.225000	0.09913	-0.438000	0.05819	TCG	.	.		0.299	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166	
POLR2H	5437	hgsc.bcm.edu	37	3	184084588	184084588	+	Splice_Site	SNP	T	T	C	rs138482713		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:184084588T>C	ENST00000456318.1	+	5	1384	c.335T>C	c.(334-336)cTc>cCc	p.L112P	POLR2H_ENST00000452961.1_Splice_Site_p.L76P|POLR2H_ENST00000443489.1_Intron|POLR2H_ENST00000429568.1_Splice_Site_p.L112P|POLR2H_ENST00000296223.3_Splice_Site_p.L112P|EIF2B5_ENST00000444495.1_Intron|POLR2H_ENST00000430783.1_Intron|POLR2H_ENST00000438240.1_Splice_Site_p.L76P	NM_001278699.1	NP_001265628.1	P52434	RPAB3_HUMAN	polymerase (RNA) II (DNA directed) polypeptide H	112					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase II, core complex (GO:0005665)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.L112P(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GCAACACGCCTGTAAGTTACG	0.458																																					p.L112P		Atlas-SNP	.											POLR2H,NS,carcinoma,0,1	POLR2H	17	.	1	Substitution - Missense(1)	breast(1)	c.T335C						.						165.0	141.0	149.0					3																	184084588		2203	4300	6503	SO:0001630	splice_region_variant	5437	exon4			CACGCCTGTAAGT		CCDS3264.1, CCDS63861.1, CCDS63862.1, CCDS63859.1, CCDS63860.1	3q28	2013-01-21			ENSG00000163882	ENSG00000163882		"""RNA polymerase subunits"""	9195	protein-coding gene	gene with protein product		606023					Standard	NM_001278698		Approved	RPB8	uc003fok.2	P52434	OTTHUMG00000156746	ENST00000456318.1:c.335+1T>C	chr3.hg19:g.184084588T>C		88.0	0.0		94.0	4.0	NM_006232	C9J413|C9JBJ6|C9JCU7|C9JUA8|P53802|Q969R0	Missense_Mutation	SNP	ENST00000456318.1	hg19	CCDS3264.1	.	.	.	.	.	.	.	.	.	.	t	23.2	4.386562	0.82902	.	.	ENSG00000163882	ENST00000456318;ENST00000438240;ENST00000455712;ENST00000452961;ENST00000296223;ENST00000429568	.	.	.	5.91	5.91	0.95273	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	T	0.80798	0.4692	M	0.86178	2.8	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.83499	0.0074	9	0.62326	D	0.03	-9.4653	14.291	0.66278	0.0:0.0:0.0:1.0	.	112	P52434	RPAB3_HUMAN	P	112;76;112;76;112;112	.	ENSP00000296223:L112P	L	+	2	0	POLR2H	185567282	1.000000	0.71417	0.999000	0.59377	0.818000	0.46254	7.678000	0.84035	2.263000	0.75096	0.529000	0.55759	CTC;CTC;CTC;CTC;CTC;CTG	.	T|1.000;G|0.000		0.458	POLR2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345558.1	NM_006232	Missense_Mutation
MUC4	4585	hgsc.bcm.edu	37	3	195508423	195508423	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:195508423G>A	ENST00000463781.3	-	2	10487	c.10028C>T	c.(10027-10029)aCc>aTc	p.T3343I	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3343I|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGCACAGGGGTGGTGTCACC	0.602																																					p.T3343I		Atlas-SNP	.											.	MUC4	1505	.	0			c.C10028T						.						32.0	24.0	27.0					3																	195508423		680	1573	2253	SO:0001583	missense	4585	exon2			ACAGGGGTGGTGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10028C>T	chr3.hg19:g.195508423G>A	ENSP00000417498:p.Thr3343Ile	159.0	0.0		304.0	115.0	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	hg19	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	6.308	0.424985	0.11987	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35605	1.33;1.3	1.03	1.03	0.20045	.	.	.	.	.	T	0.17365	0.0417	N	0.14661	0.345	0.09310	N	1	P	0.47604	0.898	B	0.37346	0.247	T	0.09885	-1.0654	8	.	.	.	.	7.5882	0.28006	0.0:0.0:1.0:0.0	.	3215	E7ESK3	.	I	3343	ENSP00000417498:T3343I;ENSP00000420243:T3343I	.	T	-	2	0	MUC4	196993202	0.000000	0.05858	0.008000	0.14137	0.030000	0.12068	-1.756000	0.01813	0.494000	0.27859	0.089000	0.15464	ACC	.	.		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PIGZ	80235	hgsc.bcm.edu	37	3	196674974	196674975	+	Missense_Mutation	DNP	GC	GC	CG			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:196674974_196674975GC>CG	ENST00000412723.1	-	3	939_940	c.793_794GC>CG	c.(793-795)GCa>CGa	p.A265R	PIGZ_ENST00000443835.1_3'UTR	NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	265					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		TGTGAGGGCTGCCCCAGGGAGC	0.614																																					p.A265G|p.A265P		Atlas-SNP	.											.	PIGZ	34	.	0			c.C794G|c.G793C						.																																			SO:0001583	missense	80235	exon3			AGGGCTGCCCCAG|GGGCTGCCCCAGG	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	30596	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 4"", ""dol-P-Man dependent GPI mannosyltransferase"""	611671	"""phosphatidylinositol glycan, class Z"""			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.793_794delinsCG	chr3.hg19:g.196674974_196674975delinsCG	ENSP00000413405:p.Ala265Arg	51.0|52.0	0.0		88.0	5.0|4.0	NM_025163	Q9H9G6	Missense_Mutation	SNP	ENST00000412723.1	hg19	CCDS3324.1																																																																																			.	.		0.614	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163	
PDE6B	5158	hgsc.bcm.edu	37	4	660330	660330	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:660330A>G	ENST00000496514.1	+	20	2300	c.2279A>G	c.(2278-2280)gAc>gGc	p.D760G	PDE6B_ENST00000429163.2_Missense_Mutation_p.D481G|PDE6B_ENST00000255622.6_Missense_Mutation_p.D760G			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	760					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	CCTATGATGGACCGGAACAAG	0.637																																					p.D760G	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.A2279G						.						89.0	75.0	80.0					4																	660330		2203	4300	6503	SO:0001583	missense	5158	exon20			TGATGGACCGGAA	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"""Phosphodiesterases"""	8786	protein-coding gene	gene with protein product	"""congenital stationary night blindness 3, autosomal dominant"""	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.2279A>G	chr4.hg19:g.660330A>G	ENSP00000420295:p.Asp760Gly	71.0	0.0		106.0	5.0	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	ENST00000496514.1	hg19	CCDS33932.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.5|22.5	4.295859|4.295859	0.81025|0.81025	.|.	.|.	ENSG00000133256|ENSG00000133256	ENST00000255622;ENST00000496514;ENST00000429163;ENST00000471824|ENST00000461490	D;D;D;D|.	0.82619|.	-1.63;-1.63;-1.63;-1.63|.	4.22|4.22	4.22|4.22	0.49857|0.49857	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84419|0.84419	0.5468|0.5468	H|H	0.94698|0.94698	3.57|3.57	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.998|.	D|D	0.88109|0.88109	0.2824|0.2824	10|5	0.87932|.	D|.	0|.	.|.	11.6112|11.6112	0.51059|0.51059	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	760;760|.	P35913;P35913-2|.	PDE6B_HUMAN;.|.	G|A	760;760;481;120|41	ENSP00000255622:D760G;ENSP00000420295:D760G;ENSP00000406334:D481G;ENSP00000417852:D120G|.	ENSP00000255622:D760G|.	D|T	+|+	2|1	0|0	PDE6B|PDE6B	650330|650330	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.926000|0.926000	0.56050|0.56050	6.872000|6.872000	0.75536|0.75536	1.687000|1.687000	0.51057|0.51057	0.524000|0.524000	0.50904|0.50904	GAC|ACC	.	.		0.637	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283	
HTRA3	94031	hgsc.bcm.edu	37	4	8307696	8307696	+	Splice_Site	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:8307696A>G	ENST00000307358.2	+	9	1400		c.e9-1			NM_053044.3	NP_444272.1	P83110	HTRA3_HUMAN	HtrA serine peptidase 3						negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|prostate(1)|urinary_tract(1)	18						TCCTGTTGGCAGAGGCGGCAT	0.622																																					.		Atlas-SNP	.											.	HTRA3	39	.	0			c.1197-2A>G						.						89.0	83.0	85.0					4																	8307696		2203	4300	6503	SO:0001630	splice_region_variant	94031	exon9			GTTGGCAGAGGCG	AY040094	CCDS3400.1, CCDS75105.1	4p16.1	2008-02-05			ENSG00000170801	ENSG00000170801			30406	protein-coding gene	gene with protein product	"""pregnancy-related serine protease"""	608785				12513693, 14500695	Standard	XM_005248040		Approved	Tasp, Prsp	uc003gla.3	P83110	OTTHUMG00000090561	ENST00000307358.2:c.1197-1A>G	chr4.hg19:g.8307696A>G		99.0	0.0		96.0	5.0	NM_053044	Q7Z7A2	Splice_Site	SNP	ENST00000307358.2	hg19	CCDS3400.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.005216	0.74932	.	.	ENSG00000170801	ENST00000307358	.	.	.	4.08	4.08	0.47627	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3595	0.60648	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HTRA3	8358596	1.000000	0.71417	0.998000	0.56505	0.879000	0.50718	7.408000	0.80041	1.635000	0.50512	0.248000	0.18094	.	.	.		0.622	HTRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092669.1	NM_053044	Intron
FGFBP1	9982	hgsc.bcm.edu	37	4	15938186	15938186	+	Missense_Mutation	SNP	T	T	C	rs201240184	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:15938186T>C	ENST00000382333.1	-	3	364	c.70A>G	c.(70-72)Aaa>Gaa	p.K24E	FGFBP1_ENST00000259988.2_Missense_Mutation_p.K24E	NM_005130.4	NP_005121.1	Q14512	FGFP1_HUMAN	fibroblast growth factor binding protein 1	24					cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|signal transduction (GO:0007165)	cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|prostate(2)|skin(1)	10						ACTTTTTTTTTCCCCTCCACC	0.517													T|||	366	0.0730831	0.0227	0.072	5008	,	,		20082	0.1895		0.0885	False		,,,				2504	0.0061				p.K24E		Atlas-SNP	.											.	FGFBP1	26	.	0			c.A70G						.						67.0	71.0	70.0					4																	15938186		2200	4294	6494	SO:0001583	missense	9982	exon3			TTTTTTTCCCCTC	M60047	CCDS3418.1	4p15.32	2008-02-05			ENSG00000137440	ENSG00000137440			19695	protein-coding gene	gene with protein product		607737				11148217, 1885605	Standard	NM_005130		Approved	HBP17, FGFBP	uc003gom.3	Q14512	OTTHUMG00000097745	ENST00000382333.1:c.70A>G	chr4.hg19:g.15938186T>C	ENSP00000371770:p.Lys24Glu	145.0	0.0		152.0	7.0	NM_005130	A8K5J2	Missense_Mutation	SNP	ENST00000382333.1	hg19	CCDS3418.1	.	.	.	.	.	.	.	.	.	.	T	9.070	0.996742	0.19043	.	.	ENSG00000137440	ENST00000382333;ENST00000259988	T;T	0.15487	2.42;2.42	5.68	-4.23	0.03789	.	0.827902	0.11485	N	0.559298	T	0.12390	0.0301	L	0.42245	1.32	0.09310	N	1	B	0.21520	0.057	B	0.20955	0.032	T	0.25537	-1.0129	10	0.49607	T	0.09	.	7.7466	0.28873	0.0:0.2911:0.1875:0.5215	.	24	Q14512	FGFP1_HUMAN	E	24	ENSP00000371770:K24E;ENSP00000259988:K24E	ENSP00000259988:K24E	K	-	1	0	FGFBP1	15547284	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	-0.357000	0.07651	-0.795000	0.04462	-1.475000	0.01000	AAA	.	.		0.517	FGFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214974.1	NM_005130	
CORIN	10699	hgsc.bcm.edu	37	4	47695047	47695047	+	Missense_Mutation	SNP	C	C	T	rs143738568		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:47695047C>T	ENST00000273857.4	-	6	852	c.853G>A	c.(853-855)Ggg>Agg	p.G285R	CORIN_ENST00000505909.1_Missense_Mutation_p.G285R|CORIN_ENST00000508498.1_Missense_Mutation_p.G146R|CORIN_ENST00000504584.1_Missense_Mutation_p.G285R|CORIN_ENST00000502252.1_Missense_Mutation_p.G218R	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	285	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						TGCAGTTTCCCGGGGATGCAG	0.463																																					p.G285R		Atlas-SNP	.											.	CORIN	154	.	0			c.G853A						.						143.0	129.0	133.0					4																	47695047		2203	4300	6503	SO:0001583	missense	10699	exon6			GTTTCCCGGGGAT	AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"""Serine peptidases / Transmembrane"""	19012	protein-coding gene	gene with protein product		605236	"""corin, serine protease"""			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.853G>A	chr4.hg19:g.47695047C>T	ENSP00000273857:p.Gly285Arg	100.0	0.0		127.0	48.0	NM_006587	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Missense_Mutation	SNP	ENST00000273857.4	hg19	CCDS3477.1	.	.	.	.	.	.	.	.	.	.	T	6.621	0.483004	0.12581	.	.	ENSG00000145244	ENST00000273857;ENST00000508498;ENST00000502252;ENST00000505909;ENST00000504584	D;D;D;D;D	0.95205	-3.64;-3.64;-3.64;-3.64;-3.64	5.54	-1.94	0.07571	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.695685	0.14811	N	0.297050	T	0.79257	0.4415	N	0.02775	-0.495	0.09310	N	1	B;B;B;B;B	0.10296	0.0;0.001;0.003;0.001;0.0	B;B;B;B;B	0.13407	0.001;0.001;0.009;0.005;0.001	T	0.70070	-0.4973	10	0.14656	T	0.56	.	2.4803	0.04586	0.0963:0.2274:0.3147:0.3616	.	285;285;218;146;285	B7Z4R1;B4E2W9;B4E1Y7;B4DZA3;Q9Y5Q5	.;.;.;.;CORIN_HUMAN	R	285;146;218;285;285	ENSP00000273857:G285R;ENSP00000425597:G146R;ENSP00000424212:G218R;ENSP00000425401:G285R;ENSP00000423216:G285R	ENSP00000273857:G285R	G	-	1	0	CORIN	47389804	0.190000	0.23276	0.499000	0.27577	0.955000	0.61496	0.181000	0.16880	-0.467000	0.06932	-0.530000	0.04314	GGG	.	C|1.000;G|0.000		0.463	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2		
SLAIN2	57606	hgsc.bcm.edu	37	4	48384604	48384604	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:48384604A>G	ENST00000264313.6	+	5	1300	c.882A>G	c.(880-882)gcA>gcG	p.A294A	SLAIN2_ENST00000512093.1_Silent_p.A101A	NM_020846.1	NP_065897.1	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	294					cytoplasmic microtubule organization (GO:0031122)|microtubule nucleation (GO:0007020)|positive regulation of microtubule polymerization (GO:0031116)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)	13						AAGAATATGCAGCCACCACGT	0.338																																					p.A294A		Atlas-SNP	.											.	SLAIN2	31	.	0			c.A882G						.						50.0	45.0	47.0					4																	48384604		1936	4123	6059	SO:0001819	synonymous_variant	57606	exon5			ATATGCAGCCACC	BC006139	CCDS47051.1	4p12	2008-02-05	2006-09-12	2006-09-12	ENSG00000109171	ENSG00000109171			29282	protein-coding gene	gene with protein product		610492	"""KIAA1458"""	KIAA1458		16546155	Standard	NM_020846		Approved	FLJ21611	uc003gya.4	Q9P270	OTTHUMG00000161701	ENST00000264313.6:c.882A>G	chr4.hg19:g.48384604A>G		29.0	0.0		45.0	4.0	NM_020846	A8K4P1|Q8N5R3	Silent	SNP	ENST00000264313.6	hg19	CCDS47051.1																																																																																			.	.		0.338	SLAIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365807.4	NM_020846	
SRP72	6731	hgsc.bcm.edu	37	4	57340538	57340538	+	Missense_Mutation	SNP	A	A	C	rs200923265		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:57340538A>C	ENST00000342756.5	+	5	1312	c.591A>C	c.(589-591)aaA>aaC	p.K197N	SRP72_ENST00000504757.1_Missense_Mutation_p.K197N|SRP72_ENST00000510663.1_Missense_Mutation_p.K197N	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	197					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(7)|ovary(2)	22	Glioma(25;0.08)|all_neural(26;0.101)					AGGCCATGAAAATCCTACAAA	0.428																																					p.K197N		Atlas-SNP	.											SRP72,NS,carcinoma,0,1	SRP72	59	.	0			c.A591C						.						75.0	76.0	76.0					4																	57340538		2203	4300	6503	SO:0001583	missense	6731	exon5			CATGAAAATCCTA	AF069765	CCDS3506.1, CCDS58898.1	4q11	2013-01-10	2002-08-29		ENSG00000174780	ENSG00000174780		"""Tetratricopeptide (TTC) repeat domain containing"""	11303	protein-coding gene	gene with protein product		602122	"""signal recognition particle 72kD"""			9224693, 9857079	Standard	NM_006947		Approved		uc003hbv.3	O76094	OTTHUMG00000128843	ENST00000342756.5:c.591A>C	chr4.hg19:g.57340538A>C	ENSP00000342181:p.Lys197Asn	97.0	0.0		106.0	7.0	NM_006947	G5E9Z8|Q7Z3C0	Missense_Mutation	SNP	ENST00000342756.5	hg19	CCDS3506.1	.	.	.	.	.	.	.	.	.	.	A	9.989	1.230248	0.22542	.	.	ENSG00000174780	ENST00000342756;ENST00000537129;ENST00000510663;ENST00000505314	D;T	0.94280	-3.39;1.12	5.61	3.21	0.36854	Tetratricopeptide-like helical (1);	0.232646	0.51477	D	0.000094	D	0.87684	0.6239	L	0.33485	1.01	0.22873	N	0.998626	B;B;B	0.17852	0.001;0.024;0.016	B;B;B	0.26614	0.002;0.071;0.006	T	0.74494	-0.3647	10	0.26408	T	0.33	.	8.2429	0.31671	0.837:0.0:0.163:0.0	.	197;197;197	G5E9Z8;Q86X80;O76094	.;.;SRP72_HUMAN	N	197;203;197;2	ENSP00000342181:K197N;ENSP00000424576:K197N	ENSP00000342181:K197N	K	+	3	2	SRP72	57035295	1.000000	0.71417	1.000000	0.80357	0.376000	0.30014	1.071000	0.30666	0.425000	0.26087	-0.256000	0.11100	AAA	.	A|0.998;C|0.002		0.428	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7		
AFF1	4299	hgsc.bcm.edu	37	4	88026981	88026981	+	Missense_Mutation	SNP	T	T	C	rs141434206		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:88026981T>C	ENST00000307808.6	+	9	1759	c.1339T>C	c.(1339-1341)Tca>Cca	p.S447P	AFF1_ENST00000395146.4_Missense_Mutation_p.S454P|AFF1_ENST00000544085.1_Missense_Mutation_p.S85P	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	447					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)		GCCTCCCTCCTCATCTGCACC	0.423																																					p.S454P		Atlas-SNP	.											.	AFF1	102	.	0			c.T1360C						.						195.0	185.0	188.0					4																	88026981		2203	4300	6503	SO:0001583	missense	4299	exon10			CCCTCCTCATCTG	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.1339T>C	chr4.hg19:g.88026981T>C	ENSP00000305689:p.Ser447Pro	176.0	0.0		112.0	5.0	NM_001166693	B4DTU1|E9PBM3	Missense_Mutation	SNP	ENST00000307808.6	hg19	CCDS3616.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.47|13.47	2.247952|2.247952	0.39697|0.39697	.|.	.|.	ENSG00000172493|ENSG00000172493	ENST00000541943|ENST00000395146;ENST00000307808;ENST00000511722;ENST00000544085;ENST00000514970	.|T;T;T;T;T	.|0.63744	.|-0.06;-0.06;-0.06;-0.06;-0.06	5.91|5.91	-1.59|-1.59	0.08453|0.08453	.|.	.|0.809745	.|0.11469	.|N	.|0.560997	.|T	.|0.30198	.|0.0757	N|N	0.03000|0.03000	-0.44|-0.44	0.38468|0.38468	D|D	0.947388|0.947388	.|B;B;B	.|0.22541	.|0.071;0.071;0.071	.|B;B;B	.|0.29663	.|0.105;0.105;0.105	.|T	.|0.09164	.|-1.0687	.|10	.|0.22706	.|T	.|0.39	.|0.0102	2.4099|2.4099	0.04421|0.04421	0.3915:0.0658:0.1458:0.3969|0.3915:0.0658:0.1458:0.3969	.|.	.|454;447;447	.|E9PBM3;Q14C88;P51825	.|.;.;AFF1_HUMAN	.|P	-1|454;447;85;85;138	.|ENSP00000378578:S454P;ENSP00000305689:S447P;ENSP00000424766:S85P;ENSP00000440843:S85P;ENSP00000424881:S138P	.|ENSP00000305689:S447P	.|S	+|+	.|1	.|0	AFF1|AFF1	88246005|88246005	0.214000|0.214000	0.23563|0.23563	0.129000|0.129000	0.21949|0.21949	0.976000|0.976000	0.68499|0.68499	0.101000|0.101000	0.15251|0.15251	-0.491000|-0.491000	0.06697|0.06697	0.533000|0.533000	0.62120|0.62120	.|TCA	.	T|1.000;A|0.000		0.423	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935	
FAM13A	10144	hgsc.bcm.edu	37	4	89702436	89702436	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:89702436A>G	ENST00000264344.5	-	11	1545	c.1338T>C	c.(1336-1338)acT>acC	p.T446T	FAM13A_ENST00000502459.1_5'UTR|FAM13A_ENST00000513837.1_Silent_p.T92T|FAM13A_ENST00000508369.1_Silent_p.T120T|FAM13A_ENST00000395002.2_Silent_p.T120T|FAM13A_ENST00000511976.1_Intron|FAM13A_ENST00000503556.1_Silent_p.T106T	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	446					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						CGACTTCCTGAGTATTCAAAA	0.353																																					p.T446T		Atlas-SNP	.											.	FAM13A	181	.	0			c.T1338C						.						98.0	98.0	98.0					4																	89702436		2203	4300	6503	SO:0001819	synonymous_variant	10144	exon11			TTCCTGAGTATTC	AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"""Rho GTPase activating proteins"""	19367	protein-coding gene	gene with protein product		613299	"""family with sequence similarity 13, member A1"""	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.1338T>C	chr4.hg19:g.89702436A>G		134.0	0.0		97.0	4.0	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Silent	SNP	ENST00000264344.5	hg19	CCDS34029.1																																																																																			.	.		0.353	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1		
RAP1GDS1	5910	hgsc.bcm.edu	37	4	99313179	99313179	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:99313179T>C	ENST00000408927.3	+	6	698	c.585T>C	c.(583-585)aaT>aaC	p.N195N	RAP1GDS1_ENST00000380158.4_Silent_p.N147N|RAP1GDS1_ENST00000453712.2_Silent_p.N196N|RAP1GDS1_ENST00000339360.5_Silent_p.N196N|RAP1GDS1_ENST00000408900.3_Silent_p.N146N|RAP1GDS1_ENST00000264572.7_Intron	NM_001100426.1|NM_001100427.1|NM_021159.4	NP_001093896.1|NP_001093897.1|NP_066982.3	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1	195					myosin filament assembly (GO:0031034)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of Rho GTPase activity (GO:0032321)|vascular smooth muscle contraction (GO:0014829)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)	28				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		ACTGCCAAAATGCAGCTCTTA	0.348			T	NUP98	T-ALL																																p.N196N		Atlas-SNP	.		Dom	yes		4	4q21-q25	5910	"""RAP1, GTP-GDP dissociation stimulator 1"""		L	.	RAP1GDS1	61	.	0			c.T588C						.						101.0	97.0	98.0					4																	99313179		1847	4080	5927	SO:0001819	synonymous_variant	5910	exon6			CCAAAATGCAGCT		CCDS43253.1, CCDS43254.1, CCDS47105.1, CCDS47106.1, CCDS47107.1, CCDS47108.1	4q23-q25	2013-02-14			ENSG00000138698	ENSG00000138698		"""Armadillo repeat containing"""	9859	protein-coding gene	gene with protein product		179502				8262526, 17951244	Standard	NM_001100426		Approved	SmgGDS	uc003htw.4	P52306	OTTHUMG00000160987	ENST00000408927.3:c.585T>C	chr4.hg19:g.99313179T>C		126.0	0.0		77.0	33.0	NM_001100426	E9PH06|G5E9P9|Q499L7|Q4KMV2|Q4QQI8|Q9BUW9|Q9BUX6|Q9NYM2|Q9NZA8	Silent	SNP	ENST00000408927.3	hg19	CCDS43253.1	.	.	.	.	.	.	.	.	.	.	T	10.10	1.256495	0.22965	.	.	ENSG00000138698	ENST00000509501	.	.	.	5.75	3.3	0.37823	.	.	.	.	.	T	0.57888	0.2084	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53373	-0.8448	4	.	.	.	-18.1237	8.3318	0.32191	0.0:0.2137:0.0:0.7863	.	.	.	.	R	47	.	.	C	+	1	0	RAP1GDS1	99532202	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.469000	0.35343	0.966000	0.38159	0.374000	0.22700	TGC	.	.		0.348	RAP1GDS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363273.2	NM_001100426	
ADH4	127	hgsc.bcm.edu	37	4	100060247	100060247	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:100060247A>G	ENST00000265512.7	-	4	389	c.315T>C	c.(313-315)tgT>tgC	p.C105C	ADH4_ENST00000504581.1_5'Flank|ADH4_ENST00000508393.1_Silent_p.C124C|ADH4_ENST00000423445.1_Silent_p.C124C|RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000505590.1_Silent_p.C124C	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	105					alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		GTGGACTCAGACAAAACTTGC	0.348																																					p.C105C		Atlas-SNP	.											.	ADH4	35	.	0			c.T315C						.						94.0	88.0	90.0					4																	100060247		2203	4300	6503	SO:0001819	synonymous_variant	127	exon4			ACTCAGACAAAAC	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"""Alcohol dehydrogenases"""	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.315T>C	chr4.hg19:g.100060247A>G		119.0	0.0		100.0	4.0	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Silent	SNP	ENST00000265512.7	hg19	CCDS34032.1																																																																																			.	.		0.348	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670	
CENPE	1062	hgsc.bcm.edu	37	4	104066439	104066439	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:104066439T>C	ENST00000265148.3	-	32	4714	c.4625A>G	c.(4624-4626)gAg>gGg	p.E1542G	CENPE_ENST00000380026.3_Missense_Mutation_p.E1517G	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1542					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TTCCTGAACCTCACTAATTTG	0.303																																					p.E1542G		Atlas-SNP	.											.	CENPE	253	.	0			c.A4625G						.						75.0	70.0	72.0					4																	104066439		2202	4299	6501	SO:0001583	missense	1062	exon32			TGAACCTCACTAA	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.4625A>G	chr4.hg19:g.104066439T>C	ENSP00000265148:p.Glu1542Gly	119.0	0.0		86.0	5.0	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	T	7.302	0.613262	0.14066	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	D;T	0.81659	-1.52;-1.33	4.34	3.08	0.35506	.	.	.	.	.	D	0.86632	0.5979	M	0.75777	2.31	0.09310	N	1	D;D	0.76494	0.993;0.999	D;D	0.64144	0.91;0.922	T	0.75393	-0.3333	9	0.62326	D	0.03	.	8.9898	0.36017	0.0:0.0:0.1852:0.8148	.	1517;1542	Q02224-3;Q02224	.;CENPE_HUMAN	G	1542;1542;1517	ENSP00000265148:E1542G;ENSP00000369365:E1517G	ENSP00000265148:E1542G	E	-	2	0	CENPE	104285888	0.006000	0.16342	0.020000	0.16555	0.006000	0.05464	1.032000	0.30178	1.813000	0.52934	0.448000	0.29417	GAG	.	.		0.303	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TBCK	93627	hgsc.bcm.edu	37	4	107156504	107156504	+	Missense_Mutation	SNP	G	G	T	rs532862191		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:107156504G>T	ENST00000273980.5	-	16	1818	c.1371C>A	c.(1369-1371)aaC>aaA	p.N457K	TBCK_ENST00000361687.4_Missense_Mutation_p.N394K|TBCK_ENST00000432496.2_Missense_Mutation_p.N457K|TBCK_ENST00000394708.2_Missense_Mutation_p.N457K|TBCK_ENST00000394706.3_Missense_Mutation_p.N418K					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TCCAGATTTGGTTTTTTTTAT	0.363													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14482	0.0		0.0	False		,,,				2504	0.0				p.N457K		Atlas-SNP	.											.,1	TBCK	89	.	0			c.C1371A						.																																			SO:0001583	missense	93627	exon15			GATTTGGTTTTTT		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1371C>A	chr4.hg19:g.107156504G>T	ENSP00000273980:p.Asn457Lys	53.0	0.0		34.0	2.0	NM_001163436		Missense_Mutation	SNP	ENST00000273980.5	hg19	CCDS54788.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.104986	0.37145	.	.	ENSG00000145348	ENST00000273980;ENST00000432496;ENST00000361687;ENST00000394706;ENST00000394708	T;T;T;T;T	0.09817	2.94;2.94;2.94;2.94;2.94	5.9	0.724	0.18236	Rab-GAP/TBC domain (1);	0.000000	0.85682	D	0.000000	T	0.06645	0.0170	L	0.34521	1.04	0.48087	D	0.999586	B;P;B	0.43094	0.013;0.799;0.012	B;B;B	0.33620	0.003;0.167;0.022	T	0.39396	-0.9616	10	0.34782	T	0.22	.	10.6525	0.45657	0.6634:0.0:0.3366:0.0	.	457;418;394	Q8TEA7;Q8TEA7-2;Q8TEA7-3	TBCK_HUMAN;.;.	K	457;457;394;418;457	ENSP00000273980:N457K;ENSP00000405847:N457K;ENSP00000355338:N394K;ENSP00000378196:N418K;ENSP00000378198:N457K	ENSP00000273980:N457K	N	-	3	2	TBCK	107375953	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	2.665000	0.46791	0.157000	0.19338	-1.027000	0.02421	AAC	.	.		0.363	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115	
CYP2U1	113612	hgsc.bcm.edu	37	4	108866756	108866756	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:108866756T>C	ENST00000332884.6	+	2	1396	c.1121T>C	c.(1120-1122)gTa>gCa	p.V374A	RP11-286E11.1_ENST00000513071.1_RNA|CYP2U1_ENST00000508453.1_Missense_Mutation_p.V165A	NM_183075.2	NP_898898.1	Q7Z449	CP2U1_HUMAN	cytochrome P450, family 2, subfamily U, polypeptide 1	374					arachidonic acid metabolic process (GO:0019369)|cell death (GO:0008219)|omega-hydroxylase P450 pathway (GO:0097267)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|large_intestine(2)|lung(4)|skin(2)|urinary_tract(1)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000128)		AACCCCGATGTACAAGGTAAT	0.408																																					p.V374A		Atlas-SNP	.											.	CYP2U1	20	.	0			c.T1121C						.						127.0	124.0	125.0					4																	108866756		2203	4300	6503	SO:0001583	missense	113612	exon2			CCGATGTACAAGG	BC012027	CCDS34047.1	4q25	2012-11-23			ENSG00000155016	ENSG00000155016		"""Cytochrome P450s"""	20582	protein-coding gene	gene with protein product	"""spastic paraplegia 49"""	610670				14975754, 14660610	Standard	XM_005262717		Approved	SPG49	uc003hyp.3	Q7Z449	OTTHUMG00000161084	ENST00000332884.6:c.1121T>C	chr4.hg19:g.108866756T>C	ENSP00000333212:p.Val374Ala	84.0	0.0		68.0	4.0	NM_183075	B2RMV7|Q96EQ6	Missense_Mutation	SNP	ENST00000332884.6	hg19	CCDS34047.1	.	.	.	.	.	.	.	.	.	.	T	10.20	1.286053	0.23478	.	.	ENSG00000155016	ENST00000332884;ENST00000424249;ENST00000508453	T;T	0.72394	-0.65;-0.65	5.83	4.62	0.57501	.	0.392414	0.28659	N	0.014563	T	0.75027	0.3794	L	0.60012	1.86	0.09310	N	1	B	0.30709	0.291	P	0.45712	0.491	T	0.70103	-0.4964	10	0.87932	D	0	.	10.507	0.44839	0.2581:0.0:0.0:0.7419	.	374	Q7Z449	CP2U1_HUMAN	A	374;331;165	ENSP00000333212:V374A;ENSP00000423667:V165A	ENSP00000333212:V374A	V	+	2	0	CYP2U1	109086205	0.930000	0.31532	0.001000	0.08648	0.162000	0.22319	4.747000	0.62141	0.989000	0.38761	0.459000	0.35465	GTA	.	.		0.408	CYP2U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363691.2	NM_183075	
ANK2	287	hgsc.bcm.edu	37	4	114276005	114276005	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:114276005A>G	ENST00000357077.4	+	38	6284	c.6231A>G	c.(6229-6231)aaA>aaG	p.K2077K	ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Silent_p.K2044K|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000509550.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2077					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GAGTTAAGAAAGAAGATGCAG	0.478																																					p.K2077K		Atlas-SNP	.											.	ANK2	576	.	0			c.A6231G						.						77.0	83.0	81.0					4																	114276005		2203	4300	6503	SO:0001819	synonymous_variant	287	exon38			TAAGAAAGAAGAT	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.6231A>G	chr4.hg19:g.114276005A>G		108.0	0.0		92.0	5.0	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	hg19	CCDS3702.1																																																																																			.	.		0.478	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
CCNA2	890	hgsc.bcm.edu	37	4	122742218	122742218	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:122742218A>C	ENST00000274026.5	-	3	789	c.486T>G	c.(484-486)atT>atG	p.I162M		NM_001237.3	NP_001228	P20248	CCNA2_HUMAN	cyclin A2	162					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|organ regeneration (GO:0031100)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|response to estradiol (GO:0032355)|response to glucagon (GO:0033762)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	12						CTTCTAATATAATTGACATGT	0.343																																					p.I162M		Atlas-SNP	.											CCNA2,colon,carcinoma,0,1	CCNA2	30	.	0			c.T486G						.						196.0	187.0	190.0					4																	122742218		2203	4299	6502	SO:0001583	missense	890	exon3			TAATATAATTGAC		CCDS3723.1	4q27	2012-07-12			ENSG00000145386	ENSG00000145386			1578	protein-coding gene	gene with protein product		123835		CCNA, CCN1		1675006	Standard	NM_001237		Approved		uc003iec.4	P20248	OTTHUMG00000133072	ENST00000274026.5:c.486T>G	chr4.hg19:g.122742218A>C	ENSP00000274026:p.Ile162Met	166.0	0.0		135.0	0.0	NM_001237	A8K7B6|Q2M3U6|Q4W5P4|Q6LER8	Missense_Mutation	SNP	ENST00000274026.5	hg19	CCDS3723.1	.	.	.	.	.	.	.	.	.	.	A	13.05	2.121146	0.37436	.	.	ENSG00000145386	ENST00000274026	T	0.15256	2.44	5.86	3.55	0.40652	.	0.665471	0.12795	U	0.438573	T	0.14787	0.0357	L	0.58101	1.795	0.32550	N	0.532438	B	0.12630	0.006	B	0.12156	0.007	T	0.18429	-1.0337	10	0.33940	T	0.23	.	1.6245	0.02720	0.5393:0.1859:0.0894:0.1854	.	162	P20248	CCNA2_HUMAN	M	162	ENSP00000274026:I162M	ENSP00000274026:I162M	I	-	3	3	CCNA2	122961668	0.997000	0.39634	0.569000	0.28460	0.977000	0.68977	1.504000	0.35726	1.038000	0.40049	0.482000	0.46254	ATT	.	.		0.343	CCNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256712.2	NM_001237	
KIAA1109	84162	hgsc.bcm.edu	37	4	123145811	123145811	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:123145811A>G	ENST00000264501.4	+	23	3145	c.2772A>G	c.(2770-2772)acA>acG	p.T924T	KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000455637.1_Silent_p.T924T|KIAA1109_ENST00000388738.3_Silent_p.T924T			Q2LD37	K1109_HUMAN	KIAA1109	924					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GAAGTCTTACAGCTAAGGTCA	0.433																																					p.T924T		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A2772G						.						121.0	122.0	121.0					4																	123145811		1952	4149	6101	SO:0001819	synonymous_variant	84162	exon21			TCTTACAGCTAAG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.2772A>G	chr4.hg19:g.123145811A>G		209.0	0.0		168.0	7.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	A	9.136	1.012639	0.19277	.	.	ENSG00000138688	ENST00000424425	.	.	.	5.23	2.75	0.32379	.	.	.	.	.	T	0.45337	0.1337	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30416	-0.9979	4	.	.	.	.	2.2057	0.03935	0.6008:0.1327:0.1393:0.1271	.	.	.	.	G	756	.	.	S	+	1	0	KIAA1109	123365261	0.908000	0.30866	1.000000	0.80357	0.981000	0.71138	0.122000	0.15687	0.387000	0.25024	-0.389000	0.06534	AGC	.	.		0.433	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
SPRY1	10252	hgsc.bcm.edu	37	4	124322782	124322782	+	Silent	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:124322782G>A	ENST00000394339.2	+	2	376	c.36G>A	c.(34-36)tcG>tcA	p.S12S	SPRY1_ENST00000339241.1_Silent_p.S12S	NM_001258039.1|NM_005841.2	NP_001244968.1|NP_005832.1	O43609	SPY1_HUMAN	sprouty homolog 1, antagonist of FGF signaling (Drosophila)	12					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						GTGGCAGTTCGTTAGTTGTGA	0.453																																					p.S12S		Atlas-SNP	.											.	SPRY1	28	.	0			c.G36A						.						172.0	181.0	178.0					4																	124322782		2203	4300	6503	SO:0001819	synonymous_variant	10252	exon2			CAGTTCGTTAGTT	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.36G>A	chr4.hg19:g.124322782G>A		143.0	0.0		188.0	60.0	NM_001258039	D3DNX6|Q6PNE0	Silent	SNP	ENST00000394339.2	hg19	CCDS3731.1																																																																																			.	.		0.453	SPRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256711.1		
ANKRD50	57182	hgsc.bcm.edu	37	4	125593315	125593315	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:125593315C>T	ENST00000504087.1	-	4	2154	c.1117G>A	c.(1117-1119)Gta>Ata	p.V373I	ANKRD50_ENST00000515641.1_Missense_Mutation_p.V194I	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	373								p.V373I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						TTGGTCCATACTGCGTGATAT	0.363																																					p.V373I		Atlas-SNP	.											ANKRD50,NS,carcinoma,0,1	ANKRD50	136	.	1	Substitution - Missense(1)	endometrium(1)	c.G1117A						.						136.0	136.0	136.0					4																	125593315		2203	4300	6503	SO:0001583	missense	57182	exon4			TCCATACTGCGTG	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.1117G>A	chr4.hg19:g.125593315C>T	ENSP00000425658:p.Val373Ile	119.0	1.0		95.0	4.0	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	hg19	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.039880	0.55003	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	T;T	0.65364	-0.15;-0.13	5.29	5.29	0.74685	.	0.148679	0.46145	D	0.000307	T	0.42359	0.1199	N	0.16602	0.42	0.58432	D	0.999998	B	0.30824	0.296	B	0.19946	0.027	T	0.44802	-0.9304	10	0.05525	T	0.97	.	19.1267	0.93388	0.0:1.0:0.0:0.0	.	373	Q9ULJ7	ANR50_HUMAN	I	373;194	ENSP00000425658:V373I;ENSP00000425355:V194I	ENSP00000425658:V373I	V	-	1	0	ANKRD50	125812765	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.164000	0.77533	2.753000	0.94483	0.555000	0.69702	GTA	.	.		0.363	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
FAT4	79633	hgsc.bcm.edu	37	4	126329790	126329790	+	Missense_Mutation	SNP	G	G	C	rs370906656		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:126329790G>C	ENST00000394329.3	+	4	5774	c.5761G>C	c.(5761-5763)Ggt>Cgt	p.G1921R	FAT4_ENST00000335110.5_Missense_Mutation_p.G219R	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1921	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G1921C(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AGCAGAAGATGGTGGGGGACA	0.333																																					p.G1921R		Atlas-SNP	.											FAT4_ENST00000394329,NS,carcinoma,0,2	FAT4	1752	.	2	Substitution - Missense(2)	lung(2)	c.G5761C						.						88.0	90.0	89.0					4																	126329790		2203	4300	6503	SO:0001583	missense	79633	exon4			GAAGATGGTGGGG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.5761G>C	chr4.hg19:g.126329790G>C	ENSP00000377862:p.Gly1921Arg	82.0	0.0		97.0	0.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	18.24	3.580005	0.65992	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01787	4.64;4.64	5.2	5.2	0.72013	Cadherin (4);Cadherin-like (1);	0.000000	0.34853	U	0.003632	T	0.06872	0.0175	L	0.39397	1.21	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.97110	0.994;1.0	T	0.55921	-0.8064	10	0.27082	T	0.32	.	18.7437	0.91784	0.0:0.0:1.0:0.0	.	219;1921	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	R	1921;219	ENSP00000377862:G1921R;ENSP00000335169:G219R	ENSP00000335169:G219R	G	+	1	0	FAT4	126549240	1.000000	0.71417	0.991000	0.47740	0.328000	0.28507	9.231000	0.95317	2.420000	0.82092	0.591000	0.81541	GGT	.	.		0.333	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
RNF150	57484	hgsc.bcm.edu	37	4	141868832	141868832	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:141868832T>C	ENST00000515673.2	-	4	899	c.866A>G	c.(865-867)gAc>gGc	p.D289G	RNF150_ENST00000507500.1_Missense_Mutation_p.D289G|RNF150_ENST00000306799.3_Missense_Mutation_p.D247G|RNF150_ENST00000420921.2_Missense_Mutation_p.D148G|RNF150_ENST00000379512.2_Missense_Mutation_p.D148G|RNF150_ENST00000515057.1_5'UTR			Q9ULK6	RN150_HUMAN	ring finger protein 150	289						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(10)|lung(7)|ovary(1)	19	all_hematologic(180;0.162)					CCGGACAACGTCATTGGGCTT	0.537																																					p.D289G		Atlas-SNP	.											.	RNF150	94	.	0			c.A866G						.						152.0	119.0	130.0					4																	141868832		2203	4300	6503	SO:0001583	missense	57484	exon4			ACAACGTCATTGG	AB033040	CCDS34065.1	4q31.1	2013-01-09			ENSG00000170153	ENSG00000170153		"""RING-type (C3HC4) zinc fingers"""	23138	protein-coding gene	gene with protein product						10574462	Standard	XM_005263150		Approved	KIAA1214	uc003iio.1	Q9ULK6	OTTHUMG00000161380	ENST00000515673.2:c.866A>G	chr4.hg19:g.141868832T>C	ENSP00000425840:p.Asp289Gly	251.0	0.0		264.0	11.0	NM_020724	Q3T1D0|Q6ZNW6	Missense_Mutation	SNP	ENST00000515673.2	hg19	CCDS34065.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.724036	0.89298	.	.	ENSG00000170153	ENST00000379512;ENST00000420921;ENST00000306799;ENST00000515673;ENST00000507500;ENST00000506101	T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82	5.95	5.95	0.96441	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	0.000000	0.85682	D	0.000000	T	0.66790	0.2825	M	0.62016	1.91	0.80722	D	1	D;P;D	0.89917	0.969;0.862;1.0	P;P;D	0.91635	0.796;0.746;0.999	T	0.69472	-0.5136	10	0.87932	D	0	.	15.4149	0.74960	0.0:0.0:0.0:1.0	.	247;289;289	Q9ULK6-2;Q9ULK6-3;Q9ULK6	.;.;RN150_HUMAN	G	148;148;247;289;289;120	ENSP00000368827:D148G;ENSP00000394581:D148G;ENSP00000304321:D247G;ENSP00000425840:D289G;ENSP00000425568:D289G;ENSP00000425947:D120G	ENSP00000304321:D247G	D	-	2	0	RNF150	142088282	1.000000	0.71417	0.916000	0.36221	0.984000	0.73092	7.336000	0.79245	2.281000	0.76405	0.528000	0.53228	GAC	.	.		0.537	RNF150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364739.2	XM_291090	
USP38	84640	hgsc.bcm.edu	37	4	144135539	144135539	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:144135539T>C	ENST00000307017.4	+	9	2916	c.2410T>C	c.(2410-2412)Tca>Cca	p.S804P	USP38_ENST00000510377.1_Missense_Mutation_p.S804P	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	804	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					CTCTTCATTGTCAGAAAGTTG	0.368																																					p.S804P		Atlas-SNP	.											.	USP38	92	.	0			c.T2410C						.						76.0	74.0	75.0					4																	144135539		2203	4300	6503	SO:0001583	missense	84640	exon9			TCATTGTCAGAAA	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"""Ubiquitin-specific peptidases"""	20067	protein-coding gene	gene with protein product			"""ubiquitin specific protease 38"""			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.2410T>C	chr4.hg19:g.144135539T>C	ENSP00000303434:p.Ser804Pro	112.0	0.0		130.0	6.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Missense_Mutation	SNP	ENST00000307017.4	hg19	CCDS3758.1	.	.	.	.	.	.	.	.	.	.	T	9.491	1.100690	0.20552	.	.	ENSG00000170185	ENST00000510377;ENST00000307017	T;T	0.73681	-0.77;-0.77	5.48	4.26	0.50523	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.280229	0.35555	N	0.003132	T	0.57388	0.2050	N	0.21545	0.675	0.36598	D	0.874492	B;B	0.10296	0.003;0.002	B;B	0.12156	0.006;0.007	T	0.55315	-0.8160	10	0.33141	T	0.24	-9.7229	7.2722	0.26262	0.0:0.0729:0.1469:0.7801	.	804;804	Q8NB14;Q3ZCV1	UBP38_HUMAN;.	P	804	ENSP00000427647:S804P;ENSP00000303434:S804P	ENSP00000303434:S804P	S	+	1	0	USP38	144354989	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	0.980000	0.29513	0.967000	0.38186	0.482000	0.46254	TCA	.	.		0.368	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557	
USP38	84640	hgsc.bcm.edu	37	4	144135649	144135649	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:144135649T>C	ENST00000307017.4	+	9	3026	c.2520T>C	c.(2518-2520)taT>taC	p.Y840Y	USP38_ENST00000510377.1_Silent_p.Y840Y	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	840	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					TGGTGCCCTATCTATTAAGTT	0.403																																					p.Y840Y		Atlas-SNP	.											.	USP38	92	.	0			c.T2520C						.						104.0	98.0	100.0					4																	144135649		2203	4300	6503	SO:0001819	synonymous_variant	84640	exon9			GCCCTATCTATTA	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"""Ubiquitin-specific peptidases"""	20067	protein-coding gene	gene with protein product			"""ubiquitin specific protease 38"""			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.2520T>C	chr4.hg19:g.144135649T>C		66.0	0.0		82.0	4.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Silent	SNP	ENST00000307017.4	hg19	CCDS3758.1																																																																																			.	.		0.403	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557	
ARFIP1	27236	hgsc.bcm.edu	37	4	153803996	153803996	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:153803996A>G	ENST00000451320.2	+	7	919	c.755A>G	c.(754-756)gAt>gGt	p.D252G	ARFIP1_ENST00000429148.2_Missense_Mutation_p.D72G|ARFIP1_ENST00000405727.2_Missense_Mutation_p.D220G|ARFIP1_ENST00000356064.3_Missense_Mutation_p.D220G|ARFIP1_ENST00000353617.2_Missense_Mutation_p.D252G			P53367	ARFP1_HUMAN	ADP-ribosylation factor interacting protein 1	252	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.				intracellular protein transport (GO:0006886)|regulation of protein secretion (GO:0050708)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)			ARFIP1/FHDC1(2)	cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(180;0.093)					ACCATTGAAGATACATTAATG	0.348																																					p.D252G		Atlas-SNP	.											.	ARFIP1	69	.	0			c.A755G						.						89.0	91.0	90.0					4																	153803996		2203	4300	6503	SO:0001583	missense	27236	exon7			TTGAAGATACATT	U52521	CCDS3780.1, CCDS34080.1	4q31.3	2008-08-01	2008-08-01			ENSG00000164144			21496	protein-coding gene	gene with protein product	"""arfaptin 1"""	605928				9038142, 10413101	Standard	NM_001025595		Approved	HSU52521	uc003imz.3	P53367		ENST00000451320.2:c.755A>G	chr4.hg19:g.153803996A>G	ENSP00000395083:p.Asp252Gly	60.0	0.0		65.0	4.0	NM_001025595	Q2M2X4|Q3SYL4|Q9Y2X6	Missense_Mutation	SNP	ENST00000451320.2	hg19	CCDS34080.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.737579	0.89482	.	.	ENSG00000164144	ENST00000451320;ENST00000429148;ENST00000353617;ENST00000405727;ENST00000356064	D;D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11;-3.11	6.17	6.17	0.99709	Arfaptin-like (3);	0.000000	0.85682	D	0.000000	D	0.96476	0.8850	M	0.84948	2.725	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.96901	0.9660	10	0.87932	D	0	-24.5395	16.8222	0.85835	1.0:0.0:0.0:0.0	.	72;220;252	B4DS69;Q2M2X4;P53367	.;.;ARFP1_HUMAN	G	252;72;252;220;220	ENSP00000395083:D252G;ENSP00000396653:D72G;ENSP00000296557:D252G;ENSP00000384189:D220G;ENSP00000348360:D220G	ENSP00000296557:D252G	D	+	2	0	ARFIP1	154023446	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.371000	0.80710	0.533000	0.62120	GAT	.	.		0.348	ARFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365032.1	NM_014447	
DDX60	55601	hgsc.bcm.edu	37	4	169195111	169195111	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:169195111C>A	ENST00000393743.3	-	17	2719	c.2428G>T	c.(2428-2430)Gtg>Ttg	p.V810L		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	810	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		TACACGACCACCCCGTCGTCG	0.443																																					p.V810L		Atlas-SNP	.											.	DDX60	304	.	0			c.G2428T						.						150.0	140.0	143.0					4																	169195111		2203	4300	6503	SO:0001583	missense	55601	exon17			CGACCACCCCGTC	AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.2428G>T	chr4.hg19:g.169195111C>A	ENSP00000377344:p.Val810Leu	82.0	0.0		88.0	6.0	NM_017631	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	hg19	CCDS34097.1	.	.	.	.	.	.	.	.	.	.	C	15.96	2.985995	0.53934	.	.	ENSG00000137628	ENST00000393743	T	0.14516	2.5	4.98	4.98	0.66077	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.52532	D	0.000073	T	0.29458	0.0734	L	0.47190	1.495	0.44539	D	0.997495	D	0.55385	0.971	P	0.60286	0.872	T	0.01178	-1.1427	10	0.66056	D	0.02	.	18.2063	0.89855	0.0:1.0:0.0:0.0	.	810	Q8IY21	DDX60_HUMAN	L	810	ENSP00000377344:V810L	ENSP00000377344:V810L	V	-	1	0	DDX60	169431686	0.984000	0.35163	1.000000	0.80357	0.019000	0.09904	2.353000	0.44089	2.467000	0.83353	0.557000	0.71058	GTG	.	.		0.443	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631	
SORBS2	8470	hgsc.bcm.edu	37	4	186598318	186598318	+	Intron	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:186598318T>C	ENST00000284776.7	-	4	465				SORBS2_ENST00000431808.1_Intron|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000355634.5_Intron|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000448662.2_Intron|RP11-626E13.1_ENST00000447277.1_RNA|SORBS2_ENST00000437304.2_Missense_Mutation_p.T109A	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)		GCTGTGTGTGTCTCAGGCACT	0.488																																					p.T109A	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.A325G						.						137.0	132.0	134.0					4																	186598318		692	1591	2283	SO:0001627	intron_variant	8470	exon5			TGTGTGTCTCAGG		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+1258A>G	chr4.hg19:g.186598318T>C		133.0	0.0		139.0	6.0	NM_001145673	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	hg19	CCDS3845.1	.	.	.	.	.	.	.	.	.	.	T	9.763	1.170512	0.21621	.	.	ENSG00000154556	ENST00000437304	T	0.32023	1.47	5.91	4.54	0.55810	.	.	.	.	.	T	0.17238	0.0414	N	0.08118	0	0.58432	D	0.999999	B	0.14012	0.009	B	0.16289	0.015	T	0.05386	-1.0888	9	0.62326	D	0.03	.	11.1936	0.48700	0.0:0.0801:0.0:0.9199	.	109	E9PAW4	.	A	109	ENSP00000396008:T109A	ENSP00000396008:T109A	T	-	1	0	SORBS2	186835312	0.963000	0.33076	0.955000	0.39395	0.749000	0.42624	1.292000	0.33342	2.254000	0.74563	0.533000	0.62120	ACA	.	.		0.488	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
FAT1	2195	hgsc.bcm.edu	37	4	187517698	187517698	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:187517698A>G	ENST00000441802.2	-	25	13205	c.12996T>C	c.(12994-12996)taT>taC	p.Y4332Y	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4332					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						TCTTACTGTCATAGTCAAAGT	0.488										HNSCC(5;0.00058)																											p.Y4332Y	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T12996C						.						46.0	48.0	47.0					4																	187517698		1987	4163	6150	SO:0001819	synonymous_variant	2195	exon25			ACTGTCATAGTCA	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.12996T>C	chr4.hg19:g.187517698A>G		83.0	0.0		99.0	4.0	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	A	1.177	-0.639369	0.03557	.	.	ENSG00000083857	ENST00000512772	.	.	.	5.37	-2.77	0.05877	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4738	0.55801	0.5168:0.0:0.4832:0.0	.	.	.	.	R	100	.	.	X	-	1	0	FAT1	187754692	0.652000	0.27349	0.827000	0.32855	0.248000	0.25809	-0.012000	0.12699	-0.604000	0.05760	-0.256000	0.11100	TGA	.	.		0.488	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
ADCY2	108	hgsc.bcm.edu	37	5	7396594	7396594	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:7396594T>C	ENST00000338316.4	+	1	274	c.185T>C	c.(184-186)cTc>cCc	p.L62P		NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	62					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)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|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)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						CTCGCCCTGCTCGCCGTCTTC	0.701																																					p.L62P		Atlas-SNP	.											.	ADCY2	337	.	0			c.T185C						.						48.0	41.0	43.0					5																	7396594		2203	4300	6503	SO:0001583	missense	108	exon1			CCCTGCTCGCCGT	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"""Adenylate cyclases"""	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.185T>C	chr5.hg19:g.7396594T>C	ENSP00000342952:p.Leu62Pro	63.0	0.0		150.0	6.0	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	T	14.70	2.614340	0.46631	.	.	ENSG00000078295	ENST00000338316	T	0.79749	-1.3	3.67	3.67	0.42095	.	0.098199	0.42172	U	0.000754	T	0.70971	0.3285	L	0.36672	1.1	0.80722	D	1	B	0.15930	0.015	B	0.18263	0.021	T	0.67597	-0.5630	10	0.49607	T	0.09	.	10.0639	0.42292	0.0:0.0:0.0:1.0	.	62	Q08462	ADCY2_HUMAN	P	62	ENSP00000342952:L62P	ENSP00000342952:L62P	L	+	2	0	ADCY2	7449594	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	4.709000	0.61867	1.279000	0.44446	0.254000	0.18369	CTC	.	.		0.701	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	
FAM173B	134145	hgsc.bcm.edu	37	5	10239279	10239279	+	Missense_Mutation	SNP	G	G	T	rs367602123		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:10239279G>T	ENST00000511437.1	-	2	218	c.206C>A	c.(205-207)cCg>cAg	p.P69Q	FAM173B_ENST00000510052.1_5'UTR|FAM173B_ENST00000280330.8_5'UTR|FAM173B_ENST00000510047.1_Missense_Mutation_p.P69Q	NM_199133.3	NP_954584.2	Q6P4H8	F173B_HUMAN	family with sequence similarity 173, member B	69						integral component of membrane (GO:0016021)		p.P69L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	16						AGGTACAAACGGCAAACAGAC	0.527																																					p.P69Q		Atlas-SNP	.											FAM173B,NS,carcinoma,0,1	FAM173B	24	.	1	Substitution - Missense(1)	lung(1)	c.C206A						.						114.0	112.0	113.0					5																	10239279		2037	4176	6213	SO:0001583	missense	134145	exon2			ACAAACGGCAAAC		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.206C>A	chr5.hg19:g.10239279G>T	ENSP00000422338:p.Pro69Gln	110.0	1.0		236.0	0.0	NM_199133	B4DT41|B4DXK2|E9PBZ4	Missense_Mutation	SNP	ENST00000511437.1	hg19	CCDS43301.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.987143	0.74589	.	.	ENSG00000150756	ENST00000511437;ENST00000510047	T;T	0.25912	1.77;1.77	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.59376	0.2189	M	0.88241	2.94	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.68179	-0.5477	10	0.87932	D	0	-16.8539	17.7316	0.88379	0.0:0.0:1.0:0.0	.	69;69	E9PBZ4;Q6P4H8	.;F173B_HUMAN	Q	69	ENSP00000422338:P69Q;ENSP00000420876:P69Q	ENSP00000424210:P69Q	P	-	2	0	FAM173B	10292279	1.000000	0.71417	0.927000	0.36925	0.361000	0.29550	8.798000	0.91888	2.430000	0.82344	0.655000	0.94253	CCG	.	.		0.527	FAM173B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366048.2	NM_199133	
CTNND2	1501	hgsc.bcm.edu	37	5	11159822	11159822	+	Silent	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:11159822G>A	ENST00000304623.8	-	12	2214	c.2025C>T	c.(2023-2025)atC>atT	p.I675I	CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000458100.2_Silent_p.I242I|CTNND2_ENST00000359640.2_Silent_p.I675I|CTNND2_ENST00000511377.1_Silent_p.I584I|CTNND2_ENST00000503622.1_Silent_p.I338I	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	675					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GGGCATCCTGGATGATTGGCA	0.483																																					p.I675I		Atlas-SNP	.											.	CTNND2	289	.	0			c.C2025T						.						177.0	163.0	168.0					5																	11159822		2203	4300	6503	SO:0001819	synonymous_variant	1501	exon12			ATCCTGGATGATT	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"""Armadillo repeat containing"""	2516	protein-coding gene	gene with protein product	"""neural plakophilin-related arm-repeat protein"""	604275	"""catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"""			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.2025C>T	chr5.hg19:g.11159822G>A		185.0	0.0		323.0	66.0	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Silent	SNP	ENST00000304623.8	hg19	CCDS3881.1																																																																																			.	.		0.483	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332	
NUP155	9631	hgsc.bcm.edu	37	5	37352917	37352917	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:37352917G>A	ENST00000231498.3	-	5	681	c.478C>T	c.(478-480)Cat>Tat	p.H160Y	NUP155_ENST00000513532.1_Missense_Mutation_p.H160Y|NUP155_ENST00000381843.2_Missense_Mutation_p.H101Y	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	160					atrial cardiac muscle cell action potential (GO:0086014)|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 export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|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)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGTCGCACATGAGGTTGAAAG	0.418																																					p.H160Y		Atlas-SNP	.											.	NUP155	116	.	0			c.C478T						.						90.0	84.0	86.0					5																	37352917		2203	4300	6503	SO:0001583	missense	9631	exon5			GCACATGAGGTTG	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"""nucleoporin 155kD"""			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.478C>T	chr5.hg19:g.37352917G>A	ENSP00000231498:p.His160Tyr	67.0	0.0		102.0	6.0	NM_153485	Q9UBE9|Q9UFL5	Missense_Mutation	SNP	ENST00000231498.3	hg19	CCDS3921.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.926367	0.34002	.	.	ENSG00000113569	ENST00000231498;ENST00000381843;ENST00000434056;ENST00000513532	T;T;T	0.44083	0.93;0.93;0.93	5.85	5.85	0.93711	Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.087367	0.85682	D	0.000000	T	0.42832	0.1220	L	0.55213	1.73	0.80722	D	1	B;B	0.13145	0.004;0.007	B;B	0.19666	0.008;0.026	T	0.16100	-1.0414	10	0.28530	T	0.3	.	18.3541	0.90351	0.0:0.0:1.0:0.0	.	160;160	E9PF10;O75694	.;NU155_HUMAN	Y	160;101;122;160	ENSP00000231498:H160Y;ENSP00000371265:H101Y;ENSP00000422019:H160Y	ENSP00000231498:H160Y	H	-	1	0	NUP155	37388674	1.000000	0.71417	0.997000	0.53966	0.712000	0.41017	6.022000	0.70839	2.767000	0.95098	0.557000	0.71058	CAT	.	.		0.418	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298	
SNX18	112574	hgsc.bcm.edu	37	5	53813856	53813856	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:53813856A>G	ENST00000326277.3	+	1	264	c.74A>G	c.(73-75)gAg>gGg	p.E25G	SNX18_ENST00000381410.4_Missense_Mutation_p.E25G|SNX18_ENST00000343017.6_Missense_Mutation_p.E25G	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	25	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				CGAGAGCACGAGGTGCTGAGC	0.706																																					p.E25G		Atlas-SNP	.											.	SNX18	102	.	0			c.A74G						.						7.0	8.0	8.0					5																	53813856		2148	4207	6355	SO:0001583	missense	112574	exon1			AGCACGAGGTGCT	AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"""Sorting nexins"""	19245	protein-coding gene	gene with protein product			"""sorting nexin associated golgi protein 1"""	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000326277.3:c.74A>G	chr5.hg19:g.53813856A>G	ENSP00000317332:p.Glu25Gly	33.0	0.0		48.0	5.0	NM_052870	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Missense_Mutation	SNP	ENST00000326277.3	hg19	CCDS3962.1	.	.	.	.	.	.	.	.	.	.	A	19.48	3.835950	0.71373	.	.	ENSG00000178996	ENST00000343017;ENST00000381410;ENST00000326277	T;T;T	0.58506	0.33;0.33;0.33	3.82	3.82	0.43975	Src homology-3 domain (4);	0.142348	0.51477	D	0.000099	T	0.77164	0.4090	M	0.86805	2.84	0.58432	D	0.999998	D;D	0.71674	0.998;0.982	D;P	0.81914	0.995;0.82	T	0.81671	-0.0827	10	0.87932	D	0	-26.2397	12.4182	0.55506	1.0:0.0:0.0:0.0	.	25;25	Q96RF0;Q96RF0-2	SNX18_HUMAN;.	G	25	ENSP00000342276:E25G;ENSP00000370817:E25G;ENSP00000317332:E25G	ENSP00000317332:E25G	E	+	2	0	SNX18	53849613	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	6.472000	0.73567	1.589000	0.49982	0.254000	0.18369	GAG	.	.		0.706	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2		
ERCC8	1161	hgsc.bcm.edu	37	5	60214181	60214181	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:60214181T>C	ENST00000265038.5	-	4	352	c.310A>G	c.(310-312)Act>Gct	p.T104A	AC104113.3_ENST00000457499.1_RNA|ERCC8_ENST00000543101.1_5'UTR|ERCC8_ENST00000426742.2_Missense_Mutation_p.T46A	NM_000082.3	NP_000073.1	Q13216	ERCC8_HUMAN	excision repair cross-complementation group 8	104					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|positive regulation of DNA repair (GO:0045739)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|response to X-ray (GO:0010165)|transcription-coupled nucleotide-excision repair (GO:0006283)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|protein complex (GO:0043234)	protein complex binding (GO:0032403)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14		Lung NSC(810;1.51e-06)|Prostate(74;0.0322)|Ovarian(174;0.0481)|Breast(144;0.077)				CACTGTACAGTCTCCACACTG	0.343																																					p.T104A		Atlas-SNP	.											.	ERCC8	31	.	0			c.A310G						.						122.0	116.0	118.0					5																	60214181		2203	4299	6502	SO:0001583	missense	1161	exon4			GTACAGTCTCCAC	U28413	CCDS3978.1	5q12.1	2014-09-17	2014-03-07		ENSG00000049167	ENSG00000049167		"""WD repeat domain containing"""	3439	protein-coding gene	gene with protein product		609412	"""Cockayne syndrome 1 (classical)"", ""excision repair cross-complementing rodent repair deficiency, complementation group 8"""	CKN1		8596535	Standard	NM_000082		Approved	CSA	uc003jsm.3	Q13216	OTTHUMG00000097741	ENST00000265038.5:c.310A>G	chr5.hg19:g.60214181T>C	ENSP00000265038:p.Thr104Ala	77.0	0.0		115.0	5.0	NM_000082	B2RB64|Q6FHX5|Q96GB9	Missense_Mutation	SNP	ENST00000265038.5	hg19	CCDS3978.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.497119	0.85069	.	.	ENSG00000049167	ENST00000426742;ENST00000265038;ENST00000536596;ENST00000439176	T;T;T	0.58060	0.36;0.36;0.36	4.74	4.74	0.60224	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.34919	0.0914	N	0.05012	-0.13	0.80722	D	1	B;B	0.31351	0.084;0.32	B;B	0.36719	0.163;0.231	T	0.27191	-1.0081	10	0.27785	T	0.31	-28.586	14.4087	0.67101	0.0:0.0:0.0:1.0	.	104;104	Q13216-2;Q13216	.;ERCC8_HUMAN	A	46;104;103;46	ENSP00000400110:T46A;ENSP00000265038:T104A;ENSP00000408344:T46A	ENSP00000265038:T104A	T	-	1	0	ERCC8	60249938	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.608000	0.82898	1.995000	0.58328	0.533000	0.62120	ACT	.	.		0.343	ERCC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214971.2	NM_000082	
ZSWIM6	57688	hgsc.bcm.edu	37	5	60839780	60839780	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:60839780T>C	ENST00000252744.5	+	14	3284	c.3284T>C	c.(3283-3285)gTc>gCc	p.V1095A		NM_020928.1	NP_065979.1	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	1095					neuron projection morphogenesis (GO:0048812)|regulation of neuron migration (GO:2001222)		zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	8						CCTCTGGTGGTCAAGAGTGTC	0.502																																					p.V1095A		Atlas-SNP	.											.	ZSWIM6	51	.	0			c.T3284C						.						95.0	78.0	83.0					5																	60839780		692	1591	2283	SO:0001583	missense	57688	exon14			TGGTGGTCAAGAG	BC039438	CCDS47215.1	5q12.1	2011-03-17			ENSG00000130449	ENSG00000130449		"""Zinc fingers, SWIM-type"""	29316	protein-coding gene	gene with protein product		615951				10997877, 16427614	Standard	NM_020928		Approved	KIAA1577	uc003jsr.3	Q9HCJ5	OTTHUMG00000162388	ENST00000252744.5:c.3284T>C	chr5.hg19:g.60839780T>C	ENSP00000252744:p.Val1095Ala	83.0	0.0		143.0	7.0	NM_020928		Missense_Mutation	SNP	ENST00000252744.5	hg19	CCDS47215.1	.	.	.	.	.	.	.	.	.	.	t	21.4	4.144638	0.77888	.	.	ENSG00000130449	ENST00000252744	T	0.55413	0.52	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.70474	0.3228	M	0.75264	2.295	0.52501	D	0.999957	D	0.69078	0.997	D	0.77004	0.989	T	0.70461	-0.4865	10	0.34782	T	0.22	-2.1229	14.5911	0.68365	0.0:0.0:0.0:1.0	.	1095	Q9HCJ5	ZSWM6_HUMAN	A	1095	ENSP00000252744:V1095A	ENSP00000252744:V1095A	V	+	2	0	ZSWIM6	60875537	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.048000	0.60808	0.450000	0.29827	GTC	.	.		0.502	ZSWIM6-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368710.1	NM_020928	
GPR98	84059	hgsc.bcm.edu	37	5	89968413	89968413	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:89968413A>G	ENST00000405460.2	+	22	4899	c.4803A>G	c.(4801-4803)ggA>ggG	p.G1601G	GPR98_ENST00000450321.2_3'UTR	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1601	Calx-beta 11. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GAACCAGAGGAGCTCTGGATT	0.368																																					p.G1601G		Atlas-SNP	.											.	GPR98	605	.	0			c.A4803G						.						174.0	158.0	163.0					5																	89968413		1866	4103	5969	SO:0001819	synonymous_variant	84059	exon22			CAGAGGAGCTCTG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.4803A>G	chr5.hg19:g.89968413A>G		177.0	0.0		372.0	87.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	hg19	CCDS47246.1																																																																																			.	.		0.368	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
CHD1	1105	hgsc.bcm.edu	37	5	98194094	98194094	+	Splice_Site	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:98194094T>C	ENST00000284049.3	-	34	4726	c.4577A>G	c.(4576-4578)gAt>gGt	p.D1526G		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1526					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)	TCTTTCCACATCTGTTAGATA	0.323																																					p.D1526G		Atlas-SNP	.											.	CHD1	137	.	0			c.A4577G						.						158.0	154.0	155.0					5																	98194094		2203	4300	6503	SO:0001630	splice_region_variant	1105	exon34			TCCACATCTGTTA	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.4577-1A>G	chr5.hg19:g.98194094T>C		111.0	0.0		170.0	7.0	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	T	14.52	2.559636	0.45590	.	.	ENSG00000153922	ENST00000422663;ENST00000284049	D	0.89810	-2.57	5.12	5.12	0.69794	.	0.000000	0.34555	U	0.003862	D	0.86066	0.5844	L	0.51422	1.61	0.58432	D	0.999999	B	0.19200	0.034	B	0.17722	0.019	T	0.82520	-0.0416	10	0.37606	T	0.19	.	15.1902	0.73038	0.0:0.0:0.0:1.0	.	1526	O14646	CHD1_HUMAN	G	116;1526	ENSP00000284049:D1526G	ENSP00000284049:D1526G	D	-	2	0	CHD1	98221994	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.460000	0.80816	2.046000	0.60703	0.397000	0.26171	GAT	.	.		0.323	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	Missense_Mutation
MAN2A1	4124	hgsc.bcm.edu	37	5	109190938	109190938	+	Missense_Mutation	SNP	C	C	T	rs3217225|rs200723635	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:109190938C>T	ENST00000261483.4	+	20	4126	c.3074C>T	c.(3073-3075)tCc>tTc	p.S1025F	MAN2A1_ENST00000505313.1_3'UTR	NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	1025					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		AATAAGTTCTCCTCACCTACC	0.403																																					p.S1025F		Atlas-SNP	.											MAN2A1,colon,carcinoma,0,1	MAN2A1	136	.	0			c.C3074T						.						163.0	117.0	132.0					5																	109190938		2202	4295	6497	SO:0001583	missense	4124	exon20			AGTTCTCCTCACC		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"""golgi integral membrane protein 7"""	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.3074C>T	chr5.hg19:g.109190938C>T	ENSP00000261483:p.Ser1025Phe	48.0	2.0		81.0	8.0	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	hg19	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	C	9.575	1.122145	0.20877	.	.	ENSG00000112893	ENST00000261483	T	0.80738	-1.41	5.07	1.88	0.25563	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	1.184260	0.05825	N	0.616516	T	0.71609	0.3360	L	0.34521	1.04	0.09310	N	1	B	0.10296	0.003	B	0.19666	0.026	T	0.58521	-0.7622	10	0.56958	D	0.05	1.7459	5.1539	0.15025	0.5166:0.3102:0.0:0.1732	.	1025	Q16706	MA2A1_HUMAN	F	1025	ENSP00000261483:S1025F	ENSP00000261483:S1025F	S	+	2	0	MAN2A1	109218837	0.407000	0.25352	0.001000	0.08648	0.007000	0.05969	3.958000	0.56737	0.412000	0.25729	-0.373000	0.07131	TCC	.	.		0.403	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1		
KCNN2	3781	hgsc.bcm.edu	37	5	113698631	113698631	+	Silent	SNP	T	T	C	rs151038013|rs111266015|rs76852708|rs34641516		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:113698631T>C	ENST00000512097.3	+	2	1177	c.159T>C	c.(157-159)gcT>gcC	p.A53A	KCNN2_ENST00000264773.3_Silent_p.A53A			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	53	Poly-Ala.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transport (GO:1901379)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|protein homodimerization activity (GO:0042803)|small conductance calcium-activated potassium channel activity (GO:0016286)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Miconazole(DB01110)|Procaine(DB00721)	CTGCAGCCGCTGCCGCCGCCG	0.701																																					p.A53A		Atlas-SNP	.											.,4	KCNN2	144	.	0			c.T159C						.						7.0	7.0	7.0					5																	113698631		2067	4071	6138	SO:0001819	synonymous_variant	3781	exon1			AGCCGCTGCCGCC	AF239613	CCDS4114.1, CCDS43352.1	5q22.3	2012-07-05			ENSG00000080709	ENSG00000080709		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6291	protein-coding gene	gene with protein product		605879				16382103	Standard	NM_001278204		Approved	KCa2.2, hSK2	uc003kqo.3	Q9H2S1	OTTHUMG00000128836	ENST00000512097.3:c.159T>C	chr5.hg19:g.113698631T>C		2.0	0.0		17.0	4.0	NM_021614	A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Silent	SNP	ENST00000512097.3	hg19	CCDS4114.1																																																																																			.	.		0.701	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614	
PHAX	51808	hgsc.bcm.edu	37	5	125960441	125960441	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:125960441T>C	ENST00000297540.4	+	5	1785	c.1090T>C	c.(1090-1092)Tct>Cct	p.S364P		NM_032177.3	NP_115553.2	Q9H814	PHAX_HUMAN	phosphorylated adaptor for RNA export	364					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|protein transport (GO:0015031)|RNA metabolic process (GO:0016070)|snRNA export from nucleus (GO:0006408)|spliceosomal snRNP assembly (GO:0000387)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA binding (GO:0003723)|toxic substance binding (GO:0015643)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	8						GGCCTTGGCCTCTCTTGATGA	0.403																																					p.S364P		Atlas-SNP	.											.	PHAX	20	.	0			c.T1090C						.						107.0	106.0	106.0					5																	125960441		2203	4300	6503	SO:0001583	missense	51808	exon5			TTGGCCTCTCTTG	AK023255	CCDS4138.1	5q23.2	2011-05-24	2008-10-01	2008-10-01	ENSG00000164902	ENSG00000164902			10241	protein-coding gene	gene with protein product		604924	"""RNA U, small nuclear RNA export adaptor (phosphorylation regulated)"""	RNUXA		10786834	Standard	NM_032177		Approved	FLJ13193	uc003kua.2	Q9H814	OTTHUMG00000163273	ENST00000297540.4:c.1090T>C	chr5.hg19:g.125960441T>C	ENSP00000297540:p.Ser364Pro	103.0	0.0		160.0	7.0	NM_032177	Q9H8W1	Missense_Mutation	SNP	ENST00000297540.4	hg19	CCDS4138.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.993292	0.74703	.	.	ENSG00000164902	ENST00000297540	T	0.54675	0.56	5.62	4.47	0.54385	.	0.000000	0.85682	D	0.000000	T	0.39963	0.1098	L	0.32530	0.975	0.58432	D	0.999998	B	0.21753	0.06	B	0.14578	0.011	T	0.28839	-1.0031	10	0.40728	T	0.16	-26.0387	10.994	0.47565	0.0:0.0723:0.0:0.9277	.	364	Q9H814	PHAX_HUMAN	P	364	ENSP00000297540:S364P	ENSP00000297540:S364P	S	+	1	0	PHAX	125988340	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.457000	0.66672	2.146000	0.66826	0.460000	0.39030	TCT	.	.		0.403	PHAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250924.1	NM_032177	
PCDHB15	56121	hgsc.bcm.edu	37	5	140627002	140627002	+	Missense_Mutation	SNP	C	C	G	rs17844634	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:140627002C>G	ENST00000231173.3	+	1	1856	c.1856C>G	c.(1855-1857)gCg>gGg	p.A619G		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	619	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A619E(1)|p.A619V(1)		NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCGTGTGGGCGCACAATGGC	0.692													C|||	2	0.000399361	0.0	0.0	5008	,	,		15365	0.002		0.0	False		,,,				2504	0.0				p.A619G		Atlas-SNP	.											PCDHB15,NS,carcinoma,0,2	PCDHB15	138	.	2	Substitution - Missense(2)	lung(1)|endometrium(1)	c.C1856G						.						25.0	27.0	26.0					5																	140627002		2064	4076	6140	SO:0001583	missense	56121	exon1			TGTGGGCGCACAA	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1856C>G	chr5.hg19:g.140627002C>G	ENSP00000231173:p.Ala619Gly	7.0	1.0		35.0	11.0	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	hg19	CCDS4257.1	.	.	.	.	.	.	.	.	.	.	C	16.20	3.055284	0.55325	.	.	ENSG00000113248	ENST00000231173	T	0.52983	0.64	4.11	3.21	0.36854	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.42494	0.1205	L	0.55017	1.72	0.20563	N	0.999889	B	0.18968	0.032	B	0.30782	0.12	T	0.29912	-0.9996	9	0.35671	T	0.21	.	5.7793	0.18297	0.0:0.6715:0.0:0.3285	rs17844634	619	Q9Y5E8	PCDBF_HUMAN	G	619	ENSP00000231173:A619G	ENSP00000231173:A619G	A	+	2	0	PCDHB15	140607186	0.000000	0.05858	1.000000	0.80357	0.980000	0.70556	-1.729000	0.01856	2.032000	0.59987	0.549000	0.68633	GCG	.	.		0.692	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
ARHGEF37	389337	hgsc.bcm.edu	37	5	149006643	149006643	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:149006643T>C	ENST00000333677.6	+	11	1632	c.1469T>C	c.(1468-1470)cTc>cCc	p.L490P		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	490						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						TCCCAGCCGCTCCTTCCAGGG	0.552																																					p.L490P		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.T1469C						.						91.0	100.0	97.0					5																	149006643		2061	4206	6267	SO:0001583	missense	389337	exon11			AGCCGCTCCTTCC	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"""Rho guanine nucleotide exchange factors"""	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1469T>C	chr5.hg19:g.149006643T>C	ENSP00000328083:p.Leu490Pro	94.0	0.0		208.0	9.0	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	hg19	CCDS43385.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.260430	0.80246	.	.	ENSG00000183111	ENST00000333677	T	0.57907	0.37	5.39	5.39	0.77823	.	0.063201	0.64402	D	0.000004	T	0.67998	0.2953	L	0.58101	1.795	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.70226	-0.4930	10	0.59425	D	0.04	.	13.6429	0.62263	0.0:0.0:0.0:1.0	.	490	A1IGU5	ARH37_HUMAN	P	490	ENSP00000328083:L490P	ENSP00000328083:L490P	L	+	2	0	ARHGEF37	148986836	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	5.468000	0.66743	2.036000	0.60181	0.459000	0.35465	CTC	.	.		0.552	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
THG1L	54974	hgsc.bcm.edu	37	5	157161681	157161681	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:157161681T>C	ENST00000231198.7	+	3	710	c.466T>C	c.(466-468)Ttt>Ctt	p.F156L	AC026407.1_ENST00000599823.1_Silent_p.K15K	NM_017872.3	NP_060342.2	Q9NWX6	THG1_HUMAN	tRNA-histidine guanylyltransferase 1-like (S. cerevisiae)	156					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)			TCCCCCAGGCTTTGACGGAAG	0.498																																					p.F156L		Atlas-SNP	.											.	THG1L	31	.	0			c.T466C						.						126.0	118.0	121.0					5																	157161681		2203	4300	6503	SO:0001583	missense	54974	exon3			CCAGGCTTTGACG	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.466T>C	chr5.hg19:g.157161681T>C	ENSP00000231198:p.Phe156Leu	99.0	0.0		191.0	8.0	NM_017872	D3DQJ5|Q53G12|Q7L5R3|Q9H0S2	Missense_Mutation	SNP	ENST00000231198.7	hg19	CCDS4341.1	.	.	.	.	.	.	.	.	.	.	T	19.20	3.781232	0.70222	.	.	ENSG00000113272	ENST00000231198;ENST00000448153	T	0.70749	-0.51	5.95	5.95	0.96441	.	0.042575	0.85682	N	0.000000	D	0.85894	0.5803	H	0.96430	3.82	0.80722	D	1	P;P	0.48016	0.888;0.904	P;P	0.51135	0.489;0.66	D	0.90196	0.4253	10	0.87932	D	0	-36.0233	16.4208	0.83758	0.0:0.0:0.0:1.0	.	24;156	B4E366;Q9NWX6	.;THG1_HUMAN	L	156;31	ENSP00000231198:F156L	ENSP00000231198:F156L	F	+	1	0	THG1L	157094259	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.001000	0.88508	2.274000	0.75844	0.528000	0.53228	TTT	.	.		0.498	THG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252579.2	NM_017872	
SLIT3	6586	hgsc.bcm.edu	37	5	168212944	168212944	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:168212944T>C	ENST00000519560.1	-	12	1538	c.1119A>G	c.(1117-1119)ggA>ggG	p.G373G	SLIT3_ENST00000332966.8_Silent_p.G373G|SLIT3_ENST00000404867.3_Silent_p.G373G	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	373					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CATCAAACAGTCCCTTGACAA	0.512																																					p.G373G	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.A1119G						.						156.0	130.0	139.0					5																	168212944		2203	4300	6503	SO:0001819	synonymous_variant	6586	exon12			AAACAGTCCCTTG	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.1119A>G	chr5.hg19:g.168212944T>C		66.0	0.0		132.0	6.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.		0.512	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
EXOC2	55770	hgsc.bcm.edu	37	6	532529	532529	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:532529A>G	ENST00000230449.4	-	23	2455	c.2320T>C	c.(2320-2322)Tcc>Ccc	p.S774P	EXOC2_ENST00000448181.3_Missense_Mutation_p.S369P	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	774					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)		p.S774P(1)		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)		GGTTCTAAGGAGCCAACGATG	0.378																																					p.S774P		Atlas-SNP	.											EXOC2,NS,carcinoma,0,1	EXOC2	81	.	1	Substitution - Missense(1)	kidney(1)	c.T2320C						.						125.0	119.0	121.0					6																	532529		2203	4300	6503	SO:0001583	missense	55770	exon23			CTAAGGAGCCAAC	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.2320T>C	chr6.hg19:g.532529A>G	ENSP00000230449:p.Ser774Pro	144.0	0.0		217.0	9.0	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Missense_Mutation	SNP	ENST00000230449.4	hg19	CCDS34327.1	.	.	.	.	.	.	.	.	.	.	A	19.44	3.828161	0.71143	.	.	ENSG00000112685	ENST00000230449;ENST00000448181	T;T	0.28255	1.62;1.62	5.67	5.67	0.87782	.	0.052488	0.85682	D	0.000000	T	0.19604	0.0471	M	0.63428	1.95	0.80722	D	1	P	0.40875	0.731	B	0.32533	0.147	T	0.08106	-1.0738	10	0.59425	D	0.04	-0.0072	16.2014	0.82084	1.0:0.0:0.0:0.0	.	774	Q96KP1	EXOC2_HUMAN	P	774;369	ENSP00000230449:S774P;ENSP00000398113:S369P	ENSP00000230449:S774P	S	-	1	0	EXOC2	477529	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.880000	0.92407	2.281000	0.76405	0.533000	0.62120	TCC	.	.		0.378	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303	
SOX4	6659	hgsc.bcm.edu	37	6	21595211	21595211	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:21595211C>T	ENST00000244745.1	+	1	1240	c.446C>T	c.(445-447)tCc>tTc	p.S149F	SOX4_ENST00000543472.1_Missense_Mutation_p.S149F	NM_003107.2	NP_003098.1	Q06945	SOX4_HUMAN	SRY (sex determining region Y)-box 4	149					ascending aorta morphogenesis (GO:0035910)|atrial septum primum morphogenesis (GO:0003289)|canonical Wnt signaling pathway (GO:0060070)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle formation (GO:0003211)|cellular response to glucose stimulus (GO:0071333)|DNA damage response, detection of DNA damage (GO:0042769)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endocrine pancreas development (GO:0031018)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|kidney morphogenesis (GO:0060993)|limb bud formation (GO:0060174)|mitral valve morphogenesis (GO:0003183)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of protein ubiquitination (GO:0031397)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|noradrenergic neuron differentiation (GO:0003357)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin secretion (GO:0032024)|positive regulation of N-terminal peptidyl-lysine acetylation (GO:2000761)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of Wnt signaling pathway (GO:0030177)|pro-B cell differentiation (GO:0002328)|protein stabilization (GO:0050821)|regulation of protein stability (GO:0031647)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spinal cord development (GO:0021510)|spinal cord motor neuron differentiation (GO:0021522)|sympathetic nervous system development (GO:0048485)|T cell differentiation (GO:0030217)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.S149Y(1)		kidney(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	6	Ovarian(93;0.163)		all cancers(50;0.0751)|Epithelial(50;0.155)			GCCGCCTCCTCCAAGCCGGGG	0.716																																					p.S149F		Atlas-SNP	.											SOX4,mouth,carcinoma,0,1	SOX4	11	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C446T						.						9.0	11.0	10.0					6																	21595211		2180	4278	6458	SO:0001583	missense	6659	exon1			CCTCCTCCAAGCC	AF070669	CCDS4547.1	6p22.3	2008-02-05			ENSG00000124766	ENSG00000124766		"""SRY (sex determining region Y)-boxes"""	11200	protein-coding gene	gene with protein product		184430				8268656, 9730625	Standard	NM_003107		Approved		uc003ndi.3	Q06945	OTTHUMG00000016101	ENST00000244745.1:c.446C>T	chr6.hg19:g.21595211C>T	ENSP00000244745:p.Ser149Phe	29.0	0.0		62.0	3.0	NM_003107		Missense_Mutation	SNP	ENST00000244745.1	hg19	CCDS4547.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.332285	0.24167	.	.	ENSG00000124766	ENST00000244745;ENST00000543472	T;T	0.20332	2.08;2.08	3.43	2.54	0.30619	.	.	.	.	.	T	0.07324	0.0185	L	0.48642	1.525	0.35912	D	0.831198	P	0.38565	0.637	B	0.41813	0.367	T	0.12811	-1.0533	9	0.09338	T	0.73	.	7.8342	0.29360	0.2467:0.7532:0.0:0.0	.	149	Q06945	SOX4_HUMAN	F	149	ENSP00000244745:S149F;ENSP00000438412:S149F	ENSP00000244745:S149F	S	+	2	0	SOX4	21703190	0.003000	0.15002	0.788000	0.31933	0.314000	0.28054	1.614000	0.36911	0.591000	0.29711	0.305000	0.20034	TCC	.	.		0.716	SOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043301.1	NM_003107	
NOTCH4	4855	hgsc.bcm.edu	37	6	32191665	32191665	+	Missense_Mutation	SNP	A	A	G	rs543450919|rs150280230	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:32191665A>G	ENST00000375023.3	-	1	179	c.41T>C	c.(40-42)cTg>cCg	p.L14P		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	14					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						ACATagcagcagcagcagcag	0.637																																					p.L14P		Atlas-SNP	.											.	NOTCH4	201	.	0			c.T41C						.						74.0	56.0	62.0					6																	32191665		1510	2709	4219	SO:0001583	missense	4855	exon1			AGCAGCAGCAGCA		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.41T>C	chr6.hg19:g.32191665A>G	ENSP00000364163:p.Leu14Pro	59.0	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	.	.	.	.	.	.	.	.	.	.	A	12.18	1.861685	0.32884	.	.	ENSG00000204301	ENST00000375023	D	0.82711	-1.64	2.85	-1.26	0.09376	.	3.622260	0.01980	N	0.044758	T	0.46328	0.1387	N	0.19112	0.55	0.09310	N	0.999996	B;B	0.25667	0.131;0.063	B;B	0.15870	0.014;0.006	T	0.35276	-0.9795	10	0.30078	T	0.28	.	2.9781	0.05945	0.482:0.2361:0.2819:0.0	.	14;14	Q6P3V5;Q99466	.;NOTC4_HUMAN	P	14	ENSP00000364163:L14P	ENSP00000364163:L14P	L	-	2	0	NOTCH4	32299643	0.008000	0.16893	0.005000	0.12908	0.016000	0.09150	-0.129000	0.10515	-0.207000	0.10187	0.372000	0.22366	CTG	.	.		0.637	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
HLA-DRA	3122	hgsc.bcm.edu	37	6	32411036	32411036	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:32411036G>C	ENST00000395388.2	+	3	512	c.403G>C	c.(403-405)Gac>Cac	p.D135H	HLA-DRA_ENST00000374982.5_Splice_Site	NM_019111.4	NP_061984.2	P01903	DRA_HUMAN	major histocompatibility complex, class II, DR alpha	135	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002504)|cognition (GO:0050890)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|polysaccharide assembly with MHC class II protein complex (GO:0002506)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|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)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)	p.D135N(1)		NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19						CTGTTTCATAGACAAGTTCAC	0.522									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Kaposi Sarcoma, Familial Clustering of																												p.D135H		Atlas-SNP	.											HLA-DRA,NS,carcinoma,0,1	HLA-DRA	34	.	1	Substitution - Missense(1)	breast(1)	c.G403C						.						137.0	109.0	119.0					6																	32411036		1511	2709	4220	SO:0001583	missense	3122	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;	TTCATAGACAAGT		CCDS4750.1	6p21.3	2013-01-11			ENSG00000204287	ENSG00000204287		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4947	protein-coding gene	gene with protein product		142860		HLA-DRA1			Standard	NM_019111		Approved		uc003obh.3	P01903	OTTHUMG00000031269	ENST00000395388.2:c.403G>C	chr6.hg19:g.32411036G>C	ENSP00000378786:p.Asp135His	157.0	0.0		264.0	0.0	NM_019111	A2BET4|Q30160|Q6IAZ1|Q861I2|Q9TP70	Missense_Mutation	SNP	ENST00000395388.2	hg19	CCDS4750.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|.	7.137|7.137	0.581116|0.581116	0.13686|0.13686	.|.	.|.	ENSG00000204287|ENSG00000204287	ENST00000374982|ENST00000395388	.|T	.|0.02944	.|4.1	5.59|5.59	3.83|3.83	0.44106|0.44106	.|Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	.|0.164111	.|0.56097	.|D	.|0.000038	.|T	.|0.06600	.|0.0169	M|M	0.75085|0.75085	2.285|2.285	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	.|T	.|0.02751	.|-1.1115	.|10	.|0.87932	.|D	.|0	.|.	7.8337|7.8337	0.29358|0.29358	0.2453:0.0:0.7547:0.0|0.2453:0.0:0.7547:0.0	.|.	.|135	.|P01903	.|DRA_HUMAN	.|H	-1|135	.|ENSP00000378786:D135H	.|ENSP00000378786:D135H	.|D	+|+	.|1	.|0	HLA-DRA|HLA-DRA	32519014|32519014	0.993000|0.993000	0.37304|0.37304	0.707000|0.707000	0.30419|0.30419	0.151000|0.151000	0.21798|0.21798	2.330000|2.330000	0.43885|0.43885	0.939000|0.939000	0.37446|0.37446	0.638000|0.638000	0.83543|0.83543	.|GAC	.	.		0.522	HLA-DRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076586.2	NM_019111	
BRD2	6046	hgsc.bcm.edu	37	6	32945598	32945598	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:32945598T>C	ENST00000374825.4	+	9	3095	c.1394T>C	c.(1393-1395)gTc>gCc	p.V465A	BRD2_ENST00000395289.2_Missense_Mutation_p.V465A|BRD2_ENST00000374831.4_Missense_Mutation_p.V465A|BRD2_ENST00000443797.2_Missense_Mutation_p.V345A|BRD2_ENST00000449085.2_Missense_Mutation_p.V418A|BRD2_ENST00000395287.1_Missense_Mutation_p.V465A	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	465					chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						CCTTTACCAGTCTCTACTGCC	0.488																																					p.V465A		Atlas-SNP	.											.	BRD2	70	.	0			c.T1394C						.						126.0	135.0	132.0					6																	32945598		1511	2708	4219	SO:0001583	missense	6046	exon9			TACCAGTCTCTAC	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"""bromodomain-containing 2"""			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.1394T>C	chr6.hg19:g.32945598T>C	ENSP00000363958:p.Val465Ala	205.0	0.0		288.0	22.0	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Missense_Mutation	SNP	ENST00000374825.4	hg19	CCDS4762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.34|11.34	1.609980|1.609980	0.28712|0.28712	.|.	.|.	ENSG00000204256|ENSG00000204256	ENST00000449025|ENST00000374825;ENST00000374831;ENST00000395289;ENST00000443797;ENST00000395287;ENST00000449085	.|T;T;T;T;T;T	.|0.06933	.|3.41;3.41;3.39;3.24;3.39;3.37	5.63|5.63	4.47|4.47	0.54385|0.54385	.|Bromodomain (1);	.|0.305062	.|0.23670	.|N	.|0.045736	T|T	0.01320|0.01320	0.0043|0.0043	N|N	0.16478|0.16478	0.41|0.41	0.42077|0.42077	D|D	0.991233|0.991233	.|B;B	.|0.15141	.|0.005;0.012	.|B;B	.|0.15870	.|0.014;0.014	T|T	0.42430|0.42430	-0.9452|-0.9452	5|10	.|0.06891	.|T	.|0.86	-9.8783|-9.8783	5.5595|5.5595	0.17135|0.17135	0.0:0.1763:0.0:0.8237|0.0:0.1763:0.0:0.8237	.|.	.|465;465	.|A2AAU0;P25440	.|.;BRD2_HUMAN	P|A	471|465;465;465;345;465;418	.|ENSP00000363958:V465A;ENSP00000363964:V465A;ENSP00000378704:V465A;ENSP00000413495:V345A;ENSP00000378702:V465A;ENSP00000409145:V418A	.|ENSP00000363958:V465A	S|V	+|+	1|2	0|0	BRD2|BRD2	33053576|33053576	0.410000|0.410000	0.25376|0.25376	0.975000|0.975000	0.42487|0.42487	0.990000|0.990000	0.78478|0.78478	0.895000|0.895000	0.28363|0.28363	2.363000|2.363000	0.80096|0.80096	0.523000|0.523000	0.50628|0.50628	TCT|GTC	.	.		0.488	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2		
SCUBE3	222663	hgsc.bcm.edu	37	6	35216340	35216340	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:35216340A>G	ENST00000274938.7	+	22	2840	c.2840A>G	c.(2839-2841)aAg>aGg	p.K947R	SCUBE3_ENST00000394681.1_Missense_Mutation_p.K963R	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3											breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						CAGGACAAGAAGCTCATCAAG	0.512																																					p.K947R		Atlas-SNP	.											.	SCUBE3	99	.	0			c.A2840G						.						141.0	130.0	134.0					6																	35216340		2203	4300	6503	SO:0001583	missense	222663	exon22			ACAAGAAGCTCAT	AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"""CUB domain and EGF-like repeat containing 3"""	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.2840A>G	chr6.hg19:g.35216340A>G	ENSP00000274938:p.Lys947Arg	56.0	0.0		86.0	4.0	NM_152753		Missense_Mutation	SNP	ENST00000274938.7	hg19	CCDS4800.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.391521	0.83011	.	.	ENSG00000146197	ENST00000394681;ENST00000274938	T;D	0.83837	-1.35;-1.77	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.71719	0.3373	N	0.24115	0.695	0.80722	D	1	P;P	0.49559	0.925;0.877	P;B	0.47162	0.54;0.339	T	0.77029	-0.2739	10	0.51188	T	0.08	.	15.9698	0.80004	1.0:0.0:0.0:0.0	.	963;947	Q8IX30-2;Q8IX30	.;SCUB3_HUMAN	R	963;947	ENSP00000378174:K963R;ENSP00000274938:K947R	ENSP00000274938:K947R	K	+	2	0	SCUBE3	35324318	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.910000	0.92685	2.183000	0.69458	0.533000	0.62120	AAG	.	.		0.512	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040275.1	NM_152753	
TREML4	285852	hgsc.bcm.edu	37	6	41196606	41196606	+	Missense_Mutation	SNP	G	G	C	rs549544699	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:41196606G>C	ENST00000341495.2	+	2	322	c.218G>C	c.(217-219)tGg>tCg	p.W73S	TREML4_ENST00000448827.2_Missense_Mutation_p.W73S	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	73	Ig-like V-type.		W -> R (in dbSNP:rs9369265).			extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					TCCAAGCCCTGGACAGCAGTT	0.512																																					p.W73S		Atlas-SNP	.											TREML4,NS,carcinoma,0,1	TREML4	25	.	0			c.G218C						.						83.0	77.0	79.0					6																	41196606		2203	4300	6503	SO:0001583	missense	285852	exon2			AGCCCTGGACAGC	AF534826	CCDS34446.1	6p21.1	2013-01-11			ENSG00000188056	ENSG00000188056		"""Immunoglobulin superfamily / V-set domain containing"""	30807	protein-coding gene	gene with protein product	"""TREM like transcript 4"""	614664				12645956	Standard	NM_198153		Approved	TLT4	uc003oqc.3	Q6UXN2	OTTHUMG00000016408	ENST00000341495.2:c.218G>C	chr6.hg19:g.41196606G>C	ENSP00000342570:p.Trp73Ser	95.0	0.0		138.0	0.0	NM_198153	B7ZL92	Missense_Mutation	SNP	ENST00000341495.2	hg19	CCDS34446.1	.	.	.	.	.	.	.	.	.	.	.	4.856	0.159171	0.09236	.	.	ENSG00000188056	ENST00000341495;ENST00000445267;ENST00000448827	T;T	0.03889	3.77;3.77	4.16	-8.32	0.00996	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00496	0.0016	N	0.03608	-0.345	0.09310	N	1	B	0.31893	0.345	B	0.30251	0.113	T	0.48031	-0.9070	9	0.56958	D	0.05	-0.0212	3.7754	0.08657	0.5171:0.1297:0.2579:0.0953	.	73	Q6UXN2	TRML4_HUMAN	S	73	ENSP00000342570:W73S;ENSP00000418078:W73S	ENSP00000342570:W73S	W	+	2	0	TREML4	41304584	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-4.226000	0.00270	-2.913000	0.00307	-1.915000	0.00519	TGG	.	.		0.512	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2		
CUL7	9820	hgsc.bcm.edu	37	6	43017756	43017756	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:43017756T>C	ENST00000265348.3	-	6	1599	c.1514A>G	c.(1513-1515)gAt>gGt	p.D505G	CUL7_ENST00000478630.1_5'Flank|CUL7_ENST00000535468.1_Missense_Mutation_p.D589G			Q14999	CUL7_HUMAN	cullin 7	505					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)			GTCAGGTCCATCCAGCTTCTT	0.557																																					p.D589G		Atlas-SNP	.											.	CUL7	133	.	0			c.A1766G						.						121.0	112.0	115.0					6																	43017756		2203	4300	6503	SO:0001583	missense	9820	exon6			GGTCCATCCAGCT	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.1514A>G	chr6.hg19:g.43017756T>C	ENSP00000265348:p.Asp505Gly	70.0	0.0		97.0	5.0	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Missense_Mutation	SNP	ENST00000265348.3	hg19	CCDS4881.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.461565	0.43736	.	.	ENSG00000044090	ENST00000265348;ENST00000535468	T;T	0.66280	-0.2;-0.2	5.12	-0.858	0.10689	.	0.861913	0.10357	N	0.684436	T	0.36413	0.0966	L	0.61218	1.895	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42599	-0.9442	10	0.45353	T	0.12	-19.4144	6.1451	0.20280	0.0:0.1394:0.2509:0.6097	.	589;505	F5H0L1;Q14999	.;CUL7_HUMAN	G	505;589	ENSP00000265348:D505G;ENSP00000438788:D589G	ENSP00000265348:D505G	D	-	2	0	CUL7	43125734	0.698000	0.27777	0.032000	0.17829	0.923000	0.55619	1.018000	0.30002	-0.047000	0.13423	0.533000	0.62120	GAT	.	.		0.557	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780	
EYS	346007	hgsc.bcm.edu	37	6	66094287	66094287	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:66094287T>C	ENST00000370621.3	-	8	1817	c.1291A>G	c.(1291-1293)Aga>Gga	p.R431G	EYS_ENST00000393380.2_Missense_Mutation_p.R431G|EYS_ENST00000370618.3_Missense_Mutation_p.R431G|EYS_ENST00000370616.2_Missense_Mutation_p.R431G|EYS_ENST00000342421.5_Missense_Mutation_p.R431G|EYS_ENST00000503581.1_Missense_Mutation_p.R431G			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	431					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						ACTTTGAATCTTCCAATTATA	0.313																																					p.R431G		Atlas-SNP	.											.	EYS	527	.	0			c.A1291G						.						88.0	87.0	87.0					6																	66094287		2202	4293	6495	SO:0001583	missense	346007	exon8			TGAATCTTCCAAT		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.1291A>G	chr6.hg19:g.66094287T>C	ENSP00000359655:p.Arg431Gly	42.0	0.0		77.0	4.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	T	14.87	2.664843	0.47572	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	T;T;T;T;T;T	0.10477	2.87;2.87;2.87;2.87;2.87;2.87	6.07	-1.86	0.07760	.	.	.	.	.	T	0.00906	0.0030	N	0.05280	-0.08	0.22675	N	0.998868	B;B;B	0.18166	0.009;0.009;0.026	B;B;B	0.14578	0.007;0.007;0.011	T	0.47861	-0.9084	9	0.10636	T	0.68	.	2.1204	0.03724	0.1229:0.306:0.126:0.4451	.	431;431;431	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	G	431	ENSP00000424243:R431G;ENSP00000359655:R431G;ENSP00000359650:R431G;ENSP00000377042:R431G;ENSP00000341818:R431G;ENSP00000359652:R431G	ENSP00000341818:R431G	R	-	1	2	EYS	66151008	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	1.504000	0.35726	-0.071000	0.12886	0.533000	0.62120	AGA	.	.		0.313	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
LMBRD1	55788	hgsc.bcm.edu	37	6	70490443	70490443	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:70490443A>G	ENST00000370577.3	-	3	479	c.250T>C	c.(250-252)Tgg>Cgg	p.W84R	LMBRD1_ENST00000370570.1_Missense_Mutation_p.W11R	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	84					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						GCATTAGCCCAGTCCTAGGAT	0.338																																					p.W84R		Atlas-SNP	.											.	LMBRD1	61	.	0			c.T250C						.						112.0	108.0	109.0					6																	70490443		2203	4300	6503	SO:0001583	missense	55788	exon3			TAGCCCAGTCCTA	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.250T>C	chr6.hg19:g.70490443A>G	ENSP00000359609:p.Trp84Arg	40.0	0.0		52.0	4.0	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Missense_Mutation	SNP	ENST00000370577.3	hg19	CCDS4969.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.012555	0.75161	.	.	ENSG00000168216	ENST00000370577;ENST00000370570	T;T	0.35973	1.28;1.99	5.67	5.67	0.87782	LMBR1-like membrane protein (1);	0.000000	0.85682	D	0.000000	T	0.57740	0.2074	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.66444	-0.5922	10	0.87932	D	0	-4.874	15.0854	0.72148	1.0:0.0:0.0:0.0	.	84	Q9NUN5	LMBD1_HUMAN	R	84;11	ENSP00000359609:W84R;ENSP00000359602:W11R	ENSP00000359602:W11R	W	-	1	0	LMBRD1	70547164	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.469000	0.73555	2.149000	0.67028	0.379000	0.24179	TGG	.	.		0.338	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368	
DPPA5	340168	hgsc.bcm.edu	37	6	74063604	74063604	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:74063604A>G	ENST00000370370.3	-	2	333	c.264T>C	c.(262-264)gcT>gcC	p.A88A		NM_001025290.2	NP_001020461.1	A6NC42	DPPA5_HUMAN	developmental pluripotency associated 5	88					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|endometrium(1)|lung(5)	7						GGTGCCACTCAGCCATGGACT	0.637																																					p.A88A		Atlas-SNP	.											.	DPPA5	23	.	0			c.T264C						.						33.0	31.0	32.0					6																	74063604		2203	4300	6503	SO:0001819	synonymous_variant	340168	exon2			CCACTCAGCCATG		CCDS34483.1	6q13	2014-01-28			ENSG00000203909	ENSG00000203909			19201	protein-coding gene	gene with protein product		611111					Standard	NM_001025290		Approved	Esg1	uc003pgs.2	A6NC42	OTTHUMG00000015025	ENST00000370370.3:c.264T>C	chr6.hg19:g.74063604A>G		97.0	0.0		134.0	6.0	NM_001025290	B2RPQ7	Silent	SNP	ENST00000370370.3	hg19	CCDS34483.1																																																																																			.	.		0.637	DPPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041203.3	NM_001025290	
FAM46A	55603	hgsc.bcm.edu	37	6	82459741	82459741	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:82459741T>C	ENST00000320172.6	-	3	1314	c.1000A>G	c.(1000-1002)Aga>Gga	p.R334G	FAM46A_ENST00000369754.3_Missense_Mutation_p.R353G|FAM46A_ENST00000369756.3_Missense_Mutation_p.R415G	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	334					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		TCCAGTTTTCTCTGCTGCTCT	0.468																																					p.R334G		Atlas-SNP	.											.	FAM46A	37	.	0			c.A1000G						.						92.0	88.0	90.0					6																	82459741		2203	4300	6503	SO:0001583	missense	55603	exon3			GTTTTCTCTGCTG	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"""chromosome 6 open reading frame 37"""	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.1000A>G	chr6.hg19:g.82459741T>C	ENSP00000318298:p.Arg334Gly	116.0	0.0		139.0	6.0	NM_017633	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Missense_Mutation	SNP	ENST00000320172.6	hg19	CCDS34489.1	.	.	.	.	.	.	.	.	.	.	T	8.059	0.767657	0.15983	.	.	ENSG00000112773	ENST00000369754;ENST00000320172;ENST00000369756;ENST00000423467	T;T;T	0.26223	1.75;1.75;1.75	5.95	4.78	0.61160	Domain of unknown function DUF1693 (1);	0.000000	0.85682	D	0.000000	T	0.41511	0.1162	M	0.80028	2.48	0.80722	D	1	D;D	0.62365	0.991;0.989	D;D	0.78314	0.991;0.985	T	0.45101	-0.9284	10	0.54805	T	0.06	-1.3331	12.5901	0.56437	0.0:0.0:0.2617:0.7383	.	334;353	Q96IP4;Q96IP4-2	FA46A_HUMAN;.	G	353;334;415;68	ENSP00000358769:R353G;ENSP00000318298:R334G;ENSP00000358771:R415G	ENSP00000318298:R334G	R	-	1	2	FAM46A	82516460	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	4.959000	0.63666	1.057000	0.40506	-0.313000	0.08912	AGA	.	.		0.468	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1		
RARS2	57038	hgsc.bcm.edu	37	6	88229963	88229963	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:88229963T>C	ENST00000369536.5	-	13	1092	c.1047A>G	c.(1045-1047)ggA>ggG	p.G349G	RARS2_ENST00000497828.1_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	349					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		GCTTTTTTTGTCCTTTATCTG	0.313																																					p.G349G		Atlas-SNP	.											.	RARS2	61	.	0			c.A1047G						.						172.0	165.0	167.0					6																	88229963		2203	4300	6503	SO:0001819	synonymous_variant	57038	exon13			TTTTTGTCCTTTA	AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	21406	protein-coding gene	gene with protein product	"""arginine tRNA ligase 2, mitochondrial (putative)"""	611524	"""arginyl-tRNA synthetase-like"""	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.1047A>G	chr6.hg19:g.88229963T>C		30.0	0.0		67.0	4.0	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Silent	SNP	ENST00000369536.5	hg19	CCDS5011.1																																																																																			.	.		0.313	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320	
ASCC3	10973	hgsc.bcm.edu	37	6	101312035	101312035	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:101312035T>C	ENST00000369162.2	-	3	490	c.146A>G	c.(145-147)aAg>aGg	p.K49R	ASCC3_ENST00000369143.2_Missense_Mutation_p.K49R|ASCC3_ENST00000522650.1_Missense_Mutation_p.K49R	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	49					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)		TTTTATTATCTTCTTCCATGT	0.294																																					p.K49R		Atlas-SNP	.											.	ASCC3	205	.	0			c.A146G						.						99.0	110.0	107.0					6																	101312035		2201	4298	6499	SO:0001583	missense	10973	exon3			ATTATCTTCTTCC	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.146A>G	chr6.hg19:g.101312035T>C	ENSP00000358159:p.Lys49Arg	75.0	0.0		112.0	5.0	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.609906	0.46527	.	.	ENSG00000112249	ENST00000369162;ENST00000522650;ENST00000324723;ENST00000369143	T;T;T	0.58506	0.42;0.33;0.79	5.32	4.16	0.48862	.	0.108694	0.64402	D	0.000009	T	0.55955	0.1953	L	0.59436	1.845	0.26722	N	0.970765	B;D;B;B	0.71674	0.022;0.998;0.022;0.003	B;D;B;B	0.78314	0.018;0.991;0.018;0.005	T	0.51748	-0.8666	10	0.41790	T	0.15	.	9.1586	0.37007	0.0:0.0868:0.0:0.9132	.	49;49;49;49	Q4G1A0;Q9H5A2;E7EW23;Q8N3C0	.;.;.;HELC1_HUMAN	R	49	ENSP00000358159:K49R;ENSP00000430769:K49R;ENSP00000320777:K49R	ENSP00000320777:K49R	K	-	2	0	ASCC3	101418756	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	5.069000	0.64370	0.861000	0.35504	0.533000	0.62120	AAG	.	.		0.294	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
FIG4	9896	hgsc.bcm.edu	37	6	110112750	110112750	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:110112750A>G	ENST00000230124.3	+	20	2476	c.2352A>G	c.(2350-2352)gcA>gcG	p.A784A	FIG4_ENST00000441478.2_Silent_p.A507A	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	784					cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		TGACTGATGCAGGAGACAGTG	0.557																																					p.A784A		Atlas-SNP	.											.	FIG4	77	.	0			c.A2352G						.						44.0	45.0	44.0					6																	110112750		2203	4300	6503	SO:0001819	synonymous_variant	9896	exon20			TGATGCAGGAGAC	D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"""KIAA0274"", ""FIG4 homolog (S. cerevisiae)"", ""FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"""	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.2352A>G	chr6.hg19:g.110112750A>G		54.0	0.0		55.0	4.0	NM_014845	Q53H49|Q5TCS6	Silent	SNP	ENST00000230124.3	hg19	CCDS5078.1																																																																																			.	.		0.557	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845	
HS3ST5	222537	hgsc.bcm.edu	37	6	114383906	114383906	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:114383906T>C	ENST00000312719.5	-	4	1292	c.104A>G	c.(103-105)gAt>gGt	p.D35G	RP3-399L15.3_ENST00000519104.1_RNA|RP3-399L15.3_ENST00000519270.1_RNA|HS3ST5_ENST00000411826.1_Missense_Mutation_p.D35G|RP3-399L15.3_ENST00000523087.1_RNA			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	35					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)		CACCCACCTATCCAAGCTCCC	0.463																																					p.D35G		Atlas-SNP	.											.	HS3ST5	80	.	0			c.A104G						.						150.0	148.0	149.0					6																	114383906		2203	4300	6503	SO:0001583	missense	222537	exon1			CACCTATCCAAGC	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.104A>G	chr6.hg19:g.114383906T>C	ENSP00000427888:p.Asp35Gly	77.0	0.0		117.0	6.0	NM_153612	A8K1J2|Q52LI2|Q8N285	Missense_Mutation	SNP	ENST00000312719.5	hg19	CCDS34517.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.673016	0.88445	.	.	ENSG00000249853	ENST00000312719;ENST00000411826	T;T	0.48522	0.81;0.81	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.41419	0.1158	N	0.19112	0.55	0.58432	D	0.999999	D	0.57571	0.98	D	0.68192	0.956	T	0.32161	-0.9917	10	0.20046	T	0.44	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	35	Q8IZT8	HS3S5_HUMAN	G	35	ENSP00000427888:D35G;ENSP00000440332:D35G	ENSP00000427888:D35G	D	-	2	0	HS3ST5	114490599	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.218000	0.77991	2.326000	0.78906	0.533000	0.62120	GAT	.	.		0.463	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612	
RWDD1	51389	hgsc.bcm.edu	37	6	116901503	116901503	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:116901503A>G	ENST00000466444.2	+	2	335	c.119A>G	c.(118-120)gAg>gGg	p.E40G	RWDD1_ENST00000392526.1_5'UTR|RWDD1_ENST00000487832.2_5'UTR|RWDD1_ENST00000517800.1_3'UTR	NM_015952.2	NP_057036.2	Q9H446	RWDD1_HUMAN	RWD domain containing 1	40	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.									NS(1)|breast(2)|central_nervous_system(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)	12		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.0312)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)|Epithelial(106;0.161)		GTGACGTCTGAGGCTGGAGAA	0.348																																					p.E40G		Atlas-SNP	.											.	RWDD1	21	.	0			c.A119G						.						52.0	49.0	50.0					6																	116901503		2203	4300	6503	SO:0001583	missense	51389	exon2			CGTCTGAGGCTGG	AF092134	CCDS34520.1, CCDS43496.1	6q13-q22.33	2012-12-07			ENSG00000111832	ENSG00000111832			20993	protein-coding gene	gene with protein product						10810093	Standard	NM_016104		Approved	PTD013	uc003pxd.3	Q9H446	OTTHUMG00000015441	ENST00000466444.2:c.119A>G	chr6.hg19:g.116901503A>G	ENSP00000420357:p.Glu40Gly	41.0	0.0		68.0	4.0	NM_015952	A8K3W2|A8MT24|Q9Y313|Q9Y6B3	Missense_Mutation	SNP	ENST00000466444.2	hg19	CCDS34520.1	.	.	.	.	.	.	.	.	.	.	A	19.98	3.926828	0.73327	.	.	ENSG00000111832	ENST00000466444	T	0.44881	0.91	5.95	5.95	0.96441	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.049815	0.85682	D	0.000000	T	0.40791	0.1131	M	0.71581	2.175	0.80722	D	1	B	0.22983	0.078	B	0.36922	0.236	T	0.41910	-0.9482	10	0.54805	T	0.06	-29.7264	16.4116	0.83717	1.0:0.0:0.0:0.0	.	40	Q9H446	RWDD1_HUMAN	G	40	ENSP00000420357:E40G	ENSP00000420357:E40G	E	+	2	0	RWDD1	117008196	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.649000	0.91067	2.276000	0.75962	0.528000	0.53228	GAG	.	.		0.348	RWDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041952.2	NM_015952	
TRDN	10345	hgsc.bcm.edu	37	6	123594509	123594510	+	Splice_Site	DNP	CT	CT	TA	rs147062785|rs386359375|rs535166955	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:123594509_123594510CT>TA	ENST00000398178.3	-	28	1619		c.e28-1		TRDN_ENST00000334268.4_Splice_Site	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin						cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		TCAGATATAGCTAAAATAAATA	0.233																																					.		Atlas-SNP	.											.	TRDN	88	.	0			c.1598-1G>A|c.1598-2A>T						.																																			SO:0001630	splice_region_variant	10345	exon29			ATATAGCTAAAAT|TATAGCTAAAATA	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1598_1598delinsTA	chr6.hg19:g.123594509_123594510delinsTA		33.0|32.0	0.0		76.0|74.0	6.0|5.0	NM_006073	A5D6W5|F5H2W7|Q6NSB8	Splice_Site	SNP	ENST00000398178.3	hg19	CCDS55053.1																																																																																			.	.		0.233	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			Intron
TPD52L1	7164	hgsc.bcm.edu	37	6	125541327	125541327	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:125541327A>G	ENST00000534000.1	+	2	419	c.123A>G	c.(121-123)gcA>gcG	p.A41A	TPD52L1_ENST00000392482.2_Silent_p.A12A|TPD52L1_ENST00000534199.1_Silent_p.A12A|TPD52L1_ENST00000527711.1_Silent_p.A41A|TPD52L1_ENST00000304877.13_Silent_p.A41A|TPD52L1_ENST00000524679.1_Silent_p.A12A|TPD52L1_ENST00000368402.5_Silent_p.A41A|TPD52L1_ENST00000528193.1_Silent_p.A41A|TPD52L1_ENST00000532429.1_Silent_p.A12A|HDDC2_ENST00000608456.1_Intron|TPD52L1_ENST00000368388.2_Silent_p.A41A	NM_003287.2	NP_003278.1	Q16890	TPD53_HUMAN	tumor protein D52-like 1	41					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|prostate(1)	5			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)		AGTTAAAAGCAGAGTTAGTTC	0.368																																					p.A41A		Atlas-SNP	.											.	TPD52L1	14	.	0			c.A123G						.						128.0	124.0	125.0					6																	125541327		2203	4300	6503	SO:0001819	synonymous_variant	7164	exon2			AAAAGCAGAGTTA	U44427	CCDS5130.1, CCDS34527.1, CCDS34528.1, CCDS43502.1, CCDS75513.1, CCDS75514.1	6q22-q23	2008-07-29			ENSG00000111907	ENSG00000111907			12006	protein-coding gene	gene with protein product		604069				8812487, 16112108	Standard	NM_003287		Approved	D53, hD53	uc003pzu.1	Q16890	OTTHUMG00000015505	ENST00000534000.1:c.123A>G	chr6.hg19:g.125541327A>G		95.0	0.0		121.0	5.0	NM_001003396	A8K757|A8K772|A8MUD2|A8MUJ7|A8MW70|F6V707|O43397|Q5TC99|Q5TDQ0|Q9BUQ6|Q9C054	Silent	SNP	ENST00000534000.1	hg19	CCDS5130.1																																																																																			.	.		0.368	TPD52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042065.2		
HINT3	135114	hgsc.bcm.edu	37	6	126278232	126278232	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:126278232A>C	ENST00000229633.5	+	1	306	c.109A>C	c.(109-111)Aag>Cag	p.K37Q		NM_138571.4	NP_612638.3	Q9NQE9	HINT3_HUMAN	histidine triad nucleotide binding protein 3	37						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)		AGCCGCTGGCAAGTCACCAGA	0.677											OREG0017649	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K37Q		Atlas-SNP	.											.	HINT3	14	.	0			c.A109C						.						27.0	21.0	23.0					6																	126278232		1869	3645	5514	SO:0001583	missense	135114	exon1			GCTGGCAAGTCAC	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.109A>C	chr6.hg19:g.126278232A>C	ENSP00000229633:p.Lys37Gln	117.0	0.0	1548	187.0	8.0	NM_138571	B3KQ91|Q8N0Y9	Missense_Mutation	SNP	ENST00000229633.5	hg19	CCDS5133.1	.	.	.	.	.	.	.	.	.	.	A	9.072	0.997150	0.19043	.	.	ENSG00000111911	ENST00000229633	D	0.91351	-2.83	4.51	-1.37	0.09056	Histidine triad-like motif (1);	1.335400	0.04646	N	0.406141	T	0.63861	0.2547	N	0.19112	0.55	0.09310	N	1	B	0.23806	0.091	B	0.19148	0.024	T	0.56111	-0.8033	10	0.19147	T	0.46	-33.9008	4.8889	0.13717	0.3582:0.2836:0.3582:0.0	.	37	Q9NQE9	HINT3_HUMAN	Q	37	ENSP00000229633:K37Q	ENSP00000229633:K37Q	K	+	1	0	HINT3	126319925	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.402000	0.07223	-0.523000	0.06409	0.374000	0.22700	AAG	.	.		0.677	HINT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042090.1	NM_138571	
TRMT11	60487	hgsc.bcm.edu	37	6	126319442	126319442	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:126319442A>G	ENST00000334379.5	+	5	489	c.368A>G	c.(367-369)gAg>gGg	p.E123G	TRMT11_ENST00000368332.3_Missense_Mutation_p.E123G|TRMT11_ENST00000450358.1_Missense_Mutation_p.E123G	NM_001031712.2	NP_001026882.2	Q7Z4G4	TRM11_HUMAN	tRNA methyltransferase 11 homolog (S. cerevisiae)	123					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)		ACACAAGAAGAGAAAATCAAG	0.299																																					p.E123G		Atlas-SNP	.											.	TRMT11	43	.	0			c.A368G						.						39.0	38.0	39.0					6																	126319442		2175	4293	6468	SO:0001583	missense	60487	exon5			AAGAAGAGAAAAT	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.368A>G	chr6.hg19:g.126319442A>G	ENSP00000333934:p.Glu123Gly	54.0	0.0		64.0	4.0	NM_001031712	E1P570|Q5JY11|Q6PGQ5|Q9HC13	Missense_Mutation	SNP	ENST00000334379.5	hg19	CCDS35496.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.164128	0.78339	.	.	ENSG00000066651	ENST00000334379;ENST00000450358;ENST00000368332;ENST00000444121;ENST00000446681	T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82	5.95	5.95	0.96441	.	0.135400	0.64402	D	0.000003	T	0.62588	0.2440	M	0.86502	2.82	0.53688	D	0.999974	P;P	0.52577	0.954;0.514	P;B	0.56700	0.804;0.106	T	0.69935	-0.5010	10	0.62326	D	0.03	-24.7641	16.4237	0.83790	1.0:0.0:0.0:0.0	.	123;123	Q7Z4G4-2;Q7Z4G4	.;TRM11_HUMAN	G	123;123;123;60;60	ENSP00000333934:E123G;ENSP00000405140:E123G;ENSP00000357316:E123G;ENSP00000406230:E60G;ENSP00000415724:E60G	ENSP00000333934:E123G	E	+	2	0	TRMT11	126361135	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.137000	0.94496	2.279000	0.76181	0.533000	0.62120	GAG	.	.		0.299	TRMT11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_021820	
C6orf58	352999	hgsc.bcm.edu	37	6	127902409	127902409	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:127902409T>C	ENST00000329722.7	+	4	668	c.656T>C	c.(655-657)aTc>aCc	p.I219T		NM_001010905.1	NP_001010905.1	Q6P5S2	CF058_HUMAN	chromosome 6 open reading frame 58	219						extracellular vesicular exosome (GO:0070062)				kidney(3)|large_intestine(3)|liver(1)|lung(7)|pancreas(1)	15				GBM - Glioblastoma multiforme(226;0.0405)|all cancers(137;0.156)		GCAGATAATATCAAAAGTTTT	0.299																																					p.I219T		Atlas-SNP	.											.	C6orf58	35	.	0			c.T656C						.						89.0	86.0	87.0					6																	127902409		2203	4296	6499	SO:0001583	missense	352999	exon4			ATAATATCAAAAG	BC062712	CCDS34533.1	6q22.33	2011-12-13			ENSG00000184530	ENSG00000184530			20960	protein-coding gene	gene with protein product							Standard	NM_001010905		Approved		uc003qbh.4	Q6P5S2	OTTHUMG00000015530	ENST00000329722.7:c.656T>C	chr6.hg19:g.127902409T>C	ENSP00000328069:p.Ile219Thr	43.0	0.0		59.0	4.0	NM_001010905	B4E1I0|Q5VUP2	Missense_Mutation	SNP	ENST00000329722.7	hg19	CCDS34533.1	.	.	.	.	.	.	.	.	.	.	T	6.420	0.445667	0.12164	.	.	ENSG00000184530	ENST00000329722	T	0.40225	1.04	4.07	-7.47	0.01365	.	2.424140	0.01919	N	0.040386	T	0.05044	0.0135	N	0.11927	0.2	0.09310	N	1	B	0.29481	0.245	B	0.24006	0.05	T	0.08269	-1.0730	10	0.20046	T	0.44	3.7749	0.7466	0.00983	0.2647:0.2924:0.2581:0.1848	.	219	Q6P5S2	CF058_HUMAN	T	219	ENSP00000328069:I219T	ENSP00000328069:I219T	I	+	2	0	C6orf58	127944102	0.000000	0.05858	0.000000	0.03702	0.385000	0.30292	-0.210000	0.09345	-1.308000	0.02318	0.477000	0.44152	ATC	.	.		0.299	C6orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042152.1	NM_001010905	
PTPRK	5796	hgsc.bcm.edu	37	6	128388715	128388715	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:128388715A>G	ENST00000368215.3	-	12	2105	c.2106T>C	c.(2104-2106)gcT>gcC	p.A702A	PTPRK_ENST00000368226.4_Silent_p.A702A|PTPRK_ENST00000368227.3_Silent_p.A702A|RP11-103C16.2_ENST00000417390.1_RNA|PTPRK_ENST00000532331.1_Silent_p.A702A|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000368210.3_Silent_p.A702A|PTPRK_ENST00000368207.3_Silent_p.A702A|PTPRK_ENST00000368213.5_Silent_p.A702A			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	702					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		CTTTGCGCGGAGCCAAAGGAG	0.527																																					p.A702A		Atlas-SNP	.											.	PTPRK	330	.	0			c.T2106C						.						71.0	70.0	71.0					6																	128388715		2203	4300	6503	SO:0001819	synonymous_variant	5796	exon12			GCGCGGAGCCAAA	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.2106T>C	chr6.hg19:g.128388715A>G		45.0	0.0		82.0	4.0	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Silent	SNP	ENST00000368215.3	hg19																																																																																				.	.		0.527	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1		
PBOV1	59351	hgsc.bcm.edu	37	6	138539188	138539188	+	Silent	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:138539188C>T	ENST00000527246.2	-	1	439	c.345G>A	c.(343-345)caG>caA	p.Q115Q	KIAA1244_ENST00000251691.4_Intron	NM_021635.2	NP_067648.1	Q9GZY1	PBOV1_HUMAN	prostate and breast cancer overexpressed 1	115						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)	1	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00055)|GBM - Glioblastoma multiforme(68;0.000674)		GACCTAGGGTCTGAGTTAACT	0.403																																					p.Q115Q		Atlas-SNP	.											.	PBOV1	12	.	0			c.G345A						.						159.0	162.0	161.0					6																	138539188		2203	4300	6503	SO:0001819	synonymous_variant	59351	exon1			TAGGGTCTGAGTT	AF189269	CCDS5190.1	6q23.3	2012-02-09			ENSG00000254440	ENSG00000254440			21079	protein-coding gene	gene with protein product		605669				12553037, 11156405	Standard	NM_021635		Approved	UC28, UROC28	uc003qhv.3	Q9GZY1	OTTHUMG00000167040	ENST00000527246.2:c.345G>A	chr6.hg19:g.138539188C>T		205.0	0.0		274.0	15.0	NM_021635		Silent	SNP	ENST00000527246.2	hg19	CCDS5190.1																																																																																			.	.		0.403	PBOV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392617.1	NM_021635	
PHACTR2	9749	hgsc.bcm.edu	37	6	144086851	144086851	+	Missense_Mutation	SNP	A	A	G	rs372509172		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:144086851A>G	ENST00000427704.2	+	6	1245	c.1115A>G	c.(1114-1116)cAg>cGg	p.Q372R	PHACTR2_ENST00000305766.6_Missense_Mutation_p.Q292R|PHACTR2_ENST00000367584.4_Missense_Mutation_p.Q360R|PHACTR2_ENST00000367582.3_Missense_Mutation_p.Q303R|PHACTR2_ENST00000440869.2_Missense_Mutation_p.Q383R	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	372							protein phosphatase inhibitor activity (GO:0004864)			NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		GACCCAAGTCAGCTTCTTTGG	0.517																																					p.Q383R	Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)	Atlas-SNP	.											.	PHACTR2	99	.	0			c.A1148G						.	A	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	1,3903		0,1,1951	86.0	84.0	85.0		1148,908,875,1115	-2.1	0.1	6		85	1,8285		0,1,4142	no	missense,missense,missense,missense	PHACTR2	NM_001100164.1,NM_001100165.1,NM_001100166.1,NM_014721.2	43,43,43,43	0,2,6093	GG,GA,AA		0.0121,0.0256,0.0164	benign,benign,benign,benign	383/646,303/566,292/555,372/635	144086851	2,12188	1952	4143	6095	SO:0001583	missense	9749	exon6			CAAGTCAGCTTCT	AB014580	CCDS43512.1, CCDS47492.1, CCDS47493.1, CCDS47494.1	6q24.1	2013-01-24	2004-05-20	2004-05-20	ENSG00000112419	ENSG00000112419		"""Phosphatase and actin regulators"""	20956	protein-coding gene	gene with protein product		608724	"""chromosome 6 open reading frame 56"""	C6orf56		9734811, 15107502	Standard	NM_001100164		Approved	KIAA0680	uc010khi.3	O75167	OTTHUMG00000015732	ENST00000427704.2:c.1115A>G	chr6.hg19:g.144086851A>G	ENSP00000391763:p.Gln372Arg	60.0	0.0		73.0	4.0	NM_001100164	A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Missense_Mutation	SNP	ENST00000427704.2	hg19	CCDS47492.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.290420	0.40494	2.56E-4	1.21E-4	ENSG00000112419	ENST00000367584;ENST00000427704;ENST00000305766;ENST00000440869;ENST00000367582	T;T;T;T;T	0.30981	1.51;1.95;1.53;1.95;1.53	5.22	-2.09	0.07232	.	1.212500	0.05664	N	0.587411	T	0.07593	0.0191	L	0.34521	1.04	0.09310	N	0.999991	B;B;B;B	0.26258	0.145;0.0;0.0;0.0	B;B;B;B	0.26864	0.074;0.001;0.001;0.0	T	0.34900	-0.9810	10	0.19590	T	0.45	.	8.4382	0.32799	0.2972:0.5516:0.1512:0.0	.	383;292;303;372	O75167-4;O75167-5;O75167-2;O75167	.;.;.;PHAR2_HUMAN	R	360;372;292;383;303	ENSP00000356556:Q360R;ENSP00000391763:Q372R;ENSP00000305530:Q292R;ENSP00000417038:Q383R;ENSP00000356554:Q303R	ENSP00000305530:Q292R	Q	+	2	0	PHACTR2	144128544	0.926000	0.31397	0.118000	0.21660	0.977000	0.68977	0.054000	0.14205	-0.633000	0.05545	-0.290000	0.09829	CAG	.	.		0.517	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721	
RAET1L	154064	hgsc.bcm.edu	37	6	150343212	150343212	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:150343212T>G	ENST00000367341.1	-	2	252	c.253A>C	c.(253-255)Atg>Ctg	p.M85L	RAET1L_ENST00000286380.2_Missense_Mutation_p.M85L			Q5VY80	RET1L_HUMAN	retinoic acid early transcript 1L	85	MHC class I alpha-1 like. {ECO:0000250}.		M -> T (in dbSNP:rs912565). {ECO:0000269|PubMed:11827464, ECO:0000269|PubMed:15489334}.		antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5		Ovarian(120;0.028)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.4e-12)		TTCCAGGCCATTGTGACATTT	0.483																																					p.M85L		Atlas-SNP	.											RAET1L,NS,carcinoma,0,2	RAET1L	21	.	0			c.A253C						.																																			SO:0001583	missense	154064	exon2			AGGCCATTGTGAC	AY039682	CCDS5224.1	6q24.1-25.1	2008-02-05			ENSG00000155918	ENSG00000155918			16798	protein-coding gene	gene with protein product		611047				11827464	Standard	NM_130900		Approved		uc011eei.2	Q5VY80	OTTHUMG00000015809	ENST00000367341.1:c.253A>C	chr6.hg19:g.150343212T>G	ENSP00000356310:p.Met85Leu	208.0	1.0		354.0	0.0	NM_130900	A3KME4|Q8TE74	Missense_Mutation	SNP	ENST00000367341.1	hg19	CCDS5224.1	.	.	.	.	.	.	.	.	.	.	t	6.430	0.447513	0.12223	.	.	ENSG00000155918	ENST00000367341;ENST00000286380	T;T	0.06218	3.33;3.33	1.91	-2.05	0.07321	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.00967	0.0032	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.47548	-0.9109	9	0.87932	D	0	.	5.9233	0.19094	0.0:0.5665:0.0:0.4335	.	85	Q5VY80	RET1L_HUMAN	L	85	ENSP00000356310:M85L;ENSP00000286380:M85L	ENSP00000286380:M85L	M	-	1	0	RAET1L	150384905	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.287000	0.01151	-0.549000	0.06191	0.402000	0.26972	ATG	.	.		0.483	RAET1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042676.1	NM_130900	
AKAP12	9590	hgsc.bcm.edu	37	6	151672185	151672185	+	Missense_Mutation	SNP	A	A	G	rs61748676	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:151672185A>G	ENST00000253332.1	+	3	2848	c.2659A>G	c.(2659-2661)Agt>Ggt	p.S887G	AKAP12_ENST00000359755.5_Missense_Mutation_p.S782G|AKAP12_ENST00000354675.6_Missense_Mutation_p.S789G|AKAP12_ENST00000402676.2_Missense_Mutation_p.S887G			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	887					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		GCTCAGCGAGAGTCAGGTTCA	0.532																																					p.S887G	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.A2659G						.						73.0	80.0	78.0					6																	151672185		2203	4300	6503	SO:0001583	missense	9590	exon4			AGCGAGAGTCAGG	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"""A-kinase anchor proteins"""	370	protein-coding gene	gene with protein product	"""gravin"", ""Src-Suppressed C Kinase Substrate"""	604698	"""A kinase (PRKA) anchor protein (gravin) 12"""			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.2659A>G	chr6.hg19:g.151672185A>G	ENSP00000253332:p.Ser887Gly	84.0	0.0		123.0	6.0	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	hg19	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	A	4.061	0.009112	0.07912	.	.	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.06687	3.27;3.27;3.28;3.28	5.4	3.03	0.35002	.	1.136460	0.06613	N	0.755988	T	0.01905	0.0060	L	0.33485	1.01	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.11329	0.006;0.006;0.003	T	0.46261	-0.9204	10	0.20046	T	0.44	.	4.6169	0.12432	0.5207:0.0:0.4793:0.0	.	782;789;887	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	G	887;887;789;782	ENSP00000384537:S887G;ENSP00000253332:S887G;ENSP00000346702:S789G;ENSP00000352794:S782G	ENSP00000253332:S887G	S	+	1	0	AKAP12	151713878	0.348000	0.24861	0.192000	0.23308	0.015000	0.08874	0.815000	0.27253	0.888000	0.36160	0.459000	0.35465	AGT	.	A|0.978;T|0.022		0.532	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
SYNE1	23345	hgsc.bcm.edu	37	6	152589207	152589207	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:152589207T>C	ENST00000367255.5	-	100	19400	c.18799A>G	c.(18799-18801)Acc>Gcc	p.T6267A	SYNE1_ENST00000341594.5_Missense_Mutation_p.T5879A|SYNE1_ENST00000423061.1_Missense_Mutation_p.T6196A|SYNE1_ENST00000356820.4_Missense_Mutation_p.T791A|SYNE1_ENST00000265368.4_Missense_Mutation_p.T6267A|SYNE1_ENST00000448038.1_Missense_Mutation_p.T6196A	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6267					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCACCAGAGGTCTCTGCCGCC	0.428										HNSCC(10;0.0054)																											p.T6267A		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A18799G						.						101.0	98.0	99.0					6																	152589207		2203	4300	6503	SO:0001583	missense	23345	exon100			CAGAGGTCTCTGC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.18799A>G	chr6.hg19:g.152589207T>C	ENSP00000356224:p.Thr6267Ala	92.0	0.0		112.0	5.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	0.032	-1.326150	0.01309	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.53206	0.72;0.71;0.63;0.71;0.82;2.73	5.74	-0.38	0.12490	.	0.819818	0.11015	N	0.609069	T	0.06781	0.0173	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.42103	-0.9471	10	0.07813	T	0.8	.	7.0886	0.25272	0.0:0.4353:0.1405:0.4242	.	6267;6267;6196	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	A	6267;6196;6267;6196;5879;791	ENSP00000356224:T6267A;ENSP00000396024:T6196A;ENSP00000265368:T6267A;ENSP00000390975:T6196A;ENSP00000341887:T5879A;ENSP00000349276:T791A	ENSP00000265368:T6267A	T	-	1	0	SYNE1	152630900	0.000000	0.05858	0.127000	0.21898	0.122000	0.20287	-1.644000	0.02002	-0.010000	0.14271	0.460000	0.39030	ACC	.	.		0.428	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
CLDN20	49861	hgsc.bcm.edu	37	6	155596902	155596902	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	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	177.0	0.0		231.0	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	
ARID1B	57492	hgsc.bcm.edu	37	6	157099949	157099949	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:157099949A>G	ENST00000350026.5	+	1	887	c.886A>G	c.(886-888)Aac>Gac	p.N296D	ARID1B_ENST00000275248.4_Missense_Mutation_p.N238D|RP11-230C9.2_ENST00000603191.1_lincRNA|ARID1B_ENST00000367148.1_Missense_Mutation_p.N296D|RP11-230C9.3_ENST00000604792.1_RNA|ARID1B_ENST00000346085.5_Missense_Mutation_p.N296D|MIR4466_ENST00000606121.1_RNA	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	296	Gly-rich.				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)		CAGCCAGTGCAACCATTATCC	0.746																																					p.N296D		Atlas-SNP	.											.	ARID1B	320	.	0			c.A886G						.						2.0	3.0	2.0					6																	157099949		1113	2290	3403	SO:0001583	missense	57492	exon1			CAGTGCAACCATT	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.886A>G	chr6.hg19:g.157099949A>G	ENSP00000055163:p.Asn296Asp	23.0	0.0		37.0	4.0	NM_017519	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	hg19	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	a	4.021	0.001387	0.07819	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248	T;T;T;T	0.02103	4.45;4.5;4.48;4.48	2.12	2.12	0.27331	.	0.340062	0.18727	U	0.132842	T	0.00440	0.0014	N	0.08118	0	0.23425	N	0.997701	P;P;P	0.48694	0.86;0.914;0.914	B;B;B	0.34418	0.089;0.182;0.182	T	0.52689	-0.8542	10	0.87932	D	0	.	7.4066	0.26993	1.0:0.0:0.0:0.0	.	296;296;238	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	D	296;296;296;238	ENSP00000344546:N296D;ENSP00000055163:N296D;ENSP00000356116:N296D;ENSP00000275248:N238D	ENSP00000275248:N238D	N	+	1	0	ARID1B	157141641	1.000000	0.71417	0.933000	0.37362	0.635000	0.38103	1.408000	0.34668	0.726000	0.32339	0.128000	0.15822	AAC	.	.		0.746	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
TAGAP	117289	hgsc.bcm.edu	37	6	159464683	159464683	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:159464683T>C	ENST00000367066.3	-	4	417	c.86A>G	c.(85-87)gAt>gGt	p.D29G	TAGAP_ENST00000338313.5_Missense_Mutation_p.D29G|RP1-111C20.4_ENST00000606466.1_RNA|TAGAP_ENST00000326965.6_5'UTR|RP1-111C20.4_ENST00000606470.1_RNA|RP1-111C20.4_ENST00000607796.1_RNA|RP1-111C20.4_ENST00000607391.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	29					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		TTCCTTGATATCACCCTAAAA	0.348																																					p.D29G		Atlas-SNP	.											.	TAGAP	75	.	0			c.A86G						.						156.0	159.0	158.0					6																	159464683		2203	4300	6503	SO:0001583	missense	117289	exon4			TTGATATCACCCT	AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"""Rho GTPase activating proteins"""	15669	protein-coding gene	gene with protein product		609667	"""T-cell activation GTPase activating protein"""			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.86A>G	chr6.hg19:g.159464683T>C	ENSP00000356033:p.Asp29Gly	103.0	0.0		159.0	7.0	NM_138810	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	hg19	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	T	14.14	2.447965	0.43429	.	.	ENSG00000164691	ENST00000367066;ENST00000338313	T;T	0.26373	1.74;1.85	5.52	5.52	0.82312	.	0.224065	0.37761	N	0.001951	T	0.09158	0.0226	L	0.32530	0.975	0.45502	D	0.998466	B;P	0.44429	0.037;0.835	B;B	0.39119	0.046;0.291	T	0.10917	-1.0609	10	0.15952	T	0.53	-18.011	13.0162	0.58759	0.0:0.0:0.0:1.0	.	29;29	Q8N103-4;Q8N103	.;TAGAP_HUMAN	G	29	ENSP00000356033:D29G;ENSP00000340217:D29G	ENSP00000340217:D29G	D	-	2	0	TAGAP	159384671	0.266000	0.24112	0.907000	0.35723	0.925000	0.55904	3.660000	0.54496	2.100000	0.63781	0.533000	0.62120	GAT	.	.		0.348	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114	
SLC22A2	6582	hgsc.bcm.edu	37	6	160671613	160671613	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:160671613T>C	ENST00000366953.3	-	3	898	c.640A>G	c.(640-642)Agc>Ggc	p.S214G	SLC22A2_ENST00000366952.1_Missense_Mutation_p.S193G|SLC22A2_ENST00000491092.1_5'UTR	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN	solute carrier family 22 (organic cation transporter), member 2	214					body fluid secretion (GO:0007589)|drug transmembrane transport (GO:0006855)|histamine transport (GO:0051608)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|organic cation transport (GO:0015695)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|steroid binding (GO:0005496)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)	Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Chlorphenamine(DB01114)|Choline(DB00122)|Cimetidine(DB00501)|Cisplatin(DB00515)|Cladribine(DB00242)|Cocaine(DB00907)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Desipramine(DB01151)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Famotidine(DB00927)|Flurazepam(DB00690)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Memantine(DB01043)|Metformin(DB00331)|Metoprolol(DB00264)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Oxprenolol(DB01580)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Propranolol(DB00571)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Reserpine(DB00206)|Thiamine(DB00152)|Tubocurarine(DB01199)|Vinblastine(DB00570)|Zidovudine(DB00495)	CCTGCTTTGCTGACCAGTCCT	0.458																																					p.S214G		Atlas-SNP	.											.	SLC22A2	78	.	0			c.A640G						.						126.0	117.0	120.0					6																	160671613		2203	4300	6503	SO:0001583	missense	6582	exon3			CTTTGCTGACCAG	X98333	CCDS5276.1	6q25.3	2013-05-22			ENSG00000112499	ENSG00000112499		"""Solute carriers"""	10966	protein-coding gene	gene with protein product		602608				9605850	Standard	NM_003058		Approved	OCT2	uc003qtf.3	O15244	OTTHUMG00000015950	ENST00000366953.3:c.640A>G	chr6.hg19:g.160671613T>C	ENSP00000355920:p.Ser214Gly	125.0	0.0		87.0	4.0	NM_003058	Q5T7Q6|Q6PIQ8|Q8NG62|Q9NQB9	Missense_Mutation	SNP	ENST00000366953.3	hg19	CCDS5276.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.268361	0.40095	.	.	ENSG00000112499	ENST00000366953;ENST00000366952	T;T	0.74209	-0.82;-0.82	5.43	5.43	0.79202	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.103676	0.64402	D	0.000002	T	0.69628	0.3132	M	0.70275	2.135	0.36461	D	0.866699	P;B;B	0.36330	0.548;0.337;0.315	P;B;B	0.44673	0.457;0.261;0.169	T	0.69888	-0.5023	10	0.20046	T	0.44	.	15.6414	0.77006	0.0:0.0:0.0:1.0	.	214;214;214	O15244-3;O15244;O15244-2	.;S22A2_HUMAN;.	G	214;193	ENSP00000355920:S214G;ENSP00000355919:S193G	ENSP00000355919:S193G	S	-	1	0	SLC22A2	160591603	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.767000	0.62286	2.279000	0.76181	0.533000	0.62120	AGC	.	.		0.458	SLC22A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042943.1	NM_003058	
LPA	4018	hgsc.bcm.edu	37	6	161022116	161022116	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:161022116T>C	ENST00000316300.5	-	19	3004	c.2960A>G	c.(2959-2961)aAc>aGc	p.N987S	LPA_ENST00000447678.1_Missense_Mutation_p.N987S			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3495	Kringle 9. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TCGGCAGTAGTTCTTGATCAA	0.443																																					p.N987S		Atlas-SNP	.											.	LPA	237	.	0			c.A2960G						.						67.0	70.0	69.0					6																	161022116		2164	4289	6453	SO:0001583	missense	4018	exon20			CAGTAGTTCTTGA	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.2960A>G	chr6.hg19:g.161022116T>C	ENSP00000321334:p.Asn987Ser	136.0	0.0		73.0	4.0	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	hg19	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	t	15.59	2.877383	0.51801	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.71934	-0.61;-0.61	2.31	2.31	0.28768	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.79143	0.4396	M	0.92691	3.335	0.20489	N	0.999899	P	0.50156	0.932	D	0.67103	0.949	T	0.67910	-0.5548	9	0.72032	D	0.01	.	6.4002	0.21634	0.0:0.0:0.0:1.0	.	3495	P08519	APOA_HUMAN	S	987	ENSP00000321334:N987S;ENSP00000395608:N987S	ENSP00000321334:N987S	N	-	2	0	LPA	160942106	1.000000	0.71417	0.726000	0.30738	0.371000	0.29859	4.141000	0.58038	1.041000	0.40125	0.172000	0.16884	AAC	.	.		0.443	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
DLL1	28514	hgsc.bcm.edu	37	6	170592565	170592565	+	Missense_Mutation	SNP	T	T	C	rs573197356	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:170592565T>C	ENST00000366756.3	-	9	2135	c.1802A>G	c.(1801-1803)gAc>gGc	p.D601G		NM_005618.3	NP_005609.3	O00548	DLL1_HUMAN	delta-like 1 (Drosophila)	601					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|cell-cell signaling (GO:0007267)|compartment pattern specification (GO:0007386)|determination of left/right symmetry (GO:0007368)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|inner ear development (GO:0048839)|left/right axis specification (GO:0070986)|loop of Henle development (GO:0072070)|negative regulation of auditory receptor cell differentiation (GO:0045608)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of myeloid cell differentiation (GO:0045638)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|regulation of cell adhesion (GO:0030155)|somite specification (GO:0001757)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|Notch binding (GO:0005112)			NS(2)|breast(1)|endometrium(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	33		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584)		GACTGAGATGTCCTTCTCACG	0.632																																					p.D601G		Atlas-SNP	.											DLL1,caecum,carcinoma,0,1	DLL1	72	.	0			c.A1802G						.						210.0	185.0	193.0					6																	170592565		2203	4300	6503	SO:0001583	missense	28514	exon9			GAGATGTCCTTCT	AF003522	CCDS5313.1	6q13-q22.33	2008-07-28	2001-12-03		ENSG00000198719	ENSG00000198719			2908	protein-coding gene	gene with protein product		606582	"""delta (Drosophila)-like 1"""				Standard	NM_005618		Approved		uc003qxm.3	O00548	OTTHUMG00000016078	ENST00000366756.3:c.1802A>G	chr6.hg19:g.170592565T>C	ENSP00000355718:p.Asp601Gly	44.0	0.0		108.0	5.0	NM_005618	B2RAK7|B5M0B3|Q9NU41|Q9UJV2	Missense_Mutation	SNP	ENST00000366756.3	hg19	CCDS5313.1	.	.	.	.	.	.	.	.	.	.	T	18.62	3.663252	0.67700	.	.	ENSG00000198719	ENST00000366756	D	0.86497	-2.13	5.38	2.88	0.33553	.	0.138436	0.64402	D	0.000004	D	0.86556	0.5961	M	0.77616	2.38	0.58432	D	0.999995	D	0.55385	0.971	P	0.57324	0.818	D	0.84563	0.0651	10	0.44086	T	0.13	.	7.5209	0.27626	0.1265:0.0694:0.0:0.804	.	601	O00548	DLL1_HUMAN	G	601	ENSP00000355718:D601G	ENSP00000355718:D601G	D	-	2	0	DLL1	170434490	1.000000	0.71417	0.497000	0.27552	0.992000	0.81027	7.932000	0.87634	0.389000	0.25086	0.533000	0.62120	GAC	.	.		0.632	DLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043254.1		
PDCD2	5134	hgsc.bcm.edu	37	6	170886715	170886715	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:170886715T>C	ENST00000541970.1	-	6	1045	c.967A>G	c.(967-969)Agc>Ggc	p.S323G	PDCD2_ENST00000392090.2_Missense_Mutation_p.S290G	NM_001199462.1|NM_002598.3	NP_001186391.1|NP_002589.2	Q16342	PDCD2_HUMAN	programmed cell death 2	323					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)		AAGCTGCAGCTCTCAGCACAG	0.473																																					p.S323G	Colon(60;1476 1726 39478)	Atlas-SNP	.											.	PDCD2	13	.	0			c.A967G						.						96.0	87.0	90.0					6																	170886715		2203	4300	6503	SO:0001583	missense	5134	exon6			TGCAGCTCTCAGC	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.967A>G	chr6.hg19:g.170886715T>C	ENSP00000439467:p.Ser323Gly	103.0	0.0		167.0	7.0	NM_002598	E9PCU7|F5GYS7|Q58HM9|Q58HN0|Q9UH12	Missense_Mutation	SNP	ENST00000541970.1	hg19	CCDS5316.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.933045	0.92458	.	.	ENSG00000071994	ENST00000541970;ENST00000392090	.	.	.	5.48	5.48	0.80851	Programmed cell death protein 2, C-terminal (1);	0.074954	0.85682	D	0.000000	D	0.83635	0.5297	M	0.93375	3.41	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.966	D	0.88443	0.3043	8	.	.	.	-22.8436	15.5971	0.76595	0.0:0.0:0.0:1.0	.	323;290	Q16342;Q58HN0	PDCD2_HUMAN;.	G	323;290	.	.	S	-	1	0	PDCD2	170728640	1.000000	0.71417	0.969000	0.41365	0.974000	0.67602	7.576000	0.82467	2.072000	0.62099	0.528000	0.53228	AGC	.	.		0.473	PDCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043269.2	NM_002598	
FOXK1	221937	hgsc.bcm.edu	37	7	4722303	4722303	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:4722303A>G	ENST00000328914.4	+	1	364	c.364A>G	c.(364-366)Agc>Ggc	p.S122G	FOXK1_ENST00000446823.1_Intron	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		GCGCCAGCCCAGCGTCACCAT	0.726																																					p.S122G		Atlas-SNP	.											.	FOXK1	64	.	0			c.A364G						.						18.0	16.0	17.0					7																	4722303		2196	4295	6491	SO:0001583	missense	221937	exon1			CAGCCCAGCGTCA	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"""Forkhead boxes"""	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.364A>G	chr7.hg19:g.4722303A>G	ENSP00000328720:p.Ser122Gly	66.0	0.0		78.0	5.0	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	hg19	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	a	15.04	2.716642	0.48622	.	.	ENSG00000164916	ENST00000328914;ENST00000545598	T	0.35973	1.28	2.93	-0.257	0.12979	Forkhead-associated (FHA) domain (2);SMAD/FHA domain (1);	0.308602	0.29066	U	0.013244	T	0.18841	0.0452	L	0.32530	0.975	0.80722	D	1	B;B	0.19331	0.035;0.013	B;B	0.19391	0.018;0.025	T	0.06643	-1.0815	10	0.19147	T	0.46	.	2.0879	0.03650	0.3237:0.0:0.2029:0.4735	.	122;5	P85037;F5H8G8	FOXK1_HUMAN;.	G	122;5	ENSP00000328720:S122G	ENSP00000328720:S122G	S	+	1	0	FOXK1	4688829	0.993000	0.37304	0.997000	0.53966	0.967000	0.64934	1.459000	0.35234	0.167000	0.19631	0.228000	0.17796	AGC	.	.		0.726	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2		
ABCB5	340273	hgsc.bcm.edu	37	7	20698161	20698161	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:20698161T>C	ENST00000404938.2	+	14	2221	c.1569T>C	c.(1567-1569)gcT>gcC	p.A523A	ABCB5_ENST00000443026.2_Silent_p.A78A|ABCB5_ENST00000258738.6_Silent_p.A78A|ABCB5_ENST00000406935.1_Silent_p.A78A	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	523	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						AAAAAGGAGCTCAAATGAGTG	0.423																																					p.A523A		Atlas-SNP	.											.	ABCB5	357	.	0			c.T1569C						.						102.0	93.0	96.0					7																	20698161		2203	4300	6503	SO:0001819	synonymous_variant	340273	exon14			AGGAGCTCAAATG	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"""ATP binding cassette transporters / subfamily B"""	46	protein-coding gene	gene with protein product	"""P-glycoprotein ABCB5"", ""ATP-binding cassette protein"""	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.1569T>C	chr7.hg19:g.20698161T>C		89.0	0.0		83.0	6.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Silent	SNP	ENST00000404938.2	hg19	CCDS55090.1																																																																																			.	.		0.423	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
RFC2	5982	hgsc.bcm.edu	37	7	73651756	73651756	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:73651756T>C	ENST00000055077.3	-	9	836	c.776A>G	c.(775-777)cAc>cGc	p.H259R	RFC2_ENST00000352131.3_Missense_Mutation_p.H225R	NM_181471.1	NP_852136.1	P35250	RFC2_HUMAN	replication factor C (activator 1) 2, 40kDa	259					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)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(3)	8						CAGCAGTGGGTGGGGCTCGTC	0.592																																					p.H259R		Atlas-SNP	.											.	RFC2	27	.	0			c.A776G						.						77.0	55.0	62.0					7																	73651756		2203	4299	6502	SO:0001583	missense	5982	exon9			AGTGGGTGGGGCT		CCDS5567.1, CCDS5568.1, CCDS75618.1	7q11.23	2010-04-21	2002-08-29		ENSG00000049541	ENSG00000049541		"""ATPases / AAA-type"""	9970	protein-coding gene	gene with protein product	"""activator 1"""	600404	"""replication factor C (activator 1) 2 (40kD)"""			1313560, 7774928	Standard	NM_181471		Approved	A1, RFC40	uc003uaj.3	P35250	OTTHUMG00000023239	ENST00000055077.3:c.776A>G	chr7.hg19:g.73651756T>C	ENSP00000055077:p.His259Arg	63.0	0.0		123.0	5.0	NM_181471	B5BU07|D3DXG3|P32846|Q9BU93	Missense_Mutation	SNP	ENST00000055077.3	hg19	CCDS5568.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.972365	0.74246	.	.	ENSG00000049541	ENST00000352131;ENST00000055077	T;T	0.42900	0.96;0.96	5.16	5.16	0.70880	Replication factor C (1);DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.58736	0.2143	L	0.59436	1.845	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	T	0.54807	-0.8238	10	0.27082	T	0.32	.	14.1544	0.65407	0.0:0.0:0.0:1.0	.	225;225;259	P35250-2;Q75MT5;P35250	.;.;RFC2_HUMAN	R	225;259	ENSP00000275627:H225R;ENSP00000055077:H259R	ENSP00000055077:H259R	H	-	2	0	RFC2	73289692	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	7.578000	0.82498	2.081000	0.62600	0.533000	0.62120	CAC	.	.		0.592	RFC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252459.2	NM_181471	
HIP1	3092	hgsc.bcm.edu	37	7	75221727	75221727	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:75221727T>C	ENST00000336926.6	-	3	316	c.290A>G	c.(289-291)cAt>cGt	p.H97R	HIP1_ENST00000434438.2_Missense_Mutation_p.H97R	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	97	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						GTGGAACACATGGCAGAACTT	0.577			T	PDGFRB	CMML																																p.H97R		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.A290G						.						83.0	67.0	73.0					7																	75221727		2203	4300	6503	SO:0001583	missense	3092	exon3			AACACATGGCAGA	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.290A>G	chr7.hg19:g.75221727T>C	ENSP00000336747:p.His97Arg	77.0	0.0		92.0	4.0	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Missense_Mutation	SNP	ENST00000336926.6	hg19	CCDS34669.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.817059	0.90790	.	.	ENSG00000127946	ENST00000336926;ENST00000434438;ENST00000420909	T;T;T	0.31510	1.49;1.49;1.49	5.78	5.78	0.91487	ENTH/VHS (2);ANTH (1);Epsin-like, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.54351	0.1853	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.51148	-0.8742	10	0.23891	T	0.37	-27.4743	14.9254	0.70875	0.0:0.0:0.0:1.0	.	97	O00291	HIP1_HUMAN	R	97;97;68	ENSP00000336747:H97R;ENSP00000410300:H97R;ENSP00000414280:H68R	ENSP00000336747:H97R	H	-	2	0	HIP1	75059663	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	7.698000	0.84413	2.208000	0.71279	0.455000	0.32223	CAT	.	.		0.577	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338	
GNAT3	346562	hgsc.bcm.edu	37	7	80103636	80103636	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:80103636A>G	ENST00000398291.3	-	5	614	c.521T>C	c.(520-522)gTt>gCt	p.V174A	CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3	174					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of visible light (GO:0009584)|platelet activation (GO:0030168)|response to nicotine (GO:0035094)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|synaptic transmission (GO:0007268)	acrosomal vesicle (GO:0001669)|apical plasma membrane (GO:0016324)|axoneme (GO:0005930)|heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	9						AGAATGGAGAACATCTTGTTC	0.313																																					p.V174A		Atlas-SNP	.											.	GNAT3	65	.	0			c.T521C						.						67.0	62.0	64.0					7																	80103636		1835	4106	5941	SO:0001583	missense	346562	exon5			TGGAGAACATCTT		CCDS47625.1	7q21.11	2007-06-13			ENSG00000214415	ENSG00000214415			22800	protein-coding gene	gene with protein product		139395					Standard	NM_001102386		Approved	gustducin, GDCA	uc011kgu.2	A8MTJ3	OTTHUMG00000155401	ENST00000398291.3:c.521T>C	chr7.hg19:g.80103636A>G	ENSP00000381339:p.Val174Ala	90.0	0.0		95.0	4.0	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Missense_Mutation	SNP	ENST00000398291.3	hg19	CCDS47625.1	.	.	.	.	.	.	.	.	.	.	A	32	5.115798	0.94339	.	.	ENSG00000214415	ENST00000398291	D	0.90385	-2.66	5.99	5.99	0.97316	G protein alpha subunit, helical insertion (1);	0.069591	0.56097	U	0.000026	D	0.96119	0.8735	M	0.92219	3.285	0.80722	D	1	P	0.52061	0.95	P	0.62014	0.897	D	0.96744	0.9549	9	.	.	.	.	16.1526	0.81632	1.0:0.0:0.0:0.0	.	174	A8MTJ3	GNAT3_HUMAN	A	174	ENSP00000381339:V174A	.	V	-	2	0	GNAT3	79941572	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	8.987000	0.93497	2.300000	0.77407	0.533000	0.62120	GTT	.	.		0.313	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370	
SEMA3D	223117	hgsc.bcm.edu	37	7	84644405	84644405	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:84644405G>A	ENST00000284136.6	-	14	1716	c.1673C>T	c.(1672-1674)gCa>gTa	p.A558V	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	558	PSI.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						TCGAGAGCATGCATTTCCATC	0.453																																					p.A558V	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.C1673T						.						126.0	114.0	118.0					7																	84644405		2203	4300	6503	SO:0001583	missense	223117	exon14			GAGCATGCATTTC	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"""Semaphorins"", ""Immunoglobulin superfamily / V-set domain containing"""	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.1673C>T	chr7.hg19:g.84644405G>A	ENSP00000284136:p.Ala558Val	148.0	0.0		157.0	34.0	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	hg19	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.760243	0.69763	.	.	ENSG00000153993	ENST00000284136	T	0.21932	1.98	5.75	5.75	0.90469	.	0.381500	0.32935	N	0.005473	T	0.23054	0.0557	L	0.50993	1.605	0.80722	D	1	B	0.33583	0.418	B	0.24394	0.053	T	0.02610	-1.1134	10	0.72032	D	0.01	.	19.9361	0.97143	0.0:0.0:1.0:0.0	.	558	O95025	SEM3D_HUMAN	V	558	ENSP00000284136:A558V	ENSP00000284136:A558V	A	-	2	0	SEMA3D	84482341	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	7.674000	0.83992	2.720000	0.93068	0.561000	0.74099	GCA	.	.		0.453	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754	
AKAP9	10142	hgsc.bcm.edu	37	7	91726654	91726654	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:91726654T>A	ENST00000359028.2	+	41	10618	c.10393T>A	c.(10393-10395)Tat>Aat	p.Y3465N	AKAP9_ENST00000356239.3_Missense_Mutation_p.Y3461N|AKAP9_ENST00000358100.2_Missense_Mutation_p.Y3411N			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3465					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AAGAATTCTGTATCAGAACCT	0.343			T	BRAF	papillary thyroid																																p.Y3461N		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.T10381A						.						27.0	28.0	28.0					7																	91726654		2156	4283	6439	SO:0001583	missense	10142	exon41			ATTCTGTATCAGA	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.10393T>A	chr7.hg19:g.91726654T>A	ENSP00000351922:p.Tyr3465Asn	40.0	0.0		56.0	4.0	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	hg19		.	.	.	.	.	.	.	.	.	.	T	10.60	1.395114	0.25205	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.03386	4.04;4.04;4.05;3.95	5.47	2.87	0.33458	.	0.418583	0.17737	N	0.163696	T	0.04815	0.0130	L	0.57536	1.79	0.21220	N	0.999752	B;B;B;B;B	0.27416	0.035;0.178;0.112;0.178;0.178	B;B;B;B;B	0.33521	0.021;0.165;0.05;0.107;0.107	T	0.40270	-0.9572	10	0.09084	T	0.74	.	8.0957	0.30826	0.127:0.0:0.2348:0.6382	.	736;3465;3465;3461;3453	B3KQF9;Q99996-6;Q99996;Q99996-2;Q99996-3	.;.;AKAP9_HUMAN;.;.	N	3461;3465;3411;3465;1307	ENSP00000348573:Y3461N;ENSP00000351922:Y3465N;ENSP00000350813:Y3411N;ENSP00000378042:Y1307N	ENSP00000348573:Y3461N	Y	+	1	0	AKAP9	91564590	0.636000	0.27207	0.999000	0.59377	0.989000	0.77384	0.696000	0.25541	0.975000	0.38392	0.533000	0.62120	TAT	.	.		0.343	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
CYP3A4	1576	hgsc.bcm.edu	37	7	99364063	99364063	+	Nonsense_Mutation	SNP	G	G	A	rs138105638		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:99364063G>A	ENST00000336411.2	-	9	985	c.802C>T	c.(802-804)Cga>Tga	p.R268*	CYP3A4_ENST00000354593.2_Nonsense_Mutation_p.R118*|RP11-757A13.1_ENST00000608397.1_RNA	NM_001202855.2|NM_017460.5	NP_001189784.1|NP_059488.2	P08684	CP3A4_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 4	268					alkaloid catabolic process (GO:0009822)|androgen metabolic process (GO:0008209)|calcitriol biosynthetic process from calciol (GO:0036378)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|lipid metabolic process (GO:0006629)|monoterpenoid metabolic process (GO:0016098)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	albendazole monooxygenase activity (GO:0047638)|caffeine oxidase activity (GO:0034875)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)|quinine 3-monooxygenase activity (GO:0050591)|steroid binding (GO:0005496)|steroid hydroxylase activity (GO:0008395)|taurochenodeoxycholate 6alpha-hydroxylase activity (GO:0033780)|testosterone 6-beta-hydroxylase activity (GO:0050649)|vitamin D 24-hydroxylase activity (GO:0070576)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(3)|central_nervous_system(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Abiraterone(DB05812)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetazolamide(DB00819)|Adinazolam(DB00546)|ado-trastuzumab emtansine(DB05773)|Albendazole(DB00518)|Alclometasone(DB00240)|Aldesleukin(DB00041)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Alimemazine(DB01246)|Aliskiren(DB01258)|Allylestrenol(DB01431)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alosetron(DB00969)|Alprazolam(DB00404)|Ambroxol(DB06742)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Arsenic trioxide(DB01169)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atazanavir(DB01072)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Avanafil(DB06237)|Axitinib(DB06626)|Azatadine(DB00719)|Azelastine(DB00972)|Azithromycin(DB00207)|Bedaquiline(DB08903)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bezafibrate(DB01393)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bisoprolol(DB00612)|Boceprevir(DB08873)|Bortezomib(DB00188)|Bosentan(DB00559)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Brinzolamide(DB01194)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Brompheniramine(DB00835)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Busulfan(DB01008)|Cabazitaxel(DB06772)|Cabergoline(DB00248)|Cabozantinib(DB08875)|Caffeine(DB00201)|Calcitriol(DB00136)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Caspofungin(DB00520)|Cefradine(DB01333)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chenodeoxycholic acid(DB06777)|Chloramphenicol(DB00446)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clemastine(DB00283)|Clevidipine(DB04920)|Clindamycin(DB01190)|Clobazam(DB00349)|Clofazimine(DB00845)|Clofibrate(DB00636)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonazepam(DB01068)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Colchicine(DB01394)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cortisone acetate(DB01380)|Crizotinib(DB08865)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Cytarabine(DB00987)|Dabrafenib(DB08912)|Dalfopristin(DB01764)|Danazol(DB01406)|Dantrolene(DB01219)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Deferasirox(DB01609)|Delavirdine(DB00705)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Dicloxacillin(DB00485)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydrocodeine(DB01551)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Disopyramide(DB00280)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dofetilide(DB00204)|Dolasetron(DB00757)|Dolutegravir(DB08930)|Domperidone(DB01184)|Donepezil(DB00843)|Dorzolamide(DB00869)|Doxepin(DB01142)|Doxorubicin(DB00997)|Doxycycline(DB00254)|Dronabinol(DB00470)|Dronedarone(DB04855)|Dutasteride(DB01126)|Econazole(DB01127)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Epinephrine(DB00668)|Eplerenone(DB00700)|Ergocalciferol(DB00153)|Ergoloid mesylate(DB01049)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Estradiol valerate/Dienogest(DB08866)|Estradiol(DB00783)|Estramustine(DB01196)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Etravirine(DB06414)|Everolimus(DB01590)|Exemestane(DB00990)|Ezetimibe(DB00973)|Famciclovir(DB00426)|Felbamate(DB00949)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Finasteride(DB01216)|Fingolimod(DB08868)|Flucloxacillin(DB00301)|Fluconazole(DB00196)|Flunisolide(DB00180)|Flunitrazepam(DB01544)|Fluorometholone(DB00324)|Fluoxetine(DB00472)|Flurazepam(DB00690)|Flutamide(DB00499)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosamprenavir(DB01319)|Fosphenytoin(DB01320)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Glipizide(DB01067)|Glyburide(DB01016)|Granisetron(DB00889)|Griseofulvin(DB00400)|Guanethidine(DB01170)|Guanfacine(DB01018)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Hydralazine(DB01275)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|Indacaterol(DB05039)|Indapamide(DB00808)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Irinotecan(DB00762)|Isoniazid(DB00951)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ixabepilone(DB04845)|Josamycin(DB01321)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Levomethadyl Acetate(DB01227)|Levomilnacipran(DB08918)|Levonorgestrel(DB00367)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Lisuride(DB00589)|Lomitapide(DB08827)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumefantrine(DB06708)|Lurasidone(DB08815)|MACITENTAN(DB08932)|Maraviroc(DB04835)|Mebendazole(DB00643)|Medroxyprogesterone Acetate(DB00603)|Mefloquine(DB00358)|Meloxicam(DB00814)|Mequitazine(DB01071)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Methylergometrine(DB00353)|Methylprednisolone(DB00959)|Methyltestosterone(DB06710)|Metronidazole(DB00916)|Metyrapone(DB01011)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Mitoxantrone(DB01204)|Modafinil(DB00745)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nafcillin(DB00607)|Naloxone(DB01183)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nitric Oxide(DB00435)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Omeprazole(DB00338)|Ondansetron(DB00904)|Orlistat(DB01083)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paramethasone(DB01384)|Paricalcitol(DB00910)|Pazopanib(DB06589)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perampanel(DB08883)|Pergolide(DB01186)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenoxybenzamine(DB00925)|Phenprocoumon(DB00946)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pilocarpine(DB01085)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Prazepam(DB01588)|Praziquantel(DB01058)|Prednisolone(DB00860)|Prednisone(DB00635)|Primaquine(DB01087)|Primidone(DB00794)|Probenecid(DB01032)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Pyridostigmine(DB00545)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Quinupristin(DB01369)|Rabeprazole(DB01129)|Raloxifene(DB00481)|Ramelteon(DB00980)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Regorafenib(DB08896)|Repaglinide(DB00912)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rifapentine(DB01201)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Rimonabant(DB06155)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rivastigmine(DB00989)|Rolitetracycline(DB01301)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosuvastatin(DB01098)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Rufinamide(DB06201)|Ruxolitinib(DB08877)|Salbutamol(DB01001)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sevoflurane(DB01236)|Sibutramine(DB01105)|Sildenafil(DB00203)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Sitaxentan(DB06268)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sufentanil(DB00708)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfanilamide(DB00259)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tasosartan(DB01349)|Telaprevir(DB05521)|Telithromycin(DB00976)|Temazepam(DB00231)|Temozolomide(DB00853)|Temsirolimus(DB06287)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Thiopental(DB00599)|Thiotepa(DB04572)|Tiagabine(DB00906)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tioconazole(DB01007)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tofisopam(DB08811)|Tolterodine(DB01036)|Tolvaptan(DB06212)|Topiramate(DB00273)|Topotecan(DB01030)|Toremifene(DB00539)|Trabectedin(DB05109)|Tramadol(DB00193)|Trametinib(DB08911)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Tretinoin(DB00755)|Triamcinolone(DB00620)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vandetanib(DB05294)|Vardenafil(DB00862)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Zidovudine(DB00495)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909)|Zopiclone(DB01198)	AAATCCACTCGGTGCTAGAAG	0.448																																					p.R268X		Atlas-SNP	.											.	CYP3A4	56	.	0			c.C802T						.	G	stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	94.0	92.0	93.0		799,802	1.9	0.2	7	dbSNP_134	93	0,8600		0,0,4300	no	stop-gained,stop-gained	CYP3A4	NM_001202855.2,NM_017460.5	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	267/503,268/504	99364063	1,13005	2203	4300	6503	SO:0001587	stop_gained	1576	exon9			CCACTCGGTGCTA	AF280107	CCDS5674.1	7q21.1	2011-06-21	2003-01-14		ENSG00000160868	ENSG00000160868	1.1.1.161	"""Cytochrome P450s"""	2637	protein-coding gene	gene with protein product		124010	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 4"""	CYP3A3		8269949, 1391968	Standard	NM_001202855		Approved		uc003urv.2	P08684	OTTHUMG00000156651	ENST00000336411.2:c.802C>T	chr7.hg19:g.99364063G>A	ENSP00000337915:p.Arg268*	159.0	0.0		187.0	26.0	NM_017460	P05184|Q16757|Q9UK50	Nonsense_Mutation	SNP	ENST00000336411.2	hg19	CCDS5674.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.267773	0.80469	2.27E-4	0.0	ENSG00000160868	ENST00000354593;ENST00000336411	.	.	.	3.87	1.92	0.25849	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.6971	0.12809	0.1102:0.0:0.5124:0.3773	.	.	.	.	X	118;268	.	ENSP00000337915:R268X	R	-	1	2	CYP3A4	99201999	0.290000	0.24343	0.204000	0.23530	0.958000	0.62258	0.489000	0.22387	0.193000	0.20303	0.491000	0.48974	CGA	.	G|1.000;A|0.000		0.448	CYP3A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345059.1		
ATXN7L1	222255	hgsc.bcm.edu	37	7	105283324	105283324	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:105283324C>G	ENST00000419735.3	-	5	868	c.823G>C	c.(823-825)Ggc>Cgc	p.G275R	ATXN7L1_ENST00000472910.1_5'UTR|ATXN7L1_ENST00000477775.1_Missense_Mutation_p.G151R	NM_020725.1	NP_065776.1	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1	275										endometrium(1)|large_intestine(4)|lung(5)	10						TTTTTGGTGCCATTTTGGTGT	0.463																																					p.G275R		Atlas-SNP	.											.	ATXN7L1	56	.	0			c.G823C						.						446.0	342.0	373.0					7																	105283324		692	1591	2283	SO:0001583	missense	222255	exon5			TGGTGCCATTTTG	AB033044	CCDS34727.1, CCDS47682.1, CCDS47683.1	7q22.1	2007-11-13			ENSG00000146776	ENSG00000146776			22210	protein-coding gene	gene with protein product			"""ataxin 7-like 4"""	ATXN7L4		15115762	Standard	NM_152749		Approved	KIAA1218, MGC33190	uc003vde.2	Q9ULK2	OTTHUMG00000157521	ENST00000419735.3:c.823G>C	chr7.hg19:g.105283324C>G	ENSP00000410759:p.Gly275Arg	309.0	0.0		475.0	126.0	NM_020725	A4D0Q2|B4DTS1|Q8N2T0	Missense_Mutation	SNP	ENST00000419735.3	hg19	CCDS47682.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.285886	0.80803	.	.	ENSG00000146776	ENST00000419735;ENST00000477775;ENST00000472195	T;T;T	0.15487	2.46;2.43;2.42	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000001	T	0.36441	0.0967	L	0.36672	1.1	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.961;1.0	T	0.00802	-1.1560	10	0.52906	T	0.07	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	59;151;275	A4D0Q3;Q9ULK2-3;Q9ULK2	.;.;AT7L1_HUMAN	R	275;151;151	ENSP00000410759:G275R;ENSP00000418476:G151R;ENSP00000419566:G151R	ENSP00000410759:G275R	G	-	1	0	ATXN7L1	105070560	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.546000	0.60705	2.941000	0.99782	0.655000	0.94253	GGC	.	.		0.463	ATXN7L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349037.2		
CCDC136	64753	hgsc.bcm.edu	37	7	128455707	128455707	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:128455707A>C	ENST00000297788.4	+	16	3452	c.3085A>C	c.(3085-3087)Aaa>Caa	p.K1029Q	CCDC136_ENST00000464832.1_Intron|CCDC136_ENST00000471729.1_Intron|CCDC136_ENST00000487361.1_Intron|CCDC136_ENST00000378685.4_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	1029						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						CAGCCAGAGGAAATTAGATGG	0.507																																					p.K1029Q		Atlas-SNP	.											.	CCDC136	170	.	0			c.A3085C						.						34.0	34.0	34.0					7																	128455707		1946	4129	6075	SO:0001583	missense	64753	exon16			CAGAGGAAATTAG		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.3085A>C	chr7.hg19:g.128455707A>C	ENSP00000297788:p.Lys1029Gln	102.0	0.0		146.0	73.0	NM_022742	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	ENST00000297788.4	hg19	CCDS47704.1	.	.	.	.	.	.	.	.	.	.	A	7.458	0.644011	0.14451	.	.	ENSG00000128596	ENST00000297788;ENST00000397697	T	0.31510	1.49	4.82	0.68	0.17980	.	1.619910	0.03252	N	0.181948	T	0.19327	0.0464	L	0.34521	1.04	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.10450	0.005;0.003	T	0.10086	-1.0645	10	0.08837	T	0.75	0.8604	1.0683	0.01616	0.222:0.2189:0.3982:0.1609	.	1029;1029	Q96JN2-4;Q96JN2	.;CC136_HUMAN	Q	1029	ENSP00000297788:K1029Q	ENSP00000297788:K1029Q	K	+	1	0	CCDC136	128242943	0.000000	0.05858	0.000000	0.03702	0.057000	0.15508	0.216000	0.17585	0.004000	0.14682	-0.468000	0.05107	AAA	.	.		0.507	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742	
EXOC4	60412	hgsc.bcm.edu	37	7	133580480	133580480	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:133580480A>G	ENST00000253861.4	+	12	1892	c.1863A>G	c.(1861-1863)gcA>gcG	p.A621A	EXOC4_ENST00000539845.1_Silent_p.A520A|EXOC4_ENST00000545148.1_Silent_p.A231A|EXOC4_ENST00000460346.1_3'UTR	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	621					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				CCTGCACTGCAGCTTACAGGT	0.453																																					p.A621A		Atlas-SNP	.											.	EXOC4	118	.	0			c.A1863G						.						129.0	110.0	117.0					7																	133580480		2203	4300	6503	SO:0001819	synonymous_variant	60412	exon12			CACTGCAGCTTAC	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"""SEC8-like 1 (S. cerevisiae)"""	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.1863A>G	chr7.hg19:g.133580480A>G		87.0	0.0		131.0	6.0	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Silent	SNP	ENST00000253861.4	hg19	CCDS5829.1																																																																																			.	.		0.453	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	
CNTNAP2	26047	hgsc.bcm.edu	37	7	147844667	147844667	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:147844667A>G	ENST00000361727.3	+	17	3155	c.2639A>G	c.(2638-2640)gAc>gGc	p.D880G	CNTNAP2_ENST00000538075.1_5'UTR	NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	880	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CTCAACGATGACCAGTGGCAC	0.567										HNSCC(39;0.1)																											p.D880G		Atlas-SNP	.											.	CNTNAP2	392	.	0			c.A2639G						.						130.0	120.0	124.0					7																	147844667		2203	4300	6503	SO:0001583	missense	26047	exon17			ACGATGACCAGTG	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.2639A>G	chr7.hg19:g.147844667A>G	ENSP00000354778:p.Asp880Gly	87.0	0.0		117.0	5.0	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation	SNP	ENST00000361727.3	hg19	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.615335	0.87359	.	.	ENSG00000174469	ENST00000361727	T	0.71341	-0.56	5.34	5.34	0.76211	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.85682	D	0.000000	T	0.56441	0.1985	N	0.04018	-0.295	0.80722	D	1	B	0.34103	0.437	P	0.44422	0.449	T	0.57207	-0.7851	10	0.17832	T	0.49	.	14.1814	0.65577	1.0:0.0:0.0:0.0	.	880	Q9UHC6	CNTP2_HUMAN	G	880	ENSP00000354778:D880G	ENSP00000354778:D880G	D	+	2	0	CNTNAP2	147475600	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.233000	0.95337	2.029000	0.59856	0.459000	0.35465	GAC	.	.		0.567	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1		
ZNF777	27153	hgsc.bcm.edu	37	7	149152609	149152609	+	Missense_Mutation	SNP	A	A	G	rs3823695		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:149152609A>G	ENST00000247930.4	-	2	828	c.505T>C	c.(505-507)Tct>Cct	p.S169P		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	169					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			ACTGCAGAAGAGATCTGGAAA	0.607																																					p.S169P		Atlas-SNP	.											.	ZNF777	63	.	0			c.T505C						.						74.0	84.0	81.0					7																	149152609		2011	4178	6189	SO:0001583	missense	27153	exon2			CAGAAGAGATCTG	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"""Zinc fingers, C2H2-type"", ""-"""	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.505T>C	chr7.hg19:g.149152609A>G	ENSP00000247930:p.Ser169Pro	66.0	0.0		103.0	5.0	NM_015694	Q8N2R2|Q8N659	Missense_Mutation	SNP	ENST00000247930.4	hg19	CCDS43675.1	.	.	.	.	.	.	.	.	.	.	A	16.52	3.145832	0.57044	.	.	ENSG00000196453	ENST00000247930	T	0.05717	3.4	4.57	3.43	0.39272	.	0.000000	0.44097	D	0.000494	T	0.04452	0.0122	L	0.27053	0.805	0.31089	N	0.711009	B	0.12013	0.005	B	0.12156	0.007	T	0.08207	-1.0733	10	0.36615	T	0.2	-9.9234	6.0597	0.19830	0.8861:0.0:0.1139:0.0	.	169	Q9ULD5-2	.	P	169	ENSP00000247930:S169P	ENSP00000247930:S169P	S	-	1	0	ZNF777	148783542	0.999000	0.42202	0.997000	0.53966	0.925000	0.55904	1.474000	0.35398	1.708000	0.51301	0.460000	0.39030	TCT	.	.		0.607	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694	
ABCB8	11194	hgsc.bcm.edu	37	7	150739104	150739104	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:150739104A>G	ENST00000297504.6	+	15	1791	c.1725A>G	c.(1723-1725)gaA>gaG	p.E575E	ABCB8_ENST00000542328.1_Silent_p.E470E|ABCB8_ENST00000356058.4_3'UTR|ABCB8_ENST00000358849.4_Silent_p.E558E|ABCB8_ENST00000498578.1_Silent_p.E558E			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	575	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	GGAAGCTGGAAGCTTCCGATG	0.562																																					p.E558E		Atlas-SNP	.											.	ABCB8	65	.	0			c.A1674G						.						61.0	64.0	63.0					7																	150739104		2203	4300	6503	SO:0001819	synonymous_variant	11194	exon14			GCTGGAAGCTTCC	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.1725A>G	chr7.hg19:g.150739104A>G		51.0	0.0		95.0	4.0	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Silent	SNP	ENST00000297504.6	hg19																																																																																				.	.		0.562	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188	
WDR60	55112	hgsc.bcm.edu	37	7	158719144	158719144	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:158719144T>C	ENST00000407559.3	+	19	2581	c.2423T>C	c.(2422-2424)cTc>cCc	p.L808P		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	808					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		AGTGGGGTTCTCAATGTATGG	0.542																																					p.L808P		Atlas-SNP	.											.	WDR60	94	.	0			c.T2423C						.						38.0	36.0	36.0					7																	158719144		1925	4130	6055	SO:0001583	missense	55112	exon19			GGGTTCTCAATGT		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"""WD repeat domain containing"""	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.2423T>C	chr7.hg19:g.158719144T>C	ENSP00000384290:p.Leu808Pro	134.0	0.0		195.0	8.0	NM_018051	Q9NW58	Missense_Mutation	SNP	ENST00000407559.3	hg19	CCDS47757.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.974786	0.74360	.	.	ENSG00000126870	ENST00000407559	T	0.69926	-0.44	5.95	5.95	0.96441	WD40 repeat-like-containing domain (1);	0.000000	0.64402	D	0.000001	D	0.82540	0.5059	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.987;0.994	D	0.84970	0.0882	10	0.87932	D	0	-19.656	15.6048	0.76658	0.0:0.0:0.0:1.0	.	291;808	A4D230;Q8WVS4	.;WDR60_HUMAN	P	808	ENSP00000384290:L808P	ENSP00000384290:L808P	L	+	2	0	WDR60	158411905	1.000000	0.71417	1.000000	0.80357	0.708000	0.40852	6.194000	0.72082	2.279000	0.76181	0.533000	0.62120	CTC	.	.		0.542	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051	
ZDHHC2	51201	hgsc.bcm.edu	37	8	17067945	17067945	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:17067945T>C	ENST00000262096.8	+	10	1601	c.906T>C	c.(904-906)ccT>ccC	p.P302P		NM_016353.4	NP_057437.1	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2	302					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|recycling endosome membrane (GO:0055038)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|pancreas(1)|stomach(1)	8				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		ACCAGGATCCTGAACAAGCAT	0.348																																					p.P302P		Atlas-SNP	.											.	ZDHHC2	25	.	0			c.T906C						.						77.0	72.0	73.0					8																	17067945		1835	4094	5929	SO:0001819	synonymous_variant	51201	exon10			GGATCCTGAACAA	AB023584	CCDS47810.1	8p22	2008-05-15			ENSG00000104219	ENSG00000104219		"""Zinc fingers, DHHC-type"""	18469	protein-coding gene	gene with protein product						10918388	Standard	NM_016353		Approved	ZNF372	uc003wxe.3	Q9UIJ5	OTTHUMG00000163860	ENST00000262096.8:c.906T>C	chr8.hg19:g.17067945T>C		74.0	0.0		63.0	4.0	NM_016353	D3DSP5	Silent	SNP	ENST00000262096.8	hg19	CCDS47810.1																																																																																			.	.		0.348	ZDHHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376014.2	NM_016353	
INTS10	55174	hgsc.bcm.edu	37	8	19675087	19675087	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:19675087A>G	ENST00000397977.3	+	1	437	c.39A>G	c.(37-39)cgA>cgG	p.R13R	INTS10_ENST00000521758.1_3'UTR	NM_018142.2	NP_060612.2	Q9NVR2	INT10_HUMAN	integrator complex subunit 10	13					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	20				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		TGGTGCAGCGAGCCCGGGAGT	0.677																																					p.R13R		Atlas-SNP	.											.	INTS10	46	.	0			c.A39G						.						18.0	26.0	24.0					8																	19675087		2036	4179	6215	SO:0001819	synonymous_variant	55174	exon1			GCAGCGAGCCCGG	AK001431	CCDS6011.2	8p21.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000104613	ENSG00000104613			25548	protein-coding gene	gene with protein product		611353	"""chromosome 8 open reading frame 35"""	C8orf35		16239144	Standard	XM_005273558		Approved	FLJ10569, INT10	uc003wzj.3	Q9NVR2	OTTHUMG00000131065	ENST00000397977.3:c.39A>G	chr8.hg19:g.19675087A>G		89.0	0.0		61.0	4.0	NM_018142	Q6IA93|Q7L538|Q7L8C8|Q9H3W8	Silent	SNP	ENST00000397977.3	hg19	CCDS6011.2																																																																																			.	.		0.677	INTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253724.2	NM_018142	
PDLIM2	64236	hgsc.bcm.edu	37	8	22452076	22452076	+	IGR	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:22452076T>C	ENST00000397760.4	+	0	1837				PDLIM2_ENST00000265810.4_Missense_Mutation_p.S339P|AC037459.4_ENST00000430850.2_Intron			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00579)|Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0626)		AATGAGATTGTCACTGGAAGC	0.527																																					p.S339P		Atlas-SNP	.											.	PDLIM2	42	.	0			c.T1015C						.						168.0	169.0	169.0					8																	22452076		2203	4300	6503	SO:0001628	intergenic_variant	64236	exon10			AGATTGTCACTGG	AY007729	CCDS34860.1, CCDS6032.1, CCDS34861.1, CCDS6032.2	8p21.3	2012-06-27			ENSG00000120913	ENSG00000120913			13992	protein-coding gene	gene with protein product		609722					Standard	NM_021630		Approved		uc003xby.4	Q96JY6	OTTHUMG00000164270		chr8.hg19:g.22452076T>C		85.0	0.0		57.0	4.0	NM_176871	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Missense_Mutation	SNP	ENST00000397760.4	hg19		.	.	.	.	.	.	.	.	.	.	T	12.83	2.054956	0.36277	.	.	ENSG00000120913	ENST00000265810	T	0.13901	2.55	1.84	1.84	0.25277	.	.	.	.	.	T	0.08980	0.0222	.	.	.	0.09310	N	0.999999	B	0.13145	0.007	B	0.06405	0.002	T	0.25467	-1.0131	8	0.45353	T	0.12	.	5.7188	0.17974	0.0:0.0:0.0:1.0	.	339	Q96JY6-3	.	P	339	ENSP00000265810:S339P	ENSP00000265810:S339P	S	+	1	0	PDLIM2	22508021	0.021000	0.18746	0.007000	0.13788	0.015000	0.08874	0.862000	0.27899	1.108000	0.41662	0.402000	0.26972	TCA	.	.		0.527	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1		
DOCK5	80005	hgsc.bcm.edu	37	8	25182970	25182970	+	Nonsense_Mutation	SNP	A	A	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:25182970A>T	ENST00000276440.7	+	18	1854	c.1810A>T	c.(1810-1812)Aaa>Taa	p.K604*		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	604	DHR-1.				positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		TCAAGCATCCAAAAACCTGGT	0.458																																					p.K604X	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.A1810T						.						135.0	124.0	128.0					8																	25182970		2203	4300	6503	SO:0001587	stop_gained	80005	exon18			GCATCCAAAAACC		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.1810A>T	chr8.hg19:g.25182970A>T	ENSP00000276440:p.Lys604*	167.0	0.0		137.0	7.0	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Nonsense_Mutation	SNP	ENST00000276440.7	hg19	CCDS6047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	40|40	7.961131|7.961131	0.98583|0.98583	.|.	.|.	ENSG00000147459|ENSG00000147459	ENST00000276440|ENST00000444569	.|.	.|.	.|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	2.143080|.	0.01481|.	N|.	0.016688|.	.|T	.|0.65770	.|0.2723	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.70781	.|-0.4779	.|3	0.02654|.	T|.	1|.	.|.	14.3564|14.3564	0.66740|0.66740	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	604|375	.|.	ENSP00000276440:K604X|.	K|Q	+|+	1|2	0|0	DOCK5|DOCK5	25238887|25238887	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.362000|0.362000	0.29581|0.29581	4.167000|4.167000	0.58209|0.58209	2.129000|2.129000	0.65627|0.65627	0.533000|0.533000	0.62120|0.62120	AAA|CAA	.	.		0.458	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
PBK	55872	hgsc.bcm.edu	37	8	27668599	27668599	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:27668599T>C	ENST00000301905.4	-	7	1111	c.648A>G	c.(646-648)gaA>gaG	p.E216E	PBK_ENST00000522944.1_Silent_p.E227E|ESCO2_ENST00000397418.2_Intron	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	216	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		CCTCCACAGCTTCTTTGGGTT	0.433																																					p.E216E		Atlas-SNP	.											.	PBK	29	.	0			c.A648G						.						127.0	110.0	116.0					8																	27668599		2203	4300	6503	SO:0001819	synonymous_variant	55872	exon7			CACAGCTTCTTTG	AB027249	CCDS6063.1, CCDS64858.1	8p21.2	2009-08-06			ENSG00000168078	ENSG00000168078			18282	protein-coding gene	gene with protein product	"""T-LAK cell-originated protein kinase"", ""cancer/testis antigen 84"""	611210				10781613, 10779557	Standard	NM_018492		Approved	TOPK, FLJ14385, Nori-3, SPK, CT84	uc003xgi.3	Q96KB5	OTTHUMG00000102113	ENST00000301905.4:c.648A>G	chr8.hg19:g.27668599T>C		139.0	0.0		94.0	4.0	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Silent	SNP	ENST00000301905.4	hg19	CCDS6063.1																																																																																			.	.		0.433	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492	
KIF13B	23303	hgsc.bcm.edu	37	8	28928094	28928094	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:28928094G>A	ENST00000524189.1	-	40	5446	c.5408C>T	c.(5407-5409)tCg>tTg	p.S1803L	KIF13B_ENST00000404075.3_Missense_Mutation_p.S322L|CTD-2647L4.5_ENST00000560714.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1803					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		AGCTGTCAGCGAGGCCAGGTT	0.706																																					p.S1803L		Atlas-SNP	.											.	KIF13B	192	.	0			c.C5408T						.						11.0	14.0	13.0					8																	28928094		1957	4149	6106	SO:0001583	missense	23303	exon40			GTCAGCGAGGCCA	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"""Kinesins"""	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.5408C>T	chr8.hg19:g.28928094G>A	ENSP00000427900:p.Ser1803Leu	78.0	0.0		47.0	4.0	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	hg19	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.321783	0.81580	.	.	ENSG00000197892	ENST00000524189;ENST00000523130;ENST00000404075	T;D;D	0.82619	-1.25;-1.63;-1.62	4.63	3.76	0.43208	.	0.169623	0.36740	N	0.002423	T	0.67116	0.2859	N	0.14661	0.345	0.40215	D	0.977676	P;B	0.34412	0.453;0.054	B;B	0.23716	0.048;0.007	T	0.69760	-0.5058	10	0.54805	T	0.06	.	12.7104	0.57086	0.0797:0.0:0.9203:0.0	.	322;1803	B4DGY5;F8VPJ2	.;.	L	1803;395;322	ENSP00000427900:S1803L;ENSP00000429106:S395L;ENSP00000384054:S322L	ENSP00000384054:S322L	S	-	2	0	KIF13B	28984013	1.000000	0.71417	0.962000	0.40283	0.736000	0.42039	6.729000	0.74775	1.179000	0.42884	0.561000	0.74099	TCG	.	.		0.706	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1		
KIF13B	23303	hgsc.bcm.edu	37	8	28999714	28999714	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:28999714T>C	ENST00000524189.1	-	19	2332	c.2294A>G	c.(2293-2295)gAc>gGc	p.D765G	CTD-2647L4.1_ENST00000523661.1_RNA|RN7SL781P_ENST00000582428.1_RNA|CTD-2647L4.1_ENST00000517632.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	765					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		CTGATAAAGGTCTCTCATATC	0.398																																					p.D765G		Atlas-SNP	.											.	KIF13B	192	.	0			c.A2294G						.						168.0	148.0	154.0					8																	28999714		1835	4093	5928	SO:0001583	missense	23303	exon19			TAAAGGTCTCTCA	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"""Kinesins"""	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.2294A>G	chr8.hg19:g.28999714T>C	ENSP00000427900:p.Asp765Gly	97.0	0.0		78.0	5.0	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	hg19	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	T	18.25	3.581706	0.65992	.	.	ENSG00000197892	ENST00000524189	T	0.80653	-1.4	5.28	5.28	0.74379	.	0.044544	0.85682	D	0.000000	T	0.78641	0.4315	L	0.49778	1.585	0.80722	D	1	B	0.27679	0.185	B	0.32090	0.14	T	0.78555	-0.2159	10	0.87932	D	0	.	15.3876	0.74714	0.0:0.0:0.0:1.0	.	765	F8VPJ2	.	G	765	ENSP00000427900:D765G	ENSP00000427900:D765G	D	-	2	0	KIF13B	29055633	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.436000	0.80404	2.217000	0.71921	0.533000	0.62120	GAC	.	.		0.398	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1		
TEX15	56154	hgsc.bcm.edu	37	8	30703400	30703400	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:30703400T>C	ENST00000256246.2	-	1	3208	c.3134A>G	c.(3133-3135)gAc>gGc	p.D1045G	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1045					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		ACCTTGAAGGTCACAACTTTC	0.333																																					p.D1045G		Atlas-SNP	.											.	TEX15	350	.	0			c.A3134G						.						66.0	70.0	68.0					8																	30703400		2203	4295	6498	SO:0001583	missense	56154	exon1			TGAAGGTCACAAC	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.3134A>G	chr8.hg19:g.30703400T>C	ENSP00000256246:p.Asp1045Gly	99.0	0.0		69.0	4.0	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	hg19	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	T	18.15	3.560018	0.65538	.	.	ENSG00000133863	ENST00000256246	T	0.26957	1.7	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000005	T	0.46054	0.1373	L	0.55481	1.735	0.43766	D	0.99628	D	0.89917	1.0	D	0.81914	0.995	T	0.42682	-0.9437	10	0.87932	D	0	.	13.5087	0.61499	0.0:0.0:0.0:1.0	.	1045	Q9BXT5	TEX15_HUMAN	G	1045	ENSP00000256246:D1045G	ENSP00000256246:D1045G	D	-	2	0	TEX15	30822942	1.000000	0.71417	1.000000	0.80357	0.707000	0.40811	4.331000	0.59273	2.180000	0.69256	0.383000	0.25322	GAC	.	.		0.333	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
WHSC1L1	54904	hgsc.bcm.edu	37	8	38178646	38178646	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:38178646A>G	ENST00000317025.8	-	8	2270	c.1753T>C	c.(1753-1755)Tct>Cct	p.S585P	WHSC1L1_ENST00000525081.1_5'Flank|WHSC1L1_ENST00000316985.3_Missense_Mutation_p.S585P|WHSC1L1_ENST00000433384.2_Missense_Mutation_p.S585P|WHSC1L1_ENST00000527502.1_Missense_Mutation_p.S585P	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	585					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)			TCTGATTCAGAACGAGTTCTA	0.358			T	NUP98	AML																																p.S585P		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.T1753C						.						176.0	159.0	165.0					8																	38178646		2203	4300	6503	SO:0001583	missense	54904	exon8			ATTCAGAACGAGT	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.1753T>C	chr8.hg19:g.38178646A>G	ENSP00000313983:p.Ser585Pro	83.0	0.0		82.0	4.0	NM_017778	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation	SNP	ENST00000317025.8	hg19	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.770502	0.90108	.	.	ENSG00000147548	ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502;ENST00000316985;ENST00000528627	D;D;D;T	0.95238	-3.65;-3.65;-3.65;-0.9	5.71	5.71	0.89125	.	0.000000	0.47455	U	0.000226	D	0.96175	0.8753	L	0.50333	1.59	0.58432	D	0.999995	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.91635	0.994;0.997;0.999;0.994	D	0.96409	0.9303	10	0.56958	D	0.05	.	15.9628	0.79945	1.0:0.0:0.0:0.0	.	585;585;585;585	B7ZL11;Q9BZ95-2;Q9BZ95-3;Q9BZ95	.;.;.;NSD3_HUMAN	P	585;585;522;585;585;51	ENSP00000393284:S585P;ENSP00000313983:S585P;ENSP00000434730:S585P;ENSP00000313410:S585P	ENSP00000313410:S585P	S	-	1	0	WHSC1L1	38297803	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.060000	0.89464	2.166000	0.68216	0.482000	0.46254	TCT	.	.		0.358	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034	
ARFGEF1	10565	hgsc.bcm.edu	37	8	68113709	68113709	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:68113709G>C	ENST00000262215.3	-	37	5649	c.5260C>G	c.(5260-5262)Ctt>Gtt	p.L1754V	ARFGEF1_ENST00000520381.1_Missense_Mutation_p.L1208V|ARFGEF1_ENST00000518230.1_Missense_Mutation_p.L592V|ARFGEF1_ENST00000517955.1_5'UTR	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1754					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)			TACTTCAAAAGCCTCTGCTGG	0.587																																					p.L1754V		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.C5260G						.						63.0	58.0	59.0					8																	68113709		2203	4300	6503	SO:0001583	missense	10565	exon37			TCAAAAGCCTCTG	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.5260C>G	chr8.hg19:g.68113709G>C	ENSP00000262215:p.Leu1754Val	106.0	0.0		349.0	17.0	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	hg19	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.514446	0.64522	.	.	ENSG00000066777	ENST00000520381;ENST00000262215;ENST00000518789;ENST00000518230	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	5.42	5.42	0.78866	.	0.144113	0.48286	D	0.000193	T	0.71779	0.3380	M	0.88842	2.985	0.58432	D	0.99999	D;P;B;P	0.89917	1.0;0.89;0.435;0.89	D;P;B;P	0.87578	0.998;0.486;0.266;0.486	T	0.74973	-0.3481	10	0.51188	T	0.08	.	12.5629	0.56293	0.0772:0.0:0.9228:0.0	.	1754;1232;578;1208	Q9Y6D6;Q59FY5;B3KMS9;E5RIF2	BIG1_HUMAN;.;.;.	V	1208;1754;85;592	ENSP00000428429:L1208V;ENSP00000262215:L1754V;ENSP00000429560:L85V;ENSP00000430891:L592V	ENSP00000262215:L1754V	L	-	1	0	ARFGEF1	68276263	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.826000	0.62715	2.717000	0.92951	0.650000	0.86243	CTT	.	.		0.587	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421	
OC90	729330	hgsc.bcm.edu	37	8	133036828	133036828	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:133036828T>C	ENST00000443356.2	-	15	1468	c.1382A>G	c.(1381-1383)gAc>gGc	p.D461G	OC90_ENST00000603859.1_Missense_Mutation_p.D445G|OC90_ENST00000262283.5_Missense_Mutation_p.D657G|OC90_ENST00000254627.3_Missense_Mutation_p.D445G			Q02509	OC90_HUMAN	otoconin 90	461					lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			CTCCTCGCTGTCCTCCTCAGA	0.652																																					p.D445G		Atlas-SNP	.											OC90_ENST00000262283,caecum,carcinoma,0,2	OC90	163	.	0			c.A1334G						.						22.0	25.0	24.0					8																	133036828		1933	4127	6060	SO:0001583	missense	729330	exon14			TCGCTGTCCTCCT	Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.1382A>G	chr8.hg19:g.133036828T>C	ENSP00000390050:p.Asp461Gly	52.0	0.0		187.0	10.0	NM_001080399	B4DNG8	Missense_Mutation	SNP	ENST00000443356.2	hg19		.	.	.	.	.	.	.	.	.	.	T	11.74	1.729548	0.30684	.	.	ENSG00000253117;ENSG00000253117;ENSG00000258417	ENST00000254627;ENST00000443356;ENST00000262283	T;T;T	0.31769	1.51;1.51;1.48	5.85	2.04	0.26737	.	0.704021	0.14765	N	0.299776	T	0.13798	0.0334	N	0.14661	0.345	0.22541	N	0.999008	B;B	0.33171	0.4;0.278	B;B	0.30855	0.121;0.057	T	0.17531	-1.0366	10	0.56958	D	0.05	-5.1902	0.9521	0.01378	0.1744:0.1368:0.1819:0.5069	.	445;461	Q02509-2;Q02509	.;OC90_HUMAN	G	445;461;657	ENSP00000254627:D445G;ENSP00000390050:D461G;ENSP00000262283:D657G	ENSP00000254627:D445G	D	-	2	0	RP11-240B13.2;OC90	133106010	0.988000	0.35896	0.976000	0.42696	0.071000	0.16799	0.804000	0.27098	0.407000	0.25591	0.533000	0.62120	GAC	.	.		0.652	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399	
PTK2	5747	hgsc.bcm.edu	37	8	141749131	141749131	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:141749131T>C	ENST00000522684.1	-	21	2040	c.1811A>G	c.(1810-1812)gAc>gGc	p.D604G	PTK2_ENST00000538769.1_Missense_Mutation_p.D272G|PTK2_ENST00000521059.1_Missense_Mutation_p.D604G|PTK2_ENST00000519465.1_Missense_Mutation_p.D232G|PTK2_ENST00000519419.1_Missense_Mutation_p.D648G|PTK2_ENST00000340930.3_Missense_Mutation_p.D604G|PTK2_ENST00000535192.1_Missense_Mutation_p.D604G|PTK2_ENST00000517887.1_Missense_Mutation_p.D648G|PTK2_ENST00000395218.2_Missense_Mutation_p.D604G	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	604	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			CATCCATACGTCACTAGCTGA	0.279																																					p.D626G		Atlas-SNP	.											.	PTK2	311	.	0			c.A1877G						.						61.0	60.0	60.0					8																	141749131		2203	4300	6503	SO:0001583	missense	5747	exon21			CATACGTCACTAG	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9611	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 71"""	600758	"""PTK2 protein tyrosine kinase 2"""			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.1811A>G	chr8.hg19:g.141749131T>C	ENSP00000429911:p.Asp604Gly	26.0	0.0		116.0	5.0	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	hg19	CCDS6381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.23|18.23	3.577129|3.577129	0.65878|0.65878	.|.	.|.	ENSG00000169398|ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000521986;ENST00000342207|ENST00000519654	D;D;D;D;D;D;D;D;D;D;D|.	0.88818|.	-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43|.	5.07|5.07	3.91|3.91	0.45181|0.45181	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);|.	0.046536|.	0.85682|.	N|.	0.000000|.	D|.	0.87633|.	0.6226|.	H|H	0.98629|0.98629	4.285|4.285	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0|.	D;D;D;D;D;D;D;D;D;D|.	0.97110|.	1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0|.	D|.	0.89457|.	0.3734|.	10|.	0.87932|.	D|.	0|.	.|.	10.7871|10.7871	0.46411|0.46411	0.0:0.0746:0.0:0.9254|0.0:0.0746:0.0:0.9254	.|.	604;299;524;604;626;604;556;452;272;232|.	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4|.	.;.;.;FAK1_HUMAN;.;.;.;.;.;.|.	G|W	604;604;232;648;604;556;604;525;299;276;604;272;648;302;450|614	ENSP00000429911:D604G;ENSP00000438009:D604G;ENSP00000429170:D232G;ENSP00000429082:D648G;ENSP00000429474:D604G;ENSP00000378644:D604G;ENSP00000428492:D276G;ENSP00000341189:D604G;ENSP00000445742:D272G;ENSP00000429129:D648G;ENSP00000430603:D302G|.	ENSP00000341189:D604G|.	D|X	-|-	2|3	0|0	PTK2|PTK2	141818313|141818313	1.000000|1.000000	0.71417|0.71417	0.880000|0.880000	0.34516|0.34516	0.777000|0.777000	0.43975|0.43975	7.859000|7.859000	0.86982|0.86982	0.782000|0.782000	0.33613|0.33613	-0.290000|-0.290000	0.09829|0.09829	GAC|TGA	.	.		0.279	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	
EPPK1	83481	hgsc.bcm.edu	37	8	144940597	144940597	+	Silent	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:144940597G>A	ENST00000525985.1	-	2	6896	c.6825C>T	c.(6823-6825)ccC>ccT	p.P2275P				P58107	EPIPL_HUMAN	epiplakin 1	2275						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)			GGTTGCGCACGGGGTCGATGA	0.721																																					p.P2275P		Atlas-SNP	.											.	EPPK1	199	.	0			c.C6825T						.						50.0	47.0	48.0					8																	144940597		2163	4239	6402	SO:0001819	synonymous_variant	83481	exon1			GCGCACGGGGTCG	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.6825C>T	chr8.hg19:g.144940597G>A		1.0	0.0		39.0	4.0	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	hg19																																																																																				.	.		0.721	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
KIFC2	90990	hgsc.bcm.edu	37	8	145693366	145693366	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:145693366C>T	ENST00000301332.2	+	7	1183	c.806C>T	c.(805-807)cCg>cTg	p.P269L	CYHR1_ENST00000306145.5_5'Flank|KIFC2_ENST00000301331.5_Missense_Mutation_p.P17L|CYHR1_ENST00000403000.2_5'Flank|CYHR1_ENST00000424149.2_5'Flank|CYHR1_ENST00000438911.2_5'Flank|CTD-2517M22.16_ENST00000525461.1_RNA	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	269	Gln-rich.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			ATCAGGGCTCCGCAGGTACTC	0.677																																					p.P269L		Atlas-SNP	.											.	KIFC2	53	.	0			c.C806T						.						12.0	15.0	14.0					8																	145693366		2178	4270	6448	SO:0001583	missense	90990	exon7			GGGCTCCGCAGGT	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.806C>T	chr8.hg19:g.145693366C>T	ENSP00000301332:p.Pro269Leu	42.0	0.0		218.0	25.0	NM_145754	E9PHB2|Q96NN6	Missense_Mutation	SNP	ENST00000301332.2	hg19	CCDS6427.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.755500	0.49362	.	.	ENSG00000167702	ENST00000301332;ENST00000301331	T;T	0.71461	-0.57;-0.51	4.22	2.34	0.29019	.	0.251086	0.21037	N	0.081232	T	0.49236	0.1545	N	0.24115	0.695	0.23640	N	0.997228	B	0.16802	0.019	B	0.14578	0.011	T	0.23762	-1.0179	10	0.14252	T	0.57	-9.219	6.5852	0.22616	0.1789:0.7215:0.0:0.0996	.	269	Q96AC6	KIFC2_HUMAN	L	269;17	ENSP00000301332:P269L;ENSP00000301331:P17L	ENSP00000301331:P17L	P	+	2	0	KIFC2	145664174	0.000000	0.05858	0.331000	0.25455	0.036000	0.12997	0.282000	0.18829	0.486000	0.27676	0.655000	0.94253	CCG	.	.		0.677	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754	
RFX3	5991	hgsc.bcm.edu	37	9	3275558	3275558	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:3275558T>C	ENST00000382004.3	-	10	1339	c.1028A>G	c.(1027-1029)gAt>gGt	p.D343G	RFX3_ENST00000358730.2_Missense_Mutation_p.D343G|RFX3_ENST00000302303.1_Missense_Mutation_p.D343G	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	343					cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		GGTAGTACCATCTGGCAGAGA	0.418																																					p.D343G		Atlas-SNP	.											.	RFX3	156	.	0			c.A1028G						.						120.0	114.0	116.0					9																	3275558		2203	4300	6503	SO:0001583	missense	5991	exon10			GTACCATCTGGCA	AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298			9984	protein-coding gene	gene with protein product		601337				8289803	Standard	XM_005251534		Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.1028A>G	chr9.hg19:g.3275558T>C	ENSP00000371434:p.Asp343Gly	88.0	0.0		68.0	4.0	NM_134428	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	hg19	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.460186	0.63401	.	.	ENSG00000080298	ENST00000382004;ENST00000358730;ENST00000302303	T;T;T	0.58797	0.32;0.31;0.31	5.83	5.83	0.93111	.	0.048134	0.85682	D	0.000000	T	0.61565	0.2357	L	0.39147	1.195	0.80722	D	1	D;B;B	0.58970	0.984;0.003;0.001	P;B;B	0.56042	0.79;0.011;0.003	T	0.55872	-0.8072	10	0.17369	T	0.5	-14.9945	16.2141	0.82191	0.0:0.0:0.0:1.0	.	343;343;343	P48380-3;P48380-2;P48380	.;.;RFX3_HUMAN	G	343	ENSP00000371434:D343G;ENSP00000351574:D343G;ENSP00000303847:D343G	ENSP00000303847:D343G	D	-	2	0	RFX3	3265558	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.186000	0.72026	2.224000	0.72417	0.528000	0.53228	GAT	.	.		0.418	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919	
KIAA2026	158358	hgsc.bcm.edu	37	9	5921058	5921058	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:5921058T>C	ENST00000399933.3	-	8	4937	c.4938A>G	c.(4936-4938)tcA>tcG	p.S1646S	KIAA2026_ENST00000381461.2_Silent_p.S1616S	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1646										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		CTGCTCTTGCTGAAGAAACCA	0.428																																					p.S1646S		Atlas-SNP	.											.	KIAA2026	231	.	0			c.A4938G						.						99.0	94.0	96.0					9																	5921058		1856	4100	5956	SO:0001819	synonymous_variant	158358	exon8			TCTTGCTGAAGAA	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.4938A>G	chr9.hg19:g.5921058T>C		51.0	0.0		72.0	5.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	hg19																																																																																				.	.		0.428	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969	
MPDZ	8777	hgsc.bcm.edu	37	9	13125334	13125334	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:13125334T>C	ENST00000319217.7	-	35	4935	c.4688A>G	c.(4687-4689)gAg>gGg	p.E1563G	MPDZ_ENST00000536827.1_Missense_Mutation_p.E1530G|MPDZ_ENST00000381022.2_Missense_Mutation_p.E1563G|MPDZ_ENST00000541093.1_5'UTR|MPDZ_ENST00000541718.1_Missense_Mutation_p.E1563G|MPDZ_ENST00000546205.1_Missense_Mutation_p.E1577G|MPDZ_ENST00000381015.4_Missense_Mutation_p.E1563G|MPDZ_ENST00000447879.1_Missense_Mutation_p.E1530G|MPDZ_ENST00000538841.1_Missense_Mutation_p.E422G	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1563	PDZ 9. {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)		ATCTGGATTCTCAGCATGGAT	0.473																																					p.E1563G		Atlas-SNP	.											.	MPDZ	324	.	0			c.A4688G						.						115.0	111.0	112.0					9																	13125334		1883	4118	6001	SO:0001583	missense	8777	exon35			GGATTCTCAGCAT	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.4688A>G	chr9.hg19:g.13125334T>C	ENSP00000320006:p.Glu1563Gly	135.0	0.0		114.0	6.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	hg19		.	.	.	.	.	.	.	.	.	.	T	12.59	1.983258	0.35036	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000438511;ENST00000545857;ENST00000538841;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.83	5.83	0.93111	PDZ/DHR/GLGF (3);	0.139426	0.32719	N	0.005734	T	0.33933	0.0880	L	0.46614	1.455	0.80722	D	1	B;B;B;B;B;B;B	0.25235	0.121;0.0;0.018;0.089;0.054;0.089;0.032	B;B;B;B;B;B;B	0.26969	0.034;0.001;0.021;0.075;0.05;0.075;0.028	T	0.16778	-1.0391	10	0.22109	T	0.4	.	8.4452	0.32838	0.1222:0.0:0.1424:0.7354	.	1530;422;268;1530;1443;1563;1563	B7ZMI4;B7ZB24;B4DGX5;O75970-3;E7EPZ1;O75970-2;O75970	.;.;.;.;.;.;MPDZ_HUMAN	G	1563;1563;1563;132;499;422;1530;1530;1563;1443;1577	ENSP00000320006:E1563G;ENSP00000439807:E1563G;ENSP00000370410:E1563G;ENSP00000415964:E132G;ENSP00000444230:E499G;ENSP00000444717:E422G;ENSP00000444151:E1530G;ENSP00000415208:E1530G;ENSP00000370403:E1563G;ENSP00000446358:E1577G	ENSP00000320006:E1563G	E	-	2	0	MPDZ	13115334	0.986000	0.35501	0.980000	0.43619	0.403000	0.30841	1.508000	0.35769	2.228000	0.72767	0.528000	0.53228	GAG	.	.		0.473	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
FREM1	158326	hgsc.bcm.edu	37	9	14863881	14863881	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:14863881A>G	ENST00000380880.3	-	3	1038	c.255T>C	c.(253-255)ctT>ctC	p.L85L	FREM1_ENST00000380881.4_Silent_p.L85L|FREM1_ENST00000422223.2_Silent_p.L85L			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	85					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		CTTCGTTGGGAAGGAAATGGC	0.413																																					p.L85L		Atlas-SNP	.											.	FREM1	261	.	0			c.T255C						.						108.0	103.0	105.0					9																	14863881		1935	4139	6074	SO:0001819	synonymous_variant	158326	exon4			GTTGGGAAGGAAA	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.255T>C	chr9.hg19:g.14863881A>G		112.0	0.0		100.0	4.0	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	hg19	CCDS47952.1																																																																																			.	.		0.413	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
DENND4C	55667	hgsc.bcm.edu	37	9	19346888	19346888	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:19346888C>T	ENST00000380432.2	+	18	3299	c.3266C>T	c.(3265-3267)tCt>tTt	p.S1089F	DENND4C_ENST00000434457.2_Missense_Mutation_p.S1374F|DENND4C_ENST00000602925.1_Missense_Mutation_p.S1325F			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1089					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CGTTCAACTTCTTTGTCAGCA	0.468																																					p.S1325F		Atlas-SNP	.											DENND4C,colon,carcinoma,0,1	DENND4C	120	.	0			c.C3974T						.						64.0	63.0	63.0					9																	19346888		2203	4300	6503	SO:0001583	missense	55667	exon22			CAACTTCTTTGTC	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.3266C>T	chr9.hg19:g.19346888C>T	ENSP00000369797:p.Ser1089Phe	36.0	0.0		72.0	4.0	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	hg19		.	.	.	.	.	.	.	.	.	.	C	22.4	4.285076	0.80803	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024	T;T	0.57752	0.38;0.38	5.31	5.31	0.75309	.	2.141580	0.01702	N	0.027243	T	0.74535	0.3729	L	0.59436	1.845	0.80722	D	1	P;D;D;P	0.54397	0.768;0.966;0.959;0.943	B;P;P;P	0.61397	0.396;0.873;0.888;0.75	T	0.58634	-0.7602	10	0.87932	D	0	-16.8913	18.9763	0.92738	0.0:1.0:0.0:0.0	.	419;1089;271;1089	B7Z660;Q5VZ89-5;Q5VZ89-3;Q5VZ89	.;.;.;DEN4C_HUMAN	F	1089;562;271;419;562;271;86	ENSP00000305795:S562F;ENSP00000443804:S419F	ENSP00000305795:S562F	S	+	2	0	DENND4C	19336888	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	7.263000	0.78421	2.483000	0.83821	0.585000	0.79938	TCT	.	.		0.468	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
ACO1	48	hgsc.bcm.edu	37	9	32425907	32425907	+	Silent	SNP	T	T	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:32425907T>G	ENST00000309951.6	+	11	1398	c.1260T>G	c.(1258-1260)acT>acG	p.T420T	ACO1_ENST00000379923.1_Silent_p.T420T|ACO1_ENST00000541043.1_Silent_p.T321T	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	420					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)		ATGATAACACTGAATTCACCC	0.383																																					p.T420T		Atlas-SNP	.											ACO1_ENST00000379923,NS,carcinoma,0,2	ACO1	149	.	0			c.T1260G						.						137.0	107.0	117.0					9																	32425907		2203	4300	6503	SO:0001819	synonymous_variant	48	exon11			TAACACTGAATTC	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.1260T>G	chr9.hg19:g.32425907T>G		121.0	0.0		97.0	4.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Silent	SNP	ENST00000309951.6	hg19	CCDS6525.1																																																																																			.	.		0.383	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197	
CHMP5	51510	hgsc.bcm.edu	37	9	33271180	33271180	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:33271180A>G	ENST00000223500.8	+	5	483	c.346A>G	c.(346-348)Atg>Gtg	p.M116V	CHMP5_ENST00000419016.2_Missense_Mutation_p.M116V	NM_016410.5	NP_057494.3	Q9NZZ3	CHMP5_HUMAN	charged multivesicular body protein 5	116					endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of receptor recycling (GO:0001919)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10			LUSC - Lung squamous cell carcinoma(29;0.00506)			AGTAAAGGAAATGAAGAAGGC	0.353																																					p.M116V		Atlas-SNP	.											.	CHMP5	15	.	0			c.A346G						.						164.0	144.0	151.0					9																	33271180		2203	4300	6503	SO:0001583	missense	51510	exon5			AAGGAAATGAAGA	AF132968	CCDS6537.1, CCDS56569.1	9p13.3	2011-09-21	2011-09-21	2005-08-09	ENSG00000086065	ENSG00000086065		"""Charged multivesicular body proteins"""	26942	protein-coding gene	gene with protein product		610900	"""chromosome 9 open reading frame 83"", ""chromatin modifying protein 5"""	C9orf83, SNF7DC2		15644320, 11559748	Standard	NM_016410		Approved	HSPC177, CGI-34, Vps60	uc003zsm.4	Q9NZZ3	OTTHUMG00000019765	ENST00000223500.8:c.346A>G	chr9.hg19:g.33271180A>G	ENSP00000223500:p.Met116Val	64.0	0.0		82.0	6.0	NM_016410	B2RD95|B4DIR6|Q5VXW2|Q96AV2|Q9HB68|Q9NYS4|Q9Y323	Missense_Mutation	SNP	ENST00000223500.8	hg19	CCDS6537.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.172728	0.78452	.	.	ENSG00000086065	ENST00000223500;ENST00000419016	T;T	0.79653	-1.29;-1.29	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.86222	0.5881	M	0.87328	2.875	0.58432	D	0.999999	P;B	0.36712	0.566;0.416	B;B	0.43990	0.438;0.403	D	0.88094	0.2815	10	0.87932	D	0	-9.9225	14.049	0.64725	1.0:0.0:0.0:0.0	.	116;116	B4DIR6;Q9NZZ3	.;CHMP5_HUMAN	V	116	ENSP00000223500:M116V;ENSP00000442725:M116V	ENSP00000223500:M116V	M	+	1	0	CHMP5	33261180	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.879000	0.92398	2.259000	0.74868	0.529000	0.55759	ATG	.	.		0.353	CHMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052040.3	NM_016410	
NFX1	4799	hgsc.bcm.edu	37	9	33295418	33295418	+	Silent	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:33295418G>A	ENST00000379540.3	+	2	1088	c.1026G>A	c.(1024-1026)acG>acA	p.T342T	NFX1_ENST00000379521.4_Silent_p.T342T|NFX1_ENST00000318524.6_Silent_p.T342T	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	342					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)		ATGTGGAAACGCACACAGGTA	0.363																																					p.T342T		Atlas-SNP	.											.	NFX1	85	.	0			c.G1026A						.						57.0	55.0	56.0					9																	33295418		2203	4300	6503	SO:0001819	synonymous_variant	4799	exon2			GGAAACGCACACA	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.1026G>A	chr9.hg19:g.33295418G>A		27.0	0.0		33.0	14.0	NM_147134	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Silent	SNP	ENST00000379540.3	hg19	CCDS6538.1																																																																																			.	.		0.363	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1		
C9orf24	84688	hgsc.bcm.edu	37	9	34385753	34385753	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:34385753A>G	ENST00000297623.2	-	2	360	c.162T>C	c.(160-162)caT>caC	p.H54H		NM_032596.3	NP_115985.2	Q8NCR6	SMRP1_HUMAN	chromosome 9 open reading frame 24	54					cell differentiation (GO:0030154)|cellular protein complex assembly (GO:0043623)|spermatogenesis (GO:0007283)	manchette (GO:0002177)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.123)		CGGGATCCACATGTCGCTCCA	0.557																																					p.H54H		Atlas-SNP	.											.	C9orf24	15	.	0			c.T162C						.						104.0	99.0	101.0					9																	34385753		2203	4300	6503	SO:0001819	synonymous_variant	84688	exon2			ATCCACATGTCGC	BC029484	CCDS6553.1, CCDS6554.1, CCDS6555.1, CCDS59121.1	9p11.2	2013-01-11			ENSG00000164972	ENSG00000164972			19919	protein-coding gene	gene with protein product	"""ciliated bronchial epithelium 1"", ""spermatid-specific manchette-related protein 1"""					12029067	Standard	NM_147168		Approved	bA573M23.4, NYD-SP22, MGC32921, MGC33614, CBE1, SMRP1	uc003zuh.1	Q8NCR6	OTTHUMG00000000437	ENST00000297623.2:c.162T>C	chr9.hg19:g.34385753A>G		95.0	0.0		95.0	4.0	NM_032596	Q5T598|Q5T599|Q5T5A0|Q8N9G4|Q96KD1|Q96LN1	Silent	SNP	ENST00000297623.2	hg19	CCDS6554.1	.	.	.	.	.	.	.	.	.	.	A	0.144	-1.098945	0.01843	.	.	ENSG00000164972	ENST00000444429	.	.	.	5.89	-11.8	0.00035	.	.	.	.	.	T	0.26738	0.0654	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.25984	-1.0116	4	.	.	.	-6.9167	11.3006	0.49302	0.1352:0.171:0.6092:0.0846	.	.	.	.	R	20	.	.	C	-	1	0	C9orf24	34375753	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-1.545000	0.02190	-2.668000	0.00415	-0.250000	0.11733	TGT	.	.		0.557	C9orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001098.3	NM_147169	
SIGMAR1	10280	hgsc.bcm.edu	37	9	34635688	34635688	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:34635688A>G	ENST00000277010.4	-	4	686	c.613T>C	c.(613-615)Tcc>Ccc	p.S205P	SIGMAR1_ENST00000477726.1_Missense_Mutation_p.S174P|SIGMAR1_ENST00000461426.1_5'UTR|SIGMAR1_ENST00000378892.1_Missense_Mutation_p.S116P	NM_001282208.1|NM_005866.2	NP_001269137.1|NP_005857.1	Q99720	SGMR1_HUMAN	sigma non-opioid intracellular receptor 1	205					cell death (GO:0008219)|lipid transport (GO:0006869)|nervous system development (GO:0007399)|regulation of neuron apoptotic process (GO:0043523)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lipid particle (GO:0005811)|nuclear envelope (GO:0005635)	drug binding (GO:0008144)|opioid receptor activity (GO:0004985)			large_intestine(1)|lung(1)	2					Amitriptyline(DB00321)|Dextromethorphan(DB00514)|Nortriptyline(DB00540)|Pentazocine(DB00652)|Remoxipride(DB00409)	CGAGCATAGGAGCGAAGAGTA	0.627																																					p.S205P		Atlas-SNP	.											.	SIGMAR1	6	.	0			c.T613C						.						108.0	95.0	100.0					9																	34635688		2203	4300	6503	SO:0001583	missense	10280	exon4			CATAGGAGCGAAG	BC004899	CCDS6562.1, CCDS6563.1	9p13.3	2008-12-18	2008-12-18	2008-12-18	ENSG00000147955	ENSG00000147955			8157	protein-coding gene	gene with protein product		601978	"""opioid receptor, sigma 1"""	OPRS1		8954936, 9453537	Standard	NM_005866		Approved	SR-BP1	uc003zvb.3	Q99720	OTTHUMG00000019829	ENST00000277010.4:c.613T>C	chr9.hg19:g.34635688A>G	ENSP00000277010:p.Ser205Pro	134.0	0.0		161.0	7.0	NM_005866	D3DRM7|O00673|O00725|Q0Z9W6|Q153Z1|Q2TSD1|Q53GN2|Q7Z653|Q8N7H3|Q9NYX0	Missense_Mutation	SNP	ENST00000277010.4	hg19	CCDS6562.1	.	.	.	.	.	.	.	.	.	.	A	14.82	2.649224	0.47362	.	.	ENSG00000147955	ENST00000378892;ENST00000277010;ENST00000360710;ENST00000477726	T;T;T	0.63255	-0.03;-0.03;-0.03	4.43	1.08	0.20341	.	0.278543	0.34750	N	0.003713	T	0.37376	0.1001	N	0.08118	0	0.25052	N	0.991129	B;B;P	0.38420	0.202;0.119;0.63	B;B;B	0.32289	0.072;0.143;0.131	T	0.21586	-1.0241	10	0.42905	T	0.14	-10.9058	14.248	0.66001	0.1673:0.8327:0.0:0.0	.	174;205;185	A2A3U5;Q99720;Q99720-2	.;SGMR1_HUMAN;.	P	116;205;171;174	ENSP00000368170:S116P;ENSP00000277010:S205P;ENSP00000420022:S174P	ENSP00000277010:S205P	S	-	1	0	SIGMAR1	34625688	0.903000	0.30736	0.812000	0.32479	0.995000	0.86356	1.916000	0.39986	0.006000	0.14734	0.379000	0.24179	TCC	.	.		0.627	SIGMAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052204.1	NM_005866	
TLN1	7094	hgsc.bcm.edu	37	9	35717439	35717439	+	Splice_Site	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:35717439T>C	ENST00000314888.9	-	19	2517		c.e19-2		TLN1_ENST00000540444.1_Splice_Site	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TGCCACCACCTGTAGGTAAAG	0.557																																					.		Atlas-SNP	.											.	TLN1	185	.	0			c.2164-2A>G						.						64.0	59.0	61.0					9																	35717439		2203	4300	6503	SO:0001630	splice_region_variant	7094	exon20			ACCACCTGTAGGT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.2164-2A>G	chr9.hg19:g.35717439T>C		66.0	0.0		73.0	4.0	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Splice_Site	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.044061	0.75732	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7766	0.78224	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TLN1	35707439	1.000000	0.71417	0.967000	0.41034	0.795000	0.44927	8.040000	0.89188	2.143000	0.66587	0.459000	0.35465	.	.	.		0.557	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	Intron
HRCT1	646962	hgsc.bcm.edu	37	9	35906303	35906303	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:35906303A>G	ENST00000354323.2	+	1	115	c.19A>G	c.(19-21)Agc>Ggc	p.S7G		NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	7						integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						CCTCCTGGGGAGCACAGCCCT	0.652																																					p.S7G		Atlas-SNP	.											.	HRCT1	14	.	0			c.A19G						.						22.0	24.0	23.0					9																	35906303		2202	4300	6502	SO:0001583	missense	646962	exon1			CTGGGGAGCACAG		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	ENST00000354323.2:c.19A>G	chr9.hg19:g.35906303A>G	ENSP00000346283:p.Ser7Gly	68.0	0.0		100.0	7.0	NM_001039792	B7ZBJ1	Missense_Mutation	SNP	ENST00000354323.2	hg19	CCDS35012.1	.	.	.	.	.	.	.	.	.	.	A	14.26	2.481596	0.44147	.	.	ENSG00000196196	ENST00000354323	.	.	.	3.83	2.69	0.31865	.	0.379917	0.19341	N	0.116648	T	0.24314	0.0589	N	0.19112	0.55	0.22866	N	0.998639	B	0.17667	0.023	B	0.14023	0.01	T	0.12889	-1.0530	9	0.41790	T	0.15	-13.1954	5.9057	0.19001	0.8813:0.0:0.1187:0.0	.	7	Q6UXD1	HRCT1_HUMAN	G	7	.	ENSP00000346283:S7G	S	+	1	0	HRCT1	35896303	0.999000	0.42202	0.989000	0.46669	0.649000	0.38597	1.385000	0.34408	0.827000	0.34685	0.533000	0.62120	AGC	.	.		0.652	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792	
FRMPD1	22844	hgsc.bcm.edu	37	9	37707505	37707505	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:37707505T>C	ENST00000539465.1	+	3	787	c.194T>C	c.(193-195)cTc>cCc	p.L65P	FRMPD1_ENST00000377765.3_Missense_Mutation_p.L65P|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	65	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		AAAGACACCCTCCTCCAGGAC	0.527																																					p.L65P		Atlas-SNP	.											.	FRMPD1	237	.	0			c.T194C						.						126.0	124.0	125.0					9																	37707505		2203	4300	6503	SO:0001583	missense	22844	exon3			ACACCCTCCTCCA	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.194T>C	chr9.hg19:g.37707505T>C	ENSP00000444411:p.Leu65Pro	72.0	0.0		86.0	4.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	hg19	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	T	19.80	3.895589	0.72639	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.26957	1.7;1.7	5.97	4.82	0.62117	PDZ/DHR/GLGF (3);	0.757041	0.12892	N	0.430536	T	0.31918	0.0812	L	0.27053	0.805	0.80722	D	1	D	0.57257	0.979	P	0.58331	0.837	T	0.01935	-1.1244	10	0.54805	T	0.06	-4.9713	9.1518	0.36967	0.0:0.0828:0.0:0.9172	.	65	Q5SYB0	FRPD1_HUMAN	P	65	ENSP00000366995:L65P;ENSP00000444411:L65P	ENSP00000366995:L65P	L	+	2	0	FRMPD1	37697505	0.899000	0.30636	0.923000	0.36655	0.985000	0.73830	2.208000	0.42797	1.062000	0.40625	0.533000	0.62120	CTC	.	.		0.527	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
PSAT1	29968	hgsc.bcm.edu	37	9	80923403	80923403	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:80923403A>G	ENST00000376588.3	+	6	712	c.644A>G	c.(643-645)gAc>gGc	p.D215G	PSAT1_ENST00000347159.2_Missense_Mutation_p.D215G	NM_058179.2	NP_478059.1	Q9Y617	SERC_HUMAN	phosphoserine aminotransferase 1	215					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-serine biosynthetic process (GO:0006564)|pyridoxine biosynthetic process (GO:0008615)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	O-phospho-L-serine:2-oxoglutarate aminotransferase activity (GO:0004648)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	20						GTCCGTGATGACCTGCTGGGG	0.517																																					p.D215G	Colon(34;187 791 10662 18313 37609)	Atlas-SNP	.											.	PSAT1	33	.	0			c.A644G						.						141.0	119.0	127.0					9																	80923403		2203	4300	6503	SO:0001583	missense	29968	exon6			GTGATGACCTGCT	BC004863	CCDS6659.1, CCDS6660.1	9q21.2	2008-08-11			ENSG00000135069	ENSG00000135069			19129	protein-coding gene	gene with protein product		610936				12633500, 3651428	Standard	NM_058179		Approved	PSA	uc004ala.3	Q9Y617	OTTHUMG00000020066	ENST00000376588.3:c.644A>G	chr9.hg19:g.80923403A>G	ENSP00000365773:p.Asp215Gly	192.0	0.0		145.0	6.0	NM_021154	Q5T7G5|Q5T7G6|Q96AW2|Q9BQ12	Missense_Mutation	SNP	ENST00000376588.3	hg19	CCDS6660.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.929233	0.92389	.	.	ENSG00000135069	ENST00000421149;ENST00000347159;ENST00000376588	T;T	0.65732	-0.17;-0.17	5.59	5.59	0.84812	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.000000	0.85682	D	0.000000	D	0.83083	0.5177	M	0.91717	3.235	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.73380	0.945;0.98	D	0.87222	0.2254	10	0.87932	D	0	-13.1243	15.7658	0.78126	1.0:0.0:0.0:0.0	.	215;215	Q9Y617-2;Q9Y617	.;SERC_HUMAN	G	39;215;215	ENSP00000317606:D215G;ENSP00000365773:D215G	ENSP00000317606:D215G	D	+	2	0	PSAT1	80113223	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.899000	0.92544	2.131000	0.65755	0.455000	0.32223	GAC	.	.		0.517	PSAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052777.1	NM_021154	
UBQLN1	29979	hgsc.bcm.edu	37	9	86284243	86284243	+	Splice_Site	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:86284243C>T	ENST00000376395.4	-	7	1629		c.e7-1		UBQLN1_ENST00000257468.7_Splice_Site	NM_013438.4|NM_053067.2	NP_038466.2|NP_444295.1	Q9UMX0	UBQL1_HUMAN	ubiquilin 1						cellular response to hypoxia (GO:0071456)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|regulation of protein ubiquitination (GO:0031396)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|protein complex (GO:0043234)	kinase binding (GO:0019900)			breast(4)|endometrium(2)|kidney(4)|large_intestine(6)|lung(10)|prostate(1)	27						AACATACTAGCTGAAAGTTTG	0.328																																					.	Melanoma(186;1284 2073 12755 14558 18426)	Atlas-SNP	.											.	UBQLN1	49	.	0			c.1106-1G>A						.						97.0	87.0	91.0					9																	86284243		2203	4300	6503	SO:0001630	splice_region_variant	29979	exon8			TACTAGCTGAAAG	AF176069	CCDS6663.1, CCDS6664.1	9q22	2013-02-12			ENSG00000135018	ENSG00000135018		"""Ubiquilin family"""	12508	protein-coding gene	gene with protein product		605046				9303440, 10807547	Standard	NM_013438		Approved	DSK2, PLIC-1, XDRP1, DA41	uc004amv.3	Q9UMX0	OTTHUMG00000020104	ENST00000376395.4:c.1106-1G>A	chr9.hg19:g.86284243C>T		78.0	0.0		80.0	5.0	NM_013438	Q5T6J5|Q5T6J9|Q8IXS9|Q8N2Q3|Q9H0T8|Q9H3R4|Q9HAZ5	Splice_Site	SNP	ENST00000376395.4	hg19	CCDS6663.1	.	.	.	.	.	.	.	.	.	.	C	19.68	3.872873	0.72180	.	.	ENSG00000135018	ENST00000376395;ENST00000257468	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8548	0.96752	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	UBQLN1	85474063	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.054000	0.57434	2.687000	0.91594	0.655000	0.94253	.	.	.		0.328	UBQLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052834.1	NM_013438	Intron
SLC28A3	64078	hgsc.bcm.edu	37	9	86920237	86920237	+	Missense_Mutation	SNP	G	G	C	rs570175390		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:86920237G>C	ENST00000376238.4	-	4	315	c.266C>G	c.(265-267)aCa>aGa	p.T89R	SLC28A3_ENST00000495823.1_5'UTR|SLC28A3_ENST00000537648.1_Missense_Mutation_p.T20R	NM_001199633.1|NM_022127.2	NP_001186562.1|NP_071410.1	Q9HAS3	S28A3_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 3	89					pyrimidine nucleoside transport (GO:0015864)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|purine-specific nucleoside:sodium symporter activity (GO:0015390)|pyrimidine- and adenine-specific:sodium symporter activity (GO:0015389)	p.T89I(1)		endometrium(2)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31					Adenosine(DB00640)|Cladribine(DB00242)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Ribavirin(DB00811)	ACCACATACTGTGTCATACCT	0.398																																					p.T89R	Ovarian(106;425 1539 34835 42413 43572)	Atlas-SNP	.											SLC28A3,NS,carcinoma,0,1	SLC28A3	72	.	1	Substitution - Missense(1)	endometrium(1)	c.C266G						.						138.0	126.0	130.0					9																	86920237		2203	4300	6503	SO:0001583	missense	64078	exon4			CATACTGTGTCAT	AF305210	CCDS6670.1	9q21.33	2013-07-17	2013-07-17		ENSG00000197506	ENSG00000197506		"""Solute carriers"""	16484	protein-coding gene	gene with protein product		608269	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"""			11032837	Standard	NM_001199633		Approved	CNT3	uc010mpz.3	Q9HAS3	OTTHUMG00000020117	ENST00000376238.4:c.266C>G	chr9.hg19:g.86920237G>C	ENSP00000365413:p.Thr89Arg	114.0	0.0		145.0	0.0	NM_001199633	A8K9Y4|B1AML0|B2RA51|B4E2S8|F5GYE3	Missense_Mutation	SNP	ENST00000376238.4	hg19	CCDS6670.1	.	.	.	.	.	.	.	.	.	.	G	0.037	-1.300979	0.01364	.	.	ENSG00000197506	ENST00000376238;ENST00000537648	T;T	0.01838	4.8;4.61	5.49	-5.3	0.02738	.	1.406730	0.04062	N	0.306495	T	0.01222	0.0040	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.46303	-0.9201	10	0.08381	T	0.77	6.5937	2.532	0.04705	0.1242:0.2813:0.2153:0.3792	.	20;89	B4E2S8;Q9HAS3	.;S28A3_HUMAN	R	89;20	ENSP00000365413:T89R;ENSP00000446438:T20R	ENSP00000365413:T89R	T	-	2	0	SLC28A3	86110057	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.234000	0.09028	-0.818000	0.04329	-0.140000	0.14226	ACA	.	.		0.398	SLC28A3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052874.1	NM_022127	
COL15A1	1306	hgsc.bcm.edu	37	9	101765842	101765842	+	Silent	SNP	G	G	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:101765842G>T	ENST00000375001.3	+	8	1596	c.1173G>T	c.(1171-1173)acG>acT	p.T391T		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	391	4 X tandem repeats.|Nonhelical region 1 (NC1).		T -> M (in dbSNP:rs10988532).		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)	p.T391T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				CTATGTCCACGGAGAACCCAG	0.622																																					p.T391T		Atlas-SNP	.											COL15A1,NS,carcinoma,0,1	COL15A1	211	.	1	Substitution - coding silent(1)	endometrium(1)	c.G1173T						.						57.0	61.0	60.0					9																	101765842		2203	4300	6503	SO:0001819	synonymous_variant	1306	exon8			GTCCACGGAGAAC	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.1173G>T	chr9.hg19:g.101765842G>T		180.0	1.0		196.0	0.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	hg19	CCDS35081.1																																																																																			.	.		0.622	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
TMEFF1	8577	hgsc.bcm.edu	37	9	103279042	103279042	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:103279042A>G	ENST00000374879.4	+	5	981	c.549A>G	c.(547-549)gcA>gcG	p.A183A	TMEFF1_ENST00000334943.6_Silent_p.A144A|MSANTD3-TMEFF1_ENST00000502978.1_Missense_Mutation_p.R147G	NM_003692.4	NP_003683.2	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 1	183					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(7)|lung(9)|stomach(1)	19		Acute lymphoblastic leukemia(62;0.0452)				ATGAAGATGCAGAAAATGTTG	0.393																																					p.A257A		Atlas-SNP	.											.	.	.	.	0			c.A771G						.						123.0	104.0	111.0					9																	103279042		2203	4300	6503	SO:0001819	synonymous_variant	100526694	exon5			AGATGCAGAAAAT	U19878	CCDS6750.1	9q31	2010-05-04			ENSG00000241697	ENSG00000241697			11866	protein-coding gene	gene with protein product	"""tomoregulin-1"", ""cancer/testis antigen family 120, member 1"""	603421		C9orf2		9730596	Standard	NM_003692		Approved	H7365, CT120.1		Q8IYR6	OTTHUMG00000020367	ENST00000374879.4:c.549A>G	chr9.hg19:g.103279042A>G		86.0	0.0		113.0	5.0	NM_001198812	Q13086|Q8N3T8	Silent	SNP	ENST00000374879.4	hg19	CCDS6750.1	.	.	.	.	.	.	.	.	.	.	A	8.992	0.977907	0.18812	.	.	ENSG00000251349	ENST00000502978	.	.	.	5.74	1.96	0.26148	.	.	.	.	.	T	0.45994	0.1370	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29731	-1.0002	4	.	.	.	-30.1287	3.3496	0.07147	0.568:0.0:0.2675:0.1644	.	.	.	.	G	147	.	.	R	+	1	2	C9orf30-TMEFF1	102318863	1.000000	0.71417	1.000000	0.80357	0.763000	0.43281	1.435000	0.34969	0.552000	0.29026	0.460000	0.39030	AGA	.	.		0.393	TMEFF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053418.1	NM_003692	
RNF20	56254	hgsc.bcm.edu	37	9	104323165	104323165	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:104323165A>G	ENST00000389120.3	+	17	2555	c.2465A>G	c.(2464-2466)gAg>gGg	p.E822G		NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	822					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		GGGGAGAAAGAGCTGGGTCTT	0.418																																					p.E822G		Atlas-SNP	.											.	RNF20	110	.	0			c.A2465G						.						83.0	85.0	84.0					9																	104323165		2203	4300	6503	SO:0001583	missense	56254	exon17			AGAAAGAGCTGGG	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"""RING-type (C3HC4) zinc fingers"""	10062	protein-coding gene	gene with protein product	"""BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"""	607699	"""ring finger protein 20"""			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.2465A>G	chr9.hg19:g.104323165A>G	ENSP00000373772:p.Glu822Gly	101.0	0.0		134.0	6.0	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	hg19	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.680329	0.88542	.	.	ENSG00000155827	ENST00000389120	T	0.38887	1.11	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.66076	0.2753	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.70230	-0.4929	10	0.66056	D	0.02	-24.4215	15.5321	0.75970	1.0:0.0:0.0:0.0	.	822	Q5VTR2	BRE1A_HUMAN	G	822	ENSP00000373772:E822G	ENSP00000373772:E822G	E	+	2	0	RNF20	103362986	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	8.962000	0.93254	2.204000	0.70986	0.528000	0.53228	GAG	.	.		0.418	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592	
RAD23B	5887	hgsc.bcm.edu	37	9	110091920	110091920	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:110091920A>G	ENST00000358015.3	+	10	1564	c.1213A>G	c.(1213-1215)Aac>Gac	p.N405D	RAD23B_ENST00000416373.2_Missense_Mutation_p.N333D	NM_001244713.1|NM_002874.4	NP_001231642.1|NP_002865.1	P54727	RD23B_HUMAN	RAD23 homolog B (S. cerevisiae)	405					DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|XPC complex (GO:0071942)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)			breast(3)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						TCTACAGCAGAACTTTGATGA	0.398								Direct reversal of damage;Nucleotide excision repair (NER)																													p.N405D		Atlas-SNP	.											.	RAD23B	31	.	0			c.A1213G						.						77.0	77.0	77.0					9																	110091920		2203	4300	6503	SO:0001583	missense	5887	exon10			CAGCAGAACTTTG		CCDS6769.1, CCDS59138.1	9q31.2	2008-07-21	2001-11-28		ENSG00000119318	ENSG00000119318			9813	protein-coding gene	gene with protein product	"""XP-C repair complementing protein"", ""XP-C repair complementing complex 58 kDa"""	600062	"""RAD23 (S. cerevisiae) homolog B"""			7851894, 8168482	Standard	NM_002874		Approved	HHR23B, P58, HR23B	uc004bde.3	P54727	OTTHUMG00000020446	ENST00000358015.3:c.1213A>G	chr9.hg19:g.110091920A>G	ENSP00000350708:p.Asn405Asp	85.0	0.0		71.0	4.0	NM_002874	B3KWK8|G5E9P0|Q7Z5K8|Q8WUB0	Missense_Mutation	SNP	ENST00000358015.3	hg19	CCDS6769.1	.	.	.	.	.	.	.	.	.	.	A	16.99	3.272855	0.59649	.	.	ENSG00000119318	ENST00000358015;ENST00000416373	T;T	0.55052	0.54;0.54	4.85	4.85	0.62838	UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.62356	0.2421	L	0.38531	1.155	0.80722	D	1	D;P	0.63880	0.993;0.609	D;B	0.70935	0.971;0.168	T	0.64106	-0.6485	10	0.51188	T	0.08	-2.3866	14.7172	0.69277	1.0:0.0:0.0:0.0	.	384;405	B7Z4W4;P54727	.;RD23B_HUMAN	D	405;333	ENSP00000350708:N405D;ENSP00000405623:N333D	ENSP00000350708:N405D	N	+	1	0	RAD23B	109131741	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.943000	0.63554	1.942000	0.56320	0.460000	0.39030	AAC	.	.		0.398	RAD23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053548.1	NM_002874	
RABGAP1	23637	hgsc.bcm.edu	37	9	125835865	125835865	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:125835865A>G	ENST00000373647.4	+	16	2152	c.2018A>G	c.(2017-2019)aAg>aGg	p.K673R	RABGAP1_ENST00000493854.1_3'UTR|RABGAP1_ENST00000373643.5_Missense_Mutation_p.K12R	NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	673	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				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						GTTCTGGTCAAGATCATGTTT	0.443																																					p.K673R		Atlas-SNP	.											.	RABGAP1	164	.	0			c.A2018G						.						173.0	164.0	167.0					9																	125835865		2203	4300	6503	SO:0001583	missense	23637	exon16			TGGTCAAGATCAT	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.2018A>G	chr9.hg19:g.125835865A>G	ENSP00000362751:p.Lys673Arg	126.0	0.0		96.0	4.0	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Missense_Mutation	SNP	ENST00000373647.4	hg19	CCDS6848.2	.	.	.	.	.	.	.	.	.	.	A	28.6	4.930181	0.92389	.	.	ENSG00000011454	ENST00000373647;ENST00000373643	T;T	0.11495	2.77;2.77	6.17	6.17	0.99709	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.12561	0.0305	L	0.37800	1.135	0.80722	D	1	B	0.31026	0.304	B	0.36244	0.22	T	0.18840	-1.0324	10	0.20046	T	0.44	-24.4333	16.8222	0.85835	1.0:0.0:0.0:0.0	.	673	Q9Y3P9	RBGP1_HUMAN	R	673;12	ENSP00000362751:K673R;ENSP00000362747:K12R	ENSP00000362747:K12R	K	+	2	0	RABGAP1	124875686	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.371000	0.80710	0.533000	0.62120	AAG	.	.		0.443	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197	
WDR38	401551	hgsc.bcm.edu	37	9	127619900	127619900	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:127619900T>C	ENST00000373574.1	+	9	992	c.936T>C	c.(934-936)ccT>ccC	p.P312P		NM_001045476.1|NM_001276374.1	NP_001038941.1|NP_001263303.1	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	312					hematopoietic progenitor cell differentiation (GO:0002244)					breast(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						CCAGGGACCCTCAAACCTAAC	0.567																																					p.P313P		Atlas-SNP	.											.	WDR38	21	.	0			c.T939C						.						63.0	69.0	67.0					9																	127619900		2135	4240	6375	SO:0001819	synonymous_variant	401551	exon9			GGACCCTCAAACC		CCDS43876.1, CCDS75898.1, CCDS75899.1	9q33.3	2013-01-09			ENSG00000136918	ENSG00000136918		"""WD repeat domain containing"""	23745	protein-coding gene	gene with protein product							Standard	NM_001276375		Approved		uc011lzo.3	Q5JTN6	OTTHUMG00000020664	ENST00000373574.1:c.936T>C	chr9.hg19:g.127619900T>C		50.0	0.0		95.0	4.0	NM_001276374	A0PK24	Silent	SNP	ENST00000373574.1	hg19	CCDS43876.1																																																																																			.	.		0.567	WDR38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054048.1	NM_001045476	
NUP214	8021	hgsc.bcm.edu	37	9	134015961	134015961	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:134015961T>C	ENST00000359428.5	+	11	1302	c.1158T>C	c.(1156-1158)gcT>gcC	p.A386A	RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|RP11-544A12.4_ENST00000588378.1_RNA|RP11-544A12.4_ENST00000587408.1_RNA|NUP214_ENST00000451030.1_Silent_p.A386A|RP11-544A12.4_ENST00000586290.1_RNA|NUP214_ENST00000411637.2_Silent_p.A386A|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	386	Seven-bladed beta propeller.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTCCTCCTGCTCCAGTTCTCA	0.393			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																p.A386A	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.T1158C						.						130.0	132.0	132.0					9																	134015961		2203	4300	6503	SO:0001819	synonymous_variant	8021	exon11			TCCTGCTCCAGTT	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.1158T>C	chr9.hg19:g.134015961T>C		88.0	0.0		112.0	5.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Silent	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	T	11.52	1.664693	0.29604	.	.	ENSG00000126883	ENST00000530863	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	T	0.59348	0.2187	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59558	-0.7432	4	.	.	.	-25.847	7.8314	0.29344	0.1356:0.0:0.1413:0.723	.	.	.	.	P	58	.	.	S	+	1	0	NUP214	133005782	0.992000	0.36948	1.000000	0.80357	0.995000	0.86356	0.143000	0.16115	2.206000	0.71126	0.533000	0.62120	TCC	.	.		0.393	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
C9orf171	389799	hgsc.bcm.edu	37	9	135374145	135374145	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:135374145C>T	ENST00000343036.2	+	3	415	c.367C>T	c.(367-369)Ctc>Ttc	p.L123F	C9orf171_ENST00000393215.3_Missense_Mutation_p.L87F|C9orf171_ENST00000393216.2_Missense_Mutation_p.L87F	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	123										large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						TAATTATGGACTCTACATCCG	0.577																																					p.L123F		Atlas-SNP	.											.	C9orf171	53	.	0			c.C367T						.						30.0	30.0	30.0					9																	135374145		2203	4300	6503	SO:0001583	missense	389799	exon3			TATGGACTCTACA	AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.367C>T	chr9.hg19:g.135374145C>T	ENSP00000343290:p.Leu123Phe	51.0	0.0		52.0	5.0	NM_207417	Q147X1	Missense_Mutation	SNP	ENST00000343036.2	hg19	CCDS6949.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.648559	0.47258	.	.	ENSG00000188523	ENST00000393215;ENST00000343036;ENST00000393216	T;T;T	0.23754	1.89;1.89;1.89	5.14	4.22	0.49857	.	0.265059	0.31507	N	0.007537	T	0.35941	0.0949	L	0.46157	1.445	0.31780	N	0.631044	P;D	0.71674	0.794;0.998	B;D	0.67548	0.31;0.952	T	0.26224	-1.0109	10	0.30854	T	0.27	.	7.5683	0.27892	0.1656:0.7478:0.0:0.0866	.	87;123	Q6ZQR2-2;Q6ZQR2	.;CI171_HUMAN	F	87;123;87	ENSP00000376908:L87F;ENSP00000343290:L123F;ENSP00000376909:L87F	ENSP00000343290:L123F	L	+	1	0	C9orf171	134363966	0.976000	0.34144	0.999000	0.59377	0.505000	0.33919	0.449000	0.21744	2.545000	0.85829	0.655000	0.94253	CTC	.	.		0.577	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417	
SDCCAG3	10807	hgsc.bcm.edu	37	9	139301956	139301956	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:139301956C>T	ENST00000357365.3	-	5	589	c.460G>A	c.(460-462)Ggg>Agg	p.G154R	SDCCAG3_ENST00000371725.3_Missense_Mutation_p.G81R|SDCCAG3_ENST00000298537.7_Missense_Mutation_p.G131R|SDCCAG3_ENST00000461693.1_5'Flank	NM_001039707.1	NP_001034796.1	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	154						cytoplasm (GO:0005737)				NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	16		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)		AGGCCATACCCGCCGGTTTGG	0.537																																					p.G154R		Atlas-SNP	.											.	SDCCAG3	41	.	0			c.G460A						.						24.0	30.0	28.0					9																	139301956		1887	4104	5991	SO:0001583	missense	10807	exon5			CATACCCGCCGGT	AF039688	CCDS6999.2, CCDS43903.1, CCDS43904.1	9q34.3	2010-10-27			ENSG00000165689	ENSG00000165689			10667	protein-coding gene	gene with protein product						9610721	Standard	XM_005266050		Approved	NY-CO-3	uc004chi.3	Q96C92	OTTHUMG00000020928	ENST00000357365.3:c.460G>A	chr9.hg19:g.139301956C>T	ENSP00000349929:p.Gly154Arg	50.0	0.0		72.0	4.0	NM_001039707	A6NCP1|O60525|Q5SXN1|Q5SXN2|Q5SXN3|Q5SXN4|Q5SXN8|Q6V704|Q9NVY5	Missense_Mutation	SNP	ENST00000357365.3	hg19	CCDS43904.1	.	.	.	.	.	.	.	.	.	.	C	8.678	0.904540	0.17760	.	.	ENSG00000165689	ENST00000357365;ENST00000298537;ENST00000371725;ENST00000371723	T;T;T;T	0.34072	2.46;2.53;2.52;1.38	5.27	4.36	0.52297	.	0.059281	0.64402	D	0.000004	T	0.34948	0.0915	L	0.56769	1.78	0.09310	N	1	B;P;B	0.35600	0.324;0.511;0.324	B;B;B	0.35770	0.119;0.21;0.158	T	0.39941	-0.9589	10	0.66056	D	0.02	-14.9586	11.2499	0.49020	0.0:0.9119:0.0:0.0881	.	81;131;154	Q96C92-4;Q96C92-2;Q96C92	.;.;SDCG3_HUMAN	R	154;131;81;104	ENSP00000349929:G154R;ENSP00000298537:G131R;ENSP00000360790:G81R;ENSP00000360788:G104R	ENSP00000298537:G131R	G	-	1	0	SDCCAG3	138421777	0.031000	0.19500	0.126000	0.21872	0.026000	0.11368	2.663000	0.46774	2.454000	0.82982	0.650000	0.86243	GGG	.	.		0.537	SDCCAG3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055060.2	NM_006643	
ABCA2	20	hgsc.bcm.edu	37	9	139906582	139906582	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:139906582T>C	ENST00000371605.3	-	33	5476	c.5329A>G	c.(5329-5331)Acc>Gcc	p.T1777A	ABCA2_ENST00000341511.6_Missense_Mutation_p.T1778A|ABCA2_ENST00000265662.5_Missense_Mutation_p.T1778A			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1777					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CTGGCGCTGGTCTTATTCATG	0.692																																					p.T1808A		Atlas-SNP	.											.	ABCA2	113	.	0			c.A5422G						.						88.0	90.0	89.0					9																	139906582		2021	4172	6193	SO:0001583	missense	20	exon34			CGCTGGTCTTATT	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"""ATP binding cassette transporters / subfamily A"""	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.5329A>G	chr9.hg19:g.139906582T>C	ENSP00000360666:p.Thr1777Ala	56.0	0.0		83.0	6.0	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Missense_Mutation	SNP	ENST00000371605.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.52|14.52	2.561208|2.561208	0.45590|0.45590	.|.	.|.	ENSG00000107331|ENSG00000107331	ENST00000477420|ENST00000265662;ENST00000371605;ENST00000355090;ENST00000341511	.|D;D;D	.|0.87887	.|-2.31;-2.31;-2.31	4.31|4.31	4.31|4.31	0.51392|0.51392	.|.	.|0.332898	.|0.33813	.|N	.|0.004537	D|D	0.86301|0.86301	0.5900|0.5900	M|M	0.68317|0.68317	2.08|2.08	0.58432|0.58432	D|D	0.999996|0.999996	.|P;P	.|0.45634	.|0.773;0.863	.|B;B	.|0.42495	.|0.389;0.389	D|D	0.88115|0.88115	0.2828|0.2828	5|10	.|0.72032	.|D	.|0.01	.|.	13.2697|13.2697	0.60153|0.60153	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1777;1808	.|Q9BZC7;E7ETC3	.|ABCA2_HUMAN;.	G|A	189|1778;1777;1808;1778	.|ENSP00000265662:T1778A;ENSP00000360666:T1777A;ENSP00000344155:T1778A	.|ENSP00000265662:T1778A	D|T	-|-	2|1	0|0	ABCA2|ABCA2	139026403|139026403	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.183000|0.183000	0.23260|0.23260	5.318000|5.318000	0.65829|0.65829	1.807000|1.807000	0.52817|0.52817	0.254000|0.254000	0.18369|0.18369	GAC|ACC	.	.		0.692	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606	
CACNA1B	774	hgsc.bcm.edu	37	9	140772543	140772543	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:140772543C>T	ENST00000371372.1	+	1	303	c.158C>T	c.(157-159)gCg>gTg	p.A53V	CACNA1B_ENST00000277551.2_Missense_Mutation_p.A53V|RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000371363.1_Missense_Mutation_p.A53V|CACNA1B_ENST00000371355.4_Missense_Mutation_p.A53V|CACNA1B_ENST00000371357.1_Missense_Mutation_p.A53V|CACNA1B_ENST00000277549.5_5'UTR	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	53					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GCGCAGCGCGCGCGGACCATG	0.721																																					p.A53V		Atlas-SNP	.											.	CACNA1B	266	.	0			c.C158T						.						24.0	28.0	27.0					9																	140772543		2013	4175	6188	SO:0001583	missense	774	exon1			AGCGCGCGCGGAC	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.158C>T	chr9.hg19:g.140772543C>T	ENSP00000360423:p.Ala53Val	99.0	0.0		170.0	75.0	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708039	0.89018	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.97404	-4.36;-4.37;-4.32;-4.34;-4.35	3.46	3.46	0.39613	.	0.000000	0.64402	U	0.000003	D	0.96219	0.8767	M	0.83953	2.67	0.80722	D	1	B	0.24533	0.105	B	0.11329	0.006	D	0.95823	0.8851	10	0.87932	D	0	.	13.975	0.64268	0.0:1.0:0.0:0.0	.	53	B1AQK6	.	V	53	ENSP00000360423:A53V;ENSP00000277551:A53V;ENSP00000360414:A53V;ENSP00000360408:A53V;ENSP00000360406:A53V	ENSP00000277551:A53V	A	+	2	0	CACNA1B	139892364	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.994000	0.63901	1.497000	0.48584	0.298000	0.19748	GCG	.	.		0.721	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
FAM208B	54906	hgsc.bcm.edu	37	10	5803302	5803302	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:5803302A>G	ENST00000328090.5	+	19	7667	c.7042A>G	c.(7042-7044)Agt>Ggt	p.S2348G		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	2348																	GTCATTTCAGAGTGCAAATAT	0.328																																					p.S2348G		Atlas-SNP	.											.	.	.	.	0			c.A7042G						.						118.0	111.0	113.0					10																	5803302		1877	4113	5990	SO:0001583	missense	54906	exon19			TTTCAGAGTGCAA	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.7042A>G	chr10.hg19:g.5803302A>G	ENSP00000328426:p.Ser2348Gly	127.0	0.0		113.0	5.0	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	hg19	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	A	7.721	0.697098	0.15106	.	.	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.42131	0.98	6.06	2.48	0.30137	.	0.223507	0.40908	N	0.000991	T	0.28034	0.0691	L	0.41027	1.25	0.26465	N	0.975389	B	0.14012	0.009	B	0.14578	0.011	T	0.13710	-1.0499	10	0.30854	T	0.27	.	4.5273	0.11988	0.5083:0.1643:0.3274:0.0	.	2348	Q5VWN6	F208B_HUMAN	G	2348;1543	ENSP00000328426:S2348G	ENSP00000328426:S2348G	S	+	1	0	C10orf18	5843308	1.000000	0.71417	0.994000	0.49952	0.207000	0.24258	2.952000	0.49097	0.514000	0.28300	-0.256000	0.11100	AGT	.	.		0.328	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
TAF3	83860	hgsc.bcm.edu	37	10	8007022	8007022	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:8007022T>C	ENST00000344293.5	+	3	1755	c.1549T>C	c.(1549-1551)Tcc>Ccc	p.S517P		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	517	Lys-rich.				maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						CAAGCTGCCTTCCTCCGTGGA	0.433																																					p.S517P		Atlas-SNP	.											.	TAF3	93	.	0			c.T1549C						.						73.0	69.0	70.0					10																	8007022		1854	4100	5954	SO:0001583	missense	83860	exon3			CTGCCTTCCTCCG	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"""Zinc fingers, PHD-type"""	17303	protein-coding gene	gene with protein product		606576	"""TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"""			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.1549T>C	chr10.hg19:g.8007022T>C	ENSP00000340271:p.Ser517Pro	82.0	0.0		85.0	4.0	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	hg19	CCDS41487.1	.	.	.	.	.	.	.	.	.	.	T	0.779	-0.763054	0.02996	.	.	ENSG00000165632	ENST00000344293	T	0.19669	2.13	5.82	0.777	0.18538	.	0.449719	0.20668	N	0.087889	T	0.10723	0.0262	L	0.28504	0.86	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.27088	-1.0084	10	0.19147	T	0.46	-1.1284	2.9263	0.05785	0.1143:0.1303:0.1274:0.6279	.	517	Q5VWG9	TAF3_HUMAN	P	517	ENSP00000340271:S517P	ENSP00000340271:S517P	S	+	1	0	TAF3	8047028	0.254000	0.23992	0.000000	0.03702	0.147000	0.21601	0.768000	0.26590	0.100000	0.17581	-0.341000	0.08007	TCC	.	.		0.433	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923	
TAF3	83860	hgsc.bcm.edu	37	10	8007368	8007368	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:8007368A>G	ENST00000344293.5	+	3	2101	c.1895A>G	c.(1894-1896)aAg>aGg	p.K632R		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	632	Lys-rich.				maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						gataaagataagagagagaaa	0.423																																					p.K632R		Atlas-SNP	.											TAF3,NS,carcinoma,0,1	TAF3	93	.	0			c.A1895G						.						44.0	47.0	46.0					10																	8007368		1855	4095	5950	SO:0001583	missense	83860	exon3			AAGATAAGAGAGA	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"""Zinc fingers, PHD-type"""	17303	protein-coding gene	gene with protein product		606576	"""TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"""			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.1895A>G	chr10.hg19:g.8007368A>G	ENSP00000340271:p.Lys632Arg	28.0	0.0		37.0	2.0	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	hg19	CCDS41487.1	.	.	.	.	.	.	.	.	.	.	A	18.30	3.592708	0.66219	.	.	ENSG00000165632	ENST00000344293	T	0.23552	1.9	5.82	4.68	0.58851	.	0.093307	0.44483	N	0.000459	T	0.30759	0.0775	M	0.80183	2.485	0.58432	D	0.999995	B	0.25390	0.125	B	0.24848	0.056	T	0.06338	-1.0832	10	0.22109	T	0.4	-18.2116	11.3896	0.49806	0.9288:0.0:0.0712:0.0	.	632	Q5VWG9	TAF3_HUMAN	R	632	ENSP00000340271:K632R	ENSP00000340271:K632R	K	+	2	0	TAF3	8047374	1.000000	0.71417	0.737000	0.30932	0.903000	0.53119	6.895000	0.75660	1.034000	0.39945	0.528000	0.53228	AAG	.	.		0.423	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923	
OPTN	10133	hgsc.bcm.edu	37	10	13152401	13152401	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:13152401G>A	ENST00000378748.3	+	5	656	c.294G>A	c.(292-294)atG>atA	p.M98I	OPTN_ENST00000378764.2_Missense_Mutation_p.M98I|OPTN_ENST00000378747.3_Missense_Mutation_p.M98I|OPTN_ENST00000378752.3_Missense_Mutation_p.M98I|OPTN_ENST00000378757.2_Missense_Mutation_p.M98I|OPTN_ENST00000482140.1_Intron|OPTN_ENST00000263036.5_Missense_Mutation_p.M98I	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	98	Interaction with Rab8.		M -> K (may modify intraocular pressure and increase risk of GLC1E and NPG, induces TFRC degradation leading to autophagic death in retinal ganglion cells; may be a common polymorphism; dbSNP:rs11258194). {ECO:0000269|PubMed:11834836, ECO:0000269|PubMed:14627677, ECO:0000269|PubMed:15498064, ECO:0000269|PubMed:15557444}.		cell death (GO:0008219)|defense response to Gram-negative bacterium (GO:0050829)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi organization (GO:0007030)|Golgi ribbon formation (GO:0090161)|Golgi to plasma membrane protein transport (GO:0043001)|macroautophagy (GO:0016236)|mitotic cell cycle (GO:0000278)|negative regulation of receptor recycling (GO:0001920)|protein targeting to Golgi (GO:0000042)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	polyubiquitin binding (GO:0031593)|protein C-terminus binding (GO:0008022)|Rab GTPase binding (GO:0017137)	p.M98I(1)		breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22						AGCGTCTAATGGCCTTGAGTC	0.438																																					p.M98I		Atlas-SNP	.											OPTN,NS,carcinoma,0,1	OPTN	57	.	1	Substitution - Missense(1)	lung(1)	c.G294A						.						105.0	118.0	113.0					10																	13152401		2203	4300	6503	SO:0001583	missense	10133	exon4			TCTAATGGCCTTG	AF420371	CCDS7094.1	10p14	2014-01-28	2003-09-08		ENSG00000123240	ENSG00000123240			17142	protein-coding gene	gene with protein product		602432	"""glaucoma 1, open angle, E (adult-onset)"""	GLC1E		11834836, 9488477	Standard	NM_001008211		Approved	FIP2, HYPL, FIP-2, TFIIIA-INTP, NRP, HIP7	uc001ilx.1	Q96CV9	OTTHUMG00000017690	ENST00000378748.3:c.294G>A	chr10.hg19:g.13152401G>A	ENSP00000368022:p.Met98Ile	149.0	0.0		155.0	0.0	NM_001008212	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Missense_Mutation	SNP	ENST00000378748.3	hg19	CCDS7094.1	.	.	.	.	.	.	.	.	.	.	G	10.29	1.308852	0.23821	.	.	ENSG00000123240	ENST00000263036;ENST00000378764;ENST00000378757;ENST00000378752;ENST00000378748;ENST00000430081;ENST00000378747	D;D;D;D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58	5.98	1.37	0.22104	NF-kappa-B essential modulator NEMO, N-terminal (1);	0.586858	0.21037	N	0.081226	T	0.63861	0.2547	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.11329	0.004;0.006	T	0.53802	-0.8387	10	0.38643	T	0.18	-3.4751	8.4113	0.32644	0.5199:0.0:0.4801:0.0	.	98;98	Q96CV9-2;Q96CV9	.;OPTN_HUMAN	I	98;98;98;98;98;41;98	ENSP00000263036:M98I;ENSP00000368040:M98I;ENSP00000368032:M98I;ENSP00000368027:M98I;ENSP00000368022:M98I;ENSP00000414747:M41I;ENSP00000368021:M98I	ENSP00000263036:M98I	M	+	3	0	OPTN	13192407	0.000000	0.05858	0.644000	0.29465	0.643000	0.38383	-0.333000	0.07894	0.376000	0.24707	0.655000	0.94253	ATG	.	.		0.438	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980	
FRMD4A	55691	hgsc.bcm.edu	37	10	13838525	13838525	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:13838525T>C	ENST00000357447.2	-	5	638	c.270A>G	c.(268-270)tcA>tcG	p.S90S	FRMD4A_ENST00000358621.4_Silent_p.S75S|FRMD4A_ENST00000378503.1_Silent_p.S90S|FRMD4A_ENST00000342409.2_Silent_p.S106S	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	90	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)				breast(4)|endometrium(9)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	41						CCACGGGTCCTGACTTTTTAG	0.428																																					p.S90S		Atlas-SNP	.											.	FRMD4A	108	.	0			c.A270G						.						150.0	148.0	149.0					10																	13838525		2203	4300	6503	SO:0001819	synonymous_variant	55691	exon5			GGGTCCTGACTTT	AB037715	CCDS7101.1	10p14	2004-07-15	2004-07-15	2004-07-15	ENSG00000151474	ENSG00000151474			25491	protein-coding gene	gene with protein product			"""FERM domain containing 4"""	FRMD4		10718198	Standard	NM_018027		Approved	FLJ10210, KIAA1294, bA295P9.4	uc001ims.3	Q9P2Q2	OTTHUMG00000017708	ENST00000357447.2:c.270A>G	chr10.hg19:g.13838525T>C		64.0	0.0		84.0	4.0	NM_018027	A7E2Y3|Q5T377	Silent	SNP	ENST00000357447.2	hg19	CCDS7101.1																																																																																			.	.		0.428	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027	
NSUN6	221078	hgsc.bcm.edu	37	10	18837156	18837156	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:18837156A>G	ENST00000377304.4	-	10	1500	c.1082T>C	c.(1081-1083)cTg>cCg	p.L361P	NSUN6_ENST00000493816.1_5'UTR|RP11-499P20.2_ENST00000425669.1_RNA	NM_182543.2	NP_872349.1	Q8TEA1	NSUN6_HUMAN	NOP2/Sun domain family, member 6	361							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15						TGGCTTCAGCAGCTGAACCGC	0.433																																					p.L361P		Atlas-SNP	.											.	NSUN6	46	.	0			c.T1082C						.						61.0	57.0	58.0					10																	18837156		2203	4300	6503	SO:0001583	missense	221078	exon10			TTCAGCAGCTGAA	BC035778	CCDS7130.1	10p13	2014-06-23	2009-11-23	2004-08-26	ENSG00000241058	ENSG00000241058		"""NOP2/Sun domain containing"""	23529	protein-coding gene	gene with protein product			"""NOL1/NOP2/Sun domain family 6"", ""NOL1/NOP2/Sun domain family, member 6"", ""ARL5B antisense RNA 1"""	NOPD1, ARL5B-AS1			Standard	XM_005252394		Approved	FLJ23743	uc010qcp.1	Q8TEA1	OTTHUMG00000017767	ENST00000377304.4:c.1082T>C	chr10.hg19:g.18837156A>G	ENSP00000366519:p.Leu361Pro	105.0	0.0		92.0	4.0	NM_182543	B0YJ54	Missense_Mutation	SNP	ENST00000377304.4	hg19	CCDS7130.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.516697	0.85495	.	.	ENSG00000241058	ENST00000377304	T	0.26223	1.75	5.87	5.87	0.94306	Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p (1);	0.000000	0.85682	D	0.000000	T	0.64659	0.2618	H	0.95365	3.66	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.76049	-0.3101	10	0.66056	D	0.02	.	16.2813	0.82687	1.0:0.0:0.0:0.0	.	361	Q8TEA1	NSUN6_HUMAN	P	361	ENSP00000366519:L361P	ENSP00000366519:L361P	L	-	2	0	NSUN6	18877162	1.000000	0.71417	0.975000	0.42487	0.991000	0.79684	8.737000	0.91562	2.244000	0.73946	0.533000	0.62120	CTG	.	.		0.433	NSUN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047083.1	NM_182543	
MYO3A	53904	hgsc.bcm.edu	37	10	26462846	26462846	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:26462846T>C	ENST00000265944.5	+	30	3819	c.3653T>C	c.(3652-3654)gTc>gCc	p.V1218A	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1218					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CAGAAGTCTGTCAAAGACCTG	0.413																																					p.V1218A		Atlas-SNP	.											.	MYO3A	371	.	0			c.T3653C						.						96.0	99.0	98.0					10																	26462846		2203	4300	6503	SO:0001583	missense	53904	exon30			AGTCTGTCAAAGA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3653T>C	chr10.hg19:g.26462846T>C	ENSP00000265944:p.Val1218Ala	90.0	0.0		106.0	5.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	T	3.997	-0.003383	0.07773	.	.	ENSG00000095777	ENST00000265944	T	0.77098	-1.07	5.18	-1.67	0.08238	.	1.632550	0.02541	N	0.094604	T	0.54224	0.1845	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.44081	-0.9351	10	0.07644	T	0.81	.	1.2475	0.01975	0.304:0.1362:0.1072:0.4527	.	1218	Q8NEV4	MYO3A_HUMAN	A	1218	ENSP00000265944:V1218A	ENSP00000265944:V1218A	V	+	2	0	MYO3A	26502852	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.373000	0.07494	0.058000	0.16222	-0.301000	0.09380	GTC	.	.		0.413	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
SVIL	6840	hgsc.bcm.edu	37	10	29839664	29839664	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:29839664A>G	ENST00000355867.4	-	6	1441	c.689T>C	c.(688-690)tTc>tCc	p.F230S	SVIL_ENST00000375400.3_Missense_Mutation_p.F230S|SVIL_ENST00000375398.2_Missense_Mutation_p.F230S	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	230					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				AGAGAAAGAGAAGGTCGAGGA	0.627																																					p.F230S		Atlas-SNP	.											.	SVIL	226	.	0			c.T689C						.						76.0	77.0	77.0					10																	29839664		2203	4300	6503	SO:0001583	missense	6840	exon8			AAAGAGAAGGTCG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.689T>C	chr10.hg19:g.29839664A>G	ENSP00000348128:p.Phe230Ser	70.0	0.0		81.0	5.0	NM_003174	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	A	9.667	1.145566	0.21288	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.50277	0.75;0.75;0.75	5.35	1.71	0.24356	.	0.674623	0.16241	N	0.223158	T	0.40040	0.1101	M	0.64997	1.995	0.80722	D	1	B;B	0.20887	0.013;0.049	B;B	0.19666	0.022;0.026	T	0.11227	-1.0596	9	.	.	.	-1.7418	6.397	0.21618	0.7264:0.1332:0.1404:0.0	.	230;230	O95425-2;O95425	.;SVIL_HUMAN	S	230	ENSP00000364549:F230S;ENSP00000364547:F230S;ENSP00000348128:F230S	.	F	-	2	0	SVIL	29879670	0.895000	0.30542	0.033000	0.17914	0.035000	0.12851	1.543000	0.36147	0.040000	0.15660	0.533000	0.62120	TTC	.	.		0.627	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
EGR2	1959	hgsc.bcm.edu	37	10	64573486	64573486	+	Silent	SNP	G	G	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:64573486G>T	ENST00000242480.3	-	2	1237	c.912C>A	c.(910-912)gcC>gcA	p.A304A	EGR2_ENST00000411732.1_Silent_p.A254A|EGR2_ENST00000439032.1_Silent_p.A304A|EGR2_ENST00000493899.2_5'Flank	NM_000399.3|NM_001136177.1	NP_000390.2|NP_001129649.1	P11161	EGR2_HUMAN	early growth response 2	304	Poly-Ala.				brain development (GO:0007420)|brain segmentation (GO:0035284)|cell death (GO:0008219)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|facial nerve structural organization (GO:0021612)|fat cell differentiation (GO:0045444)|learning or memory (GO:0007611)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein sumoylation (GO:0016925)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ossification (GO:0030278)|response to insulin (GO:0032868)|rhombomere 3 formation (GO:0021660)|rhombomere 5 formation (GO:0021666)|rhythmic behavior (GO:0007622)|Schwann cell differentiation (GO:0014037)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	36	Prostate(12;0.0297)|all_hematologic(501;0.228)					CGGCGGCGGCGGCTGCTGCTG	0.697																																					p.A304A		Atlas-SNP	.											EGR2,colon,carcinoma,0,4	EGR2	77	.	0			c.C912A						.						9.0	12.0	11.0					10																	64573486		2044	4120	6164	SO:0001819	synonymous_variant	1959	exon2			GGCGGCGGCTGCT	BC035625	CCDS7267.1, CCDS44409.1	10q21.1	2014-09-17	2009-04-23		ENSG00000122877	ENSG00000122877		"""Zinc fingers, C2H2-type"""	3239	protein-coding gene	gene with protein product	"""Krox-20 homolog, Drosophila"""	129010	"""early growth response 2 (Krox-20 homolog, Drosophila)"""	KROX20			Standard	NM_000399		Approved		uc001jmi.3	P11161	OTTHUMG00000018308	ENST00000242480.3:c.912C>A	chr10.hg19:g.64573486G>T		33.0	0.0		60.0	3.0	NM_000399	B2R724|B3KRD7|Q68CZ5|Q8IV26|Q9UNA6	Silent	SNP	ENST00000242480.3	hg19	CCDS7267.1	.	.	.	.	.	.	.	.	.	.	g	0.001	-3.014627	0.00042	.	.	ENSG00000122877	ENST00000432380	.	.	.	0.361	-0.721	0.11189	.	.	.	.	.	T	0.26268	0.0641	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.30060	-0.9991	4	0.87932	D	0	-4.9521	.	.	.	.	.	.	.	Q	245	.	ENSP00000410985:P245Q	P	-	2	0	EGR2	64243492	0.326000	0.24669	0.000000	0.03702	0.001000	0.01503	0.923000	0.28757	-3.054000	0.00259	-3.099000	0.00064	CCG	.	.		0.697	EGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048245.2	NM_000399	
JMJD1C	221037	hgsc.bcm.edu	37	10	64967219	64967219	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:64967219C>T	ENST00000399262.2	-	10	4428	c.4210G>A	c.(4210-4212)Gat>Aat	p.D1404N	JMJD1C_ENST00000399251.1_Missense_Mutation_p.D1185N|JMJD1C_ENST00000402544.1_Missense_Mutation_p.D1185N|JMJD1C_ENST00000542921.1_Missense_Mutation_p.D1222N	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1404					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					CTGGTAGTATCGGCAGCAGAT	0.418																																					p.D1404N		Atlas-SNP	.											.	JMJD1C	347	.	0			c.G4210A						.						125.0	123.0	124.0					10																	64967219		1923	4129	6052	SO:0001583	missense	221037	exon10			TAGTATCGGCAGC	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.4210G>A	chr10.hg19:g.64967219C>T	ENSP00000382204:p.Asp1404Asn	113.0	0.0		100.0	4.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	C	6.132	0.392627	0.11638	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T;T;T;T	0.52754	1.0;0.65;2.57;1.0	5.72	1.98	0.26296	.	0.606592	0.18492	N	0.139603	T	0.19604	0.0471	N	0.08118	0	0.21290	N	0.999736	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.04013	0.001;0.001;0.001	T	0.17806	-1.0357	10	0.11794	T	0.64	-1.5356	2.8573	0.05576	0.2438:0.069:0.1268:0.5604	.	945;1404;1222	A6PW35;Q15652;A0T124	.;JHD2C_HUMAN;.	N	1404;1185;1185;1222	ENSP00000382204:D1404N;ENSP00000384990:D1185N;ENSP00000382195:D1185N;ENSP00000444682:D1222N	ENSP00000382195:D1185N	D	-	1	0	JMJD1C	64637225	0.000000	0.05858	0.995000	0.50966	0.582000	0.36321	-0.354000	0.07681	0.070000	0.16634	-0.469000	0.05056	GAT	.	.		0.418	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
PPA1	5464	hgsc.bcm.edu	37	10	71969413	71969413	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	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		211.0	0.0		238.0	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	
PLA2G12B	84647	hgsc.bcm.edu	37	10	74702445	74702445	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:74702445C>A	ENST00000373032.3	-	2	357	c.265G>T	c.(265-267)Ggc>Tgc	p.G89C		NM_032562.2	NP_115951.2	Q9BX93	PG12B_HUMAN	phospholipase A2, group XIIB	89					cholesterol homeostasis (GO:0042632)|lipid catabolic process (GO:0016042)|triglyceride homeostasis (GO:0070328)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(2)|skin(2)	9	Prostate(51;0.0198)					AAATAGGAGCCGCAGCCATTG	0.468																																					p.G89C		Atlas-SNP	.											.	PLA2G12B	19	.	0			c.G265T						.						49.0	49.0	49.0					10																	74702445		2203	4300	6503	SO:0001583	missense	84647	exon2			AGGAGCCGCAGCC	AF349540	CCDS7319.1	10q22.1	2008-09-19	2004-01-13	2004-01-14	ENSG00000138308	ENSG00000138308	3.1.1.4		18555	protein-coding gene	gene with protein product		611653	"""phospholipase A2, group XIII"""	PLA2G13			Standard	NM_032562		Approved		uc001jtf.1	Q9BX93	OTTHUMG00000018446	ENST00000373032.3:c.265G>T	chr10.hg19:g.74702445C>A	ENSP00000362123:p.Gly89Cys	58.0	0.0		61.0	27.0	NM_032562	B7ZL23|Q52LB2|Q96Q99	Missense_Mutation	SNP	ENST00000373032.3	hg19	CCDS7319.1	.	.	.	.	.	.	.	.	.	.	C	18.31	3.595133	0.66219	.	.	ENSG00000138308	ENST00000373032	.	.	.	5.17	1.18	0.20946	Phospholipase A2 (1);	0.114987	0.85682	D	0.000000	T	0.58424	0.2121	L	0.56280	1.765	0.36214	D	0.851564	P;D	0.55172	0.949;0.97	P;P	0.57846	0.828;0.776	T	0.64525	-0.6387	9	0.87932	D	0	-8.8295	9.261	0.37612	0.0:0.2118:0.0:0.7882	.	89;89	B7ZL23;Q9BX93	.;PG12B_HUMAN	C	89	.	ENSP00000362123:G89C	G	-	1	0	PLA2G12B	74372451	1.000000	0.71417	0.999000	0.59377	0.936000	0.57629	1.490000	0.35573	0.046000	0.15833	-0.459000	0.05422	GGC	.	.		0.468	PLA2G12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048598.1	NM_032562	
ZMIZ1	57178	hgsc.bcm.edu	37	10	81058316	81058316	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:81058316A>G	ENST00000334512.5	+	15	2217	c.1645A>G	c.(1645-1647)Agc>Ggc	p.S549G		NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	549	Pro-rich.				artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			GCCAAATATGAGCGCTCTGCC	0.672																																					p.S549G		Atlas-SNP	.											ZMIZ1,right_upper_lobe,carcinoma,0,1	ZMIZ1	101	.	0			c.A1645G						.						95.0	95.0	95.0					10																	81058316		2203	4300	6503	SO:0001583	missense	57178	exon15			AATATGAGCGCTC	AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"""Zinc fingers, MIZ-type"""	16493	protein-coding gene	gene with protein product		607159	"""retinoic acid induced 17"""	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.1645A>G	chr10.hg19:g.81058316A>G	ENSP00000334474:p.Ser549Gly	73.0	0.0		77.0	4.0	NM_020338	Q5JSH9|Q7Z7E6	Missense_Mutation	SNP	ENST00000334512.5	hg19	CCDS7357.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.451507	0.63290	.	.	ENSG00000108175	ENST00000334512;ENST00000360331;ENST00000372347	T	0.49139	0.79	5.12	5.12	0.69794	.	0.130904	0.33309	N	0.005050	T	0.43787	0.1263	L	0.51422	1.61	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.30650	-0.9971	10	0.37606	T	0.19	-22.1592	14.9189	0.70818	1.0:0.0:0.0:0.0	.	549	Q9ULJ6	ZMIZ1_HUMAN	G	549;479;456	ENSP00000334474:S549G	ENSP00000334474:S549G	S	+	1	0	ZMIZ1	80728322	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	8.882000	0.92420	1.936000	0.56123	0.379000	0.24179	AGC	.	.		0.672	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338	
PCGF5	84333	hgsc.bcm.edu	37	10	93000241	93000241	+	Splice_Site	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:93000241T>C	ENST00000336126.5	+	3	345	c.113T>C	c.(112-114)tTc>tCc	p.F38S	PCGF5_ENST00000543648.1_Splice_Site_p.F38S	NM_001257101.1|NM_032373.4	NP_001244030.1|NP_115749.2	Q86SE9	PCGF5_HUMAN	polycomb group ring finger 5	38					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)	zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)	12						TTCTTCTTAGTCTGTAAGACT	0.348																																					p.F38S	Colon(178;732 2696 46441 50370)	Atlas-SNP	.											.	PCGF5	29	.	0			c.T113C						.						125.0	133.0	131.0					10																	93000241		2203	4300	6503	SO:0001630	splice_region_variant	84333	exon3			TCTTAGTCTGTAA	AL832003	CCDS7413.1	10q23.33	2013-01-09	2005-01-17	2005-01-19	ENSG00000180628	ENSG00000180628		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	28264	protein-coding gene	gene with protein product			"""ring finger protein (C3HC4 type) 159"""	RNF159		8076819	Standard	NM_001256549		Approved	MGC16202	uc001khh.4	Q86SE9	OTTHUMG00000018740	ENST00000336126.5:c.113-1T>C	chr10.hg19:g.93000241T>C		76.0	0.0		58.0	4.0	NM_001256549	B7Z892|D3DR33|Q6PK47|Q86TD0	Missense_Mutation	SNP	ENST00000336126.5	hg19	CCDS7413.1	.	.	.	.	.	.	.	.	.	.	T	18.97	3.735227	0.69189	.	.	ENSG00000180628	ENST00000543648;ENST00000336126	T;T	0.33865	1.39;1.39	6.0	6.0	0.97389	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type, conserved site (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	T	0.62490	0.2432	H	0.98866	4.355	0.80722	D	1	B	0.18968	0.032	B	0.26614	0.071	T	0.68945	-0.5275	9	.	.	.	.	16.5561	0.84485	0.0:0.0:0.0:1.0	.	38	Q86SE9	PCGF5_HUMAN	S	38	ENSP00000445704:F38S;ENSP00000337500:F38S	.	F	+	2	0	PCGF5	92990221	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.951000	0.87819	2.310000	0.77875	0.451000	0.29950	TTC	.	.		0.348	PCGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049363.1	NM_032373	Missense_Mutation
ARHGAP19	84986	hgsc.bcm.edu	37	10	99025639	99025639	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:99025639A>G	ENST00000358531.4	-	2	328	c.300T>C	c.(298-300)tcT>tcC	p.S100S	ARHGAP19_ENST00000371027.1_Silent_p.S91S|ARHGAP19-SLIT1_ENST00000316676.8_Silent_p.S100S|ARHGAP19_ENST00000355366.5_Silent_p.S91S|ARHGAP19-SLIT1_ENST00000358308.3_Silent_p.S100S|ARHGAP19-SLIT1_ENST00000453547.2_Silent_p.S100S	NM_001204300.1|NM_032900.5	NP_001191229.1|NP_116289.4	Q14CB8	RHG19_HUMAN	Rho GTPase activating protein 19	100					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|urinary_tract(1)	13		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)		GAGACATGAGAGACCGGAAGA	0.557																																					p.S100S		Atlas-SNP	.											.	ARHGAP19	72	.	0			c.T300C						.						92.0	88.0	89.0					10																	99025639		2203	4300	6503	SO:0001819	synonymous_variant	84986	exon2			CATGAGAGACCGG	AK074122	CCDS7454.2, CCDS58092.1, CCDS73175.1	10q24.2	2011-06-29			ENSG00000213390	ENSG00000213390		"""Rho GTPase activating proteins"""	23724	protein-coding gene	gene with protein product		611587					Standard	NM_032900		Approved	FLJ00194, MGC14258	uc001knb.3	Q14CB8	OTTHUMG00000018845	ENST00000358531.4:c.300T>C	chr10.hg19:g.99025639A>G		62.0	0.0		84.0	4.0	NM_001204300	A1XCP1|B4DZR1|Q14CF2|Q5J8M2|Q5T460|Q5T462|Q68DG6|Q8N9X1|Q8NF34|Q8TEK1	Silent	SNP	ENST00000358531.4	hg19	CCDS7454.2																																																																																			.	.		0.557	ARHGAP19-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049647.2	NM_032900	
SEC31B	25956	hgsc.bcm.edu	37	10	102275905	102275905	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:102275905T>C	ENST00000370345.3	-	3	248	c.151A>G	c.(151-153)Agg>Ggg	p.R51G	SEC31B_ENST00000451524.1_Missense_Mutation_p.R51G|SEC31B_ENST00000370329.5_Missense_Mutation_p.R51G|NDUFB8_ENST00000557395.1_3'UTR|NDUFB8_ENST00000531258.1_3'UTR|SEC31B_ENST00000535773.1_5'UTR	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	51					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)		GAAGGGTCCCTGAAATCAACC	0.458																																					p.R51G		Atlas-SNP	.											.	SEC31B	84	.	0			c.A151G						.						93.0	88.0	89.0					10																	102275905		2203	4300	6503	SO:0001583	missense	25956	exon3			GGTCCCTGAAATC	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.151A>G	chr10.hg19:g.102275905T>C	ENSP00000359370:p.Arg51Gly	116.0	0.0		91.0	4.0	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	hg19	CCDS7495.1	.	.	.	.	.	.	.	.	.	.	T	12.44	1.938920	0.34189	.	.	ENSG00000075826	ENST00000370345;ENST00000451524;ENST00000370329	T;T;T	0.57595	0.76;0.39;0.49	5.89	3.53	0.40419	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.215458	0.49916	D	0.000121	T	0.32376	0.0827	N	0.19112	0.55	0.80722	D	1	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.001;0.001	T	0.06643	-1.0815	10	0.33141	T	0.24	-12.9283	5.7669	0.18231	0.0:0.1432:0.1424:0.7144	.	51;51;51;51	B4DGE3;Q9NQW1-5;E9PKR7;Q9NQW1	.;.;.;SC31B_HUMAN	G	51	ENSP00000359370:R51G;ENSP00000391178:R51G;ENSP00000359354:R51G	ENSP00000359354:R51G	R	-	1	2	SEC31B	102265895	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.025000	0.30090	0.473000	0.27368	0.454000	0.30748	AGG	.	.		0.458	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
PDZD7	79955	hgsc.bcm.edu	37	10	102777929	102777929	+	Silent	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:102777929G>A	ENST00000370215.3	-	9	1674	c.1449C>T	c.(1447-1449)gaC>gaT	p.D483D		NM_024895.4	NP_079171.1	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	483						cilium (GO:0005929)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		CTCTGCGCCCGTCCCGCGCTA	0.617																																					p.D483D		Atlas-SNP	.											.	PDZD7	101	.	0			c.C1449T						.						81.0	77.0	79.0					10																	102777929		2203	4300	6503	SO:0001819	synonymous_variant	79955	exon9			GCGCCCGTCCCGC	AK026862	CCDS31269.1, CCDS73182.1	10q24.32	2006-01-24		2006-01-24	ENSG00000186862	ENSG00000186862			26257	protein-coding gene	gene with protein product		612971		PDZK7		12477932	Standard	NM_024895		Approved	FLJ23209, bA108L7.8	uc021pxc.1	Q9H5P4	OTTHUMG00000018916	ENST00000370215.3:c.1449C>T	chr10.hg19:g.102777929G>A		104.0	0.0		138.0	39.0	NM_001195263	D5FJ77|Q8N321	Silent	SNP	ENST00000370215.3	hg19	CCDS31269.1	.	.	.	.	.	.	.	.	.	.	G	0.204	-1.042112	0.01997	.	.	ENSG00000186862	ENST00000433616	.	.	.	4.12	-4.62	0.03370	.	.	.	.	.	T	0.35278	0.0926	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.34079	-0.9843	4	.	.	.	.	13.4053	0.60908	0.6497:0.0:0.3503:0.0	.	.	.	.	M	58	.	.	T	-	2	0	PDZD7	102767919	0.000000	0.05858	0.003000	0.11579	0.079000	0.17450	-1.754000	0.01816	-1.446000	0.01945	-1.164000	0.01763	ACG	.	.		0.617	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895	
FBXW4	6468	hgsc.bcm.edu	37	10	103433426	103433426	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:103433426T>C	ENST00000331272.7	-	3	979	c.361A>G	c.(361-363)Atg>Gtg	p.M121V		NM_022039.3	NP_071322.1	P57775	FBXW4_HUMAN	F-box and WD repeat domain containing 4	121					cartilage development (GO:0051216)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|positive regulation of mesenchymal cell proliferation (GO:0002053)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	ubiquitin ligase complex (GO:0000151)				breast(3)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	15		Colorectal(252;0.123)		Epithelial(162;4.35e-08)|all cancers(201;1.92e-06)		ATCCAGGGCATCTGACTGAAA	0.428																																					p.M121V		Atlas-SNP	.											.	FBXW4	39	.	0			c.A361G						.						59.0	60.0	60.0					10																	103433426		2203	4300	6503	SO:0001583	missense	6468	exon3			AGGGCATCTGACT	AF281859	CCDS31271.1	10q24	2013-01-09	2007-02-08	2005-03-12	ENSG00000107829	ENSG00000107829		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	10847	protein-coding gene	gene with protein product		608071	"""split hand/foot malformation (ectrodactyly) type 3"", ""F-box and WD-40 domain protein 4"""	SHFM3		8723077, 7912888	Standard	XM_005270053		Approved	Fbw4, dactylin	uc001kto.3	P57775	OTTHUMG00000018938	ENST00000331272.7:c.361A>G	chr10.hg19:g.103433426T>C	ENSP00000359149:p.Met121Val	85.0	0.0		90.0	4.0	NM_022039	Q5SVS1|Q96IM6	Missense_Mutation	SNP	ENST00000331272.7	hg19	CCDS31271.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.637031	0.47049	.	.	ENSG00000107829	ENST00000331272;ENST00000389046;ENST00000457105;ENST00000431477	T	0.72505	-0.66	5.23	5.23	0.72850	.	0.043313	0.85682	D	0.000000	T	0.56920	0.2018	L	0.29908	0.895	0.42535	D	0.993059	B	0.26195	0.144	B	0.26969	0.075	T	0.54166	-0.8334	10	0.07175	T	0.84	-19.5873	15.4089	0.74902	0.0:0.0:0.0:1.0	.	121	P57775	FBXW4_HUMAN	V	121;121;34;77	ENSP00000359149:M121V	ENSP00000359149:M121V	M	-	1	0	FBXW4	103423416	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	4.676000	0.61627	2.103000	0.63969	0.397000	0.26171	ATG	.	.		0.428	FBXW4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049979.2	NM_022039	
TMEM180	79847	hgsc.bcm.edu	37	10	104230585	104230585	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:104230585A>G	ENST00000238936.4	+	5	652	c.415A>G	c.(415-417)Acg>Gcg	p.T139A	TMEM180_ENST00000366277.2_Intron|TMEM180_ENST00000369931.3_Intron	NM_024789.3	NP_079065.2	Q14CX5	TM180_HUMAN	transmembrane protein 180	139						integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|large_intestine(3)|lung(1)|ovary(3)|skin(1)	13		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		TGGCTTCCTGACGCTCGTGGA	0.662																																					p.T139A		Atlas-SNP	.											.	TMEM180	33	.	0			c.A415G						.						96.0	93.0	94.0					10																	104230585		2203	4300	6503	SO:0001583	missense	79847	exon5			TTCCTGACGCTCG	AK026182	CCDS7535.1	10q24.32	2011-02-09	2006-10-12	2006-10-12	ENSG00000138111	ENSG00000138111			26196	protein-coding gene	gene with protein product				C10orf77		12477932	Standard	XM_006717971		Approved	FLJ22529, bA18I14.8	uc001kvt.3	Q14CX5	OTTHUMG00000018961	ENST00000238936.4:c.415A>G	chr10.hg19:g.104230585A>G	ENSP00000238936:p.Thr139Ala	103.0	0.0		123.0	5.0	NM_024789	Q6NWM8|Q6NWM9|Q6PEZ7|Q9H679	Missense_Mutation	SNP	ENST00000238936.4	hg19	CCDS7535.1	.	.	.	.	.	.	.	.	.	.	A	32	5.138864	0.94560	.	.	ENSG00000138111	ENST00000238936	T	0.78003	-1.14	5.74	5.74	0.90152	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.88485	0.6449	M	0.81341	2.54	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89522	0.3779	10	0.59425	D	0.04	.	16.0229	0.80512	1.0:0.0:0.0:0.0	.	139	Q14CX5	TM180_HUMAN	A	139	ENSP00000238936:T139A	ENSP00000238936:T139A	T	+	1	0	TMEM180	104220575	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.339000	0.96797	2.189000	0.69895	0.459000	0.35465	ACG	.	.		0.662	TMEM180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050075.2	NM_024789	
PDCD11	22984	hgsc.bcm.edu	37	10	105174798	105174798	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:105174798G>A	ENST00000369797.3	+	12	1502	c.1408G>A	c.(1408-1410)Gtg>Atg	p.V470M		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	470	S1 motif 5. {ECO:0000255|PROSITE- ProRule:PRU00180}.				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)		TGGGATGCTGGTGAAGGTGGG	0.517																																					p.V470M		Atlas-SNP	.											.	PDCD11	160	.	0			c.G1408A						.						109.0	92.0	98.0					10																	105174798		2203	4300	6503	SO:0001583	missense	22984	exon12			ATGCTGGTGAAGG	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.1408G>A	chr10.hg19:g.105174798G>A	ENSP00000358812:p.Val470Met	110.0	0.0		151.0	48.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	hg19	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	G	18.59	3.656309	0.67586	.	.	ENSG00000148843	ENST00000369797;ENST00000543503	T	0.71103	-0.54	5.35	2.44	0.29823	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);RNA-binding domain, S1 (1);Ribosomal protein S1, RNA-binding domain (2);	0.115848	0.64402	D	0.000018	D	0.84848	0.5563	H	0.95260	3.645	0.58432	D	0.999998	D	0.58268	0.982	P	0.59761	0.863	D	0.84585	0.0663	10	0.34782	T	0.22	-8.7672	11.3229	0.49433	0.0:0.1226:0.6225:0.2549	.	470	Q14690	RRP5_HUMAN	M	470	ENSP00000358812:V470M	ENSP00000358812:V470M	V	+	1	0	PDCD11	105164788	1.000000	0.71417	0.997000	0.53966	0.769000	0.43574	5.224000	0.65288	0.324000	0.23333	-0.183000	0.12914	GTG	.	.		0.517	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
CFAP43	80217	hgsc.bcm.edu	37	10	105971830	105971830	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:105971830A>G	ENST00000278064.2	-	5	785	c.460T>C	c.(460-462)Tat>Cat	p.Y154H	WDR96_ENST00000357060.3_Missense_Mutation_p.Y224H|WDR96_ENST00000369719.1_Missense_Mutation_p.Y154H|WDR96_ENST00000369720.1_Missense_Mutation_p.Y154H|WDR96_ENST00000428666.1_Missense_Mutation_p.Y224H																NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						ACGGGACCATAGATGAGATCT	0.493																																					p.Y224H		Atlas-SNP	.											.	WDR96	183	.	0			c.T670C						.						86.0	79.0	82.0					10																	105971830		2203	4300	6503	SO:0001583	missense	80217	exon5			GACCATAGATGAG																												ENST00000278064.2:c.460T>C	chr10.hg19:g.105971830A>G	ENSP00000278064:p.Tyr154His	72.0	0.0		64.0	4.0	NM_025145		Missense_Mutation	SNP	ENST00000278064.2	hg19		.	.	.	.	.	.	.	.	.	.	A	14.99	2.699136	0.48307	.	.	ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064;ENST00000369720;ENST00000369719	T;T;T;T;T	0.48201	2.41;2.4;2.39;1.41;0.82	5.51	5.51	0.81932	WD40 repeat-like-containing domain (1);	0.000000	0.34676	N	0.003774	T	0.57330	0.2046	M	0.74258	2.255	0.31682	N	0.642947	B;P;P	0.51653	0.41;0.947;0.786	B;P;B	0.50270	0.113;0.636;0.321	T	0.65446	-0.6166	10	0.27082	T	0.32	.	14.6028	0.68453	1.0:0.0:0.0:0.0	.	224;224;224	Q8NDM7-5;B4DHB6;Q8NDM7	.;.;WDR96_HUMAN	H	224;224;154;154;154	ENSP00000349568:Y224H;ENSP00000400289:Y224H;ENSP00000278064:Y154H;ENSP00000358734:Y154H;ENSP00000358733:Y154H	ENSP00000278064:Y154H	Y	-	1	0	WDR96	105961820	1.000000	0.71417	1.000000	0.80357	0.565000	0.35776	3.888000	0.56204	2.101000	0.63845	0.533000	0.62120	TAT	.	.		0.493	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1		
CFAP58	159686	hgsc.bcm.edu	37	10	106121791	106121791	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:106121791A>G	ENST00000369704.3	+	3	436	c.302A>G	c.(301-303)aAg>aGg	p.K101R	CCDC147_ENST00000312902.5_5'UTR	NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		101						extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		GAAATTGAAAAGGCCTGGAAG	0.438																																					p.K101R		Atlas-SNP	.											.	CCDC147	137	.	0			c.A302G						.						84.0	79.0	81.0					10																	106121791		2203	4300	6503	SO:0001583	missense	159686	exon3			TTGAAAAGGCCTG																												ENST00000369704.3:c.302A>G	chr10.hg19:g.106121791A>G	ENSP00000358718:p.Lys101Arg	56.0	0.0		90.0	4.0	NM_001008723	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	hg19	CCDS31282.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.859253	0.91433	.	.	ENSG00000120051	ENST00000369704	T	0.36699	1.24	6.17	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.53449	0.1797	M	0.76328	2.33	0.80722	D	1	D	0.55605	0.972	P	0.58130	0.833	T	0.53662	-0.8407	10	0.40728	T	0.16	-24.7135	12.297	0.54854	0.9345:0.0:0.0655:0.0	.	101	Q5T655	CC147_HUMAN	R	101	ENSP00000358718:K101R	ENSP00000358718:K101R	K	+	2	0	CCDC147	106111781	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.347000	0.79356	1.158000	0.42547	0.533000	0.62120	AAG	.	.		0.438	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1		
XPNPEP1	7511	hgsc.bcm.edu	37	10	111635319	111635319	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:111635319T>C	ENST00000502935.1	-	15	1477	c.1358A>G	c.(1357-1359)gAg>gGg	p.E453G	XPNPEP1_ENST00000322238.8_Intron|XPNPEP1_ENST00000369683.1_Missense_Mutation_p.E339G|XPNPEP1_ENST00000369680.4_Missense_Mutation_p.E410G					X-prolyl aminopeptidase (aminopeptidase P) 1, soluble											endometrium(2)|kidney(9)|large_intestine(4)|lung(9)|ovary(3)|pancreas(2)|skin(1)|urinary_tract(1)	31		Breast(234;0.174)		Epithelial(162;1.64e-05)|all cancers(201;0.000564)|BRCA - Breast invasive adenocarcinoma(275;0.0721)		AAGGTACACCTCATCCAGGGA	0.438																																					p.E453G		Atlas-SNP	.											.	XPNPEP1	110	.	0			c.A1358G						.						127.0	103.0	111.0					10																	111635319		2203	4300	6503	SO:0001583	missense	7511	exon15			TACACCTCATCCA		CCDS7560.1, CCDS7560.2, CCDS53576.1	10q25.3	2006-01-16	2002-07-17		ENSG00000108039	ENSG00000108039	3.4.11.9		12822	protein-coding gene	gene with protein product		602443	"""X-prolyl aminopeptidase (aminopeptidase P)-like"""	XPNPEP, XPNPEPL1, XPNPEPL			Standard	NM_020383		Approved		uc001kyp.2	Q9NQW7	OTTHUMG00000019029	ENST00000502935.1:c.1358A>G	chr10.hg19:g.111635319T>C	ENSP00000421566:p.Glu453Gly	112.0	0.0		90.0	5.0	NM_020383		Missense_Mutation	SNP	ENST00000502935.1	hg19	CCDS7560.2	.	.	.	.	.	.	.	.	.	.	T	25.6	4.659386	0.88154	.	.	ENSG00000108039	ENST00000502935;ENST00000369683;ENST00000369680	T;T;T	0.77358	-1.09;-1.09;-1.09	5.43	5.43	0.79202	Peptidase M24, structural domain (3);	0.000000	0.85682	D	0.000000	T	0.77425	0.4128	N	0.24115	0.695	0.54753	D	0.999988	D	0.89917	1.0	D	0.77557	0.99	T	0.71813	-0.4479	10	0.06891	T	0.86	-23.1133	14.3486	0.66685	0.0:0.0:0.0:1.0	.	410	Q9NQW7	XPP1_HUMAN	G	453;339;410	ENSP00000421566:E453G;ENSP00000358697:E339G;ENSP00000358694:E410G	ENSP00000358694:E410G	E	-	2	0	XPNPEP1	111625309	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	5.682000	0.68182	2.179000	0.69175	0.533000	0.62120	GAG	.	.		0.438	XPNPEP1-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050264.2		
GPAM	57678	hgsc.bcm.edu	37	10	113935417	113935417	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:113935417T>C	ENST00000348367.4	-	6	551	c.354A>G	c.(352-354)cgA>cgG	p.R118R	GPAM_ENST00000423155.1_Silent_p.R118R|GPAM_ENST00000369425.1_Silent_p.R118R			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	118					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)		TATGCACATCTCGCTCTTGAA	0.473																																					p.R118R	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.A354G						.						167.0	148.0	154.0					10																	113935417		2203	4300	6503	SO:0001819	synonymous_variant	57678	exon6			CACATCTCGCTCT	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.354A>G	chr10.hg19:g.113935417T>C		73.0	0.0		60.0	4.0	NM_001244949	Q5VW51|Q86TA3	Silent	SNP	ENST00000348367.4	hg19	CCDS7570.1																																																																																			.	.		0.473	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918	
FAM160B1	57700	hgsc.bcm.edu	37	10	116608429	116608429	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:116608429A>G	ENST00000369248.4	+	13	2071	c.1736A>G	c.(1735-1737)gAc>gGc	p.D579G	FAM160B1_ENST00000369250.3_Missense_Mutation_p.D579G	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	579										NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						GTACCGGATGACGCAAAATCC	0.403																																					p.D579G		Atlas-SNP	.											.	FAM160B1	107	.	0			c.A1736G						.						112.0	88.0	96.0					10																	116608429		2203	4300	6503	SO:0001583	missense	57700	exon13			CGGATGACGCAAA	AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"""KIAA1600"""	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.1736A>G	chr10.hg19:g.116608429A>G	ENSP00000358251:p.Asp579Gly	94.0	0.0		99.0	4.0	NM_020940	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Missense_Mutation	SNP	ENST00000369248.4	hg19	CCDS31290.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.803348	0.70682	.	.	ENSG00000151553	ENST00000369248;ENST00000369250	T;T	0.66460	-0.21;-0.21	5.58	5.58	0.84498	.	0.083461	0.85682	D	0.000000	T	0.47801	0.1465	N	0.08118	0	0.80722	D	1	B;B	0.11235	0.002;0.004	B;B	0.18561	0.022;0.005	T	0.41502	-0.9505	10	0.21540	T	0.41	-13.1897	16.0529	0.80775	1.0:0.0:0.0:0.0	.	579;579	Q5W0V3-2;Q5W0V3	.;F16B1_HUMAN	G	579	ENSP00000358251:D579G;ENSP00000358253:D579G	ENSP00000358251:D579G	D	+	2	0	FAM160B1	116598419	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.971000	0.93419	2.257000	0.74773	0.459000	0.35465	GAC	.	.		0.403	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351	
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118231366	118231366	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:118231366A>G	ENST00000369230.3	+	10	1293	c.1147A>G	c.(1147-1149)Aaa>Gaa	p.K383E		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	383	PLAT.				lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		GGCAGTTAGGAAAACTGGGGA	0.483																																					p.K383E		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.A1147G						.						128.0	136.0	133.0					10																	118231366		2203	4300	6503	SO:0001583	missense	119548	exon10			GTTAGGAAAACTG	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.1147A>G	chr10.hg19:g.118231366A>G	ENSP00000358232:p.Lys383Glu	132.0	0.0		118.0	6.0	NM_001011709		Missense_Mutation	SNP	ENST00000369230.3	hg19	CCDS31292.1	.	.	.	.	.	.	.	.	.	.	A	12.17	1.858868	0.32884	.	.	ENSG00000203837	ENST00000369230	T	0.64991	-0.13	4.18	1.81	0.25067	Lipoxygenase, LH2 (2);Lipase/lipooxygenase, PLAT/LH2 (1);	0.871930	0.09589	N	0.781766	T	0.54838	0.1883	L	0.47716	1.5	0.09310	N	1	B	0.16396	0.017	B	0.26614	0.071	T	0.51426	-0.8707	10	0.62326	D	0.03	.	6.8165	0.23833	0.8008:0.0:0.1992:0.0	.	383	Q17RR3	LIPR3_HUMAN	E	383	ENSP00000358232:K383E	ENSP00000358232:K383E	K	+	1	0	PNLIPRP3	118221356	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.003000	0.12901	0.252000	0.21531	0.482000	0.46254	AAA	.	.		0.483	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
TACC2	10579	hgsc.bcm.edu	37	10	124008566	124008566	+	Splice_Site	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:124008566A>G	ENST00000369005.1	+	21	8895	c.8555A>G	c.(8554-8556)aAt>aGt	p.N2852S	TACC2_ENST00000368999.1_Splice_Site_p.N942S|TACC2_ENST00000453444.2_Splice_Site_p.N2779S|TACC2_ENST00000515273.1_Splice_Site_p.N2779S|TACC2_ENST00000369001.1_Splice_Site_p.N479S|TACC2_ENST00000369004.3_Splice_Site_p.N912S|TACC2_ENST00000513429.1_Splice_Site_p.N998S|TACC2_ENST00000369000.1_Splice_Site_p.N475S|TACC2_ENST00000260733.3_Splice_Site_p.N930S|TACC2_ENST00000334433.3_Splice_Site_p.N2852S|TACC2_ENST00000515603.1_Splice_Site_p.N2730S|TACC2_ENST00000358010.1_Splice_Site_p.N998S|TACC2_ENST00000360561.3_Splice_Site_p.N900S	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2852					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)				CTGTGTCAGAATGAAGAGGTG	0.587																																					p.N2852S		Atlas-SNP	.											.	TACC2	271	.	0			c.A8555G						.						76.0	73.0	74.0					10																	124008566		2203	4300	6503	SO:0001630	splice_region_variant	10579	exon21			GTCAGAATGAAGA	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.8554-1A>G	chr10.hg19:g.124008566A>G		87.0	0.0		77.0	4.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	hg19	CCDS7626.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.41|17.41	3.382677|3.382677	0.61845|0.61845	.|.	.|.	ENSG00000138162|ENSG00000138162	ENST00000490979|ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000369001;ENST00000369000;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733	.|T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.68025	.|-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.04|5.04	3.91|3.91	0.45181|0.45181	.|.	.|0.000000	.|0.39341	.|N	.|0.001387	T|T	0.78742|0.78742	0.4331|0.4331	M|M	0.70842|0.70842	2.15|2.15	0.49213|0.49213	D|D	0.999767|0.999767	.|D;D;D;D;D;D;D;D;D	.|0.89917	.|0.998;0.999;1.0;0.999;1.0;0.984;1.0;0.984;1.0	.|D;D;D;D;D;D;D;D;D	.|0.91635	.|0.999;0.996;0.999;0.999;0.999;0.973;0.999;0.973;0.999	T|T	0.78841|0.78841	-0.2045|-0.2045	5|10	.|0.59425	.|D	.|0.04	-16.0554|-16.0554	10.8205|10.8205	0.46601|0.46601	0.9252:0.0:0.0748:0.0|0.9252:0.0:0.0748:0.0	.|.	.|2779;912;2730;2779;900;930;475;998;2852	.|E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-2;O95359-5;O95359	.|.;.;.;.;.;.;.;.;TACC2_HUMAN	V|S	96|2852;998;2779;2730;2852;998;2779;2765;479;475;900;942;912;930	.|ENSP00000358001:N2852S;ENSP00000425062:N998S;ENSP00000424467:N2779S;ENSP00000427618:N2730S;ENSP00000334280:N2852S;ENSP00000350701:N998S;ENSP00000395048:N2779S;ENSP00000357997:N479S;ENSP00000357996:N475S;ENSP00000353763:N900S;ENSP00000357995:N942S;ENSP00000422815:N912S;ENSP00000260733:N930S	.|ENSP00000260733:N930S	M|N	+|+	1|2	0|0	TACC2|TACC2	123998556|123998556	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.469000|0.469000	0.32828|0.32828	9.197000|9.197000	0.94985|0.94985	0.875000|0.875000	0.35847|0.35847	-0.256000|-0.256000	0.11100|0.11100	ATG|AAT	.	.		0.587	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		Missense_Mutation
DMBT1	1755	hgsc.bcm.edu	37	10	124402895	124402895	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:124402895G>A	ENST00000338354.3	+	53	7329	c.7223G>A	c.(7222-7224)cGa>cAa	p.R2408Q	DMBT1_ENST00000368956.2_Missense_Mutation_p.R1780Q|DMBT1_ENST00000368955.3_Missense_Mutation_p.R2398Q|DMBT1_ENST00000359586.6_Missense_Mutation_p.R1128Q|DMBT1_ENST00000330163.4_Missense_Mutation_p.R1780Q|DMBT1_ENST00000344338.3_Missense_Mutation_p.R2398Q|DMBT1_ENST00000368909.3_Missense_Mutation_p.R2408Q			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	2408					defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CCCCCACGCCGAGAAGAGGAG	0.622																																					p.R2408Q	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,colon,carcinoma,0,3	DMBT1	677	.	0			c.G7223A						.						29.0	32.0	31.0					10																	124402895		1942	4134	6076	SO:0001583	missense	1755	exon53			CACGCCGAGAAGA		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.7223G>A	chr10.hg19:g.124402895G>A	ENSP00000342210:p.Arg2408Gln	117.0	0.0		165.0	50.0	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	G	10.20	1.284184	0.23392	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000344467;ENST00000359586	T;T;T;T;T;T;T	0.23950	1.93;1.92;1.88;1.93;1.92;1.88;1.91	4.38	-8.09	0.01090	.	0.736603	0.10817	U	0.630867	T	0.06234	0.0161	N	0.08118	0	0.09310	N	1	B;P;B;B;B;B;B	0.39717	0.013;0.684;0.013;0.013;0.013;0.013;0.007	B;B;B;B;B;B;B	0.26094	0.003;0.066;0.002;0.004;0.004;0.004;0.002	T	0.19128	-1.0315	10	0.49607	T	0.09	.	1.2818	0.02042	0.2559:0.1826:0.3749:0.1866	.	1128;2388;1657;2537;1780;2398;2408	F8WEF7;Q9UGM3-5;Q9UGM3-8;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;.;.;DMBT1_HUMAN	Q	2408;2537;2408;2408;2408;2407;1780;2398;1780;1780;2408;2398;1780;554;1128	ENSP00000342210:R2408Q;ENSP00000343175:R2398Q;ENSP00000327747:R1780Q;ENSP00000357905:R2408Q;ENSP00000357951:R2398Q;ENSP00000357952:R1780Q;ENSP00000352593:R1128Q	ENSP00000331522:R1780Q	R	+	2	0	DMBT1	124392885	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.977000	0.03782	-2.400000	0.00579	-2.511000	0.00188	CGA	.	.		0.622	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
PSTK	118672	hgsc.bcm.edu	37	10	124742793	124742793	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:124742793T>A	ENST00000368887.3	+	3	954	c.514T>A	c.(514-516)Ttg>Atg	p.L172M	PSTK_ENST00000405485.1_Missense_Mutation_p.L172M|PSTK_ENST00000497219.1_3'UTR	NM_153336.2	NP_699167.2	Q8IV42	PSTK_HUMAN	phosphoseryl-tRNA kinase	172					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|tRNA binding (GO:0000049)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|skin(1)|stomach(2)	13		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0725)		TTCAGATTCGTTGGGCTTTTG	0.378																																					p.L172M		Atlas-SNP	.											PSTK,NS,lymphoid_neoplasm,0,1	PSTK	34	.	0			c.T514A						.						52.0	51.0	52.0					10																	124742793		2203	4300	6503	SO:0001583	missense	118672	exon3			GATTCGTTGGGCT	AK127173	CCDS7633.1	10q26.13	2007-04-17	2007-04-17	2007-04-17	ENSG00000179988	ENSG00000179988			28578	protein-coding gene	gene with protein product		611310	"""chromosome 10 open reading frame 89"""	C10orf89		15317934	Standard	NM_153336		Approved	MGC35392	uc001lgy.1	Q8IV42	OTTHUMG00000019191	ENST00000368887.3:c.514T>A	chr10.hg19:g.124742793T>A	ENSP00000357882:p.Leu172Met	94.0	0.0		104.0	0.0	NM_153336	Q6ZSS9	Missense_Mutation	SNP	ENST00000368887.3	hg19	CCDS7633.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.987176	0.53934	.	.	ENSG00000179988	ENST00000368887;ENST00000405485	T;T	0.30448	1.53;1.53	5.86	0.849	0.18972	.	0.153654	0.41605	D	0.000841	T	0.45175	0.1329	M	0.73962	2.25	0.09310	N	1	P	0.52692	0.955	P	0.57244	0.816	T	0.34900	-0.9810	10	0.52906	T	0.07	-19.4718	9.706	0.40216	0.0:0.3732:0.0:0.6268	.	172	Q8IV42	PSTK_HUMAN	M	172	ENSP00000357882:L172M;ENSP00000384764:L172M	ENSP00000357882:L172M	L	+	1	2	PSTK	124732783	0.114000	0.22134	0.002000	0.10522	0.932000	0.56968	0.517000	0.22832	-0.087000	0.12528	0.460000	0.39030	TTG	.	.		0.378	PSTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050811.1	NM_153336	
MUC2	4583	hgsc.bcm.edu	37	11	1094691	1094691	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:1094691G>T	ENST00000441003.2	+	31	5806	c.5779G>T	c.(5779-5781)Ggg>Tgg	p.G1927W	MUC2_ENST00000361558.6_Missense_Mutation_p.G65W|MUC2_ENST00000333592.6_Missense_Mutation_p.G215W	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4289					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TACCACGACCGGGTCATCTTC	0.632																																					p.G1923W		Atlas-SNP	.											.	MUC2	614	.	0			c.G5767T						.						78.0	97.0	90.0					11																	1094691		2117	4220	6337	SO:0001583	missense	4583	exon32			ACGACCGGGTCAT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5779G>T	chr11.hg19:g.1094691G>T	ENSP00000415183:p.Gly1927Trp	101.0	0.0		164.0	7.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	G	10.79	1.449554	0.26074	.	.	ENSG00000198788	ENST00000441003;ENST00000361558;ENST00000333592	T;T;T	0.41758	2.56;0.99;2.9	1.97	-1.24	0.09435	.	.	.	.	.	T	0.40171	0.1106	L	0.51422	1.61	0.09310	N	1	D	0.63880	0.993	P	0.49665	0.618	T	0.31613	-0.9937	9	0.66056	D	0.02	.	5.8132	0.18477	0.5036:0.0:0.4964:0.0	.	1927	E7EUV1	.	W	1927;65;215	ENSP00000415183:G1927W;ENSP00000354885:G65W;ENSP00000331373:G215W	ENSP00000331373:G215W	G	+	1	0	MUC2	1084691	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-2.996000	0.00655	-0.225000	0.09913	0.479000	0.44913	GGG	.	.		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR51A7	119687	hgsc.bcm.edu	37	11	4929062	4929062	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:4929062T>G	ENST00000359350.4	+	1	463	c.463T>G	c.(463-465)Tta>Gta	p.L155V	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	155						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(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		GAGCATTCTCTTAGTGATTCC	0.393																																					p.L155V		Atlas-SNP	.											OR51A7,NS,carcinoma,0,1	OR51A7	86	.	0			c.T463G						.						99.0	98.0	98.0					11																	4929062		2201	4298	6499	SO:0001583	missense	119687	exon1			ATTCTCTTAGTGA	AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"""GPCR / Class A : Olfactory receptors"""	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.463T>G	chr11.hg19:g.4929062T>G	ENSP00000352305:p.Leu155Val	94.0	0.0		149.0	0.0	NM_001004749	Q6IFH8	Missense_Mutation	SNP	ENST00000359350.4	hg19	CCDS31364.1	.	.	.	.	.	.	.	.	.	.	T	5.845	0.340128	0.11069	.	.	ENSG00000176895	ENST00000359350;ENST00000545959;ENST00000544684	T	0.72282	-0.64	5.02	2.68	0.31781	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37095	N	0.002254	T	0.64670	0.2619	L	0.41710	1.295	0.09310	N	1	P	0.44195	0.828	P	0.54924	0.764	T	0.53648	-0.8409	10	0.09590	T	0.72	.	3.7568	0.08588	0.157:0.1825:0.0:0.6605	.	155	Q8NH64	O51A7_HUMAN	V	155;155;144	ENSP00000352305:L155V	ENSP00000352305:L155V	L	+	1	2	OR51A7	4885638	0.000000	0.05858	0.059000	0.19551	0.360000	0.29518	-1.244000	0.02902	0.379000	0.24794	-0.250000	0.11733	TTA	.	.		0.393	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749	
CNGA4	1262	hgsc.bcm.edu	37	11	6265177	6265177	+	Splice_Site	SNP	A	A	G	rs34385295		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:6265177A>G	ENST00000379936.2	+	6	1382		c.e6-1			NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4						phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATGAGCCACAGGGAACATGT	0.552																																					.		Atlas-SNP	.											.	CNGA4	96	.	0			c.1268-2A>G						.						50.0	49.0	50.0					11																	6265177		2201	4296	6497	SO:0001630	splice_region_variant	1262	exon6			AGCCACAGGGAAC	AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2152	protein-coding gene	gene with protein product		609472	"""cyclic nucleotide gated channel beta 2"""	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.1268-1A>G	chr11.hg19:g.6265177A>G		32.0	0.0		46.0	4.0	NM_001037329		Splice_Site	SNP	ENST00000379936.2	hg19	CCDS31408.1	.	.	.	.	.	.	.	.	.	.	A	18.26	3.585347	0.66105	.	.	ENSG00000132259	ENST00000379936	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5724	0.56344	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CNGA4	6221753	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.111000	0.71541	2.185000	0.69588	0.514000	0.50259	.	.	.		0.552	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329	Intron
TRIM3	10612	hgsc.bcm.edu	37	11	6472208	6472208	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:6472208T>C	ENST00000525074.1	-	9	2178	c.1784A>G	c.(1783-1785)aAg>aGg	p.K595R	TRIM3_ENST00000345851.3_Missense_Mutation_p.K595R|TRIM3_ENST00000537602.1_Missense_Mutation_p.K517R|TRIM3_ENST00000536344.1_Missense_Mutation_p.K476R|TRIM3_ENST00000359518.3_Missense_Mutation_p.K595R	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	595					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCAGCAAGACTTGTTGTCGAC	0.572																																					p.K595R	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.A1784G						.						78.0	75.0	76.0					11																	6472208		2201	4296	6497	SO:0001583	missense	10612	exon9			CAAGACTTGTTGT	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10064	protein-coding gene	gene with protein product	"""ring finger protein 22"", ""brain expressed ring finger"", ""tripartite motif protein TRIM3"""	605493	"""tripartite motif-containing 3"""	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.1784A>G	chr11.hg19:g.6472208T>C	ENSP00000433102:p.Lys595Arg	55.0	0.0		93.0	4.0	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Missense_Mutation	SNP	ENST00000525074.1	hg19	CCDS7764.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.884841	0.91814	.	.	ENSG00000110171	ENST00000530899;ENST00000525074;ENST00000545029;ENST00000345851;ENST00000336043;ENST00000537602;ENST00000359518;ENST00000536344	T;T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6;-0.6	5.14	5.14	0.70334	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.67382	0.2887	L	0.39020	1.185	0.80722	D	1	P;P	0.48911	0.917;0.833	P;P	0.51055	0.657;0.6	T	0.62492	-0.6843	10	0.12430	T	0.62	-20.4211	13.9521	0.64123	0.0:0.0:0.0:1.0	.	476;595	F5H2Q8;O75382	.;TRIM3_HUMAN	R	595;595;595;595;584;517;595;476	ENSP00000433102:K595R;ENSP00000340797:K595R;ENSP00000441091:K517R;ENSP00000352508:K595R;ENSP00000445460:K476R	ENSP00000337094:K584R	K	-	2	0	TRIM3	6428784	1.000000	0.71417	0.995000	0.50966	0.980000	0.70556	7.868000	0.87116	2.155000	0.67459	0.460000	0.39030	AAG	.	.		0.572	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458	
DCHS1	8642	hgsc.bcm.edu	37	11	6653852	6653852	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:6653852T>C	ENST00000299441.3	-	6	3302	c.2891A>G	c.(2890-2892)cAt>cGt	p.H964R	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	964	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTCCAGCTCATGGGCTGGCCC	0.662																																					p.H964R		Atlas-SNP	.											.	DCHS1	277	.	0			c.A2891G						.						10.0	10.0	10.0					11																	6653852		2177	4263	6440	SO:0001583	missense	8642	exon6			AGCTCATGGGCTG	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.2891A>G	chr11.hg19:g.6653852T>C	ENSP00000299441:p.His964Arg	38.0	0.0		86.0	4.0	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	T	11.57	1.678686	0.29783	.	.	ENSG00000166341	ENST00000299441	T	0.52295	0.67	4.34	4.34	0.51931	Cadherin (4);Cadherin-like (1);	0.146542	0.31542	N	0.007479	T	0.46927	0.1418	M	0.71581	2.175	0.38604	D	0.95072	P	0.35821	0.523	B	0.33846	0.171	T	0.57659	-0.7773	10	0.52906	T	0.07	.	13.1399	0.59428	0.0:0.0:0.0:1.0	.	964	Q96JQ0	PCD16_HUMAN	R	964	ENSP00000299441:H964R	ENSP00000299441:H964R	H	-	2	0	DCHS1	6610428	1.000000	0.71417	0.992000	0.48379	0.442000	0.32017	3.518000	0.53451	1.952000	0.56665	0.459000	0.35465	CAT	.	.		0.662	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
PIK3C2A	5286	hgsc.bcm.edu	37	11	17113160	17113160	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:17113160A>G	ENST00000265970.7	-	30	4685	c.4686T>C	c.(4684-4686)gcT>gcC	p.A1562A	PIK3C2A_ENST00000531428.1_5'UTR|PIK3C2A_ENST00000540361.1_Silent_p.A1182A	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1562	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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						ATAATTTCACAGCTCCTCCTA	0.378																																					p.A1562A		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.T4686C						.						104.0	97.0	99.0					11																	17113160		2200	4294	6494	SO:0001819	synonymous_variant	5286	exon30			TTTCACAGCTCCT	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.4686T>C	chr11.hg19:g.17113160A>G		134.0	0.0		170.0	7.0	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Silent	SNP	ENST00000265970.7	hg19	CCDS7824.1																																																																																			.	.		0.378	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645	
HPS5	11234	hgsc.bcm.edu	37	11	18305405	18305405	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:18305405T>C	ENST00000349215.3	-	21	3272	c.2995A>G	c.(2995-2997)Aga>Gga	p.R999G	HPS5_ENST00000438420.2_Missense_Mutation_p.R885G|HPS5_ENST00000396253.3_Missense_Mutation_p.R885G|HPS5_ENST00000537258.1_Missense_Mutation_p.R106G|HPS5_ENST00000352460.3_5'UTR	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	999					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						GCCTCTCTTCTTCTCTCCAGC	0.408									Hermansky-Pudlak syndrome																												p.R999G		Atlas-SNP	.											.	HPS5	70	.	0			c.A2995G						.						132.0	128.0	129.0					11																	18305405		2199	4293	6492	SO:0001583	missense	11234	exon21	Familial Cancer Database	HPS, HPS1-8	CTCTTCTTCTCTC	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.2995A>G	chr11.hg19:g.18305405T>C	ENSP00000265967:p.Arg999Gly	47.0	0.0		89.0	4.0	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	hg19	CCDS7836.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.345007	0.82022	.	.	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215;ENST00000537258	T;T;T	0.63913	-0.07;-0.07;-0.0	5.98	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.74680	0.3748	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76176	-0.3055	10	0.72032	D	0.01	.	12.2493	0.54589	0.0:0.0664:0.0:0.9336	.	999	Q9UPZ3	HPS5_HUMAN	G	885;885;999;106	ENSP00000379552:R885G;ENSP00000399590:R885G;ENSP00000265967:R999G	ENSP00000265967:R999G	R	-	1	2	HPS5	18261981	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.345000	0.59360	1.078000	0.41014	0.482000	0.46254	AGA	.	.		0.408	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	
PTPN5	84867	hgsc.bcm.edu	37	11	18763990	18763990	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:18763990G>A	ENST00000358540.2	-	7	974	c.544C>T	c.(544-546)Cgc>Tgc	p.R182C	PTPN5_ENST00000477854.1_5'UTR|PTPN5_ENST00000396167.2_Missense_Mutation_p.R150C|PTPN5_ENST00000496201.2_5'UTR|PTPN5_ENST00000396168.1_Missense_Mutation_p.R158C|PTPN5_ENST00000396170.1_Missense_Mutation_p.R150C|PTPN5_ENST00000396171.4_Missense_Mutation_p.R182C|RP11-1081L13.4_ENST00000527285.1_RNA	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	182					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						ACTGACTGGCGCCTGTCCTCA	0.632																																					p.R182C		Atlas-SNP	.											PTPN5_ENST00000358540,NS,carcinoma,0,2	PTPN5	163	.	0			c.C544T						.						47.0	50.0	49.0					11																	18763990		2199	4293	6492	SO:0001583	missense	84867	exon7			ACTGGCGCCTGTC	BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.544C>T	chr11.hg19:g.18763990G>A	ENSP00000351342:p.Arg182Cys	95.0	0.0		120.0	59.0	NM_032781	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Missense_Mutation	SNP	ENST00000358540.2	hg19	CCDS7845.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.699138	0.88830	.	.	ENSG00000110786	ENST00000358540;ENST00000396170;ENST00000396171;ENST00000396167;ENST00000396168	T;T;T;T;T	0.05025	3.51;3.68;3.51;3.68;3.54	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.15565	0.0375	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.02797	-1.1109	10	0.87932	D	0	.	16.3618	0.83270	0.0:0.0:1.0:0.0	.	182;150	P54829;B3KXG7	PTN5_HUMAN;.	C	182;150;182;150;158	ENSP00000351342:R182C;ENSP00000379473:R150C;ENSP00000379474:R182C;ENSP00000379470:R150C;ENSP00000379471:R158C	ENSP00000351342:R182C	R	-	1	0	PTPN5	18720566	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.080000	0.94040	2.290000	0.77057	0.561000	0.74099	CGC	.	.		0.632	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970	
TCP11L1	55346	hgsc.bcm.edu	37	11	33079469	33079469	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:33079469T>C	ENST00000334274.4	+	5	822	c.422T>C	c.(421-423)cTc>cCc	p.L141P	TCP11L1_ENST00000530171.1_3'UTR|TCP11L1_ENST00000531632.2_Missense_Mutation_p.L141P|TCP11L1_ENST00000324357.9_5'Flank|TCP11L1_ENST00000432887.1_Missense_Mutation_p.L141P	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	141						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						TTGTAGACTCTCTTATCTTTC	0.368																																					p.L141P		Atlas-SNP	.											.	TCP11L1	40	.	0			c.T422C						.						56.0	55.0	55.0					11																	33079469		2202	4298	6500	SO:0001583	missense	55346	exon5			AGACTCTCTTATC	BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"""t-complex 11 (mouse) like 1"""				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.422T>C	chr11.hg19:g.33079469T>C	ENSP00000335595:p.Leu141Pro	77.0	0.0		96.0	4.0	NM_001145541	D3DR01|Q8IVX4	Missense_Mutation	SNP	ENST00000334274.4	hg19	CCDS7882.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.263626	0.80358	.	.	ENSG00000176148	ENST00000530419;ENST00000334274;ENST00000531632;ENST00000432887	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.63628	0.2527	M	0.89534	3.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72557	-0.4257	10	0.87932	D	0	-20.0459	15.5323	0.75974	0.0:0.0:0.0:1.0	.	141	Q9NUJ3	T11L1_HUMAN	P	141	ENSP00000436428:L141P;ENSP00000335595:L141P;ENSP00000433067:L141P;ENSP00000395070:L141P	ENSP00000335595:L141P	L	+	2	0	TCP11L1	33036045	1.000000	0.71417	0.704000	0.30370	0.917000	0.54804	8.040000	0.89188	2.074000	0.62210	0.402000	0.26972	CTC	.	.		0.368	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393	
TCP11L1	55346	hgsc.bcm.edu	37	11	33083146	33083146	+	Silent	SNP	C	C	T	rs145755006		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:33083146C>T	ENST00000334274.4	+	7	1246	c.846C>T	c.(844-846)caC>caT	p.H282H	TCP11L1_ENST00000531632.2_Silent_p.H282H|TCP11L1_ENST00000324357.9_Silent_p.H61H|TCP11L1_ENST00000432887.1_Silent_p.H282H	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	282						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						AGTATAAACACGCCCTGCCAG	0.532																																					p.H282H		Atlas-SNP	.											TCP11L1_ENST00000324357,NS,carcinoma,0,2	TCP11L1	40	.	0			c.C846T						.	C	,	0,4404		0,0,2202	56.0	56.0	56.0		846,846	-2.5	0.5	11	dbSNP_134	56	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous,coding-synonymous	TCP11L1	NM_001145541.1,NM_018393.3	,	0,2,6498	TT,TC,CC		0.0233,0.0,0.0154	,	282/510,282/510	33083146	2,12998	2202	4298	6500	SO:0001819	synonymous_variant	55346	exon7			TAAACACGCCCTG	BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"""t-complex 11 (mouse) like 1"""				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.846C>T	chr11.hg19:g.33083146C>T		92.0	0.0		123.0	29.0	NM_001145541	D3DR01|Q8IVX4	Silent	SNP	ENST00000334274.4	hg19	CCDS7882.1																																																																																			.	C|1.000;T|0.000		0.532	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393	
LDLRAD3	143458	hgsc.bcm.edu	37	11	36119988	36119988	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:36119988A>G	ENST00000315571.5	+	4	452	c.431A>G	c.(430-432)gAg>gGg	p.E144G	LDLRAD3_ENST00000524419.1_Missense_Mutation_p.E95G|LDLRAD3_ENST00000528989.1_Missense_Mutation_p.E95G	NM_174902.2	NP_777562.1	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain containing 3	144	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				receptor-mediated endocytosis (GO:0006898)|regulation of protein processing (GO:0070613)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(7)|skin(1)	28	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				AACAGTGATGAGGAAAGCTGT	0.468																																					p.E144G		Atlas-SNP	.											.	LDLRAD3	52	.	0			c.A431G						.						97.0	83.0	88.0					11																	36119988		2202	4298	6500	SO:0001583	missense	143458	exon4			GTGATGAGGAAAG	AK075546	CCDS31462.1	11p13	2014-06-05			ENSG00000179241	ENSG00000179241			27046	protein-coding gene	gene with protein product						21795536	Standard	NM_174902		Approved	LRAD3	uc001mwk.1	Q86YD5	OTTHUMG00000166313	ENST00000315571.5:c.431A>G	chr11.hg19:g.36119988A>G	ENSP00000318607:p.Glu144Gly	56.0	0.0		123.0	5.0	NM_174902	B7Z1U3|B9EG81|Q8NBJ0	Missense_Mutation	SNP	ENST00000315571.5	hg19	CCDS31462.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.430084	0.83776	.	.	ENSG00000179241	ENST00000528989;ENST00000524419;ENST00000545142;ENST00000315571	D;D;D	0.98876	-5.2;-5.2;-5.2	4.97	4.97	0.65823	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99513	0.9826	H	0.98721	4.31	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.992	D	0.97862	1.0281	10	0.87932	D	0	.	14.1219	0.65192	1.0:0.0:0.0:0.0	.	95;144	B7Z1U3;Q86YD5	.;LRAD3_HUMAN	G	95;95;130;144	ENSP00000433954:E95G;ENSP00000434313:E95G;ENSP00000318607:E144G	ENSP00000318607:E144G	E	+	2	0	LDLRAD3	36076564	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	8.190000	0.89714	1.996000	0.58369	0.533000	0.62120	GAG	.	.		0.468	LDLRAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389085.1	NM_174902	
OR8I2	120586	hgsc.bcm.edu	37	11	55861691	55861691	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:55861691T>C	ENST00000302124.2	+	1	939	c.908T>C	c.(907-909)gTc>gCc	p.V303A		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	303						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					CTTCTGAGAGTCATACATAGA	0.373																																					p.V303A		Atlas-SNP	.											.	OR8I2	119	.	0			c.T908C						.						23.0	23.0	23.0					11																	55861691		2200	4275	6475	SO:0001583	missense	120586	exon1			TGAGAGTCATACA	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"""GPCR / Class A : Olfactory receptors"""	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.908T>C	chr11.hg19:g.55861691T>C	ENSP00000303864:p.Val303Ala	24.0	0.0		48.0	4.0	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	hg19	CCDS31517.1	.	.	.	.	.	.	.	.	.	.	T	8.935	0.964439	0.18583	.	.	ENSG00000172154	ENST00000302124	T	0.38240	1.15	4.0	4.0	0.46444	.	0.440276	0.16412	U	0.215536	T	0.19046	0.0457	N	0.16368	0.405	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.19614	-1.0300	10	0.13470	T	0.59	-4.5772	7.0122	0.24869	0.2033:0.0:0.0:0.7967	.	303	Q8N0Y5	OR8I2_HUMAN	A	303	ENSP00000303864:V303A	ENSP00000303864:V303A	V	+	2	0	OR8I2	55618267	.	.	0.002000	0.10522	0.234000	0.25298	.	.	1.580000	0.49851	0.367000	0.22151	GTC	.	.		0.373	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750	
OR8J1	219477	hgsc.bcm.edu	37	11	56128630	56128630	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:56128630A>G	ENST00000303039.3	+	1	940	c.908A>G	c.(907-909)cAg>cGg	p.Q303R		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	303						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)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					ACTGCTCTACAGAGATTCATG	0.358																																					p.Q303R		Atlas-SNP	.											.	OR8J1	87	.	0			c.A908G						.						71.0	65.0	67.0					11																	56128630		2201	4296	6497	SO:0001583	missense	219477	exon1			CTCTACAGAGATT	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"""GPCR / Class A : Olfactory receptors"""	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.908A>G	chr11.hg19:g.56128630A>G	ENSP00000304060:p.Gln303Arg	76.0	0.0		125.0	5.0	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	hg19	CCDS31529.1	.	.	.	.	.	.	.	.	.	.	A	1.442	-0.567393	0.03910	.	.	ENSG00000172487	ENST00000303039	T	0.34072	1.38	4.02	2.89	0.33648	.	0.477293	0.21088	N	0.080372	T	0.11793	0.0287	N	0.01679	-0.765	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20706	-1.0267	10	0.25751	T	0.34	.	5.5946	0.17319	0.6885:0.0:0.3114:0.0	.	303	Q8NGP2	OR8J1_HUMAN	R	303	ENSP00000304060:Q303R	ENSP00000304060:Q303R	Q	+	2	0	OR8J1	55885206	0.000000	0.05858	0.925000	0.36789	0.053000	0.15095	-0.480000	0.06559	0.711000	0.32018	0.448000	0.29417	CAG	.	.		0.358	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205	
OR5M11	219487	hgsc.bcm.edu	37	11	56310224	56310224	+	Silent	SNP	G	G	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:56310224G>T	ENST00000528616.2	-	1	533	c.510C>A	c.(508-510)tcC>tcA	p.S170S		NM_001005245.1	NP_001005245.1	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M, member 11	170						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(2)|large_intestine(1)|lung(14)	18						TGATGACACTGGATCTACAGA	0.488																																					p.S170S		Atlas-SNP	.											.	OR5M11	60	.	0			c.C510A						.						45.0	47.0	46.0					11																	56310224		2091	4226	6317	SO:0001819	synonymous_variant	219487	exon1			GACACTGGATCTA	AP002517	CCDS53629.1	11q11	2012-08-09				ENSG00000255223		"""GPCR / Class A : Olfactory receptors"""	15291	protein-coding gene	gene with protein product							Standard	NM_001005245		Approved	OR11-199	uc010rjl.2	Q96RB7		ENST00000528616.2:c.510C>A	chr11.hg19:g.56310224G>T		84.0	0.0		131.0	7.0	NM_001005245	B2RNL5|B2RNL7	Silent	SNP	ENST00000528616.2	hg19	CCDS53629.1																																																																																			.	.		0.488	OR5M11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391608.1	NM_001005245	
SERPING1	710	hgsc.bcm.edu	37	11	57367406	57367406	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:57367406A>G	ENST00000278407.4	+	3	333	c.106A>G	c.(106-108)Agt>Ggt	p.S36G	SERPING1_ENST00000378323.4_Missense_Mutation_p.S41G|SERPING1_ENST00000378324.2_5'UTR|SERPING1_ENST00000340687.6_Missense_Mutation_p.S36G|SERPING1_ENST00000403558.1_Missense_Mutation_p.S70G	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	36					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						GGATCCAGAGAGTTTGCAAGA	0.478																																					p.S36G		Atlas-SNP	.											.	SERPING1	57	.	0			c.A106G	GRCh37	CD961868	SERPING1	D		.						115.0	115.0	115.0					11																	57367406		2201	4296	6497	SO:0001583	missense	710	exon2			CCAGAGAGTTTGC	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.106A>G	chr11.hg19:g.57367406A>G	ENSP00000278407:p.Ser36Gly	96.0	0.0		156.0	7.0	NM_001032295	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Missense_Mutation	SNP	ENST00000278407.4	hg19	CCDS7962.1	.	.	.	.	.	.	.	.	.	.	A	11.52	1.663237	0.29515	.	.	ENSG00000149131	ENST00000405496;ENST00000278407;ENST00000457869;ENST00000340687;ENST00000378323;ENST00000403558;ENST00000433668	D;D;T;D;D;D	0.89875	-2.58;-1.93;-1.42;-1.98;-1.99;-2.03	4.76	-0.369	0.12534	.	1.223870	0.05423	N	0.544623	T	0.81403	0.4815	L	0.46157	1.445	0.09310	N	1	B;P;B;B	0.39480	0.118;0.675;0.118;0.118	B;B;B;B	0.28553	0.026;0.091;0.037;0.026	T	0.69716	-0.5070	10	0.59425	D	0.04	.	4.704	0.12841	0.5712:0.1563:0.2725:0.0	.	41;70;36;36	B4E1F0;E9PGN7;E9KL26;P05155	.;.;.;IC1_HUMAN	G	36;36;70;36;41;70;36	ENSP00000384561:S36G;ENSP00000278407:S36G;ENSP00000399746:S70G;ENSP00000341861:S36G;ENSP00000367574:S41G;ENSP00000384420:S70G	ENSP00000278407:S36G	S	+	1	0	SERPING1	57123982	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	0.428000	0.21395	-0.144000	0.11314	0.402000	0.26972	AGT	.	.		0.478	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062	
FADS3	3995	hgsc.bcm.edu	37	11	61658711	61658711	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:61658711A>G	ENST00000278829.2	-	1	295	c.143T>C	c.(142-144)aTc>aCc	p.I48T	FADS3_ENST00000529525.1_5'UTR|FADS3_ENST00000540820.1_Missense_Mutation_p.I48T|FADS3_ENST00000527697.1_Intron|FADS3_ENST00000525588.1_Missense_Mutation_p.I48T	NM_021727.3	NP_068373.1	Q9Y5Q0	FADS3_HUMAN	fatty acid desaturase 3	48	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.				unsaturated fatty acid biosynthetic process (GO:0006636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water (GO:0016717)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CCAGCGGCTGATGTCGTAGAC	0.711																																					p.I48T		Atlas-SNP	.											.	FADS3	29	.	0			c.T143C						.						5.0	6.0	6.0					11																	61658711		2043	4012	6055	SO:0001583	missense	3995	exon1			CGGCTGATGTCGT		CCDS8013.1	11q12-q13.1	2013-01-25			ENSG00000221968	ENSG00000221968	1.14.19.3	"""Fatty acid desaturases"""	3576	protein-coding gene	gene with protein product	"""delta-9-desaturase"""	606150		LLCDL3			Standard	NM_021727		Approved	CYB5RP	uc001nsm.3	Q9Y5Q0	OTTHUMG00000167500	ENST00000278829.2:c.143T>C	chr11.hg19:g.61658711A>G	ENSP00000278829:p.Ile48Thr	43.0	0.0		96.0	4.0	NM_021727	O60426	Missense_Mutation	SNP	ENST00000278829.2	hg19	CCDS8013.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.626385	0.66901	.	.	ENSG00000221968	ENST00000278829;ENST00000540820;ENST00000525588	T;T;T	0.81330	-1.48;-1.48;-1.48	3.65	3.65	0.41850	Cytochrome b5 (4);	0.117094	0.34555	U	0.003864	D	0.85371	0.5681	M	0.79123	2.44	0.39950	D	0.974528	B	0.31318	0.319	P	0.46339	0.513	D	0.87215	0.2250	10	0.66056	D	0.02	-8.2834	11.5368	0.50641	1.0:0.0:0.0:0.0	.	48	Q9Y5Q0	FADS3_HUMAN	T	48	ENSP00000278829:I48T;ENSP00000439308:I48T;ENSP00000432206:I48T	ENSP00000278829:I48T	I	-	2	0	FADS3	61415287	1.000000	0.71417	0.993000	0.49108	0.999000	0.98932	7.106000	0.77039	1.657000	0.50732	0.533000	0.62120	ATC	.	.		0.711	FADS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394836.1		
FERMT3	83706	hgsc.bcm.edu	37	11	63988014	63988014	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:63988014T>C	ENST00000279227.5	+	12	1525	c.1430T>C	c.(1429-1431)cTc>cCc	p.L477P	FERMT3_ENST00000345728.5_Missense_Mutation_p.L473P	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	477	FERM.				integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|platelet aggregation (GO:0070527)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|podosome (GO:0002102)	integrin binding (GO:0005178)			breast(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	18						CTGGCCTTCCTCAGCCTGCAG	0.711																																					p.L477P		Atlas-SNP	.											.	FERMT3	51	.	0			c.T1430C						.						12.0	14.0	13.0					11																	63988014		2184	4270	6454	SO:0001583	missense	83706	exon12			CCTTCCTCAGCCT	L25343	CCDS8059.1, CCDS8060.1	11q13.1	2014-09-17	2010-06-24		ENSG00000149781	ENSG00000149781		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	23151	protein-coding gene	gene with protein product	"""kindlin-3"""	607901	"""fermitin family homolog 3 (Drosophila)"""				Standard	NM_178443		Approved	URP2, KIND3, MIG2B, MGC10966, MIG-2, UNC112C	uc001nym.2	Q86UX7	OTTHUMG00000167790	ENST00000279227.5:c.1430T>C	chr11.hg19:g.63988014T>C	ENSP00000279227:p.Leu477Pro	46.0	0.0		94.0	4.0	NM_178443	Q8IUA1|Q8N207|Q9BT48	Missense_Mutation	SNP	ENST00000279227.5	hg19	CCDS8060.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.1|22.1	4.249925|4.249925	0.80024|0.80024	.|.	.|.	ENSG00000149781|ENSG00000149781	ENST00000345728;ENST00000279227|ENST00000545896	T;T|T	0.77098|0.56941	-1.07;-1.07|0.43	4.31|4.31	4.31|4.31	0.51392|0.51392	Band 4.1 domain (1);FERM central domain (2);|.	0.000000|.	0.64402|.	D|.	0.000004|.	T|T	0.65059|0.65059	0.2655|0.2655	M|M	0.73598|0.73598	2.24|2.24	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	T|T	0.66654|0.66654	-0.5869|-0.5869	10|6	0.87932|.	D|.	0|.	-34.5898|-34.5898	12.87|12.87	0.57960|0.57960	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	473;477|.	Q86UX7-2;Q86UX7|.	.;URP2_HUMAN|.	P|P	473;477|36	ENSP00000339950:L473P;ENSP00000279227:L477P|ENSP00000440209:S36P	ENSP00000279227:L477P|.	L|S	+|+	2|1	0|0	FERMT3|FERMT3	63744590|63744590	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.915000|0.915000	0.54546|0.54546	5.707000|5.707000	0.68370|0.68370	1.940000|1.940000	0.56252|0.56252	0.459000|0.459000	0.35465|0.35465	CTC|TCA	.	.		0.711	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471	
SCYL1	57410	hgsc.bcm.edu	37	11	65294460	65294460	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:65294460T>C	ENST00000270176.5	+	6	798	c.721T>C	c.(721-723)Tgt>Cgt	p.C241R	SCYL1_ENST00000533862.1_Missense_Mutation_p.C241R|SCYL1_ENST00000527009.1_Missense_Mutation_p.C98R|SCYL1_ENST00000420247.2_Missense_Mutation_p.C241R|SCYL1_ENST00000279270.6_Missense_Mutation_p.C241R|SCYL1_ENST00000524944.1_Missense_Mutation_p.C241R|SCYL1_ENST00000525364.1_Missense_Mutation_p.C241R	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	241	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)			ovary(1)|skin(1)	2						GCCCCATTACTGTGAGCTGGT	0.627																																					p.C241R		Atlas-SNP	.											.	SCYL1	76	.	0			c.T721C						.						39.0	43.0	42.0					11																	65294460		1941	4131	6072	SO:0001583	missense	57410	exon6			CATTACTGTGAGC	AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"""teratoma-associated tyrosine kinase"", ""telomerase transcriptional elements-interacting factor"", ""telomerase regulation-associated protein"""	607982	"""N-terminal kinase-like"""	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.721T>C	chr11.hg19:g.65294460T>C	ENSP00000270176:p.Cys241Arg	120.0	0.0		143.0	6.0	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Missense_Mutation	SNP	ENST00000270176.5	hg19	CCDS41672.1	.	.	.	.	.	.	.	.	.	.	T	11.65	1.700715	0.30142	.	.	ENSG00000142186	ENST00000270176;ENST00000525364;ENST00000420247;ENST00000533862;ENST00000527630;ENST00000349495;ENST00000279270;ENST00000524944;ENST00000417543;ENST00000527009	T;T;T;T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63	4.64	4.64	0.57946	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.047838	0.85682	D	0.000000	T	0.53318	0.1789	N	0.21508	0.67	0.80722	D	1	B;B;B;B	0.28470	0.004;0.009;0.009;0.213	B;B;B;B	0.30401	0.055;0.032;0.032;0.115	T	0.48833	-0.9000	10	0.07325	T	0.83	-5.9943	12.3316	0.55043	0.0:0.0:0.0:1.0	.	241;241;241;241	E9PS17;Q96KG9-6;Q96KG9-2;Q96KG9	.;.;.;NTKL_HUMAN	R	241;241;241;241;241;241;241;241;241;98	ENSP00000270176:C241R;ENSP00000431635:C241R;ENSP00000408192:C241R;ENSP00000437254:C241R;ENSP00000433450:C241R;ENSP00000279270:C241R;ENSP00000432175:C241R;ENSP00000436993:C98R	ENSP00000270176:C241R	C	+	1	0	SCYL1	65051036	1.000000	0.71417	0.998000	0.56505	0.935000	0.57460	6.943000	0.75934	1.870000	0.54199	0.459000	0.35465	TGT	.	.		0.627	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680	
MYEOV	26579	hgsc.bcm.edu	37	11	69063723	69063723	+	Missense_Mutation	SNP	T	T	C	rs552116583	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:69063723T>C	ENST00000308946.3	+	3	1256	c.806T>C	c.(805-807)cTg>cCg	p.L269P	MYEOV_ENST00000535407.1_Missense_Mutation_p.L211P|MYEOV_ENST00000441339.2_Missense_Mutation_p.L269P	NM_138768.2	NP_620123.2	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	269										endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|urinary_tract(1)	24	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)		GTTGAGGCCCTGGGGGGGTGG	0.677																																					p.L269P		Atlas-SNP	.											.,1	MYEOV	42	.	0			c.T806C						.						46.0	49.0	48.0					11																	69063723		2200	4294	6494	SO:0001583	missense	26579	exon3			AGGCCCTGGGGGG	AJ223366	CCDS8190.1, CCDS73340.1	11q13.2	2013-03-27	2013-03-27			ENSG00000172927			7563	protein-coding gene	gene with protein product		605625	"""myeloma overexpressed (in a subset of t(11;14) positive multiple myelomas)"""			10753852	Standard	XM_005273908		Approved	OCIM	uc001oov.3	Q96EZ4		ENST00000308946.3:c.806T>C	chr11.hg19:g.69063723T>C	ENSP00000308330:p.Leu269Pro	86.0	2.0		145.0	8.0	NM_138768	Q9UGN6|Q9UGN7	Missense_Mutation	SNP	ENST00000308946.3	hg19	CCDS8190.1	.	.	.	.	.	.	.	.	.	.	T	2.171	-0.389831	0.04932	.	.	ENSG00000172927	ENST00000441339;ENST00000308946;ENST00000535407	T;T;T	0.27402	1.68;1.68;1.67	1.59	-3.17	0.05202	.	.	.	.	.	T	0.13200	0.0320	N	0.08118	0	0.09310	N	1	P	0.47910	0.902	B	0.41135	0.348	T	0.16335	-1.0406	9	0.87932	D	0	.	4.1225	0.10112	0.1762:0.0:0.3642:0.4596	.	269	Q96EZ4	MYEOV_HUMAN	P	269;269;211	ENSP00000412482:L269P;ENSP00000308330:L269P;ENSP00000438100:L211P	ENSP00000308330:L269P	L	+	2	0	MYEOV	68820299	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.789000	0.04609	-2.394000	0.00583	-2.303000	0.00259	CTG	.	.		0.677	MYEOV-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396548.1		
RNF121	55298	hgsc.bcm.edu	37	11	71671841	71671841	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:71671841T>C	ENST00000361756.3	+	3	508	c.147T>C	c.(145-147)gcT>gcC	p.A49A	RNF121_ENST00000545854.1_5'UTR|RNF121_ENST00000490867.1_3'UTR|RNF121_ENST00000393713.3_Silent_p.A17A|RNF121_ENST00000533380.1_Silent_p.A17A|RNF121_ENST00000530137.1_Silent_p.A17A	NM_018320.4	NP_060790.2	Q9H920	RN121_HUMAN	ring finger protein 121	49						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|urinary_tract(1)	13						GCCATGAAGCTATGCATGCTG	0.552																																					p.A49A		Atlas-SNP	.											.	RNF121	19	.	0			c.T147C						.						143.0	102.0	116.0					11																	71671841		2200	4293	6493	SO:0001819	synonymous_variant	55298	exon3			TGAAGCTATGCAT	AK001961	CCDS8203.1, CCDS73343.1	11q13.3	2008-02-05			ENSG00000137522	ENSG00000137522		"""RING-type (C3HC4) zinc fingers"""	21070	protein-coding gene	gene with protein product							Standard	NM_018320		Approved	FLJ11099	uc001ora.3	Q9H920	OTTHUMG00000157023	ENST00000361756.3:c.147T>C	chr11.hg19:g.71671841T>C		85.0	0.0		119.0	5.0	NM_018320	B3KSW8|Q6IA57|Q6P449|Q96DB4	Silent	SNP	ENST00000361756.3	hg19	CCDS8203.1																																																																																			.	.		0.552	RNF121-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347132.1	NM_018320	
C11orf30	56946	hgsc.bcm.edu	37	11	76255832	76255832	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76255832T>C	ENST00000529032.1	+	18	3239	c.3239T>C	c.(3238-3240)cTc>cCc	p.L1080P	C11orf30_ENST00000525919.1_Missense_Mutation_p.L1081P|C11orf30_ENST00000524767.1_Missense_Mutation_p.L1095P|C11orf30_ENST00000334736.3_Missense_Mutation_p.L1080P|C11orf30_ENST00000524490.1_Missense_Mutation_p.L982P|C11orf30_ENST00000525038.1_Missense_Mutation_p.L1081P|C11orf30_ENST00000343878.3_Missense_Mutation_p.L1080P|C11orf30_ENST00000533248.1_Missense_Mutation_p.L989P			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	1080	Gln-rich.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						CAAATGTCGCTCCCAGCTTCT	0.478																																					p.L1080P		Atlas-SNP	.											.	C11orf30	123	.	0			c.T3239C						.						64.0	77.0	73.0					11																	76255832		2200	4292	6492	SO:0001583	missense	56946	exon19			TGTCGCTCCCAGC	AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.3239T>C	chr11.hg19:g.76255832T>C	ENSP00000432327:p.Leu1080Pro	55.0	0.0		63.0	4.0	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Missense_Mutation	SNP	ENST00000529032.1	hg19	CCDS8244.1	.	.	.	.	.	.	.	.	.	.	T	13.05	2.121128	0.37436	.	.	ENSG00000158636	ENST00000524490;ENST00000334736;ENST00000343878;ENST00000393457;ENST00000524767;ENST00000533248;ENST00000525919;ENST00000525038;ENST00000529032;ENST00000532719	.	.	.	5.24	4.1	0.47936	.	0.183972	0.49916	D	0.000136	T	0.53786	0.1818	N	0.19112	0.55	0.58432	D	0.999998	D;P;P;D;D;D;D	0.69078	0.996;0.94;0.94;0.99;0.976;0.997;0.976	D;P;P;P;P;P;P	0.67725	0.953;0.462;0.462;0.836;0.454;0.879;0.454	T	0.50923	-0.8770	9	0.36615	T	0.2	-1.3643	11.4725	0.50278	0.1349:0.0:0.0:0.8651	.	989;1081;1095;434;1081;982;1080	B7ZKT8;B7ZKU2;B7ZKU0;B3KWW8;Q17RM7;E9PMC9;Q7Z589	.;.;.;.;.;.;EMSY_HUMAN	P	982;1080;1080;762;1095;989;1081;1081;1080;220	.	ENSP00000334130:L1080P	L	+	2	0	C11orf30	75933480	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.574000	0.53863	0.815000	0.34398	0.383000	0.25322	CTC	.	.		0.478	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193	
NARS2	79731	hgsc.bcm.edu	37	11	78154722	78154722	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:78154722T>C	ENST00000281038.5	-	12	1622	c.1247A>G	c.(1246-1248)gAg>gGg	p.E416G	RP11-452H21.1_ENST00000534168.1_RNA|NARS2_ENST00000528850.1_Missense_Mutation_p.E189G	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	416					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	TAAGCGCTCCTCTAAGAAATG	0.438																																					p.E416G		Atlas-SNP	.											.	NARS2	62	.	0			c.A1247G						.						96.0	91.0	92.0					11																	78154722		2200	4292	6492	SO:0001583	missense	79731	exon12			CGCTCCTCTAAGA	BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"""Aminoacyl tRNA synthetases / Class II"""	26274	protein-coding gene	gene with protein product	"""asparagine tRNA ligase 2, mitochondrial (putative)"""	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.1247A>G	chr11.hg19:g.78154722T>C	ENSP00000281038:p.Glu416Gly	75.0	0.0		82.0	4.0	NM_024678	G3V178	Missense_Mutation	SNP	ENST00000281038.5	hg19	CCDS8261.1	.	.	.	.	.	.	.	.	.	.	T	15.87	2.961013	0.53400	.	.	ENSG00000137513	ENST00000281038;ENST00000528850	T;T	0.80480	-1.38;-1.38	4.96	3.8	0.43715	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.452209	0.27572	N	0.018770	D	0.83275	0.5219	M	0.86953	2.85	0.38088	D	0.93686	P	0.39920	0.695	B	0.41374	0.355	D	0.85761	0.1349	10	0.59425	D	0.04	-7.8818	12.1094	0.53830	0.0:0.0:0.1439:0.8561	.	416	Q96I59	SYNM_HUMAN	G	416;189	ENSP00000281038:E416G;ENSP00000432635:E189G	ENSP00000281038:E416G	E	-	2	0	NARS2	77832370	0.891000	0.30450	1.000000	0.80357	0.991000	0.79684	3.084000	0.50143	0.992000	0.38840	0.482000	0.46254	GAG	.	.		0.438	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678	
PCF11	51585	hgsc.bcm.edu	37	11	82877693	82877693	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:82877693T>C	ENST00000298281.4	+	5	2206	c.1754T>C	c.(1753-1755)gTa>gCa	p.V585A		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	585					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						AAGGAGAATGTAGAAAACTGG	0.393																																					p.V585A		Atlas-SNP	.											.	PCF11	220	.	0			c.T1754C						.						67.0	66.0	66.0					11																	82877693		1815	4038	5853	SO:0001583	missense	51585	exon5			AGAATGTAGAAAA	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.1754T>C	chr11.hg19:g.82877693T>C	ENSP00000298281:p.Val585Ala	100.0	0.0		122.0	58.0	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	T	4.321	0.058962	0.08339	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.50548	1.75;0.74;0.76	6.07	6.07	0.98685	.	0.819345	0.10731	N	0.640597	T	0.28797	0.0714	N	0.08118	0	0.09310	N	0.999999	B;B	0.10296	0.003;0.0	B;B	0.04013	0.001;0.001	T	0.15578	-1.0432	9	.	.	.	.	11.1894	0.48677	0.0:0.0761:0.0:0.9239	.	585;585	E9PQ01;O94913	.;PCF11_HUMAN	A	585	ENSP00000298281:V585A;ENSP00000434540:V585A;ENSP00000431567:V585A	.	V	+	2	0	PCF11	82555341	1.000000	0.71417	0.653000	0.29593	0.954000	0.61252	4.381000	0.59587	2.326000	0.78906	0.533000	0.62120	GTA	.	.		0.393	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
KIAA1731	85459	hgsc.bcm.edu	37	11	93412715	93412715	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:93412715T>C	ENST00000325212.6	+	7	924	c.762T>C	c.(760-762)gcT>gcC	p.A254A	KIAA1731_ENST00000411936.1_Silent_p.A254A|KIAA1731_ENST00000344196.4_5'UTR			Q9C0D2	K1731_HUMAN	KIAA1731	254						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TCCATTTGGCTCAAGTAAGAC	0.413																																					p.A254A		Atlas-SNP	.											.	KIAA1731	173	.	0			c.T762C						.						111.0	117.0	115.0					11																	93412715		692	1591	2283	SO:0001819	synonymous_variant	85459	exon7			TTTGGCTCAAGTA	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.762T>C	chr11.hg19:g.93412715T>C		68.0	0.0		134.0	6.0	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Silent	SNP	ENST00000325212.6	hg19	CCDS44708.1																																																																																			.	.		0.413	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
PANX1	24145	hgsc.bcm.edu	37	11	93912932	93912932	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:93912932T>C	ENST00000227638.3	+	4	1095	c.710T>C	c.(709-711)cTc>cCc	p.L237P	PANX1_ENST00000436171.2_Missense_Mutation_p.L237P	NM_015368.3	NP_056183.2	Q96RD7	PANX1_HUMAN	pannexin 1	237					calcium ion transport (GO:0006816)|cation transport (GO:0006812)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|protein hexamerization (GO:0034214)|response to ATP (GO:0033198)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	bleb (GO:0032059)|endoplasmic reticulum (GO:0005783)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium channel activity (GO:0005262)|gap junction hemi-channel activity (GO:0055077)|leak channel activity (GO:0022840)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Probenecid(DB01032)	TACTTCAGCCTCTCCTCACTC	0.448																																					p.L237P		Atlas-SNP	.											.	PANX1	38	.	0			c.T710C						.						124.0	110.0	115.0					11																	93912932		2201	4298	6499	SO:0001583	missense	24145	exon4			TCAGCCTCTCCTC	AF093239	CCDS8296.1	11q14-q21	2011-12-02			ENSG00000110218	ENSG00000110218		"""Ion channels / Pannexins"""	8599	protein-coding gene	gene with protein product	"""innexin"""	608420				14597722	Standard	NM_015368		Approved	MRS1, UNQ2529, PX1	uc001per.3	Q96RD7	OTTHUMG00000167757	ENST00000227638.3:c.710T>C	chr11.hg19:g.93912932T>C	ENSP00000227638:p.Leu237Pro	90.0	0.0		117.0	7.0	NM_015368	O75968|Q543A0|Q6UW26|Q96AM9|Q96L77|Q96RS5	Missense_Mutation	SNP	ENST00000227638.3	hg19	CCDS8296.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.312663	0.60414	.	.	ENSG00000110218	ENST00000227638;ENST00000436171	T;T	0.20598	2.07;2.06	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.50222	0.1603	M	0.83483	2.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.49643	-0.8918	10	0.35671	T	0.21	-30.008	16.0852	0.81042	0.0:0.0:0.0:1.0	.	237;237	Q96RD7;Q96RD7-2	PANX1_HUMAN;.	P	237	ENSP00000227638:L237P;ENSP00000411461:L237P	ENSP00000227638:L237P	L	+	2	0	PANX1	93552580	1.000000	0.71417	0.949000	0.38748	0.564000	0.35744	7.538000	0.82048	2.279000	0.76181	0.533000	0.62120	CTC	.	.		0.448	PANX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396121.1	NM_015368	
DYNC2H1	79659	hgsc.bcm.edu	37	11	102991458	102991458	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:102991458T>C	ENST00000375735.2	+	8	1319	c.1175T>C	c.(1174-1176)aTt>aCt	p.I392T	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.I392T|DYNC2H1_ENST00000334267.7_Missense_Mutation_p.I392T	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	392	Stem. {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)		GAAAAGATTATTGCACCTGCG	0.308																																					p.I392T		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T1175C						.						37.0	36.0	36.0					11																	102991458		1807	4061	5868	SO:0001583	missense	79659	exon8			AGATTATTGCACC	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.1175T>C	chr11.hg19:g.102991458T>C	ENSP00000364887:p.Ile392Thr	38.0	0.0		72.0	4.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	18.15	3.560736	0.65538	.	.	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093	T;T;T	0.56776	0.44;0.44;0.44	5.2	4.08	0.47627	Dynein heavy chain, domain-1 (1);	0.537912	0.15256	U	0.272042	T	0.66416	0.2787	M	0.73598	2.24	0.53688	D	0.999979	B;P;P	0.41188	0.084;0.741;0.734	B;P;P	0.53809	0.022;0.735;0.617	T	0.66460	-0.5918	10	0.87932	D	0	.	10.8046	0.46509	0.0:0.0744:0.0:0.9256	.	392;392;392	Q8NCM8-3;Q8NCM8;Q8NCM8-2	.;DYHC2_HUMAN;.	T	392	ENSP00000364887:I392T;ENSP00000334021:I392T;ENSP00000381167:I392T	ENSP00000334021:I392T	I	+	2	0	DYNC2H1	102496668	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.790000	0.62453	0.939000	0.37446	0.528000	0.53228	ATT	.	.		0.308	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103153740	103153740	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:103153740T>C	ENST00000375735.2	+	73	10960	c.10816T>C	c.(10816-10818)Tct>Cct	p.S3606P	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.S3613P|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3606					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)		ATTAAAGGACTCTCAACAAAA	0.313																																					p.S3613P		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T10837C						.						60.0	59.0	59.0					11																	103153740		1810	4063	5873	SO:0001583	missense	79659	exon74			AAGGACTCTCAAC	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.10816T>C	chr11.hg19:g.103153740T>C	ENSP00000364887:p.Ser3606Pro	81.0	0.0		175.0	7.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	11.75	1.732659	0.30684	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.28454	1.61;1.61	5.14	2.55	0.30701	.	0.647467	0.15994	N	0.234658	T	0.34716	0.0907	L	0.40543	1.245	0.37071	D	0.898524	P;P	0.52316	0.952;0.941	P;P	0.54815	0.761;0.648	T	0.18935	-1.0321	10	0.28530	T	0.3	.	9.7604	0.40528	0.272:0.0:0.0:0.728	.	3606;3613	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	P	3606;3613	ENSP00000364887:S3606P;ENSP00000381167:S3613P	ENSP00000364887:S3606P	S	+	1	0	DYNC2H1	102658950	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.010000	0.40913	0.842000	0.35045	0.377000	0.23210	TCT	.	.		0.313	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
POU2AF1	5450	hgsc.bcm.edu	37	11	111225126	111225126	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:111225126A>G	ENST00000393067.3	-	5	1145	c.631T>C	c.(631-633)Tct>Cct	p.S211P		NM_006235.2	NP_006226.2	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	211					humoral immune response (GO:0006959)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(2)|lung(2)	5		all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;3.12e-06)|all cancers(92;1.8e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0364)		TCTGGGATAGAGATGGGGAGC	0.622			T	BCL6	NHL																																p.S211P		Atlas-SNP	.		Dom	yes		11	11q23.1	5450	"""POU domain, class 2, associating factor 1 (OBF1)"""		L	.	POU2AF1	23	.	0			c.T631C						.						55.0	58.0	57.0					11																	111225126		2201	4297	6498	SO:0001583	missense	5450	exon5			GGATAGAGATGGG		CCDS31675.1	11q23.1	2011-06-01	2007-07-13			ENSG00000110777			9211	protein-coding gene	gene with protein product		601206	"""POU domain class 2, associating factor 1"""			8617501	Standard	NM_006235		Approved	OBF1	uc001plg.4	Q16633		ENST00000393067.3:c.631T>C	chr11.hg19:g.111225126A>G	ENSP00000376786:p.Ser211Pro	155.0	0.0		199.0	8.0	NM_006235	B2R8Z9|Q14983	Missense_Mutation	SNP	ENST00000393067.3	hg19	CCDS31675.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.167841	0.78339	.	.	ENSG00000110777	ENST00000393067	T	0.32023	1.47	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.45397	0.1340	L	0.41710	1.295	0.44880	D	0.997894	D	0.89917	1.0	D	0.91635	0.999	T	0.24584	-1.0156	10	0.33141	T	0.24	-3.9004	14.4288	0.67236	1.0:0.0:0.0:0.0	.	211	Q16633	OBF1_HUMAN	P	211	ENSP00000376786:S211P	ENSP00000376786:S211P	S	-	1	0	POU2AF1	110730336	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	4.228000	0.58619	2.067000	0.61834	0.460000	0.39030	TCT	.	.		0.622	POU2AF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391002.1	NM_006235	
SIK3	23387	hgsc.bcm.edu	37	11	116744713	116744713	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:116744713T>C	ENST00000292055.4	-	12	1348	c.1313A>G	c.(1312-1314)cAg>cGg	p.Q438R	SIK3_ENST00000375288.1_5'UTR|SIK3_ENST00000542607.1_Missense_Mutation_p.Q390R|SIK3_ENST00000446921.2_Missense_Mutation_p.Q448R|SIK3_ENST00000375300.1_Missense_Mutation_p.Q496R|SIK3_ENST00000434315.2_Missense_Mutation_p.Q337R	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	438					protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						GAATGGAGCCTGGGGGTTGAC	0.478																																					p.Q438R		Atlas-SNP	.											.	SIK3	112	.	0			c.A1313G						.						99.0	101.0	100.0					11																	116744713		2201	4296	6497	SO:0001583	missense	23387	exon12			GGAGCCTGGGGGT	AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.1313A>G	chr11.hg19:g.116744713T>C	ENSP00000292055:p.Gln438Arg	90.0	0.0		127.0	31.0	NM_025164	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	hg19	CCDS8379.1	.	.	.	.	.	.	.	.	.	.	T	17.92	3.506538	0.64410	.	.	ENSG00000160584	ENST00000375300;ENST00000292055;ENST00000542607;ENST00000434315	T;T;T;T	0.72835	-0.56;-0.6;-0.69;-0.18	5.33	4.18	0.49190	Protein kinase-like domain (1);	0.000000	0.37530	U	0.002048	T	0.75287	0.3829	L	0.38531	1.155	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.75020	0.985;0.918;0.985	T	0.72679	-0.4220	10	0.36615	T	0.2	.	12.3471	0.55126	0.0:0.0:0.1415:0.8585	.	390;337;438	A1A5A8;A1A5A9;Q9Y2K2	.;.;SIK3_HUMAN	R	496;438;390;337	ENSP00000364449:Q496R;ENSP00000292055:Q438R;ENSP00000438108:Q390R;ENSP00000415873:Q337R	ENSP00000292055:Q438R	Q	-	2	0	SIK3	116249923	1.000000	0.71417	0.409000	0.26459	0.484000	0.33280	7.503000	0.81632	0.843000	0.35070	-0.321000	0.08615	CAG	.	.		0.478	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164	
CEP164	22897	hgsc.bcm.edu	37	11	117222658	117222658	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	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	38.0	0.0		70.0	6.0	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	
TMPRSS13	84000	hgsc.bcm.edu	37	11	117782565	117782565	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:117782565T>C	ENST00000430170.2	-	6	907	c.820A>G	c.(820-822)Aca>Gca	p.T274A	TMPRSS13_ENST00000445164.2_Missense_Mutation_p.T274A|TMPRSS13_ENST00000526090.1_Missense_Mutation_p.T274A|TMPRSS13_ENST00000528626.1_Missense_Mutation_p.T239A|TMPRSS13_ENST00000524993.1_Missense_Mutation_p.T274A	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	274	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		ACCTCGGTTGTCCGGTGAGCA	0.582																																					p.T274A		Atlas-SNP	.											.	TMPRSS13	75	.	0			c.A820G						.						65.0	69.0	68.0					11																	117782565		1944	4141	6085	SO:0001583	missense	84000	exon6			CGGTTGTCCGGTG	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.820A>G	chr11.hg19:g.117782565T>C	ENSP00000387702:p.Thr274Ala	52.0	0.0		86.0	4.0	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000430170.2	hg19	CCDS58185.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.336595	0.60963	.	.	ENSG00000137747	ENST00000528626;ENST00000336500;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81	5.35	5.35	0.76521	.	0.366933	0.26535	N	0.023832	T	0.43964	0.1271	L	0.53729	1.69	0.39913	D	0.974055	B;B	0.33637	0.234;0.42	B;B	0.35240	0.198;0.061	T	0.39860	-0.9593	10	0.25751	T	0.34	.	12.7014	0.57035	0.0:0.0:0.0:1.0	.	269;274	Q9BYE2-4;E9PRA0	.;.	A	239;269;274;274;274;274	ENSP00000435813:T239A;ENSP00000434279:T274A;ENSP00000387702:T274A;ENSP00000394114:T274A;ENSP00000436502:T274A	ENSP00000337113:T269A	T	-	1	0	TMPRSS13	117287775	1.000000	0.71417	0.995000	0.50966	0.508000	0.34012	4.419000	0.59835	2.024000	0.59613	0.459000	0.35465	ACA	.	.		0.582	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
CLMP	79827	hgsc.bcm.edu	37	11	122968546	122968546	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:122968546T>C	ENST00000448775.2	-	2	483	c.143A>G	c.(142-144)gAt>gGt	p.D48G		NM_024769.2	NP_079045.1	Q9H6B4	CLMP_HUMAN	CXADR-like membrane protein	48	Ig-like C2-type 1.				digestive tract development (GO:0048565)	cell surface (GO:0009986)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	14						CCATTCAATATCCAGAGTGTC	0.502																																					p.D48G		Atlas-SNP	.											.	CLMP	39	.	0			c.A143G						.						152.0	147.0	149.0					11																	122968546		2202	4299	6501	SO:0001583	missense	79827	exon2			TCAATATCCAGAG	BC009371	CCDS8441.1	11q24	2013-01-29			ENSG00000166250	ENSG00000166250		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24039	protein-coding gene	gene with protein product	"""adipocyte-specific adhesion molecule"", ""coxsackie- and adenovirus receptor-like membrane protein"", ""adipocyte adhesion molecule"""	611693				12851705, 14573622	Standard	NM_024769		Approved	ASAM, FLJ22415, ACAM	uc001pyt.3	Q9H6B4		ENST00000448775.2:c.143A>G	chr11.hg19:g.122968546T>C	ENSP00000405577:p.Asp48Gly	97.0	0.0		127.0	6.0	NM_024769		Missense_Mutation	SNP	ENST00000448775.2	hg19	CCDS8441.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.280885	0.80692	.	.	ENSG00000166250	ENST00000448775	T	0.66638	-0.22	5.34	5.34	0.76211	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.80110	0.4563	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78919	-0.2014	10	0.32370	T	0.25	.	13.8471	0.63474	0.0:0.0:0.0:1.0	.	48	Q9H6B4	CLMP_HUMAN	G	48	ENSP00000405577:D48G	ENSP00000405577:D48G	D	-	2	0	CLMP	122473756	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.069000	0.64370	2.161000	0.67846	0.379000	0.24179	GAT	.	.		0.502	CLMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387542.1	NM_024769	
NTM	50863	hgsc.bcm.edu	37	11	132177637	132177637	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:132177637A>G	ENST00000374786.1	+	4	1060	c.581A>G	c.(580-582)gAg>gGg	p.E194G	NTM_ENST00000374791.3_Missense_Mutation_p.E194G|NTM_ENST00000474900.1_3'UTR|NTM_ENST00000539799.1_Missense_Mutation_p.E194G|NTM_ENST00000425719.2_Missense_Mutation_p.E194G|NTM_ENST00000427481.2_Missense_Mutation_p.E185G|NTM_ENST00000374784.1_Missense_Mutation_p.E194G	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	194	Ig-like C2-type 2.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						ATCACCAGGGAGCAGTCAGGG	0.527																																					p.E194G		Atlas-SNP	.											.	NTM	253	.	0			c.A581G						.						97.0	87.0	90.0					11																	132177637		2201	4297	6498	SO:0001583	missense	50863	exon4			CCAGGGAGCAGTC	AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"""Immunoglobulin superfamily / I-set domain containing"""	17941	protein-coding gene	gene with protein product	"""neurotrimin"", ""IgLON family member 2"""	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.581A>G	chr11.hg19:g.132177637A>G	ENSP00000363918:p.Glu194Gly	50.0	0.0		115.0	5.0	NM_001144059	A0MTT2|Q6UXJ3|Q86VJ9	Missense_Mutation	SNP	ENST00000374786.1	hg19	CCDS8491.1	.	.	.	.	.	.	.	.	.	.	A	12.94	2.087205	0.36855	.	.	ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000550167;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784	T;T;T;T;T;T;T	0.39406	1.44;1.44;1.08;1.44;1.44;1.44;1.44	5.62	4.43	0.53597	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.089217	0.85682	D	0.000000	T	0.30603	0.0770	L	0.28776	0.89	0.52501	D	0.99995	B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0;0.001	B;B;B;B;B;B	0.15484	0.013;0.004;0.003;0.002;0.003;0.001	T	0.07404	-1.0774	10	0.22706	T	0.39	-29.9428	13.2973	0.60305	0.8689:0.1311:0.0:0.0	.	194;185;194;194;194;194	B7Z1Z5;B7Z1I4;Q9P121-4;Q9P121;Q9P121-3;Q9P121-2	.;.;.;NTRI_HUMAN;.;.	G	194;194;185;185;194;194;194	ENSP00000363923:E194G;ENSP00000437668:E194G;ENSP00000448104:E185G;ENSP00000416320:E185G;ENSP00000363918:E194G;ENSP00000396722:E194G;ENSP00000363916:E194G	ENSP00000363916:E194G	E	+	2	0	NTM	131682847	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.007000	0.76335	2.267000	0.75376	0.383000	0.25322	GAG	.	.		0.527	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522	
TEAD4	7004	hgsc.bcm.edu	37	12	3128311	3128311	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:3128311T>C	ENST00000397122.2	+	6	456	c.171T>C	c.(169-171)gcT>gcC	p.A57A	TEAD4_ENST00000358409.2_Silent_p.A143A|TEAD4_ENST00000359864.2_Silent_p.A186A	NM_201443.2	NP_958851.1	Q15561	TEAD4_HUMAN	TEA domain family member 4	186					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)			AAACCTATGCTGTCCAGCCTC	0.682																																					p.A186A		Atlas-SNP	.											.	TEAD4	45	.	0			c.T558C						.						93.0	76.0	81.0					12																	3128311		2203	4300	6503	SO:0001819	synonymous_variant	7004	exon8			CTATGCTGTCCAG	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.171T>C	chr12.hg19:g.3128311T>C		115.0	0.0		92.0	5.0	NM_003213	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Silent	SNP	ENST00000397122.2	hg19	CCDS41737.1	.	.	.	.	.	.	.	.	.	.	T	10.85	1.467103	0.26335	.	.	ENSG00000197905	ENST00000544666	.	.	.	5.0	3.86	0.44501	.	.	.	.	.	T	0.57257	0.2041	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52071	-0.8624	4	.	.	.	0.4751	7.3544	0.26711	0.0:0.1698:0.0:0.8302	.	.	.	.	R	109	.	.	C	+	1	0	TEAD4	2998572	0.993000	0.37304	0.979000	0.43373	0.925000	0.55904	0.744000	0.26245	0.759000	0.33084	0.459000	0.35465	TGT	.	.		0.682	TEAD4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398477.1	NM_003213	
PZP	5858	hgsc.bcm.edu	37	12	9349247	9349247	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:9349247T>C	ENST00000261336.2	-	9	930	c.902A>G	c.(901-903)cAc>cGc	p.H301R	PZP_ENST00000381997.2_Missense_Mutation_p.H170R	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	301					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CATTTTGGTGTGTACTTGTTG	0.398																																					p.H301R	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.A902G						.						146.0	141.0	143.0					12																	9349247		2203	4300	6503	SO:0001583	missense	5858	exon9			TTGGTGTGTACTT	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.902A>G	chr12.hg19:g.9349247T>C	ENSP00000261336:p.His301Arg	84.0	0.0		68.0	4.0	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	hg19	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	5.429	0.264282	0.10294	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.32753	1.64;1.44	3.57	2.4	0.29515	.	0.940200	0.08770	N	0.896414	T	0.10937	0.0267	N	0.01352	-0.895	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.26258	-1.0108	10	0.34782	T	0.22	.	5.8195	0.18520	0.0:0.1321:0.0:0.8679	.	170;301	P20742-2;P20742	.;PZP_HUMAN	R	301;170	ENSP00000261336:H301R;ENSP00000371427:H170R	ENSP00000261336:H301R	H	-	2	0	PZP	9240514	0.003000	0.15002	0.016000	0.15963	0.006000	0.05464	0.144000	0.16135	0.546000	0.28920	0.374000	0.22700	CAC	.	.		0.398	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
CLEC1B	51266	hgsc.bcm.edu	37	12	10147781	10147781	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:10147781T>C	ENST00000298527.6	-	5	682	c.503A>G	c.(502-504)gAg>gGg	p.E168G	CLEC1B_ENST00000348658.4_Missense_Mutation_p.E135G|CLEC1B_ENST00000428126.2_Missense_Mutation_p.E135G	NM_016509.3	NP_057593.3	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B	168	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|platelet formation (GO:0030220)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						CTTCCAGACCTCATTCGACTT	0.408																																					p.E168G		Atlas-SNP	.											.	CLEC1B	39	.	0			c.A503G						.						270.0	262.0	265.0					12																	10147781		1869	4096	5965	SO:0001583	missense	51266	exon5			CAGACCTCATTCG	AF124841	CCDS41751.1, CCDS41752.1	12p13.31	2006-04-12				ENSG00000165682		"""C-type lectin domain containing"""	24356	protein-coding gene	gene with protein product		606783				10671229, 11745369	Standard	NM_016509		Approved	CLEC2	uc001qwu.3	Q9P126		ENST00000298527.6:c.503A>G	chr12.hg19:g.10147781T>C	ENSP00000298527:p.Glu168Gly	56.0	0.0		36.0	4.0	NM_016509	Q6UWX7|Q8NHR6	Missense_Mutation	SNP	ENST00000298527.6	hg19	CCDS41752.1	.	.	.	.	.	.	.	.	.	.	T	7.016	0.557656	0.13436	.	.	ENSG00000165682	ENST00000398937;ENST00000428126;ENST00000298527;ENST00000348658;ENST00000398939	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	3.83	2.78	0.32641	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.888420	0.09391	N	0.808501	T	0.05777	0.0151	N	0.05177	-0.1	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.001;0.003	T	0.43196	-0.9406	10	0.22109	T	0.4	.	3.0056	0.06027	0.0:0.3524:0.0:0.6476	.	135;168	Q9P126-2;Q9P126	.;CLC1B_HUMAN	G	75;135;168;135;75	ENSP00000381910:E75G;ENSP00000406338:E135G;ENSP00000298527:E168G;ENSP00000327169:E135G	ENSP00000298527:E168G	E	-	2	0	CLEC1B	10039048	0.001000	0.12720	0.001000	0.08648	0.470000	0.32858	0.827000	0.27421	0.560000	0.29169	0.248000	0.18094	GAG	.	.		0.408	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509	
TAS2R8	50836	hgsc.bcm.edu	37	12	10958681	10958681	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:10958681A>G	ENST00000240615.2	-	1	1211	c.899T>C	c.(898-900)cTg>cCg	p.L300P		NM_023918.1	NP_076407.1	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	300					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)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TCTACATGTCAGCATTCTGAC	0.318																																					p.L300P		Atlas-SNP	.											.	TAS2R8	42	.	0			c.T899C						.						27.0	28.0	28.0					12																	10958681		2197	4291	6488	SO:0001583	missense	50836	exon1			CATGTCAGCATTC	AF227134	CCDS8632.1	12p13	2012-08-22			ENSG00000121314	ENSG00000121314		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14915	protein-coding gene	gene with protein product		604794				10761934, 10766242	Standard	NM_023918		Approved	T2R8, TRB5	uc010shh.2	Q9NYW2	OTTHUMG00000168506	ENST00000240615.2:c.899T>C	chr12.hg19:g.10958681A>G	ENSP00000240615:p.Leu300Pro	127.0	0.0		127.0	7.0	NM_023918	Q4KN29|Q645Y2	Missense_Mutation	SNP	ENST00000240615.2	hg19	CCDS8632.1	.	.	.	.	.	.	.	.	.	.	A	11.97	1.797846	0.31777	.	.	ENSG00000121314	ENST00000240615	T	0.01323	5.01	3.95	1.51	0.23008	.	0.699272	0.11364	N	0.571658	T	0.09291	0.0229	M	0.91768	3.24	0.09310	N	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.10520	-1.0626	10	0.87932	D	0	.	5.7189	0.17976	0.7703:0.0:0.2297:0.0	.	300	Q9NYW2	TA2R8_HUMAN	P	300	ENSP00000240615:L300P	ENSP00000240615:L300P	L	-	2	0	TAS2R8	10849948	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	0.519000	0.22862	0.207000	0.20607	-0.256000	0.11100	CTG	.	.		0.318	TAS2R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399932.1		
PLBD1	79887	hgsc.bcm.edu	37	12	14693776	14693776	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:14693776T>C	ENST00000240617.5	-	4	1132	c.480A>G	c.(478-480)agA>agG	p.R160R		NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	160					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						AGCCTGTATGTCTCCAAAATG	0.393																																					p.R160R		Atlas-SNP	.											.	PLBD1	36	.	0			c.A480G						.						205.0	198.0	200.0					12																	14693776		2203	4300	6503	SO:0001819	synonymous_variant	79887	exon4			TGTATGTCTCCAA	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.480A>G	chr12.hg19:g.14693776T>C		170.0	0.0		116.0	5.0	NM_024829	A8K4E9|Q9BVV3|Q9H625	Silent	SNP	ENST00000240617.5	hg19	CCDS31751.1																																																																																			.	.		0.393	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401203.1	NM_024829	
PLCZ1	89869	hgsc.bcm.edu	37	12	18872429	18872429	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:18872429A>G	ENST00000266505.7	-	5	768	c.505T>C	c.(505-507)Tca>Cca	p.S169P	PLCZ1_ENST00000435379.1_Intron|PLCZ1_ENST00000447925.2_Missense_Mutation_p.S167P|PLCZ1_ENST00000539875.1_Intron|PLCZ1_ENST00000541695.1_Missense_Mutation_p.S32P|RP11-361I14.2_ENST00000536931.1_RNA					phospholipase C, zeta 1											NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					GTGTTATGTGAAGATGAAATA	0.264																																					p.S169P		Atlas-SNP	.											.	PLCZ1	107	.	0			c.T505C						.						56.0	58.0	57.0					12																	18872429		2202	4289	6491	SO:0001583	missense	89869	exon5			TATGTGAAGATGA	AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"""EF-hand domain containing"""	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000266505.7:c.505T>C	chr12.hg19:g.18872429A>G	ENSP00000266505:p.Ser169Pro	104.0	0.0		80.0	4.0	NM_033123		Missense_Mutation	SNP	ENST00000266505.7	hg19	CCDS8680.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.443784	0.83993	.	.	ENSG00000139151	ENST00000266505;ENST00000447925;ENST00000541695;ENST00000541966	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	5.28	5.28	0.74379	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.000000	0.64402	D	0.000001	D	0.86973	0.6062	H	0.98407	4.225	0.54753	D	0.999988	D	0.89917	1.0	D	0.97110	1.0	D	0.91848	0.5489	10	0.87932	D	0	.	14.3734	0.66857	1.0:0.0:0.0:0.0	.	169	Q86YW0	PLCZ1_HUMAN	P	169;167;32;65	ENSP00000266505:S169P;ENSP00000402358:S167P;ENSP00000443349:S32P;ENSP00000444383:S65P	ENSP00000266505:S169P	S	-	1	0	PLCZ1	18763696	1.000000	0.71417	0.993000	0.49108	0.937000	0.57800	8.664000	0.91139	1.994000	0.58287	0.482000	0.46254	TCA	.	.		0.264	PLCZ1-001	KNOWN	NAGNAG_splice_site|non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401667.3	NM_033123	
PLCZ1	89869	hgsc.bcm.edu	37	12	18876315	18876315	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:18876315T>C	ENST00000266505.7	-	4	560	c.297A>G	c.(295-297)gaA>gaG	p.E99E	PLCZ1_ENST00000435379.1_Intron|PLCZ1_ENST00000447925.2_Silent_p.E97E|PLCZ1_ENST00000539875.1_Intron|RP11-361I14.2_ENST00000536931.1_RNA					phospholipase C, zeta 1											NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					CTGCATATTGTTCTTGTGTCA	0.343																																					p.E99E		Atlas-SNP	.											.	PLCZ1	107	.	0			c.A297G						.						89.0	85.0	87.0					12																	18876315		2202	4299	6501	SO:0001819	synonymous_variant	89869	exon4			ATATTGTTCTTGT	AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"""EF-hand domain containing"""	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000266505.7:c.297A>G	chr12.hg19:g.18876315T>C		119.0	0.0		88.0	4.0	NM_033123		Silent	SNP	ENST00000266505.7	hg19	CCDS8680.1																																																																																			.	.		0.343	PLCZ1-001	KNOWN	NAGNAG_splice_site|non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401667.3	NM_033123	
ABCC9	10060	hgsc.bcm.edu	37	12	22012588	22012588	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:22012588T>C	ENST00000261201.4	-	20	2436	c.2437A>G	c.(2437-2439)Agt>Ggt	p.S813G	ABCC9_ENST00000345162.2_Missense_Mutation_p.S777G|RP11-729I10.2_ENST00000539874.1_RNA|ABCC9_ENST00000261200.4_Missense_Mutation_p.S813G	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	813	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	TGTCCCCCACTCAGGTTGATG	0.383																																					p.S813G		Atlas-SNP	.											.	ABCC9	411	.	0			c.A2437G						.						170.0	171.0	170.0					12																	22012588		2203	4300	6503	SO:0001583	missense	10060	exon20			CCCCACTCAGGTT	AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"""ATP binding cassette transporters / subfamily C"""	60	protein-coding gene	gene with protein product	"""sulfonylurea receptor 2"""	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.2437A>G	chr12.hg19:g.22012588T>C	ENSP00000261201:p.Ser813Gly	78.0	0.0		62.0	5.0	NM_005691	O60707	Missense_Mutation	SNP	ENST00000261201.4	hg19	CCDS8694.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.169044	0.78339	.	.	ENSG00000069431	ENST00000261200;ENST00000544039;ENST00000261201;ENST00000345162	D;D;D;D	0.98822	-5.16;-5.16;-5.16;-5.16	4.71	4.71	0.59529	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.99530	0.9832	H	0.99211	4.47	0.80722	D	1	P;D	0.89917	0.941;1.0	P;D	0.91635	0.766;0.999	D	0.97698	1.0183	10	0.87932	D	0	-17.5591	14.3377	0.66603	0.0:0.0:0.0:1.0	.	813;813	O60706;O60706-2	ABCC9_HUMAN;.	G	813;440;813;777	ENSP00000261200:S813G;ENSP00000440521:S440G;ENSP00000261201:S813G;ENSP00000261202:S777G	ENSP00000261200:S813G	S	-	1	0	ABCC9	21903855	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.854000	0.86942	1.982000	0.57802	0.383000	0.25322	AGT	.	.		0.383	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691	
KRAS	3845	hgsc.bcm.edu	37	12	25368464	25368464	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:25368464T>C	ENST00000256078.4	-	5	544	c.481A>G	c.(481-483)Agg>Ggg	p.R161G	KRAS_ENST00000557334.1_Intron|KRAS_ENST00000311936.3_Intron	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	161					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			CGGATCTCCCTCACCAATGTA	0.348		119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.R161G	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	.	KRAS	30930	.	0			c.A481G						.						119.0	114.0	116.0					12																	25368464		2203	4300	6503	SO:0001583	missense	3845	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	TCTCCCTCACCAA	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.481A>G	chr12.hg19:g.25368464T>C	ENSP00000256078:p.Arg161Gly	138.0	0.0		67.0	4.0	NM_033360	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	T	19.90	3.913542	0.72983	.	.	ENSG00000133703	ENST00000256078	T	0.71579	-0.58	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.85225	0.5648	M	0.88906	2.99	0.80722	D	1	D	0.71674	0.998	D	0.70016	0.967	D	0.87762	0.2599	10	0.87932	D	0	.	12.0477	0.53489	0.0:0.0:0.1538:0.8462	.	161	P01116	RASK_HUMAN	G	161	ENSP00000256078:R161G	ENSP00000256078:R161G	R	-	1	2	KRAS	25259731	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.695000	0.54749	2.254000	0.74563	0.482000	0.46254	AGG	.	.		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
ITPR2	3709	hgsc.bcm.edu	37	12	26809378	26809378	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:26809378A>G	ENST00000381340.3	-	19	2712	c.2296T>C	c.(2296-2298)Tcg>Ccg	p.S766P		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	766					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)	CTCTCATCCGACACACACCGC	0.567																																					p.S766P		Atlas-SNP	.											.	ITPR2	270	.	0			c.T2296C						.						67.0	73.0	71.0					12																	26809378		2066	4200	6266	SO:0001583	missense	3709	exon19			CATCCGACACACA	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.2296T>C	chr12.hg19:g.26809378A>G	ENSP00000370744:p.Ser766Pro	104.0	0.0		83.0	4.0	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	A	18.32	3.598181	0.66332	.	.	ENSG00000123104	ENST00000381340	D	0.92348	-3.02	4.62	4.62	0.57501	.	0.056272	0.64402	D	0.000001	D	0.91703	0.7377	M	0.76574	2.34	0.80722	D	1	P	0.37330	0.59	B	0.38880	0.284	D	0.92449	0.5968	10	0.59425	D	0.04	.	14.4962	0.67688	1.0:0.0:0.0:0.0	.	766	Q14571	ITPR2_HUMAN	P	766	ENSP00000370744:S766P	ENSP00000370744:S766P	S	-	1	0	ITPR2	26700645	1.000000	0.71417	0.966000	0.40874	0.432000	0.31715	4.744000	0.62118	2.059000	0.61396	0.533000	0.62120	TCG	.	.		0.567	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
SENP1	29843	hgsc.bcm.edu	37	12	48477423	48477423	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:48477423A>G	ENST00000004980.5	-	6	981	c.503T>C	c.(502-504)cTt>cCt	p.L168P	SENP1_ENST00000547886.1_5'UTR|SENP1_ENST00000549518.1_Missense_Mutation_p.L168P|SENP1_ENST00000551330.1_Missense_Mutation_p.L168P|RNU6-1203P_ENST00000410703.1_RNA|SENP1_ENST00000448372.1_Missense_Mutation_p.L168P|SENP1_ENST00000549595.1_Missense_Mutation_p.L168P|SENP1_ENST00000339976.6_3'UTR			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	168	Ser-rich.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)			large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				GGGGCTCAAAAGACTTCGACG	0.413																																					p.L168P		Atlas-SNP	.											.	SENP1	44	.	0			c.T503C						.						121.0	112.0	115.0					12																	48477423		1855	4091	5946	SO:0001583	missense	29843	exon6			CTCAAAAGACTTC	AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"""SUMO1/sentrin specific protease 1"""			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.503T>C	chr12.hg19:g.48477423A>G	ENSP00000004980:p.Leu168Pro	124.0	0.0		100.0	4.0	NM_001267594	A8K7P5|Q86XC8	Missense_Mutation	SNP	ENST00000004980.5	hg19	CCDS44868.2	.	.	.	.	.	.	.	.	.	.	A	17.78	3.472698	0.63737	.	.	ENSG00000079387	ENST00000004980;ENST00000448372;ENST00000551330;ENST00000549595;ENST00000549518	T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99	4.2	3.01	0.34805	.	0.610158	0.15739	N	0.247034	T	0.24005	0.0581	N	0.24115	0.695	0.80722	D	1	D;D	0.58620	0.971;0.983	P;P	0.56700	0.641;0.804	T	0.02546	-1.1143	10	0.72032	D	0.01	-11.7182	9.0643	0.36453	0.8359:0.0:0.0:0.1641	.	168;168	Q9P0U3;Q9P0U3-2	SENP1_HUMAN;.	P	168	ENSP00000004980:L168P;ENSP00000394791:L168P;ENSP00000446681:L168P;ENSP00000450076:L168P;ENSP00000447328:L168P	ENSP00000004980:L168P	L	-	2	0	SENP1	46763690	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.478000	0.53158	0.900000	0.36469	0.533000	0.62120	CTT	.	.		0.413	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554	
CERS5	91012	hgsc.bcm.edu	37	12	50532384	50532384	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:50532384T>C	ENST00000317551.6	-	5	633	c.509A>G	c.(508-510)gAc>gGc	p.D170G	CERS5_ENST00000422340.2_Missense_Mutation_p.D112G	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	170	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										CTGTCGGATGTCCCAGAACCA	0.453																																					p.D170G		Atlas-SNP	.											.	.	.	.	0			c.A509G						.						216.0	203.0	207.0					12																	50532384		2203	4300	6503	SO:0001583	missense	91012	exon5			CGGATGTCCCAGA		CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"""Homeoboxes / CERS class"""	23749	protein-coding gene	gene with protein product		615335	"""LAG1 longevity assurance homolog 5 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 5"""	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.509A>G	chr12.hg19:g.50532384T>C	ENSP00000325485:p.Asp170Gly	101.0	0.0		109.0	5.0	NM_147190	B4DV54	Missense_Mutation	SNP	ENST00000317551.6	hg19	CCDS8801.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.0|27.0	4.794249|4.794249	0.90453|0.90453	.|.	.|.	ENSG00000139624|ENSG00000139624	ENST00000551005;ENST00000317551;ENST00000422340|ENST00000547800	T;T;T|.	0.27402|.	1.67;2.66;2.48|.	5.12|5.12	5.12|5.12	0.69794|0.69794	TRAM/LAG1/CLN8 homology domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80768|0.80768	0.4686|0.4686	M|M	0.88512|0.88512	2.96|2.96	0.80722|0.80722	D|D	1|1	P;D;D|.	0.71674|.	0.881;0.957;0.998|.	P;P;D|.	0.68192|.	0.794;0.833;0.956|.	D|D	0.85025|0.85025	0.0914|0.0914	10|6	0.87932|0.87932	D|D	0|0	-17.9584|-17.9584	15.4003|15.4003	0.74834|0.74834	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	112;170;89|.	B4DV54;Q8N5B7;F8W0U5|.	.;CERS5_HUMAN;.|.	G|A	89;170;112|105	ENSP00000447556:D89G;ENSP00000325485:D170G;ENSP00000389050:D112G|.	ENSP00000325485:D170G|ENSP00000369536:T151A	D|T	-|-	2|1	0|0	CERS5|CERS5	48818651|48818651	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	7.787000|7.787000	0.85759|0.85759	2.288000|2.288000	0.76882|0.76882	0.533000|0.533000	0.62120|0.62120	GAC|ACA	.	.		0.453	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190	
FAM186A	121006	hgsc.bcm.edu	37	12	50749223	50749223	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	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		78.0	0.0		107.0	5.0	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	
CSAD	51380	hgsc.bcm.edu	37	12	53553669	53553669	+	Splice_Site	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:53553669A>G	ENST00000444623.1	-	15	1486		c.e15+1		CSAD_ENST00000379843.3_Splice_Site|CSAD_ENST00000453446.2_Splice_Site|CSAD_ENST00000379846.1_Splice_Site|RP11-1136G11.8_ENST00000550908.1_lincRNA|CSAD_ENST00000267085.4_Splice_Site	NM_001244705.1	NP_001231634.1	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase						cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)		pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(4)	14					L-Cysteine(DB00151)	AAGGGGTCCTACCTCCATGAC	0.552											OREG0021859	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.	Ovarian(109;252 1546 16882 28524 44645)	Atlas-SNP	.											.	CSAD	66	.	0			c.519+2T>C						.						48.0	48.0	48.0					12																	53553669		2203	4300	6503	SO:0001630	splice_region_variant	51380	exon7			GGTCCTACCTCCA	AB044561	CCDS8848.2, CCDS58235.1	12q13.11-q14.3	2008-08-04			ENSG00000139631	ENSG00000139631			18966	protein-coding gene	gene with protein product	"""P-selectin cytoplasmic tail-associated protein"""					15489334	Standard	NM_015989		Approved	PCAP, CSD	uc001sbz.3	Q9Y600	OTTHUMG00000048076	ENST00000444623.1:c.1218+1T>C	chr12.hg19:g.53553669A>G		107.0	0.0	993	101.0	5.0	NM_001244706	A8K0U4|Q4QQH9|Q9UNJ5|Q9Y601	Splice_Site	SNP	ENST00000444623.1	hg19	CCDS58235.1	.	.	.	.	.	.	.	.	.	.	A	11.02	1.514972	0.27123	.	.	ENSG00000139631	ENST00000308926;ENST00000379843;ENST00000267085;ENST00000379850;ENST00000379846;ENST00000444623;ENST00000398047;ENST00000453446	.	.	.	4.68	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.554	0.61749	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CSAD	51839936	1.000000	0.71417	0.945000	0.38365	0.089000	0.18198	7.633000	0.83260	2.101000	0.63845	0.533000	0.62120	.	.	.		0.552	CSAD-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343697.1	NM_015989	Intron
ATP5G2	517	hgsc.bcm.edu	37	12	54063089	54063089	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:54063089A>G	ENST00000549164.1	-	4	341	c.154T>C	c.(154-156)Tca>Cca	p.S52P	ATP5G2_ENST00000602871.1_Missense_Mutation_p.S52P|ATP5G2_ENST00000394349.3_Missense_Mutation_p.S109P|ATP5G2_ENST00000338662.5_Missense_Mutation_p.S68P|ATP5G2_ENST00000550241.1_5'Flank			Q06055	AT5G2_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9)	52					ATP hydrolysis coupled proton transport (GO:0015991)|ATP synthesis coupled proton transport (GO:0015986)|response to ethanol (GO:0045471)	integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|lipid binding (GO:0008289)|transporter activity (GO:0005215)			kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6						GAGACAAGTGAGGTAAGGGGA	0.498																																					p.S109P		Atlas-SNP	.											.	ATP5G2	16	.	0			c.T325C						.						46.0	44.0	44.0					12																	54063089		2203	4300	6503	SO:0001583	missense	517	exon4			CAAGTGAGGTAAG	X69908	CCDS8863.2, CCDS31812.1	12q13.13	2012-10-12	2010-06-11		ENSG00000135390	ENSG00000135390		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	842	protein-coding gene	gene with protein product		603193	"""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9), isoform 2"", ""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)"""			8328972	Standard	NM_005176		Approved		uc001sec.3	Q06055	OTTHUMG00000133442	ENST00000549164.1:c.154T>C	chr12.hg19:g.54063089A>G	ENSP00000447317:p.Ser52Pro	62.0	0.0		69.0	4.0	NM_005176	B3KQQ6	Missense_Mutation	SNP	ENST00000549164.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.44	1.937443	0.34189	.	.	ENSG00000135390	ENST00000394349;ENST00000549164;ENST00000338662	T;T;T	0.26373	1.74;1.79;1.76	5.26	4.08	0.47627	.	0.477592	0.22598	N	0.058000	T	0.25195	0.0612	M	0.69358	2.11	0.27892	N	0.939296	B;B;B	0.18310	0.009;0.004;0.027	B;B;B	0.23275	0.016;0.015;0.045	T	0.16837	-1.0389	10	0.31617	T	0.26	0.0319	6.6517	0.22965	0.7525:0.0:0.2475:0.0	.	52;68;109	Q06055;Q06055-3;Q06055-2	AT5G2_HUMAN;.;.	P	109;52;68	ENSP00000377878:S109P;ENSP00000447317:S52P;ENSP00000340315:S68P	ENSP00000340315:S68P	S	-	1	0	ATP5G2	52349356	0.973000	0.33851	0.990000	0.47175	0.737000	0.42083	1.442000	0.35046	1.096000	0.41439	0.533000	0.62120	TCA	.	.		0.498	ATP5G2-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000407403.1	NM_005176	
ITGA5	3678	hgsc.bcm.edu	37	12	54796806	54796806	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:54796806T>C	ENST00000293379.4	-	19	2204	c.1943A>G	c.(1942-1944)gAc>gGc	p.D648G	RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	648					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|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)|memory (GO:0007613)|negative regulation of anoikis (GO:2000811)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|viral process (GO:0016032)|wound healing, spreading of epidermal cells (GO:0035313)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	metal ion binding (GO:0046872)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	34						ACAGATGTTGTCTTCTCCACA	0.547																																					p.D648G		Atlas-SNP	.											.	ITGA5	99	.	0			c.A1943G						.						111.0	97.0	102.0					12																	54796806		2203	4300	6503	SO:0001583	missense	3678	exon19			ATGTTGTCTTCTC		CCDS8880.1	12q11-q13	2010-03-23				ENSG00000161638		"""CD molecules"", ""Integrins"""	6141	protein-coding gene	gene with protein product		135620		FNRA		2454952	Standard	NM_002205		Approved	CD49e	uc001sga.3	P08648	OTTHUMG00000169841	ENST00000293379.4:c.1943A>G	chr12.hg19:g.54796806T>C	ENSP00000293379:p.Asp648Gly	108.0	0.0		113.0	5.0	NM_002205	Q96HA5	Missense_Mutation	SNP	ENST00000293379.4	hg19	CCDS8880.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.517798	0.85495	.	.	ENSG00000161638	ENST00000293379	T	0.72725	-0.68	4.94	4.94	0.65067	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	D	0.84620	0.5512	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87017	0.2126	10	0.72032	D	0.01	.	12.8536	0.57871	0.0:0.0:0.0:1.0	.	648	P08648	ITA5_HUMAN	G	648	ENSP00000293379:D648G	ENSP00000293379:D648G	D	-	2	0	ITGA5	53083073	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.680000	0.84062	2.006000	0.58801	0.454000	0.30748	GAC	.	.		0.547	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1		
DGKA	1606	hgsc.bcm.edu	37	12	56346928	56346928	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56346928T>C	ENST00000331886.5	+	22	2501	c.2047T>C	c.(2047-2049)Tct>Cct	p.S683P	DGKA_ENST00000551156.1_Missense_Mutation_p.S683P|DGKA_ENST00000394147.1_Missense_Mutation_p.S683P|DGKA_ENST00000549079.2_3'UTR	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	683					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	GGCCAAGTGCTCTGAGATCAC	0.567																																					p.S683P		Atlas-SNP	.											.	DGKA	70	.	0			c.T2047C						.						86.0	84.0	85.0					12																	56346928		2203	4300	6503	SO:0001583	missense	1606	exon22			AAGTGCTCTGAGA	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"""EF-hand domain containing"""	2849	protein-coding gene	gene with protein product		125855	"""diacylglycerol kinase, alpha (80kD)"""	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.2047T>C	chr12.hg19:g.56346928T>C	ENSP00000328405:p.Ser683Pro	86.0	0.0		99.0	6.0	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Missense_Mutation	SNP	ENST00000331886.5	hg19	CCDS8896.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.968503	0.74131	.	.	ENSG00000065357	ENST00000331886;ENST00000394147;ENST00000551156	T;T;T	0.46063	0.88;0.88;0.88	4.83	3.64	0.41730	Diacylglycerol kinase, accessory domain (2);	0.057410	0.64402	D	0.000001	T	0.68348	0.2991	M	0.91459	3.21	0.53005	D	0.999968	D	0.67145	0.996	D	0.75020	0.985	T	0.73353	-0.4009	10	0.87932	D	0	.	10.8775	0.46919	0.0:0.0:0.1583:0.8417	.	683	P23743	DGKA_HUMAN	P	683	ENSP00000328405:S683P;ENSP00000377703:S683P;ENSP00000450359:S683P	ENSP00000328405:S683P	S	+	1	0	DGKA	54633195	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.875000	0.69660	0.752000	0.32923	0.459000	0.35465	TCT	.	.		0.567	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1		
PA2G4	5036	hgsc.bcm.edu	37	12	56503708	56503708	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56503708A>G	ENST00000303305.6	+	7	1037	c.618A>G	c.(616-618)acA>acG	p.T206T	PA2G4_ENST00000552766.1_Silent_p.T206T|RP11-603J24.17_ENST00000548595.1_RNA	NM_006191.2	NP_006182.2	Q9UQ80	PA2G4_HUMAN	proliferation-associated 2G4, 38kDa	206					cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of translation (GO:0006417)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(18;0.0739)			AGAATCCCACAGACCAGCAGA	0.438																																					p.T206T		Atlas-SNP	.											.	PA2G4	24	.	0			c.A618G						.						106.0	97.0	100.0					12																	56503708		2203	4300	6503	SO:0001819	synonymous_variant	5036	exon7			TCCCACAGACCAG	U59435, BC007561	CCDS8902.1	12q13.2	2008-09-05	2002-08-29		ENSG00000170515	ENSG00000170515			8550	protein-coding gene	gene with protein product		602145	"""proliferation-associated 2G4, 38kD"""			9345902	Standard	NM_006191		Approved		uc001sjm.3	Q9UQ80	OTTHUMG00000170173	ENST00000303305.6:c.618A>G	chr12.hg19:g.56503708A>G		105.0	0.0		113.0	5.0	NM_006191	O43846|Q9UM59	Silent	SNP	ENST00000303305.6	hg19	CCDS8902.1																																																																																			.	.		0.438	PA2G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407767.1	NM_006191	
MYL6	4637	hgsc.bcm.edu	37	12	56553921	56553921	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56553921T>C	ENST00000550697.1	+	4	579	c.338T>C	c.(337-339)cTt>cCt	p.L113P	MYL6_ENST00000547649.1_Missense_Mutation_p.L113P|MYL6_ENST00000548293.1_Missense_Mutation_p.L113P|MYL6_ENST00000348108.4_Missense_Mutation_p.L114P|MYL6_ENST00000536128.1_Missense_Mutation_p.L206P|MYL6_ENST00000549566.1_Missense_Mutation_p.L158P|RP11-977G19.5_ENST00000553176.1_RNA|MYL6_ENST00000551589.1_Missense_Mutation_p.L113P|MYL6_ENST00000293422.5_Missense_Mutation_p.L114P|MYL6_ENST00000548400.1_Missense_Mutation_p.L77P|MYL6_ENST00000548580.1_Missense_Mutation_p.L65P|RP11-603J24.14_ENST00000548731.1_RNA|MYL6_ENST00000547408.1_Missense_Mutation_p.L113P|MYL6_ENST00000549017.1_Missense_Mutation_p.L9P	NM_021019.4	NP_066299.2	P60660	MYL6_HUMAN	myosin, light chain 6, alkali, smooth muscle and non-muscle	113	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle tissue development (GO:0007519)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|unconventional myosin complex (GO:0016461)|vesicle (GO:0031982)	actin-dependent ATPase activity (GO:0030898)|calcium ion binding (GO:0005509)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			large_intestine(1)|lung(1)|ovary(1)|prostate(3)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(18;0.0979)			CGGCATGTTCTTGTCACACTG	0.502																																					p.L113P		Atlas-SNP	.											.	MYL6	16	.	0			c.T338C						.						75.0	71.0	72.0					12																	56553921		2203	4300	6503	SO:0001583	missense	4637	exon4			ATGTTCTTGTCAC	AB046613	CCDS8906.1, CCDS31834.1	12q13.13	2013-01-10	2006-09-29			ENSG00000092841		"""Myosins / Light chain"", ""EF-hand domain containing"""	7587	protein-coding gene	gene with protein product		609931	"""myosin, light polypeptide 6, alkali, smooth muscle and non-muscle"""			8188229, 2304459, 2722814	Standard	NM_021019		Approved	ESMLC, MLC3NM, MLC1SM	uc001sjx.2	P60660		ENST00000550697.1:c.338T>C	chr12.hg19:g.56553921T>C	ENSP00000446955:p.Leu113Pro	75.0	0.0		84.0	4.0	NM_079423	P16475|P24572|P24573|Q12790|Q561V9|Q6IAZ0|Q6IPY5	Missense_Mutation	SNP	ENST00000550697.1	hg19	CCDS8906.1	.	.	.	.	.	.	.	.	.	.	T	19.39	3.818926	0.71028	.	.	ENSG00000092841	ENST00000550697;ENST00000548580;ENST00000293422;ENST00000348108;ENST00000549017;ENST00000549566;ENST00000536128;ENST00000547649;ENST00000547408;ENST00000551589;ENST00000553056;ENST00000549392;ENST00000548400;ENST00000548293	D;D;D;D;T;D;D;D;D;D;D;D;D	0.91577	-2.87;-2.87;-2.87;-2.87;0.37;-2.87;-2.87;-2.87;-2.87;-2.87;-2.87;-2.87;-2.87	4.19	4.19	0.49359	EF-hand-like domain (1);	0.000000	0.64402	D	0.000001	D	0.97365	0.9138	H	0.99600	4.65	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.98068	1.0397	10	0.87932	D	0	.	12.662	0.56820	0.0:0.0:0.0:1.0	.	206;113;113;113	B7Z6Z4;P60660-2;P60660;F8W1R7	.;.;MYL6_HUMAN;.	P	113;65;114;114;9;158;206;113;113;113;113;101;77;113	ENSP00000446955:L113P;ENSP00000446640:L65P;ENSP00000293422:L114P;ENSP00000301540:L114P;ENSP00000449086:L9P;ENSP00000446709:L158P;ENSP00000441750:L206P;ENSP00000446714:L113P;ENSP00000446721:L113P;ENSP00000446687:L113P;ENSP00000450116:L101P;ENSP00000448859:L77P;ENSP00000448101:L113P	ENSP00000293422:L114P	L	+	2	0	MYL6	54840188	1.000000	0.71417	0.966000	0.40874	0.988000	0.76386	7.856000	0.86956	1.898000	0.54952	0.379000	0.24179	CTT	.	.		0.502	MYL6-003	KNOWN	NAGNAG_splice_site|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407928.3		
BAZ2A	11176	hgsc.bcm.edu	37	12	56997486	56997486	+	Splice_Site	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56997486T>C	ENST00000551812.1	-	17	3238		c.e17-2		BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000379441.3_Splice_Site|BAZ2A_ENST00000179765.5_Splice_Site|BAZ2A_ENST00000549884.1_Splice_Site	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A						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						GTTTTCAGCCTTGAAATAGAT	0.542																																					.		Atlas-SNP	.											.	BAZ2A	263	.	0			c.3045-2A>G						.						42.0	40.0	41.0					12																	56997486		1932	4135	6067	SO:0001630	splice_region_variant	11176	exon18			TCAGCCTTGAAAT	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.3045-2A>G	chr12.hg19:g.56997486T>C		67.0	0.0		77.0	4.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Splice_Site	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	T	13.93	2.385176	0.42308	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549884	.	.	.	4.82	4.82	0.62117	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0842	0.48078	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	BAZ2A	55283753	1.000000	0.71417	0.985000	0.45067	0.517000	0.34286	4.145000	0.58065	1.940000	0.56252	0.533000	0.62120	.	.	.		0.542	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449	Intron
KIF5A	3798	hgsc.bcm.edu	37	12	57974761	57974761	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:57974761T>C	ENST00000455537.2	+	24	2835	c.2561T>C	c.(2560-2562)cTg>cCg	p.L854P	KIF5A_ENST00000286452.5_Missense_Mutation_p.L765P	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	854					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						AATGCAGATCTGCGTTGTGAG	0.557																																					p.L854P		Atlas-SNP	.											.	KIF5A	143	.	0			c.T2561C						.						66.0	58.0	61.0					12																	57974761		2203	4300	6503	SO:0001583	missense	3798	exon24			CAGATCTGCGTTG	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"""Kinesins"""	6323	protein-coding gene	gene with protein product		602821	"""spastic paraplegia 10 (autosomal dominant)"""	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.2561T>C	chr12.hg19:g.57974761T>C	ENSP00000408979:p.Leu854Pro	74.0	0.0		92.0	4.0	NM_004984	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	hg19	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.431502	0.83776	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	D;D	0.87729	-2.29;-2.29	4.97	4.97	0.65823	.	0.000000	0.64402	D	0.000005	D	0.94291	0.8166	M	0.89904	3.07	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	D	0.95266	0.8373	10	0.87932	D	0	.	14.0734	0.64874	0.0:0.0:0.0:1.0	.	765;854	B7Z2M7;Q12840	.;KIF5A_HUMAN	P	854;765	ENSP00000408979:L854P;ENSP00000286452:L765P	ENSP00000286452:L765P	L	+	2	0	KIF5A	56261028	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.700000	0.84556	2.225000	0.72522	0.533000	0.62120	CTG	.	.		0.557	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984	
SRGAP1	57522	hgsc.bcm.edu	37	12	64472776	64472776	+	Silent	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:64472776C>T	ENST00000355086.3	+	9	1727	c.1203C>T	c.(1201-1203)tgC>tgT	p.C401C	SRGAP1_ENST00000543397.1_Silent_p.C361C|SRGAP1_ENST00000357825.3_Silent_p.C401C|RP11-196H14.2_ENST00000535594.1_RNA	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	401	F-BAR domain.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		TTTCTGAATGCTTCCAGCACA	0.458																																					p.C401C		Atlas-SNP	.											.	SRGAP1	146	.	0			c.C1203T						.						118.0	99.0	105.0					12																	64472776		2203	4300	6503	SO:0001819	synonymous_variant	57522	exon9			TGAATGCTTCCAG	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"""Rho GTPase activating proteins"""	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.1203C>T	chr12.hg19:g.64472776C>T		78.0	0.0		83.0	4.0	NM_020762	Q9H8A3|Q9P2P2	Silent	SNP	ENST00000355086.3	hg19	CCDS8967.1																																																																																			.	.		0.458	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1		
C12orf66	144577	hgsc.bcm.edu	37	12	64609570	64609570	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:64609570T>C	ENST00000398055.3	-	2	462	c.409A>G	c.(409-411)Atg>Gtg	p.M137V	C12orf66_ENST00000311915.8_Missense_Mutation_p.M137V|C12orf66_ENST00000544871.1_Missense_Mutation_p.M84V	NM_152440.4	NP_689653	Q96MD2	CL066_HUMAN	chromosome 12 open reading frame 66	137										central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)	5						GCCATCTCCATCCGAGCCTGA	0.527																																					p.M137V		Atlas-SNP	.											.	C12orf66	28	.	0			c.A409G						.						64.0	64.0	64.0					12																	64609570		2024	4203	6227	SO:0001583	missense	144577	exon2			TCTCCATCCGAGC		CCDS41803.1, CCDS73490.1	12q14.2	2008-08-08			ENSG00000174206	ENSG00000174206			26517	protein-coding gene	gene with protein product						12477932	Standard	NM_152440		Approved	FLJ32549	uc001srw.4	Q96MD2	OTTHUMG00000168763	ENST00000398055.3:c.409A>G	chr12.hg19:g.64609570T>C	ENSP00000381132:p.Met137Val	117.0	0.0		115.0	5.0	NM_152440	C9JX54|Q8IYA0	Missense_Mutation	SNP	ENST00000398055.3	hg19	CCDS41803.1	.	.	.	.	.	.	.	.	.	.	T	11.49	1.653358	0.29425	.	.	ENSG00000174206	ENST00000311915;ENST00000544871;ENST00000398055	T;T;T	0.34859	1.34;1.34;1.34	5.95	4.82	0.62117	.	0.188542	0.64402	D	0.000003	T	0.26738	0.0654	L	0.38838	1.175	0.46542	D	0.999091	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.06356	-1.0831	9	.	.	.	-21.9238	10.6315	0.45538	0.0:0.1006:0.0:0.8994	.	84;137	F5H2Q3;Q96MD2	.;CL066_HUMAN	V	137;84;137	ENSP00000311486:M137V;ENSP00000445481:M84V;ENSP00000381132:M137V	.	M	-	1	0	C12orf66	62895837	1.000000	0.71417	0.997000	0.53966	0.912000	0.54170	3.179000	0.50887	2.279000	0.76181	0.402000	0.26972	ATG	.	.		0.527	C12orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400921.1	NM_152440	
TBC1D15	64786	hgsc.bcm.edu	37	12	72300901	72300901	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:72300901T>C	ENST00000550746.1	+	12	1398	c.1334T>C	c.(1333-1335)aTg>aCg	p.M445T	TBC1D15_ENST00000548679.1_3'UTR|TBC1D15_ENST00000319106.8_Missense_Mutation_p.M436T|TBC1D15_ENST00000485960.2_Missense_Mutation_p.M428T|TBC1D15_ENST00000393309.3_Missense_Mutation_p.M199T	NM_001146213.1|NM_022771.4	NP_001139685.2|NP_073608.4	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15	445	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	Rab GTPase activator activity (GO:0005097)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ACCTACTGTATGTATGATTTT	0.289																																					p.M445T		Atlas-SNP	.											.	TBC1D15	99	.	0			c.T1334C						.						177.0	159.0	165.0					12																	72300901		2202	4298	6500	SO:0001583	missense	64786	exon12			ACTGTATGTATGA	AL157464	CCDS31858.1, CCDS53814.1, CCDS55849.1	12q15	2013-07-09			ENSG00000121749	ENSG00000121749			25694	protein-coding gene	gene with protein product		612662				16055087	Standard	NM_022771		Approved	FLJ12085, DKFZp761D0223	uc001swu.3	Q8TC07	OTTHUMG00000158553	ENST00000550746.1:c.1334T>C	chr12.hg19:g.72300901T>C	ENSP00000448182:p.Met445Thr	89.0	0.0		97.0	4.0	NM_022771	B4DMT9|B9A6L6|J3KNI9|Q9HA83	Missense_Mutation	SNP	ENST00000550746.1	hg19	CCDS31858.1	.	.	.	.	.	.	.	.	.	.	T	18.67	3.673062	0.67928	.	.	ENSG00000121749	ENST00000550746;ENST00000319106;ENST00000485960;ENST00000393309	T;T;T;T	0.04234	3.67;3.67;3.67;3.67	5.09	5.09	0.68999	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.19604	0.0471	M	0.68317	2.08	0.80722	D	1	D;D;D	0.65815	0.995;0.994;0.993	D;D;P	0.77004	0.989;0.981;0.901	T	0.00256	-1.1873	10	0.72032	D	0.01	-13.8343	14.8798	0.70522	0.0:0.0:0.0:1.0	.	436;428;445	E9PH93;Q8TC07-2;Q8TC07	.;.;TBC15_HUMAN	T	445;436;428;199	ENSP00000448182:M445T;ENSP00000318262:M436T;ENSP00000420678:M428T;ENSP00000376986:M199T	ENSP00000318262:M436T	M	+	2	0	TBC1D15	70587168	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	1.919000	0.55581	0.528000	0.53228	ATG	.	.		0.289	TBC1D15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351266.2	NM_022771	
SLC6A15	55117	hgsc.bcm.edu	37	12	85264404	85264404	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:85264404T>C	ENST00000266682.5	-	9	1889	c.1348A>G	c.(1348-1350)Atg>Gtg	p.M450V	SLC6A15_ENST00000551388.1_5'Flank|SLC6A15_ENST00000552192.1_Missense_Mutation_p.M343V|SLC6A15_ENST00000309283.7_Missense_Mutation_p.M158V	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	450					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						AAATGTGTCATCGCTTCTGTA	0.418																																					p.M450V		Atlas-SNP	.											.	SLC6A15	159	.	0			c.A1348G						.						143.0	133.0	136.0					12																	85264404		2203	4300	6503	SO:0001583	missense	55117	exon9			GTGTCATCGCTTC	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"""Solute carriers"""	13621	protein-coding gene	gene with protein product	"""homolog of rat orphan transporter v7-3"", ""sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"""	607971	"""solute carrier family 6 (neurotransmitter transporter), member 15"""			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.1348A>G	chr12.hg19:g.85264404T>C	ENSP00000266682:p.Met450Val	97.0	0.0		80.0	4.0	NM_182767	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	hg19	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.945403	0.73672	.	.	ENSG00000072041	ENST00000309283;ENST00000266682;ENST00000318721;ENST00000552192;ENST00000551818	T;T;T	0.73152	-0.72;-0.72;-0.72	5.7	5.7	0.88788	.	0.070578	0.85682	D	0.000000	T	0.71728	0.3374	N	0.20530	0.585	0.80722	D	1	D;D	0.62365	0.991;0.985	P;D	0.63877	0.835;0.919	T	0.69950	-0.5006	10	0.25106	T	0.35	.	15.9735	0.80040	0.0:0.0:0.0:1.0	.	158;450	F8WJN6;Q9H2J7	.;S6A15_HUMAN	V	158;450;166;343;158	ENSP00000311645:M158V;ENSP00000266682:M450V;ENSP00000450145:M343V	ENSP00000266682:M450V	M	-	1	0	SLC6A15	83788535	1.000000	0.71417	0.918000	0.36340	0.993000	0.82548	7.603000	0.82811	2.159000	0.67721	0.533000	0.62120	ATG	.	.		0.418	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767	
C12orf50	160419	hgsc.bcm.edu	37	12	88383079	88383079	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:88383079T>C	ENST00000298699.2	-	8	842	c.662A>G	c.(661-663)gAg>gGg	p.E221G	C12orf50_ENST00000550553.1_Missense_Mutation_p.E221G	NM_152589.1	NP_689802.1	Q8NA57	CL050_HUMAN	chromosome 12 open reading frame 50	221										NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|urinary_tract(2)	34						GATTTCTTTCTCTTCAGTTAA	0.338																																					p.E221G		Atlas-SNP	.											.	C12orf50	70	.	0			c.A662G						.						69.0	67.0	68.0					12																	88383079		2203	4300	6503	SO:0001583	missense	160419	exon8			TCTTTCTCTTCAG	AK093140	CCDS9031.1	12q21.32	2006-02-03				ENSG00000165805			26665	protein-coding gene	gene with protein product						12477932	Standard	NM_152589		Approved	FLJ35821	uc001tam.1	Q8NA57	OTTHUMG00000169869	ENST00000298699.2:c.662A>G	chr12.hg19:g.88383079T>C	ENSP00000298699:p.Glu221Gly	44.0	0.0		60.0	4.0	NM_152589	Q6P674	Missense_Mutation	SNP	ENST00000298699.2	hg19	CCDS9031.1	.	.	.	.	.	.	.	.	.	.	T	11.78	1.742198	0.30865	.	.	ENSG00000165805	ENST00000298699;ENST00000550553;ENST00000551944	T;T	0.35421	1.31;1.31	4.96	3.81	0.43845	.	0.344430	0.24539	N	0.037650	T	0.27731	0.0682	L	0.41824	1.3	0.23731	N	0.996992	B;B	0.10296	0.003;0.001	B;B	0.09377	0.004;0.003	T	0.18053	-1.0349	10	0.44086	T	0.13	.	8.3575	0.32340	0.0:0.0924:0.0:0.9076	.	275;221	G3V208;Q8NA57	.;CL050_HUMAN	G	221;221;275	ENSP00000298699:E221G;ENSP00000448344:E221G	ENSP00000298699:E221G	E	-	2	0	C12orf50	86907210	0.852000	0.29690	0.936000	0.37596	0.615000	0.37417	1.020000	0.30027	0.758000	0.33059	-0.379000	0.06801	GAG	.	.		0.338	C12orf50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406328.1	NM_152589	
HECTD4	283450	hgsc.bcm.edu	37	12	112694221	112694221	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:112694221T>C	ENST00000430131.2	-	20	3079	c.1934A>G	c.(1933-1935)gAc>gGc	p.D645G	RP3-521E19.2_ENST00000547401.1_RNA|HECTD4_ENST00000377560.5_Missense_Mutation_p.D895G|HECTD4_ENST00000550722.1_Missense_Mutation_p.D931G			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	645					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)										TTTATAGTTGTCTCTGACGGG	0.448																																					p.D933G		Atlas-SNP	.											.	.	.	.	0			c.A2798G						.						89.0	91.0	90.0					12																	112694221		2203	4300	6503	SO:0001583	missense	283450	exon21			TAGTTGTCTCTGA	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.1934A>G	chr12.hg19:g.112694221T>C	ENSP00000404379:p.Asp645Gly	87.0	0.0		123.0	5.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	T	29.6	5.016303	0.93404	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.56444	0.46;0.47;0.64	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.60051	0.2239	N	0.24115	0.695	0.58432	D	0.999992	D;D;D	0.67145	0.996;0.993;0.996	D;D;D	0.73708	0.981;0.971;0.981	T	0.65084	-0.6254	10	0.87932	D	0	.	15.3801	0.74648	0.0:0.0:0.0:1.0	.	645;645;645	Q9Y4D8-2;Q9Y4D8;Q9Y4D8-3	.;K0614_HUMAN;.	G	895;645;931	ENSP00000366783:D895G;ENSP00000404379:D645G;ENSP00000449784:D931G	ENSP00000366783:D895G	D	-	2	0	C12orf51	111178604	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.459000	0.80802	2.275000	0.75901	0.533000	0.62120	GAC	.	.		0.448	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
PTPN11	5781	hgsc.bcm.edu	37	12	112888306	112888306	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:112888306A>G	ENST00000351677.2	+	3	520	c.322A>G	c.(322-324)Acc>Gcc	p.T108A	PTPN11_ENST00000392597.1_Missense_Mutation_p.T108A	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	108					abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						TGCAGATCCTACCTCTGAAAG	0.448			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome																												p.T108A		Atlas-SNP	.		Dom	yes		12	12q24.1	5781	"""protein tyrosine phosphatase, non-receptor type 11"""	yes	L	.	PTPN11	623	.	0			c.A322G						.						95.0	89.0	91.0					12																	112888306		2203	4300	6503	SO:0001583	missense	5781	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	GATCCTACCTCTG	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9644	protein-coding gene	gene with protein product		176876	"""Noonan syndrome 1"""	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.322A>G	chr12.hg19:g.112888306A>G	ENSP00000340944:p.Thr108Ala	70.0	0.0		97.0	4.0	NM_080601	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	hg19	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.552427	0.86127	.	.	ENSG00000179295	ENST00000392597;ENST00000351677;ENST00000392596	T;T	0.73047	-0.71;2.88	6.05	4.87	0.63330	.	0.045464	0.85682	D	0.000000	T	0.79052	0.4381	M	0.83953	2.67	0.58432	D	0.999998	P;B	0.43542	0.81;0.196	P;B	0.48952	0.596;0.199	T	0.81150	-0.1064	10	0.87932	D	0	.	12.5001	0.55950	0.8747:0.0:0.0:0.1253	.	108;108	Q06124-2;Q06124-3	.;.	A	108	ENSP00000376376:T108A;ENSP00000340944:T108A	ENSP00000340944:T108A	T	+	1	0	PTPN11	111372689	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.568000	0.82369	1.055000	0.40461	0.528000	0.53228	ACC	.	.		0.448	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2		
HIP1R	9026	hgsc.bcm.edu	37	12	123340451	123340452	+	Splice_Site	DNP	GT	GT	TG			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:123340451_123340452GT>TG	ENST00000253083.4	+	13	1253		c.e13+1			NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related						receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		CAAGCTGGAGGTGCGGGGTGGG	0.649																																					.		Atlas-SNP	.											.	HIP1R	68	.	0			c.1128+1G>T|c.1128+2T>G						.																																			SO:0001630	splice_region_variant	9026	exon13			CTGGAGGTGCGGG|TGGAGGTGCGGGG	AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	Exception_encountered	chr12.hg19:g.123340451_123340452delinsTG		85.0|84.0	0.0		118.0|115.0	7.0|9.0	NM_003959	A6NHQ6|Q6NXG8|Q9UED9	Splice_Site	SNP	ENST00000253083.4	hg19	CCDS31922.1																																																																																			.	.		0.649	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959	Intron
VPS37B	79720	hgsc.bcm.edu	37	12	123352099	123352099	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:123352099A>G	ENST00000267202.2	-	4	803	c.422T>C	c.(421-423)gTc>gCc	p.V141A	RP11-463O12.3_ENST00000537827.2_lincRNA	NM_024667.2	NP_078943.1	Q9H9H4	VP37B_HUMAN	vacuolar protein sorting 37 homolog B (S. cerevisiae)	141	Interaction with IST1.|VPS37 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00646}.				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)|midbody (GO:0030496)				breast(1)|central_nervous_system(1)|large_intestine(1)|skin(1)|urinary_tract(1)	5	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.08e-05)|Epithelial(86;0.000197)|BRCA - Breast invasive adenocarcinoma(302;0.205)		GCTCTGATAGACATCAATGAA	0.532																																					p.V141A		Atlas-SNP	.											.	VPS37B	26	.	0			c.T422C						.						107.0	111.0	109.0					12																	123352099		2203	4300	6503	SO:0001583	missense	79720	exon4			TGATAGACATCAA	AK022812	CCDS9239.1	12q24.31	2008-02-05	2006-04-04		ENSG00000139722	ENSG00000139722			25754	protein-coding gene	gene with protein product		610037	"""vacuolar protein sorting 37B (yeast)"""			15218037	Standard	NM_024667		Approved	FLJ12750	uc001udl.3	Q9H9H4	OTTHUMG00000168767	ENST00000267202.2:c.422T>C	chr12.hg19:g.123352099A>G	ENSP00000267202:p.Val141Ala	80.0	0.0		86.0	4.0	NM_024667		Missense_Mutation	SNP	ENST00000267202.2	hg19	CCDS9239.1	.	.	.	.	.	.	.	.	.	.	A	5.165	0.216049	0.09810	.	.	ENSG00000139722	ENST00000267202;ENST00000535765;ENST00000371248	T;T;T	0.75154	-0.91;-0.91;-0.91	5.59	0.21	0.15231	Modifier of rudimentary, Modr (2);	0.625852	0.16458	N	0.213530	T	0.44829	0.1312	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.23476	-1.0187	10	0.10377	T	0.69	-17.7843	4.1147	0.10076	0.395:0.0:0.2805:0.3245	.	141	Q9H9H4	VP37B_HUMAN	A	141;139;139	ENSP00000267202:V141A;ENSP00000446075:V139A;ENSP00000360294:V139A	ENSP00000267202:V141A	V	-	2	0	VPS37B	121918052	0.652000	0.27349	0.181000	0.23098	0.744000	0.42396	1.600000	0.36762	0.093000	0.17368	0.533000	0.62120	GTC	.	.		0.532	VPS37B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400946.1	NM_024667	
CENPJ	55835	hgsc.bcm.edu	37	13	25480336	25480336	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:25480336A>G	ENST00000381884.4	-	7	2025	c.1840T>C	c.(1840-1842)Tct>Cct	p.S614P	CENPJ_ENST00000545981.1_Missense_Mutation_p.S614P	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	614					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		GGGGTGGAAGACATCCGGTGA	0.433																																					p.S614P		Atlas-SNP	.											.	CENPJ	116	.	0			c.T1840C						.						94.0	92.0	93.0					13																	25480336		2203	4300	6503	SO:0001583	missense	55835	exon7			TGGAAGACATCCG	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"""centrosomal P4.1-associated protein"""	609279	"""microcephaly, primary autosomal recessive 6"""	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.1840T>C	chr13.hg19:g.25480336A>G	ENSP00000371308:p.Ser614Pro	103.0	0.0		87.0	6.0	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Missense_Mutation	SNP	ENST00000381884.4	hg19	CCDS9310.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.091830	0.76756	.	.	ENSG00000151849	ENST00000381884;ENST00000545981;ENST00000445729	T;T	0.67698	-0.28;0.25	6.02	6.02	0.97574	.	0.135337	0.49916	D	0.000122	T	0.81683	0.4874	M	0.76574	2.34	0.48901	D	0.999729	D	0.89917	1.0	D	0.85130	0.997	D	0.83582	0.0118	10	0.72032	D	0.01	.	15.5319	0.75970	1.0:0.0:0.0:0.0	.	614	Q9HC77	CENPJ_HUMAN	P	614	ENSP00000371308:S614P;ENSP00000441090:S614P	ENSP00000371308:S614P	S	-	1	0	CENPJ	24378336	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.924000	0.70054	2.299000	0.77371	0.528000	0.53228	TCT	.	.		0.433	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451	
STARD13	90627	hgsc.bcm.edu	37	13	33684128	33684128	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:33684128A>G	ENST00000336934.5	-	12	3045	c.2929T>C	c.(2929-2931)Tgg>Cgg	p.W977R	STARD13_ENST00000255486.4_Missense_Mutation_p.W969R|STARD13_ENST00000399365.3_Missense_Mutation_p.W859R	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	977	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		TCCTCGTCCCACAGGTGGCGC	0.587											OREG0022359	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W977R		Atlas-SNP	.											.	STARD13	100	.	0			c.T2929C						.						163.0	139.0	147.0					13																	33684128		2203	4300	6503	SO:0001583	missense	90627	exon12			CGTCCCACAGGTG	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.2929T>C	chr13.hg19:g.33684128A>G	ENSP00000338785:p.Trp977Arg	145.0	0.0	841	114.0	5.0	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	hg19	CCDS9348.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.589348	0.86851	.	.	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934	D;D;D	0.94457	-3.43;-3.43;-3.43	5.34	5.34	0.76211	Lipid-binding START (3);START-like domain (1);	0.000000	0.85682	D	0.000000	D	0.97751	0.9262	M	0.91717	3.235	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	0.98813	1.0744	10	0.87932	D	0	.	15.6106	0.76713	1.0:0.0:0.0:0.0	.	942;977;969	Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;STA13_HUMAN;.	R	859;969;977	ENSP00000382300:W859R;ENSP00000255486:W969R;ENSP00000338785:W977R	ENSP00000255486:W969R	W	-	1	0	STARD13	32582128	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.181000	0.94874	2.147000	0.66899	0.533000	0.62120	TGG	.	.		0.587	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
TRPC4	7223	hgsc.bcm.edu	37	13	38213437	38213437	+	Splice_Site	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:38213437C>T	ENST00000379705.3	-	9	2937		c.e9-1		TRPC4_ENST00000447043.1_Splice_Site|TRPC4_ENST00000379673.2_Splice_Site|TRPC4_ENST00000379681.3_Splice_Site|TRPC4_ENST00000355779.2_Splice_Site|TRPC4_ENST00000426868.2_Splice_Site|TRPC4_ENST00000338947.5_Splice_Site|TRPC4_ENST00000379679.1_Splice_Site|TRPC4_ENST00000358477.2_Splice_Site			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4						axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		CAGCTCGCCTCTGAAAAGGAA	0.303																																					.		Atlas-SNP	.											TRPC4_ENST00000379681,NS,carcinoma,0,2	TRPC4	389	.	0			c.1885-1G>A						.						118.0	122.0	121.0					13																	38213437		2203	4300	6503	SO:0001630	splice_region_variant	7223	exon9			TCGCCTCTGAAAA	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2080-1G>A	chr13.hg19:g.38213437C>T		39.0	0.0		54.0	3.0	NM_001135956	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Splice_Site	SNP	ENST00000379705.3	hg19	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.699269	0.88830	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000355779;ENST00000358477;ENST00000379673;ENST00000447043	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1041	0.97884	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TRPC4	37111437	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.982000	0.70532	2.826000	0.97356	0.655000	0.94253	.	.	.		0.303	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	Intron
COG6	57511	hgsc.bcm.edu	37	13	40297514	40297514	+	Nonsense_Mutation	SNP	T	T	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:40297514T>G	ENST00000455146.3	+	16	1679	c.1629T>G	c.(1627-1629)taT>taG	p.Y543*	COG6_ENST00000416691.1_Nonsense_Mutation_p.Y543*	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	543					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)		AAGCCTCTTATGTTTTAACTA	0.343																																					p.Y543X		Atlas-SNP	.											.	COG6	49	.	0			c.T1629G						.						114.0	107.0	110.0					13																	40297514		2203	4300	6503	SO:0001587	stop_gained	57511	exon16			CTCTTATGTTTTA	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.1629T>G	chr13.hg19:g.40297514T>G	ENSP00000397441:p.Tyr543*	98.0	0.0		83.0	5.0	NM_001145079	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Nonsense_Mutation	SNP	ENST00000455146.3	hg19	CCDS9370.1	.	.	.	.	.	.	.	.	.	.	T	36	5.716747	0.96830	.	.	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000455146	.	.	.	5.66	-6.93	0.01638	.	0.055567	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.4576	16.8685	0.86035	0.0:0.5934:0.0:0.4066	.	.	.	.	X	543;574;543	.	ENSP00000255468:Y574X	Y	+	3	2	COG6	39195514	0.173000	0.23056	0.634000	0.29324	0.990000	0.78478	-0.518000	0.06267	-1.658000	0.01490	-0.280000	0.10049	TAT	.	.		0.343	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3		
AKAP11	11215	hgsc.bcm.edu	37	13	42877272	42877272	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:42877272A>G	ENST00000025301.2	+	8	4565	c.4390A>G	c.(4390-4392)Agc>Ggc	p.S1464G		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1464				LDPYRNEVSQLYSFSTSLVHSITKDA -> CGPSVELSPWK WQTRCGREGNSWKRE (in Ref. 5; BAA92117). {ECO:0000305}.	intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TCTGGTTCACAGCATAACAAA	0.378																																					p.S1464G		Atlas-SNP	.											.	AKAP11	146	.	0			c.A4390G						.						71.0	77.0	75.0					13																	42877272		2203	4300	6503	SO:0001583	missense	11215	exon8			GTTCACAGCATAA	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.4390A>G	chr13.hg19:g.42877272A>G	ENSP00000025301:p.Ser1464Gly	95.0	0.0		64.0	5.0	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	A	12.66	2.005396	0.35415	.	.	ENSG00000023516	ENST00000025301	T	0.51817	0.69	5.99	4.79	0.61399	.	0.168669	0.50627	D	0.000116	T	0.41811	0.1175	M	0.62723	1.935	0.32309	N	0.56396	P	0.34724	0.465	B	0.31101	0.124	T	0.50725	-0.8794	10	0.18710	T	0.47	.	12.4499	0.55671	0.8743:0.0:0.0:0.1257	.	1464	Q9UKA4	AKA11_HUMAN	G	1464	ENSP00000025301:S1464G	ENSP00000025301:S1464G	S	+	1	0	AKAP11	41775272	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	4.885000	0.63142	1.049000	0.40321	0.533000	0.62120	AGC	.	.		0.378	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
PHF11	51131	hgsc.bcm.edu	37	13	50098318	50098318	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:50098318A>G	ENST00000378319.3	+	8	776	c.735A>G	c.(733-735)ccA>ccG	p.P245P	PHF11_ENST00000357596.3_Silent_p.P206P|PHF11_ENST00000488958.1_Silent_p.P206P	NM_001040443.1	NP_001035533.1	Q9UIL8	PHF11_HUMAN	PHD finger protein 11	245					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			large_intestine(3)|lung(1)	4		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)		ATTCAATTCCAGAAAAACTCA	0.333																																					p.P245P		Atlas-SNP	.											.	PHF11	20	.	0			c.A735G						.						51.0	55.0	54.0					13																	50098318		2203	4296	6499	SO:0001819	synonymous_variant	51131	exon8			AATTCCAGAAAAA	AB011031	CCDS31975.1, CCDS41887.1	13q14.11	2014-05-20			ENSG00000136147	ENSG00000136147		"""Zinc fingers, PHD-type"""	17024	protein-coding gene	gene with protein product	"""IgE responsiveness (atopic)"""	607796				10508479, 15057823	Standard	XM_005266417		Approved	NY-REN-34, BCAP, IGER	uc001vdb.3	Q9UIL8	OTTHUMG00000016916	ENST00000378319.3:c.735A>G	chr13.hg19:g.50098318A>G		145.0	0.0		88.0	4.0	NM_001040443	Q5W0A4|Q5W0A6|Q9Y5A2	Silent	SNP	ENST00000378319.3	hg19	CCDS31975.1	.	.	.	.	.	.	.	.	.	.	A	0.020	-1.433803	0.01108	.	.	ENSG00000136147	ENST00000426879	.	.	.	4.27	-8.53	0.00916	.	.	.	.	.	T	0.14743	0.0356	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.20672	-1.0268	4	.	.	.	-1.7604	1.0353	0.01547	0.2341:0.1021:0.3428:0.321	.	.	.	.	R	200	.	.	Q	+	2	0	PHF11	48996319	0.020000	0.18652	0.001000	0.08648	0.000000	0.00434	-0.837000	0.04377	-1.470000	0.01888	-1.286000	0.01371	CAG	.	.		0.333	PHF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044915.1	NM_016119	
LECT1	11061	hgsc.bcm.edu	37	13	53277943	53277943	+	Silent	SNP	C	C	T	rs368102754		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:53277943C>T	ENST00000377962.3	-	7	870	c.792G>A	c.(790-792)caG>caA	p.Q264Q	LECT1_ENST00000448904.2_Splice_Site			O75829	LECT1_HUMAN	leukocyte cell derived chemotaxin 1	264					cartilage development (GO:0051216)|endothelial cell morphogenesis (GO:0001886)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|proteoglycan metabolic process (GO:0006029)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.38e-08)		CCCCTTCCTGCTGCTGTGAAA	0.403																																					p.Q264Q		Atlas-SNP	.											.	LECT1	44	.	0			c.G792A						.	C	,	0,4406		0,0,2203	68.0	65.0	66.0		,792	4.3	1.0	13		66	1,8599	1.2+/-3.3	0,1,4299	no	splice-3,coding-synonymous	LECT1	NM_001011705.1,NM_007015.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	,264/335	53277943	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11061	exon7			TTCCTGCTGCTGT	AB006000	CCDS9437.1, CCDS45051.1	13q14.3	2012-10-10			ENSG00000136110	ENSG00000136110		"""BRICHOS domain containing"""	17005	protein-coding gene	gene with protein product	"""BRICHOS domain containing 3"""	605147	"""multiple myeloma tumor suppressor 1"""	MYETS1		9731231, 10103018	Standard	XM_006719760		Approved	CHM-I, CHM1, chondromodulin, BRICD3	uc001vhf.2	O75829	OTTHUMG00000016980	ENST00000377962.3:c.792G>A	chr13.hg19:g.53277943C>T		74.0	0.0		77.0	4.0	NM_007015	Q5TAM4|Q8TAY6|Q9UM18	Silent	SNP	ENST00000377962.3	hg19	CCDS9437.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.235196	0.58886	0.0	1.16E-4	ENSG00000136110	ENST00000448904	.	.	.	5.23	4.3	0.51218	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2671	0.60139	0.0:0.8717:0.0:0.1283	.	.	.	.	.	-1	.	.	.	-	.	.	LECT1	52175944	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.554000	0.23407	2.717000	0.92951	0.585000	0.79938	.	.	.		0.403	LECT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045110.3		
IPO5	3843	hgsc.bcm.edu	37	13	98658548	98658548	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:98658548A>G	ENST00000490680.1	+	14	1727	c.1662A>G	c.(1660-1662)agA>agG	p.R554R	IPO5_ENST00000493492.2_3'UTR|IPO5_ENST00000539640.1_Silent_p.R429R|IPO5_ENST00000261574.5_Silent_p.R572R			O00410	IPO5_HUMAN	importin 5	554					cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						GACTTCTGAGAGGAAAAACTA	0.313																																					p.R572R		Atlas-SNP	.											.	IPO5	90	.	0			c.A1716G						.						78.0	78.0	78.0					13																	98658548		2203	4300	6503	SO:0001819	synonymous_variant	3843	exon17			TCTGAGAGGAAAA	U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"""Importins"""	6402	protein-coding gene	gene with protein product		602008	"""karyopherin (importin) beta 3"", ""RAN binding protein 5"""	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.1662A>G	chr13.hg19:g.98658548A>G		113.0	0.0		211.0	12.0	NM_002271	B4DZA0|O15257|Q5T578|Q86XC7	Silent	SNP	ENST00000490680.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.07	1.249378	0.22880	.	.	ENSG00000065150	ENST00000469360	.	.	.	5.1	2.65	0.31530	.	.	.	.	.	T	0.58293	0.2112	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51172	-0.8739	4	.	.	.	-2.596	9.2079	0.37300	0.8505:0.0:0.1495:0.0	.	.	.	.	G	556	.	.	E	+	2	0	IPO5	97456549	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	1.071000	0.30666	0.358000	0.24211	0.377000	0.23210	GAG	.	.		0.313	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271	
COL4A1	1282	hgsc.bcm.edu	37	13	110827094	110827094	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:110827094T>C	ENST00000375820.4	-	38	3322	c.3201A>G	c.(3199-3201)ggA>ggG	p.G1067G		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1067	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			TCCCTTGATCTCCCTGCAAGT	0.463																																					p.G1067G		Atlas-SNP	.											.	COL4A1	372	.	0			c.A3201G						.						147.0	159.0	155.0					13																	110827094		2203	4300	6503	SO:0001819	synonymous_variant	1282	exon38			TTGATCTCCCTGC	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.3201A>G	chr13.hg19:g.110827094T>C		62.0	0.0		94.0	6.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	hg19	CCDS9511.1																																																																																			.	.		0.463	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
OR4Q3	441669	hgsc.bcm.edu	37	14	20215940	20215940	+	Silent	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:20215940C>T	ENST00000331723.1	+	1	354	c.354C>T	c.(352-354)gtC>gtT	p.V118V		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	118						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V118V(1)		NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TGCTGACAGTCATGGCCTATG	0.498																																					p.V118V		Atlas-SNP	.											OR4Q3,NS,carcinoma,0,1	OR4Q3	117	.	1	Substitution - coding silent(1)	lung(1)	c.C354T						.						93.0	94.0	94.0					14																	20215940		2203	4299	6502	SO:0001819	synonymous_variant	441669	exon1			GACAGTCATGGCC	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"""GPCR / Class A : Olfactory receptors"""	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.354C>T	chr14.hg19:g.20215940C>T		139.0	0.0		145.0	10.0	NM_172194	Q6IEX4	Silent	SNP	ENST00000331723.1	hg19	CCDS32020.1																																																																																			.	.		0.498	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2		
KLHL33	123103	hgsc.bcm.edu	37	14	20897683	20897683	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:20897683T>C	ENST00000344581.4	-	3	1249	c.1027A>G	c.(1027-1029)Aac>Gac	p.N343D		NM_001109997.2	NP_001103467.2	A6NCF5	KLH33_HUMAN	kelch-like family member 33	343												all_cancers(95;0.00123)		Epithelial(56;7.57e-08)|all cancers(55;8.63e-07)	GBM - Glioblastoma multiforme(265;0.0223)|READ - Rectum adenocarcinoma(17;0.193)		AGCTCAGGGTTGTAGGTCTCC	0.507																																					p.N343D		Atlas-SNP	.											.	KLHL33	37	.	0			c.A1027G						.						200.0	174.0	182.0					14																	20897683		692	1591	2283	SO:0001583	missense	123103	exon3			CAGGGTTGTAGGT		CCDS53882.1	14q11.2	2013-10-15	2013-02-22		ENSG00000185271	ENSG00000185271		"""Kelch-like"""	31952	protein-coding gene	gene with protein product			"""kelch-like 33 (Drosophila)"""				Standard	NM_001109997		Approved		uc010tli.2	A6NCF5	OTTHUMG00000170982	ENST00000344581.4:c.1027A>G	chr14.hg19:g.20897683T>C	ENSP00000341549:p.Asn343Asp	80.0	0.0		73.0	4.0	NM_001109997		Missense_Mutation	SNP	ENST00000344581.4	hg19	CCDS53882.1	.	.	.	.	.	.	.	.	.	.	T	4.145	0.025222	0.08054	.	.	ENSG00000185271	ENST00000344581	T	0.63255	-0.03	5.34	-2.6	0.06190	Kelch-type beta propeller (1);	0.630757	0.16343	N	0.218571	T	0.23532	0.0569	N	0.01751	-0.74	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.35895	-0.9770	10	0.02654	T	1	.	7.0021	0.24815	0.0:0.5093:0.1629:0.3279	.	343	A6NCF5	KLH33_HUMAN	D	343	ENSP00000341549:N343D	ENSP00000341549:N343D	N	-	1	0	KLHL33	19967523	0.000000	0.05858	0.940000	0.37924	0.958000	0.62258	-0.376000	0.07465	-0.329000	0.08527	-0.250000	0.11733	AAC	.	.		0.507	KLHL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411038.1	XM_063481	
PRMT5	10419	hgsc.bcm.edu	37	14	23393312	23393312	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:23393312T>C	ENST00000324366.8	-	12	1503	c.1280A>G	c.(1279-1281)gAg>gGg	p.E427G	PRMT5_ENST00000538452.1_Missense_Mutation_p.E321G|PRMT5-AS1_ENST00000457443.2_RNA|PRMT5_ENST00000553897.1_Missense_Mutation_p.E383G|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5-AS1_ENST00000424245.2_RNA|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000553641.1_5'Flank|PRMT5_ENST00000397440.4_Missense_Mutation_p.E256G|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5_ENST00000397441.2_Missense_Mutation_p.E410G|PRMT5_ENST00000216350.8_Missense_Mutation_p.E366G|PRMT5-AS1_ENST00000609885.1_RNA|PRMT5-AS1_ENST00000587245.2_RNA	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	427	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)		GTCTGCTTTCTCTGGAGCCAC	0.502																																					p.E427G		Atlas-SNP	.											.	PRMT5	101	.	0			c.A1280G						.						91.0	81.0	85.0					14																	23393312		2203	4300	6503	SO:0001583	missense	10419	exon12			GCTTTCTCTGGAG	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.1280A>G	chr14.hg19:g.23393312T>C	ENSP00000319169:p.Glu427Gly	110.0	0.0		117.0	5.0	NM_006109	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Missense_Mutation	SNP	ENST00000324366.8	hg19	CCDS9579.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.567072	0.86439	.	.	ENSG00000100462	ENST00000324366;ENST00000397441;ENST00000397440;ENST00000216350;ENST00000555454;ENST00000538452;ENST00000553897	T;T;T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87;1.87;1.87	5.5	5.5	0.81552	.	0.089755	0.85682	D	0.000000	T	0.53867	0.1823	M	0.83692	2.655	0.80722	D	1	D;D;D;D;D	0.71674	0.997;0.986;0.998;0.998;0.996	D;D;D;D;D	0.75020	0.974;0.944;0.985;0.956;0.978	T	0.59043	-0.7528	10	0.59425	D	0.04	-23.0779	14.731	0.69383	0.0:0.0:0.0:1.0	.	383;366;256;427;410	G3V5W5;B4DX49;A8MTP3;O14744;A8MZ91	.;.;.;ANM5_HUMAN;.	G	427;410;256;366;26;321;383	ENSP00000319169:E427G;ENSP00000380583:E410G;ENSP00000380582:E256G;ENSP00000216350:E366G;ENSP00000451245:E26G;ENSP00000444915:E321G;ENSP00000452555:E383G	ENSP00000216350:E366G	E	-	2	0	PRMT5	22463152	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.304000	0.78882	2.313000	0.78055	0.454000	0.30748	GAG	.	.		0.502	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3		
IPO4	79711	hgsc.bcm.edu	37	14	24653232	24653232	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:24653232A>G	ENST00000354464.6	-	18	2017	c.1841T>C	c.(1840-1842)cTg>cCg	p.L614P	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	614					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		ACGCAGTGACAGCAGCATGAG	0.612																																					p.L614P		Atlas-SNP	.											.	IPO4	74	.	0			c.T1841C						.						44.0	44.0	44.0					14																	24653232		1978	4148	6126	SO:0001583	missense	79711	exon18			AGTGACAGCAGCA	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1841T>C	chr14.hg19:g.24653232A>G	ENSP00000346453:p.Leu614Pro	80.0	0.0		100.0	4.0	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	hg19	CCDS9616.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.698050	0.30142	.	.	ENSG00000196497	ENST00000354464;ENST00000399536	T	0.04654	3.58	5.93	3.28	0.37604	Armadillo-like helical (1);Armadillo-type fold (1);	0.240418	0.33457	N	0.004891	T	0.05502	0.0145	L	0.48642	1.525	0.80722	D	1	B;B	0.25904	0.084;0.137	B;B	0.33339	0.106;0.162	T	0.36383	-0.9750	10	0.30854	T	0.27	-2.2341	5.7616	0.18203	0.7089:0.0:0.1599:0.1312	.	614;614	Q8TEX9;Q8TEX9-2	IPO4_HUMAN;.	P	614;290	ENSP00000346453:L614P	ENSP00000346453:L614P	L	-	2	0	IPO4	23723072	0.052000	0.20516	0.980000	0.43619	0.984000	0.73092	1.876000	0.39588	1.076000	0.40961	0.533000	0.62120	CTG	.	.		0.612	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
TM9SF1	10548	hgsc.bcm.edu	37	14	24662001	24662001	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:24662001T>C	ENST00000261789.4	-	3	1178	c.820A>G	c.(820-822)Acc>Gcc	p.T274A	RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000528669.1_Missense_Mutation_p.T274A|TM9SF1_ENST00000524835.1_Missense_Mutation_p.T187A|TM9SF1_ENST00000530611.1_Missense_Mutation_p.T483A|TM9SF1_ENST00000396854.4_Missense_Mutation_p.T274A|TM9SF1_ENST00000556387.1_Missense_Mutation_p.T483A	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	274					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		GCAGAGGTGGTCTCCTCATCT	0.498																																					p.T274A		Atlas-SNP	.											.	TM9SF1	58	.	0			c.A820G						.						141.0	130.0	134.0					14																	24662001		2203	4300	6503	SO:0001583	missense	10548	exon3			AGGTGGTCTCCTC	U94831	CCDS9617.1, CCDS41934.1, CCDS73623.1	14q11.2	2005-10-11			ENSG00000100926	ENSG00000100926			11864	protein-coding gene	gene with protein product						9332367	Standard	NM_006405		Approved	MP70, HMP70	uc010tob.1	O15321	OTTHUMG00000029322	ENST00000261789.4:c.820A>G	chr14.hg19:g.24662001T>C	ENSP00000261789:p.Thr274Ala	137.0	0.0		123.0	5.0	NM_001014842	D3DS65|Q86SZ6|Q96FI8	Missense_Mutation	SNP	ENST00000261789.4	hg19	CCDS9617.1	.	.	.	.	.	.	.	.	.	.	T	4.994	0.184632	0.09495	.	.	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000396854;ENST00000528895;ENST00000530563;ENST00000530611	T;T;T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02;1.02;1.02	5.1	3.94	0.45596	.	0.451250	0.24580	N	0.037304	T	0.14485	0.0350	N	0.02708	-0.52	0.31439	N	0.672171	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.20042	-1.0287	10	0.09590	T	0.72	-6.1289	4.8739	0.13646	0.0:0.0982:0.2058:0.696	.	274;274;274	E9PJM1;Q86SZ6;O15321	.;.;TM9S1_HUMAN	A	274;274;483;187;274;274;187;483	ENSP00000261789:T274A;ENSP00000432997:T274A;ENSP00000451949:T483A;ENSP00000434387:T187A;ENSP00000380063:T274A;ENSP00000431447:T274A;ENSP00000437127:T187A;ENSP00000433967:T483A	ENSP00000433967:T483A	T	-	1	0	TM9SF1;RP11-468E2.1	23731841	1.000000	0.71417	0.929000	0.37066	0.889000	0.51656	4.087000	0.57671	2.137000	0.66172	0.533000	0.62120	ACC	.	.		0.498	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405	
RIPK3	11035	hgsc.bcm.edu	37	14	24805506	24805506	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:24805506C>T	ENST00000216274.5	-	10	1650	c.1432G>A	c.(1432-1434)Ggc>Agc	p.G478S	ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000554068.2_5'Flank|RP11-934B9.3_ENST00000555591.1_Intron|ADCY4_ENST00000396747.3_5'Flank|ADCY4_ENST00000558563.1_5'Flank|RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000418030.2_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	478					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)		GGTGCCAAGCCCCATGTGGGC	0.567																																					p.G478S	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.G1432A						.						89.0	91.0	90.0					14																	24805506		2203	4300	6503	SO:0001583	missense	11035	exon10			CCAAGCCCCATGT	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.1432G>A	chr14.hg19:g.24805506C>T	ENSP00000216274:p.Gly478Ser	88.0	0.0		98.0	37.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Missense_Mutation	SNP	ENST00000216274.5	hg19	CCDS9628.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.524751	0.44969	.	.	ENSG00000129465	ENST00000216274	T	0.77098	-1.07	4.2	-2.27	0.06846	.	1.815640	0.02715	N	0.113376	T	0.62539	0.2436	L	0.27053	0.805	0.09310	N	1	B	0.26363	0.147	B	0.18263	0.021	T	0.43653	-0.9378	10	0.29301	T	0.29	1.2926	5.4134	0.16360	0.0:0.2791:0.4437:0.2772	.	478	Q9Y572	RIPK3_HUMAN	S	478	ENSP00000216274:G478S	ENSP00000216274:G478S	G	-	1	0	RIPK3	23875346	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.006000	0.03671	-0.484000	0.06763	-0.176000	0.13171	GGC	.	.		0.567	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871	
PRPF39	55015	hgsc.bcm.edu	37	14	45571779	45571779	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:45571779A>G	ENST00000355765.6	+	5	787	c.617A>G	c.(616-618)gAc>gGc	p.D206G		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	206					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						TTCCGTTCTGACAGACTGTGG	0.358																																					p.D206G		Atlas-SNP	.											.	PRPF39	46	.	0			c.A617G						.						101.0	105.0	104.0					14																	45571779		2203	4300	6503	SO:0001583	missense	55015	exon5			GTTCTGACAGACT	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"""PRP39 pre-mRNA processing factor 39 homolog (yeast)"", ""PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"""				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.617A>G	chr14.hg19:g.45571779A>G	ENSP00000348010:p.Asp206Gly	98.0	0.0		90.0	4.0	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	hg19	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	A	26.8	4.770121	0.90108	.	.	ENSG00000185246	ENST00000355765;ENST00000355846	T	0.29655	1.56	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.48277	0.1491	L	0.50993	1.605	0.80722	D	1	P;D	0.89917	0.86;1.0	P;D	0.87578	0.661;0.998	T	0.30416	-0.9979	10	0.20046	T	0.44	-8.4025	15.4843	0.75551	1.0:0.0:0.0:0.0	.	206;85	Q86UA1;F5H1P0	PRP39_HUMAN;.	G	206;85	ENSP00000348010:D206G	ENSP00000348010:D206G	D	+	2	0	PRPF39	44641529	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.339000	0.96797	2.137000	0.66172	0.533000	0.62120	GAC	.	.		0.358	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2		
SOS2	6655	hgsc.bcm.edu	37	14	50647366	50647366	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:50647366T>C	ENST00000216373.5	-	7	1167	c.893A>G	c.(892-894)cAg>cGg	p.Q298R	SOS2_ENST00000555794.1_5'UTR|SOS2_ENST00000543680.1_Missense_Mutation_p.Q298R	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	298	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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 small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					AAGAATGTCCTGTGATAATGT	0.313																																					p.Q298R		Atlas-SNP	.											.	SOS2	195	.	0			c.A893G						.						77.0	77.0	77.0					14																	50647366		2203	4300	6503	SO:0001583	missense	6655	exon7			ATGTCCTGTGATA	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11188	protein-coding gene	gene with protein product		601247	"""son of sevenless (Drosophilia) homolog 2"""			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.893A>G	chr14.hg19:g.50647366T>C	ENSP00000216373:p.Gln298Arg	48.0	0.0		56.0	4.0	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	hg19	CCDS9697.1	.	.	.	.	.	.	.	.	.	.	T	8.883	0.952136	0.18431	.	.	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.62941	-0.01;-0.01	5.6	5.6	0.85130	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.46833	0.1413	N	0.25485	0.75	0.80722	D	1	B;B	0.14805	0.011;0.002	B;B	0.16289	0.015;0.01	T	0.43196	-0.9406	10	0.06099	T	0.92	.	15.829	0.78736	0.0:0.0:0.0:1.0	.	298;298	B7ZKT6;Q07890	.;SOS2_HUMAN	R	298	ENSP00000216373:Q298R;ENSP00000445328:Q298R	ENSP00000216373:Q298R	Q	-	2	0	SOS2	49717116	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.033000	0.88852	2.122000	0.65172	0.529000	0.55759	CAG	.	.		0.313	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
PYGL	5836	hgsc.bcm.edu	37	14	51375542	51375542	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:51375542T>C	ENST00000216392.7	-	18	2641	c.2309A>G	c.(2308-2310)gAc>gGc	p.D770G	PYGL_ENST00000532462.1_Missense_Mutation_p.D770G|PYGL_ENST00000544180.2_Missense_Mutation_p.D736G	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	770					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|necroptotic process (GO:0070266)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	AMP binding (GO:0016208)|ATP binding (GO:0005524)|bile acid binding (GO:0032052)|drug binding (GO:0008144)|glucose binding (GO:0005536)|glycogen phosphorylase activity (GO:0008184)|protein homodimerization activity (GO:0042803)|purine nucleobase binding (GO:0002060)|pyridoxal phosphate binding (GO:0030170)|vitamin binding (GO:0019842)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(3)	25	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)	AACTCACCTGTCATGATAAAA	0.383																																					p.D770G		Atlas-SNP	.											.	PYGL	77	.	0			c.A2309G						.						237.0	251.0	247.0					14																	51375542		2203	4300	6503	SO:0001583	missense	5836	exon18			CACCTGTCATGAT		CCDS32080.1, CCDS53894.1	14q11.2-q24.3	2013-03-01	2008-07-31		ENSG00000100504	ENSG00000100504	2.4.1.1	"""Glycogen phosphorylases"""	9725	protein-coding gene	gene with protein product	"""Hers disease"", ""glycogen storage disease type VI"", ""glycogen phosphorylase, liver form"""	613741	"""phosphorylase, glycogen; liver"""			2877458	Standard	NM_002863		Approved		uc001wyu.3	P06737	OTTHUMG00000166596	ENST00000216392.7:c.2309A>G	chr14.hg19:g.51375542T>C	ENSP00000216392:p.Asp770Gly	109.0	0.0		93.0	5.0	NM_002863	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Missense_Mutation	SNP	ENST00000216392.7	hg19	CCDS32080.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.808688	0.90707	.	.	ENSG00000100504	ENST00000532462;ENST00000544180;ENST00000216392	D;D;D	0.96265	-3.96;-3.96;-3.96	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.98833	0.9606	H	0.97491	4.015	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.83275	0.992;0.996;0.996	D	0.99585	1.0974	10	0.87932	D	0	.	14.8423	0.70235	0.0:0.0:0.0:1.0	.	736;736;770	F5H816;B4DUB7;P06737	.;.;PYGL_HUMAN	G	770;736;770	ENSP00000431657:D770G;ENSP00000443787:D736G;ENSP00000216392:D770G	ENSP00000216392:D770G	D	-	2	0	PYGL	50445292	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	8.040000	0.89188	2.187000	0.69744	0.533000	0.62120	GAC	.	.		0.383	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863	
KTN1	3895	hgsc.bcm.edu	37	14	56126388	56126388	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:56126388C>T	ENST00000395314.3	+	31	3034	c.2966C>T	c.(2965-2967)tCt>tTt	p.S989F	KTN1_ENST00000395309.3_Missense_Mutation_p.S989F|KTN1_ENST00000555573.1_5'Flank|KTN1_ENST00000438792.2_Missense_Mutation_p.S989F|KTN1_ENST00000416613.1_Missense_Mutation_p.S989F|KTN1_ENST00000413890.2_Missense_Mutation_p.S966F|KTN1_ENST00000554507.1_Missense_Mutation_p.S284F|KTN1_ENST00000395311.1_Missense_Mutation_p.S966F|KTN1_ENST00000395308.1_Missense_Mutation_p.S966F	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	989					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						TGATAGGCATCTTCTTTTCCC	0.274			T	RET	papillary thryoid																																p.S989F		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.C2966T						.						70.0	81.0	77.0					14																	56126388		2199	4283	6482	SO:0001583	missense	3895	exon31			AGGCATCTTCTTT		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.2966C>T	chr14.hg19:g.56126388C>T	ENSP00000378725:p.Ser989Phe	59.0	0.0		97.0	5.0	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Missense_Mutation	SNP	ENST00000395314.3	hg19	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.409650	0.62399	.	.	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613;ENST00000554507	T;T;T;T;T;T;T;T	0.37411	1.39;1.38;1.2;1.38;1.39;1.39;1.38;1.2	4.68	4.68	0.58851	.	0.000000	0.43579	D	0.000546	T	0.48114	0.1482	L	0.50333	1.59	0.34812	D	0.737796	B;D;B;B;P	0.52996	0.429;0.957;0.429;0.343;0.744	B;P;B;B;P	0.56127	0.421;0.792;0.323;0.311;0.503	T	0.61431	-0.7064	10	0.56958	D	0.05	-0.0373	15.1455	0.72647	0.0:1.0:0.0:0.0	.	989;284;989;966;989	B4DZ88;G3V4Y7;Q86UP2-2;Q17RZ5;Q86UP2	.;.;.;.;KTN1_HUMAN	F	966;989;989;989;966;966;989;284	ENSP00000394992:S966F;ENSP00000378720:S989F;ENSP00000391964:S989F;ENSP00000378725:S989F;ENSP00000378719:S966F;ENSP00000378722:S966F;ENSP00000388807:S989F;ENSP00000452073:S284F	ENSP00000378719:S966F	S	+	2	0	KTN1	55196141	0.982000	0.34865	0.998000	0.56505	0.993000	0.82548	1.978000	0.40598	2.418000	0.82041	0.563000	0.77884	TCT	.	.		0.274	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		
AP5M1	55745	hgsc.bcm.edu	37	14	57741096	57741096	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:57741096A>G	ENST00000261558.3	+	2	615	c.209A>G	c.(208-210)gAg>gGg	p.E70G	AP5M1_ENST00000431972.2_Missense_Mutation_p.E84G	NM_018229.3	NP_060699.3	Q9H0R1	AP5M1_HUMAN	adaptor-related protein complex 5, mu 1 subunit	70					endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytosol (GO:0005829)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)											GACTTCGTTGAGAGTCGTGAT	0.408																																					p.E70G		Atlas-SNP	.											.	.	.	.	0			c.A209G						.						109.0	101.0	104.0					14																	57741096		2203	4300	6503	SO:0001583	missense	55745	exon2			TCGTTGAGAGTCG	AF094583	CCDS9729.1	14q22.2	2012-03-20	2012-03-20	2012-03-20	ENSG00000053770	ENSG00000053770			20192	protein-coding gene	gene with protein product	"""Mu-2 related death-inducing gene"""	614368	"""chromosome 14 open reading frame 108"", ""MU-2/AP1M2 domain containing, death-inducing"""	C14orf108, MUDENG		18395520	Standard	NM_018229		Approved	FLJ10813, MuD, mu5	uc001xcv.3	Q9H0R1	OTTHUMG00000140318	ENST00000261558.3:c.209A>G	chr14.hg19:g.57741096A>G	ENSP00000261558:p.Glu70Gly	105.0	0.0		114.0	5.0	NM_018229	O95354|Q6ZMD7|Q96DX3|Q9NVC5	Missense_Mutation	SNP	ENST00000261558.3	hg19	CCDS9729.1	.	.	.	.	.	.	.	.	.	.	A	9.012	0.982620	0.18889	.	.	ENSG00000053770	ENST00000261558;ENST00000431972	T;T	0.36878	1.24;1.23	5.56	4.4	0.53042	.	0.136995	0.64402	D	0.000004	T	0.38374	0.1038	M	0.67953	2.075	0.48830	D	0.999715	B;P	0.38078	0.038;0.617	B;B	0.37144	0.045;0.242	T	0.32640	-0.9899	10	0.62326	D	0.03	.	12.9714	0.58515	0.8647:0.1353:0.0:0.0	.	70;70	Q9H0R1;Q9H0R1-2	MUDEN_HUMAN;.	G	70;84	ENSP00000261558:E70G;ENSP00000390531:E84G	ENSP00000261558:E70G	E	+	2	0	MUDENG	56810849	0.999000	0.42202	0.010000	0.14722	0.091000	0.18340	4.322000	0.59215	1.026000	0.39733	-0.438000	0.05819	GAG	.	.		0.408	AP5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276922.1	NM_018229	
SLC38A6	145389	hgsc.bcm.edu	37	14	61497161	61497161	+	Splice_Site	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:61497161A>G	ENST00000267488.4	+	6	519		c.e6-1		SLC38A6_ENST00000456840.2_Splice_Site|SLC38A6_ENST00000354886.2_Splice_Site	NM_153811.2	NP_722518.2	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6						amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		ATTCTTTTGCAGCTATGTCAT	0.303																																					.		Atlas-SNP	.											.	SLC38A6	87	.	0			c.404-2A>G						.						56.0	58.0	57.0					14																	61497161		2202	4294	6496	SO:0001630	splice_region_variant	145389	exon6			TTTTGCAGCTATG	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"""Solute carriers"""	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000267488.4:c.404-1A>G	chr14.hg19:g.61497161A>G		112.0	0.0		97.0	5.0	NM_153811	C9JWA6|Q86SY5	Splice_Site	SNP	ENST00000267488.4	hg19	CCDS9751.1	.	.	.	.	.	.	.	.	.	.	A	15.69	2.908374	0.52333	.	.	ENSG00000139974	ENST00000354886;ENST00000267488;ENST00000451406;ENST00000456840;ENST00000526105;ENST00000533744	.	.	.	5.08	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3669	0.55234	0.8589:0.1411:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC38A6	60566914	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	5.449000	0.66619	0.874000	0.35823	-0.291000	0.09656	.	.	.		0.303	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1		Intron
SIPA1L1	26037	hgsc.bcm.edu	37	14	72152235	72152235	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:72152235T>C	ENST00000555818.1	+	10	3609	c.3261T>C	c.(3259-3261)agT>agC	p.S1087S	SIPA1L1_ENST00000358550.2_Silent_p.S1087S|SIPA1L1_ENST00000537413.1_Silent_p.S562S|SIPA1L1_ENST00000381232.3_Silent_p.S1087S	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1087					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		AGGTGCAGAGTCCCATGACCT	0.547																																					p.S1087S		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.T3261C						.						52.0	50.0	51.0					14																	72152235		2203	4300	6503	SO:0001819	synonymous_variant	26037	exon10			GCAGAGTCCCATG	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.3261T>C	chr14.hg19:g.72152235T>C		88.0	0.0		97.0	5.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	hg19	CCDS9807.1																																																																																			.	.		0.547	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	
FAM161B	145483	hgsc.bcm.edu	37	14	74409383	74409383	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:74409383T>C	ENST00000534936.1	-	4	1066	c.961A>G	c.(961-963)Aga>Gga	p.R321G	FAM161B_ENST00000286544.3_Missense_Mutation_p.R384G			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	321										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						TCCAGGGCTCTCATTTGGATG	0.537																																					p.R384G		Atlas-SNP	.											.	FAM161B	67	.	0			c.A1150G						.						68.0	74.0	72.0					14																	74409383		2203	4300	6503	SO:0001583	missense	145483	exon4			GGGCTCTCATTTG	AA356453	CCDS9822.1, CCDS9822.2	14q24.2	2008-06-05	2008-06-05	2008-06-05		ENSG00000156050			19854	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 44"""	C14orf44			Standard	NM_152445		Approved	FLJ31697	uc001xpd.3	Q96MY7		ENST00000534936.1:c.961A>G	chr14.hg19:g.74409383T>C	ENSP00000445326:p.Arg321Gly	68.0	0.0		70.0	4.0	NM_152445	B7Z882|J3KNA2	Missense_Mutation	SNP	ENST00000534936.1	hg19		.	.	.	.	.	.	.	.	.	.	T	20.7	4.035816	0.75617	.	.	ENSG00000156050	ENST00000286544;ENST00000534936	T;T	0.37915	1.17;1.17	5.5	-0.0292	0.13919	.	0.061993	0.64402	D	0.000016	T	0.62196	0.2408	M	0.86953	2.85	0.51012	D	0.999902	D	0.89917	1.0	D	0.91635	0.999	T	0.71130	-0.4682	10	0.87932	D	0	-14.4659	14.7771	0.69738	0.0:0.0:0.507:0.493	.	321	Q96MY7	F161B_HUMAN	G	384;321	ENSP00000286544:R384G;ENSP00000445326:R321G	ENSP00000286544:R384G	R	-	1	2	FAM161B	73479136	1.000000	0.71417	0.994000	0.49952	0.969000	0.65631	1.711000	0.37930	0.134000	0.18681	0.533000	0.62120	AGA	.	.		0.537	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445	
IRF2BPL	64207	hgsc.bcm.edu	37	14	77493060	77493060	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:77493060T>C	ENST00000238647.3	-	1	1974	c.1076A>G	c.(1075-1077)gAg>gGg	p.E359G		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	359					development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						GCGCAGGCTCTCGCTCAGCTC	0.682																																					p.E359G		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.A1076G						.						31.0	29.0	30.0					14																	77493060		2200	4299	6499	SO:0001583	missense	64207	exon1			AGGCTCTCGCTCA	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"""enhanced at puberty 1"""	611720	"""chromosome 14 open reading frame 4"""	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.1076A>G	chr14.hg19:g.77493060T>C	ENSP00000238647:p.Glu359Gly	66.0	0.0		100.0	5.0	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Missense_Mutation	SNP	ENST00000238647.3	hg19	CCDS9854.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.980023	0.74474	.	.	ENSG00000119669	ENST00000238647	T	0.20463	2.07	4.03	4.03	0.46877	.	0.083770	0.45606	U	0.000343	T	0.34890	0.0913	L	0.58810	1.83	0.52099	D	0.999942	D	0.60575	0.988	P	0.57204	0.815	T	0.15607	-1.0431	10	0.87932	D	0	7.8519	11.9534	0.52968	0.0:0.0:0.0:1.0	.	359	Q9H1B7	I2BPL_HUMAN	G	359	ENSP00000238647:E359G	ENSP00000238647:E359G	E	-	2	0	IRF2BPL	76562813	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.635000	0.67841	1.696000	0.51158	0.379000	0.24179	GAG	.	.		0.682	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496	
AHSA1	10598	hgsc.bcm.edu	37	14	77935521	77935521	+	Silent	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:77935521C>A	ENST00000216479.3	+	9	1106	c.946C>A	c.(946-948)Cga>Aga	p.R316R	SNORA46_ENST00000391069.1_RNA|AHSA1_ENST00000555457.1_3'UTR	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		163.0	0.0		166.0	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	
SEL1L	6400	hgsc.bcm.edu	37	14	81970628	81970628	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:81970628T>C	ENST00000336735.4	-	5	647	c.531A>G	c.(529-531)agA>agG	p.R177R	SEL1L_ENST00000555824.1_Silent_p.R177R	NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	177	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		GCATCTGCCGTCTCTTAGCAG	0.353																																					p.R177R		Atlas-SNP	.											.	SEL1L	67	.	0			c.A531G						.						205.0	182.0	190.0					14																	81970628		2203	4300	6503	SO:0001819	synonymous_variant	6400	exon5			CTGCCGTCTCTTA		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"""sel-1 suppressor of lin-12-like 1 (C. elegans)"""	602329	"""sel-1 (suppressor of lin-12, C.elegans)-like"""			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.531A>G	chr14.hg19:g.81970628T>C		146.0	0.0		142.0	6.0	NM_001244984	Q6UWT6|Q9P1T9|Q9UHK7	Silent	SNP	ENST00000336735.4	hg19	CCDS9876.1																																																																																			.	.		0.353	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065	
GALC	2581	hgsc.bcm.edu	37	14	88429767	88429767	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:88429767A>G	ENST00000261304.2	-	10	1228	c.1122T>C	c.(1120-1122)acT>acC	p.T374T	GALC_ENST00000393569.2_Silent_p.T348T|GALC_ENST00000393568.4_Silent_p.T351T|GALC_ENST00000544807.2_Silent_p.T318T	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	374					carbohydrate metabolic process (GO:0005975)|galactosylceramide catabolic process (GO:0006683)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	galactosylceramidase activity (GO:0004336)			endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CTAAGCCATCAGTCAGAGCTA	0.383																																					p.T374T		Atlas-SNP	.											.	GALC	48	.	0			c.T1122C						.						139.0	130.0	132.0					14																	88429767		1897	4114	6011	SO:0001819	synonymous_variant	2581	exon10			GCCATCAGTCAGA	L23116	CCDS9878.2, CCDS55936.1, CCDS55937.1	14q31	2009-01-06	2005-11-29		ENSG00000054983	ENSG00000054983	3.2.1.46		4115	protein-coding gene	gene with protein product	"""Krabbe disease"""	606890	"""galactosylceramidase (Krabbe disease)"""				Standard	NM_000153		Approved		uc001xvt.3	P54803	OTTHUMG00000028646	ENST00000261304.2:c.1122T>C	chr14.hg19:g.88429767A>G		90.0	0.0		102.0	6.0	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Silent	SNP	ENST00000261304.2	hg19	CCDS9878.2																																																																																			.	.		0.383	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2		
EML5	161436	hgsc.bcm.edu	37	14	89172628	89172628	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:89172628T>C	ENST00000380664.5	-	11	1799	c.1800A>G	c.(1798-1800)aaA>aaG	p.K600K	EML5_ENST00000352093.5_Silent_p.K600K|EML5_ENST00000554922.1_Silent_p.K600K			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	600						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GAACAGCATCTTTCAGTTTTC	0.368																																					p.K600K		Atlas-SNP	.											.	EML5	141	.	0			c.A1800G						.						108.0	105.0	106.0					14																	89172628		1841	4086	5927	SO:0001819	synonymous_variant	161436	exon11			AGCATCTTTCAGT	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.1800A>G	chr14.hg19:g.89172628T>C		96.0	0.0		87.0	4.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Silent	SNP	ENST00000380664.5	hg19	CCDS45148.1																																																																																			.	.		0.368	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
BTBD7	55727	hgsc.bcm.edu	37	14	93712578	93712578	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:93712578T>C	ENST00000334746.5	-	10	2483	c.2176A>G	c.(2176-2178)Aca>Gca	p.T726A	BTBD7_ENST00000554565.1_Missense_Mutation_p.T375A|BTBD7_ENST00000393170.2_Missense_Mutation_p.T300A	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	726					multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		TGTCTCATTGTCAAGAGTGGA	0.403																																					p.T726A		Atlas-SNP	.											.	BTBD7	112	.	0			c.A2176G						.						106.0	106.0	106.0					14																	93712578		2203	4300	6503	SO:0001583	missense	55727	exon10			TCATTGTCAAGAG	AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"""BTB/POZ domain containing"""	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.2176A>G	chr14.hg19:g.93712578T>C	ENSP00000335615:p.Thr726Ala	113.0	0.0		130.0	6.0	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Missense_Mutation	SNP	ENST00000334746.5	hg19	CCDS32146.1	.	.	.	.	.	.	.	.	.	.	T	15.40	2.821766	0.50633	.	.	ENSG00000011114	ENST00000334746;ENST00000554565;ENST00000553975;ENST00000393170	T;T	0.39997	1.41;1.05	5.75	5.75	0.90469	.	0.044520	0.85682	D	0.000000	T	0.24812	0.0602	N	0.08118	0	0.53688	D	0.999978	B;B;B	0.27625	0.183;0.1;0.002	B;B;B	0.22601	0.04;0.022;0.004	T	0.09037	-1.0693	10	0.23891	T	0.37	.	16.0605	0.80836	0.0:0.0:0.0:1.0	.	300;375;726	E7ERI4;Q9P203-5;Q9P203	.;.;BTBD7_HUMAN	A	726;375;341;300	ENSP00000335615:T726A;ENSP00000451010:T375A	ENSP00000335615:T726A	T	-	1	0	BTBD7	92782331	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.126000	0.57937	2.193000	0.70182	0.528000	0.53228	ACA	.	.		0.403	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860	
DDX24	57062	hgsc.bcm.edu	37	14	94519409	94519409	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:94519409T>C	ENST00000330836.5	-	8	2374	c.2243A>G	c.(2242-2244)cAc>cGc	p.H748R	DDX24_ENST00000555054.1_Missense_Mutation_p.H705R|DDX24_ENST00000544005.1_Missense_Mutation_p.H498R|DDX24_ENST00000553400.1_5'Flank	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	748					RNA metabolic process (GO:0016070)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		CCAAGAGTTGTGCAGGCAAGC	0.483																																					p.H748R		Atlas-SNP	.											.	DDX24	82	.	0			c.A2243G						.						68.0	66.0	67.0					14																	94519409		2203	4300	6503	SO:0001583	missense	57062	exon8			GAGTTGTGCAGGC	AF214731	CCDS9918.1	14q32	2013-07-16	2013-07-16			ENSG00000089737		"""DEAD-boxes"""	13266	protein-coding gene	gene with protein product		606181	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 24"""			10936056, 18289627	Standard	NM_020414		Approved		uc001ycj.3	Q9GZR7		ENST00000330836.5:c.2243A>G	chr14.hg19:g.94519409T>C	ENSP00000328690:p.His748Arg	106.0	0.0		81.0	4.0	NM_020414	E7EMJ4|Q4V9L5	Missense_Mutation	SNP	ENST00000330836.5	hg19	CCDS9918.1	.	.	.	.	.	.	.	.	.	.	T	19.34	3.807978	0.70797	.	.	ENSG00000089737	ENST00000330836;ENST00000544005;ENST00000440370;ENST00000543787;ENST00000555054;ENST00000542247	T;T;T	0.03358	4.05;3.96;4.05	5.61	5.61	0.85477	.	0.047415	0.85682	D	0.000000	T	0.06325	0.0163	L	0.43152	1.355	0.58432	D	0.999993	B	0.30146	0.27	B	0.34489	0.184	T	0.28776	-1.0033	10	0.59425	D	0.04	-10.2535	16.0977	0.81139	0.0:0.0:0.0:1.0	.	748	Q9GZR7	DDX24_HUMAN	R	748;498;693;374;705;705	ENSP00000328690:H748R;ENSP00000440623:H498R;ENSP00000452145:H705R	ENSP00000328690:H748R	H	-	2	0	DDX24	93589162	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	8.029000	0.88807	2.269000	0.75478	0.533000	0.62120	CAC	.	.		0.483	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414	
ATG2B	55102	hgsc.bcm.edu	37	14	96761480	96761480	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:96761480A>G	ENST00000359933.4	-	36	6136	c.5243T>C	c.(5242-5244)gTc>gCc	p.V1748A	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1748					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		ACTGCAGGTGACATCAGCTCC	0.373																																					p.V1748A		Atlas-SNP	.											.	ATG2B	169	.	0			c.T5243C						.						73.0	70.0	71.0					14																	96761480		2203	4300	6503	SO:0001583	missense	55102	exon36			CAGGTGACATCAG	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.5243T>C	chr14.hg19:g.96761480A>G	ENSP00000353010:p.Val1748Ala	110.0	0.0		89.0	5.0	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	A	17.89	3.500390	0.64298	.	.	ENSG00000066739	ENST00000359933	T	0.10005	2.92	5.52	5.52	0.82312	.	0.089600	0.44285	D	0.000476	T	0.11665	0.0284	L	0.42245	1.32	0.49483	D	0.999796	P	0.47302	0.893	B	0.44315	0.446	T	0.04840	-1.0923	10	0.06099	T	0.92	.	15.9319	0.79668	1.0:0.0:0.0:0.0	.	1748	Q96BY7	ATG2B_HUMAN	A	1748	ENSP00000353010:V1748A	ENSP00000261834:V392A	V	-	2	0	ATG2B	95831233	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.927000	0.75840	2.225000	0.72522	0.459000	0.35465	GTC	.	.		0.373	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
CCNK	8812	hgsc.bcm.edu	37	14	99976694	99976694	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:99976694T>C	ENST00000389879.5	+	11	1441	c.1318T>C	c.(1318-1320)Tct>Cct	p.S440P	CCNK_ENST00000555049.1_Intron|RP11-688G15.3_ENST00000557733.1_RNA	NM_001099402.1	NP_001092872.1	O75909	CCNK_HUMAN	cyclin K	440					cellular response to DNA damage stimulus (GO:0006974)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of cell cycle arrest (GO:0071157)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cyclin K-CDK12 complex (GO:0002944)|cyclin K-CDK13 complex (GO:0002945)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase binding (GO:0019901)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(1)|endometrium(2)|lung(3)	6		all_cancers(154;0.224)|all_epithelial(191;0.0643)|Melanoma(154;0.0866)				CTCCTACATGTCTGGAGAGGG	0.697																																					p.S440P		Atlas-SNP	.											.	CCNK	32	.	0			c.T1318C						.						20.0	22.0	22.0					14																	99976694		1957	4123	6080	SO:0001583	missense	8812	exon11			TACATGTCTGGAG	AF060515	CCDS45160.1	14q32.2	2014-07-03			ENSG00000090061	ENSG00000090061			1596	protein-coding gene	gene with protein product		603544				9632813, 10574912	Standard	NM_001099402		Approved	CPR4	uc001ygi.4	O75909	OTTHUMG00000171495	ENST00000389879.5:c.1318T>C	chr14.hg19:g.99976694T>C	ENSP00000374529:p.Ser440Pro	130.0	0.0		139.0	6.0	NM_001099402	Q59FT6|Q86U16|Q96B63|Q9NNY9	Missense_Mutation	SNP	ENST00000389879.5	hg19	CCDS45160.1	.	.	.	.	.	.	.	.	.	.	T	15.81	2.944018	0.53079	.	.	ENSG00000090061	ENST00000437596;ENST00000389879	T	0.27720	1.65	3.96	3.96	0.45880	.	0.292105	0.33496	N	0.004854	T	0.30541	0.0768	N	0.24115	0.695	0.80722	D	1	D	0.65815	0.995	P	0.54889	0.763	T	0.02596	-1.1136	10	0.21014	T	0.42	-6.8107	13.0066	0.58707	0.0:0.0:0.0:1.0	.	440	O75909	CCNK_HUMAN	P	460;440	ENSP00000374529:S440P	ENSP00000374529:S440P	S	+	1	0	CCNK	99046447	1.000000	0.71417	0.994000	0.49952	0.985000	0.73830	7.023000	0.76437	1.665000	0.50811	0.397000	0.26171	TCT	.	.		0.697	CCNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413721.1		
DYNC1H1	1778	hgsc.bcm.edu	37	14	102431079	102431079	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:102431079A>G	ENST00000360184.4	+	1	215	c.51A>G	c.(49-51)gaA>gaG	p.E17E		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	17					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						CCGGATTGGAAGTGTCGGCCG	0.726																																					p.E17E		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A51G						.						7.0	9.0	8.0					14																	102431079		1982	3991	5973	SO:0001819	synonymous_variant	1778	exon1			ATTGGAAGTGTCG	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.51A>G	chr14.hg19:g.102431079A>G		25.0	0.0		43.0	4.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	hg19	CCDS9966.1																																																																																			.	.		0.726	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
AMN	81693	hgsc.bcm.edu	37	14	103395267	103395267	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:103395267T>C	ENST00000299155.5	+	5	501	c.468T>C	c.(466-468)ccT>ccC	p.P156P		NM_030943.3	NP_112205.2	Q9BXJ7	AMNLS_HUMAN	amnion associated transmembrane protein	156					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|excretion (GO:0007588)|Golgi to plasma membrane protein transport (GO:0043001)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			kidney(2)|large_intestine(1)|lung(2)|skin(1)	6				Colorectal(3;0.00739)|READ - Rectum adenocarcinoma(2;0.0336)|Epithelial(152;0.0363)|all cancers(159;0.147)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GGCTCGGCCCTGGCGCTAGCC	0.721																																					p.P156P		Atlas-SNP	.											.	AMN	13	.	0			c.T468C						.						25.0	25.0	25.0					14																	103395267		2199	4296	6495	SO:0001819	synonymous_variant	81693	exon5			CGGCCCTGGCGCT	AF328788	CCDS9977.1	14q32.32	2014-09-17	2012-12-07		ENSG00000166126	ENSG00000166126			14604	protein-coding gene	gene with protein product		605799	"""amnionless homolog (mouse)"""			11279523	Standard	NM_030943		Approved	amnionless	uc001ymg.4	Q9BXJ7		ENST00000299155.5:c.468T>C	chr14.hg19:g.103395267T>C		32.0	0.0		53.0	4.0	NM_030943	Q6UX83	Silent	SNP	ENST00000299155.5	hg19	CCDS9977.1																																																																																			.	.		0.721	AMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415704.1		
CDC42BPB	9578	hgsc.bcm.edu	37	14	103414077	103414077	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:103414077T>C	ENST00000361246.2	-	27	3800	c.3512A>G	c.(3511-3513)gAt>gGt	p.D1171G		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		ACATGGAATATCTCGGCGTGT	0.443																																					p.D1171G		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.A3512G						.						113.0	114.0	113.0					14																	103414077		2200	4293	6493	SO:0001583	missense	9578	exon27			GGAATATCTCGGC	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"""CDC42-binding protein kinase beta (DMPK-like)"""			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.3512A>G	chr14.hg19:g.103414077T>C	ENSP00000355237:p.Asp1171Gly	65.0	0.0		96.0	4.0	NM_006035		Missense_Mutation	SNP	ENST00000361246.2	hg19	CCDS9978.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.165233	0.78339	.	.	ENSG00000198752	ENST00000361246;ENST00000541396	T	0.40476	1.03	5.63	5.63	0.86233	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.046925	0.85682	D	0.000000	T	0.71459	0.3342	M	0.90082	3.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.78352	-0.2237	10	0.87932	D	0	.	16.1721	0.81825	0.0:0.0:0.0:1.0	.	1171;1171	A9JR72;Q9Y5S2	.;MRCKB_HUMAN	G	1171;282	ENSP00000355237:D1171G	ENSP00000355237:D1171G	D	-	2	0	CDC42BPB	102483830	1.000000	0.71417	0.955000	0.39395	0.671000	0.39405	7.483000	0.81158	2.281000	0.76405	0.524000	0.50904	GAT	.	.		0.443	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035	
MTA1	9112	hgsc.bcm.edu	37	14	105916421	105916421	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:105916421C>T	ENST00000331320.7	+	5	482	c.268C>T	c.(268-270)Ccg>Tcg	p.P90S	MTA1_ENST00000406191.1_Missense_Mutation_p.P90S|MTA1_ENST00000405646.1_Missense_Mutation_p.P73S	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	90	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		AATGGAGAACCCGGAAATGGT	0.627																																					p.P90S		Atlas-SNP	.											MTA1,NS,carcinoma,0,1	MTA1	61	.	0			c.C268T						.						61.0	66.0	64.0					14																	105916421		2203	4300	6503	SO:0001583	missense	9112	exon5			GAGAACCCGGAAA	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"""GATA zinc finger domain containing"""	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.268C>T	chr14.hg19:g.105916421C>T	ENSP00000333633:p.Pro90Ser	179.0	0.0		157.0	0.0	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	hg19	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	C	19.02	3.746070	0.69418	.	.	ENSG00000182979	ENST00000331320;ENST00000406191;ENST00000405646;ENST00000498644	D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02	4.14	4.14	0.48551	Bromo adjacent homology (BAH) domain (3);	0.000000	0.85682	U	0.000000	D	0.83367	0.5239	L	0.56396	1.775	0.80722	D	1	P	0.38250	0.624	B	0.39465	0.3	D	0.83910	0.0295	10	0.41790	T	0.15	-11.5496	14.9627	0.71169	0.0:1.0:0.0:0.0	.	90	Q13330	MTA1_HUMAN	S	90;90;73;4	ENSP00000333633:P90S;ENSP00000385702:P90S;ENSP00000384180:P73S;ENSP00000448146:P4S	ENSP00000333633:P90S	P	+	1	0	MTA1	104987466	1.000000	0.71417	0.914000	0.36105	0.674000	0.39518	3.448000	0.52943	1.839000	0.53478	0.306000	0.20318	CCG	.	.		0.627	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15		
APBA2	321	hgsc.bcm.edu	37	15	29397672	29397672	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:29397672A>G	ENST00000558402.1	+	12	2214	c.1615A>G	c.(1615-1617)Agc>Ggc	p.S539G	APBA2_ENST00000561069.1_Missense_Mutation_p.S539G|APBA2_ENST00000558259.1_Missense_Mutation_p.S539G|APBA2_ENST00000411764.1_Missense_Mutation_p.S527G|APBA2_ENST00000558330.1_Missense_Mutation_p.S527G			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	539	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)		CGAAGACTTGAGCCAGAAGGA	0.562																																					p.S539G		Atlas-SNP	.											.	APBA2	132	.	0			c.A1615G						.						160.0	113.0	129.0					15																	29397672		2202	4300	6502	SO:0001583	missense	321	exon10			GACTTGAGCCAGA	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.1615A>G	chr15.hg19:g.29397672A>G	ENSP00000453293:p.Ser539Gly	86.0	0.0		123.0	5.0	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	hg19	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.155937	0.57259	.	.	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.06218	3.33	4.23	4.23	0.50019	Phosphotyrosine interaction domain (1);PDZ/DHR/GLGF (1);	0.159368	0.51477	D	0.000082	T	0.15478	0.0373	L	0.41492	1.28	0.80722	D	1	P;D;B	0.71674	0.856;0.998;0.089	B;D;B	0.73380	0.352;0.98;0.042	T	0.01884	-1.1254	10	0.39692	T	0.17	.	12.9273	0.58266	1.0:0.0:0.0:0.0	.	527;527;539	Q5XKC0;E9PGI4;Q99767	.;.;APBA2_HUMAN	G	527;539	ENSP00000409312:S527G	ENSP00000219865:S539G	S	+	1	0	APBA2	27184964	1.000000	0.71417	1.000000	0.80357	0.321000	0.28281	5.828000	0.69307	1.880000	0.54463	0.402000	0.26972	AGC	.	.		0.562	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
NUTM1	256646	hgsc.bcm.edu	37	15	34649310	34649310	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:34649310A>G	ENST00000333756.4	+	7	3172	c.3017A>G	c.(3016-3018)aAg>aGg	p.K1006R	NUTM1_ENST00000438749.3_Missense_Mutation_p.K1024R|NUTM1_ENST00000537011.1_Missense_Mutation_p.K1034R	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	1006						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.K1006M(1)									AAGGAGAAAAAGAAAAAGGAA	0.478																																					p.K1006R		Atlas-SNP	.											C15orf55_ENST00000333756,lymph_node,lymphoid_neoplasm,0,1	C15orf55	110	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A3017G						.						53.0	45.0	47.0					15																	34649310		2201	4298	6499	SO:0001583	missense	256646	exon7			AGAAAAAGAAAAA	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"""nuclear protein in testis"""	608963	"""chromosome 15 open reading frame 55"""	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.3017A>G	chr15.hg19:g.34649310A>G	ENSP00000329448:p.Lys1006Arg	55.0	0.0		56.0	3.0	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	hg19	CCDS32190.1	.	.	.	.	.	.	.	.	.	.	A	4.528	0.097981	0.08681	.	.	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000333756	T;T;T	0.08807	3.05;3.05;3.06	4.06	-1.03	0.10102	.	2.094490	0.02876	N	0.132249	T	0.04679	0.0127	N	0.14661	0.345	0.09310	N	1	B;B;B	0.11235	0.003;0.004;0.003	B;B;B	0.08055	0.001;0.003;0.001	T	0.35773	-0.9775	10	0.12766	T	0.61	.	3.9357	0.09305	0.4982:0.1883:0.3135:0.0	.	1024;1034;1006	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	R	1034;1024;1006	ENSP00000444896:K1034R;ENSP00000407031:K1024R;ENSP00000329448:K1006R	ENSP00000329448:K1006R	K	+	2	0	C15orf55	32436602	0.013000	0.17824	0.000000	0.03702	0.016000	0.09150	1.969000	0.40510	-0.188000	0.10499	0.533000	0.62120	AAG	.	.		0.478	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741	
DPH6	89978	hgsc.bcm.edu	37	15	35742950	35742950	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:35742950T>C	ENST00000256538.4	-	5	467	c.441A>G	c.(439-441)gaA>gaG	p.E147E		NM_080650.3	NP_542381.1	Q7L8W6	DPH6_HUMAN	diphthamine biosynthesis 6	147					peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)		ATP binding (GO:0005524)|diphthine-ammonia ligase activity (GO:0017178)										TGAGCAAATCTTCCTGGTTTC	0.378																																					p.E147E		Atlas-SNP	.											.	ATPBD4	30	.	0			c.A441G						.						145.0	129.0	134.0					15																	35742950		2201	4298	6499	SO:0001819	synonymous_variant	89978	exon5			CAAATCTTCCTGG		CCDS10043.1, CCDS45213.1	15q14	2013-06-19	2013-06-19	2013-05-02	ENSG00000134146	ENSG00000134146	6.3.1.14		30543	protein-coding gene	gene with protein product	"""diphthine--ammonia ligase"""		"""ATP binding domain 4"", ""DPH6 homolog (S. cerevisiae)"""	ATPBD4		23169644, 23468660	Standard	NM_080650		Approved	MGC14798		Q7L8W6	OTTHUMG00000129759	ENST00000256538.4:c.441A>G	chr15.hg19:g.35742950T>C		112.0	0.0		96.0	4.0	NM_080650	B3KWG1|Q96HJ6	Silent	SNP	ENST00000256538.4	hg19	CCDS10043.1																																																																																			.	.		0.378	DPH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251973.1	NM_080650	
NDUFAF1	51103	hgsc.bcm.edu	37	15	41688824	41688824	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:41688824C>A	ENST00000260361.4	-	2	815	c.434G>T	c.(433-435)gGa>gTa	p.G145V		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	145					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		ACTTCTGCCTCCAATCGTCTT	0.488																																					p.G145V		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.G434T						.						91.0	86.0	88.0					15																	41688824		2203	4300	6503	SO:0001583	missense	51103	exon2			CTGCCTCCAATCG	AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"""Mitochondrial respiratory chain complex assembly factors"""	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.434G>T	chr15.hg19:g.41688824C>A	ENSP00000260361:p.Gly145Val	250.0	0.0		270.0	94.0	NM_016013	Q9BVZ5	Missense_Mutation	SNP	ENST00000260361.4	hg19	CCDS10075.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.487384	0.84854	.	.	ENSG00000137806	ENST00000260361	D	0.88741	-2.42	4.7	4.7	0.59300	NADH:ubiquinone oxidoreductase intermediate-associated protein 30 (1);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.95544	0.8552	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96545	0.9403	10	0.87932	D	0	-13.2143	18.0656	0.89389	0.0:1.0:0.0:0.0	.	145	Q9Y375	CIA30_HUMAN	V	145	ENSP00000260361:G145V	ENSP00000260361:G145V	G	-	2	0	NDUFAF1	39476116	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.624000	0.83124	2.334000	0.79466	0.449000	0.29647	GGA	.	.		0.488	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013	
ITPKA	3706	hgsc.bcm.edu	37	15	41794627	41794627	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:41794627T>C	ENST00000260386.5	+	5	1089	c.1036T>C	c.(1036-1038)Ttc>Ctc	p.F346L		NM_002220.2	NP_002211.1	P23677	IP3KA_HUMAN	inositol-trisphosphate 3-kinase A	346					actin cytoskeleton organization (GO:0030036)|dendritic spine maintenance (GO:0097062)|inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|positive regulation of dendritic spine morphogenesis (GO:0061003)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendritic spine (GO:0043197)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			kidney(1)|lung(3)|skin(1)	5		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;7.63e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		CAGCACCGACTTCAAGACTAC	0.612																																					p.F346L		Atlas-SNP	.											.	ITPKA	19	.	0			c.T1036C						.						60.0	65.0	63.0					15																	41794627		2203	4300	6503	SO:0001583	missense	3706	exon5			ACCGACTTCAAGA	X54938	CCDS10076.1	15q15.1	2011-04-28	2011-04-28		ENSG00000137825	ENSG00000137825	2.7.1.127		6178	protein-coding gene	gene with protein product		147521	"""inositol 1,4,5-trisphosphate 3-kinase A"""			1330886, 2175886	Standard	NM_002220		Approved	IP3KA, IP3-3KA	uc001znz.3	P23677	OTTHUMG00000130343	ENST00000260386.5:c.1036T>C	chr15.hg19:g.41794627T>C	ENSP00000260386:p.Phe346Leu	79.0	0.0		96.0	5.0	NM_002220	Q8TAN3	Missense_Mutation	SNP	ENST00000260386.5	hg19	CCDS10076.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.888794	0.91814	.	.	ENSG00000137825	ENST00000425927;ENST00000260386	T;T	0.17370	2.28;2.28	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.39545	0.1082	M	0.71920	2.185	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.19353	-1.0308	10	0.54805	T	0.06	-3.0312	12.219	0.54423	0.0:0.0:0.0:1.0	.	346	P23677	IP3KA_HUMAN	L	241;346	ENSP00000396560:F241L;ENSP00000260386:F346L	ENSP00000260386:F346L	F	+	1	0	ITPKA	39581919	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.791000	0.69045	2.020000	0.59435	0.533000	0.62120	TTC	.	.		0.612	ITPKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252695.3	NM_002220	
LTK	4058	hgsc.bcm.edu	37	15	41797008	41797008	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:41797008A>G	ENST00000263800.6	-	17	2179	c.2083T>C	c.(2083-2085)Ttc>Ctc	p.F695L	LTK_ENST00000453182.2_Missense_Mutation_p.F565L|LTK_ENST00000355166.5_Missense_Mutation_p.F634L|LTK_ENST00000561619.1_Missense_Mutation_p.F393L	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	695	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		CCCTCCAGGAAGGCCTCTGGG	0.582										TSP Lung(18;0.14)																											p.F695L		Atlas-SNP	.											.	LTK	117	.	0			c.T2083C						.						52.0	58.0	56.0					15																	41797008		2203	4300	6503	SO:0001583	missense	4058	exon17			CCAGGAAGGCCTC	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.2083T>C	chr15.hg19:g.41797008A>G	ENSP00000263800:p.Phe695Leu	76.0	0.0		99.0	4.0	NM_002344	A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	ENST00000263800.6	hg19	CCDS10077.1	.	.	.	.	.	.	.	.	.	.	A	13.89	2.371410	0.42003	.	.	ENSG00000062524	ENST00000355166;ENST00000263800;ENST00000453182	T;T;T	0.79940	-1.32;-1.32;-1.32	4.6	2.28	0.28536	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.245905	0.21107	N	0.080057	T	0.45975	0.1369	N	0.00313	-1.665	0.43234	D	0.995131	B;B;B;B	0.30763	0.02;0.028;0.107;0.294	B;B;B;B	0.35470	0.043;0.017;0.052;0.203	T	0.22347	-1.0219	10	0.18276	T	0.48	.	6.5018	0.22174	0.7502:0.0:0.2498:0.0	.	565;565;634;695	E9PFX4;B4DL89;P29376-4;P29376	.;.;.;LTK_HUMAN	L	634;695;565	ENSP00000347293:F634L;ENSP00000263800:F695L;ENSP00000392196:F565L	ENSP00000263800:F695L	F	-	1	0	LTK	39584300	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	3.712000	0.54875	0.306000	0.22856	0.533000	0.62120	TTC	.	.		0.582	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2		
UBR1	197131	hgsc.bcm.edu	37	15	43314950	43314950	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:43314950T>C	ENST00000290650.4	-	26	2867	c.2789A>G	c.(2788-2790)cAa>cGa	p.Q930R	UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	930					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)		AGGAGCTTTTTGAAGCTGTTG	0.348																																					p.Q930R		Atlas-SNP	.											.	UBR1	124	.	0			c.A2789G						.						98.0	99.0	99.0					15																	43314950		2203	4298	6501	SO:0001583	missense	197131	exon26			GCTTTTTGAAGCT		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.2789A>G	chr15.hg19:g.43314950T>C	ENSP00000290650:p.Gln930Arg	54.0	0.0		65.0	4.0	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	hg19	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	T	18.32	3.597076	0.66332	.	.	ENSG00000159459	ENST00000290650;ENST00000546274	T	0.58506	0.33	4.77	4.77	0.60923	.	0.125005	0.53938	D	0.000041	T	0.51058	0.1652	L	0.53249	1.67	0.80722	D	1	P;P	0.38922	0.57;0.651	B;B	0.35114	0.196;0.165	T	0.51996	-0.8634	10	0.29301	T	0.29	-13.5412	14.7539	0.69549	0.0:0.0:0.0:1.0	.	930;930	B4DYL2;Q8IWV7	.;UBR1_HUMAN	R	930	ENSP00000290650:Q930R	ENSP00000290650:Q930R	Q	-	2	0	UBR1	41102242	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.280000	0.65603	2.134000	0.65973	0.528000	0.53228	CAA	.	.		0.348	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	
MYO5C	55930	hgsc.bcm.edu	37	15	52571842	52571842	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:52571842A>G	ENST00000261839.7	-	3	329	c.168T>C	c.(166-168)tcT>tcC	p.S56S	MYO5C_ENST00000541028.1_5'UTR|MYO5C_ENST00000443683.2_5'UTR|MIR1266_ENST00000408125.1_RNA	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	56						extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		GTGGAGGCAGAGATTCTGGAT	0.468																																					p.S56S		Atlas-SNP	.											.	MYO5C	162	.	0			c.T168C						.						47.0	46.0	46.0					15																	52571842		1862	4110	5972	SO:0001819	synonymous_variant	55930	exon3			AGGCAGAGATTCT	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"""Myosins / Myosin superfamily : Class V"""	7604	protein-coding gene	gene with protein product	"""myosin 5C"""	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.168T>C	chr15.hg19:g.52571842A>G		61.0	0.0		78.0	6.0	NM_018728	Q6P1W8	Silent	SNP	ENST00000261839.7	hg19	CCDS42036.1																																																																																			.	.		0.468	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728	
MYO5A	4644	hgsc.bcm.edu	37	15	52645812	52645812	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:52645812T>C	ENST00000399231.3	-	27	3854	c.3611A>G	c.(3610-3612)gAg>gGg	p.E1204G	MYO5A_ENST00000399233.2_Missense_Mutation_p.E1204G|MYO5A_ENST00000358212.6_Missense_Mutation_p.E1204G|MYO5A_ENST00000553916.1_Missense_Mutation_p.E1204G|MYO5A_ENST00000356338.6_Missense_Mutation_p.E1204G	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1204					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)		CTTGAGTGACTCATATTCCAG	0.348																																					p.E1204G		Atlas-SNP	.											.	MYO5A	145	.	0			c.A3611G						.						113.0	110.0	111.0					15																	52645812		1818	4078	5896	SO:0001583	missense	4644	exon27			AGTGACTCATATT		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.3611A>G	chr15.hg19:g.52645812T>C	ENSP00000382177:p.Glu1204Gly	139.0	0.0		151.0	7.0	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	hg19	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.817687	0.90790	.	.	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.39091	0.1065	L	0.40543	1.245	0.80722	D	1	B;D	0.89917	0.012;1.0	B;D	0.85130	0.015;0.997	T	0.06935	-1.0799	10	0.48119	T	0.1	.	16.3631	0.83280	0.0:0.0:0.0:1.0	.	1204;1204	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	G	1204;738;1204;1204;1204;834;1204	ENSP00000382177:E1204G;ENSP00000382179:E1204G;ENSP00000348693:E1204G;ENSP00000350945:E1204G;ENSP00000451109:E1204G	ENSP00000348693:E1204G	E	-	2	0	MYO5A	50433104	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.138000	0.77305	2.266000	0.75297	0.533000	0.62120	GAG	.	.		0.348	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
MYZAP	100820829	hgsc.bcm.edu	37	15	57967220	57967220	+	Missense_Mutation	SNP	G	G	C	rs146505887	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:57967220G>C	ENST00000267853.5	+	12	1352	c.1258G>C	c.(1258-1260)Gaa>Caa	p.E420Q	GCOM1_ENST00000380561.2_Missense_Mutation_p.E361Q|GCOM1_ENST00000380568.3_Missense_Mutation_p.E420Q|GCOM1_ENST00000574161.1_Missense_Mutation_p.E420Q|GCOM1_ENST00000572390.1_Missense_Mutation_p.E392Q|GCOM1_ENST00000380560.2_Missense_Mutation_p.E351Q|GCOM1_ENST00000396180.1_Missense_Mutation_p.E389Q|GCOM1_ENST00000380569.2_Missense_Mutation_p.E420Q|POLR2M_ENST00000380563.2_5'UTR|MYZAP_ENST00000380565.4_Missense_Mutation_p.E392Q|GCOM1_ENST00000587652.1_Missense_Mutation_p.E420Q			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	420					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)											GGCCAAGACTGAAGTGGAAAC	0.378																																					p.E420Q		Atlas-SNP	.											GCOM1_ENST00000574161,NS,carcinoma,0,2	GCOM1	66	.	0			c.G1258C						.						99.0	102.0	101.0					15																	57967220		2192	4292	6484	SO:0001583	missense	145781	exon12			AAGACTGAAGTGG	FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"""myocardium-enriched zonula adherens protein"""	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.1258G>C	chr15.hg19:g.57967220G>C	ENSP00000267853:p.Glu420Gln	104.0	0.0		104.0	0.0	NM_001018090	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Missense_Mutation	SNP	ENST00000267853.5	hg19	CCDS10162.1	.	.	.	.	.	.	.	.	.	.	G	13.73	2.325088	0.41197	.	.	ENSG00000137878	ENST00000380569;ENST00000380561;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380565;ENST00000380568	T;T;T;T;T;T;T	0.26373	1.85;1.82;1.87;1.87;1.84;1.74;1.85	5.55	4.64	0.57946	.	0.474041	0.25222	N	0.032236	T	0.20292	0.0488	L	0.27053	0.805	0.80722	D	1	P;B;B;B	0.39903	0.694;0.374;0.385;0.015	B;B;B;B	0.42422	0.387;0.334;0.387;0.043	T	0.03433	-1.1037	10	0.27082	T	0.32	-6.0611	10.3407	0.43877	0.0905:0.0:0.9095:0.0	.	420;420;392;420	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	Q	420;361;389;351;420;392;420	ENSP00000369943:E420Q;ENSP00000369935:E361Q;ENSP00000379483:E389Q;ENSP00000369933:E351Q;ENSP00000267853:E420Q;ENSP00000369939:E392Q;ENSP00000369942:E420Q	ENSP00000267853:E420Q	E	+	1	0	GCOM1	55754512	0.849000	0.29639	0.974000	0.42286	0.747000	0.42532	2.916000	0.48813	1.342000	0.45619	-0.136000	0.14681	GAA	.	G|0.999;A|0.001		0.378	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100	
GCNT3	9245	hgsc.bcm.edu	37	15	59910958	59910958	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:59910958A>G	ENST00000396065.1	+	3	969	c.521A>G	c.(520-522)gAg>gGg	p.E174G	GCNT3_ENST00000560585.1_Missense_Mutation_p.E174G	NM_004751.2	NP_004742.1	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin type	174					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|immunoglobulin production in mucosal tissue (GO:0002426)|intestinal absorption (GO:0050892)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|tissue morphogenesis (GO:0048729)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0047225)|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ACTTTCAAAGAGGCGGTCAAA	0.473																																					p.E174G		Atlas-SNP	.											.	GCNT3	42	.	0			c.A521G						.						104.0	101.0	102.0					15																	59910958		2190	4290	6480	SO:0001583	missense	9245	exon3			TCAAAGAGGCGGT	AF102542	CCDS10172.1	15q22	2013-02-25			ENSG00000140297	ENSG00000140297	2.4.1.102, 2.4.1.150	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4205	protein-coding gene	gene with protein product		606836				9915862, 9988682	Standard	NM_004751		Approved	C2GnT-M, C2/4GnT, C2GnT2	uc002age.3	O95395	OTTHUMG00000132726	ENST00000396065.1:c.521A>G	chr15.hg19:g.59910958A>G	ENSP00000379377:p.Glu174Gly	93.0	0.0		93.0	4.0	NM_004751		Missense_Mutation	SNP	ENST00000396065.1	hg19	CCDS10172.1	.	.	.	.	.	.	.	.	.	.	A	9.148	1.015453	0.19355	.	.	ENSG00000140297	ENST00000396065	T	0.13089	2.62	6.16	3.76	0.43208	.	0.485335	0.23151	N	0.051359	T	0.13286	0.0322	L	0.51914	1.62	0.35243	D	0.778048	B	0.31459	0.324	B	0.31390	0.129	T	0.13522	-1.0506	10	0.34782	T	0.22	.	9.4683	0.38826	0.7526:0.1268:0.0:0.1206	.	174	O95395	GCNT3_HUMAN	G	174	ENSP00000379377:E174G	ENSP00000379377:E174G	E	+	2	0	GCNT3	57698250	0.600000	0.26899	0.521000	0.27850	0.374000	0.29953	2.343000	0.44001	0.505000	0.28104	0.528000	0.53228	GAG	.	.		0.473	GCNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256068.1	NM_004751	
TLN2	83660	hgsc.bcm.edu	37	15	62948266	62948266	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:62948266T>G	ENST00000561311.1	+	7	871	c.641T>G	c.(640-642)cTg>cGg	p.L214R	TLN2_ENST00000306829.6_Missense_Mutation_p.L214R			Q9Y4G6	TLN2_HUMAN	talin 2	214	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CCCGTGCAGCTGAACTTGCTT	0.468																																					p.L214R		Atlas-SNP	.											.	TLN2	253	.	0			c.T641G						.						108.0	92.0	97.0					15																	62948266		2203	4300	6503	SO:0001583	missense	83660	exon5			TGCAGCTGAACTT	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.641T>G	chr15.hg19:g.62948266T>G	ENSP00000453508:p.Leu214Arg	133.0	0.0		146.0	6.0	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.583538	0.86748	.	.	ENSG00000171914	ENST00000306829	T	0.77620	-1.11	5.47	5.47	0.80525	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.85682	D	0.000000	D	0.87900	0.6294	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89418	0.3708	10	0.87932	D	0	-13.9128	15.0304	0.71701	0.0:0.0:0.0:1.0	.	214	Q9Y4G6	TLN2_HUMAN	R	214	ENSP00000303476:L214R	ENSP00000303476:L214R	L	+	2	0	TLN2	60735558	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.988000	0.88194	2.199000	0.70637	0.533000	0.62120	CTG	.	.		0.468	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
IGDCC4	57722	hgsc.bcm.edu	37	15	65689174	65689174	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:65689174A>G	ENST00000352385.2	-	6	1204	c.995T>C	c.(994-996)cTg>cCg	p.L332P		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	332						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						CGCCTCACCCAGCACACGGAG	0.701																																					p.L332P		Atlas-SNP	.											.	IGDCC4	95	.	0			c.T995C						.						10.0	11.0	11.0					15																	65689174		2179	4274	6453	SO:0001583	missense	57722	exon6			TCACCCAGCACAC		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13770	protein-coding gene	gene with protein product	"""likely ortholog of mouse neighbor of Punc E11"""						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.995T>C	chr15.hg19:g.65689174A>G	ENSP00000319623:p.Leu332Pro	36.0	0.0		82.0	4.0	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	hg19	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.074015	0.36566	.	.	ENSG00000103742	ENST00000352385	T	0.31247	1.5	4.04	4.04	0.47022	.	0.377432	0.24396	N	0.038897	T	0.37348	0.1000	M	0.79011	2.435	0.80722	D	1	B	0.20988	0.05	B	0.24394	0.053	T	0.36065	-0.9763	10	0.59425	D	0.04	-4.2363	12.9927	0.58630	1.0:0.0:0.0:0.0	.	332	Q8TDY8	IGDC4_HUMAN	P	332	ENSP00000319623:L332P	ENSP00000319623:L332P	L	-	2	0	IGDCC4	63476227	1.000000	0.71417	1.000000	0.80357	0.395000	0.30598	7.138000	0.77305	1.455000	0.47813	0.379000	0.24179	CTG	.	.		0.701	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	
VWA9	81556	hgsc.bcm.edu	37	15	65871932	65871932	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:65871932A>G	ENST00000395644.4	-	12	1706	c.1371T>C	c.(1369-1371)gcT>gcC	p.A457A	VWA9_ENST00000569491.1_Silent_p.A407A|VWA9_ENST00000567744.1_Silent_p.A493A|VWA9_ENST00000420799.2_Silent_p.A400A|VWA9_ENST00000442903.3_Silent_p.A421A|VWA9_ENST00000431261.2_Silent_p.A378A|VWA9_ENST00000313182.2_Silent_p.A457A			Q96SY0	VWA9_HUMAN	von Willebrand factor A domain containing 9	457																	CCAGCATGTCAGCCACCCCTT	0.552																																					p.A439A		Atlas-SNP	.											.	VWA9	15	.	0			c.T1317C						.						70.0	61.0	64.0					15																	65871932		2201	4299	6500	SO:0001819	synonymous_variant	81556	exon12			CATGTCAGCCACC	AL136662	CCDS55969.1, CCDS45283.1	15q22.31	2012-09-27	2012-09-27	2012-09-27	ENSG00000138614	ENSG00000138614			25372	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 44"""	C15orf44		11230166	Standard	NM_001136043		Approved	DKFZP564O1664	uc010uja.2	Q96SY0	OTTHUMG00000133159	ENST00000395644.4:c.1371T>C	chr15.hg19:g.65871932A>G		98.0	0.0		110.0	5.0	NM_001207058	B4DDI6|B4DVD5|Q49AH8|Q96HX5|Q9H0S5	Silent	SNP	ENST00000395644.4	hg19																																																																																				.	.		0.552	VWA9-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420604.3	NM_030800	
NOX5	79400	hgsc.bcm.edu	37	15	69331259	69331259	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:69331259T>C	ENST00000388866.3	+	9	1475	c.1434T>C	c.(1432-1434)taT>taC	p.Y478Y	NOX5_ENST00000530406.2_Silent_p.Y450Y|NOX5_ENST00000455873.3_Silent_p.Y443Y|NOX5_ENST00000448182.3_Silent_p.Y432Y|NOX5_ENST00000260364.5_Silent_p.Y460Y|RP11-809H16.4_ENST00000559495.1_RNA	NM_001184779.1|NM_024505.3	NP_001171708.1|NP_078781.3	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	478	C-terminal catalytic region.|FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cytokine secretion (GO:0050663)|cytokinesis (GO:0000910)|endothelial cell proliferation (GO:0001935)|oxidation-reduction process (GO:0055114)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|proton transport (GO:0015992)|regulation of fusion of sperm to egg plasma membrane (GO:0043012)|regulation of proton transport (GO:0010155)|superoxide anion generation (GO:0042554)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|hydrogen ion channel activity (GO:0015252)|NADP binding (GO:0050661)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35						ACTACTTGTATCTGAACATCC	0.522																																					p.Y478Y		Atlas-SNP	.											.	NOX5	60	.	0			c.T1434C						.						230.0	217.0	221.0					15																	69331259		2200	4298	6498	SO:0001819	synonymous_variant	79400	exon9			CTTGTATCTGAAC	AF317889	CCDS32276.1, CCDS32276.2, CCDS53953.1, CCDS53954.1	15q22.31	2013-01-10			ENSG00000255346	ENSG00000255346		"""EF-hand domain containing"""	14874	protein-coding gene	gene with protein product		606572				11483596	Standard	NM_001184779		Approved	NOX5A, NOX5B	uc002ars.2	Q96PH1	OTTHUMG00000133320	ENST00000388866.3:c.1434T>C	chr15.hg19:g.69331259T>C		148.0	0.0		165.0	7.0	NM_024505	B2RBJ4|Q08AN2|Q08AN3|Q8TEQ1|Q8TER4|Q96PH2|Q96PJ8|Q96PJ9|Q9H6E0|Q9HAM8	Silent	SNP	ENST00000388866.3	hg19	CCDS32276.2																																																																																			.	.		0.522	NOX5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257124.2	NM_024505	
MYO9A	4649	hgsc.bcm.edu	37	15	72193622	72193622	+	Silent	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:72193622G>A	ENST00000356056.5	-	23	3532	c.3060C>T	c.(3058-3060)ctC>ctT	p.L1020L	MYO9A_ENST00000444904.1_Silent_p.L1001L|MYO9A_ENST00000564571.1_Silent_p.L1020L|MYO9A_ENST00000424560.1_Silent_p.L1020L|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000566885.1_Silent_p.L640L	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1020					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						TGATTCTGCGGAGCACCTCTT	0.458																																					p.L1020L		Atlas-SNP	.											.	MYO9A	203	.	0			c.C3060T						.						114.0	97.0	102.0					15																	72193622		2199	4297	6496	SO:0001819	synonymous_variant	4649	exon23			TCTGCGGAGCACC	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.3060C>T	chr15.hg19:g.72193622G>A		132.0	0.0		141.0	57.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Silent	SNP	ENST00000356056.5	hg19	CCDS10239.1																																																																																			.	.		0.458	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
STRA6	64220	hgsc.bcm.edu	37	15	74473791	74473791	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:74473791A>G	ENST00000323940.5	-	17	1774	c.1529T>C	c.(1528-1530)cTc>cCc	p.L510P	STRA6_ENST00000563965.1_Missense_Mutation_p.L549P|STRA6_ENST00000574278.1_Missense_Mutation_p.L525P|STRA6_ENST00000449139.2_Missense_Mutation_p.L510P|STRA6_ENST00000395105.4_Missense_Mutation_p.L510P|STRA6_ENST00000574439.1_5'UTR|STRA6_ENST00000416286.3_Missense_Mutation_p.L502P|STRA6_ENST00000423167.2_Missense_Mutation_p.L501P|STRA6_ENST00000535552.1_Missense_Mutation_p.L547P|RP11-665J16.1_ENST00000561647.1_RNA	NM_001142617.1|NM_001142618.1|NM_001142619.1	NP_001136089.1|NP_001136090.1|NP_001136091.1	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid 6	510					adrenal gland development (GO:0030325)|alveolar primary septum development (GO:0061143)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|cognition (GO:0050890)|developmental growth (GO:0048589)|diaphragm development (GO:0060539)|digestive tract morphogenesis (GO:0048546)|ductus arteriosus closure (GO:0097070)|ear development (GO:0043583)|embryonic camera-type eye formation (GO:0060900)|embryonic digestive tract development (GO:0048566)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|feeding behavior (GO:0007631)|female genitalia development (GO:0030540)|head development (GO:0060322)|head morphogenesis (GO:0060323)|heart development (GO:0007507)|kidney development (GO:0001822)|learning (GO:0007612)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung vasculature development (GO:0060426)|neuromuscular process (GO:0050905)|nose morphogenesis (GO:0043585)|paramesonephric duct development (GO:0061205)|phototransduction, visible light (GO:0007603)|positive regulation of behavior (GO:0048520)|positive regulation of JAK-STAT cascade (GO:0046427)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol transport (GO:0034633)|smooth muscle tissue development (GO:0048745)|uterus morphogenesis (GO:0061038)|ventricular septum development (GO:0003281)|vitamin A import (GO:0071939)|vocal learning (GO:0042297)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	receptor activity (GO:0004872)|vitamin transporter activity (GO:0051183)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|stomach(2)	26						GGCTGCATAGAGCACTCGCCT	0.602																																					p.L549P		Atlas-SNP	.											.	STRA6	66	.	0			c.T1646C						.						64.0	56.0	59.0					15																	74473791		2198	4297	6495	SO:0001583	missense	64220	exon17			GCATAGAGCACTC	AF352728	CCDS10261.1, CCDS45301.1, CCDS45302.1, CCDS55973.1, CCDS55974.1, CCDS58387.1	15q24.1	2014-07-14	2012-12-07		ENSG00000137868	ENSG00000137868			30650	protein-coding gene	gene with protein product	"""retinol binding protein 4 receptor"""	610745	"""stimulated by retinoic acid gene 6 homolog (mouse)"", ""stimulated by retinoic acid 6 homolog (mouse)"""			17255476, 17273977	Standard	NM_022369		Approved	FLJ12541	uc002axj.3	Q9BX79	OTTHUMG00000138998	ENST00000323940.5:c.1529T>C	chr15.hg19:g.74473791A>G	ENSP00000326085:p.Leu510Pro	67.0	0.0		100.0	4.0	NM_001199042	A8K7F1|B7Z5M9|B7Z862|D3DW54|F5GYI8|I3L1G8|Q6PJF8|Q71RB9|Q7L9G1|Q7Z3U9|Q8TB21|Q9BX78|Q9H9U8	Missense_Mutation	SNP	ENST00000323940.5	hg19	CCDS10261.1	.	.	.	.	.	.	.	.	.	.	A	17.99	3.522404	0.64747	.	.	ENSG00000137868	ENST00000395105;ENST00000323940;ENST00000416286;ENST00000545137;ENST00000449139;ENST00000423167;ENST00000535552;ENST00000536129	D;D;T;D;D	0.83755	-1.76;-1.76;-1.47;-1.76;-1.76	4.72	4.72	0.59763	.	0.068022	0.64402	D	0.000012	D	0.89952	0.6864	M	0.72894	2.215	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.85130	0.996;0.996;0.996;0.997;0.996;0.996	D	0.91199	0.4990	10	0.87932	D	0	-37.6285	14.2323	0.65901	1.0:0.0:0.0:0.0	.	547;548;501;510;549;319	F5GYI8;B7Z5G7;Q9BX79-3;Q9BX79;Q9BX79-4;B3KRT6	.;.;.;STRA6_HUMAN;.;.	P	510;510;442;319;549;501;547;400	ENSP00000378537:L510P;ENSP00000326085:L510P;ENSP00000410221:L549P;ENSP00000413012:L501P;ENSP00000440238:L547P	ENSP00000326085:L510P	L	-	2	0	STRA6	72260844	1.000000	0.71417	0.040000	0.18447	0.257000	0.26127	7.603000	0.82811	1.769000	0.52152	0.459000	0.35465	CTC	.	.		0.602	STRA6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272891.1		
AKAP13	11214	hgsc.bcm.edu	37	15	86124122	86124122	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:86124122T>C	ENST00000394518.2	+	7	2918	c.2823T>C	c.(2821-2823)gcT>gcC	p.A941A	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Silent_p.A941A	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	941					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						AGGAAAATGCTCTCTCTTCAG	0.438																																					p.A941A	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.T2823C						.						77.0	80.0	79.0					15																	86124122		2202	4299	6501	SO:0001819	synonymous_variant	11214	exon7			AAATGCTCTCTCT	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.2823T>C	chr15.hg19:g.86124122T>C		100.0	0.0		89.0	4.0	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	hg19	CCDS32319.1																																																																																			.	.		0.438	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
KLHL25	64410	hgsc.bcm.edu	37	15	86312123	86312123	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:86312123A>G	ENST00000337975.5	-	2	1193	c.919T>C	c.(919-921)Tgt>Cgt	p.C307R	MIR1276_ENST00000408707.1_RNA|KLHL25_ENST00000559131.1_Intron|KLHL25_ENST00000536947.1_Missense_Mutation_p.C307R	NM_022480.3	NP_071925.2	Q9H0H3	KLH25_HUMAN	kelch-like family member 25	307					protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of translational initiation (GO:0006446)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)				breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	25						ATCTTGTCACACATGAAGGTC	0.642																																					p.C307R		Atlas-SNP	.											.	KLHL25	58	.	0			c.T919C						.						74.0	58.0	63.0					15																	86312123		2202	4299	6501	SO:0001583	missense	64410	exon2			TGTCACACATGAA		CCDS10339.1	15q25.3	2013-02-22	2013-02-22		ENSG00000183655	ENSG00000183655		"""Kelch-like"", ""BTB/POZ domain containing"""	25732	protein-coding gene	gene with protein product	"""ectodermal-neural cortex 2"""		"""kelch-like 25 (Drosophila)"""				Standard	XM_006720635		Approved	FLJ12587, ENC2, ENC-2	uc002bly.3	Q9H0H3	OTTHUMG00000148672	ENST00000337975.5:c.919T>C	chr15.hg19:g.86312123A>G	ENSP00000336800:p.Cys307Arg	140.0	0.0		123.0	5.0	NM_022480	B2RDH2|B3KRT7	Missense_Mutation	SNP	ENST00000337975.5	hg19	CCDS10339.1	.	.	.	.	.	.	.	.	.	.	A	17.09	3.301136	0.60195	.	.	ENSG00000183655	ENST00000337975;ENST00000538153;ENST00000536947	T;T	0.65178	-0.14;-0.14	5.13	5.13	0.70059	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.69842	0.3156	L	0.61218	1.895	0.80722	D	1	D	0.53619	0.961	P	0.53224	0.721	T	0.73110	-0.4086	10	0.56958	D	0.05	.	14.1137	0.65139	1.0:0.0:0.0:0.0	.	307	Q9H0H3	ENC2_HUMAN	R	307;276;307	ENSP00000336800:C307R;ENSP00000444739:C307R	ENSP00000336800:C307R	C	-	1	0	KLHL25	84113127	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.339000	0.96797	1.933000	0.56026	0.379000	0.24179	TGT	.	.		0.642	KLHL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309023.1	NM_022480	
CRTC3	64784	hgsc.bcm.edu	37	15	91185296	91185296	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:91185296T>C	ENST00000268184.6	+	15	1788	c.1784T>C	c.(1783-1785)cTc>cCc	p.L595P	RP11-387D10.2_ENST00000559531.1_RNA|CRTC3_ENST00000420329.2_Missense_Mutation_p.L594P			Q6UUV7	CRTC3_HUMAN	CREB regulated transcription coactivator 3	595					energy homeostasis (GO:0097009)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of lipid catabolic process (GO:0050995)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)		CRTC3/MAML2(26)	breast(1)|endometrium(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)			CTGGACGGACTCAACATGTTA	0.552			T	MAML2	salivary gland mucoepidermoid																																p.L595P		Atlas-SNP	.		Dom	yes		15	15q26.1	64784	CREB regulated transcription coactivator 3		E	.	CRTC3	47	.	0			c.T1784C						.						79.0	69.0	73.0					15																	91185296		2198	4298	6496	SO:0001583	missense	64784	exon15			ACGGACTCAACAT		CCDS32331.1, CCDS45348.1	15q26.1	2005-11-24				ENSG00000140577			26148	protein-coding gene	gene with protein product		608986				14536081, 14506290	Standard	NM_022769		Approved	FLJ21868	uc002bpp.4	Q6UUV7		ENST00000268184.6:c.1784T>C	chr15.hg19:g.91185296T>C	ENSP00000268184:p.Leu595Pro	173.0	0.0		162.0	7.0	NM_022769	Q6DK61|Q6DK62|Q8NF38|Q9H6U2	Missense_Mutation	SNP	ENST00000268184.6	hg19	CCDS32331.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.331247	0.81690	.	.	ENSG00000140577	ENST00000437186;ENST00000268184;ENST00000420329	T;T	0.29142	1.58;1.59	4.93	4.93	0.64822	Transducer of regulated CREB activity, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.53481	0.1799	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.57740	-0.7759	10	0.87932	D	0	-23.2149	12.578	0.56375	0.0:0.0:0.0:1.0	.	595;594	Q6UUV7;Q6UUV7-3	CRTC3_HUMAN;.	P	558;595;594	ENSP00000268184:L595P;ENSP00000416573:L594P	ENSP00000268184:L595P	L	+	2	0	CRTC3	88986300	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.146000	0.77373	2.079000	0.62486	0.533000	0.62120	CTC	.	.		0.552	CRTC3-001	KNOWN	NAGNAG_splice_site|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417716.2	NM_022769	
ZNF598	90850	hgsc.bcm.edu	37	16	2053113	2053113	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:2053113A>G	ENST00000563630.1	-	3	421	c.179T>C	c.(178-180)cTg>cCg	p.L60P	ZNF598_ENST00000562103.1_Missense_Mutation_p.L60P|ZNF598_ENST00000431526.1_Missense_Mutation_p.L115P			Q86UK7	ZN598_HUMAN	zinc finger protein 598	115							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						CTCGTGCTGCAGCAGCTGCCT	0.687																																					p.L115P		Atlas-SNP	.											.	ZNF598	55	.	0			c.T344C						.						8.0	11.0	10.0					16																	2053113		2009	4154	6163	SO:0001583	missense	90850	exon5			TGCTGCAGCAGCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"""Zinc fingers, C2H2-type"""	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.179T>C	chr16.hg19:g.2053113A>G	ENSP00000455882:p.Leu60Pro	52.0	0.0		59.0	4.0	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	hg19		.	.	.	.	.	.	.	.	.	.	.	20.4	3.991751	0.74703	.	.	ENSG00000167962	ENST00000431526	T	0.32272	1.46	4.73	3.65	0.41850	.	0.000000	0.64402	D	0.000002	T	0.55417	0.1919	M	0.86097	2.795	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60870	-0.7177	10	0.87932	D	0	-15.1366	8.9718	0.35910	0.912:0.0:0.088:0.0	.	115	Q86UK7	ZN598_HUMAN	P	115	ENSP00000411409:L115P	ENSP00000411409:L115P	L	-	2	0	ZNF598	1993114	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.552000	0.67281	1.773000	0.52216	0.533000	0.62120	CTG	.	.		0.687	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	
SRRM2	23524	hgsc.bcm.edu	37	16	2812846	2812846	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:2812846T>C	ENST00000301740.8	+	11	2866	c.2317T>C	c.(2317-2319)Ttg>Ctg	p.L773L		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	773	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						AAAATCTCGCTTGTCTTTGAG	0.517																																					p.L773L		Atlas-SNP	.											.	SRRM2	263	.	0			c.T2317C						.						160.0	164.0	163.0					16																	2812846		2198	4300	6498	SO:0001819	synonymous_variant	23524	exon11			TCTCGCTTGTCTT	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.2317T>C	chr16.hg19:g.2812846T>C		67.0	0.0		63.0	4.0	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	hg19	CCDS32373.1																																																																																			.	.		0.517	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
CCDC64B	146439	hgsc.bcm.edu	37	16	3079412	3079412	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:3079412T>C	ENST00000572449.1	-	7	1038	c.976A>G	c.(976-978)Acc>Gcc	p.T326A	CCDC64B_ENST00000573514.1_Missense_Mutation_p.T119A|CCDC64B_ENST00000389347.4_Missense_Mutation_p.T326A			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	326										breast(1)|endometrium(2)|large_intestine(1)	4						GCCTTTCGGGTCTTTGGGGAC	0.587																																					p.T326A		Atlas-SNP	.											.	CCDC64B	19	.	0			c.A976G						.						34.0	35.0	35.0					16																	3079412		1881	4111	5992	SO:0001583	missense	146439	exon6			TTCGGGTCTTTGG	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.976A>G	chr16.hg19:g.3079412T>C	ENSP00000459043:p.Thr326Ala	32.0	0.0		57.0	4.0	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	hg19	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	T	6.735	0.504396	0.12822	.	.	ENSG00000162069	ENST00000389347	T	0.32023	1.47	4.07	1.75	0.24633	.	1.015660	0.07866	N	0.967158	T	0.21387	0.0515	L	0.44542	1.39	0.09310	N	1	B	0.15930	0.015	B	0.13407	0.009	T	0.35943	-0.9768	10	0.09338	T	0.73	-6.8936	4.0812	0.09927	0.0:0.1167:0.2332:0.65	.	326	A1A5D9	BICR2_HUMAN	A	326	ENSP00000373998:T326A	ENSP00000373998:T326A	T	-	1	0	CCDC64B	3019413	0.049000	0.20398	0.031000	0.17742	0.089000	0.18198	0.192000	0.17096	0.251000	0.21505	0.418000	0.28097	ACC	.	.		0.587	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1		
ADCY9	115	hgsc.bcm.edu	37	16	4016885	4016885	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:4016885C>T	ENST00000294016.3	-	11	3491	c.2953G>A	c.(2953-2955)Gtc>Atc	p.V985I		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	985					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						AGAAAGAAGACGAGAACCACC	0.592																																					p.V985I		Atlas-SNP	.											ADCY9,NS,carcinoma,0,1	ADCY9	151	.	0			c.G2953A						.						69.0	76.0	74.0					16																	4016885		2197	4300	6497	SO:0001583	missense	115	exon11			AGAAGACGAGAAC	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.2953G>A	chr16.hg19:g.4016885C>T	ENSP00000294016:p.Val985Ile	60.0	0.0		69.0	3.0	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	hg19	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	C	7.751	0.703434	0.15172	.	.	ENSG00000162104	ENST00000294016	D	0.82526	-1.62	5.48	3.5	0.40072	.	0.521749	0.21639	N	0.071363	T	0.65037	0.2653	N	0.08118	0	0.28252	N	0.925232	B	0.19817	0.039	B	0.18263	0.021	T	0.52548	-0.8561	10	0.20519	T	0.43	.	10.7456	0.46179	0.0:0.7952:0.1324:0.0724	.	985	O60503	ADCY9_HUMAN	I	985	ENSP00000294016:V985I	ENSP00000294016:V985I	V	-	1	0	ADCY9	3956886	0.992000	0.36948	0.508000	0.27688	0.023000	0.10783	3.024000	0.49674	0.768000	0.33290	-0.304000	0.09214	GTC	.	.		0.592	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
TEKT5	146279	hgsc.bcm.edu	37	16	10788409	10788409	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:10788409A>G	ENST00000283025.2	-	1	393	c.322T>C	c.(322-324)Tcc>Ccc	p.S108P	RP11-109M19.1_ENST00000576710.1_RNA	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	108						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						CACAGCCGGGAGGCCTCGGCC	0.667																																					p.S108P		Atlas-SNP	.											.	TEKT5	66	.	0			c.T322C						.						60.0	70.0	67.0					16																	10788409		2197	4300	6497	SO:0001583	missense	146279	exon1			GCCGGGAGGCCTC		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.322T>C	chr16.hg19:g.10788409A>G	ENSP00000283025:p.Ser108Pro	53.0	0.0		79.0	5.0	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	hg19	CCDS10542.1	.	.	.	.	.	.	.	.	.	.	.	26.1	4.705016	0.88924	.	.	ENSG00000153060	ENST00000283025	T	0.02682	4.2	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000020	T	0.11537	0.0281	M	0.74881	2.28	0.80722	D	1	P	0.51537	0.946	P	0.56163	0.793	T	0.00254	-1.1874	10	0.62326	D	0.03	-28.5225	14.5344	0.67950	1.0:0.0:0.0:0.0	.	108	Q96M29	TEKT5_HUMAN	P	108	ENSP00000283025:S108P	ENSP00000283025:S108P	S	-	1	0	TEKT5	10695910	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	5.516000	0.67055	2.161000	0.67846	0.528000	0.53228	TCC	.	.		0.667	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
CLEC16A	23274	hgsc.bcm.edu	37	16	11272336	11272336	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:11272336T>C	ENST00000409790.1	+	24	3181	c.2951T>C	c.(2950-2952)gTc>gCc	p.V984A	CLEC16A_ENST00000381822.2_Missense_Mutation_p.V71A	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CCCAGCCTCGTCCCTGCCCGG	0.637																																					p.V984A		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.T2951C						.						61.0	74.0	70.0					16																	11272336		2154	4250	6404	SO:0001583	missense	23274	exon23			GCCTCGTCCCTGC	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2951T>C	chr16.hg19:g.11272336T>C	ENSP00000387122:p.Val984Ala	67.0	0.0		94.0	4.0	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	hg19	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.158172	0.38119	.	.	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.46819	0.86	4.64	2.36	0.29203	.	0.333921	0.31381	N	0.007755	T	0.22781	0.0550	N	0.08118	0	0.18873	N	0.999989	B;B	0.33777	0.425;0.001	B;B	0.28385	0.089;0.004	T	0.11966	-1.0566	10	0.56958	D	0.05	-8.071	7.2849	0.26333	0.0:0.1785:0.0:0.8215	.	71;984	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	A	984;984;71	ENSP00000387122:V984A	ENSP00000371244:V71A	V	+	2	0	CLEC16A	11179837	0.994000	0.37717	0.144000	0.22314	0.801000	0.45260	0.743000	0.26231	0.254000	0.21573	0.533000	0.62120	GTC	.	.		0.637	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
MKL2	57496	hgsc.bcm.edu	37	16	14346343	14346343	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:14346343A>G	ENST00000341243.5	+	13	2654	c.2654A>G	c.(2653-2655)cAg>cGg	p.Q885R	MKL2_ENST00000574045.1_Missense_Mutation_p.Q846R|MKL2_ENST00000571589.1_Missense_Mutation_p.Q896R|MKL2_ENST00000318282.5_Missense_Mutation_p.Q846R			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	885					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						CGCAGCACACAGGCCCCTCTG	0.552																																					p.Q846R		Atlas-SNP	.											.	MKL2	103	.	0			c.A2537G						.						59.0	62.0	61.0					16																	14346343		2197	4300	6497	SO:0001583	missense	57496	exon15			GCACACAGGCCCC	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.2654A>G	chr16.hg19:g.14346343A>G	ENSP00000345841:p.Gln885Arg	85.0	0.0		82.0	4.0	NM_014048	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Missense_Mutation	SNP	ENST00000341243.5	hg19		.	.	.	.	.	.	.	.	.	.	A	16.85	3.237921	0.58886	.	.	ENSG00000186260	ENST00000318282;ENST00000341243	.	.	.	5.84	3.53	0.40419	.	0.463978	0.25619	N	0.029421	T	0.40473	0.1118	M	0.68317	2.08	0.25544	N	0.987155	P;P	0.41848	0.651;0.763	B;B	0.39840	0.081;0.311	T	0.19877	-1.0292	9	0.23302	T	0.38	-1.6222	12.2411	0.54541	0.5843:0.4157:0.0:0.0	.	896;846	B4DGT8;Q9ULH7-4	.;.	R	846;885	.	ENSP00000339086:Q846R	Q	+	2	0	MKL2	14253844	0.995000	0.38212	0.007000	0.13788	0.431000	0.31685	3.515000	0.53429	0.434000	0.26340	0.533000	0.62120	CAG	.	.		0.552	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048	
ACSM1	116285	hgsc.bcm.edu	37	16	20682956	20682956	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:20682956T>C	ENST00000307493.4	-	4	716	c.649A>G	c.(649-651)Acc>Gcc	p.T217A	ACSM1_ENST00000520010.1_Missense_Mutation_p.T217A|ACSM1_ENST00000219151.4_5'UTR	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	217					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						GGGTCCAAGGTCTTTGACTTA	0.488																																					p.T217A		Atlas-SNP	.											.	ACSM1	118	.	0			c.A649G						.						136.0	115.0	122.0					16																	20682956		2201	4300	6501	SO:0001583	missense	116285	exon4			CCAAGGTCTTTGA	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"""Acyl-CoA synthetase family"""	18049	protein-coding gene	gene with protein product		614357	"""butyryl Coenzyme A synthetase 1"""	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.649A>G	chr16.hg19:g.20682956T>C	ENSP00000301956:p.Thr217Ala	81.0	0.0		114.0	5.0	NM_052956	Q08AH2|Q96A20	Missense_Mutation	SNP	ENST00000307493.4	hg19	CCDS10587.1	.	.	.	.	.	.	.	.	.	.	T	10.56	1.383779	0.25031	.	.	ENSG00000166743	ENST00000307493;ENST00000520010	T;T	0.37915	1.17;1.17	5.19	1.58	0.23477	AMP-dependent synthetase/ligase (1);	0.535492	0.17171	N	0.184277	T	0.17408	0.0418	N	0.10645	0.015	0.36941	D	0.892402	P	0.38617	0.64	B	0.40602	0.334	T	0.10337	-1.0634	10	0.34782	T	0.22	.	4.4887	0.11803	0.1446:0.166:0.0:0.6894	.	217	Q08AH1	ACSM1_HUMAN	A	217	ENSP00000301956:T217A;ENSP00000428047:T217A	ENSP00000301956:T217A	T	-	1	0	ACSM1	20590457	0.702000	0.27816	0.543000	0.28128	0.627000	0.37826	1.033000	0.30191	0.450000	0.26774	0.491000	0.48974	ACC	.	.		0.488	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956	
ACSM1	116285	hgsc.bcm.edu	37	16	20696513	20696513	+	Splice_Site	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:20696513A>G	ENST00000307493.4	-	2	471		c.e2+1		ACSM1_ENST00000520010.1_Splice_Site|ACSM1_ENST00000219151.4_Splice_Site	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1						benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						TGCATCACTGACCTGTTCGCA	0.582																																					.		Atlas-SNP	.											.	ACSM1	118	.	0			c.403+2T>C						.						119.0	92.0	101.0					16																	20696513		2201	4300	6501	SO:0001630	splice_region_variant	116285	exon3			TCACTGACCTGTT	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"""Acyl-CoA synthetase family"""	18049	protein-coding gene	gene with protein product		614357	"""butyryl Coenzyme A synthetase 1"""	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.403+1T>C	chr16.hg19:g.20696513A>G		100.0	0.0		96.0	4.0	NM_052956	Q08AH2|Q96A20	Splice_Site	SNP	ENST00000307493.4	hg19	CCDS10587.1	.	.	.	.	.	.	.	.	.	.	.	17.04	3.287478	0.59976	.	.	ENSG00000166743	ENST00000307493;ENST00000520010;ENST00000523065	.	.	.	4.38	4.38	0.52667	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4282	0.61039	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ACSM1	20604014	1.000000	0.71417	1.000000	0.80357	0.675000	0.39556	7.258000	0.78371	1.835000	0.53391	0.496000	0.49642	.	.	.		0.582	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956	Intron
DNAH3	55567	hgsc.bcm.edu	37	16	20994094	20994094	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:20994094A>G	ENST00000261383.3	-	49	7807	c.7808T>C	c.(7807-7809)gTg>gCg	p.V2603A	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2603	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TTTGTTAGCCACCAACTCTAG	0.468																																					p.V2603A		Atlas-SNP	.											DNAH3_ENST00000261383,caecum,carcinoma,0,2	DNAH3	1142	.	0			c.T7808C						.						83.0	80.0	81.0					16																	20994094		2201	4300	6501	SO:0001583	missense	55567	exon49			TTAGCCACCAACT	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.7808T>C	chr16.hg19:g.20994094A>G	ENSP00000261383:p.Val2603Ala	46.0	1.0		64.0	3.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.910029	0.92107	.	.	ENSG00000158486	ENST00000261383	T	0.42900	0.96	5.83	5.83	0.93111	Dynein heavy chain, P-loop containing D4 domain (1);	0.000000	0.64402	D	0.000002	T	0.80681	0.4669	H	0.99404	4.55	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89364	0.3670	10	0.87932	D	0	.	16.2159	0.82217	1.0:0.0:0.0:0.0	.	2603	Q8TD57	DYH3_HUMAN	A	2603	ENSP00000261383:V2603A	ENSP00000261383:V2603A	V	-	2	0	DNAH3	20901595	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	8.831000	0.92068	2.235000	0.73313	0.533000	0.62120	GTG	.	.		0.468	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
COG7	91949	hgsc.bcm.edu	37	16	23404640	23404640	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:23404640A>G	ENST00000307149.5	-	15	2101	c.1916T>C	c.(1915-1917)cTg>cCg	p.L639P	COG7_ENST00000569635.1_Intron	NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	639					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		CTCAAGATTCAGGGGGAGGGA	0.498																																					p.L639P		Atlas-SNP	.											.	COG7	62	.	0			c.T1916C						.						83.0	70.0	74.0					16																	23404640		2197	4300	6497	SO:0001583	missense	91949	exon15			AGATTCAGGGGGA	AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"""Components of oligomeric golgi complex"""	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.1916T>C	chr16.hg19:g.23404640A>G	ENSP00000305442:p.Leu639Pro	51.0	0.0		66.0	4.0	NM_153603	Q6UWU7	Missense_Mutation	SNP	ENST00000307149.5	hg19	CCDS10610.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.238246	0.79800	.	.	ENSG00000168434	ENST00000307149	T	0.49432	0.78	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.61615	0.2361	L	0.55481	1.735	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.59091	-0.7519	10	0.31617	T	0.26	-16.3661	13.8458	0.63466	1.0:0.0:0.0:0.0	.	639	P83436	COG7_HUMAN	P	639	ENSP00000305442:L639P	ENSP00000305442:L639P	L	-	2	0	COG7	23312141	1.000000	0.71417	0.997000	0.53966	0.941000	0.58515	9.307000	0.96226	1.866000	0.54105	0.533000	0.62120	CTG	.	.		0.498	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1		
GGA2	23062	hgsc.bcm.edu	37	16	23481435	23481435	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:23481435A>G	ENST00000309859.4	-	15	1584	c.1502T>C	c.(1501-1503)cTc>cCc	p.L501P	GGA2_ENST00000567468.1_Intron	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	501	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		GGAGAAGTGGAGCAGAATTCT	0.552																																					p.L501P		Atlas-SNP	.											.	GGA2	49	.	0			c.T1502C						.						69.0	70.0	69.0					16																	23481435		2197	4300	6497	SO:0001583	missense	23062	exon15			AAGTGGAGCAGAA	AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.1502T>C	chr16.hg19:g.23481435A>G	ENSP00000311962:p.Leu501Pro	87.0	0.0		71.0	5.0	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	hg19	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.182572	0.78677	.	.	ENSG00000103365	ENST00000309859	T	0.51071	0.72	4.93	4.93	0.64822	Coatomer/clathrin adaptor appendage, Ig-like subdomain (1);Clathrin adaptor, gamma-adaptin, appendage (2);Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain (2);	0.156761	0.42053	D	0.000762	T	0.69006	0.3063	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.74047	-0.3790	10	0.87932	D	0	-21.3672	12.8236	0.57707	1.0:0.0:0.0:0.0	.	501	Q9UJY4	GGA2_HUMAN	P	501	ENSP00000311962:L501P	ENSP00000311962:L501P	L	-	2	0	GGA2	23388936	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.094000	0.89533	1.958000	0.56883	0.459000	0.35465	CTC	.	.		0.552	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1		
ARHGAP17	55114	hgsc.bcm.edu	37	16	24950880	24950880	+	Missense_Mutation	SNP	C	C	A	rs78457529	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:24950880C>A	ENST00000289968.6	-	17	1598	c.1529G>T	c.(1528-1530)cGg>cTg	p.R510L	ARHGAP17_ENST00000441763.2_3'UTR|ARHGAP17_ENST00000303665.5_Intron	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	510					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)		AGTGCCACCCCGCCGGTGGGC	0.582																																					p.R510L		Atlas-SNP	.											.	ARHGAP17	138	.	0			c.G1529T						.						29.0	26.0	27.0					16																	24950880		2194	4300	6494	SO:0001583	missense	55114	exon17			CCACCCCGCCGGT	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.1529G>T	chr16.hg19:g.24950880C>A	ENSP00000289968:p.Arg510Leu	63.0	0.0		81.0	4.0	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Missense_Mutation	SNP	ENST00000289968.6	hg19	CCDS32409.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906595	0.92107	.	.	ENSG00000140750	ENST00000289968;ENST00000455311	T	0.23552	1.9	5.0	5.0	0.66597	.	0.000000	0.40144	N	0.001163	T	0.48447	0.1500	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	0.965;1.0	P;D	0.87578	0.545;0.998	T	0.39583	-0.9607	10	0.48119	T	0.1	.	15.8573	0.78989	0.0:1.0:0.0:0.0	.	510;43	Q68EM7;Q68EM7-7	RHG17_HUMAN;.	L	510	ENSP00000289968:R510L	ENSP00000289968:R510L	R	-	2	0	ARHGAP17	24858381	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	6.289000	0.72696	2.595000	0.87683	0.655000	0.94253	CGG	.	C|0.992;T|0.008		0.582	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054	
SETD1A	9739	hgsc.bcm.edu	37	16	30976976	30976976	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:30976976G>A	ENST00000262519.8	+	8	2460	c.1774G>A	c.(1774-1776)Ggc>Agc	p.G592S		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	592	Pro-rich. {ECO:0000255}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						CGACCGGGGTGGCTCACCCCC	0.677																																					p.G592S		Atlas-SNP	.											.	SETD1A	143	.	0			c.G1774A						.						23.0	27.0	25.0					16																	30976976		2194	4289	6483	SO:0001583	missense	9739	exon8			CGGGGTGGCTCAC	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.1774G>A	chr16.hg19:g.30976976G>A	ENSP00000262519:p.Gly592Ser	55.0	0.0		83.0	34.0	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	hg19	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.446036	0.43429	.	.	ENSG00000099381	ENST00000262519	D	0.93859	-3.3	4.41	4.41	0.53225	.	0.476082	0.19592	N	0.110587	T	0.80969	0.4726	N	0.11427	0.14	0.20638	N	0.999879	P	0.38473	0.633	B	0.30782	0.12	T	0.71533	-0.4564	10	0.25751	T	0.34	.	5.4932	0.16787	0.1012:0.0:0.6995:0.1993	.	592	O15047	SET1A_HUMAN	S	592	ENSP00000262519:G592S	ENSP00000262519:G592S	G	+	1	0	SETD1A	30884477	0.970000	0.33590	0.997000	0.53966	0.985000	0.73830	2.685000	0.46959	2.269000	0.75478	0.561000	0.74099	GGC	.	.		0.677	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712	
ZNF646	9726	hgsc.bcm.edu	37	16	31088375	31088375	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:31088375T>C	ENST00000394979.2	+	1	1153	c.730T>C	c.(730-732)Tgt>Cgt	p.C244R	ZNF646_ENST00000300850.5_Missense_Mutation_p.C244R|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000300849.4_5'Flank			O15015	ZN646_HUMAN	zinc finger protein 646	244					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						ATGTAGTCAGTGTGGCAAGAC	0.582																																					p.C244R		Atlas-SNP	.											ZNF646,NS,carcinoma,0,1	ZNF646	133	.	0			c.T730C						.						71.0	67.0	68.0					16																	31088375		2197	4300	6497	SO:0001583	missense	9726	exon2			AGTCAGTGTGGCA	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.730T>C	chr16.hg19:g.31088375T>C	ENSP00000378429:p.Cys244Arg	76.0	1.0		99.0	4.0	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	hg19		.	.	.	.	.	.	.	.	.	.	T	17.64	3.440009	0.63067	.	.	ENSG00000167395	ENST00000300850;ENST00000394979;ENST00000439353	D;D	0.99974	-10.2;-10.2	5.6	5.6	0.85130	.	.	.	.	.	D	0.99984	0.9995	H	0.98682	4.3	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.98834	1.0752	9	0.87932	D	0	-9.2591	14.7704	0.69671	0.0:0.0:0.0:1.0	.	244	O15015-2	.	R	244;244;9	ENSP00000300850:C244R;ENSP00000378429:C244R	ENSP00000300850:C244R	C	+	1	0	ZNF646	30995876	1.000000	0.71417	0.931000	0.37212	0.890000	0.51754	7.499000	0.81566	2.133000	0.65898	0.533000	0.62120	TGT	.	.		0.582	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
PHKB	5257	hgsc.bcm.edu	37	16	47622844	47622844	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:47622844T>C	ENST00000323584.5	+	10	923	c.899T>C	c.(898-900)aTc>aCc	p.I300T	PHKB_ENST00000566044.1_Missense_Mutation_p.I293T|PHKB_ENST00000455779.1_Missense_Mutation_p.I293T|PHKB_ENST00000299167.8_Missense_Mutation_p.I300T|PHKB_ENST00000567402.1_3'UTR	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	300					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)				CTCCCCTGCATCAGTTATCCT	0.423																																					p.I300T		Atlas-SNP	.											.	PHKB	298	.	0			c.T899C						.						92.0	86.0	88.0					16																	47622844		2201	4300	6501	SO:0001583	missense	5257	exon10			CCTGCATCAGTTA		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.899T>C	chr16.hg19:g.47622844T>C	ENSP00000313504:p.Ile300Thr	93.0	0.0		79.0	4.0	NM_000293	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	hg19	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	T	18.98	3.737779	0.69304	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.93366	-3.21;-3.21	5.58	5.58	0.84498	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.050257	0.85682	D	0.000000	D	0.96156	0.8747	M	0.79805	2.47	0.80722	D	1	P;P	0.43024	0.798;0.554	P;B	0.56474	0.799;0.295	D	0.96638	0.9472	10	0.87932	D	0	-4.5324	15.7677	0.78141	0.0:0.0:0.0:1.0	.	300;293	Q93100;Q93100-4	KPBB_HUMAN;.	T	293;293;300	ENSP00000414345:I293T;ENSP00000313504:I300T	ENSP00000299167:I293T	I	+	2	0	PHKB	46180345	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.875000	0.87205	2.124000	0.65301	0.477000	0.44152	ATC	.	.		0.423	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1		
ZNF423	23090	hgsc.bcm.edu	37	16	49672029	49672029	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:49672029T>C	ENST00000561648.1	-	4	1087	c.1034A>G	c.(1033-1035)cAc>cGc	p.H345R	ZNF423_ENST00000562520.1_Missense_Mutation_p.H285R|ZNF423_ENST00000563137.2_Missense_Mutation_p.H285R|ZNF423_ENST00000262383.2_Missense_Mutation_p.H345R|ZNF423_ENST00000535559.1_Missense_Mutation_p.H228R|ZNF423_ENST00000567169.1_Missense_Mutation_p.H228R|ZNF423_ENST00000562871.1_Missense_Mutation_p.H285R	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	345					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				GGGCTGCCGGTGGCTGTCCAG	0.632																																					p.H345R		Atlas-SNP	.											.	ZNF423	463	.	0			c.A1034G						.						54.0	48.0	50.0					16																	49672029		2198	4300	6498	SO:0001583	missense	23090	exon4			TGCCGGTGGCTGT	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1034A>G	chr16.hg19:g.49672029T>C	ENSP00000455426:p.His345Arg	72.0	0.0		89.0	6.0	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	hg19	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	T	14.04	2.417281	0.42918	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	D;D	0.88975	-2.45;-2.45	5.0	5.0	0.66597	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.046152	0.85682	D	0.000000	D	0.94003	0.8079	M	0.89904	3.07	0.44055	D	0.996797	D	0.57899	0.981	P	0.56163	0.793	D	0.94876	0.8034	9	.	.	.	.	14.7223	0.69317	0.0:0.0:0.0:1.0	.	345	Q2M1K9	ZN423_HUMAN	R	345;228	ENSP00000262383:H345R;ENSP00000442321:H228R	.	H	-	2	0	ZNF423	48229530	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.139000	0.71728	1.891000	0.54761	0.459000	0.35465	CAC	.	.		0.632	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
SALL1	6299	hgsc.bcm.edu	37	16	51173561	51173561	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:51173561G>A	ENST00000251020.4	-	2	2605	c.2572C>T	c.(2572-2574)Ctc>Ttc	p.L858F	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.L761F	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	858					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GACATCTCGAGGGGCAAAGGC	0.527																																					p.L858F	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C2572T						.						98.0	95.0	96.0					16																	51173561		2198	4300	6498	SO:0001583	missense	6299	exon2			TCTCGAGGGGCAA	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.2572C>T	chr16.hg19:g.51173561G>A	ENSP00000251020:p.Leu858Phe	155.0	0.0		183.0	8.0	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	hg19	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	6.849	0.525946	0.13066	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.57107	0.42;0.42	5.37	5.37	0.77165	.	0.382264	0.26784	N	0.022518	T	0.47691	0.1459	L	0.55990	1.75	0.37039	D	0.897036	P	0.48162	0.906	B	0.38378	0.272	T	0.53599	-0.8416	10	0.17369	T	0.5	.	19.1142	0.93331	0.0:0.0:1.0:0.0	.	858	Q9NSC2	SALL1_HUMAN	F	858;761;822	ENSP00000251020:L858F;ENSP00000407914:L761F	ENSP00000251020:L858F	L	-	1	0	SALL1	49731062	1.000000	0.71417	0.966000	0.40874	0.016000	0.09150	5.613000	0.67688	2.515000	0.84797	0.460000	0.39030	CTC	.	.		0.527	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
NUP93	9688	hgsc.bcm.edu	37	16	56867148	56867148	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:56867148A>G	ENST00000308159.5	+	13	1488	c.1367A>G	c.(1366-1368)aAc>aGc	p.N456S	NUP93_ENST00000569842.1_Missense_Mutation_p.N456S|NUP93_ENST00000542526.1_Missense_Mutation_p.N333S|NUP93_ENST00000564887.1_Missense_Mutation_p.N333S	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	456					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)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TTTACGGTGAACCAGCAACCC	0.562																																					p.N456S	Colon(33;610 796 1305 1705 38917)	Atlas-SNP	.											.	NUP93	75	.	0			c.A1367G						.						147.0	127.0	134.0					16																	56867148		2198	4300	6498	SO:0001583	missense	9688	exon13			CGGTGAACCAGCA	D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.1367A>G	chr16.hg19:g.56867148A>G	ENSP00000310668:p.Asn456Ser	127.0	0.0		150.0	6.0	NM_014669	B3KPQ8|Q14705	Missense_Mutation	SNP	ENST00000308159.5	hg19	CCDS10769.1	.	.	.	.	.	.	.	.	.	.	A	12.63	1.996597	0.35226	.	.	ENSG00000102900	ENST00000308159;ENST00000542526	T;T	0.40225	1.04;1.04	5.53	5.53	0.82687	.	0.078415	0.85682	D	0.000000	T	0.24661	0.0598	N	0.08118	0	0.48452	D	0.999656	B	0.10296	0.003	B	0.14578	0.011	T	0.09552	-1.0669	10	0.15952	T	0.53	-15.9651	15.6915	0.77457	1.0:0.0:0.0:0.0	.	456	Q8N1F7	NUP93_HUMAN	S	456;333	ENSP00000310668:N456S;ENSP00000440235:N333S	ENSP00000310668:N456S	N	+	2	0	NUP93	55424649	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	5.315000	0.65810	2.107000	0.64212	0.533000	0.62120	AAC	.	.		0.562	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669	
RSPRY1	89970	hgsc.bcm.edu	37	16	57254758	57254758	+	Splice_Site	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:57254758A>G	ENST00000537866.1	+	9	1889	c.1016A>G	c.(1015-1017)gAg>gGg	p.E339G	RSPRY1_ENST00000394420.4_Splice_Site_p.E339G			Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	339	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular region (GO:0005576)	zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|urinary_tract(3)	27						CATGGCTTAGAGGTAGGTAAT	0.463																																					p.E339G		Atlas-SNP	.											.	RSPRY1	49	.	0			c.A1016G						.						162.0	131.0	141.0					16																	57254758		2198	4300	6498	SO:0001630	splice_region_variant	89970	exon9			GCTTAGAGGTAGG	AB075852	CCDS10775.1	16q13	2014-02-12			ENSG00000159579	ENSG00000159579		"""RING-type (C3HC4) zinc fingers"""	29420	protein-coding gene	gene with protein product						11853319	Standard	NM_133368		Approved	KIAA1972	uc002elb.3	Q96DX4	OTTHUMG00000133462	ENST00000537866.1:c.1017+1A>G	chr16.hg19:g.57254758A>G		128.0	0.0		125.0	5.0	NM_133368	Q6UX21|Q8ND53	Missense_Mutation	SNP	ENST00000537866.1	hg19	CCDS10775.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.919567	0.73098	.	.	ENSG00000159579	ENST00000394420;ENST00000537866	T;T	0.73681	-0.77;-0.77	5.33	5.33	0.75918	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.051956	0.85682	D	0.000000	T	0.76371	0.3978	M	0.79805	2.47	0.80722	D	1	B	0.31752	0.338	B	0.31547	0.132	T	0.77973	-0.2386	10	0.56958	D	0.05	.	15.3204	0.74117	1.0:0.0:0.0:0.0	.	339	Q96DX4	RSPRY_HUMAN	G	339	ENSP00000377942:E339G;ENSP00000443176:E339G	ENSP00000377942:E339G	E	+	2	0	RSPRY1	55812259	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	9.236000	0.95360	2.014000	0.59158	0.533000	0.62120	GAG	.	.		0.463	RSPRY1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432953.1	NM_133368	Missense_Mutation
CNOT1	23019	hgsc.bcm.edu	37	16	58562491	58562491	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:58562491T>C	ENST00000317147.5	-	44	6673	c.6341A>G	c.(6340-6342)cAt>cGt	p.H2114R	CNOT1_ENST00000245138.4_Missense_Mutation_p.H965R|CNOT1_ENST00000569240.1_Missense_Mutation_p.H2109R	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	2114					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)		GAACCCATAATGGTAATCACA	0.398																																					p.H2114R		Atlas-SNP	.											.	CNOT1	359	.	0			c.A6341G						.						93.0	94.0	94.0					16																	58562491		2198	4300	6498	SO:0001583	missense	23019	exon44			CCATAATGGTAAT	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.6341A>G	chr16.hg19:g.58562491T>C	ENSP00000320949:p.His2114Arg	61.0	0.0		71.0	4.0	NM_016284	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	hg19	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.811403	0.90707	.	.	ENSG00000125107	ENST00000317147;ENST00000422872;ENST00000546037;ENST00000245138;ENST00000394200	T	0.56776	0.44	5.73	5.73	0.89815	CCR4-Not complex component, Not1, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80502	0.4635	H	0.94925	3.6	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.998;0.997	D	0.86096	0.1553	10	0.72032	D	0.01	.	16.0096	0.80391	0.0:0.0:0.0:1.0	.	965;2114;2109	B5MDN3;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	R	2114;808;119;965;2109	ENSP00000320949:H2114R	ENSP00000245138:H965R	H	-	2	0	CNOT1	57119992	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.015000	0.88690	2.184000	0.69523	0.477000	0.44152	CAT	.	.		0.398	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
CNOT1	23019	hgsc.bcm.edu	37	16	58608980	58608980	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:58608980A>G	ENST00000317147.5	-	15	2090	c.1758T>C	c.(1756-1758)gcT>gcC	p.A586A	CNOT1_ENST00000569240.1_Silent_p.A586A|CNOT1_ENST00000441024.2_Silent_p.A586A	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	586					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)		AAGCAAGTGCAGCAAGGTCAA	0.393																																					p.A586A		Atlas-SNP	.											.	CNOT1	359	.	0			c.T1758C						.						131.0	115.0	121.0					16																	58608980		2198	4300	6498	SO:0001819	synonymous_variant	23019	exon15			AAGTGCAGCAAGG	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.1758T>C	chr16.hg19:g.58608980A>G		82.0	0.0		90.0	4.0	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Silent	SNP	ENST00000317147.5	hg19	CCDS10799.1																																																																																			.	.		0.393	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
CBFB	865	hgsc.bcm.edu	37	16	67116231	67116231	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:67116231T>C	ENST00000290858.6	+	5	776	c.515T>C	c.(514-516)cTg>cCg	p.L172P	CBFB_ENST00000561924.2_Missense_Mutation_p.L72P|CBFB_ENST00000412916.2_Intron	NM_001755.2|NM_022845.2	NP_001746.1|NP_074036.1	Q13951	PEBB_HUMAN	core-binding factor, beta subunit	172					cell maturation (GO:0048469)|definitive hemopoiesis (GO:0060216)|lymphocyte differentiation (GO:0030098)|myeloid cell differentiation (GO:0030099)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|large_intestine(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)		TCACAGCTGCTGGCAGTAACT	0.428			T	MYH11	AML																																p.L172P		Atlas-SNP	.		Dom	yes		16	16q22	865	"""core-binding factor, beta subunit"""		L	.	CBFB	52	.	0			c.T515C						.						143.0	140.0	141.0					16																	67116231		2200	4300	6500	SO:0001583	missense	865	exon5			AGCTGCTGGCAGT	BC018509	CCDS10827.1, CCDS45508.1	16q22.1	2008-02-05			ENSG00000067955	ENSG00000067955			1539	protein-coding gene	gene with protein product		121360				8351518, 7587111	Standard	NM_001755		Approved	PEBP2B	uc002erb.3	Q13951	OTTHUMG00000137520	ENST00000290858.6:c.515T>C	chr16.hg19:g.67116231T>C	ENSP00000290858:p.Leu172Pro	86.0	0.0		96.0	4.0	NM_001755	A8K347|Q13124|Q9HCT2	Missense_Mutation	SNP	ENST00000290858.6	hg19	CCDS10827.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.811884	0.70797	.	.	ENSG00000067955	ENST00000290858	.	.	.	5.64	5.64	0.86602	.	0.504996	0.22835	N	0.055046	T	0.42245	0.1194	N	0.19112	0.55	0.80722	D	1	P	0.38440	0.631	B	0.39119	0.291	T	0.47812	-0.9088	9	0.72032	D	0.01	.	14.6719	0.68951	0.0:0.0:0.0:1.0	.	172	Q13951	PEBB_HUMAN	P	172	.	ENSP00000290858:L172P	L	+	2	0	CBFB	65673732	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.868000	0.56055	2.145000	0.66743	0.477000	0.44152	CTG	.	.		0.428	CBFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268843.2	NM_001755	
HSF4	3299	hgsc.bcm.edu	37	16	67203201	67203201	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:67203201A>G	ENST00000521374.1	+	12	1274	c.1274A>G	c.(1273-1275)gAg>gGg	p.E425G	NOL3_ENST00000432069.2_5'Flank|HSF4_ENST00000264009.8_Missense_Mutation_p.E425G|HSF4_ENST00000584272.1_Missense_Mutation_p.E395G|NOL3_ENST00000564053.1_5'Flank|HSF4_ENST00000421453.1_Missense_Mutation_p.E395G			Q9ULV5	HSF4_HUMAN	heat shock transcription factor 4	425					camera-type eye development (GO:0043010)|cell development (GO:0048468)|histone H3-K9 demethylation (GO:0033169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotrimerization (GO:0070207)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)		TTGGTTCCAGAGCGGGGTGAG	0.592																																					p.E425G		Atlas-SNP	.											.	HSF4	33	.	0			c.A1274G						.						33.0	37.0	36.0					16																	67203201		1987	4169	6156	SO:0001583	missense	3299	exon14			TTCCAGAGCGGGG	D87673	CCDS42175.1, CCDS45510.1	16q21	2013-01-22			ENSG00000102878	ENSG00000102878			5227	protein-coding gene	gene with protein product		602438	"""cataract, Marner"""	CTM		8972228, 10488131, 12089525	Standard	NM_001538		Approved		uc002erl.2	Q9ULV5	OTTHUMG00000178325	ENST00000521374.1:c.1274A>G	chr16.hg19:g.67203201A>G	ENSP00000430947:p.Glu425Gly	59.0	0.0		72.0	4.0	NM_001040667	Q99472|Q9ULV6	Missense_Mutation	SNP	ENST00000521374.1	hg19	CCDS42175.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.0|21.0	4.086265|4.086265	0.76642|0.76642	.|.	.|.	ENSG00000102878|ENSG00000102878	ENST00000421453;ENST00000264009;ENST00000517685;ENST00000521374|ENST00000520304	.|.	.|.	.|.	4.73|4.73	4.73|4.73	0.59995|0.59995	.|.	0.000000|.	0.51477|.	D|.	0.000086|.	T|T	0.47673|0.47673	0.1458|0.1458	L|L	0.32530|0.32530	0.975|0.975	0.37856|0.37856	D|D	0.929561|0.929561	D;D|.	0.89917|.	1.0;0.999|.	D;D|.	0.80764|.	0.994;0.986|.	T|T	0.49341|0.49341	-0.8950|-0.8950	9|5	0.27785|.	T|.	0.31|.	-31.7262|-31.7262	10.5258|10.5258	0.44948|0.44948	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	395;425|.	Q9ULV5-2;Q9ULV5|.	.;HSF4_HUMAN|.	G|G	395;425;349;425|101	.|.	ENSP00000264009:E425G|.	E|S	+|+	2|1	0|0	HSF4|HSF4	65760702|65760702	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.946000|0.946000	0.59487|0.59487	2.915000|2.915000	0.48805|0.48805	1.958000|1.958000	0.56883|0.56883	0.533000|0.533000	0.62120|0.62120	GAG|AGC	.	.		0.592	HSF4-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375080.1	NM_001538	
KCTD19	146212	hgsc.bcm.edu	37	16	67329298	67329298	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:67329298A>G	ENST00000304372.5	-	9	1314	c.1259T>C	c.(1258-1260)cTg>cCg	p.L420P		NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	420	BTB 2.				protein homooligomerization (GO:0051260)					endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)	23		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		GTTGGACAGCAGTTCTGGATA	0.527																																					p.L420P		Atlas-SNP	.											.	KCTD19	82	.	0			c.T1259C						.						87.0	81.0	83.0					16																	67329298		1948	4145	6093	SO:0001583	missense	146212	exon9			GACAGCAGTTCTG	AK097481	CCDS42179.1	16q22.1	2013-06-20	2013-06-20			ENSG00000168676			24753	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 19"""				Standard	NM_001100915		Approved	FLJ40162	uc002esu.2	Q17RG1		ENST00000304372.5:c.1259T>C	chr16.hg19:g.67329298A>G	ENSP00000305702:p.Leu420Pro	67.0	0.0		82.0	4.0	NM_001100915	B4DZ49|Q8N804	Missense_Mutation	SNP	ENST00000304372.5	hg19	CCDS42179.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.933643	0.73442	.	.	ENSG00000168676	ENST00000304372	T	0.52754	0.65	5.5	5.5	0.81552	BTB/POZ fold (2);	0.000000	0.47455	D	0.000237	T	0.62171	0.2406	L	0.49778	1.585	0.58432	D	0.999999	D	0.76494	0.999	D	0.78314	0.991	T	0.64846	-0.6311	10	0.72032	D	0.01	-9.0977	12.9874	0.58599	1.0:0.0:0.0:0.0	.	420	Q17RG1	KCD19_HUMAN	P	420	ENSP00000305702:L420P	ENSP00000305702:L420P	L	-	2	0	KCTD19	65886799	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.001000	0.70685	2.102000	0.63906	0.533000	0.62120	CTG	.	.		0.527	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1	XM_085367	
NFATC3	4775	hgsc.bcm.edu	37	16	68156826	68156826	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:68156826A>G	ENST00000346183.3	+	2	1064	c.1040A>G	c.(1039-1041)cAa>cGa	p.Q347R	NFATC3_ENST00000349223.5_Missense_Mutation_p.Q347R|NFATC3_ENST00000329524.4_Missense_Mutation_p.Q347R|NFATC3_ENST00000575270.1_Missense_Mutation_p.Q347R|NFATC3_ENST00000535127.2_3'UTR|RP11-67A1.2_ENST00000548144.1_RNA	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	347					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	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)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		TCTGAAGATCAAGCTGCCATA	0.473																																					p.Q347R		Atlas-SNP	.											.	NFATC3	190	.	0			c.A1040G						.						143.0	143.0	143.0					16																	68156826		2198	4300	6498	SO:0001583	missense	4775	exon2			AAGATCAAGCTGC	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"""Nuclear factor of activated T-cells"""	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.1040A>G	chr16.hg19:g.68156826A>G	ENSP00000300659:p.Gln347Arg	71.0	0.0		75.0	4.0	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	hg19	CCDS10860.1	.	.	.	.	.	.	.	.	.	.	A	11.36	1.615684	0.28801	.	.	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524	T;T;T	0.08720	3.06;3.06;3.06	5.39	4.27	0.50696	.	0.261212	0.45361	D	0.000375	T	0.06917	0.0176	L	0.29908	0.895	0.35391	D	0.790771	B;B;B;B	0.28713	0.22;0.0;0.22;0.072	B;B;B;B	0.26864	0.074;0.002;0.045;0.024	T	0.31833	-0.9929	9	.	.	.	-3.8788	12.5522	0.56233	0.8607:0.1393:0.0:0.0	.	347;347;347;347	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	R	347	ENSP00000264008:Q347R;ENSP00000300659:Q347R;ENSP00000331324:Q347R	.	Q	+	2	0	NFATC3	66714327	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.593000	0.61034	0.951000	0.37770	0.460000	0.39030	CAA	.	.		0.473	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555	
COG4	25839	hgsc.bcm.edu	37	16	70548316	70548316	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:70548316C>T	ENST00000323786.5	-	4	487	c.466G>A	c.(466-468)Gag>Aag	p.E156K	COG4_ENST00000564653.1_Missense_Mutation_p.E156K|COG4_ENST00000393612.4_Missense_Mutation_p.E152K	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	152					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				GCAGCCTGCTCATAATCTTCA	0.517																																					p.E156K		Atlas-SNP	.											.	COG4	64	.	0			c.G466A						.						110.0	94.0	99.0					16																	70548316		2198	4300	6498	SO:0001583	missense	25839	exon4			CCTGCTCATAATC	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"""Components of oligomeric golgi complex"""	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.466G>A	chr16.hg19:g.70548316C>T	ENSP00000315775:p.Glu156Lys	101.0	0.0		107.0	24.0	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Missense_Mutation	SNP	ENST00000323786.5	hg19	CCDS10892.2	.	.	.	.	.	.	.	.	.	.	C	36	5.840835	0.97009	.	.	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000393612;ENST00000534772	T;T;T	0.41758	0.99;0.99;0.99	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.69700	0.3140	M	0.83603	2.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.992;0.999	T	0.74003	-0.3804	10	0.87932	D	0	-19.7913	19.4155	0.94694	0.0:1.0:0.0:0.0	.	151;152	Q6PIW8;Q9H9E3	.;COG4_HUMAN	K	156;152;152;79	ENSP00000315775:E156K;ENSP00000377236:E152K;ENSP00000461912:E79K	ENSP00000315775:E156K	E	-	1	0	COG4	69105817	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.342000	0.79310	2.589000	0.87451	0.561000	0.74099	GAG	.	.		0.517	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3		
BCAR1	9564	hgsc.bcm.edu	37	16	75269535	75269535	+	Missense_Mutation	SNP	G	G	T	rs376153187		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:75269535G>T	ENST00000162330.5	-	5	1388	c.1262C>A	c.(1261-1263)cCg>cAg	p.P421Q	BCAR1_ENST00000546196.1_Missense_Mutation_p.P392Q|BCAR1_ENST00000393422.2_Missense_Mutation_p.P439Q|BCAR1_ENST00000542031.2_Missense_Mutation_p.P419Q|BCAR1_ENST00000393420.6_Missense_Mutation_p.P439Q|BCAR1_ENST00000535626.2_Missense_Mutation_p.P273Q|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000420641.3_Missense_Mutation_p.P439Q|BCAR1_ENST00000538440.2_Missense_Mutation_p.P421Q|BCAR1_ENST00000418647.3_Missense_Mutation_p.P467Q	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	421					actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		GCCCTCTGCCGGGGCTTCACG	0.687																																					p.P467Q		Atlas-SNP	.											.	BCAR1	184	.	0			c.C1400A						.						21.0	26.0	24.0					16																	75269535		2197	4298	6495	SO:0001583	missense	9564	exon6			TCTGCCGGGGCTT	AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"""Cas scaffolding proteins"""	971	protein-coding gene	gene with protein product	"""Crk-associated substrate"", ""Cas scaffolding protein family member 1"""	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.1262C>A	chr16.hg19:g.75269535G>T	ENSP00000162330:p.Pro421Gln	134.0	0.0		153.0	10.0	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Missense_Mutation	SNP	ENST00000162330.5	hg19	CCDS10915.1	.	.	.	.	.	.	.	.	.	.	G	1.871	-0.460203	0.04508	.	.	ENSG00000050820	ENST00000162330;ENST00000393422;ENST00000420641;ENST00000538440;ENST00000418647;ENST00000535626;ENST00000393420;ENST00000542031;ENST00000546196	T;T;T;T;T;T;T;T;T	0.37584	1.3;1.84;1.61;1.41;1.61;1.19;1.38;1.3;3.11	3.91	0.522	0.17053	.	0.693744	0.12978	N	0.423522	T	0.27697	0.0681	L	0.34521	1.04	0.09310	N	0.999999	P;P;P;P;P;P;P;P;B	0.46952	0.64;0.887;0.819;0.755;0.755;0.64;0.874;0.64;0.33	B;P;B;B;B;B;B;B;B	0.49683	0.238;0.619;0.301;0.299;0.417;0.171;0.394;0.157;0.157	T	0.09796	-1.0658	10	0.28530	T	0.3	-7.8402	0.9398	0.01353	0.2195:0.1783:0.4197:0.1826	.	439;273;467;419;439;439;421;421;211	B4DIW5;F5GXV6;E9PCL5;F5GXA2;F8WA69;E9PCV2;F5H7Z0;P56945;B3KWE2	.;.;.;.;.;.;.;BCAR1_HUMAN;.	Q	421;439;439;421;467;273;439;419;392	ENSP00000162330:P421Q;ENSP00000377074:P439Q;ENSP00000392708:P439Q;ENSP00000443841:P421Q;ENSP00000391669:P467Q;ENSP00000440370:P273Q;ENSP00000377072:P439Q;ENSP00000440415:P419Q;ENSP00000442161:P392Q	ENSP00000162330:P421Q	P	-	2	0	BCAR1	73827036	0.004000	0.15560	0.007000	0.13788	0.002000	0.02628	0.235000	0.17948	0.411000	0.25702	-0.384000	0.06662	CCG	.	.		0.687	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77327037	77327037	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:77327037C>A	ENST00000282849.5	-	20	3543	c.3125G>T	c.(3124-3126)gGc>gTc	p.G1042V	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1042	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						AAGCACACAGCCCTCCTGCAG	0.602																																					p.G1042V		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.G3125T						.						88.0	82.0	84.0					16																	77327037		2198	4300	6498	SO:0001583	missense	170692	exon20			ACACAGCCCTCCT	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.3125G>T	chr16.hg19:g.77327037C>A	ENSP00000282849:p.Gly1042Val	62.0	0.0		80.0	23.0	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	hg19	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	C	5.352	0.250201	0.10130	.	.	ENSG00000140873	ENST00000282849	T	0.59638	0.25	6.02	6.02	0.97574	.	0.159420	0.52532	D	0.000077	T	0.38585	0.1046	N	0.11131	0.1	0.58432	D	0.999998	B;B	0.10296	0.003;0.002	B;B	0.14023	0.002;0.01	T	0.25710	-1.0124	10	0.15066	T	0.55	.	15.7552	0.78018	0.0:0.8545:0.1455:0.0	.	1042;1042	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	V	1042	ENSP00000282849:G1042V	ENSP00000282849:G1042V	G	-	2	0	ADAMTS18	75884538	1.000000	0.71417	1.000000	0.80357	0.009000	0.06853	1.304000	0.33482	2.850000	0.98022	0.650000	0.86243	GGC	.	.		0.602	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
KIAA0513	9764	hgsc.bcm.edu	37	16	85112029	85112029	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:85112029A>G	ENST00000566428.1	+	7	1422	c.791A>G	c.(790-792)gAg>gGg	p.E264G	KIAA0513_ENST00000258180.3_Missense_Mutation_p.E264G|KIAA0513_ENST00000567328.1_Missense_Mutation_p.E264G|KIAA0513_ENST00000538274.1_Missense_Mutation_p.E264G			O60268	K0513_HUMAN	KIAA0513	264						cytoplasm (GO:0005737)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(9)|pancreas(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.234)		AGGGAAGACGAGAACAAACCC	0.587																																					p.E264G		Atlas-SNP	.											.	KIAA0513	43	.	0			c.A791G						.						59.0	57.0	58.0					16																	85112029		2198	4300	6498	SO:0001583	missense	9764	exon7			AAGACGAGAACAA	AB011085	CCDS32499.1, CCDS67091.1, CCDS73919.1	16q24.1	2012-11-29			ENSG00000135709	ENSG00000135709			29058	protein-coding gene	gene with protein product		611675				9628581	Standard	XM_005256265		Approved		uc002fiu.3	O60268	OTTHUMG00000176597	ENST00000566428.1:c.791A>G	chr16.hg19:g.85112029A>G	ENSP00000457408:p.Glu264Gly	95.0	0.0		121.0	5.0	NM_014732	B4DSS5|D3DUM2|Q8N6G0	Missense_Mutation	SNP	ENST00000566428.1	hg19	CCDS32499.1	.	.	.	.	.	.	.	.	.	.	A	10.72	1.430298	0.25726	.	.	ENSG00000135709	ENST00000538274;ENST00000258180	T;T	0.37058	1.22;1.22	4.97	4.97	0.65823	.	0.206732	0.49305	D	0.000141	T	0.28333	0.0700	L	0.29908	0.895	0.39812	D	0.972725	P;P	0.37370	0.592;0.457	B;B	0.37601	0.254;0.129	T	0.13980	-1.0489	10	0.45353	T	0.12	-17.9317	12.328	0.55022	1.0:0.0:0.0:0.0	.	264;264	B4DSS5;O60268	.;K0513_HUMAN	G	264	ENSP00000446439:E264G;ENSP00000258180:E264G	ENSP00000258180:E264G	E	+	2	0	KIAA0513	83669530	0.994000	0.37717	0.092000	0.20876	0.034000	0.12701	4.876000	0.63079	1.982000	0.57802	0.459000	0.35465	GAG	.	.		0.587	KIAA0513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432736.1	NM_014732	
ZNF469	84627	hgsc.bcm.edu	37	16	88498350	88498350	+	Missense_Mutation	SNP	C	C	T	rs375045076	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:88498350C>T	ENST00000437464.1	+	2	4388	c.4388C>T	c.(4387-4389)aCg>aTg	p.T1463M	ZNF469_ENST00000565624.1_Missense_Mutation_p.T1491M	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	1463	Pro-rich.				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						CCCCAGAAGACGGTGCCGTCA	0.602													C|||	4	0.000798722	0.0008	0.0014	5008	,	,		18425	0.0		0.002	False		,,,				2504	0.0				p.T1463M		Atlas-SNP	.											ZNF469,NS,carcinoma,0,1	ZNF469	121	.	0			c.C4388T						.	C	MET/THR	0,1384		0,0,692	117.0	97.0	103.0		4388	2.2	0.0	16		103	15,3167		0,15,1576	no	missense	ZNF469	NM_001127464.1	81	0,15,2268	TT,TC,CC		0.4714,0.0,0.3285	probably-damaging	1463/3926	88498350	15,4551	692	1591	2283	SO:0001583	missense	84627	exon2			AGAAGACGGTGCC	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.4388C>T	chr16.hg19:g.88498350C>T	ENSP00000402343:p.Thr1463Met	50.0	0.0		60.0	4.0	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	hg19	CCDS45544.1	.	.	.	.	.	.	.	.	.	.	C	7.011	0.556792	0.13436	0.0	0.004714	ENSG00000225614	ENST00000437464	T	0.05925	3.37	4.55	2.25	0.28309	.	.	.	.	.	T	0.02727	0.0082	N	0.08118	0	0.09310	N	1	P	0.42456	0.78	B	0.32211	0.142	T	0.42865	-0.9426	9	0.87932	D	0	.	5.3628	0.16098	0.5504:0.3532:0.0964:0.0	.	1463	Q96JG9	ZN469_HUMAN	M	1463	ENSP00000402343:T1463M	ENSP00000402343:T1463M	T	+	2	0	ZNF469	87025851	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.168000	0.16622	0.163000	0.19507	-0.410000	0.06199	ACG	.	.		0.602	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
ZNF778	197320	hgsc.bcm.edu	37	16	89294754	89294754	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:89294754T>C	ENST00000433976.2	+	6	2306	c.1974T>C	c.(1972-1974)tcT>tcC	p.S658S	RP11-46C24.6_ENST00000563182.1_RNA|ZNF778_ENST00000306502.6_Silent_p.S616S	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	658					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		GTGCCTCCTCTCACCTGCATA	0.428																																					p.S686S		Atlas-SNP	.											.	ZNF778	67	.	0			c.T2058C						.						53.0	57.0	56.0					16																	89294754		2180	4293	6473	SO:0001819	synonymous_variant	197320	exon7			CTCCTCTCACCTG	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"""Zinc fingers, C2H2-type"", ""-"""	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.1974T>C	chr16.hg19:g.89294754T>C		115.0	0.0		114.0	5.0	NM_001201407	Q08AG0	Silent	SNP	ENST00000433976.2	hg19	CCDS45550.1																																																																																			.	.		0.428	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531	
FANCA	2175	hgsc.bcm.edu	37	16	89839740	89839740	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:89839740T>C	ENST00000389301.3	-	22	1983	c.1953A>G	c.(1951-1953)ggA>ggG	p.G651G	FANCA_ENST00000567284.2_5'UTR|FANCA_ENST00000568369.1_Silent_p.G651G	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	651					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		CTGTGAGCTGTCCCAGGGGCT	0.572			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.G651G		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.A1953G						.						35.0	27.0	30.0					16																	89839740		2027	3941	5968	SO:0001819	synonymous_variant	2175	exon22	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GAGCTGTCCCAGG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1953A>G	chr16.hg19:g.89839740T>C		101.0	0.0		91.0	4.0	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	hg19	CCDS32515.1																																																																																			.	.		0.572	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
FANCA	2175	hgsc.bcm.edu	37	16	89857899	89857899	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:89857899A>G	ENST00000389301.3	-	14	1301	c.1271T>C	c.(1270-1272)cTg>cCg	p.L424P	FANCA_ENST00000568369.1_Missense_Mutation_p.L424P	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	424					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		CATGCTGTCCAGCTGGCAGCT	0.572			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.L424P		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.T1271C						.						67.0	53.0	58.0					16																	89857899		2198	4300	6498	SO:0001583	missense	2175	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTGTCCAGCTGGC	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1271T>C	chr16.hg19:g.89857899A>G	ENSP00000373952:p.Leu424Pro	62.0	0.0		82.0	4.0	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	hg19	CCDS32515.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.411386	0.42817	.	.	ENSG00000187741	ENST00000389301	D	0.98493	-4.96	5.13	2.89	0.33648	.	0.157917	0.29126	N	0.013066	D	0.98232	0.9415	M	0.73598	2.24	0.80722	D	1	D;D	0.56746	0.977;0.977	P;P	0.60236	0.871;0.871	D	0.97490	1.0053	10	0.72032	D	0.01	-4.5933	9.8979	0.41329	0.8946:0.0:0.1054:0.0	.	424;424	B4DRI7;O15360	.;FANCA_HUMAN	P	424	ENSP00000373952:L424P	ENSP00000373952:L424P	L	-	2	0	FANCA	88385400	1.000000	0.71417	0.479000	0.27329	0.150000	0.21749	2.965000	0.49200	0.322000	0.23283	0.529000	0.55759	CTG	.	.		0.572	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
ACADVL	37	hgsc.bcm.edu	37	17	7123922	7123922	+	Splice_Site	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7123922G>A	ENST00000356839.5	+	4	383		c.e4-1		ACADVL_ENST00000543245.2_Splice_Site|ACADVL_ENST00000350303.5_Splice_Site|ACADVL_ENST00000581562.1_Splice_Site|MIR324_ENST00000362183.1_RNA|DLG4_ENST00000399510.2_5'Flank	NM_000018.3|NM_001270448.1	NP_000009.1|NP_001257377.1	P49748	ACADV_HUMAN	acyl-CoA dehydrogenase, very long chain						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|energy derivation by oxidation of organic compounds (GO:0015980)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(1)|ovary(4)|skin(1)	21						TCTCTGCCCAGGAATCTAAGT	0.562																																					.		Atlas-SNP	.											.	ACADVL	43	.	0			c.274-1G>A						.						96.0	98.0	97.0					17																	7123922		2203	4300	6503	SO:0001630	splice_region_variant	37	exon5			TGCCCAGGAATCT	BC012912	CCDS11090.1, CCDS42249.1, CCDS58509.1	17p13.1	2010-04-30	2010-04-30		ENSG00000072778	ENSG00000072778			92	protein-coding gene	gene with protein product		609575	"""acyl-Coenzyme A dehydrogenase, very long chain"""			8921384	Standard	NM_000018		Approved	VLCAD, LCACD, ACAD6	uc002gev.4	P49748	OTTHUMG00000102157	ENST00000356839.5:c.205-1G>A	chr17.hg19:g.7123922G>A		93.0	0.0		65.0	4.0	NM_001270447	B4DEB6|F5H2A9|O76056|Q8WUL0	Splice_Site	SNP	ENST00000356839.5	hg19	CCDS11090.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.966479	0.92855	.	.	ENSG00000072778	ENST00000543245;ENST00000356839;ENST00000350303;ENST00000322910;ENST00000542255	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2384	0.73450	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACADVL	7064646	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.412000	0.90232	2.675000	0.91044	0.655000	0.94253	.	.	.		0.562	ACADVL-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220001.5	NM_000018	Intron
NEURL4	84461	hgsc.bcm.edu	37	17	7224736	7224736	+	Missense_Mutation	SNP	T	T	C	rs117553236	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7224736T>C	ENST00000399464.2	-	19	3157	c.3142A>G	c.(3142-3144)Atg>Gtg	p.M1048V	NEURL4_ENST00000315614.7_Missense_Mutation_p.M1046V|RP11-542C16.2_ENST00000575474.1_5'Flank|NEURL4_ENST00000570460.1_Missense_Mutation_p.M1024V|NEURL4_ENST00000574120.1_5'Flank	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	1048	NHR 5. {ECO:0000255|PROSITE- ProRule:PRU00400}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						AGGATGTGCATCGTGTCATCT	0.607																																					p.M1048V		Atlas-SNP	.											.	NEURL4	192	.	0			c.A3142G						.						104.0	113.0	110.0					17																	7224736		2147	4233	6380	SO:0001583	missense	84461	exon19			TGTGCATCGTGTC		CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"""neuralized homolog 4 (Drosophila)"""			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.3142A>G	chr17.hg19:g.7224736T>C	ENSP00000382390:p.Met1048Val	106.0	0.0		82.0	6.0	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	ENST00000399464.2	hg19	CCDS42251.1	.	.	.	.	.	.	.	.	.	.	T	13.96	2.393743	0.42410	.	.	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.33654	1.4;1.48	5.14	5.14	0.70334	NEUZ (1);	0.046596	0.85682	D	0.000000	T	0.42017	0.1184	M	0.74647	2.275	0.37491	D	0.916388	P;B	0.36712	0.566;0.275	B;B	0.41135	0.348;0.051	T	0.49466	-0.8937	10	0.38643	T	0.18	-27.0231	10.1661	0.42882	0.0:0.0:0.1675:0.8325	.	1046;1048	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	V	1046;1048	ENSP00000319826:M1046V;ENSP00000382390:M1048V	ENSP00000319826:M1046V	M	-	1	0	NEURL4	7165460	1.000000	0.71417	0.976000	0.42696	0.994000	0.84299	4.065000	0.57513	1.911000	0.55334	0.460000	0.39030	ATG	.	T|0.996;G|0.004		0.607	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442	
POLR2A	5430	hgsc.bcm.edu	37	17	7416095	7416095	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7416095A>G	ENST00000322644.6	+	28	5008	c.4609A>G	c.(4609-4611)Agt>Ggt	p.S1537G		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1537					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)|regulation of transcription, DNA-templated (GO:0006355)|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)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				CTCTATAGGGAGTGGAATGAC	0.622																																					p.S1537G		Atlas-SNP	.											.	POLR2A	157	.	0			c.A4609G						.						64.0	74.0	71.0					17																	7416095		2203	4300	6503	SO:0001583	missense	5430	exon28			ATAGGGAGTGGAA			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.4609A>G	chr17.hg19:g.7416095A>G	ENSP00000314949:p.Ser1537Gly	57.0	0.0		48.0	4.0	NM_000937	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	hg19	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	A	8.797	0.931934	0.18131	.	.	ENSG00000181222	ENST00000535204;ENST00000545644;ENST00000322644	T	0.71103	-0.54	4.04	4.04	0.47022	.	0.822365	0.10722	N	0.641652	T	0.53594	0.1806	N	0.11201	0.11	0.80722	D	1	B	0.15719	0.014	B	0.15484	0.013	T	0.47142	-0.9140	10	0.44086	T	0.13	-2.128	12.4264	0.55548	1.0:0.0:0.0:0.0	.	1537	P24928	RPB1_HUMAN	G	1493;436;1537	ENSP00000314949:S1537G	ENSP00000314949:S1537G	S	+	1	0	SLC35G6	7356819	1.000000	0.71417	0.992000	0.48379	0.254000	0.26022	8.174000	0.89682	1.819000	0.53055	0.374000	0.22700	AGT	.	.		0.622	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
SHBG	6462	hgsc.bcm.edu	37	17	7536255	7536255	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7536255T>C	ENST00000380450.4	+	7	1069	c.1038T>C	c.(1036-1038)cgT>cgC	p.R346R	SHBG_ENST00000570547.1_Intron|SHBG_ENST00000575903.1_Silent_p.R328R|SHBG_ENST00000572262.1_Silent_p.R234R|SHBG_ENST00000575314.1_Silent_p.R288R|SHBG_ENST00000576478.1_Intron|SHBG_ENST00000574539.1_Intron|SHBG_ENST00000572182.1_Intron|SHBG_ENST00000416273.3_Intron|SHBG_ENST00000340624.5_Intron|SHBG_ENST00000441599.2_Intron|SHBG_ENST00000576728.1_Intron	NM_001040.3	NP_001031.2	P04278	SHBG_HUMAN	sex hormone-binding globulin	346	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				primary spermatocyte growth (GO:0007285)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	androgen binding (GO:0005497)	p.0?(1)|p.?(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Drostanolone(DB00858)|Estradiol(DB00783)|Estropipate(DB04574)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Methyltestosterone(DB06710)|Mitotane(DB00648)|Norethindrone(DB00717)|Spironolactone(DB00421)|Testosterone(DB00624)|transdermal testosterone gel(DB05275)	CTCAAGGGCGTCTCTTCCTGG	0.562											OREG0024140	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R346R		Atlas-SNP	.											.	SHBG	21	.	2	Unknown(1)|Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)|bone(1)	c.T1038C						.						38.0	37.0	38.0					17																	7536255		2203	4300	6503	SO:0001819	synonymous_variant	6462	exon7			AGGGCGTCTCTTC		CCDS11117.1, CCDS54082.1, CCDS54083.1, CCDS58513.1, CCDS73961.1, CCDS73962.1	17p13.1	2013-09-19			ENSG00000129214	ENSG00000129214			10839	protein-coding gene	gene with protein product	"""androgen binding protein"""	182205				2587256	Standard	NM_001146279		Approved	ABP, TEBG, MGC126834, MGC138391	uc002gie.2	P04278	OTTHUMG00000108153	ENST00000380450.4:c.1038T>C	chr17.hg19:g.7536255T>C		63.0	0.0	642	43.0	4.0	NM_001040	B0FWH4|E9PGW1|F5H5Z8|I3L1N7|P14689|Q16616|Q3MIL0|Q6ISD2	Silent	SNP	ENST00000380450.4	hg19	CCDS11117.1																																																																																			.	.		0.562	SHBG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226957.2	NM_001040	
TP53	7157	hgsc.bcm.edu	37	17	7578457	7578457	+	Missense_Mutation	SNP	C	C	T	rs587782144		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7578457C>T	ENST00000269305.4	-	5	662	c.473G>A	c.(472-474)cGc>cAc	p.R158H	TP53_ENST00000359597.4_Missense_Mutation_p.R158H|TP53_ENST00000455263.2_Missense_Mutation_p.R158H|TP53_ENST00000420246.2_Missense_Mutation_p.R158H|TP53_ENST00000413465.2_Missense_Mutation_p.R158H|TP53_ENST00000445888.2_Missense_Mutation_p.R158H|TP53_ENST00000574684.1_5'Flank	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	158	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> F (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		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.R158L(77)|p.R158H(74)|p.R158P(9)|p.R65L(8)|p.0?(8)|p.R26L(8)|p.R158fs(6)|p.R158fs*11(6)|p.R65H(5)|p.R26H(5)|p.R158_A159insX(4)|p.R65fs(2)|p.R158_A159delRA(2)|p.R156_I162delRVRAMAI(2)|p.V157fs*9(2)|p.P153fs*22(2)|p.R26fs(2)|p.V157fs*22(2)|p.V157_C176del20(1)|p.R156_A161delRVRAMA(1)|p.R158F(1)|p.P151_V173del23(1)|p.R156_R158delRVR(1)|p.R156fs*18(1)|p.R26fs*11(1)|p.R156_A161del(1)|p.V157_M160delVRAM(1)|p.V157_R158delVR(1)|p.S149fs*72(1)|p.A159fs*21(1)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R65fs*11(1)|p.R156fs*20(1)|p.R158C(1)|p.V157_I162delVRAMAI(1)|p.V157fs*21(1)|p.R158fs*8(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)	GGCCATGGCGCGGACGCGGGT	0.627		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.R158H	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,adenocarcinoma,0,2	TP53	33396	.	244	Substitution - Missense(188)|Deletion - Frameshift(19)|Deletion - In frame(13)|Complex(10)|Whole gene deletion(8)|Insertion - In frame(4)|Complex - frameshift(2)	lung(78)|central_nervous_system(33)|oesophagus(20)|haematopoietic_and_lymphoid_tissue(19)|large_intestine(18)|upper_aerodigestive_tract(12)|stomach(12)|urinary_tract(9)|prostate(7)|kidney(6)|liver(6)|breast(5)|bone(4)|soft_tissue(3)|ovary(3)|pancreas(3)|thyroid(2)|biliary_tract(2)|vulva(1)|thymus(1)	c.G473A	GRCh37	CM994513	TP53	M		.						49.0	51.0	50.0					17																	7578457		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;	ATGGCGCGGACGC	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.473G>A	chr17.hg19:g.7578457C>T	ENSP00000269305:p.Arg158His	153.0	0.0		90.0	55.0	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	13.67	2.306299	0.40795	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793	D;D;D;D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	5.59	4.63	0.57726	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.110116	0.64402	D	0.000010	D	0.99809	0.9917	M	0.77486	2.375	0.58432	D	0.999999	D;P;D;D;P;P;D	0.89917	0.998;0.631;0.984;0.982;0.831;0.48;1.0	P;B;P;P;P;B;D	0.97110	0.907;0.274;0.76;0.751;0.516;0.242;1.0	D	0.96738	0.9544	10	0.87932	D	0	-10.4795	12.6491	0.56751	0.0:0.9196:0.0:0.0804	.	119;158;158;65;158;158;158	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	158;158;158;158;158;158;147;65;26;65;26;158	ENSP00000410739:R158H;ENSP00000352610:R158H;ENSP00000269305:R158H;ENSP00000398846:R158H;ENSP00000391127:R158H;ENSP00000391478:R158H;ENSP00000425104:R26H;ENSP00000423862:R65H;ENSP00000424104:R158H	ENSP00000269305:R158H	R	-	2	0	TP53	7519182	1.000000	0.71417	0.034000	0.17996	0.175000	0.22909	7.775000	0.85489	1.514000	0.48869	-0.140000	0.14226	CGC	.	.		0.627	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
DNAH2	146754	hgsc.bcm.edu	37	17	7674122	7674122	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7674122T>C	ENST00000572933.1	+	27	5693	c.4233T>C	c.(4231-4233)tcT>tcC	p.S1411S	DNAH2_ENST00000389173.2_Silent_p.S1411S			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1411	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TAGCTCTGTCTACCATGAAGG	0.488																																					p.S1411S		Atlas-SNP	.											.	DNAH2	498	.	0			c.T4233C						.						181.0	164.0	170.0					17																	7674122		2203	4300	6503	SO:0001819	synonymous_variant	146754	exon26			TCTGTCTACCATG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.4233T>C	chr17.hg19:g.7674122T>C		124.0	0.0		99.0	4.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	hg19	CCDS32551.1																																																																																			.	.		0.488	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
CHD3	1107	hgsc.bcm.edu	37	17	7802659	7802659	+	Splice_Site	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:7802659A>G	ENST00000330494.7	+	15	2493		c.e15-1		CHD3_ENST00000380358.4_Splice_Site|CHD3_ENST00000358181.4_Splice_Site	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3						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)				CTTGACTCCCAGGGCCACACA	0.557																																					.		Atlas-SNP	.											.	CHD3	169	.	0			c.2521-2A>G						.						95.0	94.0	94.0					17																	7802659		2203	4300	6503	SO:0001630	splice_region_variant	1107	exon15			ACTCCCAGGGCCA	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.2344-1A>G	chr17.hg19:g.7802659A>G		120.0	0.0		86.0	4.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Splice_Site	SNP	ENST00000330494.7	hg19	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	A	16.26	3.072821	0.55646	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3149	0.74065	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CHD3	7743384	1.000000	0.71417	0.996000	0.52242	0.704000	0.40688	9.139000	0.94554	2.266000	0.75297	0.454000	0.30748	.	.	.		0.557	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273	Intron
DNAH9	1770	hgsc.bcm.edu	37	17	11572530	11572530	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:11572530T>C	ENST00000262442.4	+	16	2949	c.2881T>C	c.(2881-2883)Tct>Cct	p.S961P	DNAH9_ENST00000454412.2_Missense_Mutation_p.S961P	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	961	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TAGGATACCATCTCTGGTGCC	0.532																																					p.S961P		Atlas-SNP	.											.	DNAH9	695	.	0			c.T2881C						.						126.0	119.0	121.0					17																	11572530		2203	4300	6503	SO:0001583	missense	1770	exon16			ATACCATCTCTGG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.2881T>C	chr17.hg19:g.11572530T>C	ENSP00000262442:p.Ser961Pro	149.0	0.0		105.0	5.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.146753	0.57151	.	.	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.27557	1.7;1.66	5.6	4.51	0.55191	.	0.143325	0.48767	D	0.000168	T	0.51941	0.1704	M	0.85041	2.73	0.80722	D	1	D	0.54601	0.967	P	0.59948	0.866	T	0.54296	-0.8315	10	0.59425	D	0.04	.	8.0065	0.30327	0.1357:0.0:0.1421:0.7222	.	961	Q9NYC9	DYH9_HUMAN	P	961	ENSP00000262442:S961P;ENSP00000414874:S961P	ENSP00000262442:S961P	S	+	1	0	DNAH9	11513255	0.990000	0.36364	0.743000	0.31040	0.601000	0.36947	2.384000	0.44362	0.924000	0.37069	0.533000	0.62120	TCT	.	.		0.532	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
RAI1	10743	hgsc.bcm.edu	37	17	17700882	17700882	+	Silent	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:17700882C>A	ENST00000353383.1	+	3	5089	c.4620C>A	c.(4618-4620)ctC>ctA	p.L1540L	RAI1_ENST00000261641.6_Silent_p.L1540L	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1540					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		GGAAGCGCCTCACTCGGGGCC	0.667																																					p.L1540L		Atlas-SNP	.											.	RAI1	121	.	0			c.C4620A						.						57.0	69.0	65.0					17																	17700882		2203	4300	6503	SO:0001819	synonymous_variant	10743	exon3			GCGCCTCACTCGG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.4620C>A	chr17.hg19:g.17700882C>A		227.0	0.0		256.0	89.0	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	hg19	CCDS11188.1																																																																																			.	.		0.667	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
SLC47A1	55244	hgsc.bcm.edu	37	17	19451395	19451395	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:19451395T>C	ENST00000270570.4	+	4	490	c.404T>C	c.(403-405)cTc>cCc	p.L135P	SLC47A1_ENST00000571335.1_5'UTR|SLC47A1_ENST00000584348.1_3'UTR|SLC47A1_ENST00000457293.1_Missense_Mutation_p.L135P|SLC47A1_ENST00000395585.1_Missense_Mutation_p.L135P|SLC47A1_ENST00000575023.1_Missense_Mutation_p.L135P|SLC47A1_ENST00000436810.2_Missense_Mutation_p.L112P|SLC47A1_ENST00000542886.1_Missense_Mutation_p.L135P	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	135					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	GCGCTCTTTCTCAACACCCAG	0.617																																					p.L135P		Atlas-SNP	.											.	SLC47A1	55	.	0			c.T404C						.						114.0	93.0	100.0					17																	19451395		2203	4300	6503	SO:0001583	missense	55244	exon4			TCTTTCTCAACAC		CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"""Solute carriers"""	25588	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 1"""	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.404T>C	chr17.hg19:g.19451395T>C	ENSP00000270570:p.Leu135Pro	77.0	0.0		95.0	4.0	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Missense_Mutation	SNP	ENST00000270570.4	hg19	CCDS11209.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.127766	0.77549	.	.	ENSG00000142494	ENST00000436810;ENST00000270570;ENST00000457293;ENST00000542886;ENST00000395585	T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38	4.99	4.99	0.66335	.	0.285709	0.37219	N	0.002181	T	0.59335	0.2186	M	0.76002	2.32	0.54753	D	0.999981	D;D;D;D	0.69078	0.997;0.997;0.993;0.982	D;D;D;P	0.73380	0.98;0.974;0.976;0.891	T	0.64698	-0.6346	10	0.87932	D	0	-12.738	13.8392	0.63428	0.0:0.0:0.0:1.0	.	112;135;135;135	E7EX57;B4DYV3;Q96FL8;Q96FL8-3	.;.;S47A1_HUMAN;.	P	112;135;135;135;135	ENSP00000407155:L112P;ENSP00000270570:L135P;ENSP00000415586:L135P;ENSP00000440435:L135P;ENSP00000378951:L135P	ENSP00000270570:L135P	L	+	2	0	SLC47A1	19391987	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	7.403000	0.79983	1.879000	0.54435	0.379000	0.24179	CTC	.	.		0.617	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242	
SLC47A2	146802	hgsc.bcm.edu	37	17	19583316	19583316	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:19583316C>A	ENST00000325411.5	-	16	1587	c.1537G>T	c.(1537-1539)Gca>Tca	p.A513S	SLC47A2_ENST00000350657.5_Missense_Mutation_p.A491S|SLC47A2_ENST00000463318.1_5'UTR	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	513					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)			endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	GTGCTCTCTGCTCTCTGCTGC	0.493																																					p.A513S		Atlas-SNP	.											.	SLC47A2	61	.	0			c.G1537T						.						107.0	89.0	95.0					17																	19583316		2203	4300	6503	SO:0001583	missense	146802	exon16			TCTCTGCTCTCTG	AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"""Solute carriers"""	26439	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 2"""	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.1537G>T	chr17.hg19:g.19583316C>A	ENSP00000326671:p.Ala513Ser	64.0	0.0		86.0	28.0	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Missense_Mutation	SNP	ENST00000325411.5	hg19	CCDS11211.1	.	.	.	.	.	.	.	.	.	.	C	4.854	0.158712	0.09236	.	.	ENSG00000180638	ENST00000350657;ENST00000325411	T;T	0.29397	1.57;1.59	4.04	-8.08	0.01094	.	2.099700	0.02651	U	0.106463	T	0.12008	0.0292	N	0.14661	0.345	0.09310	N	1	B;B;B	0.24186	0.099;0.037;0.001	B;B;B	0.25405	0.06;0.048;0.002	T	0.24584	-1.0156	10	0.06891	T	0.86	1.1802	1.9074	0.03280	0.2094:0.2109:0.1039:0.4758	.	477;491;513	Q86VL8-3;Q86VL8-4;Q86VL8	.;.;S47A2_HUMAN	S	491;513	ENSP00000338084:A491S;ENSP00000326671:A513S	ENSP00000326671:A513S	A	-	1	0	SLC47A2	19523908	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.977000	0.01495	-2.180000	0.00766	-0.251000	0.11542	GCA	.	.		0.493	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908	
FOXN1	8456	hgsc.bcm.edu	37	17	26857795	26857795	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:26857795A>G	ENST00000226247.2	+	5	888	c.859A>G	c.(859-861)Agt>Ggt	p.S287G	FOXN1_ENST00000579795.1_Missense_Mutation_p.S287G	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	287					defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					CCTTAAGAACAGTAAAACTGG	0.537																																					p.S287G		Atlas-SNP	.											.	FOXN1	51	.	0			c.A859G						.						104.0	101.0	102.0					17																	26857795		2203	4300	6503	SO:0001583	missense	8456	exon5			AAGAACAGTAAAA	Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"""Forkhead boxes"""	12765	protein-coding gene	gene with protein product		600838	"""winged-helix nude"", ""Rowett nude"""	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.859A>G	chr17.hg19:g.26857795A>G	ENSP00000226247:p.Ser287Gly	143.0	0.0		158.0	9.0	NM_003593	B2R9Q7|O15352	Missense_Mutation	SNP	ENST00000226247.2	hg19	CCDS11232.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.006365	0.93287	.	.	ENSG00000109101	ENST00000226247	D	0.96554	-4.05	5.84	5.84	0.93424	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	D	0.000000	D	0.98707	0.9566	H	0.95645	3.7	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	D	0.99719	1.1009	10	0.87932	D	0	.	16.2045	0.82114	1.0:0.0:0.0:0.0	.	287	O15353	FOXN1_HUMAN	G	287	ENSP00000226247:S287G	ENSP00000226247:S287G	S	+	1	0	FOXN1	23881922	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.339000	0.96797	2.234000	0.73211	0.459000	0.35465	AGT	.	.		0.537	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1		
SSH2	85464	hgsc.bcm.edu	37	17	27959313	27959313	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:27959313A>G	ENST00000269033.3	-	15	2969	c.2818T>C	c.(2818-2820)Tct>Cct	p.S940P	RP11-68I3.2_ENST00000581474.1_RNA|SSH2_ENST00000540801.1_Missense_Mutation_p.S967P	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	940					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCAGCCTCAGACCCACTGTAT	0.532																																					p.S940P		Atlas-SNP	.											.	SSH2	107	.	0			c.T2818C						.						136.0	135.0	136.0					17																	27959313		2203	4300	6503	SO:0001583	missense	85464	exon15			CCTCAGACCCACT	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30580	protein-coding gene	gene with protein product		606779	"""slingshot homolog 2 (Drosophila)"""			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.2818T>C	chr17.hg19:g.27959313A>G	ENSP00000269033:p.Ser940Pro	63.0	0.0		98.0	4.0	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	hg19	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	A	1.170	-0.641203	0.03557	.	.	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.10477	2.87;2.87	5.47	-4.85	0.03142	.	0.751587	0.12524	N	0.461421	T	0.07683	0.0193	L	0.60455	1.87	0.09310	N	0.999998	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.37174	-0.9717	10	0.24483	T	0.36	-0.0038	2.7204	0.05199	0.37:0.2765:0.2626:0.0909	.	967;940	F5H527;Q76I76	.;SSH2_HUMAN	P	940;967	ENSP00000269033:S940P;ENSP00000444743:S967P	ENSP00000269033:S940P	S	-	1	0	SSH2	24983439	0.000000	0.05858	0.030000	0.17652	0.234000	0.25298	-0.060000	0.11712	-0.938000	0.03714	-1.139000	0.01908	TCT	.	.		0.532	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389	
CPD	1362	hgsc.bcm.edu	37	17	28791765	28791765	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:28791765T>C	ENST00000225719.4	+	21	4152	c.4076T>C	c.(4075-4077)cTc>cCc	p.L1359P	CPD_ENST00000543464.2_Missense_Mutation_p.L1112P	NM_001304.4	NP_001295.2	O75976	CBPD_HUMAN	carboxypeptidase D	1359						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metallocarboxypeptidase activity (GO:0004181)|serine-type carboxypeptidase activity (GO:0004185)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(13)|skin(5)|stomach(1)|urinary_tract(1)	36						AAGAAGTCCCTCCTAAGCCAT	0.413																																					p.L1359P		Atlas-SNP	.											.	CPD	89	.	0			c.T4076C						.						147.0	139.0	142.0					17																	28791765		2203	4300	6503	SO:0001583	missense	1362	exon21			AGTCCCTCCTAAG	U65090	CCDS11257.1, CCDS56025.1	17q11.2	2012-02-10			ENSG00000108582	ENSG00000108582	3.4.17.22		2301	protein-coding gene	gene with protein product	"""metallocarboxypeptidase D"""	603102				9628828, 9355738	Standard	NM_001304		Approved	GP180	uc002hfb.2	O75976	OTTHUMG00000132797	ENST00000225719.4:c.4076T>C	chr17.hg19:g.28791765T>C	ENSP00000225719:p.Leu1359Pro	80.0	0.0		97.0	6.0	NM_001304	B7Z7T9|B7ZAU4|F5GZH6|O15377|Q86SH9|Q86XE6	Missense_Mutation	SNP	ENST00000225719.4	hg19	CCDS11257.1	.	.	.	.	.	.	.	.	.	.	T	16.26	3.074156	0.55646	.	.	ENSG00000108582	ENST00000225719;ENST00000543464	T;T	0.25250	1.81;2.93	5.6	5.6	0.85130	.	1.657100	0.02876	N	0.132188	T	0.42404	0.1201	N	0.14661	0.345	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.05683	-1.0870	10	0.87932	D	0	-22.1691	15.0117	0.71555	0.0:0.0:0.0:1.0	.	1112;1359	F5GZH6;O75976	.;CBPD_HUMAN	P	1359;1112	ENSP00000225719:L1359P;ENSP00000444443:L1112P	ENSP00000225719:L1359P	L	+	2	0	CPD	25815891	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.282000	0.78630	2.118000	0.64928	0.529000	0.55759	CTC	.	.		0.413	CPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256214.3	NM_001304	
NLE1	54475	hgsc.bcm.edu	37	17	33460449	33460449	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:33460449A>G	ENST00000442241.4	-	11	1322	c.1283T>C	c.(1282-1284)cTc>cCc	p.L428P	NLE1_ENST00000360831.5_Missense_Mutation_p.L386P|NLE1_ENST00000586869.1_Missense_Mutation_p.L136P	NM_001014445.1|NM_018096.3	NP_001014445.1|NP_060566.2	Q9NVX2	NLE1_HUMAN	notchless homolog 1 (Drosophila)	428					hematopoietic stem cell homeostasis (GO:0061484)|inner cell mass cell differentiation (GO:0001826)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)|negative regulation of mitotic cell cycle (GO:0045930)|Notch signaling pathway (GO:0007219)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|ribosomal large subunit biogenesis (GO:0042273)	nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	22		Ovarian(249;0.17)				GCTGACCAGGAGCCGACTGTC	0.617																																					p.L428P		Atlas-SNP	.											.	NLE1	42	.	0			c.T1283C						.						41.0	36.0	38.0					17																	33460449		2203	4300	6503	SO:0001583	missense	54475	exon11			ACCAGGAGCCGAC		CCDS11291.1, CCDS45647.1	17q12	2013-01-10		2005-08-09	ENSG00000073536	ENSG00000073536		"""WD repeat domain containing"""	19889	protein-coding gene	gene with protein product	"""Notchless gene homolog, (Drosophila)"""						Standard	XM_005257989		Approved	FLJ10458	uc002hiy.1	Q9NVX2	OTTHUMG00000132928	ENST00000442241.4:c.1283T>C	chr17.hg19:g.33460449A>G	ENSP00000413572:p.Leu428Pro	97.0	0.0		102.0	6.0	NM_018096	O60868|Q59GJ8|Q9BU54	Missense_Mutation	SNP	ENST00000442241.4	hg19	CCDS11291.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.5|23.5	4.428386|4.428386	0.83667|0.83667	.|.	.|.	ENSG00000073536|ENSG00000073536	ENST00000442241;ENST00000360831;ENST00000537697|ENST00000436188	T|.	0.63255|.	-0.03|.	5.14|5.14	5.14|5.14	0.70334|0.70334	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86176|0.86176	0.5870|0.5870	H|H	0.95402|0.95402	3.665|3.665	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.997;1.0|.	D|D	0.89897|0.89897	0.4041|0.4041	10|5	0.72032|.	D|.	0.01|.	-15.3864|-15.3864	12.9593|12.9593	0.58449|0.58449	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	404;428|.	B4E074;Q9NVX2|.	.;NLE1_HUMAN|.	P|P	428;136;404|247	ENSP00000413572:L428P|.	ENSP00000354075:L136P|.	L|S	-|-	2|1	0|0	NLE1|NLE1	30484562|30484562	1.000000|1.000000	0.71417|0.71417	0.922000|0.922000	0.36590|0.36590	0.987000|0.987000	0.75469|0.75469	8.531000|8.531000	0.90610|0.90610	2.144000|2.144000	0.66660|0.66660	0.460000|0.460000	0.39030|0.39030	CTC|TCC	.	.		0.617	NLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256441.2	NM_018096	
THRA	7067	hgsc.bcm.edu	37	17	38230771	38230771	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:38230771T>C	ENST00000264637.4	+	2	610	c.30T>C	c.(28-30)tgT>tgC	p.C10C	THRA_ENST00000546243.1_Silent_p.C10C|THRA_ENST00000394121.4_Silent_p.C10C|THRA_ENST00000450525.2_Silent_p.C10C|THRA_ENST00000584985.1_Silent_p.C10C	NM_003250.5	NP_003241.2	P10827	THA_HUMAN	thyroid hormone receptor, alpha	10	Modulating.				cartilage condensation (GO:0001502)|cytoplasmic sequestering of transcription factor (GO:0042994)|erythrocyte differentiation (GO:0030218)|female courtship behavior (GO:0008050)|gene expression (GO:0010467)|hormone-mediated signaling pathway (GO:0009755)|learning or memory (GO:0007611)|negative regulation of DNA-templated transcription, initiation (GO:2000143)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of female receptivity (GO:0045925)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart contraction (GO:0008016)|regulation of lipid catabolic process (GO:0050994)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cold (GO:0009409)|thyroid gland development (GO:0030878)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Type I pneumocyte differentiation (GO:0060509)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|steroid receptor RNA activator RNA binding (GO:0002153)|TBP-class protein binding (GO:0017025)|thyroid hormone binding (GO:0070324)|thyroid hormone receptor activity (GO:0004887)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|prostate(1)	11	Colorectal(19;0.000442)	Myeloproliferative disorder(1115;0.0255)			Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	AGGTGGAGTGTGGGTCAGACC	0.582																																					p.C10C		Atlas-SNP	.											.	THRA	88	.	0			c.T30C						.						191.0	161.0	171.0					17																	38230771		2203	4300	6503	SO:0001819	synonymous_variant	7067	exon2			GGAGTGTGGGTCA	J03239	CCDS11360.1, CCDS42316.1, CCDS58546.1	17q21.1	2013-01-16	2011-05-19		ENSG00000126351	ENSG00000126351		"""Nuclear hormone receptors"""	11796	protein-coding gene	gene with protein product		190120	"""thyroid hormone receptor, alpha (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog)"", ""thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-a) oncogene homolog, avian)"""	THRA1, THRA2, ERBA1		6323162, 6589608	Standard	NM_003250		Approved	EAR-7.1/EAR-7.2, THRA3, AR7, ERBA, NR1A1	uc002htw.3	P10827	OTTHUMG00000133332	ENST00000264637.4:c.30T>C	chr17.hg19:g.38230771T>C		83.0	0.0		117.0	6.0	NM_001190918	A8K3B5|P21205|Q8N6A1|Q96H73	Silent	SNP	ENST00000264637.4	hg19	CCDS11360.1																																																																																			.	.		0.582	THRA-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257160.2		
WIPF2	147179	hgsc.bcm.edu	37	17	38430226	38430226	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:38430226T>C	ENST00000323571.4	+	6	1395	c.1155T>C	c.(1153-1155)tcT>tcC	p.S385S	WIPF2_ENST00000585043.1_Silent_p.S385S|WIPF2_ENST00000536600.1_Silent_p.S127S|WIPF2_ENST00000394103.3_Silent_p.S127S|WIPF2_ENST00000583130.1_Silent_p.S385S|WIPF2_ENST00000494757.1_3'UTR	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	385					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						ACAGAGATTCTATCACCACTG	0.602										HNSCC(43;0.11)																											p.S385S		Atlas-SNP	.											.	WIPF2	55	.	0			c.T1155C						.						136.0	114.0	121.0					17																	38430226		2203	4300	6503	SO:0001819	synonymous_variant	147179	exon6			AGATTCTATCACC	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.1155T>C	chr17.hg19:g.38430226T>C		52.0	0.0		68.0	24.0	NM_133264	A8K0L3|Q658J8|Q71RE1|Q8TE44	Silent	SNP	ENST00000323571.4	hg19	CCDS11364.1																																																																																			.	.		0.602	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264	
AARSD1	80755	hgsc.bcm.edu	37	17	41113229	41113229	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:41113229T>C	ENST00000427569.2	-	3	346	c.311A>G	c.(310-312)gAc>gGc	p.D104G	AARSD1_ENST00000416949.1_5'UTR|PTGES3L-AARSD1_ENST00000421990.2_Missense_Mutation_p.D278G|PTGES3L-AARSD1_ENST00000409399.1_Missense_Mutation_p.D278G|PTGES3L-AARSD1_ENST00000360221.4_Missense_Mutation_p.D217G|PTGES3L-AARSD1_ENST00000409103.1_Missense_Mutation_p.D187G	NM_001261434.1	NP_001248363.1	Q9BTE6	AASD1_HUMAN	alanyl-tRNA synthetase domain containing 1	104					alanyl-tRNA aminoacylation (GO:0006419)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	alanine-tRNA ligase activity (GO:0004813)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|Ser-tRNA(Ala) hydrolase activity (GO:0002196)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|skin(1)	17		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)		CTGCATGTGGTCAAACCTCCG	0.562																																					p.D278G		Atlas-SNP	.											.	PTGES3L-AARSD1	15	.	0			c.A833G						.						232.0	221.0	225.0					17																	41113229		2203	4300	6503	SO:0001583	missense	100885850	exon8			ATGTGGTCAAACC	BC004172	CCDS11447.1, CCDS45691.1, CCDS58552.1	17q21.31	2012-10-05			ENSG00000266967	ENSG00000266967			28417	protein-coding gene	gene with protein product		613212					Standard	NM_001261434		Approved	MGC2744		Q9BTE6	OTTHUMG00000153515	ENST00000427569.2:c.311A>G	chr17.hg19:g.41113229T>C	ENSP00000400870:p.Asp104Gly	114.0	0.0		156.0	8.0	NM_001136042	B4DI73	Missense_Mutation	SNP	ENST00000427569.2	hg19	CCDS58552.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.8|24.8	4.565951|4.565951	0.86439|0.86439	.|.	.|.	ENSG00000108825|ENSG00000108825	ENST00000360221;ENST00000409399;ENST00000421990;ENST00000427569;ENST00000409103|ENST00000441280;ENST00000430739	T;T|.	0.50548|.	0.74;0.74|.	4.18|4.18	4.18|4.18	0.49190|0.49190	Alanyl-tRNA synthetase, class IIc, core domain (1);Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80722|0.80722	0.4677|0.4677	M|M	0.91459|0.91459	3.21|3.21	.|.	.|.	.|.	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	0.999;0.999;1.0;0.999;1.0|.	D|D	0.87911|0.87911	0.2697|0.2697	9|4	0.41790|.	T|.	0.15|.	-22.4336|-22.4336	13.4037|13.4037	0.60898|0.60898	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	217;278;187;235;104|.	Q9BTE6-2;B4DI73;C9J5N1;B3KSP9;Q9BTE6|.	.;.;.;.;AASD1_HUMAN|.	G|A	217;278;278;104;187|110	ENSP00000386621:D278G;ENSP00000409924:D278G|.	ENSP00000353355:D217G|.	D|T	-|-	2|1	0|0	AARSD1|AARSD1	38366755|38366755	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.688000|7.688000	0.84153|0.84153	1.752000|1.752000	0.51891|0.51891	0.443000|0.443000	0.29094|0.29094	GAC|ACC	.	.		0.562	AARSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467729.1	NM_001261434	
DHX8	1659	hgsc.bcm.edu	37	17	41582144	41582144	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:41582144A>G	ENST00000262415.3	+	12	1751	c.1679A>G	c.(1678-1680)gAg>gGg	p.E560G	DHX8_ENST00000540306.1_Missense_Mutation_p.E560G	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	560					ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		TCAATCCTTGAGCAGAGGGAG	0.463																																					p.E560G	NSCLC(56;1548 1661 49258 49987)	Atlas-SNP	.											.	DHX8	98	.	0			c.A1679G						.						108.0	107.0	107.0					17																	41582144		2203	4300	6503	SO:0001583	missense	1659	exon12			TCCTTGAGCAGAG	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"""DEAH-boxes"""	2749	protein-coding gene	gene with protein product		600396	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"""	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.1679A>G	chr17.hg19:g.41582144A>G	ENSP00000262415:p.Glu560Gly	97.0	0.0		116.0	5.0	NM_004941		Missense_Mutation	SNP	ENST00000262415.3	hg19	CCDS11464.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.913858	0.72983	.	.	ENSG00000067596	ENST00000540306;ENST00000262415	T;T	0.08634	3.07;3.07	5.36	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.25975	0.0633	M	0.84511	2.7	0.80722	D	1	D;P	0.62365	0.991;0.95	P;P	0.58721	0.844;0.703	T	0.01982	-1.1235	10	0.87932	D	0	.	10.3646	0.44015	0.9228:0.0:0.0772:0.0	.	560;560	F5H658;Q14562	.;DHX8_HUMAN	G	560	ENSP00000437886:E560G;ENSP00000262415:E560G	ENSP00000262415:E560G	E	+	2	0	DHX8	38937670	1.000000	0.71417	0.990000	0.47175	0.557000	0.35523	9.237000	0.95368	0.884000	0.36064	0.454000	0.30748	GAG	.	.		0.463	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1		
ATXN7L3	56970	hgsc.bcm.edu	37	17	42273429	42273429	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:42273429T>C	ENST00000454077.2	-	6	516	c.517A>G	c.(517-519)Aga>Gga	p.R173G	CTB-175E5.7_ENST00000586560.1_RNA|ATXN7L3_ENST00000593073.1_Intron|ATXN7L3_ENST00000389384.4_Missense_Mutation_p.R166G	NM_020218.1	NP_064603.1			ataxin 7-like 3											kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	12		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GACTTGGATCTTCGAGGGGAA	0.502																																					p.R173G		Atlas-SNP	.											.	ATXN7L3	31	.	0			c.A517G						.						91.0	89.0	90.0					17																	42273429		1852	4093	5945	SO:0001583	missense	56970	exon6			TGGATCTTCGAGG	AK056002	CCDS42345.1, CCDS45697.1	17q21	2010-03-10			ENSG00000087152	ENSG00000087152			25416	protein-coding gene	gene with protein product						15115762	Standard	NM_001098833		Approved	DKFZp761G2113	uc002ifz.3	Q14CW9		ENST00000454077.2:c.517A>G	chr17.hg19:g.42273429T>C	ENSP00000397259:p.Arg173Gly	95.0	0.0		76.0	4.0	NM_020218		Missense_Mutation	SNP	ENST00000454077.2	hg19	CCDS45697.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.674091	0.47781	.	.	ENSG00000087152	ENST00000454077;ENST00000389384	.	.	.	4.95	3.8	0.43715	.	0.000000	0.85682	D	0.000000	T	0.66499	0.2795	L	0.46157	1.445	0.58432	D	0.999999	D;D	0.61080	0.982;0.989	P;D	0.75020	0.715;0.985	T	0.67975	-0.5531	9	0.59425	D	0.04	.	10.5191	0.44907	0.0:0.0:0.1623:0.8377	.	166;173	Q14CW9;Q14CW9-2	AT7L3_HUMAN;.	G	173;166	.	ENSP00000374035:R166G	R	-	1	2	ATXN7L3	39628955	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.526000	0.60566	1.858000	0.53909	0.454000	0.30748	AGA	.	.		0.502	ATXN7L3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457724.1		
OSBPL7	114881	hgsc.bcm.edu	37	17	45888158	45888158	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:45888158T>C	ENST00000007414.3	-	17	1972	c.1781A>G	c.(1780-1782)gAg>gGg	p.E594G	OSBPL7_ENST00000392507.3_Missense_Mutation_p.E594G	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	594					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						GGCGAAGTTCTCAGACTCTGC	0.592																																					p.E594G		Atlas-SNP	.											.	OSBPL7	65	.	0			c.A1781G						.						39.0	38.0	38.0					17																	45888158		2203	4300	6503	SO:0001583	missense	114881	exon17			AAGTTCTCAGACT	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.1781A>G	chr17.hg19:g.45888158T>C	ENSP00000007414:p.Glu594Gly	63.0	0.0		87.0	5.0	NM_145798	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	hg19	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	T	16.38	3.107490	0.56291	.	.	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.31510	1.49;1.49	4.49	4.49	0.54785	.	0.235041	0.42294	D	0.000726	T	0.28732	0.0712	L	0.48935	1.535	0.52501	D	0.999959	P	0.34587	0.458	B	0.35413	0.202	T	0.07501	-1.0769	10	0.42905	T	0.14	-22.3097	12.7769	0.57453	0.0:0.0:0.0:1.0	.	594	Q9BZF2	OSBL7_HUMAN	G	594	ENSP00000007414:E594G;ENSP00000376295:E594G	ENSP00000007414:E594G	E	-	2	0	OSBPL7	43243157	0.728000	0.28080	1.000000	0.80357	0.924000	0.55760	2.838000	0.48199	1.650000	0.50662	0.402000	0.26972	GAG	.	.		0.592	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	
HOXB2	3212	hgsc.bcm.edu	37	17	46622272	46622272	+	Start_Codon_SNP	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:46622272A>G	ENST00000330070.4	-	1	1169	c.2T>C	c.(1-3)aTg>aCg	p.M1T	HOXB-AS1_ENST00000502764.2_RNA|HOXB2_ENST00000504772.3_5'Flank|HOXB-AS1_ENST00000508688.1_RNA|HOXB-AS1_ENST00000504972.3_RNA|HOXB-AS1_ENST00000435312.1_RNA	NM_002145.3	NP_002136.1	P14652	HXB2_HUMAN	homeobox B2	1					anterior/posterior pattern specification (GO:0009952)|blood circulation (GO:0008015)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|neural nucleus development (GO:0048857)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	11						TTCAAAATTCATGGCTTTCAA	0.567																																					p.M1T		Atlas-SNP	.											.	HOXB2	23	.	0			c.T2C						.						24.0	28.0	27.0					17																	46622272		2203	4300	6503	SO:0001582	initiator_codon_variant	3212	exon1			AAATTCATGGCTT		CCDS11527.1	17q21.32	2012-02-22	2005-12-22		ENSG00000173917	ENSG00000173917		"""Homeoboxes / ANTP class : HOXL subclass"""	5113	protein-coding gene	gene with protein product		142967	"""homeo box B2"""	HOX2, HOX2H		1973146, 1358459	Standard	XM_005257276		Approved		uc002inm.3	P14652	OTTHUMG00000159930	ENST00000330070.4:c.2T>C	chr17.hg19:g.46622272A>G	ENSP00000331741:p.Met1Thr	37.0	0.0		61.0	4.0	NM_002145	P10913|P17485	Missense_Mutation	SNP	ENST00000330070.4	hg19	CCDS11527.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.024521	0.75390	.	.	ENSG00000173917	ENST00000330070	D	0.91464	-2.85	4.53	4.53	0.55603	.	0.149462	0.56097	D	0.000022	D	0.94863	0.8340	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.95403	0.8491	9	0.87932	D	0	.	13.2918	0.60274	1.0:0.0:0.0:0.0	.	1	P14652	HXB2_HUMAN	T	1	ENSP00000331741:M1T	ENSP00000331741:M1T	M	-	2	0	HOXB2	43977271	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.612000	0.90909	2.031000	0.59945	0.477000	0.44152	ATG	.	.		0.567	HOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358384.2		Missense_Mutation
RNF43	54894	hgsc.bcm.edu	37	17	56448298	56448298	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:56448298G>T	ENST00000584437.1	-	2	2304	c.349C>A	c.(349-351)Cgc>Agc	p.R117S	RNF43_ENST00000407977.2_Missense_Mutation_p.R117S|RNF43_ENST00000577625.1_5'UTR|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000581868.1_5'UTR|RNF43_ENST00000577716.1_Missense_Mutation_p.R117S|RNF43_ENST00000583753.1_Intron|RNF43_ENST00000500597.2_Intron			Q68DV7	RNF43_HUMAN	ring finger protein 43	117			R -> H (in dbSNP:rs2257205).		negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGGCAGGGGCGGGGGGCCCGT	0.607																																					p.R117S		Atlas-SNP	.											.,6	RNF43	157	.	0			c.C349A						.						55.0	51.0	52.0					17																	56448298		2203	4300	6503	SO:0001583	missense	54894	exon3			AGGGGCGGGGGGC		CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.349C>A	chr17.hg19:g.56448298G>T	ENSP00000463069:p.Arg117Ser	82.0	0.0		129.0	0.0	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	hg19	CCDS11607.1	.	.	.	.	.	.	.	.	.	.	G	18.67	3.673770	0.67928	.	.	ENSG00000108375	ENST00000407977	T	0.41065	1.01	5.45	5.45	0.79879	.	0.368624	0.26753	N	0.022674	T	0.41442	0.1159	N	0.24115	0.695	0.80722	D	1	D	0.58620	0.983	P	0.52267	0.694	T	0.36817	-0.9732	10	0.72032	D	0.01	-4.475	13.8474	0.63477	0.0:0.0:0.8373:0.1627	.	117	Q68DV7	RNF43_HUMAN	S	117	ENSP00000385328:R117S	ENSP00000385328:R117S	R	-	1	0	RNF43	53803297	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.888000	0.63164	2.555000	0.86185	0.655000	0.94253	CGC	.	.		0.607	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
VMP1	81671	hgsc.bcm.edu	37	17	57808841	57808841	+	Missense_Mutation	SNP	C	C	T	rs543321998		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:57808841C>T	ENST00000262291.4	+	2	344	c.34C>T	c.(34-36)Cgt>Tgt	p.R12C	VMP1_ENST00000537567.1_5'UTR|VMP1_ENST00000536180.1_5'UTR|VMP1_ENST00000545362.1_Missense_Mutation_p.R12C|VMP1_ENST00000539763.1_5'UTR	NM_030938.3	NP_112200.2	Q96GC9	VMP1_HUMAN	vacuole membrane protein 1	12					autophagy (GO:0006914)|cell junction assembly (GO:0034329)|embryo implantation (GO:0007566)|regulation of autophagy (GO:0010506)|single organismal cell-cell adhesion (GO:0016337)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|pre-autophagosomal structure (GO:0000407)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|skin(2)	16						TGACCAGAGACGTGTAGCAAT	0.348													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14778	0.0		0.0	False		,,,				2504	0.0				p.R12C		Atlas-SNP	.											.	VMP1	49	.	0			c.C34T						.						107.0	104.0	105.0					17																	57808841		2203	4300	6503	SO:0001583	missense	81671	exon2			CAGAGACGTGTAG		CCDS11619.1	17q23.1	2014-05-20	2011-03-02	2011-03-02	ENSG00000062716	ENSG00000062716			29559	protein-coding gene	gene with protein product	"""ectopic P-granules autophagy protein 3 homolog (C. elegans)"", ""transport and golgi organization 5 homolog (Drosophila)"""	611753	"""transmembrane protein 49"""	TMEM49		11230166, 11785947	Standard	NM_030938		Approved	EPG3, TANGO5	uc002ixu.4	Q96GC9	OTTHUMG00000179882	ENST00000262291.4:c.34C>T	chr17.hg19:g.57808841C>T	ENSP00000262291:p.Arg12Cys	84.0	0.0		120.0	31.0	NM_030938	B4DVV9|Q9H0P4|Q9P089	Missense_Mutation	SNP	ENST00000262291.4	hg19	CCDS11619.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.508102	0.85282	.	.	ENSG00000062716	ENST00000262291;ENST00000545362	.	.	.	5.04	5.04	0.67666	.	0.226055	0.44285	D	0.000464	T	0.60090	0.2242	L	0.40543	1.245	0.80722	D	1	D;D	0.64830	0.994;0.987	P;B	0.50049	0.629;0.409	T	0.64114	-0.6483	9	0.56958	D	0.05	-6.6801	18.4015	0.90518	0.0:1.0:0.0:0.0	.	12;12	F5H2J3;Q96GC9	.;VMP1_HUMAN	C	12	.	ENSP00000262291:R12C	R	+	1	0	VMP1	55163623	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.624000	0.61254	2.320000	0.78422	0.460000	0.39030	CGT	.	.		0.348	VMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448793.1	NM_030938	
ACE	1636	hgsc.bcm.edu	37	17	61568576	61568576	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:61568576A>G	ENST00000290866.4	+	19	2770	c.2746A>G	c.(2746-2748)Acg>Gcg	p.T916A	ACE_ENST00000290863.6_Missense_Mutation_p.T342A|ACE_ENST00000413513.3_Missense_Mutation_p.T342A|ACE_ENST00000490216.2_Missense_Mutation_p.T342A|ACE_ENST00000421982.2_Missense_Mutation_p.T162A|ACE_ENST00000428043.1_Missense_Mutation_p.T916A|ACE_ENST00000577647.1_Missense_Mutation_p.T342A	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	916	Peptidase M2 2.		T -> M (in dbSNP:rs3730043).		angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	GCAGGGCTGGACGCCCAGGAG	0.617																																					p.T916A		Atlas-SNP	.											.	ACE	187	.	0			c.A2746G						.						47.0	47.0	47.0					17																	61568576		2203	4300	6503	SO:0001583	missense	1636	exon19			GGCTGGACGCCCA	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"""CD molecules"""	2707	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	106180	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"""	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.2746A>G	chr17.hg19:g.61568576A>G	ENSP00000290866:p.Thr916Ala	62.0	0.0		82.0	4.0	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	hg19	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	A	12.83	2.054984	0.36277	.	.	ENSG00000159640	ENST00000290866;ENST00000428043;ENST00000290863;ENST00000413513;ENST00000421982	T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2	5.28	5.28	0.74379	.	0.101804	0.64402	D	0.000002	T	0.69637	0.3133	H	0.94847	3.59	0.80722	D	1	P;D;P;P	0.56035	0.722;0.974;0.931;0.894	P;D;P;B	0.68765	0.688;0.96;0.681;0.422	T	0.78964	-0.1996	10	0.62326	D	0.03	-10.8333	15.2126	0.73238	1.0:0.0:0.0:0.0	.	162;342;342;916	F6X3S4;B4DXI3;P12821-3;P12821	.;.;.;ACE_HUMAN	A	916;916;342;342;162	ENSP00000290866:T916A;ENSP00000397593:T916A;ENSP00000290863:T342A;ENSP00000392247:T342A;ENSP00000387760:T162A	ENSP00000290863:T342A	T	+	1	0	ACE	58922308	1.000000	0.71417	0.996000	0.52242	0.501000	0.33797	5.279000	0.65597	1.975000	0.57531	0.459000	0.35465	ACG	.	.		0.617	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2		
SCN4A	6329	hgsc.bcm.edu	37	17	62048557	62048557	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:62048557A>G	ENST00000435607.1	-	5	744	c.668T>C	c.(667-669)gTg>gCg	p.V223A	CTC-264K15.6_ENST00000577329.1_lincRNA|SCN4A_ENST00000578147.1_Missense_Mutation_p.V223A	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	223					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)	GGCCCGCAGCACCCGGAAGGT	0.642																																					p.V223A		Atlas-SNP	.											.	SCN4A	205	.	0			c.T668C						.						24.0	27.0	26.0					17																	62048557		1917	4132	6049	SO:0001583	missense	6329	exon5			CGCAGCACCCGGA	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.668T>C	chr17.hg19:g.62048557A>G	ENSP00000396320:p.Val223Ala	42.0	0.0		71.0	5.0	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	hg19	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.228631	0.79576	.	.	ENSG00000007314	ENST00000435607	D	0.98835	-5.17	4.22	4.22	0.49857	Ion transport (1);	0.124247	0.53938	D	0.000053	D	0.98969	0.9649	M	0.83852	2.665	0.54753	D	0.999984	D	0.63880	0.993	D	0.72075	0.976	D	0.99421	1.0933	10	0.72032	D	0.01	.	12.5717	0.56341	1.0:0.0:0.0:0.0	.	223	P35499	SCN4A_HUMAN	A	223	ENSP00000396320:V223A	ENSP00000396320:V223A	V	-	2	0	SCN4A	59402289	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.087000	0.94110	1.894000	0.54839	0.379000	0.24179	GTG	.	.		0.642	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
GNA13	10672	hgsc.bcm.edu	37	17	63014373	63014373	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:63014373G>A	ENST00000439174.2	-	3	804	c.559C>T	c.(559-561)Cca>Tca	p.P187S	GNA13_ENST00000541118.1_Missense_Mutation_p.P92S	NM_006572.4	NP_006563.2	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein), alpha 13	187					activation of phospholipase D activity (GO:0031584)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|in utero embryonic development (GO:0001701)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 1 angiotensin receptor binding (GO:0031702)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(14)|kidney(2)|large_intestine(4)|lung(6)|urinary_tract(1)	34						ACACTTACTGGTTCTCCAAGT	0.303																																					p.P187S		Atlas-SNP	.											.	GNA13	69	.	0			c.C559T						.						132.0	139.0	137.0					17																	63014373		2203	4299	6502	SO:0001583	missense	10672	exon3			TTACTGGTTCTCC	L22075	CCDS11661.1, CCDS62302.1	17q24.1	2014-09-04			ENSG00000120063	ENSG00000120063			4381	protein-coding gene	gene with protein product		604406				7791744	Standard	NM_006572		Approved	G13, MGC46138	uc002jfc.3	Q14344	OTTHUMG00000179316	ENST00000439174.2:c.559C>T	chr17.hg19:g.63014373G>A	ENSP00000400717:p.Pro187Ser	200.0	0.0		236.0	57.0	NM_006572	B2R977|B7Z7R0|F5H1G8|Q8TD70	Missense_Mutation	SNP	ENST00000439174.2	hg19	CCDS11661.1	.	.	.	.	.	.	.	.	.	.	G	11.58	1.679744	0.29783	.	.	ENSG00000120063	ENST00000439174;ENST00000541118;ENST00000239138	D;D	0.89123	-2.47;-2.47	4.95	0.565	0.17309	G protein alpha subunit, helical insertion (2);	0.864625	0.10553	N	0.661221	D	0.82921	0.5142	L	0.48260	1.515	0.47009	D	0.999289	B	0.02656	0.0	B	0.01281	0.0	T	0.75048	-0.3455	10	0.37606	T	0.19	.	7.1178	0.25427	0.1565:0.2824:0.5612:0.0	.	187	Q14344	GNA13_HUMAN	S	187;92;162	ENSP00000400717:P187S;ENSP00000439647:P92S	ENSP00000239138:P162S	P	-	1	0	GNA13	60444835	0.839000	0.29477	1.000000	0.80357	0.996000	0.88848	0.044000	0.13992	0.679000	0.31345	0.655000	0.94253	CCA	.	.		0.303	GNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445720.1	NM_006572	
PSMD12	5718	hgsc.bcm.edu	37	17	65346373	65346373	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:65346373T>C	ENST00000356126.3	-	4	484	c.377A>G	c.(376-378)gAt>gGt	p.D126G	PSMD12_ENST00000581618.1_Intron|PSMD12_ENST00000357146.4_Missense_Mutation_p.D106G	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	126					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)					TCGTAGAGTATCAATTAATCG	0.333																																					p.D126G		Atlas-SNP	.											.	PSMD12	32	.	0			c.A377G						.						84.0	78.0	80.0					17																	65346373		2203	4300	6503	SO:0001583	missense	5718	exon4			AGAGTATCAATTA	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.377A>G	chr17.hg19:g.65346373T>C	ENSP00000348442:p.Asp126Gly	109.0	0.0		131.0	6.0	NM_002816	A6NP15|Q53HA2|Q6P053	Missense_Mutation	SNP	ENST00000356126.3	hg19	CCDS11669.1	.	.	.	.	.	.	.	.	.	.	T	19.74	3.883153	0.72410	.	.	ENSG00000197170	ENST00000356126;ENST00000357146	T;T	0.41758	0.99;0.99	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.55862	0.1947	M	0.80616	2.505	0.80722	D	1	P;P	0.48230	0.907;0.907	P;P	0.49953	0.489;0.627	T	0.61753	-0.6998	10	0.48119	T	0.1	-22.0817	14.4325	0.67259	0.0:0.0:0.0:1.0	.	106;126	A6NP15;O00232	.;PSD12_HUMAN	G	126;106	ENSP00000348442:D126G;ENSP00000349667:D106G	ENSP00000348442:D126G	D	-	2	0	PSMD12	62776835	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.280000	0.78610	1.944000	0.56390	0.383000	0.25322	GAT	.	.		0.333	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871	
FDXR	2232	hgsc.bcm.edu	37	17	72860316	72860316	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:72860316T>C	ENST00000293195.5	-	9	1034	c.956A>G	c.(955-957)gAt>gGt	p.D319G	FDXR_ENST00000581969.1_5'Flank|FDXR_ENST00000413947.2_Missense_Mutation_p.D350G|FDXR_ENST00000582944.1_Missense_Mutation_p.D311G|FDXR_ENST00000544854.1_Missense_Mutation_p.D267G|FDXR_ENST00000442102.2_Missense_Mutation_p.D362G|GRIN2C_ENST00000578159.1_5'Flank|FDXR_ENST00000455107.2_Missense_Mutation_p.D275G|FDXR_ENST00000581530.1_Missense_Mutation_p.D325G|FDXR_ENST00000420580.2_Missense_Mutation_p.D279G|FDXR_ENST00000583917.1_Missense_Mutation_p.D291G	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase	319					cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	CCGCCGCCCATCTGGTGAGGG	0.672																																					p.D362G		Atlas-SNP	.											.	FDXR	68	.	0			c.A1085G						.						22.0	27.0	25.0					17																	72860316		2199	4293	6492	SO:0001583	missense	2232	exon9			CGCCCATCTGGTG	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"""adrenodoxin-NADP(+) reductase"", ""adrenodoxin reductase"""	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.956A>G	chr17.hg19:g.72860316T>C	ENSP00000293195:p.Asp319Gly	54.0	0.0		93.0	7.0	NM_001258012	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Missense_Mutation	SNP	ENST00000293195.5	hg19	CCDS58593.1	.	.	.	.	.	.	.	.	.	.	T	15.54	2.864812	0.51482	.	.	ENSG00000161513	ENST00000420580;ENST00000544854;ENST00000293195;ENST00000455107;ENST00000442102;ENST00000413947	T;T;T;T;T	0.26067	1.76;2.72;2.72;2.72;2.72	4.58	4.58	0.56647	.	0.100098	0.64402	D	0.000003	T	0.26593	0.0650	L	0.41236	1.265	0.80722	D	1	B;B;B;B;B;B;B;B;B;B	0.24651	0.043;0.108;0.001;0.012;0.0;0.001;0.0;0.012;0.0;0.006	B;B;B;B;B;B;B;B;B;B	0.33799	0.025;0.17;0.006;0.032;0.002;0.005;0.007;0.032;0.007;0.019	T	0.08289	-1.0729	10	0.52906	T	0.07	-6.4927	13.6354	0.62219	0.0:0.0:0.0:1.0	.	279;362;350;317;267;350;319;311;319;325	B4DQQ4;B4DHX5;E7EQC1;B4DDI9;B7Z7G2;B4DDI7;Q6GSK2;B4DX24;P22570;P22570-2	.;.;.;.;.;.;.;.;ADRO_HUMAN;.	G	279;267;325;275;362;350	ENSP00000414172:D279G;ENSP00000445432:D267G;ENSP00000390875:D275G;ENSP00000416515:D362G;ENSP00000408595:D350G	ENSP00000293195:D325G	D	-	2	0	FDXR	70371911	0.569000	0.26643	0.742000	0.31022	0.940000	0.58332	2.017000	0.40981	1.713000	0.51359	0.459000	0.35465	GAT	.	.		0.672	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110	
TNRC6C	57690	hgsc.bcm.edu	37	17	76075517	76075517	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:76075517A>G	ENST00000588061.1	+	12	3979	c.3252A>G	c.(3250-3252)gcA>gcG	p.A1084A	TNRC6C_ENST00000335749.4_Silent_p.A1081A|TNRC6C_ENST00000588847.1_Silent_p.A1081A|TNRC6C_ENST00000301624.4_Silent_p.A1084A|TNRC6C_ENST00000544502.1_Silent_p.A1081A|TNRC6C_ENST00000541771.1_Silent_p.A1084A			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	1084					embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|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)|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 gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			ATAGTGGAGCAGCACAAGCCA	0.527																																					p.A1084A		Atlas-SNP	.											.	TNRC6C	173	.	0			c.A3252G						.						99.0	108.0	105.0					17																	76075517		2153	4260	6413	SO:0001819	synonymous_variant	57690	exon11			TGGAGCAGCACAA	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"""Trinucleotide (CAG) repeat containing"""	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.3252A>G	chr17.hg19:g.76075517A>G		88.0	0.0		149.0	6.0	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Silent	SNP	ENST00000588061.1	hg19	CCDS45798.1																																																																																			.	.		0.527	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996	
USP36	57602	hgsc.bcm.edu	37	17	76799861	76799861	+	Missense_Mutation	SNP	G	G	C	rs537129179		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:76799861G>C	ENST00000542802.3	-	16	2859	c.2416C>G	c.(2416-2418)Cag>Gag	p.Q806E	USP36_ENST00000312010.6_Missense_Mutation_p.Q806E|USP36_ENST00000449938.2_Intron			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	806			Q -> R (in dbSNP:rs3088040). {ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			GAGGGGCTCTGGGGGGGCTCA	0.632																																					p.Q806E		Atlas-SNP	.											.,2	USP36	243	.	0			c.C2416G						.						38.0	46.0	43.0					17																	76799861		2167	4248	6415	SO:0001583	missense	57602	exon16			GGCTCTGGGGGGG	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"""Ubiquitin-specific peptidases"""	20062	protein-coding gene	gene with protein product		612543	"""ubiquitin specific protease 36"""			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.2416C>G	chr17.hg19:g.76799861G>C	ENSP00000441214:p.Gln806Glu	52.0	0.0		80.0	0.0	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Missense_Mutation	SNP	ENST00000542802.3	hg19	CCDS32755.1	.	.	.	.	.	.	.	.	.	.	G	3.509	-0.100119	0.07010	.	.	ENSG00000055483	ENST00000312010;ENST00000542802	T;T	0.06449	3.3;3.3	5.42	1.16	0.20824	.	2.568530	0.00751	N	0.001065	T	0.06096	0.0158	L	0.44542	1.39	0.09310	N	0.999999	B;B	0.14438	0.006;0.01	B;B	0.15870	0.006;0.014	T	0.42172	-0.9467	10	0.02654	T	1	0.0129	5.3078	0.15813	0.2332:0.0:0.6269:0.1399	.	806;806	Q9P275;Q9P275-2	UBP36_HUMAN;.	E	806	ENSP00000310590:Q806E;ENSP00000441214:Q806E	ENSP00000310590:Q806E	Q	-	1	0	USP36	74311456	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.402000	0.20965	0.268000	0.21939	-0.137000	0.14449	CAG	.	.		0.632	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090	
CBX2	84733	hgsc.bcm.edu	37	17	77755868	77755868	+	Intron	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:77755868T>C	ENST00000310942.4	+	4	392				CBX2_ENST00000269399.5_Missense_Mutation_p.S186P	NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2						cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|development of primary sexual characteristics (GO:0045137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GGTGGCAGGGTCAAACTGCTG	0.647																																					p.S186P		Atlas-SNP	.											.	CBX2	50	.	0			c.T556C						.						39.0	44.0	42.0					17																	77755868		2203	4298	6501	SO:0001627	intron_variant	84733	exon4			GCAGGGTCAAACT	BC004252, BG354579	CCDS11764.1, CCDS32757.1	17q25.3	2010-07-06	2010-06-24		ENSG00000173894	ENSG00000173894			1552	protein-coding gene	gene with protein product	"""Pc class homolog (Drosophila)"""	602770	"""chromobox homolog 2 (Drosophila Pc class)"", ""cell division cycle associated 6"""	CDCA6		7782071, 2477932	Standard	NM_005189		Approved	MGC10561	uc002jxc.3	Q14781		ENST00000310942.4:c.288+268T>C	chr17.hg19:g.77755868T>C		72.0	0.0		131.0	6.0	NM_032647	Q0VDA5|Q9BTB1	Missense_Mutation	SNP	ENST00000310942.4	hg19	CCDS32757.1	.	.	.	.	.	.	.	.	.	.	T	13.59	2.281458	0.40394	.	.	ENSG00000173894	ENST00000269399	.	.	.	3.0	-1.23	0.09465	.	.	.	.	.	T	0.21962	0.0529	.	.	.	0.09310	N	1	B	0.14438	0.01	B	0.13407	0.009	T	0.22977	-1.0201	6	.	.	.	.	4.8624	0.13590	0.0:0.1508:0.554:0.2952	.	186	Q14781-2	.	P	186	.	.	S	+	1	0	CBX2	75370463	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.195000	0.09546	-0.051000	0.13334	0.454000	0.30748	TCA	.	.		0.647	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
CBX4	8535	hgsc.bcm.edu	37	17	77812826	77812826	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:77812826T>C	ENST00000269397.4	-	2	274	c.97A>G	c.(97-99)Aga>Gga	p.R33G	CBX4_ENST00000448310.1_Missense_Mutation_p.R33G	NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	33	Chromo. {ECO:0000255|PROSITE- ProRule:PRU00053}.|Interaction with BMI1.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GACCAGCCTCTCCATTTCACC	0.751																																					p.R33G		Atlas-SNP	.											.	CBX4	40	.	0			c.A97G						.						13.0	12.0	12.0					17																	77812826		2137	4199	6336	SO:0001583	missense	8535	exon2			AGCCTCTCCATTT	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"""NS5ATP1-binding protein 16"", ""Pc class 2 homolog (Drosophila)"""	603079	"""chromobox homolog 4 (Drosophila Pc class)"""			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.97A>G	chr17.hg19:g.77812826T>C	ENSP00000269397:p.Arg33Gly	54.0	0.0		91.0	5.0	NM_003655	B1PJR7|Q6TPI8|Q96C04	Missense_Mutation	SNP	ENST00000269397.4	hg19	CCDS32758.1	.	.	.	.	.	.	.	.	.	.	T	7.386	0.629745	0.14257	.	.	ENSG00000141582	ENST00000269397;ENST00000343048	T	0.73469	-0.75	2.41	-0.374	0.12512	Chromo domain (1);Chromo domain subgroup (1);Chromo domain-like (1);Chromo domain/shadow (2);Chromo domain, conserved site (1);	0.075581	0.49305	U	0.000152	T	0.70710	0.3255	M	0.85041	2.73	0.41740	D	0.989608	B	0.09022	0.002	B	0.12837	0.008	T	0.63967	-0.6517	10	0.87932	D	0	-40.4506	5.0543	0.14524	0.0:0.1178:0.1823:0.6999	.	33	O00257	CBX4_HUMAN	G	33	ENSP00000269397:R33G	ENSP00000269397:R33G	R	-	1	2	CBX4	75427421	1.000000	0.71417	0.988000	0.46212	0.149000	0.21700	1.228000	0.32588	-0.020000	0.14032	0.358000	0.22013	AGA	.	.		0.751	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655	
AATK	9625	hgsc.bcm.edu	37	17	79094085	79094085	+	Silent	SNP	C	C	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:79094085C>G	ENST00000326724.4	-	11	3675	c.3651G>C	c.(3649-3651)ctG>ctC	p.L1217L	AATK_ENST00000417379.1_Silent_p.L1114L	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1217					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			AGGTCTCGGACAGCAGGCTGG	0.667																																					p.L1217L		Atlas-SNP	.											.	AATK	102	.	0			c.G3651C						.						26.0	31.0	30.0					17																	79094085		2147	4235	6382	SO:0001819	synonymous_variant	9625	exon11			CTCGGACAGCAGG	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"""lemur tyrosine kinase 1"", ""protein phosphatase 1, regulatory subunit 77"""	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.3651G>C	chr17.hg19:g.79094085C>G		105.0	0.0		173.0	39.0	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	hg19	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	C	8.746	0.920116	0.17982	.	.	ENSG00000181409	ENST00000417379	.	.	.	3.98	2.9	0.33743	.	.	.	.	.	T	0.56381	0.1981	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50792	-0.8786	4	.	.	.	.	7.9182	0.29831	0.0:0.5191:0.3869:0.094	.	.	.	.	S	1170	.	.	C	-	2	0	AATK	76708680	0.013000	0.17824	0.991000	0.47740	0.832000	0.47134	-0.192000	0.09587	0.843000	0.35070	0.313000	0.20887	TGT	.	.		0.667	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920	
DUS1L	64118	hgsc.bcm.edu	37	17	80020818	80020818	+	Silent	SNP	A	A	G	rs372985546		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:80020818A>G	ENST00000354321.7	-	4	914	c.429T>C	c.(427-429)ccT>ccC	p.P143P	DUS1L_ENST00000306796.5_Silent_p.P143P			Q6P1R4	DUS1L_HUMAN	dihydrouridine synthase 1-like (S. cerevisiae)	143							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	6	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)			TGCACGTGACAGGAACAGAGA	0.612																																					p.P143P		Atlas-SNP	.											.	DUS1L	25	.	0			c.T429C						.						60.0	59.0	59.0					17																	80020818		2202	4300	6502	SO:0001819	synonymous_variant	64118	exon5			CGTGACAGGAACA		CCDS32775.1	17q25.3	2005-08-09				ENSG00000169718			30086	protein-coding gene	gene with protein product						12477932	Standard	NM_022156		Approved	PP3111, DUS1	uc002kdr.4	Q6P1R4		ENST00000354321.7:c.429T>C	chr17.hg19:g.80020818A>G		47.0	0.0		55.0	4.0	NM_022156	A6NHV4|Q96AI3	Silent	SNP	ENST00000354321.7	hg19	CCDS32775.1																																																																																			.	.		0.612	DUS1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442347.1	NM_022156	
SMCHD1	23347	hgsc.bcm.edu	37	18	2750117	2750117	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:2750117C>A	ENST00000320876.6	+	31	4342	c.4004C>A	c.(4003-4005)cCt>cAt	p.P1335H	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.P1335H	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1335					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						GTTTTTGCCCCTAGGTAAGAA	0.368																																					p.P1335H		Atlas-SNP	.											.	SMCHD1	88	.	0			c.C4004A						.						121.0	108.0	112.0					18																	2750117		1839	4087	5926	SO:0001583	missense	23347	exon31			TTGCCCCTAGGTA	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.4004C>A	chr18.hg19:g.2750117C>A	ENSP00000326603:p.Pro1335His	106.0	0.0		94.0	23.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	C	15.77	2.932066	0.52866	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.28454	1.61;1.62	5.96	5.96	0.96718	.	0.052669	0.85682	D	0.000000	T	0.52484	0.1737	M	0.67953	2.075	0.43133	D	0.994877	D	0.76494	0.999	P	0.60173	0.87	T	0.51942	-0.8641	10	0.72032	D	0.01	-7.2361	18.1738	0.89754	0.0:1.0:0.0:0.0	.	1335	A6NHR9	SMHD1_HUMAN	H	1335	ENSP00000326603:P1335H;ENSP00000261598:P1335H	ENSP00000261598:P1335H	P	+	2	0	SMCHD1	2740117	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.754000	0.62191	2.826000	0.97356	0.655000	0.94253	CCT	.	.		0.368	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
MYOM1	8736	hgsc.bcm.edu	37	18	3151804	3151804	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:3151804A>G	ENST00000356443.4	-	12	2064	c.1731T>C	c.(1729-1731)ggT>ggC	p.G577G	MYOM1_ENST00000400569.3_Silent_p.G577G|MYOM1_ENST00000261606.7_Silent_p.G577G	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	577	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TATAGGAACGACCTTCGATCA	0.502											OREG0024839	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G577G		Atlas-SNP	.											.	MYOM1	192	.	0			c.T1731C						.						94.0	92.0	93.0					18																	3151804		1923	4144	6067	SO:0001819	synonymous_variant	8736	exon12			GGAACGACCTTCG	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.1731T>C	chr18.hg19:g.3151804A>G		91.0	0.0	609	98.0	4.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	hg19	CCDS45824.1																																																																																			.	.		0.502	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
ZBTB14	7541	hgsc.bcm.edu	37	18	5291325	5291325	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:5291325C>A	ENST00000357006.4	-	4	1220	c.882G>T	c.(880-882)aaG>aaT	p.K294N	ZBTB14_ENST00000400143.3_Missense_Mutation_p.K294N	NM_001143823.2|NM_001243704.1	NP_001137295.1|NP_001230633.1	O43829	ZBT14_HUMAN	zinc finger and BTB domain containing 14	294					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)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)										GTTTCTCATGCTTCCTCAATC	0.478																																					p.K294N		Atlas-SNP	.											.	.	.	.	0			c.G882T						.						98.0	89.0	92.0					18																	5291325		2203	4300	6503	SO:0001583	missense	7541	exon4			CTCATGCTTCCTC	D89859	CCDS11837.1	18p11.31	2013-09-19	2013-01-08	2013-01-08	ENSG00000198081	ENSG00000198081		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12860	protein-coding gene	gene with protein product		602126	"""zinc finger protein 161 homolog (mouse)"", ""zinc finger protein 161"", ""ZFP161 zinc finger protein"""	ZFP161		9244432	Standard	NM_001243702		Approved	ZNF478	uc010dkp.3	O43829	OTTHUMG00000131563	ENST00000357006.4:c.882G>T	chr18.hg19:g.5291325C>A	ENSP00000349503:p.Lys294Asn	115.0	0.0		122.0	43.0	NM_001243702	O00403|Q2TB80	Missense_Mutation	SNP	ENST00000357006.4	hg19	CCDS11837.1	.	.	.	.	.	.	.	.	.	.	C	9.860	1.195990	0.22037	.	.	ENSG00000198081	ENST00000357006;ENST00000400143	T;T	0.20598	2.06;2.06	5.8	3.05	0.35203	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.103499	0.64402	D	0.000006	T	0.18509	0.0444	L	0.33668	1.02	0.54753	D	0.999989	D	0.57257	0.979	P	0.48368	0.575	T	0.02031	-1.1226	10	0.33940	T	0.23	-20.0419	7.9098	0.29785	0.0:0.5701:0.0:0.4299	.	294	O43829	ZF161_HUMAN	N	294	ENSP00000349503:K294N;ENSP00000383009:K294N	ENSP00000349503:K294N	K	-	3	2	ZFP161	5281325	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	0.666000	0.25097	0.361000	0.24292	0.650000	0.86243	AAG	.	.		0.478	ZBTB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254425.1	NM_003409	
CEP76	79959	hgsc.bcm.edu	37	18	12673464	12673464	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:12673464T>C	ENST00000262127.2	-	12	2105	c.1880A>G	c.(1879-1881)gAc>gGc	p.D627G	PSMG2_ENST00000589405.1_Intron|RP11-973H7.3_ENST00000585877.1_RNA|CEP76_ENST00000423709.2_Missense_Mutation_p.D552G|PSMG2_ENST00000585331.2_Intron	NM_024899.2	NP_079175.2	Q8TAP6	CEP76_HUMAN	centrosomal protein 76kDa	627					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TCGCACTTGGTCTCCACGGCA	0.363																																					p.D627G		Atlas-SNP	.											.	CEP76	45	.	0			c.A1880G						.						102.0	101.0	102.0					18																	12673464		2203	4300	6503	SO:0001583	missense	79959	exon12			ACTTGGTCTCCAC	BC026307	CCDS11861.1, CCDS62390.1	18p11.21	2014-02-20	2005-12-01	2005-12-01	ENSG00000101624	ENSG00000101624			25727	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 9"""	C18orf9		14654843	Standard	NM_024899		Approved	HsT1705, FLJ12542	uc002kri.4	Q8TAP6	OTTHUMG00000131701	ENST00000262127.2:c.1880A>G	chr18.hg19:g.12673464T>C	ENSP00000262127:p.Asp627Gly	126.0	0.0		150.0	6.0	NM_024899	B0YJB2|B4DXG5|B4DZW1|Q658N5|Q9H9U7	Missense_Mutation	SNP	ENST00000262127.2	hg19	CCDS11861.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.656210	0.88056	.	.	ENSG00000101624	ENST00000262127;ENST00000423709	T;T	0.35048	1.33;1.33	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.55955	0.1953	L	0.60845	1.875	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.989	T	0.51268	-0.8727	10	0.33141	T	0.24	-3.0266	16.1307	0.81436	0.0:0.0:0.0:1.0	.	552;627	Q8TAP6-2;Q8TAP6	.;CEP76_HUMAN	G	627;552	ENSP00000262127:D627G;ENSP00000403074:D552G	ENSP00000262127:D627G	D	-	2	0	CEP76	12663464	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.263000	0.75096	0.533000	0.62120	GAC	.	.		0.363	CEP76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254611.1	NM_024899	
LAMA3	3909	hgsc.bcm.edu	37	18	21494402	21494402	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:21494402T>C	ENST00000313654.9	+	57	7599	c.7358T>C	c.(7357-7359)gTt>gCt	p.V2453A	LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Missense_Mutation_p.V844A|LAMA3_ENST00000587184.1_Missense_Mutation_p.V788A|LAMA3_ENST00000399516.3_Missense_Mutation_p.V2397A	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2453	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GGCATGGCAGTTGTGGATGGC	0.542																																					p.V2453A		Atlas-SNP	.											.	LAMA3	397	.	0			c.T7358C						.						83.0	77.0	79.0					18																	21494402		2203	4300	6503	SO:0001583	missense	3909	exon57			TGGCAGTTGTGGA	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.7358T>C	chr18.hg19:g.21494402T>C	ENSP00000324532:p.Val2453Ala	63.0	0.0		65.0	4.0	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	T	15.50	2.852232	0.51270	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.75821	-0.97;-0.97;-0.97	5.25	5.25	0.73442	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.82346	0.5017	M	0.77820	2.39	0.23371	N	0.997819	B;P;P;P	0.49185	0.309;0.549;0.866;0.92	B;B;P;P	0.51657	0.197;0.32;0.676;0.578	T	0.76556	-0.2916	9	0.72032	D	0.01	.	15.1529	0.72717	0.0:0.0:0.0:1.0	.	788;844;2397;2453	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	A	2453;2397;844	ENSP00000324532:V2453A;ENSP00000382432:V2397A;ENSP00000269217:V844A	ENSP00000269217:V844A	V	+	2	0	LAMA3	19748400	0.965000	0.33210	0.009000	0.14445	0.147000	0.21601	6.957000	0.76019	1.977000	0.57605	0.459000	0.35465	GTT	.	.		0.542	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
LAMA3	3909	hgsc.bcm.edu	37	18	21494698	21494698	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:21494698A>G	ENST00000313654.9	+	58	7759	c.7518A>G	c.(7516-7518)ggA>ggG	p.G2506G	LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Silent_p.G897G|LAMA3_ENST00000587184.1_Silent_p.G841G|LAMA3_ENST00000399516.3_Silent_p.G2450G	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2506	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					ACACCAAAGGAGCCACATCCA	0.328																																					p.G2506G		Atlas-SNP	.											.	LAMA3	397	.	0			c.A7518G						.						60.0	60.0	60.0					18																	21494698		2203	4300	6503	SO:0001819	synonymous_variant	3909	exon58			CAAAGGAGCCACA	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.7518A>G	chr18.hg19:g.21494698A>G		109.0	0.0		113.0	5.0	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.		0.328	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
DSG2	1829	hgsc.bcm.edu	37	18	29125991	29125991	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:29125991C>T	ENST00000261590.8	+	15	2851	c.2642C>T	c.(2641-2643)aCc>aTc	p.T881I	RP11-75N4.2_ENST00000583706.1_RNA	NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	881					apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			TCAGAGAATACCTACTCCTCT	0.403																																					p.T881I		Atlas-SNP	.											.	DSG2	115	.	0			c.C2642T						.						70.0	68.0	69.0					18																	29125991		1870	4100	5970	SO:0001583	missense	1829	exon15			AGAATACCTACTC	Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"""Cadherins / Major cadherins"""	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.2642C>T	chr18.hg19:g.29125991C>T	ENSP00000261590:p.Thr881Ile	65.0	0.0		79.0	4.0	NM_001943	Q4KKU6	Missense_Mutation	SNP	ENST00000261590.8	hg19	CCDS42423.1	.	.	.	.	.	.	.	.	.	.	C	8.610	0.888861	0.17540	.	.	ENSG00000046604	ENST00000261590	T	0.59906	0.23	5.63	3.82	0.43975	.	0.971478	0.08457	N	0.943034	T	0.47820	0.1466	L	0.36672	1.1	0.24752	N	0.992975	P	0.42785	0.79	B	0.36719	0.231	T	0.31943	-0.9925	10	0.59425	D	0.04	.	10.6835	0.45828	0.0:0.7952:0.1331:0.0717	.	881	Q14126	DSG2_HUMAN	I	881	ENSP00000261590:T881I	ENSP00000261590:T881I	T	+	2	0	DSG2	27379989	0.001000	0.12720	0.000000	0.03702	0.034000	0.12701	0.662000	0.25038	0.705000	0.31890	0.591000	0.81541	ACC	.	.		0.403	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943	
ASXL3	80816	hgsc.bcm.edu	37	18	31320093	31320093	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:31320093T>C	ENST00000269197.5	+	11	2725	c.2725T>C	c.(2725-2727)Tca>Cca	p.S909P		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	909					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(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						GCAATATATCTCATCAGTGGA	0.393																																					p.S909P		Atlas-SNP	.											.	ASXL3	405	.	0			c.T2725C						.						89.0	85.0	86.0					18																	31320093		1860	4098	5958	SO:0001583	missense	80816	exon11			TATATCTCATCAG	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.2725T>C	chr18.hg19:g.31320093T>C	ENSP00000269197:p.Ser909Pro	108.0	0.0		100.0	4.0	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	T	0.159	-1.083017	0.01888	.	.	ENSG00000141431	ENST00000269197	T	0.15487	2.42	5.86	2.29	0.28610	.	1.176010	0.06075	N	0.660859	T	0.10165	0.0249	N	0.17082	0.46	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39418	-0.9615	10	0.21540	T	0.41	.	4.3564	0.11181	0.1347:0.2186:0.0:0.6467	.	909	Q9C0F0	ASXL3_HUMAN	P	909	ENSP00000269197:S909P	ENSP00000269197:S909P	S	+	1	0	ASXL3	29574091	0.083000	0.21467	0.001000	0.08648	0.039000	0.13416	0.095000	0.15127	0.168000	0.19655	0.533000	0.62120	TCA	.	.		0.393	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
EPG5	57724	hgsc.bcm.edu	37	18	43532416	43532416	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:43532416A>G	ENST00000282041.5	-	3	1236	c.1202T>C	c.(1201-1203)cTc>cCc	p.L401P		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	401					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TGAACTACTGAGCAATGCATA	0.423																																					p.L401P		Atlas-SNP	.											.	EPG5	199	.	0			c.T1202C						.						106.0	102.0	103.0					18																	43532416		1934	4137	6071	SO:0001583	missense	57724	exon3			CTACTGAGCAATG	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.1202T>C	chr18.hg19:g.43532416A>G	ENSP00000282041:p.Leu401Pro	91.0	0.0		100.0	4.0	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	hg19	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	A	18.28	3.588365	0.66105	.	.	ENSG00000152223	ENST00000282041	T	0.80994	-1.44	5.38	5.38	0.77491	.	0.556823	0.18742	N	0.132439	D	0.87517	0.6197	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.68483	0.958;0.958	D	0.88122	0.2832	10	0.66056	D	0.02	-8.0382	15.6912	0.77453	1.0:0.0:0.0:0.0	.	401;401	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	P	401	ENSP00000282041:L401P	ENSP00000282041:L401P	L	-	2	0	EPG5	41786414	1.000000	0.71417	0.784000	0.31847	0.520000	0.34377	8.473000	0.90410	2.170000	0.68504	0.460000	0.39030	CTC	.	.		0.423	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
DCC	1630	hgsc.bcm.edu	37	18	50278698	50278698	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:50278698A>G	ENST00000442544.2	+	2	982	c.366A>G	c.(364-366)ggA>ggG	p.G122G	DCC_ENST00000412726.1_5'UTR	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	122	Ig-like C2-type 1.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CATCTTTAGGAGATTCTGGCT	0.443																																					p.G122G		Atlas-SNP	.											.	DCC	360	.	0			c.A366G						.						128.0	119.0	122.0					18																	50278698		2203	4300	6503	SO:0001819	synonymous_variant	1630	exon2			TTTAGGAGATTCT	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.366A>G	chr18.hg19:g.50278698A>G		146.0	0.0		163.0	7.0	NM_005215		Silent	SNP	ENST00000442544.2	hg19	CCDS11952.1																																																																																			.	.		0.443	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
POLI	11201	hgsc.bcm.edu	37	18	51807238	51807238	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:51807238T>C	ENST00000579534.1	+	5	904	c.761T>C	c.(760-762)cTt>cCt	p.L254P	POLI_ENST00000217800.5_Missense_Mutation_p.L128P|POLI_ENST00000406285.3_Intron|POLI_ENST00000579434.1_Missense_Mutation_p.L151P	NM_007195.2	NP_009126.2	Q9UNA4	POLI_HUMAN	polymerase (DNA directed) iota	254	UmuC. {ECO:0000255|PROSITE- ProRule:PRU00216}.				DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)	intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(5)|ovary(3)|urinary_tract(1)	26				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		TGTCAACATCTTATTCATAGT	0.279								DNA polymerases (catalytic subunits)																													p.L254P		Atlas-SNP	.											.	POLI	132	.	0			c.T761C						.						58.0	61.0	60.0					18																	51807238		2203	4300	6503	SO:0001583	missense	11201	exon5			AACATCTTATTCA		CCDS11954.2	18q21.1	2012-05-18			ENSG00000101751	ENSG00000101751		"""DNA polymerases"""	9182	protein-coding gene	gene with protein product		605252		RAD3OB, RAD30B		17609217	Standard	NM_007195		Approved		uc002lfj.4	Q9UNA4	OTTHUMG00000132704	ENST00000579534.1:c.761T>C	chr18.hg19:g.51807238T>C	ENSP00000462664:p.Leu254Pro	74.0	0.0		76.0	4.0	NM_007195	Q8N590|Q9H0S1|Q9NYH6	Missense_Mutation	SNP	ENST00000579534.1	hg19	CCDS11954.2	.	.	.	.	.	.	.	.	.	.	T	12.86	2.065191	0.36470	.	.	ENSG00000101751	ENST00000217800	.	.	.	5.72	5.72	0.89469	DNA-repair protein, UmuC-like, N-terminal (1);	0.123680	0.56097	D	0.000032	T	0.81800	0.4899	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85130	0.0974	9	0.72032	D	0.01	-6.7447	13.816	0.63292	0.0:0.0:0.0:1.0	.	254	Q9UNA4	POLI_HUMAN	P	254	.	ENSP00000217800:L254P	L	+	2	0	POLI	50061236	1.000000	0.71417	1.000000	0.80357	0.787000	0.44495	4.985000	0.63845	2.304000	0.77564	0.528000	0.53228	CTT	.	.		0.279	POLI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256002.3	NM_007195	
WDR7	23335	hgsc.bcm.edu	37	18	54547190	54547190	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:54547190T>C	ENST00000254442.3	+	21	3531	c.3320T>C	c.(3319-3321)gTc>gCc	p.V1107A	WDR7_ENST00000589935.1_Intron|WDR7_ENST00000357574.3_Missense_Mutation_p.V1074A	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	1107					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		TTATCAAGTGTCCCACAAATG	0.363																																					p.V1107A		Atlas-SNP	.											WDR7,colon,carcinoma,0,1	WDR7	166	.	0			c.T3320C						.						73.0	68.0	70.0					18																	54547190		2203	4300	6503	SO:0001583	missense	23335	exon21			CAAGTGTCCCACA	AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"""WD repeat domain containing"""	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.3320T>C	chr18.hg19:g.54547190T>C	ENSP00000254442:p.Val1107Ala	92.0	0.0		131.0	6.0	NM_015285	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Missense_Mutation	SNP	ENST00000254442.3	hg19	CCDS11962.1	.	.	.	.	.	.	.	.	.	.	T	4.589	0.109480	0.08780	.	.	ENSG00000091157	ENST00000254442;ENST00000357574;ENST00000444065;ENST00000398311	T;T	0.69926	-0.44;1.47	5.37	4.21	0.49690	.	0.358804	0.29508	N	0.011960	T	0.44498	0.1296	N	0.14661	0.345	0.30187	N	0.799835	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.32428	-0.9907	10	0.09084	T	0.74	.	10.8785	0.46925	0.0:0.0749:0.0:0.9251	.	1074;1107	Q9Y4E6-2;Q9Y4E6	.;WDR7_HUMAN	A	1107;1074;432;1074	ENSP00000254442:V1107A;ENSP00000350187:V1074A	ENSP00000254442:V1107A	V	+	2	0	WDR7	52698188	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	3.661000	0.54503	0.991000	0.38814	0.533000	0.62120	GTC	.	.		0.363	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1		
ST8SIA3	51046	hgsc.bcm.edu	37	18	55024466	55024466	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:55024466A>G	ENST00000324000.3	+	3	2659	c.625A>G	c.(625-627)Acc>Gcc	p.T209A		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	209					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		CAATCTTACCACCTTCAACCC	0.403																																					p.T209A		Atlas-SNP	.											.	ST8SIA3	73	.	0			c.A625G						.						66.0	68.0	67.0					18																	55024466		2203	4300	6503	SO:0001583	missense	51046	exon3			CTTACCACCTTCA	AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"""Sialyltransferases"""	14269	protein-coding gene	gene with protein product	"""ST8Sia III"""	609478	"""sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"""	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.625A>G	chr18.hg19:g.55024466A>G	ENSP00000320431:p.Thr209Ala	69.0	0.0		92.0	4.0	NM_015879	A8K0F2|Q6B085|Q9NS41	Missense_Mutation	SNP	ENST00000324000.3	hg19	CCDS32834.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.147013	0.77888	.	.	ENSG00000177511	ENST00000541833;ENST00000324000	T	0.32988	1.43	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.63117	0.2484	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.70799	-0.4774	10	0.87932	D	0	-10.9553	15.897	0.79341	1.0:0.0:0.0:0.0	.	209	O43173	SIA8C_HUMAN	A	316;209	ENSP00000320431:T209A	ENSP00000320431:T209A	T	+	1	0	ST8SIA3	53175464	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.936000	0.92931	2.238000	0.73509	0.533000	0.62120	ACC	.	.		0.403	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879	
ST8SIA3	51046	hgsc.bcm.edu	37	18	55027237	55027237	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:55027237A>G	ENST00000324000.3	+	4	2906	c.872A>G	c.(871-873)aAc>aGc	p.N291S		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	291					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		TACTGGAAAAACAAACATTTG	0.423																																					p.N291S		Atlas-SNP	.											.	ST8SIA3	73	.	0			c.A872G						.						85.0	81.0	82.0					18																	55027237		2203	4300	6503	SO:0001583	missense	51046	exon4			GGAAAAACAAACA	AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"""Sialyltransferases"""	14269	protein-coding gene	gene with protein product	"""ST8Sia III"""	609478	"""sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"""	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.872A>G	chr18.hg19:g.55027237A>G	ENSP00000320431:p.Asn291Ser	101.0	0.0		94.0	4.0	NM_015879	A8K0F2|Q6B085|Q9NS41	Missense_Mutation	SNP	ENST00000324000.3	hg19	CCDS32834.1	.	.	.	.	.	.	.	.	.	.	A	13.27	2.187544	0.38609	.	.	ENSG00000177511	ENST00000541833;ENST00000324000	T	0.28069	1.63	6.11	4.95	0.65309	.	0.084546	0.85682	N	0.000000	T	0.15609	0.0376	N	0.10809	0.05	0.48452	D	0.999657	B	0.26002	0.139	B	0.25506	0.061	T	0.06588	-1.0818	10	0.09843	T	0.71	-12.7948	11.8217	0.52242	0.9313:0.0:0.0687:0.0	.	291	O43173	SIA8C_HUMAN	S	398;291	ENSP00000320431:N291S	ENSP00000320431:N291S	N	+	2	0	ST8SIA3	53178235	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.683000	0.54663	1.125000	0.41998	0.533000	0.62120	AAC	.	.		0.423	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879	
ARID3A	1820	hgsc.bcm.edu	37	19	932477	932477	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:932477A>G	ENST00000263620.3	+	3	755	c.428A>G	c.(427-429)gAg>gGg	p.E143G		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	143	Acidic.|Glu-rich.					cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|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)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gaggaggaggaggaggaggat	0.652																																					p.E143G	Pancreas(29;54 1022 32760 50921)	Atlas-SNP	.											.	ARID3A	35	.	0			c.A428G						.						13.0	12.0	12.0					19																	932477		2185	4277	6462	SO:0001583	missense	1820	exon3			AGGAGGAGGAGGA	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"""-"""	3031	protein-coding gene	gene with protein product		603265	"""dead ringer-like 1 (Drosophila)"", ""AT rich interactive domain 3A (BRIGHT- like)"""	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.428A>G	chr19.hg19:g.932477A>G	ENSP00000263620:p.Glu143Gly	48.0	0.0		71.0	4.0	NM_005224	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Missense_Mutation	SNP	ENST00000263620.3	hg19	CCDS12050.1	.	.	.	.	.	.	.	.	.	.	A	14.27	2.484176	0.44147	.	.	ENSG00000116017	ENST00000263620	T	0.13307	2.6	3.66	3.66	0.41972	.	0.324761	0.26159	N	0.025998	T	0.09686	0.0238	L	0.29908	0.895	0.36972	D	0.893854	P	0.34522	0.455	B	0.31614	0.133	T	0.29518	-1.0009	10	0.30854	T	0.27	.	11.2668	0.49114	1.0:0.0:0.0:0.0	.	143	Q99856	ARI3A_HUMAN	G	143	ENSP00000263620:E143G	ENSP00000263620:E143G	E	+	2	0	ARID3A	883477	0.996000	0.38824	0.184000	0.23157	0.675000	0.39556	3.832000	0.55783	1.527000	0.49086	0.375000	0.23000	GAG	.	.		0.652	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224	
MKNK2	2872	hgsc.bcm.edu	37	19	2041918	2041918	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:2041918A>G	ENST00000591601.1	-	10	901	c.866T>C	c.(865-867)cTc>cCc	p.L289P	MKNK2_ENST00000250896.3_Missense_Mutation_p.L289P|MKNK2_ENST00000591142.1_Missense_Mutation_p.L33P|MKNK2_ENST00000588014.1_Missense_Mutation_p.L33P|MKNK2_ENST00000309340.7_Missense_Mutation_p.L289P|MKNK2_ENST00000541165.1_Missense_Mutation_p.L158P|MKNK2_ENST00000591588.1_Missense_Mutation_p.L33P			Q9HBH9	MKNK2_HUMAN	MAP kinase interacting serine/threonine kinase 2	289	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|cellular response to arsenic-containing substance (GO:0071243)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|hemopoiesis (GO:0030097)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(3)|large_intestine(3)|lung(3)	10		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTAGCCGCTGAGTAGGATATA	0.687																																					p.L289P		Atlas-SNP	.											.	MKNK2	56	.	0			c.T866C						.						26.0	22.0	23.0					19																	2041918		2129	4174	6303	SO:0001583	missense	2872	exon11			CCGCTGAGTAGGA	AF125532	CCDS12079.1, CCDS12080.1	19p13.3	2012-12-20			ENSG00000099875	ENSG00000099875			7111	protein-coding gene	gene with protein product	"""Putative map kinase interacting kinase"""	605069	"""G protein-coupled receptor kinase 7"""	GPRK7		11013076	Standard	NM_199054		Approved	MNK2	uc002lus.2	Q9HBH9	OTTHUMG00000180020	ENST00000591601.1:c.866T>C	chr19.hg19:g.2041918A>G	ENSP00000467811:p.Leu289Pro	71.0	0.0		54.0	4.0	NM_017572	Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6	Missense_Mutation	SNP	ENST00000591601.1	hg19	CCDS12080.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.150244	0.57151	.	.	ENSG00000099875	ENST00000309340;ENST00000250896;ENST00000541165;ENST00000545627	T;T;T	0.53206	0.63;0.63;0.63	4.08	4.08	0.47627	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000003	T	0.79470	0.4451	H	0.98487	4.245	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.998;0.999	D	0.86533	0.1823	10	0.87932	D	0	-9.2055	12.3786	0.55293	1.0:0.0:0.0:0.0	.	94;289;289;191	Q59GN5;Q9HBH9;Q9HBH9-2;Q9NT28	.;MKNK2_HUMAN;.;.	P	289;289;158;229	ENSP00000309485:L289P;ENSP00000250896:L289P;ENSP00000438904:L158P	ENSP00000250896:L289P	L	-	2	0	MKNK2	1992918	1.000000	0.71417	1.000000	0.80357	0.116000	0.19942	8.803000	0.91915	1.712000	0.51347	0.454000	0.30748	CTC	.	.		0.687	MKNK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449312.1	NM_199054	
AP3D1	8943	hgsc.bcm.edu	37	19	2123875	2123875	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:2123875A>G	ENST00000345016.5	-	10	1091	c.860T>C	c.(859-861)cTc>cCc	p.L287P	AP3D1_ENST00000355272.6_Missense_Mutation_p.L287P|AP3D1_ENST00000350812.6_Missense_Mutation_p.L118P|AP3D1_ENST00000590683.1_5'UTR|AP3D1_ENST00000356926.4_Missense_Mutation_p.L196P	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	287					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCGAGATGAGCACTGCAAC	0.687																																					p.L287P		Atlas-SNP	.											.	AP3D1	81	.	0			c.T860C						.						90.0	101.0	97.0					19																	2123875		2192	4285	6477	SO:0001583	missense	8943	exon10			GAGATGAGCACTG	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.860T>C	chr19.hg19:g.2123875A>G	ENSP00000344055:p.Leu287Pro	136.0	0.0		147.0	8.0	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Missense_Mutation	SNP	ENST00000345016.5	hg19	CCDS42459.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.673405	0.88445	.	.	ENSG00000065000	ENST00000356926;ENST00000345016;ENST00000355272;ENST00000343722;ENST00000350812	T;T;T;T	0.24538	1.85;1.85;1.85;1.85	5.07	5.07	0.68467	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000001	T	0.47619	0.1455	M	0.63208	1.945	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.43507	-0.9387	10	0.48119	T	0.1	-38.2157	13.9963	0.64405	1.0:0.0:0.0:0.0	.	287;287;196	O14617-5;O14617;G5E988	.;AP3D1_HUMAN;.	P	196;287;287;287;118	ENSP00000349398:L196P;ENSP00000344055:L287P;ENSP00000347416:L287P;ENSP00000342321:L118P	ENSP00000341579:L287P	L	-	2	0	AP3D1	2074875	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	8.755000	0.91646	1.909000	0.55274	0.460000	0.39030	CTC	.	.		0.687	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1		
JSRP1	126306	hgsc.bcm.edu	37	19	2254202	2254202	+	Silent	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:2254202C>T	ENST00000300961.6	-	4	310	c.246G>A	c.(244-246)agG>agA	p.R82R	JSRP1_ENST00000586471.2_Silent_p.R82R	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	82					protein localization to membrane (GO:0072657)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|skeletal muscle contraction (GO:0003009)	membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|pancreas(1)|urinary_tract(1)	6				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGCTTTCAGCCTCTCCTTCC	0.637											OREG0025137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R82R		Atlas-SNP	.											.	JSRP1	18	.	0			c.G246A						.						133.0	132.0	132.0					19																	2254202		2203	4300	6503	SO:0001819	synonymous_variant	126306	exon4			TTTCAGCCTCTCC	AK056978	CCDS12086.1	19p13.3	2010-03-23			ENSG00000167476	ENSG00000167476			24963	protein-coding gene	gene with protein product	"""homolog of mouse skeletal muscle sarcoplasmic reticulum protein JP-45"""	608743				12871958	Standard	NM_144616		Approved	JP-45, FLJ32416	uc002lvj.2	Q96MG2		ENST00000300961.6:c.246G>A	chr19.hg19:g.2254202C>T		72.0	0.0	602	89.0	4.0	NM_144616		Silent	SNP	ENST00000300961.6	hg19	CCDS12086.1																																																																																			.	.		0.637	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616	
ZNF556	80032	hgsc.bcm.edu	37	19	2877368	2877368	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:2877368A>G	ENST00000307635.2	+	4	499	c.412A>G	c.(412-414)Aag>Gag	p.K138E	ZNF556_ENST00000586426.1_Missense_Mutation_p.K137E	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	138					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(7)|lung(10)|pancreas(1)|prostate(3)|skin(7)	31				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCATCTGCGCAAGAATTGTTG	0.433																																					p.K138E		Atlas-SNP	.											.	ZNF556	73	.	0			c.A412G						.						131.0	114.0	120.0					19																	2877368		2203	4300	6503	SO:0001583	missense	80032	exon4			CTGCGCAAGAATT	BC009374	CCDS12097.1, CCDS74254.1	19p13.3	2013-09-20			ENSG00000172000	ENSG00000172000		"""Zinc fingers, C2H2-type"", ""-"""	25669	protein-coding gene	gene with protein product						12477932	Standard	XM_005259647		Approved	FLJ11637	uc002lwp.1	Q9HAH1	OTTHUMG00000180501	ENST00000307635.2:c.412A>G	chr19.hg19:g.2877368A>G	ENSP00000302603:p.Lys138Glu	119.0	0.0		95.0	4.0	NM_024967	Q96GM3	Missense_Mutation	SNP	ENST00000307635.2	hg19	CCDS12097.1	.	.	.	.	.	.	.	.	.	.	A	4.609	0.113209	0.08831	.	.	ENSG00000172000	ENST00000307635	T	0.05855	3.38	1.95	0.854	0.19007	.	.	.	.	.	T	0.03695	0.0105	N	0.16708	0.43	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.43228	-0.9404	9	0.62326	D	0.03	.	1.8371	0.03142	0.5443:0.0:0.1805:0.2752	.	138	Q9HAH1	ZN556_HUMAN	E	138	ENSP00000302603:K138E	ENSP00000302603:K138E	K	+	1	0	ZNF556	2828368	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	0.208000	0.17415	0.058000	0.16222	0.334000	0.21626	AAG	.	.		0.433	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967	
SMARCA4	6597	hgsc.bcm.edu	37	19	11150224	11150224	+	Intron	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:11150224T>C	ENST00000429416.3	+	31	4451				SMARCA4_ENST00000413806.3_Intron|SMARCA4_ENST00000538456.3_3'UTR|SMARCA4_ENST00000590574.1_Intron|SMARCA4_ENST00000589677.1_Intron|SMARCA4_ENST00000541122.2_Intron|SMARCA4_ENST00000358026.2_Missense_Mutation_p.S1421P|SMARCA4_ENST00000344626.4_Intron|SMARCA4_ENST00000444061.3_Intron|SMARCA4_ENST00000450717.3_Intron	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4						aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CACACGTGCGTCAAAGGTGGG	0.527			"""F, N, Mis"""		NSCLC																																p.S1421P		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.T4261C						.						56.0	52.0	53.0					19																	11150224		1566	3580	5146	SO:0001627	intron_variant	6597	exon30			CGTGCGTCAAAGG	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.4171-1759T>C	chr19.hg19:g.11150224T>C		121.0	0.0		112.0	5.0	NM_001128849	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.53|12.53	1.966007|1.966007	0.34659|0.34659	.|.	.|.	ENSG00000127616|ENSG00000127616	ENST00000358026|ENST00000538456	D|.	0.87256|.	-2.23|.	0.727|0.727	0.727|0.727	0.18254|0.18254	.|.	.|.	.|.	.|.	.|.	T|T	0.16685|0.16685	0.0401|0.0401	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	P|.	0.39520|.	0.676|.	B|.	0.39706|.	0.307|.	T|T	0.28202|0.28202	-1.0051|-1.0051	8|4	0.38643|.	T|.	0.18|.	.|.	.|.	.|.	.|.	.|.	1421|.	Q9HBD4|.	.|.	P|A	1421|157	ENSP00000350720:S1421P|.	ENSP00000350720:S1421P|.	S|V	+|+	1|2	0|0	SMARCA4|SMARCA4	11011224|11011224	0.015000|0.015000	0.18098|0.18098	0.007000|0.007000	0.13788|0.13788	0.981000|0.981000	0.71138|0.71138	0.614000|0.614000	0.24314|0.24314	0.555000|0.555000	0.29079|0.29079	0.260000|0.260000	0.18958|0.18958	TCA|GTC	.	.		0.527	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
ELAVL3	1995	hgsc.bcm.edu	37	19	11565448	11565448	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:11565448T>C	ENST00000359227.3	-	7	1421	c.997A>G	c.(997-999)Acc>Gcc	p.T333A	ELAVL3_ENST00000438662.2_Missense_Mutation_p.T326A	NM_001420.3|NM_032281.2	NP_001411.2|NP_115657.2	Q14576	ELAV3_HUMAN	ELAV like neuron-specific RNA binding protein 3	333	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)		AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			breast(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15						TCATAGTTGGTCATGGTCACG	0.587																																					p.T333A		Atlas-SNP	.											.	ELAVL3	58	.	0			c.A997G						.						157.0	112.0	127.0					19																	11565448		2203	4300	6503	SO:0001583	missense	1995	exon7			AGTTGGTCATGGT		CCDS32912.1, CCDS45978.1	19p13.2	2013-10-03	2013-10-03			ENSG00000196361		"""RNA binding motif (RRM) containing"""	3314	protein-coding gene	gene with protein product	"""Hu antigen C"", ""paraneoplastic limbic encephalitis antigen 21"", ""paraneoplastic cerebellar degeneration-associated antigen"", ""ELAV-like protein 3"""	603458	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)"""			9799595	Standard	NM_001420		Approved	HUC, PLE21, DKFZp547J036, HUCL, MGC20653	uc002mry.1	Q14576		ENST00000359227.3:c.997A>G	chr19.hg19:g.11565448T>C	ENSP00000352162:p.Thr333Ala	108.0	0.0		127.0	7.0	NM_001420	Q16135|Q96CL8|Q96QS9	Missense_Mutation	SNP	ENST00000359227.3	hg19	CCDS32912.1	.	.	.	.	.	.	.	.	.	.	T	15.22	2.769848	0.49680	.	.	ENSG00000196361	ENST00000359227;ENST00000438662	T;T	0.15487	2.42;2.42	4.59	3.55	0.40652	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.105378	0.64402	D	0.000005	T	0.07999	0.0200	N	0.03115	-0.41	0.53688	D	0.999978	B;B	0.27951	0.195;0.075	B;B	0.31016	0.123;0.051	T	0.30238	-0.9985	10	0.37606	T	0.19	.	9.5834	0.39501	0.1575:0.0:0.0:0.8425	.	333;326	Q14576;Q14576-2	ELAV3_HUMAN;.	A	333;326	ENSP00000352162:T333A;ENSP00000390878:T326A	ENSP00000352162:T333A	T	-	1	0	ELAVL3	11426448	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.576000	0.82467	0.598000	0.29829	0.352000	0.21897	ACC	.	.		0.587	ELAVL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458827.2	NM_001420	
NOTCH3	4854	hgsc.bcm.edu	37	19	15292438	15292438	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:15292438G>C	ENST00000263388.2	-	17	2816	c.2741C>G	c.(2740-2742)cCa>cGa	p.P914R		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	914	EGF-like 23; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.P914L(1)		breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			TCCGTAGCCTGGCGGGCAGGT	0.697																																					p.P914R		Atlas-SNP	.											NOTCH3,NS,carcinoma,0,1	NOTCH3	340	.	1	Substitution - Missense(1)	lung(1)	c.C2741G						.						13.0	11.0	11.0					19																	15292438		2094	4050	6144	SO:0001583	missense	4854	exon17			TAGCCTGGCGGGC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.2741C>G	chr19.hg19:g.15292438G>C	ENSP00000263388:p.Pro914Arg	281.0	0.0		296.0	0.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.001631	0.54254	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.96200	-3.94	5.45	5.45	0.79879	EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.32015	N	0.006713	D	0.96153	0.8746	L	0.41492	1.28	0.58432	D	0.999999	D;D	0.58620	0.983;0.975	P;P	0.62649	0.88;0.905	D	0.96302	0.9222	10	0.54805	T	0.06	.	18.0459	0.89332	0.0:0.0:1.0:0.0	.	865;914	Q59FL3;Q9UM47	.;NOTC3_HUMAN	R	914;864	ENSP00000263388:P914R	ENSP00000263388:P914R	P	-	2	0	NOTCH3	15153438	1.000000	0.71417	0.035000	0.18076	0.010000	0.07245	5.641000	0.67881	2.569000	0.86673	0.561000	0.74099	CCA	.	.		0.697	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
CYP4F12	66002	hgsc.bcm.edu	37	19	15807241	15807241	+	Splice_Site	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:15807241T>C	ENST00000550308.1	+	12	1696	c.1316T>C	c.(1315-1317)gTc>gCc	p.V439A	CYP4F12_ENST00000324632.10_Splice_Site_p.V439A	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	439					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CACCTGCAGGTCTACGACCCC	0.537																																					p.V439A		Atlas-SNP	.											.	CYP4F12	89	.	0			c.T1316C						.						109.0	105.0	107.0					19																	15807241		2202	4300	6502	SO:0001630	splice_region_variant	66002	exon12			TGCAGGTCTACGA	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.1315-1T>C	chr19.hg19:g.15807241T>C		95.0	0.0		127.0	6.0	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	hg19	CCDS42517.1	.	.	.	.	.	.	.	.	.	.	.	11.30	1.597846	0.28445	.	.	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.79033	-1.23;-1.23	2.31	2.31	0.28768	.	0.188665	0.32106	U	0.006572	T	0.82038	0.4950	L	0.54863	1.705	0.40773	D	0.983102	D	0.62365	0.991	D	0.70016	0.967	T	0.82418	-0.0467	10	0.72032	D	0.01	.	8.4933	0.33112	0.0:0.0:0.0:1.0	.	439	Q9HCS2	CP4FC_HUMAN	A	439	ENSP00000448998:V439A;ENSP00000321821:V439A	ENSP00000321821:V439A	V	+	2	0	CYP4F12	15668241	1.000000	0.71417	0.998000	0.56505	0.190000	0.23558	4.375000	0.59549	1.308000	0.44962	0.260000	0.18958	GTC	.	.		0.537	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		Missense_Mutation
UNC13A	23025	hgsc.bcm.edu	37	19	17758258	17758258	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:17758258T>C	ENST00000519716.2	-	17	1859	c.1860A>G	c.(1858-1860)acA>acG	p.T620T	UNC13A_ENST00000552293.1_Silent_p.T620T|UNC13A_ENST00000550896.1_Silent_p.T618T|UNC13A_ENST00000551649.1_Silent_p.T620T|UNC13A_ENST00000252773.7_Silent_p.T620T|UNC13A_ENST00000428389.2_Silent_p.T708T	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	620					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						TGATGTTCTGTGTCCGGTCCT	0.642																																					p.T620T		Atlas-SNP	.											.	UNC13A	299	.	0			c.A1860G						.						76.0	79.0	78.0					19																	17758258		2153	4284	6437	SO:0001819	synonymous_variant	23025	exon16			GTTCTGTGTCCGG	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.1860A>G	chr19.hg19:g.17758258T>C		117.0	0.0		109.0	5.0	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	hg19	CCDS46013.2																																																																																			.	.		0.642	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
PDE4C	5143	hgsc.bcm.edu	37	19	18322644	18322644	+	Silent	SNP	T	T	C	rs577328081		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:18322644T>C	ENST00000355502.3	-	18	2587	c.1716A>G	c.(1714-1716)ggA>ggG	p.G572G	PDE4C_ENST00000594465.3_Silent_p.G572G|PDE4C_ENST00000262805.12_Silent_p.G540G|PDE4C_ENST00000447275.3_Silent_p.G466G|PDE4C_ENST00000598111.2_Silent_p.G287G|PDE4C_ENST00000597297.1_Silent_p.G342G|PDE4C_ENST00000594617.3_Silent_p.G572G|AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000539010.1_Silent_p.G341G|AC068499.10_ENST00000599416.2_RNA			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	572					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)	GCTCGCGGTCTCCCTGCTGGA	0.627																																					p.G572G		Atlas-SNP	.											.	PDE4C	80	.	0			c.A1716G						.						112.0	93.0	99.0					19																	18322644		2203	4300	6503	SO:0001819	synonymous_variant	5143	exon15			GCGGTCTCCCTGC		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.1716A>G	chr19.hg19:g.18322644T>C		120.0	0.0		135.0	7.0	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Silent	SNP	ENST00000355502.3	hg19	CCDS12373.1																																																																																			.	.		0.627	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1		
PBX4	80714	hgsc.bcm.edu	37	19	19681414	19681414	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:19681414T>C	ENST00000251203.9	-	3	708	c.422A>G	c.(421-423)gAg>gGg	p.E141G		NM_025245.2	NP_079521.1	Q9BYU1	PBX4_HUMAN	pre-B-cell leukemia homeobox 4	141					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						TTTCTCTAGCTCAGAGTGGTA	0.483																																					p.E141G		Atlas-SNP	.											.	PBX4	34	.	0			c.A422G						.						73.0	68.0	70.0					19																	19681414		2203	4300	6503	SO:0001583	missense	80714	exon3			TCTAGCTCAGAGT	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.422A>G	chr19.hg19:g.19681414T>C	ENSP00000251203:p.Glu141Gly	90.0	0.0		123.0	6.0	NM_025245	A5D8Y0|B3KUK9	Missense_Mutation	SNP	ENST00000251203.9	hg19	CCDS12406.1	.	.	.	.	.	.	.	.	.	.	T	19.16	3.773765	0.69992	.	.	ENSG00000105717	ENST00000251203	T	0.50813	0.73	3.47	3.47	0.39725	PBX (1);	0.000000	0.85682	D	0.000000	T	0.66829	0.2829	M	0.80616	2.505	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.70669	-0.4808	10	0.87932	D	0	-15.0187	10.0195	0.42035	0.0:0.0:0.0:1.0	.	141	Q9BYU1	PBX4_HUMAN	G	141	ENSP00000251203:E141G	ENSP00000251203:E141G	E	-	2	0	PBX4	19542414	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.825000	0.75293	1.451000	0.47736	0.414000	0.27820	GAG	.	.		0.483	PBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417784.6		
ZNF626	199777	hgsc.bcm.edu	37	19	20807353	20807353	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:20807353T>C	ENST00000601440.1	-	4	1476	c.1330A>G	c.(1330-1332)Agg>Ggg	p.R444G	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	444					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|lung(3)|skin(1)	6						TGAATTCTCCTATGTGTAGTA	0.373																																					p.R444G		Atlas-SNP	.											ZNF626_ENST00000392298,bladder,carcinoma,0,1	ZNF626	121	.	0			c.A1330G						.						65.0	59.0	61.0					19																	20807353		2108	4259	6367	SO:0001583	missense	199777	exon4			TTCTCCTATGTGT	BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"""Zinc fingers, C2H2-type"", ""-"""	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.1330A>G	chr19.hg19:g.20807353T>C	ENSP00000469958:p.Arg444Gly	24.0	0.0		39.0	4.0	NM_001076675	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	hg19	CCDS42535.1	.	.	.	.	.	.	.	.	.	.	N	0.713	-0.786488	0.02907	.	.	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	.	.	.	0.832	0.832	0.18867	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.50718	0.1632	L	0.58101	1.795	0.80722	D	1	B	0.23806	0.091	B	0.33121	0.158	T	0.49447	-0.8939	8	0.87932	D	0	.	3.5311	0.07777	0.0:0.0:0.4169:0.583	.	444	Q68DY1	ZN626_HUMAN	G	444;368;444	.	ENSP00000445201:R444G	R	-	1	2	ZNF626	20599193	0.121000	0.22262	0.006000	0.13384	0.006000	0.05464	0.065000	0.14466	0.148000	0.19059	0.147000	0.16070	AGG	.	.		0.373	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297	
ZNF536	9745	hgsc.bcm.edu	37	19	30935844	30935844	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:30935844C>T	ENST00000355537.3	+	2	1522	c.1375C>T	c.(1375-1377)Ccc>Tcc	p.P459S		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	459					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)					GGGCGAGCTGCCCATGAAGGA	0.647																																					p.P459S		Atlas-SNP	.											.	ZNF536	424	.	0			c.C1375T						.						31.0	33.0	32.0					19																	30935844		2199	4299	6498	SO:0001583	missense	9745	exon2			GAGCTGCCCATGA		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.1375C>T	chr19.hg19:g.30935844C>T	ENSP00000347730:p.Pro459Ser	82.0	0.0		73.0	4.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	C	2.002	-0.429180	0.04701	.	.	ENSG00000198597	ENST00000355537	T	0.07327	3.2	5.44	1.79	0.24919	.	0.228755	0.45867	D	0.000336	T	0.07503	0.0189	L	0.27053	0.805	0.37911	D	0.931372	B;B	0.24258	0.1;0.1	B;B	0.24541	0.054;0.054	T	0.24764	-1.0151	10	0.45353	T	0.12	-18.4226	15.9244	0.79603	0.0:0.5869:0.4131:0.0	.	459;459	A7E228;O15090	.;ZN536_HUMAN	S	459	ENSP00000347730:P459S	ENSP00000347730:P459S	P	+	1	0	ZNF536	35627684	1.000000	0.71417	0.886000	0.34754	0.033000	0.12548	2.772000	0.47678	0.599000	0.29845	0.591000	0.81541	CCC	.	.		0.647	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
ZNF536	9745	hgsc.bcm.edu	37	19	31039960	31039960	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:31039960T>C	ENST00000355537.3	+	4	3581	c.3434T>C	c.(3433-3435)gTc>gCc	p.V1145A		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1145					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)					GAAGAGGATGTCCCCATCCTG	0.547																																					p.V1145A		Atlas-SNP	.											ZNF536,colon,carcinoma,0,1	ZNF536	424	.	0			c.T3434C						.						73.0	70.0	71.0					19																	31039960		2203	4300	6503	SO:0001583	missense	9745	exon4			AGGATGTCCCCAT		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.3434T>C	chr19.hg19:g.31039960T>C	ENSP00000347730:p.Val1145Ala	97.0	0.0		113.0	6.0	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	t	0.008	-1.871054	0.00542	.	.	ENSG00000198597	ENST00000355537	T	0.06933	3.24	5.59	1.07	0.20283	.	0.656971	0.15796	N	0.244188	T	0.02688	0.0081	N	0.03608	-0.345	0.19300	N	0.999974	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46512	-0.9186	10	0.02654	T	1	-9.6809	7.7337	0.28802	0.0:0.6861:0.1173:0.1966	.	1145;1145	A7E228;O15090	.;ZN536_HUMAN	A	1145	ENSP00000347730:V1145A	ENSP00000347730:V1145A	V	+	2	0	ZNF536	35731800	0.159000	0.22864	0.250000	0.24296	0.402000	0.30811	1.115000	0.31209	0.047000	0.15862	-0.866000	0.03004	GTC	.	.		0.547	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
ATP4A	495	hgsc.bcm.edu	37	19	36048637	36048637	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:36048637T>C	ENST00000262623.3	-	11	1641	c.1613A>G	c.(1612-1614)gAg>gGg	p.E538G		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	538					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	CAGCGGCAGCTCCTGGCCCTT	0.706																																					p.E538G		Atlas-SNP	.											.	ATP4A	123	.	0			c.A1613G						.						13.0	14.0	14.0					19																	36048637		2187	4280	6467	SO:0001583	missense	495	exon11			GGCAGCTCCTGGC		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"""ATPases / P-type"""	819	protein-coding gene	gene with protein product	"""gastric H,K-ATPase alpha subunit"", ""H(+)-K(+)-ATPase alpha subunit"", ""proton pump"""	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.1613A>G	chr19.hg19:g.36048637T>C	ENSP00000262623:p.Glu538Gly	127.0	0.0		155.0	9.0	NM_000704	O00738	Missense_Mutation	SNP	ENST00000262623.3	hg19	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.034699	0.93575	.	.	ENSG00000105675	ENST00000262623	D	0.81659	-1.52	3.8	3.8	0.43715	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.52532	D	0.000061	D	0.84329	0.5448	L	0.49778	1.585	0.53005	D	0.999969	P	0.51240	0.943	D	0.64321	0.924	D	0.84894	0.0838	10	0.62326	D	0.03	.	10.5596	0.45138	0.0:0.0:0.0:1.0	.	538	P20648	ATP4A_HUMAN	G	538	ENSP00000262623:E538G	ENSP00000262623:E538G	E	-	2	0	ATP4A	40740477	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.736000	0.84948	1.598000	0.50083	0.397000	0.26171	GAG	.	.		0.706	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704	
NPHS1	4868	hgsc.bcm.edu	37	19	36333298	36333298	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:36333298A>G	ENST00000378910.5	-	18	2488	c.2489T>C	c.(2488-2490)cTc>cCc	p.L830P	NPHS1_ENST00000353632.6_Missense_Mutation_p.L830P	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	830	Ig-like C2-type 7.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AACAAGACGGAGCAGCCGTCG	0.582																																					p.L830P		Atlas-SNP	.											.	NPHS1	165	.	0			c.T2489C						.						65.0	58.0	60.0					19																	36333298		2203	4300	6503	SO:0001583	missense	4868	exon18			AGACGGAGCAGCC		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.2489T>C	chr19.hg19:g.36333298A>G	ENSP00000368190:p.Leu830Pro	37.0	0.0		71.0	5.0	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	hg19	CCDS32996.1	.	.	.	.	.	.	.	.	.	.	A	11.69	1.712724	0.30413	.	.	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.14766	2.48;2.48	4.57	2.39	0.29439	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.512179	0.20255	N	0.095982	T	0.09992	0.0245	L	0.38175	1.15	0.31825	N	0.62543	B	0.18166	0.026	B	0.24269	0.052	T	0.05162	-1.0902	10	0.72032	D	0.01	-18.1196	4.0947	0.09985	0.6786:0.2128:0.1087:0.0	.	830	O60500	NPHN_HUMAN	P	830	ENSP00000368190:L830P;ENSP00000343634:L830P	ENSP00000343634:L830P	L	-	2	0	NPHS1	41025138	0.986000	0.35501	1.000000	0.80357	0.859000	0.49053	2.140000	0.42159	1.936000	0.56123	0.456000	0.33151	CTC	.	.		0.582	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
GRIK5	2901	hgsc.bcm.edu	37	19	42510910	42510910	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:42510910A>G	ENST00000262895.3	-	15	1923	c.1924T>C	c.(1924-1926)Ttc>Ctc	p.F642L	GRIK5_ENST00000301218.4_Missense_Mutation_p.F642L|GRIK5_ENST00000593562.1_Missense_Mutation_p.F642L	NM_002088.4	NP_002079.3	Q16478	GRIK5_HUMAN	glutamate receptor, ionotropic, kainate 5	642					cellular response to glucose stimulus (GO:0071333)|establishment of localization in cell (GO:0051649)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|positive regulation of neuron apoptotic process (GO:0043525)|protein retention in ER lumen (GO:0006621)|receptor clustering (GO:0043113)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	35		Prostate(69;0.059)				ACGGTGAGGAAGGCGGCCAGG	0.627																																					p.F642L		Atlas-SNP	.											.	GRIK5	220	.	0			c.T1924C						.						68.0	54.0	59.0					19																	42510910		2203	4300	6503	SO:0001583	missense	2901	exon15			TGAGGAAGGCGGC		CCDS12595.1	19q13.2	2012-08-29			ENSG00000105737	ENSG00000105737		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4583	protein-coding gene	gene with protein product		600283		GRIK2		7527545	Standard	NM_002088		Approved	GluK5, KA2	uc002osj.2	Q16478	OTTHUMG00000044573	ENST00000262895.3:c.1924T>C	chr19.hg19:g.42510910A>G	ENSP00000262895:p.Phe642Leu	84.0	0.0		94.0	4.0	NM_002088	Q8WWG8	Missense_Mutation	SNP	ENST00000262895.3	hg19	CCDS12595.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	32|32	5.171401|5.171401	0.94807|0.94807	.|.	.|.	ENSG00000105737|ENSG00000105737	ENST00000262895;ENST00000301218|ENST00000454993	T;T|.	0.56941|.	0.43;0.43|.	5.18|5.18	5.18|5.18	0.71444|0.71444	Ionotropic glutamate receptor (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85940|0.85940	0.5814|0.5814	H|H	0.94886|0.94886	3.595|3.595	0.58432|0.58432	D|D	0.999998|0.999998	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.89859|0.89859	0.4015|0.4015	10|5	0.87932|.	D|.	0|.	.|.	14.0093|14.0093	0.64486|0.64486	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	642|.	Q16478|.	GRIK5_HUMAN|.	L|P	642|18	ENSP00000262895:F642L;ENSP00000301218:F642L|.	ENSP00000262895:F642L|.	F|L	-|-	1|2	0|0	GRIK5|GRIK5	47202750|47202750	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.324000|9.324000	0.96373|0.96373	1.959000|1.959000	0.56917|0.56917	0.460000|0.460000	0.39030|0.39030	TTC|CTT	.	.		0.627	GRIK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463453.1		
ERCC2	2068	hgsc.bcm.edu	37	19	45867515	45867515	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:45867515T>C	ENST00000391945.4	-	9	870	c.793A>G	c.(793-795)Acc>Gcc	p.T265A	ERCC2_ENST00000485403.2_Missense_Mutation_p.T241A|ERCC2_ENST00000221481.6_3'UTR|ERCC2_ENST00000391940.4_Missense_Mutation_p.T241A|ERCC2_ENST00000391944.3_Missense_Mutation_p.T187A	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	265	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TTCTGCAGGGTCTCCAGGTTG	0.682			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.T265A		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"""		E	.	ERCC2	78	.	0			c.A793G						.						35.0	39.0	38.0					19																	45867515		2201	4300	6501	SO:0001583	missense	2068	exon9	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GCAGGGTCTCCAG		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"""General transcription factor IIH complex subunits"""	3434	protein-coding gene	gene with protein product	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 protein"", ""TFIIH basal transcription factor complex helicase XPB subunit"""	126340	"""xeroderma pigmentosum complementary group D"", ""excision repair cross-complementing rodent repair deficiency, complementation group 2"""	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.793A>G	chr19.hg19:g.45867515T>C	ENSP00000375809:p.Thr265Ala	83.0	0.0		114.0	6.0	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	hg19	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	T	13.32	2.201219	0.38905	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944;ENST00000391940	T;D;T	0.82081	-1.4;-1.57;-0.25	4.72	4.72	0.59763	Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	0.107907	0.64402	D	0.000010	T	0.70613	0.3244	N	0.21448	0.665	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.12837	0.001;0.008;0.0	T	0.64546	-0.6382	10	0.15499	T	0.54	-54.599	12.4641	0.55749	0.0:0.0:0.0:1.0	.	187;241;265	E7EVE9;Q7KZU6;P18074	.;.;ERCC2_HUMAN	A	215;241;265;187;241	ENSP00000375809:T265A;ENSP00000375808:T187A;ENSP00000375804:T241A	ENSP00000375804:T241A	T	-	1	0	ERCC2	50559355	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	4.054000	0.57434	2.102000	0.63906	0.459000	0.35465	ACC	.	.		0.682	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400	
ARHGAP35	2909	hgsc.bcm.edu	37	19	47422735	47422735	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:47422735A>G	ENST00000404338.3	+	1	803	c.803A>G	c.(802-804)cAg>cGg	p.Q268R		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	268					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										CAGCAGAGTCAGCAGATAGCT	0.453																																					p.Q268R		Atlas-SNP	.											.	.	.	.	0			c.A803G						.						72.0	73.0	72.0					19																	47422735		2023	4202	6225	SO:0001583	missense	2909	exon1			AGAGTCAGCAGAT	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"""Rho GTPase activating proteins"""	4591	protein-coding gene	gene with protein product		605277	"""glucocorticoid receptor DNA binding factor 1"""	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.803A>G	chr19.hg19:g.47422735A>G	ENSP00000385720:p.Gln268Arg	73.0	0.0		99.0	5.0	NM_004491	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	hg19	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.646163	0.67358	.	.	ENSG00000160007	ENST00000317082;ENST00000501576;ENST00000404338	T	0.09073	3.02	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.20414	0.0491	L	0.55990	1.75	0.80722	D	1	P	0.48834	0.916	P	0.55345	0.774	T	0.00061	-1.2159	10	0.87932	D	0	-32.9111	15.4607	0.75353	1.0:0.0:0.0:0.0	.	268	Q9NRY4-2	.	R	268	ENSP00000385720:Q268R	ENSP00000324820:Q268R	Q	+	2	0	ARHGAP35	52114575	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.339000	0.96797	2.288000	0.76882	0.528000	0.53228	CAG	.	.		0.453	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491	
SLC6A16	28968	hgsc.bcm.edu	37	19	49813309	49813309	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:49813309A>G	ENST00000335875.4	-	4	929	c.688T>C	c.(688-690)Tct>Cct	p.S230P	MIR4324_ENST00000584846.1_RNA|SLC6A16_ENST00000454748.3_Missense_Mutation_p.S230P	NM_014037.2	NP_054756.2	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	230					neurotransmitter transport (GO:0006836)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)		AAGCCACTAGAGTTCATCGTT	0.473																																					p.S230P		Atlas-SNP	.											.	SLC6A16	62	.	0			c.T688C						.						88.0	77.0	80.0					19																	49813309		1885	4124	6009	SO:0001583	missense	28968	exon4			CACTAGAGTTCAT	AF265578	CCDS42590.1	19q13.33	2013-05-22			ENSG00000063127	ENSG00000063127		"""Solute carriers"""	13622	protein-coding gene	gene with protein product	"""NTT5 protein"""	607972	"""solute carrier family 6 (neurotransmitter transporter), member 16"""			10471414, 11112352	Standard	XM_005258820		Approved	NTT5	uc002pmz.3	Q9GZN6		ENST00000335875.4:c.688T>C	chr19.hg19:g.49813309A>G	ENSP00000338627:p.Ser230Pro	160.0	0.0		147.0	6.0	NM_014037	Q8IYV4|Q9Y5I9	Missense_Mutation	SNP	ENST00000335875.4	hg19	CCDS42590.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.694629	0.30052	.	.	ENSG00000063127	ENST00000335875;ENST00000454748	T;T	0.75477	-0.94;-0.94	4.58	-0.138	0.13464	.	0.788296	0.12019	N	0.507196	D	0.83344	0.5234	M	0.86268	2.805	0.28862	N	0.895465	D;D	0.67145	0.996;0.996	D;D	0.68192	0.956;0.956	T	0.72931	-0.4142	10	0.39692	T	0.17	.	6.9237	0.24403	0.3769:0.4712:0.0:0.1518	.	230;230	Q8IYV4;Q9GZN6	.;S6A16_HUMAN	P	230	ENSP00000338627:S230P;ENSP00000404022:S230P	ENSP00000338627:S230P	S	-	1	0	SLC6A16	54505121	0.913000	0.31002	0.910000	0.35882	0.003000	0.03518	-0.247000	0.08866	-0.127000	0.11661	-0.327000	0.08410	TCT	.	.		0.473	SLC6A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465503.2	NM_014037	
SIGLEC12	89858	hgsc.bcm.edu	37	19	52002448	52002448	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:52002448T>C	ENST00000291707.3	-	4	1166	c.1111A>G	c.(1111-1113)Act>Gct	p.T371A	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.T253A	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	371	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		TGGAAGACAGTCATGGTCAAG	0.567																																					p.T371A		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.A1111G						.						120.0	102.0	108.0					19																	52002448		2203	4300	6503	SO:0001583	missense	89858	exon4			AGACAGTCATGGT	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15482	protein-coding gene	gene with protein product		606094	"""SIGLEC-like 1"", ""sialic acid binding Ig-like lectin 12"""	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1111A>G	chr19.hg19:g.52002448T>C	ENSP00000291707:p.Thr371Ala	137.0	0.0		141.0	6.0	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	hg19	CCDS12833.1	.	.	.	.	.	.	.	.	.	.	.	10.75	1.439444	0.25900	.	.	ENSG00000254521	ENST00000291707	T	0.41758	0.99	2.07	2.07	0.26955	Immunoglobulin-like (1);	0.896444	0.09202	N	0.834571	T	0.42607	0.1210	M	0.69248	2.105	0.09310	N	1	P;P	0.37612	0.602;0.567	B;B	0.40901	0.343;0.343	T	0.34625	-0.9821	10	0.41790	T	0.15	.	6.0661	0.19864	0.0:0.0:0.0:1.0	.	371;253	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	A	371	ENSP00000291707:T371A	ENSP00000291707:T371A	T	-	1	0	SIGLEC12	56694260	0.000000	0.05858	0.002000	0.10522	0.591000	0.36615	0.002000	0.13061	0.975000	0.38392	0.329000	0.21502	ACT	.	.		0.567	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003	
ZNF841	284371	hgsc.bcm.edu	37	19	52569542	52569542	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:52569542A>G	ENST00000426391.2	-	5	1796	c.1245T>C	c.(1243-1245)caT>caC	p.H415H	ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000594295.1_Silent_p.H531H|ZNF841_ENST00000389534.4_Silent_p.H531H|CTC-471J1.2_ENST00000569091.1_RNA|ZNF841_ENST00000359973.2_Intron			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	415					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(3)|lung(3)	11						GAATTCTCTGATGTACAGTTA	0.398																																					p.H531H		Atlas-SNP	.											.	ZNF841	183	.	0			c.T1593C						.						99.0	91.0	94.0					19																	52569542		692	1591	2283	SO:0001819	synonymous_variant	284371	exon7			TCTCTGATGTACA	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"""Zinc fingers, C2H2-type"", ""-"""	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.1245T>C	chr19.hg19:g.52569542A>G		52.0	0.0		36.0	4.0	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Silent	SNP	ENST00000426391.2	hg19																																																																																				.	.		0.398	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155	
ZNF347	84671	hgsc.bcm.edu	37	19	53645764	53645764	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:53645764T>C	ENST00000334197.7	-	5	385	c.317A>G	c.(316-318)aAg>aGg	p.K106R	ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000601469.2_Missense_Mutation_p.K107R|ZNF347_ENST00000452676.2_Missense_Mutation_p.K107R	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	106					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(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		TGTATTACTCTTCCCTTTGTG	0.358																																					p.K107R	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											.	ZNF347	87	.	0			c.A320G						.						60.0	53.0	55.0					19																	53645764		2203	4299	6502	SO:0001583	missense	84671	exon5			TTACTCTTCCCTT	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"""Zinc fingers, C2H2-type"", ""-"""	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.317A>G	chr19.hg19:g.53645764T>C	ENSP00000334146:p.Lys106Arg	118.0	0.0		119.0	5.0	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	hg19	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	T	3.500	-0.102088	0.06967	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.07021	3.23;3.23	2.57	-1.34	0.09143	.	.	.	.	.	T	0.02727	0.0082	N	0.08118	0	0.09310	N	1	P;B	0.42908	0.793;0.316	B;B	0.37780	0.258;0.098	T	0.28138	-1.0053	9	0.18710	T	0.47	.	0.3772	0.00389	0.2189:0.1429:0.2244:0.4138	.	107;106	G5E9N4;Q96SE7	.;ZN347_HUMAN	R	106;107	ENSP00000334146:K106R;ENSP00000405218:K107R	ENSP00000334146:K106R	K	-	2	0	ZNF347	58337576	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.782000	0.04643	-0.596000	0.05821	-0.256000	0.11100	AAG	.	.		0.358	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584	
ZNF845	91664	hgsc.bcm.edu	37	19	53855284	53855284	+	Silent	SNP	G	G	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:53855284G>A	ENST00000595091.1	+	5	1575	c.1356G>A	c.(1354-1356)tcG>tcA	p.S452S	ZNF845_ENST00000458035.1_Silent_p.S452S			Q96IR2	ZN845_HUMAN	zinc finger protein 845	452					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.S452S(2)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						GTTTCAAATCGAACCTTGAAA	0.398																																					p.S452S		Atlas-SNP	.											ZNF845,NS,carcinoma,0,1	ZNF845	101	.	2	Substitution - coding silent(2)	prostate(1)|kidney(1)	c.G1356A						.						26.0	24.0	25.0					19																	53855284		692	1590	2282	SO:0001819	synonymous_variant	91664	exon4			CAAATCGAACCTT	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.1356G>A	chr19.hg19:g.53855284G>A		45.0	1.0		55.0	3.0	NM_138374		Silent	SNP	ENST00000595091.1	hg19	CCDS46170.1																																																																																			.	.		0.398	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
ZNF761	388561	hgsc.bcm.edu	37	19	53959189	53959189	+	RNA	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:53959189T>C	ENST00000454407.1	+	0	1881							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		AAGCTTTCCGTTTCAAATCAA	0.423																																					p.R476R		Atlas-SNP	.											.	ZNF761	104	.	0			c.T1428C						.						76.0	80.0	78.0					19																	53959189		2203	4300	6503			388561	exon7			TTTCCGTTTCAAA	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"""Zinc fingers, C2H2-type"""	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		chr19.hg19:g.53959189T>C		41.0	0.0		39.0	10.0	NM_001008401	Q6ZNB9	Silent	SNP	ENST00000454407.1	hg19																																																																																				.	.		0.423	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401	
DPRX	503834	hgsc.bcm.edu	37	19	54140025	54140025	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:54140025T>A	ENST00000376650.1	+	3	410	c.359T>A	c.(358-360)gTg>gAg	p.V120E		NM_001012728.1	NP_001012746.1	A6NFQ7	DPRX_HUMAN	divergent-paired related homeobox	120					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(4)|large_intestine(1)|lung(7)	12	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.013)		ATCGGCCTGGTGTACACGGGT	0.562																																					p.V120E		Atlas-SNP	.											.	DPRX	34	.	0			c.T359A						.						133.0	105.0	114.0					19																	54140025		2203	4300	6503	SO:0001583	missense	503834	exon3			GCCTGGTGTACAC		CCDS33103.1	19q13.42	2011-06-20			ENSG00000204595	ENSG00000204595		"""Homeoboxes / PRD class"""	32166	protein-coding gene	gene with protein product		611165					Standard	NM_001012728		Approved		uc002qcf.1	A6NFQ7		ENST00000376650.1:c.359T>A	chr19.hg19:g.54140025T>A	ENSP00000365838:p.Val120Glu	158.0	0.0		160.0	52.0	NM_001012728		Missense_Mutation	SNP	ENST00000376650.1	hg19	CCDS33103.1	.	.	.	.	.	.	.	.	.	.	t	9.525	1.109197	0.20714	.	.	ENSG00000204595	ENST00000376650	D	0.94376	-3.41	1.45	1.45	0.22620	.	.	.	.	.	D	0.91432	0.7296	N	0.24115	0.695	0.09310	N	1	D	0.76494	0.999	D	0.71184	0.972	T	0.82014	-0.0667	9	0.29301	T	0.29	.	5.0324	0.14417	0.0:0.0:0.0:1.0	.	120	A6NFQ7	DPRX_HUMAN	E	120	ENSP00000365838:V120E	ENSP00000365838:V120E	V	+	2	0	DPRX	58831837	0.014000	0.17966	0.004000	0.12327	0.002000	0.02628	1.273000	0.33121	0.918000	0.36919	0.459000	0.35465	GTG	.	.		0.562	DPRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409880.1	NM_001012728	
NLRP7	199713	hgsc.bcm.edu	37	19	55445101	55445101	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:55445101T>C	ENST00000590030.1	-	7	2518	c.2478A>G	c.(2476-2478)gaA>gaG	p.E826E	NLRP7_ENST00000446217.1_Silent_p.E854E|NLRP7_ENST00000592784.1_Silent_p.E826E|NLRP7_ENST00000328092.5_Silent_p.E798E|NLRP7_ENST00000448121.2_Silent_p.E798E|NLRP7_ENST00000340844.2_Silent_p.E826E|NLRP7_ENST00000588756.1_Silent_p.E826E			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	826							ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		GACGACAGTTTTCCAACCTGC	0.478																																					p.E826E		Atlas-SNP	.											.	NLRP7	411	.	0			c.A2478G						.						81.0	78.0	79.0					19																	55445101		2203	4300	6503	SO:0001819	synonymous_variant	199713	exon8			ACAGTTTTCCAAC	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.2478A>G	chr19.hg19:g.55445101T>C		78.0	0.0		97.0	4.0	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	hg19	CCDS33109.1																																																																																			.	.		0.478	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
SSC5D	284297	hgsc.bcm.edu	37	19	56028719	56028719	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:56028719T>C	ENST00000389623.6	+	14	3099	c.3076T>C	c.(3076-3078)Tcc>Ccc	p.S1026P		NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	1026	Pro-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						GACCTCTGACTCCAGTCGAGA	0.721																																					p.S1026P		Atlas-SNP	.											.	SSC5D	65	.	0			c.T3076C						.						15.0	17.0	16.0					19																	56028719		692	1591	2283	SO:0001583	missense	284297	exon14			TCTGACTCCAGTC		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.3076T>C	chr19.hg19:g.56028719T>C	ENSP00000374274:p.Ser1026Pro	94.0	0.0		99.0	5.0	NM_001144950	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Missense_Mutation	SNP	ENST00000389623.6	hg19	CCDS46196.1	.	.	.	.	.	.	.	.	.	.	-	14.23	2.473475	0.43942	.	.	ENSG00000179954	ENST00000389623	T	0.01613	4.73	3.15	3.15	0.36227	.	.	.	.	.	T	0.02767	0.0083	L	0.58669	1.825	0.09310	N	1	B	0.30193	0.272	B	0.31495	0.131	T	0.34279	-0.9835	9	0.51188	T	0.08	.	8.004	0.30315	0.0:0.0:0.0:1.0	.	1026	A1L4H1	SRCRL_HUMAN	P	1026	ENSP00000374274:S1026P	ENSP00000374274:S1026P	S	+	1	0	SSC5D	60720531	0.000000	0.05858	0.016000	0.15963	0.058000	0.15608	-0.009000	0.12765	1.453000	0.47775	0.381000	0.24937	TCC	.	.		0.721	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
PEG3	5178	hgsc.bcm.edu	37	19	57326604	57326604	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:57326604T>C	ENST00000326441.9	-	10	3569	c.3206A>G	c.(3205-3207)gAt>gGt	p.D1069G	PEG3_ENST00000423103.2_Missense_Mutation_p.D1069G|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000593711.1_Intron|ZIM2_ENST00000599935.1_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.D943G|PEG3_ENST00000598410.1_Missense_Mutation_p.D945G|ZIM2_ENST00000601070.1_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1069					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		CTCCTCCCCATCAGTATTCTC	0.493																																					p.D1069G		Atlas-SNP	.											.	PEG3	414	.	0			c.A3206G						.						148.0	134.0	139.0					19																	57326604		2203	4300	6503	SO:0001583	missense	5178	exon9			TCCCCATCAGTAT	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.3206A>G	chr19.hg19:g.57326604T>C	ENSP00000326581:p.Asp1069Gly	84.0	0.0		115.0	5.0	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	hg19	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.882305	0.00532	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02737	4.18;4.18	2.5	-0.933	0.10431	.	2.678910	0.01592	N	0.021597	T	0.01905	0.0060	N	0.08118	0	.	.	.	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.002	T	0.44605	-0.9317	9	0.22706	T	0.39	0.3141	5.7766	0.18283	0.0:0.4641:0.0:0.5359	.	945;1069;1004	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	G	1069	ENSP00000326581:D1069G;ENSP00000403051:D1069G	ENSP00000326581:D1069G	D	-	2	0	ZIM2	62018416	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.306000	0.02735	-0.307000	0.08804	-0.290000	0.09829	GAT	.	.		0.493	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2		
CSNK2A1	1457	hgsc.bcm.edu	37	20	469379	469379	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:469379T>C	ENST00000217244.3	-	11	1142	c.767A>G	c.(766-768)gAc>gGc	p.D256G	CSNK2A1_ENST00000349736.5_Missense_Mutation_p.D256G|CSNK2A1_ENST00000400217.2_Missense_Mutation_p.D120G|CSNK2A1_ENST00000400227.3_Missense_Mutation_p.D256G	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	256	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			D -> G (in Ref. 3; CAA49758). {ECO:0000305}.	axon guidance (GO:0007411)|chaperone-mediated protein folding (GO:0061077)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	ATP binding (GO:0005524)|Hsp90 protein binding (GO:0051879)|protein N-terminus binding (GO:0047485)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.0969)			GTCAATATAGTCATATAAATC	0.338																																					p.D256G		Atlas-SNP	.											.	CSNK2A1	36	.	0			c.A767G						.						139.0	128.0	132.0					20																	469379		2203	4300	6503	SO:0001583	missense	1457	exon10			ATATAGTCATATA	M55265	CCDS13003.1, CCDS13004.1	20p13	2013-01-17			ENSG00000101266	ENSG00000101266			2457	protein-coding gene	gene with protein product		115440				2174700, 1766873	Standard	NM_177559		Approved		uc002wdx.1	P68400	OTTHUMG00000031636	ENST00000217244.3:c.767A>G	chr20.hg19:g.469379T>C	ENSP00000217244:p.Asp256Gly	73.0	0.0		111.0	6.0	NM_001895	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Missense_Mutation	SNP	ENST00000217244.3	hg19	CCDS13003.1	.	.	.	.	.	.	.	.	.	.	T	13.52	2.262675	0.39995	.	.	ENSG00000101266	ENST00000400227;ENST00000349736;ENST00000217244;ENST00000381973;ENST00000400217	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.44	5.44	0.79542	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.086149	0.85682	D	0.000000	T	0.64746	0.2626	M	0.69248	2.105	0.80722	D	1	B	0.06786	0.001	B	0.16722	0.016	T	0.60372	-0.7276	10	0.23302	T	0.38	-3.5424	14.836	0.70183	0.0:0.0:0.0:1.0	.	256	P68400	CSK21_HUMAN	G	256;256;256;256;120	ENSP00000383086:D256G;ENSP00000339247:D256G;ENSP00000217244:D256G;ENSP00000383076:D120G	ENSP00000217244:D256G	D	-	2	0	CSNK2A1	417379	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.978000	0.70501	2.285000	0.76669	0.533000	0.62120	GAC	.	.		0.338	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895	
PAK7	57144	hgsc.bcm.edu	37	20	9538333	9538333	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:9538333A>G	ENST00000378429.3	-	8	2211	c.1665T>C	c.(1663-1665)gcT>gcC	p.A555A	PAK7_ENST00000353224.5_Silent_p.A555A|PAK7_ENST00000378423.1_Silent_p.A555A	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	555	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> S (in dbSNP:rs34102290). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			GGTAGGAGAGAGCTCTCAGAA	0.433																																					p.A555A		Atlas-SNP	.											.	PAK7	194	.	0			c.T1665C						.						141.0	122.0	128.0					20																	9538333		2203	4300	6503	SO:0001819	synonymous_variant	57144	exon7			GGAGAGAGCTCTC	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"""p21(CDKN1A)-activated kinase 7"""			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1665T>C	chr20.hg19:g.9538333A>G		79.0	0.0		96.0	4.0	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Silent	SNP	ENST00000378429.3	hg19	CCDS13107.1																																																																																			.	.		0.433	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1		
SNX5	27131	hgsc.bcm.edu	37	20	17950850	17950850	+	5'Flank	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:17950850T>C	ENST00000377768.3	-	0	0				MGME1_ENST00000377704.4_Silent_p.D116D|SNX5_ENST00000606602.1_5'Flank|MGME1_ENST00000377710.5_Silent_p.D116D|MGME1_ENST00000467391.1_3'UTR|MGME1_ENST00000377709.1_Intron|SNX5_ENST00000486039.1_5'Flank|SNX5_ENST00000481323.1_5'Flank|SNX5_ENST00000377759.4_5'Flank|SNX5_ENST00000606557.1_5'Flank	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5						intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						ATGCAAGTGATCCTTCAGTTC	0.448																																					p.D116D		Atlas-SNP	.											.	.	.	.	0			c.T348C						.						84.0	89.0	87.0					20																	17950850		2203	4300	6503	SO:0001631	upstream_gene_variant	92667	exon2			AAGTGATCCTTCA	AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"""Sorting nexins"""	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953		chr20.hg19:g.17950850T>C	Exception_encountered	131.0	0.0		119.0	5.0	NM_052865	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Silent	SNP	ENST00000377768.3	hg19	CCDS13130.1																																																																																			.	.		0.448	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4		
PXMP4	11264	hgsc.bcm.edu	37	20	32302502	32302502	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:32302502T>C	ENST00000409299.3	-	2	246	c.154A>G	c.(154-156)Acc>Gcc	p.T52A	PXMP4_ENST00000344022.3_Missense_Mutation_p.T52A|PXMP4_ENST00000217398.3_Missense_Mutation_p.T52A	NM_007238.4	NP_009169.3	Q9Y6I8	PXMP4_HUMAN	peroxisomal membrane protein 4, 24kDa	52						integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|large_intestine(2)|lung(8)	13						AAGAGAAAGGTCATGACCAGC	0.502																																					p.T52A		Atlas-SNP	.											.	PXMP4	20	.	0			c.A154G						.						167.0	151.0	156.0					20																	32302502		2203	4300	6503	SO:0001583	missense	11264	exon2			GAAAGGTCATGAC	AF072864	CCDS13225.1, CCDS13226.1	20q11.22	2008-07-02	2002-08-29		ENSG00000101417	ENSG00000101417			15920	protein-coding gene	gene with protein product	"""24 kDa peroxisomal intrinsic membrane protein"""		"""peroxisomal membrane protein 4 (24kD)"""			10366717	Standard	NM_183397		Approved	PMP24	uc002wzv.3	Q9Y6I8	OTTHUMG00000032273	ENST00000409299.3:c.154A>G	chr20.hg19:g.32302502T>C	ENSP00000386385:p.Thr52Ala	144.0	0.0		150.0	6.0	NM_183397	A2A2I7|Q9H0T4	Missense_Mutation	SNP	ENST00000409299.3	hg19	CCDS13225.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.694169	0.88735	.	.	ENSG00000101417	ENST00000409299;ENST00000344022;ENST00000217398	T	0.31510	1.49	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.52208	0.1720	M	0.64567	1.98	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.997	D;D;D	0.85130	0.997;0.996;0.957	T	0.49735	-0.8908	10	0.39692	T	0.17	-40.2422	14.8622	0.70389	0.0:0.0:0.0:1.0	.	52;52;52	B4DWH1;A2A2I7;Q9Y6I8	.;.;PXMP4_HUMAN	A	52	ENSP00000386385:T52A	ENSP00000217398:T52A	T	-	1	0	PXMP4	31766163	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	7.943000	0.87716	1.996000	0.58369	0.368000	0.22195	ACC	.	.		0.502	PXMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078739.2	NM_007238	
EIF2S2	8894	hgsc.bcm.edu	37	20	32686360	32686360	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:32686360T>C	ENST00000374980.2	-	4	598	c.377A>G	c.(376-378)aAg>aGg	p.K126R		NM_003908.3	NP_003899.2	P20042	IF2B_HUMAN	eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa	126	Poly-Lys.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|male germ cell proliferation (GO:0002176)|male gonad development (GO:0008584)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 2 complex (GO:0005850)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|prostate(3)|upper_aerodigestive_tract(1)	11						CTTCTTTTTCTTCTTTTTATT	0.383																																					p.K126R		Atlas-SNP	.											.	EIF2S2	32	.	0			c.A377G						.						105.0	101.0	103.0					20																	32686360		2203	4300	6503	SO:0001583	missense	8894	exon4			TTTTTCTTCTTTT	M29536	CCDS13231.1	20q11.2	2012-04-17	2002-08-29		ENSG00000125977	ENSG00000125977		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	3266	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 67"""	603908	"""eukaryotic translation initiation factor 2, subunit 2 (beta, 38kD )"""	EIF2		3044606	Standard	XM_005260605		Approved	EIF2beta, PPP1R67	uc031rsu.1	P20042	OTTHUMG00000032287	ENST00000374980.2:c.377A>G	chr20.hg19:g.32686360T>C	ENSP00000364119:p.Lys126Arg	81.0	0.0		72.0	4.0	NM_003908	Q9BVU0|Q9UJE4	Missense_Mutation	SNP	ENST00000374980.2	hg19	CCDS13231.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.461514	0.63513	.	.	ENSG00000125977	ENST00000374980	T	0.55588	0.51	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.66470	0.2792	L	0.55017	1.72	0.80722	D	1	B;P;P	0.52842	0.002;0.956;0.956	B;P;P	0.62184	0.003;0.899;0.899	T	0.66073	-0.6014	10	0.46703	T	0.11	-14.8695	16.1549	0.81657	0.0:0.0:0.0:1.0	.	126;126;126	B5BU01;Q6IBR8;P20042	.;.;IF2B_HUMAN	R	126	ENSP00000364119:K126R	ENSP00000364119:K126R	K	-	2	0	EIF2S2	32150021	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.412000	0.73303	2.207000	0.71202	0.528000	0.53228	AAG	.	.		0.383	EIF2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078765.2	NM_003908	
CEP250	11190	hgsc.bcm.edu	37	20	34092346	34092346	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:34092346A>G	ENST00000397527.1	+	30	6869	c.6149A>G	c.(6148-6150)gAg>gGg	p.E2050G	CEP250_ENST00000342580.4_Missense_Mutation_p.E1994G	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	2050	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			AGGGATGAAGAGCTGAGACAT	0.557																																					p.E2050G		Atlas-SNP	.											.	CEP250	141	.	0			c.A6149G						.						30.0	31.0	31.0					20																	34092346		2203	4300	6503	SO:0001583	missense	11190	exon30			ATGAAGAGCTGAG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.6149A>G	chr20.hg19:g.34092346A>G	ENSP00000380661:p.Glu2050Gly	71.0	0.0		79.0	4.0	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	A	18.40	3.616285	0.66672	.	.	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.57907	2.42;2.36;0.37	4.83	4.83	0.62350	.	0.000000	0.56097	D	0.000026	T	0.60547	0.2277	M	0.68952	2.095	0.34852	D	0.741764	P	0.49559	0.925	P	0.49752	0.621	T	0.75374	-0.3340	10	0.72032	D	0.01	.	14.2031	0.65716	1.0:0.0:0.0:0.0	.	2050	Q9BV73	CP250_HUMAN	G	2050;1994;538	ENSP00000380661:E2050G;ENSP00000341541:E1994G;ENSP00000395992:E538G	ENSP00000341541:E1994G	E	+	2	0	CEP250	33555760	0.976000	0.34144	0.880000	0.34516	0.991000	0.79684	2.566000	0.45948	2.021000	0.59480	0.533000	0.62120	GAG	.	.		0.557	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
TGIF2	60436	hgsc.bcm.edu	37	20	35219773	35219773	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:35219773A>G	ENST00000373874.2	+	3	852	c.653A>G	c.(652-654)cAg>cGg	p.Q218R	RP5-977B1.11_ENST00000561134.1_RNA|TGIF2_ENST00000373872.4_Missense_Mutation_p.Q218R|TGIF2-C20orf24_ENST00000558530.1_Intron	NM_001199514.1|NM_001199515.1	NP_001186443.1|NP_001186444.1	Q9GZN2	TGIF2_HUMAN	TGFB-induced factor homeobox 2	218	Repressive function.				gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nodal signaling pathway (GO:0038092)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|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)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				CAGAAGCAGCAGGACCCATCA	0.577																																					p.Q218R		Atlas-SNP	.											.	TGIF2	26	.	0			c.A653G						.						127.0	125.0	125.0					20																	35219773		2200	4295	6495	SO:0001583	missense	60436	exon3			AGCAGCAGGACCC	AB042646	CCDS13278.1	20q11.23	2012-12-12	2007-02-07		ENSG00000118707	ENSG00000118707		"""Homeoboxes / TALE class"""	15764	protein-coding gene	gene with protein product		607294	"""TGFB-induced factor 2 (TALE family homeobox)"""			11006116	Standard	NM_021809		Approved		uc021wcv.1	Q9GZN2	OTTHUMG00000172332	ENST00000373874.2:c.653A>G	chr20.hg19:g.35219773A>G	ENSP00000362981:p.Gln218Arg	112.0	0.0		117.0	6.0	NM_021809	B2R9U3|E1P5T9|H0YNI0	Missense_Mutation	SNP	ENST00000373874.2	hg19	CCDS13278.1	.	.	.	.	.	.	.	.	.	.	A	14.18	2.457346	0.43634	.	.	ENSG00000118707	ENST00000373874;ENST00000373872	T;T	0.65732	-0.17;-0.17	5.5	5.5	0.81552	.	0.750110	0.13143	N	0.410470	T	0.53142	0.1778	L	0.39898	1.24	0.80722	D	1	B	0.11235	0.004	B	0.04013	0.001	T	0.51529	-0.8694	10	0.56958	D	0.05	-22.1275	9.2083	0.37302	0.9107:0.0:0.0893:0.0	.	218	Q9GZN2	TGIF2_HUMAN	R	218	ENSP00000362981:Q218R;ENSP00000362979:Q218R	ENSP00000362979:Q218R	Q	+	2	0	TGIF2	34653187	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.798000	0.55522	2.077000	0.62373	0.459000	0.35465	CAG	.	.		0.577	TGIF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079004.2	NM_021809	
CHD6	84181	hgsc.bcm.edu	37	20	40084597	40084597	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:40084597T>C	ENST00000373233.3	-	19	3029	c.2852A>G	c.(2851-2853)gAg>gGg	p.E951G	CHD6_ENST00000309279.7_Intron	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	951	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)				GTCCTCCACCTCCATTTTTGA	0.448																																					p.E951G		Atlas-SNP	.											.	CHD6	312	.	0			c.A2852G						.						174.0	164.0	167.0					20																	40084597		2203	4300	6503	SO:0001583	missense	84181	exon19			TCCACCTCCATTT	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.2852A>G	chr20.hg19:g.40084597T>C	ENSP00000362330:p.Glu951Gly	137.0	0.0		119.0	5.0	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.736086	0.89482	.	.	ENSG00000124177	ENST00000373233	T	0.75589	-0.95	5.73	5.73	0.89815	Helicase, C-terminal (1);	0.000000	0.64402	D	0.000017	D	0.90707	0.7084	H	0.96080	3.765	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.93516	0.6857	10	0.87932	D	0	-29.5288	16.3123	0.82883	0.0:0.0:0.0:1.0	.	951	Q8TD26	CHD6_HUMAN	G	951	ENSP00000362330:E951G	ENSP00000362330:E951G	E	-	2	0	CHD6	39518011	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.040000	0.89188	2.308000	0.77769	0.533000	0.62120	GAG	.	.		0.448	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1		
PREX1	57580	hgsc.bcm.edu	37	20	47342873	47342873	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:47342873A>G	ENST00000371941.3	-	5	597	c.575T>C	c.(574-576)cTg>cCg	p.L192P	PREX1_ENST00000396220.1_Missense_Mutation_p.L192P	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	192	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)			CGGAGACAACAGGTAGCCTTC	0.512																																					p.L192P		Atlas-SNP	.											.	PREX1	441	.	0			c.T575C						.						101.0	83.0	89.0					20																	47342873		2203	4300	6503	SO:0001583	missense	57580	exon5			GACAACAGGTAGC	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.575T>C	chr20.hg19:g.47342873A>G	ENSP00000361009:p.Leu192Pro	126.0	0.0		89.0	5.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	a	25.4	4.636544	0.87760	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	D;D	0.84298	-1.83;-1.83	5.51	5.51	0.81932	Guanine-nucleotide dissociation stimulator, CDC24, conserved site (1);Dbl homology (DH) domain (5);	0.000000	0.42294	U	0.000728	D	0.95510	0.8541	H	0.98542	4.26	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97213	0.9872	10	0.87932	D	0	.	14.906	0.70718	1.0:0.0:0.0:0.0	.	192	Q8TCU6	PREX1_HUMAN	P	192	ENSP00000361009:L192P;ENSP00000379522:L192P	ENSP00000361009:L192P	L	-	2	0	PREX1	46776280	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.471000	0.90403	2.215000	0.71742	0.529000	0.55759	CTG	.	.		0.512	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
NPEPL1	79716	hgsc.bcm.edu	37	20	57269500	57269500	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:57269500T>C	ENST00000356091.6	+	3	647	c.359T>C	c.(358-360)gTc>gCc	p.V120A	NPEPL1_ENST00000525817.1_Missense_Mutation_p.V72A|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Missense_Mutation_p.V92A	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	120						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			CAGCCGGAGGTCTTTGCTTCC	0.652																																					p.V120A		Atlas-SNP	.											.	NPEPL1	36	.	0			c.T359C						.						69.0	76.0	74.0					20																	57269500		2041	4187	6228	SO:0001583	missense	79716	exon3			CGGAGGTCTTTGC	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.359T>C	chr20.hg19:g.57269500T>C	ENSP00000348395:p.Val120Ala	69.0	0.0		107.0	5.0	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	hg19	CCDS46621.1	.	.	.	.	.	.	.	.	.	.	T	10.51	1.370083	0.24771	.	.	ENSG00000215440	ENST00000525967;ENST00000525817;ENST00000356091	T;T;T	0.32023	1.47;1.49;1.48	4.58	3.49	0.39957	.	0.057690	0.64402	N	0.000002	T	0.23370	0.0565	L	0.52206	1.635	0.58432	D	0.99999	B;B;B;B	0.14438	0.0;0.0;0.001;0.01	B;B;B;B	0.22753	0.003;0.007;0.003;0.041	T	0.05937	-1.0855	10	0.14656	T	0.56	-24.6563	5.9423	0.19199	0.0:0.1513:0.0:0.8487	.	120;72;92;120	Q8NDH3;G5EA34;E9PN47;Q8NDH3-3	PEPL1_HUMAN;.;.;.	A	92;72;120	ENSP00000434810:V92A;ENSP00000437112:V72A;ENSP00000348395:V120A	ENSP00000348395:V120A	V	+	2	0	NPEPL1	56702907	1.000000	0.71417	0.319000	0.25293	0.122000	0.20287	3.234000	0.51320	0.693000	0.31634	0.449000	0.29647	GTC	.	.		0.652	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
SYCP2	10388	hgsc.bcm.edu	37	20	58489043	58489043	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:58489043C>T	ENST00000357552.3	-	12	1042	c.817G>A	c.(817-819)Gga>Aga	p.G273R	SYCP2_ENST00000371001.2_Missense_Mutation_p.G273R			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	273					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			CTTTTGTCTCCAAGCATGCCA	0.294																																					p.G273R		Atlas-SNP	.											.	SYCP2	204	.	0			c.G817A						.						68.0	65.0	66.0					20																	58489043		2201	4298	6499	SO:0001583	missense	10388	exon11			TGTCTCCAAGCAT	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.817G>A	chr20.hg19:g.58489043C>T	ENSP00000350162:p.Gly273Arg	126.0	0.0		148.0	6.0	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.152350	0.78001	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.04809	3.55;3.55;3.55	4.91	4.91	0.64330	.	0.101773	0.43110	D	0.000601	T	0.24812	0.0602	M	0.80422	2.495	0.44282	D	0.99714	D;D	0.89917	1.0;1.0	D;D	0.87578	0.995;0.998	T	0.01743	-1.1283	10	0.87932	D	0	-22.4929	18.4759	0.90792	0.0:1.0:0.0:0.0	.	273;273	A2A341;Q9BX26	.;SYCP2_HUMAN	R	273	ENSP00000360040:G273R;ENSP00000350162:G273R;ENSP00000402456:G273R	ENSP00000350162:G273R	G	-	1	0	SYCP2	57922438	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.736000	0.68597	2.430000	0.82344	0.655000	0.94253	GGA	.	.		0.294	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	
CDH26	60437	hgsc.bcm.edu	37	20	58547020	58547020	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:58547020T>C	ENST00000244047.5	+	4	546	c.235T>C	c.(235-237)Ttc>Ctc	p.F79L	CDH26_ENST00000348616.4_Missense_Mutation_p.F79L			Q8IXH8	CAD26_HUMAN	cadherin 26	79	Cadherin 1. {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)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			CTTCCAGCTGTTCAATAATAT	0.353																																					p.F79L		Atlas-SNP	.											.	CDH26	229	.	0			c.T235C						.						122.0	115.0	117.0					20																	58547020		2203	4300	6503	SO:0001583	missense	60437	exon4			CAGCTGTTCAATA	AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"""Cadherins / Major cadherins"""	15902	protein-coding gene	gene with protein product			"""cadherin-like 26"""				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.235T>C	chr20.hg19:g.58547020T>C	ENSP00000244047:p.Phe79Leu	104.0	0.0		70.0	4.0	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Missense_Mutation	SNP	ENST00000244047.5	hg19		.	.	.	.	.	.	.	.	.	.	T	16.94	3.261979	0.59431	.	.	ENSG00000124215	ENST00000244047;ENST00000348616	T;T	0.57907	0.37;0.46	5.13	4.03	0.46877	.	0.055201	0.64402	D	0.000001	T	0.63896	0.2550	M	0.75447	2.3	0.46376	D	0.999011	P	0.40602	0.723	P	0.52758	0.708	T	0.62234	-0.6897	10	0.41790	T	0.15	.	10.0199	0.42037	0.0:0.0816:0.0:0.9184	.	79	Q8IXH8-4	.	L	79	ENSP00000244047:F79L;ENSP00000339390:F79L	ENSP00000244047:F79L	F	+	1	0	CDH26	57980415	1.000000	0.71417	0.951000	0.38953	0.718000	0.41266	4.458000	0.60095	0.904000	0.36572	0.528000	0.53228	TTC	.	.		0.353	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980	
OGFR	11054	hgsc.bcm.edu	37	20	61443731	61443731	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:61443731A>G	ENST00000290291.6	+	7	789	c.764A>G	c.(763-765)gAc>gGc	p.D255G	OGFR_ENST00000370461.1_Missense_Mutation_p.D203G	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	255					opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					AGTGCCCTGGACTACTTCATG	0.706																																					p.D255G		Atlas-SNP	.											.	OGFR	63	.	0			c.A764G						.						12.0	12.0	12.0					20																	61443731		2160	4254	6414	SO:0001583	missense	11054	exon7			CCCTGGACTACTT	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.764A>G	chr20.hg19:g.61443731A>G	ENSP00000290291:p.Asp255Gly	47.0	0.0		78.0	6.0	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	hg19	CCDS13504.1	.	.	.	.	.	.	.	.	.	.	A	18.28	3.589434	0.66105	.	.	ENSG00000060491	ENST00000290291;ENST00000370468;ENST00000357163;ENST00000370469;ENST00000370461	T;T;T	0.52754	1.55;0.65;1.08	4.57	4.57	0.56435	Opioid growth factor receptor (OGFr) conserved domain (1);	0.106918	0.64402	N	0.000007	T	0.46639	0.1403	M	0.65975	2.015	0.45490	D	0.998451	B;B;B	0.33171	0.4;0.4;0.4	B;B;B	0.30251	0.113;0.113;0.113	T	0.53620	-0.8413	10	0.72032	D	0.01	-43.7867	13.9168	0.63902	1.0:0.0:0.0:0.0	.	255;238;255	B3KMQ6;Q05BV5;Q9NZT2	.;.;OGFR_HUMAN	G	255;255;255;110;203	ENSP00000290291:D255G;ENSP00000359499:D255G;ENSP00000359491:D203G	ENSP00000290291:D255G	D	+	2	0	OGFR	60914176	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.834000	0.92094	1.664000	0.50801	0.459000	0.35465	GAC	.	.		0.706	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
DIDO1	11083	hgsc.bcm.edu	37	20	61513462	61513462	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:61513462T>C	ENST00000266070.4	-	16	4171	c.3846A>G	c.(3844-3846)gcA>gcG	p.A1282A	DIDO1_ENST00000395343.1_Silent_p.A1282A	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1282	Pro-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GGCTGGGGGCTGCAGGTTTGA	0.652																																					p.A1282A	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.A3846G						.						62.0	68.0	66.0					20																	61513462		2202	4299	6501	SO:0001819	synonymous_variant	11083	exon16			GGGGGCTGCAGGT	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.3846A>G	chr20.hg19:g.61513462T>C		75.0	0.0		104.0	5.0	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	hg19	CCDS33506.1																																																																																			.	.		0.652	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
TMPRSS15	5651	hgsc.bcm.edu	37	21	19704485	19704485	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:19704485A>G	ENST00000284885.3	-	14	1603	c.1570T>C	c.(1570-1572)Tgt>Cgt	p.C524R		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	524	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						GGTCCTCCACAGTCCGCTGAA	0.383																																					p.C524R		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.T1570C						.						114.0	112.0	113.0					21																	19704485		2203	4300	6503	SO:0001583	missense	5651	exon14			CTCCACAGTCCGC		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1570T>C	chr21.hg19:g.19704485A>G	ENSP00000284885:p.Cys524Arg	73.0	0.0		92.0	5.0	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	hg19	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	A	18.79	3.698574	0.68386	.	.	ENSG00000154646	ENST00000284885	D	0.95377	-3.69	5.43	5.43	0.79202	CUB (5);	0.000000	0.85682	D	0.000000	D	0.98626	0.9540	H	0.97918	4.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99651	1.0991	9	.	.	.	.	14.6004	0.68438	1.0:0.0:0.0:0.0	.	524	P98073	ENTK_HUMAN	R	524	ENSP00000284885:C524R	.	C	-	1	0	TMPRSS15	18626356	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	6.228000	0.72288	2.184000	0.69523	0.528000	0.53228	TGT	.	.		0.383	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
KRTAP19-8	728299	hgsc.bcm.edu	37	21	32410759	32410759	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:32410759T>C	ENST00000382822.2	-	1	36	c.4A>G	c.(4-6)Agc>Ggc	p.S2G		NM_001099219.1	NP_001092689.1	Q3LI54	KR198_HUMAN	keratin associated protein 19-8	2						intermediate filament (GO:0005882)				endometrium(2)|upper_aerodigestive_tract(1)	3						CTGTAGTAGCTCATGGTTCAG	0.507																																					p.S2G		Atlas-SNP	.											.	KRTAP19-8	9	.	0			c.A4G						.						108.0	121.0	117.0					21																	32410759		2203	4300	6503	SO:0001583	missense	728299	exon1			AGTAGCTCATGGT	AB096964	CCDS42917.1	21q22.11	2007-11-23			ENSG00000206102	ENSG00000206102		"""Keratin associated proteins"""	33898	protein-coding gene	gene with protein product							Standard	NM_001099219		Approved		uc010glt.3	Q3LI54	OTTHUMG00000057787	ENST00000382822.2:c.4A>G	chr21.hg19:g.32410759T>C	ENSP00000372272:p.Ser2Gly	130.0	0.0		139.0	6.0	NM_001099219		Missense_Mutation	SNP	ENST00000382822.2	hg19	CCDS42917.1	.	.	.	.	.	.	.	.	.	.	T	7.608	0.674208	0.14841	.	.	ENSG00000206102	ENST00000382822	T	0.11821	2.74	4.04	-3.48	0.04739	.	1.705140	0.04349	U	0.355326	T	0.09069	0.0224	.	.	.	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.41822	-0.9487	9	0.87932	D	0	.	3.1895	0.06612	0.4744:0.1745:0.0:0.3511	.	2	Q3LI54	KR198_HUMAN	G	2	ENSP00000372272:S2G	ENSP00000372272:S2G	S	-	1	0	KRTAP19-8	31332630	0.014000	0.17966	0.054000	0.19295	0.026000	0.11368	-0.308000	0.08156	-0.357000	0.08175	-0.876000	0.02978	AGC	.	.		0.507	KRTAP19-8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000128239.3	NM_001099219	
SYNJ1	8867	hgsc.bcm.edu	37	21	34053824	34053824	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:34053824A>G	ENST00000322229.7	-	10	1334	c.1335T>C	c.(1333-1335)gcT>gcC	p.A445A	SYNJ1_ENST00000433931.2_Silent_p.A484A|SYNJ1_ENST00000382499.2_Silent_p.A484A|SYNJ1_ENST00000357345.3_Silent_p.A445A|SYNJ1_ENST00000382491.3_Silent_p.A445A			O43426	SYNJ1_HUMAN	synaptojanin 1	445					cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						TCCCTTCAAGAGCTCCAGTTC	0.378																																					p.A484A		Atlas-SNP	.											.	SYNJ1	253	.	0			c.T1452C						.						161.0	159.0	160.0					21																	34053824		2203	4300	6503	SO:0001819	synonymous_variant	8867	exon11			TTCAAGAGCTCCA	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.1335T>C	chr21.hg19:g.34053824A>G		104.0	0.0		112.0	5.0	NM_203446	O43425|O94984|Q4KMR1	Silent	SNP	ENST00000322229.7	hg19	CCDS54484.1																																																																																			.	.		0.378	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
LCA5L	150082	hgsc.bcm.edu	37	21	40800338	40800338	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:40800338C>T	ENST00000358268.2	-	4	610	c.82G>A	c.(82-84)Gca>Aca	p.A28T	LCA5L_ENST00000380671.2_Missense_Mutation_p.A28T|LCA5L_ENST00000485895.2_Missense_Mutation_p.A28T|LCA5L_ENST00000288350.3_Missense_Mutation_p.A28T			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	28										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)				CTCTTGCATGCTGCAGACCTC	0.408																																					p.A28T		Atlas-SNP	.											.	LCA5L	57	.	0			c.G82A						.						126.0	120.0	122.0					21																	40800338		2203	4300	6503	SO:0001583	missense	150082	exon4			TGCATGCTGCAGA	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.82G>A	chr21.hg19:g.40800338C>T	ENSP00000351008:p.Ala28Thr	150.0	0.0		146.0	6.0	NM_152505	D3DSI0|Q3ZCT0	Missense_Mutation	SNP	ENST00000358268.2	hg19	CCDS13665.1	.	.	.	.	.	.	.	.	.	.	C	14.19	2.461870	0.43736	.	.	ENSG00000157578	ENST00000288350;ENST00000380671;ENST00000358268;ENST00000418018;ENST00000448288;ENST00000434281;ENST00000438404;ENST00000411566;ENST00000415863;ENST00000426783;ENST00000456017	T;T;T;T;T;T;T;T;T;T;T	0.68479	0.5;0.5;0.5;0.91;0.9;0.9;0.9;0.9;0.88;0.87;-0.33	5.43	3.57	0.40892	.	0.433618	0.21726	N	0.070045	T	0.45756	0.1358	N	0.14661	0.345	0.09310	N	1	B;B	0.26547	0.02;0.152	B;B	0.20955	0.023;0.032	T	0.40384	-0.9566	10	0.72032	D	0.01	-9.476	7.4124	0.27025	0.0:0.59:0.32:0.09	.	28;28	C9JFB6;O95447	.;LCA5L_HUMAN	T	28	ENSP00000288350:A28T;ENSP00000370046:A28T;ENSP00000351008:A28T;ENSP00000404521:A28T;ENSP00000405598:A28T;ENSP00000400086:A28T;ENSP00000405130:A28T;ENSP00000412691:A28T;ENSP00000395593:A28T;ENSP00000414784:A28T;ENSP00000407065:A28T	ENSP00000288350:A28T	A	-	1	0	LCA5L	39722208	0.000000	0.05858	0.001000	0.08648	0.134000	0.20937	0.328000	0.19681	0.632000	0.30432	0.655000	0.94253	GCA	.	.		0.408	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505	
IGSF5	150084	hgsc.bcm.edu	37	21	41143130	41143130	+	Silent	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:41143130C>A	ENST00000380588.4	+	4	809	c.706C>A	c.(706-708)Cgg>Agg	p.R236R	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	236					single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.R236W(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				CACTGTGATTCGGTGTCCCCA	0.468																																					p.R236R		Atlas-SNP	.											IGSF5,caecum,carcinoma,0,1	IGSF5	62	.	1	Substitution - Missense(1)	large_intestine(1)	c.C706A						.						70.0	71.0	71.0					21																	41143130		2203	4300	6503	SO:0001819	synonymous_variant	150084	exon4			GTGATTCGGTGTC		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5952	protein-coding gene	gene with protein product	"""junctional adhesion molecule 4"""	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.706C>A	chr21.hg19:g.41143130C>A		98.0	0.0		70.0	3.0	NM_001080444		Silent	SNP	ENST00000380588.4	hg19	CCDS33562.1																																																																																			.	.		0.468	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1		
DSCAM	1826	hgsc.bcm.edu	37	21	41434820	41434820	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:41434820T>C	ENST00000400454.1	-	28	5372	c.4895A>G	c.(4894-4896)aAg>aGg	p.K1632R		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1632					cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				AGCTAAACTCTTTGCATCTGG	0.348																																					p.K1632R	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.A4895G						.						127.0	117.0	120.0					21																	41434820		1865	4102	5967	SO:0001583	missense	1826	exon28			AAACTCTTTGCAT	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.4895A>G	chr21.hg19:g.41434820T>C	ENSP00000383303:p.Lys1632Arg	96.0	0.0		88.0	4.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.845118	0.91197	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.60040	0.22;0.34	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.60869	0.2302	L	0.36672	1.1	0.42313	D	0.992225	D	0.63880	0.993	P	0.54629	0.757	T	0.60677	-0.7216	10	0.38643	T	0.18	.	15.5822	0.76452	0.0:0.0:0.0:1.0	.	1632	O60469	DSCAM_HUMAN	R	1632;1384	ENSP00000383303:K1632R;ENSP00000385342:K1384R	ENSP00000383303:K1632R	K	-	2	0	DSCAM	40356690	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.349000	0.79376	2.210000	0.71456	0.533000	0.62120	AAG	.	.		0.348	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
AGPAT3	56894	hgsc.bcm.edu	37	21	45389012	45389012	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:45389012T>C	ENST00000398063.2	+	4	854	c.362T>C	c.(361-363)cTc>cCc	p.L121P	AGPAT3_ENST00000291572.8_Missense_Mutation_p.L121P|AGPAT3_ENST00000327505.2_Missense_Mutation_p.L121P|AGPAT3_ENST00000546158.1_Missense_Mutation_p.L121P|AGPAT3_ENST00000398061.1_Missense_Mutation_p.L121P|AGPAT3_ENST00000479117.1_3'UTR|AGPAT3_ENST00000398058.1_Missense_Mutation_p.L121P	NM_001037553.1	NP_001032642.1	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3	121					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			large_intestine(4)|lung(5)|ovary(1)|prostate(1)	11				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		TCCAAGGTCCTCGCTAAGAAG	0.637																																					p.L121P	Pancreas(60;623 1650 5574 52796)	Atlas-SNP	.											.	AGPAT3	37	.	0			c.T362C						.						112.0	87.0	95.0					21																	45389012		2203	4300	6503	SO:0001583	missense	56894	exon4			AGGTCCTCGCTAA	AF156774	CCDS13703.1	21q22.3	2013-02-05			ENSG00000160216	ENSG00000160216	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	326	protein-coding gene	gene with protein product		614794					Standard	XM_005261159		Approved	LPAAT-gamma	uc002zdw.3	Q9NRZ7	OTTHUMG00000086892	ENST00000398063.2:c.362T>C	chr21.hg19:g.45389012T>C	ENSP00000381140:p.Leu121Pro	119.0	0.0		119.0	5.0	NM_001037553	D3DSL2|Q3ZCU2|Q6UWP6|Q6ZUC6|Q8N3Q7|Q9NRZ6	Missense_Mutation	SNP	ENST00000398063.2	hg19	CCDS13703.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.200300	0.79015	.	.	ENSG00000160216	ENST00000291572;ENST00000398061;ENST00000327505;ENST00000445582;ENST00000398063;ENST00000438598;ENST00000398058;ENST00000457068;ENST00000422850;ENST00000546158	D;D;D;D;D;D;D;D	0.94330	-3.4;-3.4;-3.4;-3.4;-3.4;-3.4;-3.4;-3.4	4.5	4.5	0.54988	Phospholipid/glycerol acyltransferase (2);	0.000000	0.64402	D	0.000001	D	0.96500	0.8858	M	0.82517	2.595	0.80722	D	1	D;D	0.89917	1.0;0.995	D;D	0.79784	0.993;0.971	D	0.96997	0.9726	10	0.72032	D	0.01	-14.3743	13.8003	0.63196	0.0:0.0:0.0:1.0	.	141;121	Q9NRZ7-3;Q9NRZ7	.;PLCC_HUMAN	P	121	ENSP00000291572:L121P;ENSP00000381138:L121P;ENSP00000332989:L121P;ENSP00000381140:L121P;ENSP00000381135:L121P;ENSP00000413906:L121P;ENSP00000414440:L121P;ENSP00000443510:L121P	ENSP00000291572:L121P	L	+	2	0	AGPAT3	44213440	1.000000	0.71417	0.684000	0.30055	0.948000	0.59901	7.470000	0.80973	1.667000	0.50832	0.402000	0.26972	CTC	.	.		0.637	AGPAT3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195722.1	NM_020132	
PWP2	5822	hgsc.bcm.edu	37	21	45547852	45547852	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:45547852T>C	ENST00000291576.7	+	18	2307	c.2180T>C	c.(2179-2181)aTc>aCc	p.I727T	PWP2_ENST00000494310.1_3'UTR	NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	727					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		GGACTCCTCATCTACTCCCTG	0.582																																					p.I727T		Atlas-SNP	.											.	PWP2	64	.	0			c.T2180C						.						42.0	41.0	41.0					21																	45547852		2200	4300	6500	SO:0001583	missense	5822	exon18			TCCTCATCTACTC		CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"""WD repeat domain containing"""	9711	protein-coding gene	gene with protein product		601475	"""PWP2 (periodic tryptophan protein, yeast) homolog"""	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.2180T>C	chr21.hg19:g.45547852T>C	ENSP00000291576:p.Ile727Thr	69.0	0.0		90.0	4.0	NM_005049	B2RAG8|Q96A77	Missense_Mutation	SNP	ENST00000291576.7	hg19	CCDS33579.1	.	.	.	.	.	.	.	.	.	.	T	16.95	3.263433	0.59431	.	.	ENSG00000241945	ENST00000291576	T	0.65364	-0.15	4.47	4.47	0.54385	WD40/YVTN repeat-like-containing domain (1);	0.281959	0.38381	N	0.001703	T	0.60612	0.2282	M	0.69248	2.105	0.54753	D	0.999981	B	0.14438	0.01	B	0.10450	0.005	T	0.63269	-0.6675	10	0.72032	D	0.01	-18.2125	13.0243	0.58806	0.0:0.0:0.0:1.0	.	727	Q15269	PWP2_HUMAN	T	727	ENSP00000291576:I727T	ENSP00000291576:I727T	I	+	2	0	PWP2	44372280	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.201000	0.77847	1.956000	0.56807	0.533000	0.62120	ATC	.	.		0.582	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049	
CECR1	51816	hgsc.bcm.edu	37	22	17662863	17662863	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:17662863A>G	ENST00000399839.1	-	9	1559	c.1289T>C	c.(1288-1290)aTg>aCg	p.M430T	CECR1_ENST00000399837.2_Missense_Mutation_p.M430T|CECR1_ENST00000330232.4_Missense_Mutation_p.M189T|CECR1_ENST00000449907.2_Missense_Mutation_p.M388T|CECR1_ENST00000262607.3_Missense_Mutation_p.M430T	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	430					adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				CCCAGTGGCCATCAGAGTGGC	0.512																																					p.M430T		Atlas-SNP	.											.	CECR1	77	.	0			c.T1289C						.						86.0	76.0	79.0					22																	17662863		2203	4300	6503	SO:0001583	missense	51816	exon8			GTGGCCATCAGAG	AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.1289T>C	chr22.hg19:g.17662863A>G	ENSP00000382733:p.Met430Thr	64.0	0.0		72.0	4.0	NM_017424	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Missense_Mutation	SNP	ENST00000399839.1	hg19	CCDS13742.1	.	.	.	.	.	.	.	.	.	.	A	14.53	2.564220	0.45694	.	.	ENSG00000093072	ENST00000399839;ENST00000330232;ENST00000262607;ENST00000449907;ENST00000399837	D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62	3.92	3.92	0.45320	Adenosine/AMP deaminase (1);	0.124034	0.64402	D	0.000001	D	0.90940	0.7152	M	0.86028	2.79	0.49687	D	0.99981	D;D	0.89917	1.0;0.982	D;P	0.81914	0.995;0.875	D	0.92061	0.5656	10	0.72032	D	0.01	.	12.8002	0.57582	1.0:0.0:0.0:0.0	.	430;189	Q9NZK5;Q9NZK5-2	CECR1_HUMAN;.	T	430;189;430;388;430	ENSP00000382733:M430T;ENSP00000332871:M189T;ENSP00000262607:M430T;ENSP00000406443:M388T;ENSP00000382731:M430T	ENSP00000262607:M430T	M	-	2	0	CECR1	16042863	1.000000	0.71417	0.162000	0.22713	0.435000	0.31806	6.006000	0.70724	1.407000	0.46875	0.454000	0.30748	ATG	.	.		0.512	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1		
CLTCL1	8218	hgsc.bcm.edu	37	22	19188997	19188998	+	Missense_Mutation	DNP	TC	TC	CT			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:19188997_19188998TC>CT	ENST00000263200.10	-	23	3679_3680	c.3607_3608GA>AG	c.(3607-3609)GAc>AGc	p.D1203S	CLTCL1_ENST00000442042.2_5'UTR|CLTCL1_ENST00000427926.1_Splice_Site_p.G1203E|CLTCL1_ENST00000353891.5_Missense_Mutation_p.D1203S	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1203	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					GTAACAGCGGTCTCCAACTACG	0.485			T	?	ALCL																																p.D1203G|p.D1203N		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.A3608G|c.G3607A						.																																			SO:0001583	missense	8218	exon23			CAGCGGTCTCCAA|AGCGGTCTCCAAC		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.3607_3608delinsCT	chr22.hg19:g.19188997_19188998delinsCT	ENSP00000445677:p.Asp1203Ser	107.0|105.0	0.0		107.0|106.0	5.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	hg19	CCDS46662.1																																																																																			.	.		0.485	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
TANGO2	128989	hgsc.bcm.edu	37	22	20024329	20024329	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:20024329T>C	ENST00000327374.4	+	2	186	c.8T>C	c.(7-9)aTc>aCc	p.I3T	TANGO2_ENST00000479679.1_3'UTR|TANGO2_ENST00000447208.2_Missense_Mutation_p.I3T|TANGO2_ENST00000432883.1_Missense_Mutation_p.I3T|TANGO2_ENST00000434570.2_5'UTR|TANGO2_ENST00000456048.1_5'Flank|TANGO2_ENST00000401833.1_5'UTR|TANGO2_ENST00000398042.2_Missense_Mutation_p.I3T|TANGO2_ENST00000420290.2_5'UTR|TANGO2_ENST00000401886.1_Missense_Mutation_p.I3T	NM_001283106.1|NM_001283116.1|NM_001283148.1|NM_001283154.1|NM_152906.4	NP_001270035.1|NP_001270045.1|NP_001270077.1|NP_001270083.1|NP_690870.3	Q6ICL3	TNG2_HUMAN	transport and golgi organization 2 homolog (Drosophila)	3																	ACCATGTGCATCATCTTCTTT	0.587																																					p.I3T		Atlas-SNP	.											.	TANGO2	4	.	0			c.T8C						.						197.0	150.0	166.0					22																	20024329		2203	4300	6503	SO:0001583	missense	128989	exon2			TGTGCATCATCTT		CCDS13772.1, CCDS63404.1, CCDS63405.1, CCDS63406.1, CCDS63407.1, CCDS74821.1, CCDS74822.1	22q11.21	2012-12-13	2012-12-13	2012-12-13	ENSG00000183597	ENSG00000183597			25439	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 25"""	C22orf25		12477932	Standard	XM_005261222		Approved	DKFZp761P1121	uc002zrc.1	Q6ICL3	OTTHUMG00000150510	ENST00000327374.4:c.8T>C	chr22.hg19:g.20024329T>C	ENSP00000332721:p.Ile3Thr	98.0	0.0		125.0	5.0	NM_152906	A8MUE9|B7WNV6|B7Z583|B7Z730|D3DX23|Q8IW05|Q8NAL0|Q8TCS0|Q96M16	Missense_Mutation	SNP	ENST00000327374.4	hg19	CCDS13772.1	.	.	.	.	.	.	.	.	.	.	T	13.78	2.339307	0.41398	.	.	ENSG00000183597	ENST00000401886;ENST00000432198;ENST00000447208;ENST00000398042;ENST00000450664;ENST00000327374;ENST00000432883;ENST00000434168	T;T;T;T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39;1.39;1.39;1.39	4.14	3.1	0.35709	.	0.000000	0.85682	D	0.000000	T	0.58221	0.2107	M	0.82630	2.6	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;1.0;1.0;1.0;0.999	T	0.59080	-0.7521	10	0.66056	D	0.02	.	8.083	0.30756	0.0:0.102:0.0:0.898	.	3;3;3;3;3	B7Z9Q5;B7Z4A5;Q6AHY1;Q6ICL3;Q6ICL3-2	.;.;.;CV025_HUMAN;.	T	3	ENSP00000385662:I3T;ENSP00000413850:I3T;ENSP00000389797:I3T;ENSP00000381122:I3T;ENSP00000415450:I3T;ENSP00000332721:I3T;ENSP00000402926:I3T;ENSP00000411602:I3T	ENSP00000332721:I3T	I	+	2	0	C22orf25	18404329	1.000000	0.71417	1.000000	0.80357	0.365000	0.29674	6.609000	0.74173	0.721000	0.32231	-0.415000	0.06103	ATC	.	.		0.587	TANGO2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318689.2	NM_152906	
PRAME	23532	hgsc.bcm.edu	37	22	22892685	22892685	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:22892685T>C	ENST00000398741.1	-	5	722	c.416A>G	c.(415-417)aAc>aGc	p.N139S	PRAME_ENST00000402697.1_Missense_Mutation_p.N139S|PRAME_ENST00000539862.1_Missense_Mutation_p.N123S|PRAME_ENST00000405655.3_Missense_Mutation_p.N139S|PRAME_ENST00000398743.2_Missense_Mutation_p.N139S|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000424204.2_Missense_Mutation_p.N123S|PRAME_ENST00000543184.1_Missense_Mutation_p.N139S	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	139					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		ACTGGCCCTGTTTCCAGACCA	0.493																																					p.N139S	Melanoma(73;1707 1838 15168 27201)	Atlas-SNP	.											.	PRAME	78	.	0			c.A416G						.						77.0	72.0	74.0					22																	22892685		2203	4300	6503	SO:0001583	missense	23532	exon5			GCCCTGTTTCCAG	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"""-"""	9336	protein-coding gene	gene with protein product	"""cancer/testis antigen 130"""	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.416A>G	chr22.hg19:g.22892685T>C	ENSP00000381726:p.Asn139Ser	112.0	0.0		78.0	21.0	NM_206954	B2R6Y7|O43481|Q8IXN8	Missense_Mutation	SNP	ENST00000398741.1	hg19	CCDS13801.1	.	.	.	.	.	.	.	.	.	.	.	0.809	-0.752527	0.03041	.	.	ENSG00000185686	ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000539862;ENST00000402697;ENST00000424204;ENST00000439106;ENST00000420709	T;T;T;T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9;0.9;2.56;2.56	3.02	-0.399	0.12415	.	1.549960	0.03983	N	0.293671	T	0.12774	0.0310	N	0.00462	-1.47	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.11817	-1.0572	10	0.27785	T	0.31	.	3.8691	0.09029	0.1273:0.0:0.4273:0.4454	.	139	P78395	PRAME_HUMAN	S	139;139;139;139;123;139;123;139;139	ENSP00000381728:N139S;ENSP00000445675:N139S;ENSP00000381726:N139S;ENSP00000384343:N139S;ENSP00000445097:N123S;ENSP00000385198:N139S;ENSP00000407342:N123S;ENSP00000407320:N139S;ENSP00000412318:N139S	ENSP00000381726:N139S	N	-	2	0	PRAME	21222685	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	-1.283000	0.02796	-0.012000	0.14223	-0.396000	0.06452	AAC	.	.		0.493	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953	
XBP1	7494	hgsc.bcm.edu	37	22	29195079	29195079	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:29195079T>C	ENST00000216037.6	-	2	362	c.290A>G	c.(289-291)gAg>gGg	p.E97G	XBP1_ENST00000403532.3_Missense_Mutation_p.E97G|CTA-292E10.6_ENST00000585003.1_RNA|CTA-292E10.6_ENST00000458080.1_RNA|CTA-292E10.6_ENST00000418292.1_RNA|CTA-292E10.6_ENST00000451486.1_RNA|XBP1_ENST00000405219.3_Missense_Mutation_p.E47G|XBP1_ENST00000344347.5_Missense_Mutation_p.E97G	NM_001079539.1|NM_005080.3	NP_001073007.1|NP_005071.2	P17861	XBP1_HUMAN	X-box binding protein 1	97	bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to antibiotic (GO:0071236)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial cell maturation involved in salivary gland development (GO:0060691)|exocrine pancreas development (GO:0031017)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|serotonin secretion, neurotransmission (GO:0060096)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|large_intestine(1)|lung(1)	5						CTGTTCCAGCTCACTCATTCG	0.408																																					p.E97G		Atlas-SNP	.											.	XBP1	37	.	0			c.A290G						.						131.0	114.0	120.0					22																	29195079		2203	4300	6503	SO:0001583	missense	7494	exon2			TCCAGCTCACTCA	M31627	CCDS13847.1	22q12.1	2013-01-10			ENSG00000100219	ENSG00000100219		"""basic leucine zipper proteins"""	12801	protein-coding gene	gene with protein product		194355		XBP2		1718857, 2196176	Standard	NM_001079539		Approved		uc003aec.3	P17861	OTTHUMG00000151094	ENST00000216037.6:c.290A>G	chr22.hg19:g.29195079T>C	ENSP00000216037:p.Glu97Gly	86.0	0.0		112.0	6.0	NM_001079539	Q8WYK6|Q969P1|Q96BD7	Missense_Mutation	SNP	ENST00000216037.6	hg19	CCDS13847.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.934656	0.92458	.	.	ENSG00000100219	ENST00000216037;ENST00000403532;ENST00000344347;ENST00000405219	.	.	.	5.26	5.26	0.73747	.	0.048750	0.85682	D	0.000000	T	0.70290	0.3207	L	0.53671	1.685	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.977;0.996	T	0.68727	-0.5332	9	0.34782	T	0.22	.	14.0068	0.64468	0.0:0.0:0.0:1.0	.	97;47	P17861-2;B1AHH1	.;.	G	97;97;97;47	.	ENSP00000216037:E97G	E	-	2	0	XBP1	27525079	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.699000	0.74613	1.987000	0.57996	0.533000	0.62120	GAG	.	.		0.408	XBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321274.1	NM_005080	
DEPDC5	9681	hgsc.bcm.edu	37	22	32215113	32215113	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:32215113A>G	ENST00000382112.3	+	21	1842	c.1772A>G	c.(1771-1773)tAc>tGc	p.Y591C	DEPDC5_ENST00000535622.1_Missense_Mutation_p.Y591C|DEPDC5_ENST00000382111.2_Missense_Mutation_p.Y591C|DEPDC5_ENST00000400246.1_Missense_Mutation_p.Y591C|DEPDC5_ENST00000400248.2_Missense_Mutation_p.Y591C|DEPDC5_ENST00000536766.1_Missense_Mutation_p.Y563C|DEPDC5_ENST00000266091.3_Missense_Mutation_p.Y591C|DEPDC5_ENST00000400249.2_Missense_Mutation_p.Y591C|DEPDC5_ENST00000382105.2_Missense_Mutation_p.Y591C	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	591					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CCTGGTGGATACACGCCCCAG	0.562																																					p.Y591C		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A1772G						.						148.0	152.0	151.0					22																	32215113		2115	4226	6341	SO:0001583	missense	9681	exon22			GTGGATACACGCC	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.1772A>G	chr22.hg19:g.32215113A>G	ENSP00000371546:p.Tyr591Cys	130.0	0.0		140.0	8.0	NM_001242897	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	A	16.48	3.134531	0.56828	.	.	ENSG00000100150	ENST00000535622;ENST00000536766;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	T;T;T;T;T;T;T;T;T	0.31510	1.5;1.49;1.88;1.91;1.86;1.49;1.91;1.86;1.91	5.68	2.25	0.28309	.	0.128121	0.53938	N	0.000042	T	0.33177	0.0854	N	0.22421	0.69	0.80722	D	1	D;B;D;D;D;D	0.76494	0.999;0.003;0.999;0.999;0.997;0.999	P;B;D;D;D;D	0.79784	0.884;0.009;0.993;0.927;0.947;0.965	T	0.07986	-1.0744	10	0.39692	T	0.17	.	5.3509	0.16036	0.7256:0.0:0.1443:0.1301	.	591;563;591;591;591;591	B9EGN9;F5GYZ8;B4DH93;O75140-4;A8MPX9;O75140	.;.;.;.;.;DEPD5_HUMAN	C	591;563;591;591;591;591;591;591;591;591	ENSP00000440210:Y591C;ENSP00000441358:Y563C;ENSP00000266091:Y591C;ENSP00000383108:Y591C;ENSP00000383105:Y591C;ENSP00000371539:Y591C;ENSP00000371546:Y591C;ENSP00000371545:Y591C;ENSP00000383107:Y591C	ENSP00000266091:Y591C	Y	+	2	0	DEPDC5	30545113	1.000000	0.71417	0.364000	0.25888	0.883000	0.51084	3.586000	0.53950	0.436000	0.26393	0.460000	0.39030	TAC	.	.		0.562	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	
DEPDC5	9681	hgsc.bcm.edu	37	22	32266729	32266729	+	Splice_Site	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:32266729A>G	ENST00000382112.3	+	33	3527	c.3457A>G	c.(3457-3459)Agc>Ggc	p.S1153G	DEPDC5_ENST00000535622.1_Splice_Site_p.S1062G|DEPDC5_ENST00000382111.2_Splice_Site_p.S1162G|DEPDC5_ENST00000400248.2_Splice_Site_p.S1131G|DEPDC5_ENST00000539165.1_5'UTR|DEPDC5_ENST00000266091.3_Splice_Site_p.S1140G|DEPDC5_ENST00000400249.2_Splice_Site_p.S1131G|DEPDC5_ENST00000400246.1_Splice_Site_p.S1162G|DEPDC5_ENST00000382105.2_Splice_Site_p.S1084G|DEPDC5_ENST00000494060.1_3'UTR	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	1162					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CAGTGACAGCAGGTGAGATTC	0.542																																					p.S1162G		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A3484G						.						80.0	82.0	81.0					22																	32266729		1994	4167	6161	SO:0001630	splice_region_variant	9681	exon34			GACAGCAGGTGAG	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.3458+1A>G	chr22.hg19:g.32266729A>G		143.0	0.0		148.0	6.0	NM_001242896	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.95|12.95	2.091620|2.091620	0.36952|0.36952	.|.	.|.	ENSG00000100150|ENSG00000100150	ENST00000433147|ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	.|T;T;T;T;T;T;T;T	.|0.32272	.|1.52;1.94;1.94;1.89;1.46;1.9;1.89;1.94	5.95|5.95	4.92|4.92	0.64577|0.64577	.|.	.|0.466924	.|0.24573	.|N	.|0.037379	T|T	0.18425|0.18425	0.0442|0.0442	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	.|B;B;B;B;B;B	.|0.11235	.|0.0;0.003;0.0;0.004;0.0;0.001	.|B;B;B;B;B;B	.|0.13407	.|0.0;0.003;0.0;0.009;0.0;0.002	T|T	0.06770|0.06770	-1.0808|-1.0808	5|10	.|0.15952	.|T	.|0.53	.|.	9.714|9.714	0.40263|0.40263	0.9212:0.0:0.0788:0.0|0.9212:0.0:0.0788:0.0	.|.	.|1162;1062;548;1140;1153;1131	.|B9EGN9;B4DH93;O75140-7;O75140-4;A8MPX9;O75140	.|.;.;.;.;.;DEPD5_HUMAN	R|G	537|1062;1140;1131;1062;1162;1084;1153;1162;1131	.|ENSP00000440210:S1062G;ENSP00000266091:S1140G;ENSP00000383108:S1131G;ENSP00000383105:S1162G;ENSP00000371539:S1084G;ENSP00000371546:S1153G;ENSP00000371545:S1162G;ENSP00000383107:S1131G	.|ENSP00000266091:S1140G	Q|S	+|+	2|1	0|0	DEPDC5|DEPDC5	30596729|30596729	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.949000|0.949000	0.60115|0.60115	1.328000|1.328000	0.33758|0.33758	1.076000|1.076000	0.40961|0.40961	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.		0.542	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	Missense_Mutation
SSTR3	6753	hgsc.bcm.edu	37	22	37602589	37602590	+	Missense_Mutation	DNP	CA	CA	AC			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:37602589_37602590CA>AC	ENST00000328544.3	-	2	1786_1787	c.1253_1254TG>GT	c.(1252-1254)cTG>cGT	p.L418R	SSTR3_ENST00000402501.1_Missense_Mutation_p.L418R	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	418					cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	CCAGGCCCTACAGGTAGCTGAT	0.639																																					p.L418L|p.L418R		Atlas-SNP	.											.	SSTR3	42	.	0			c.G1254T|c.T1253G						.																																			SO:0001583	missense	6753	exon2			GCCCTACAGGTAG|CCCTACAGGTAGC		CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"""GPCR / Class A : Somatostatin receptors"""	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.1253_1254delinsAC	chr22.hg19:g.37602589_37602590delinsAC	ENSP00000330138:p.Leu418Arg	39.0	0.0		53.0|54.0	4.0	NM_001051	A8K550|Q53ZR7	Silent|Missense_Mutation	SNP	ENST00000328544.3	hg19	CCDS13944.1																																																																																			.	.		0.639	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1		
SOX10	6663	hgsc.bcm.edu	37	22	38379616	38379616	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:38379616T>C	ENST00000396884.2	-	2	458	c.176A>G	c.(175-177)cAg>cGg	p.Q59R	SOX10_ENST00000360880.2_Missense_Mutation_p.Q59R|SOX10_ENST00000470555.1_Intron|POLR2F_ENST00000405557.1_Intron|POLR2F_ENST00000407936.1_Intron	NM_006941.3	NP_008872.1	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10	59					anatomical structure morphogenesis (GO:0009653)|cell maturation (GO:0048469)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|enteric nervous system development (GO:0048484)|in utero embryonic development (GO:0001701)|melanocyte differentiation (GO:0030318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system development (GO:0007422)|positive regulation of gliogenesis (GO:0014015)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extrinsic component of mitochondrial outer membrane (GO:0031315)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|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 transcription factor activity involved in positive regulation of transcription (GO:0001190)|transcription coactivator activity (GO:0003713)			NS(6)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|skin(2)	20	Melanoma(58;0.045)					CTCGCCGTCCTGCTGCTCCTT	0.731																																					p.Q59R	Melanoma(39;342 1098 6220 32775 40068)|GBM(21;140 497 5227 16059 19275)	Atlas-SNP	.											.	SOX10	48	.	0			c.A176G						.						60.0	37.0	45.0					22																	38379616		2203	4300	6503	SO:0001583	missense	6663	exon2			CCGTCCTGCTGCT		CCDS13964.1	22q13.1	2014-09-17			ENSG00000100146	ENSG00000100146		"""SRY (sex determining region Y)-boxes"""	11190	protein-coding gene	gene with protein product	"""dominant megacolon, mouse, human homolog of"""	602229				9462749, 10441344, 12944398	Standard	NM_006941		Approved	DOM, WS4, WS2E	uc003aun.1	P56693	OTTHUMG00000149913	ENST00000396884.2:c.176A>G	chr22.hg19:g.38379616T>C	ENSP00000380093:p.Gln59Arg	57.0	0.0		83.0	4.0	NM_006941	B4DV62|Q6FHW7	Missense_Mutation	SNP	ENST00000396884.2	hg19	CCDS13964.1	.	.	.	.	.	.	.	.	.	.	T	9.955	1.221143	0.22457	.	.	ENSG00000100146	ENST00000396884;ENST00000360880;ENST00000416937;ENST00000427770	T;T;T	0.76578	-1.03;-1.03;-1.03	4.39	2.14	0.27477	.	0.545411	0.18672	N	0.134414	T	0.61924	0.2386	N	0.22421	0.69	0.33535	D	0.594119	B	0.15141	0.012	B	0.20384	0.029	T	0.57329	-0.7830	9	.	.	.	.	9.889	0.41279	0.0:0.0:0.3323:0.6677	.	59	P56693	SOX10_HUMAN	R	59	ENSP00000380093:Q59R;ENSP00000354130:Q59R;ENSP00000414853:Q59R	.	Q	-	2	0	SOX10	36709562	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.027000	0.41078	0.186000	0.20125	0.379000	0.24179	CAG	.	.		0.731	SOX10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313875.1	NM_006941	
PICK1	9463	hgsc.bcm.edu	37	22	38470994	38470994	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:38470994C>T	ENST00000404072.3	+	13	1450	c.1103C>T	c.(1102-1104)aCa>aTa	p.T368I	PICK1_ENST00000356976.3_Missense_Mutation_p.T368I|RP5-1039K5.13_ENST00000445483.1_RNA	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN	protein interacting with PRKCA 1	368					ATP catabolic process (GO:0006200)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|dendritic spine maintenance (GO:0097062)|dendritic spine organization (GO:0097061)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|glial cell development (GO:0021782)|long term synaptic depression (GO:0060292)|monoamine transport (GO:0015844)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|neuronal ion channel clustering (GO:0045161)|positive regulation of receptor internalization (GO:0002092)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|protein targeting (GO:0006605)|receptor clustering (GO:0043113)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endocytic vesicle membrane (GO:0030666)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein kinase C binding (GO:0005080)|receptor binding (GO:0005102)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	Melanoma(58;0.045)					GCGCACACCACATTGGCCTAT	0.617																																					p.T368I		Atlas-SNP	.											.	PICK1	30	.	0			c.C1103T						.						84.0	63.0	70.0					22																	38470994		2203	4300	6503	SO:0001583	missense	9463	exon13			ACACCACATTGGC	AL049654	CCDS13965.1	22q13.1	2006-02-14	2006-02-14	2006-02-14	ENSG00000100151	ENSG00000100151			9394	protein-coding gene	gene with protein product		605926	"""protein kinase C, alpha binding protein"", ""protein interacting with PRKCA"""	PRKCABP		10340301, 10591208	Standard	XM_006724377		Approved	dJ1039K5, MGC15204	uc003aus.3	Q9NRD5	OTTHUMG00000151159	ENST00000404072.3:c.1103C>T	chr22.hg19:g.38470994C>T	ENSP00000385205:p.Thr368Ile	107.0	0.0		116.0	46.0	NM_012407	B3KS52|O95906	Missense_Mutation	SNP	ENST00000404072.3	hg19	CCDS13965.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.863168	0.32884	.	.	ENSG00000100151	ENST00000404072;ENST00000356976	T;T	0.31510	1.49;1.49	4.33	3.21	0.36854	.	0.147994	0.64402	D	0.000013	T	0.24509	0.0594	L	0.47716	1.5	0.37753	D	0.926044	B	0.34103	0.437	B	0.27076	0.076	T	0.23547	-1.0185	10	0.32370	T	0.25	-16.1603	13.831	0.63380	0.0:0.8456:0.1544:0.0	.	368	Q9NRD5	PICK1_HUMAN	I	368	ENSP00000385205:T368I;ENSP00000349465:T368I	ENSP00000349465:T368I	T	+	2	0	PICK1	36800940	0.937000	0.31787	1.000000	0.80357	0.634000	0.38068	2.210000	0.42816	2.124000	0.65301	0.561000	0.74099	ACA	.	.		0.617	PICK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321569.2	NM_012407	
FAM83F	113828	hgsc.bcm.edu	37	22	40417739	40417739	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:40417739A>G	ENST00000333407.6	+	4	1319	c.1225A>G	c.(1225-1227)Aga>Gga	p.R409G	FAM83F_ENST00000473717.1_Missense_Mutation_p.R241G	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	409										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						TCACATGCACAGAGACCTGAA	0.662																																					p.R409G		Atlas-SNP	.											.	FAM83F	29	.	0			c.A1225G						.						32.0	26.0	28.0					22																	40417739		2203	4300	6503	SO:0001583	missense	113828	exon4			ATGCACAGAGACC		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.1225A>G	chr22.hg19:g.40417739A>G	ENSP00000330432:p.Arg409Gly	106.0	0.0		101.0	5.0	NM_138435	Q96FD6	Missense_Mutation	SNP	ENST00000333407.6	hg19	CCDS14000.2	.	.	.	.	.	.	.	.	.	.	A	11.94	1.790035	0.31685	.	.	ENSG00000133477	ENST00000333407	T	0.08008	3.14	4.42	-8.83	0.00806	.	2.532400	0.01078	N	0.004933	T	0.03390	0.0098	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.33929	-0.9849	10	0.22109	T	0.4	4.4295	4.758	0.13093	0.2899:0.168:0.452:0.09	.	409	Q8NEG4	FA83F_HUMAN	G	409	ENSP00000330432:R409G	ENSP00000330432:R409G	R	+	1	2	FAM83F	38747685	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-1.758000	0.01810	-1.733000	0.01357	0.379000	0.24179	AGA	.	.		0.662	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435	
UPK3A	7380	hgsc.bcm.edu	37	22	45681941	45681941	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:45681941A>G	ENST00000216211.4	+	2	204	c.172A>G	c.(172-174)Acc>Gcc	p.T58A	UPK3A_ENST00000396082.2_Missense_Mutation_p.T58A	NM_006953.3	NP_008884.1	O75631	UPK3A_HUMAN	uroplakin 3A	58					cell morphogenesis (GO:0000902)|epithelial cell differentiation (GO:0030855)|kidney development (GO:0001822)|potassium ion homeostasis (GO:0055075)|sodium ion homeostasis (GO:0055078)|urea transport (GO:0015840)|urinary bladder development (GO:0060157)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CCTCACTGGCACCCACGAGGT	0.572																																					p.T58A		Atlas-SNP	.											.	UPK3A	14	.	0			c.A172G						.						127.0	94.0	105.0					22																	45681941		2203	4300	6503	SO:0001583	missense	7380	exon2			ACTGGCACCCACG	AB010637	CCDS14064.1, CCDS54539.1	22q13.31	2005-11-14	2003-07-29	2003-07-30	ENSG00000100373	ENSG00000100373			12580	protein-coding gene	gene with protein product		611559	"""uroplakin 3"""	UPK3		9818021	Standard	NM_006953		Approved		uc003bfy.3	O75631	OTTHUMG00000151339	ENST00000216211.4:c.172A>G	chr22.hg19:g.45681941A>G	ENSP00000216211:p.Thr58Ala	101.0	0.0		112.0	7.0	NM_006953	B0QY25|O60261|Q32N05|Q5TII6	Missense_Mutation	SNP	ENST00000216211.4	hg19	CCDS14064.1	.	.	.	.	.	.	.	.	.	.	A	13.85	2.360497	0.41801	.	.	ENSG00000100373	ENST00000216211;ENST00000396082	T;D	0.83419	-0.06;-1.72	4.74	-9.49	0.00587	.	1.151650	0.06239	N	0.690140	T	0.65428	0.2690	L	0.36672	1.1	0.09310	N	1	B;B	0.12013	0.0;0.005	B;B	0.11329	0.001;0.006	T	0.50004	-0.8878	10	0.27082	T	0.32	-16.1587	1.1443	0.01772	0.1464:0.3123:0.2092:0.3321	.	58;58	O75631-2;O75631	.;UPK3A_HUMAN	A	58	ENSP00000216211:T58A;ENSP00000379391:T58A	ENSP00000216211:T58A	T	+	1	0	UPK3A	44060605	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.794000	0.04584	-2.021000	0.00939	-1.236000	0.01555	ACC	.	.		0.572	UPK3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322276.1	NM_006953	
SBF1	6305	hgsc.bcm.edu	37	22	50905072	50905072	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:50905072A>G	ENST00000390679.3	-	6	801	c.617T>C	c.(616-618)gTc>gCc	p.V206A	SBF1_ENST00000380817.3_Missense_Mutation_p.V206A|SBF1_ENST00000348911.6_Missense_Mutation_p.V207A			O95248	MTMR5_HUMAN	SET binding factor 1	206	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				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)		GCAGCGGCTGACGGGCAGCGA	0.632																																					p.V206A		Atlas-SNP	.											.	SBF1	211	.	0			c.T617C						.						6.0	11.0	10.0					22																	50905072		1965	4052	6017	SO:0001583	missense	6305	exon6			CGGCTGACGGGCA	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.617T>C	chr22.hg19:g.50905072A>G	ENSP00000375097:p.Val206Ala	128.0	0.0		124.0	6.0	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	hg19		.	.	.	.	.	.	.	.	.	.	A	12.66	2.004760	0.35320	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000356279;ENST00000337034;ENST00000390679	T;T;T	0.12039	2.72;2.72;2.72	4.28	4.28	0.50868	.	0.580414	0.16662	N	0.204748	T	0.15998	0.0385	L	0.56340	1.77	0.50632	D	0.99988	B;B	0.06786	0.001;0.001	B;B	0.08055	0.002;0.003	T	0.03060	-1.1077	10	0.87932	D	0	.	12.5208	0.56058	1.0:0.0:0.0:0.0	.	207;206	G5E933;O95248-4	.;.	A	206;207;217;216;206	ENSP00000370196:V206A;ENSP00000252027:V207A;ENSP00000375097:V206A	ENSP00000336522:V216A	V	-	2	0	SBF1	49251938	0.998000	0.40836	0.937000	0.37676	0.011000	0.07611	3.884000	0.56175	1.801000	0.52704	0.459000	0.35465	GTC	.	.		0.632	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
ARSF	416	hgsc.bcm.edu	37	X	2994595	2994595	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:2994595T>C	ENST00000381127.1	+	4	389	c.168T>C	c.(166-168)ccT>ccC	p.P56P	ARSF_ENST00000359361.2_Silent_p.P56P|ARSF_ENST00000537104.1_Silent_p.P56P	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	56					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)|extracellular vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		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)				tcAGGACGCCTCACATCGACC	0.612																																					p.P56P		Atlas-SNP	.											.	ARSF	97	.	0			c.T168C						.						40.0	24.0	29.0					X																	2994595		2203	4299	6502	SO:0001819	synonymous_variant	416	exon4			GACGCCTCACATC	X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"""Arylsulfatase family"""	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.168T>C	chrX.hg19:g.2994595T>C		48.0	0.0		66.0	5.0	NM_004042	Q8TCC5	Silent	SNP	ENST00000381127.1	hg19	CCDS14123.1																																																																																			.	.		0.612	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1		
MXRA5	25878	hgsc.bcm.edu	37	X	3241039	3241039	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:3241039T>C	ENST00000217939.6	-	5	2841	c.2687A>G	c.(2686-2688)gAg>gGg	p.E896G		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	896						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				AGTTATCTCCTCAGTCTTCTC	0.463																																					p.E896G		Atlas-SNP	.											.	MXRA5	815	.	0			c.A2687G						.						95.0	83.0	87.0					X																	3241039		2203	4300	6503	SO:0001583	missense	25878	exon5			ATCTCCTCAGTCT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2687A>G	chrX.hg19:g.3241039T>C	ENSP00000217939:p.Glu896Gly	106.0	0.0		112.0	5.0	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	hg19	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	t	6.662	0.490634	0.12702	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.64085	-0.08	3.33	0.722	0.18225	.	1.435640	0.04933	U	0.457118	T	0.38026	0.1025	N	0.08118	0	0.09310	N	1	B	0.23058	0.079	B	0.17098	0.017	T	0.15752	-1.0426	10	0.28530	T	0.3	.	3.2428	0.06787	0.2055:0.1216:0.0:0.6729	.	896	Q9NR99	MXRA5_HUMAN	G	896	ENSP00000217939:E896G	ENSP00000217939:E896G	E	-	2	0	MXRA5	3251039	0.002000	0.14202	0.000000	0.03702	0.014000	0.08584	0.998000	0.29744	-0.136000	0.11475	0.430000	0.28490	GAG	.	.		0.463	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
PIGA	5277	hgsc.bcm.edu	37	X	15349573	15349573	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:15349573A>G	ENST00000333590.4	-	2	564	c.480T>C	c.(478-480)gcT>gcC	p.A160A	PIGA_ENST00000428964.1_Intron|PIGA_ENST00000482148.1_Intron|PIGA_ENST00000542278.1_Intron	NM_002641.3	NP_002632.1	P37287	PIGA_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class A	160					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|positive regulation of metabolic process (GO:0009893)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)|UDP-glycosyltransferase activity (GO:0008194)			endometrium(2)|kidney(2)|large_intestine(2)|ovary(1)|prostate(2)|urinary_tract(1)	10	Hepatocellular(33;0.183)					AGCTGACATCAGCAAATCCAA	0.433																																					p.A160A		Atlas-SNP	.											.	PIGA	34	.	0			c.T480C						.						94.0	73.0	80.0					X																	15349573		2203	4300	6503	SO:0001819	synonymous_variant	5277	exon2			GACATCAGCAAAT	BC038236	CCDS14165.1, CCDS48086.1, CCDS48086.2	Xp22.1	2014-09-17	2008-07-31		ENSG00000165195	ENSG00000165195	2.4.1.198	"""Glycosyltransferase group 1 domain containing"", ""Phosphatidylinositol glycan anchor biosynthesis"""	8957	protein-coding gene	gene with protein product	"""paroxysmal nocturnal hemoglobinuria"", ""phosphatidylinositol N-acetylglucosaminyltransferase"""	311770	"""phosphatidylinositol glycan, class A (paroxysmal nocturnal hemoglobinuria)"""			8500164	Standard	NM_002641		Approved	GPI3	uc004cwr.3	P37287	OTTHUMG00000021174	ENST00000333590.4:c.480T>C	chrX.hg19:g.15349573A>G		72.0	0.0		89.0	6.0	NM_002641	B4E0V2|Q16025|Q16250	Silent	SNP	ENST00000333590.4	hg19	CCDS14165.1																																																																																			.	.		0.433	PIGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055854.1	NM_002641	
SCML1	6322	hgsc.bcm.edu	37	X	17767571	17767571	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:17767571A>G	ENST00000380041.3	+	5	578	c.250A>G	c.(250-252)Aga>Gga	p.R84G	SCML1_ENST00000398080.1_5'UTR|SCML1_ENST00000380045.3_5'UTR|SCML1_ENST00000380043.3_Missense_Mutation_p.R57G	NM_001037540.1	NP_001032629.1	Q9UN30	SCML1_HUMAN	sex comb on midleg-like 1 (Drosophila)	84					anatomical structure morphogenesis (GO:0009653)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|ovary(1)	10	Hepatocellular(33;0.183)					TGTGATTCGTAGAAAGGTTTC	0.308																																					p.R84G		Atlas-SNP	.											.	SCML1	55	.	0			c.A250G						.						101.0	92.0	95.0					X																	17767571		2203	4300	6503	SO:0001583	missense	6322	exon5			ATTCGTAGAAAGG		CCDS14182.2, CCDS35210.1, CCDS35211.1	Xp22	2013-01-10	2001-11-28		ENSG00000047634	ENSG00000047634		"""Sterile alpha motif (SAM) domain containing"""	10580	protein-coding gene	gene with protein product		300227	"""sex comb on midleg (Drosophila)-like 1"""			9570953	Standard	XM_005274578		Approved		uc004cyc.3	Q9UN30	OTTHUMG00000021206	ENST00000380041.3:c.250A>G	chrX.hg19:g.17767571A>G	ENSP00000369380:p.Arg84Gly	120.0	0.0		128.0	6.0	NM_001037540	B0FZN6|B2RA08|Q5H968|Q5H969	Missense_Mutation	SNP	ENST00000380041.3	hg19	CCDS35210.1	.	.	.	.	.	.	.	.	.	.	A	13.03	2.115816	0.37339	.	.	ENSG00000047634	ENST00000380041;ENST00000380043;ENST00000419185	.	.	.	4.96	-0.356	0.12583	.	1.217200	0.06182	N	0.679576	T	0.16428	0.0395	N	0.03050	-0.425	0.09310	N	0.999999	B;B	0.09022	0.001;0.002	B;B	0.04013	0.001;0.001	T	0.24548	-1.0157	9	0.35671	T	0.21	-0.5909	7.8214	0.29290	0.5618:0.0:0.4382:0.0	.	57;84	Q9UN30-2;Q9UN30	.;SCML1_HUMAN	G	84;57;57	.	ENSP00000369380:R84G	R	+	1	2	SCML1	17677492	0.003000	0.15002	0.000000	0.03702	0.025000	0.11179	0.162000	0.16501	-0.312000	0.08741	-0.438000	0.05819	AGA	.	.		0.308	SCML1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060495.5	NM_006746	
MAGEB16	139604	hgsc.bcm.edu	37	X	35820408	35820408	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:35820408A>G	ENST00000399989.1	+	2	374	c.95A>G	c.(94-96)aAg>aGg	p.K32R	MAGEB16_ENST00000399988.1_Missense_Mutation_p.K32R|MAGEB16_ENST00000399987.1_Missense_Mutation_p.K32R|MAGEB16_ENST00000399992.1_Missense_Mutation_p.K64R|MAGEB16_ENST00000399985.1_Missense_Mutation_p.K32R	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	32										breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						CAGGTCTCCAAGGCTCTGGAG	0.552																																					p.K32R		Atlas-SNP	.											.	MAGEB16	64	.	0			c.A95G						.						41.0	42.0	41.0					X																	35820408		2022	4171	6193	SO:0001583	missense	139604	exon2			TCTCCAAGGCTCT		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.95A>G	chrX.hg19:g.35820408A>G	ENSP00000382871:p.Lys32Arg	87.0	0.0		87.0	4.0	NM_001099921	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	hg19	CCDS43927.1	.	.	.	.	.	.	.	.	.	.	A	3.125	-0.179717	0.06380	.	.	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.04317	3.65;3.65;3.65;3.65;3.65	3.02	-6.03	0.02185	Melanoma associated antigen, MAGE, N-terminal (1);	1.111270	0.06703	N	0.771751	T	0.03651	0.0104	L	0.34521	1.04	0.09310	N	1	B	0.18013	0.025	B	0.18263	0.021	T	0.42344	-0.9457	10	0.48119	T	0.1	.	4.6746	0.12706	0.2246:0.0:0.4599:0.3155	.	32	A2A368	MAGBG_HUMAN	R	32;64;32;32;32	ENSP00000382870:K32R;ENSP00000382874:K64R;ENSP00000382869:K32R;ENSP00000382871:K32R;ENSP00000382867:K32R	ENSP00000382867:K32R	K	+	2	0	MAGEB16	35730329	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.720000	0.04969	-1.864000	0.01148	0.423000	0.28283	AAG	.	.		0.552	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1		
CXorf30	645090	hgsc.bcm.edu	37	X	36337383	36337383	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:36337383A>G	ENST00000378657.4	+	11	1390	c.742A>G	c.(742-744)Agt>Ggt	p.S248G		NM_001098843.4	NP_001092313.2	A6PW82	CX030_HUMAN	chromosome X open reading frame 30	248										breast(1)|lung(2)|stomach(1)	4						CATCTATGAGAGTTCTGCCTT	0.358																																					p.S248G		Atlas-SNP	.											.	CXorf30	76	.	0			c.A742G						.						195.0	149.0	163.0					X																	36337383		692	1591	2283	SO:0001583	missense	645090	exon12			TATGAGAGTTCTG		CCDS55396.1	Xp21.1	2014-08-07			ENSG00000205081	ENSG00000205081			27298	protein-coding gene	gene with protein product							Standard	NM_001098843		Approved		uc011mkc.3	A6PW82	OTTHUMG00000021353	ENST00000378657.4:c.742A>G	chrX.hg19:g.36337383A>G	ENSP00000367926:p.Ser248Gly	100.0	0.0		129.0	8.0	NM_001098843		Missense_Mutation	SNP	ENST00000378657.4	hg19	CCDS55396.1	.	.	.	.	.	.	.	.	.	.	A	5.695	0.312791	0.10789	.	.	ENSG00000205081	ENST00000378653;ENST00000378657	T;T	0.23348	1.91;1.91	4.32	1.78	0.24846	.	0.925700	0.08865	N	0.882454	T	0.11537	0.0281	N	0.08118	0	0.09310	N	1	B	0.23806	0.091	B	0.18871	0.023	T	0.34875	-0.9811	10	0.25751	T	0.34	-4.0206	4.6334	0.12513	0.5912:0.3006:0.1081:0.0	.	248	A6PW82	CX030_HUMAN	G	533;248	ENSP00000367922:S533G;ENSP00000367926:S248G	ENSP00000367922:S533G	S	+	1	0	CXorf30	36247304	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.452000	0.21795	0.136000	0.18733	0.486000	0.48141	AGT	.	.		0.358	CXorf30-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NP_001092313	
FAM47C	442444	hgsc.bcm.edu	37	X	37028804	37028804	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:37028804T>C	ENST00000358047.3	+	1	2373	c.2321T>C	c.(2320-2322)cTc>cCc	p.L774P		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	774										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						GTGTCCCATCTCCACCCAGAG	0.627																																					p.L774P		Atlas-SNP	.											.	FAM47C	267	.	0			c.T2321C						.						40.0	40.0	40.0					X																	37028804		2202	4300	6502	SO:0001583	missense	442444	exon1			CCCATCTCCACCC	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2321T>C	chrX.hg19:g.37028804T>C	ENSP00000367913:p.Leu774Pro	38.0	0.0		49.0	4.0	NM_001013736	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	hg19	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	-	5.808	0.333363	0.11013	.	.	ENSG00000198173	ENST00000358047	T	0.23348	1.91	0.118	0.118	0.14667	.	.	.	.	.	T	0.39784	0.1091	M	0.79258	2.445	0.22888	N	0.998603	D	0.62365	0.991	P	0.60609	0.877	T	0.21621	-1.0240	9	0.29301	T	0.29	.	4.6021	0.12359	0.0:5.0E-4:0.0:0.9995	.	774	Q5HY64	FA47C_HUMAN	P	774	ENSP00000367913:L774P	ENSP00000367913:L774P	L	+	2	0	FAM47C	36938725	0.000000	0.05858	0.004000	0.12327	0.004000	0.04260	-1.576000	0.02129	0.153000	0.19213	0.151000	0.16131	CTC	.	.		0.627	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736	
USP9X	8239	hgsc.bcm.edu	37	X	41075804	41075804	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:41075804A>G	ENST00000324545.8	+	35	6617	c.5984A>G	c.(5983-5985)aAc>aGc	p.N1995S	USP9X_ENST00000378308.2_Missense_Mutation_p.N1995S	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1995					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						CGGAAACAGAACGTACAATTC	0.388																																					p.N1995S	Ovarian(172;1807 2695 35459 49286)	Atlas-SNP	.											.	USP9X	385	.	0			c.A5984G						.						115.0	101.0	106.0					X																	41075804		2103	4228	6331	SO:0001583	missense	8239	exon35			AACAGAACGTACA	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.5984A>G	chrX.hg19:g.41075804A>G	ENSP00000316357:p.Asn1995Ser	116.0	0.0		112.0	5.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	hg19	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.047601	0.75846	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.13307	2.6;2.6	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.39545	0.1082	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.983	T	0.31916	-0.9926	10	0.87932	D	0	.	14.9222	0.70847	1.0:0.0:0.0:0.0	.	1995;1995	Q93008-1;Q93008	.;USP9X_HUMAN	S	1995	ENSP00000367558:N1995S;ENSP00000316357:N1995S	ENSP00000316357:N1995S	N	+	2	0	USP9X	40960748	1.000000	0.71417	0.963000	0.40424	0.985000	0.73830	8.952000	0.93031	1.906000	0.55180	0.481000	0.45027	AAC	.	.		0.388	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652	
KDM6A	7403	hgsc.bcm.edu	37	X	44941973	44941973	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:44941973A>G	ENST00000377967.4	+	22	3264	c.3223A>G	c.(3223-3225)Agg>Ggg	p.R1075G	KDM6A_ENST00000382899.4_Missense_Mutation_p.R1082G|KDM6A_ENST00000543216.1_Missense_Mutation_p.R996G|KDM6A_ENST00000536777.1_Missense_Mutation_p.R1030G	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1075	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						TGGGAGGAGGAGGAAAGGACC	0.338			"""D, N, F, S"""		"""renal, oesophageal SCC, MM"""																																p.R1075G	Colon(129;1273 1667 15230 27352 52914)	Atlas-SNP	.		Rec	yes		X	Xp11.2	7403	"""lysine (K)-specific demethylase 6A, UTX"""		"""E, L"""	.	KDM6A	274	.	6	Whole gene deletion(6)	oesophagus(2)|breast(2)|pancreas(2)	c.A3223G						.						113.0	103.0	106.0					X																	44941973		2203	4300	6503	SO:0001583	missense	7403	exon22			AGGAGGAGGAAAG	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"""Chromatin-modifying enzymes / K-demethylases"", ""Tetratricopeptide (TTC) repeat domain containing"""	12637	protein-coding gene	gene with protein product		300128	"""ubiquitously transcribed tetratricopeptide repeat, X chromosome"""	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.3223A>G	chrX.hg19:g.44941973A>G	ENSP00000367203:p.Arg1075Gly	78.0	0.0		72.0	5.0	NM_021140	Q52LL9|Q5JVQ7	Missense_Mutation	SNP	ENST00000377967.4	hg19	CCDS14265.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.46|14.46	2.543038|2.543038	0.45280|0.45280	.|.	.|.	ENSG00000147050|ENSG00000147050	ENST00000414389;ENST00000433797|ENST00000334516;ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216	.|T;T;T;T	.|0.79554	.|-1.28;-1.28;-1.28;-1.28	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	.|0.042744	.|0.85682	.|D	.|0.000000	T|T	0.76793|0.76793	0.4037|0.4037	N|N	0.25890|0.25890	0.77|0.77	0.80722|0.80722	D|D	1|1	.|P;B;D;B;P	.|0.54047	.|0.816;0.275;0.964;0.027;0.647	.|B;B;P;B;P	.|0.52217	.|0.091;0.109;0.693;0.011;0.653	T|T	0.77493|0.77493	-0.2567|-0.2567	5|10	.|0.46703	.|T	.|0.11	-2.9787|-2.9787	10.5922|10.5922	0.45316|0.45316	0.8411:0.1589:0.0:0.0|0.8411:0.1589:0.0:0.0	.|.	.|714;1082;1030;1127;1075	.|B4E0L8;F8W8R6;F5H6S1;B7ZKN5;O15550	.|.;.;.;.;KDM6A_HUMAN	G|G	672;717|772;1075;1030;1082;996	.|ENSP00000367203:R1075G;ENSP00000437405:R1030G;ENSP00000372355:R1082G;ENSP00000443078:R996G	.|ENSP00000334340:R772G	E|R	+|+	2|1	0|2	KDM6A|KDM6A	44826917|44826917	1.000000|1.000000	0.71417|0.71417	0.977000|0.977000	0.42913|0.42913	0.991000|0.991000	0.79684|0.79684	4.667000|4.667000	0.61561|0.61561	1.793000|1.793000	0.52555|0.52555	0.437000|0.437000	0.28790|0.28790	GAG|AGG	.	.		0.338	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140	
RBM10	8241	hgsc.bcm.edu	37	X	47041607	47041607	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:47041607A>G	ENST00000377604.3	+	17	2574	c.1832A>G	c.(1831-1833)gAg>gGg	p.E611G	RBM10_ENST00000345781.6_Missense_Mutation_p.E534G|RBM10_ENST00000329236.7_Missense_Mutation_p.E533G	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	611					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						TGGGATGGGGAGAGGCGGACC	0.577																																					p.E676G	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.A2027G						.						92.0	80.0	84.0					X																	47041607		2203	4300	6503	SO:0001583	missense	8241	exon17			ATGGGGAGAGGCG	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"""Zinc fingers, RAN-binding domain containing"", ""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.1832A>G	chrX.hg19:g.47041607A>G	ENSP00000366829:p.Glu611Gly	99.0	0.0		94.0	4.0	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	hg19	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	A	19.38	3.815946	0.70912	.	.	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	T;T;T	0.22336	2.63;1.96;2.22	4.85	4.85	0.62838	.	0.060824	0.64402	D	0.000006	T	0.45796	0.1360	M	0.79475	2.455	0.40097	D	0.976325	D;D;D;D;D	0.89917	0.99;0.993;0.984;1.0;0.991	P;D;P;D;P	0.80764	0.843;0.926;0.888;0.994;0.837	T	0.50709	-0.8796	10	0.66056	D	0.02	-18.6669	11.6162	0.51092	1.0:0.0:0.0:0.0	.	534;676;610;533;611	P98175-3;Q7Z3D7;P98175-2;P98175-4;P98175	.;.;.;.;RBM10_HUMAN	G	611;533;534	ENSP00000366829:E611G;ENSP00000328848:E533G;ENSP00000329659:E534G	ENSP00000328848:E533G	E	+	2	0	RBM10	46926551	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	9.086000	0.94088	1.713000	0.51359	0.356000	0.21956	GAG	.	.		0.577	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676	
FTSJ1	24140	hgsc.bcm.edu	37	X	48341394	48341394	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:48341394T>C	ENST00000348411.2	+	12	1301	c.978T>C	c.(976-978)agT>agC	p.S326S	FTSJ1_ENST00000456787.1_Silent_p.S324S|FTSJ1_ENST00000019019.2_Silent_p.S324S|FTSJ1_ENST00000396894.4_Silent_p.S189S|FTSJ1_ENST00000496365.1_3'UTR	NM_012280.2	NP_036412.1			FtsJ RNA methyltransferase homolog 1 (E. coli)											breast(1)|central_nervous_system(1)|lung(4)|skin(1)	7						ATGAAATGAGTTGTTCACCTT	0.338																																					p.S326S		Atlas-SNP	.											.	FTSJ1	21	.	0			c.T978C						.						156.0	138.0	144.0					X																	48341394		2203	4300	6503	SO:0001819	synonymous_variant	24140	exon12			AATGAGTTGTTCA	AJ005892	CCDS14294.1, CCDS14295.1, CCDS75972.1	Xp11.23	2012-06-12	2012-06-12		ENSG00000068438	ENSG00000068438			13254	protein-coding gene	gene with protein product	"""tRNA methyltransferase 7 homolog (S. cerevisiae)"""	300499	"""mental retardation, X-linked 9"", ""mental retardation, X-linked 44"""	MRX9, MRX44		15342698, 15162322	Standard	XR_246715		Approved	JM23, CDLIV, SPB1, TRM7, TRMT7	uc004djo.1	Q9UET6	OTTHUMG00000024118	ENST00000348411.2:c.978T>C	chrX.hg19:g.48341394T>C		60.0	0.0		60.0	4.0	NM_012280		Silent	SNP	ENST00000348411.2	hg19	CCDS14294.1																																																																																			.	.		0.338	FTSJ1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060726.1		
WDR13	64743	hgsc.bcm.edu	37	X	48458000	48458000	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:48458000T>C	ENST00000218056.5	+	4	923	c.418T>C	c.(418-420)Tca>Cca	p.S140P	WDR13_ENST00000492715.1_3'UTR|WDR13_ENST00000376729.5_Missense_Mutation_p.S140P	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	140						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						GGTGCCCACGTCAGCAGCAGA	0.612																																					p.S140P		Atlas-SNP	.											.	WDR13	96	.	0			c.T418C						.						81.0	70.0	73.0					X																	48458000		2203	4300	6503	SO:0001583	missense	64743	exon4			CCCACGTCAGCAG	AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"""WD repeat domain containing"""	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.418T>C	chrX.hg19:g.48458000T>C	ENSP00000218056:p.Ser140Pro	85.0	0.0		96.0	5.0	NM_017883	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Missense_Mutation	SNP	ENST00000218056.5	hg19	CCDS14302.1	.	.	.	.	.	.	.	.	.	.	T	14.33	2.501964	0.44455	.	.	ENSG00000101940	ENST00000376729;ENST00000218056	T;T	0.72167	-0.63;-0.63	5.48	5.48	0.80851	.	0.065767	0.64402	D	0.000005	T	0.52773	0.1755	L	0.27053	0.805	0.48236	D	0.999614	B;B	0.13145	0.007;0.004	B;B	0.09377	0.002;0.004	T	0.48340	-0.9044	10	0.19590	T	0.45	-25.0681	7.2254	0.26012	0.0:0.0991:0.0:0.9008	.	18;140	B4DVQ7;Q9H1Z4	.;WDR13_HUMAN	P	140	ENSP00000365919:S140P;ENSP00000218056:S140P	ENSP00000218056:S140P	S	+	1	0	WDR13	48342944	0.999000	0.42202	0.020000	0.16555	0.854000	0.48673	3.373000	0.52394	1.826000	0.53198	0.430000	0.28490	TCA	.	.		0.612	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2		
HDAC6	10013	hgsc.bcm.edu	37	X	48663924	48663924	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:48663924T>C	ENST00000334136.5	+	5	569	c.391T>C	c.(391-393)Ttt>Ctt	p.F131L	HDAC6_ENST00000469223.1_3'UTR|HDAC6_ENST00000376619.2_Missense_Mutation_p.F131L|HDAC6_ENST00000413163.2_Missense_Mutation_p.F76L|HDAC6_ENST00000444343.2_Missense_Mutation_p.F145L			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	131	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)	CTGCGTGTCCTTTCAGGTAAG	0.592																																					p.F131L	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.T391C						.						79.0	59.0	65.0					X																	48663924		2203	4300	6503	SO:0001583	missense	10013	exon5			GTGTCCTTTCAGG	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.391T>C	chrX.hg19:g.48663924T>C	ENSP00000334061:p.Phe131Leu	89.0	0.0		88.0	4.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	hg19	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	T	9.004	0.980811	0.18812	.	.	ENSG00000094631	ENST00000423941;ENST00000376643;ENST00000444343;ENST00000376610;ENST00000334136;ENST00000376619;ENST00000436813;ENST00000413163;ENST00000441703;ENST00000426196;ENST00000443563;ENST00000440653	T;T;T;T	0.61392	0.38;0.38;0.38;0.11	4.16	2.94	0.34122	Histone deacetylase domain (2);	0.379228	0.23422	N	0.048352	T	0.14787	0.0357	N	0.00226	-1.805	0.29091	N	0.882076	B;B;B;P	0.38335	0.321;0.002;0.321;0.627	B;B;B;B	0.36030	0.107;0.002;0.107;0.216	T	0.17776	-1.0358	10	0.10111	T	0.7	-7.3413	4.4811	0.11767	0.1971:0.0:0.2002:0.6027	.	121;76;131;131	B4DZN1;E7EUZ1;Q9UBN7;Q9BRX7	.;.;HDAC6_HUMAN;.	L	131;131;145;131;131;131;131;76;131;131;131;131	ENSP00000398566:F145L;ENSP00000334061:F131L;ENSP00000365804:F131L;ENSP00000398801:F76L	ENSP00000334061:F131L	F	+	1	0	HDAC6	48548868	0.998000	0.40836	0.988000	0.46212	0.880000	0.50808	0.772000	0.26647	0.517000	0.28361	0.242000	0.17961	TTT	.	.		0.592	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044	
AKAP4	8852	hgsc.bcm.edu	37	X	49963345	49963345	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:49963345T>C	ENST00000376056.2	-	2	209	c.59A>G	c.(58-60)tAc>tGc	p.Y20C	AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Missense_Mutation_p.Y20C|AKAP4_ENST00000376064.3_Missense_Mutation_p.Y20C|AKAP4_ENST00000358526.2_Missense_Mutation_p.Y29C					A kinase (PRKA) anchor protein 4											NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4)	41	Ovarian(276;0.236)					TTCTGGGTTGTAGAGATCTAC	0.423																																					p.Y29C		Atlas-SNP	.											.	AKAP4	131	.	0			c.A86G						.						121.0	92.0	102.0					X																	49963345		2203	4300	6503	SO:0001583	missense	8852	exon2			GGGTTGTAGAGAT	AF072756	CCDS14329.1, CCDS14330.1	Xp11.2	2009-03-12			ENSG00000147081	ENSG00000147081		"""A-kinase anchor proteins"""	374	protein-coding gene	gene with protein product	"""A-kinase anchor protein 82 kDa"", ""testis-specific gene HI"", ""protein kinase A anchoring protein 4"", ""cancer/testis antigen 99"""	300185				9822690, 9514854	Standard	NM_003886		Approved	p82, hAKAP82, AKAP82, Fsc1, HI, CT99	uc004dow.1	Q5JQC9	OTTHUMG00000021517	ENST00000376056.2:c.59A>G	chrX.hg19:g.49963345T>C	ENSP00000365224:p.Tyr20Cys	79.0	0.0		118.0	7.0	NM_003886		Missense_Mutation	SNP	ENST00000376056.2	hg19	CCDS14330.1	.	.	.	.	.	.	.	.	.	.	T	10.08	1.251060	0.22880	.	.	ENSG00000147081	ENST00000376056;ENST00000376058;ENST00000358526;ENST00000376064;ENST00000448865;ENST00000437370	T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06	5.02	5.02	0.67125	.	0.000000	0.46442	D	0.000284	T	0.62502	0.2433	M	0.78801	2.425	0.25657	N	0.986043	D;D	0.76494	0.999;0.999	D;D	0.81914	0.994;0.995	T	0.58165	-0.7684	9	.	.	.	-11.9723	10.2373	0.43290	0.0:0.0:0.0:1.0	.	29;20	Q5JQC9;A6ND82	AKAP4_HUMAN;.	C	20;20;29;20;20;20	ENSP00000365224:Y20C;ENSP00000365226:Y20C;ENSP00000351327:Y29C;ENSP00000365232:Y20C;ENSP00000402403:Y20C;ENSP00000412279:Y20C	.	Y	-	2	0	AKAP4	49850085	1.000000	0.71417	0.999000	0.59377	0.052000	0.14988	3.990000	0.56965	1.683000	0.51011	0.486000	0.48141	TAC	.	.		0.423	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886	
TRO	7216	hgsc.bcm.edu	37	X	54955827	54955827	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:54955827A>G	ENST00000173898.7	+	12	2782	c.2670A>G	c.(2668-2670)ggA>ggG	p.G890G	TRO_ENST00000375022.4_Intron|TRO_ENST00000319167.8_Intron|TRO_ENST00000375041.2_Silent_p.G493G|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000420798.2_Silent_p.G421G|TRO_ENST00000399736.1_Intron	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	890	62 X 10 AA approximate tandem repeats.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						CTGGCTTTGGAGGCATACTCA	0.547																																					p.G890G		Atlas-SNP	.											.	TRO	246	.	0			c.A2670G						.						70.0	63.0	65.0					X																	54955827		2102	4200	6302	SO:0001819	synonymous_variant	7216	exon12			CTTTGGAGGCATA	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.2670A>G	chrX.hg19:g.54955827A>G		145.0	0.0		119.0	5.0	NM_001039705	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Silent	SNP	ENST00000173898.7	hg19	CCDS43959.1																																																																																			.	.		0.547	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157	
LAS1L	81887	hgsc.bcm.edu	37	X	64754546	64754546	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:64754546T>C	ENST00000374811.3	-	1	90	c.50A>G	c.(49-51)gAt>gGt	p.D17G	LAS1L_ENST00000312391.8_Missense_Mutation_p.D17G|LAS1L_ENST00000374804.5_Missense_Mutation_p.D17G|LAS1L_ENST00000374807.5_Missense_Mutation_p.D17G	NM_031206.4	NP_112483.1	Q9Y4W2	LAS1L_HUMAN	LAS1-like (S. cerevisiae)	17					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	33						CCACACGAGATCCATCCCCTG	0.642																																					p.D17G		Atlas-SNP	.											.	LAS1L	72	.	0			c.A50G						.						115.0	77.0	90.0					X																	64754546		2198	4291	6489	SO:0001583	missense	81887	exon1			ACGAGATCCATCC	BC014545	CCDS14381.1, CCDS55433.1, CCDS55434.1	Xq12	2008-02-05			ENSG00000001497	ENSG00000001497			25726	protein-coding gene	gene with protein product						12477932	Standard	NM_031206		Approved	FLJ12525	uc004dwa.2	Q9Y4W2	OTTHUMG00000021720	ENST00000374811.3:c.50A>G	chrX.hg19:g.64754546T>C	ENSP00000363944:p.Asp17Gly	78.0	0.0		104.0	5.0	NM_031206	A9X410|Q5JXQ0|Q8TEN5|Q9H9V5	Missense_Mutation	SNP	ENST00000374811.3	hg19	CCDS14381.1	.	.	.	.	.	.	.	.	.	.	t	19.62	3.862209	0.71949	.	.	ENSG00000001497	ENST00000374807;ENST00000374811;ENST00000374804;ENST00000312391	.	.	.	4.39	4.39	0.52855	.	0.453724	0.22209	N	0.063140	T	0.53883	0.1824	L	0.32530	0.975	0.35087	D	0.763914	D;D;D	0.61080	0.964;0.964;0.989	P;P;P	0.57846	0.71;0.71;0.828	T	0.66204	-0.5982	9	0.87932	D	0	.	8.9211	0.35612	0.0:0.0:0.0:1.0	.	17;17;17	Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2	.;.;LAS1L_HUMAN	G	17	.	ENSP00000308649:D17G	D	-	2	0	LAS1L	64671271	0.998000	0.40836	0.994000	0.49952	0.838000	0.47535	1.851000	0.39338	1.928000	0.55862	0.481000	0.45027	GAT	.	.		0.642	LAS1L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056974.1	NM_031206	
SLC7A3	84889	hgsc.bcm.edu	37	X	70146023	70146023	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:70146023A>G	ENST00000374299.3	-	11	1770	c.1626T>C	c.(1624-1626)ccT>ccC	p.P542P	SLC7A3_ENST00000298085.4_Silent_p.P542P			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	542					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GAGGCAAAGCAGGCACCTGAA	0.463																																					p.P542P		Atlas-SNP	.											.	SLC7A3	76	.	0			c.T1626C						.						59.0	49.0	52.0					X																	70146023		2203	4300	6503	SO:0001819	synonymous_variant	84889	exon11			CAAAGCAGGCACC	AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"""Solute carriers"""	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.1626T>C	chrX.hg19:g.70146023A>G		69.0	0.0		87.0	4.0	NM_032803	D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Silent	SNP	ENST00000374299.3	hg19	CCDS14404.1																																																																																			.	.		0.463	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1	NM_032803	
MED12	9968	hgsc.bcm.edu	37	X	70344673	70344673	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:70344673C>A	ENST00000374080.3	+	14	2066	c.2034C>A	c.(2032-2034)gaC>gaA	p.D678E	MED12_ENST00000374102.1_Missense_Mutation_p.D678E|MED12_ENST00000333646.6_Missense_Mutation_p.D678E			Q93074	MED12_HUMAN	mediator complex subunit 12	678					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					TCTTTGAGGACATGGAGAAGC	0.468			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.D678E		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.C2034A						.						132.0	112.0	118.0					X																	70344673		1943	4114	6057	SO:0001583	missense	9968	exon14			TGAGGACATGGAG	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.2034C>A	chrX.hg19:g.70344673C>A	ENSP00000363193:p.Asp678Glu	89.0	0.0		100.0	4.0	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	hg19	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	.	8.615	0.889947	0.17540	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072	T;T;T;T	0.57907	0.37;0.38;0.38;0.38	4.49	2.72	0.32119	Mediator complex, subunit Med12, LCEWAV-domain (1);	0.053172	0.85682	D	0.000000	T	0.36303	0.0962	L	0.33485	1.01	0.47214	D	0.999355	B;B;B;B	0.25048	0.002;0.117;0.005;0.007	B;B;B;B	0.25884	0.006;0.064;0.009;0.007	T	0.07158	-1.0787	10	0.11182	T	0.66	-17.6143	9.9661	0.41725	0.0:0.8301:0.0:0.1699	.	678;525;678;678	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	E	678;678;678;678;646	ENSP00000333125:D678E;ENSP00000363215:D678E;ENSP00000363193:D678E;ENSP00000414203:D646E	ENSP00000333125:D678E	D	+	3	2	MED12	70261398	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.616000	0.24344	0.378000	0.24764	0.529000	0.55759	GAC	.	.		0.468	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
PHKA1	5255	hgsc.bcm.edu	37	X	71873287	71873287	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:71873287T>C	ENST00000373542.4	-	11	1294	c.1135A>G	c.(1135-1137)Agg>Ggg	p.R379G	PHKA1_ENST00000339490.3_Missense_Mutation_p.R379G|PHKA1_ENST00000373545.3_Missense_Mutation_p.R379G|PHKA1_ENST00000373539.3_Missense_Mutation_p.R379G|PHKA1_ENST00000541944.1_Missense_Mutation_p.R379G	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	379					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)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					TGACTCACCCTGTCAGGAGGA	0.428																																					p.R379G		Atlas-SNP	.											.	PHKA1	129	.	0			c.A1135G						.						81.0	65.0	70.0					X																	71873287		2203	4300	6503	SO:0001583	missense	5255	exon11			TCACCCTGTCAGG		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.1135A>G	chrX.hg19:g.71873287T>C	ENSP00000362643:p.Arg379Gly	88.0	0.0		85.0	4.0	NM_001172436	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	hg19	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	T	15.44	2.833627	0.50951	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.90504	-2.68;-2.68;-2.68;-2.68;-2.68	5.08	5.08	0.68730	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.047373	0.85682	D	0.000000	D	0.84284	0.5438	L	0.29908	0.895	0.41772	D	0.989773	B;B;B	0.22851	0.03;0.014;0.076	B;B;B	0.25759	0.027;0.023;0.063	T	0.79626	-0.1725	10	0.24483	T	0.36	-19.5286	11.8025	0.52135	0.0:0.0:0.0:1.0	.	379;379;379	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	G	379	ENSP00000362646:R379G;ENSP00000362643:R379G;ENSP00000441251:R379G;ENSP00000342469:R379G;ENSP00000362640:R379G	ENSP00000342469:R379G	R	-	1	2	PHKA1	71790012	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	5.416000	0.66417	1.688000	0.51068	0.430000	0.28490	AGG	.	.		0.428	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1		
HDX	139324	hgsc.bcm.edu	37	X	83577009	83577009	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:83577009T>C	ENST00000297977.5	-	10	2072	c.1961A>G	c.(1960-1962)gAt>gGt	p.D654G	HDX_ENST00000373177.2_Missense_Mutation_p.D654G|HDX_ENST00000506585.2_Missense_Mutation_p.D596G	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	654						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						AGGAGGTAAATCTGACAGCAG	0.348																																					p.D654G	Pancreas(53;231 1169 36156 43751 51139)	Atlas-SNP	.											.	HDX	124	.	0			c.A1961G						.						55.0	45.0	48.0					X																	83577009		2203	4298	6501	SO:0001583	missense	139324	exon10			GGTAAATCTGACA	BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"""Homeoboxes / POU class"""	26411	protein-coding gene	gene with protein product			"""chromosome X open reading frame 43"""	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.1961A>G	chrX.hg19:g.83577009T>C	ENSP00000297977:p.Asp654Gly	109.0	0.0		97.0	4.0	NM_144657	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	ENST00000297977.5	hg19	CCDS35342.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.571720	0.45798	.	.	ENSG00000165259	ENST00000297977;ENST00000373177;ENST00000506585	T;T;T	0.32988	1.45;1.43;1.45	5.52	5.52	0.82312	.	0.201705	0.52532	D	0.000074	T	0.26810	0.0656	L	0.27053	0.805	0.46631	D	0.999133	B	0.29531	0.247	B	0.33392	0.163	T	0.08411	-1.0723	10	0.72032	D	0.01	-21.2483	14.6824	0.69028	0.0:0.0:0.0:1.0	.	654	Q7Z353	HDX_HUMAN	G	654;596;654	ENSP00000297977:D654G;ENSP00000362272:D596G;ENSP00000423670:D654G	ENSP00000297977:D654G	D	-	2	0	HDX	83463665	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.322000	0.65852	1.848000	0.53677	0.486000	0.48141	GAT	.	.		0.348	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657	
APOOL	139322	hgsc.bcm.edu	37	X	84306506	84306506	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:84306506T>G	ENST00000373173.2	+	3	319	c.232T>G	c.(232-234)Tgg>Ggg	p.W78G		NM_198450.5	NP_940852.3	Q6UXV4	MIC27_HUMAN	apolipoprotein O-like	78						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8						TTACATTGGCTGGTGCAAGGT	0.403																																					p.W78G		Atlas-SNP	.											.	APOOL	20	.	0			c.T232G						.						82.0	73.0	76.0					X																	84306506		1869	4098	5967	SO:0001583	missense	139322	exon3			ATTGGCTGGTGCA	AK130506	CCDS48138.1	Xq21.1	2007-01-17	2007-01-17	2007-01-17	ENSG00000155008	ENSG00000155008			24009	protein-coding gene	gene with protein product			"""chromosome X open reading frame 33"", ""family with sequence similarity 121A"""	CXorf33, FAM121A		12975309	Standard	NM_198450		Approved	UNQ8193, AAIR8193	uc004eem.3	Q6UXV4	OTTHUMG00000021930	ENST00000373173.2:c.232T>G	chrX.hg19:g.84306506T>G	ENSP00000362268:p.Trp78Gly	67.0	0.0		73.0	4.0	NM_198450	Q3KNU7|Q5H9D1	Missense_Mutation	SNP	ENST00000373173.2	hg19	CCDS48138.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.907132	0.33628	.	.	ENSG00000155008	ENST00000373173;ENST00000373169	.	.	.	4.36	4.36	0.52297	.	0.192534	0.47455	D	0.000225	T	0.59376	0.2189	M	0.69463	2.115	0.43448	D	0.995632	P	0.48162	0.906	P	0.50754	0.649	T	0.56798	-0.7919	9	0.15952	T	0.53	-29.2283	8.5823	0.33637	0.0:0.0:0.1916:0.8084	.	78	Q6UXV4	APOOL_HUMAN	G	78	.	ENSP00000362264:W78G	W	+	1	0	APOOL	84193162	1.000000	0.71417	0.998000	0.56505	0.483000	0.33249	2.022000	0.41030	1.610000	0.50200	0.481000	0.45027	TGG	.	.		0.403	APOOL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057385.2	NM_198450	
CSTF2	1478	hgsc.bcm.edu	37	X	100078882	100078882	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:100078882T>C	ENST00000372972.2	+	5	468	c.452T>C	c.(451-453)gTc>gCc	p.V151A	SNORA9_ENST00000365361.1_RNA|CSTF2_ENST00000415585.2_Missense_Mutation_p.V151A	NM_001325.2	NP_001316.1	P33240	CSTF2_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa	151	Interactions with CSTF3 and SYMPK.				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)	cleavage body (GO:0071920)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	13						CAGCTCTGTGTCCAGAATAGT	0.428																																					p.V151A		Atlas-SNP	.											.	CSTF2	47	.	0			c.T452C						.						131.0	112.0	119.0					X																	100078882		2203	4300	6503	SO:0001583	missense	1478	exon5			TCTGTGTCCAGAA	BC017712	CCDS14473.1	Xq22.1	2013-02-12	2002-08-29		ENSG00000101811	ENSG00000101811		"""RNA binding motif (RRM) containing"""	2484	protein-coding gene	gene with protein product		300907	"""cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kD"""			1741396	Standard	XM_006724622		Approved		uc004egh.3	P33240	OTTHUMG00000022709	ENST00000372972.2:c.452T>C	chrX.hg19:g.100078882T>C	ENSP00000362063:p.Val151Ala	53.0	0.0		74.0	4.0	NM_001325	Q5H951|Q6LA74|Q8N502	Missense_Mutation	SNP	ENST00000372972.2	hg19	CCDS14473.1	.	.	.	.	.	.	.	.	.	.	T	18.85	3.712235	0.68730	.	.	ENSG00000101811	ENST00000415585;ENST00000372972;ENST00000458320;ENST00000413437	T;T;T	0.14640	2.67;2.72;2.49	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.21347	0.0514	L	0.35414	1.06	0.80722	D	1	B;D;B	0.53619	0.351;0.961;0.351	B;P;B	0.58454	0.444;0.839;0.262	T	0.03566	-1.1024	10	0.20046	T	0.44	-11.164	14.5729	0.68224	0.0:0.0:0.0:1.0	.	151;151;151	E7EWR4;P33240-2;P33240	.;.;CSTF2_HUMAN	A	151;151;151;142	ENSP00000387996:V151A;ENSP00000362063:V151A;ENSP00000415705:V142A	ENSP00000362063:V151A	V	+	2	0	CSTF2	99965538	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.440000	0.80464	1.822000	0.53115	0.486000	0.48141	GTC	.	.		0.428	CSTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058926.1	NM_001325	
TCEAL6	158931	hgsc.bcm.edu	37	X	101395773	101395773	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:101395773G>T	ENST00000372774.3	-	3	780	c.531C>A	c.(529-531)gaC>gaA	p.D177E	TCEAL6_ENST00000372773.1_Missense_Mutation_p.D177E	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						ACACCCCGTTGTCCCCTTGGG	0.502																																					p.D177E		Atlas-SNP	.											.	TCEAL6	27	.	0			c.C531A						.						22.0	21.0	21.0					X																	101395773		2197	4275	6472	SO:0001583	missense	158931	exon3			CCCGTTGTCCCCT	BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.531C>A	chrX.hg19:g.101395773G>T	ENSP00000361860:p.Asp177Glu	79.0	0.0		143.0	6.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.032|0.032	-1.327438|-1.327438	0.01309|0.01309	.|.	.|.	ENSG00000204071|ENSG00000204071	ENST00000372774;ENST00000372773|ENST00000536102	T;T|.	0.21191|.	2.02;2.02|.	2.82|2.82	2.82|2.82	0.32997|0.32997	.|.	0.272209|.	0.20313|.	N|.	0.094788|.	T|T	0.20455|0.20455	0.0492|0.0492	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	B|.	0.16396|.	0.017|.	B|.	0.13407|.	0.009|.	T|T	0.20638|0.20638	-1.0269|-1.0269	10|6	0.22706|0.06236	T|T	0.39|0.91	.|.	8.3639|8.3639	0.32374|0.32374	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	177|.	Q6IPX3-2|.	.|.	E|K	177|177	ENSP00000361860:D177E;ENSP00000361859:D177E|.	ENSP00000361859:D177E|ENSP00000437364:Q177K	D|Q	-|-	3|1	2|0	TCEAL6|TCEAL6	101282429|101282429	0.014000|0.014000	0.17966|0.17966	0.012000|0.012000	0.15200|0.15200	0.864000|0.864000	0.49448|0.49448	2.835000|2.835000	0.48175|0.48175	1.692000|1.692000	0.51112|0.51112	0.468000|0.468000	0.43344|0.43344	GAC|CAA	.	.		0.502	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938	
TCEAL6	158931	hgsc.bcm.edu	37	X	101395778	101395778	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	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	74.0	0.0		140.0	19.0	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	
TCEAL6	158931	hgsc.bcm.edu	37	X	101395786	101395786	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:101395786A>G	ENST00000372774.3	-	3	767	c.518T>C	c.(517-519)tTc>tCc	p.F173S	TCEAL6_ENST00000372773.1_Missense_Mutation_p.F173S	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	173					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						CCCTTGGGCGAATGGATCCTG	0.502																																					p.F173S		Atlas-SNP	.											.	TCEAL6	27	.	0			c.T518C						.						18.0	16.0	17.0					X																	101395786		2188	4247	6435	SO:0001583	missense	158931	exon3			TGGGCGAATGGAT	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.518T>C	chrX.hg19:g.101395786A>G	ENSP00000361860:p.Phe173Ser	89.0	0.0		165.0	7.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.	.	.	.	.	.	.	.	.	.	A	11.02	1.514968	0.27123	.	.	ENSG00000204071	ENST00000372774;ENST00000372773;ENST00000536102	T;T	0.10288	2.89;2.89	2.82	1.57	0.23409	.	0.407517	0.18158	N	0.149877	T	0.23965	0.0580	M	0.65498	2.005	0.09310	N	1	D	0.76494	0.999	D	0.80764	0.994	T	0.04495	-1.0947	10	0.87932	D	0	.	4.5124	0.11917	0.7069:0.0:0.0:0.2931	.	173	Q6IPX3-2	.	S	173	ENSP00000361860:F173S;ENSP00000361859:F173S	ENSP00000361859:F173S	F	-	2	0	TCEAL6	101282442	0.004000	0.15560	0.001000	0.08648	0.524000	0.34500	1.362000	0.34148	0.327000	0.23409	0.381000	0.24937	TTC	.	.		0.502	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938	
GPRASP2	114928	hgsc.bcm.edu	37	X	101970497	101970497	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:101970497T>C	ENST00000535209.1	+	4	1531	c.700T>C	c.(700-702)Tct>Cct	p.S234P	GPRASP2_ENST00000332262.5_Missense_Mutation_p.S234P|GPRASP2_ENST00000543253.1_Missense_Mutation_p.S234P			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	234						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						CTCTACAGCGTCTTCTTTCTG	0.532																																					p.S234P		Atlas-SNP	.											.	GPRASP2	89	.	0			c.T700C						.						90.0	97.0	94.0					X																	101970497		2203	4299	6502	SO:0001583	missense	114928	exon4			ACAGCGTCTTCTT	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.700T>C	chrX.hg19:g.101970497T>C	ENSP00000437394:p.Ser234Pro	92.0	0.0		79.0	4.0	NM_138437	D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	hg19	CCDS14501.1	.	.	.	.	.	.	.	.	.	.	T	10.33	1.319545	0.23994	.	.	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.25085	1.82;1.82;1.82	5.05	3.88	0.44766	.	0.144862	0.32753	N	0.005700	T	0.19327	0.0464	L	0.52126	1.63	0.19775	N	0.999954	B	0.25904	0.137	B	0.21151	0.033	T	0.20739	-1.0266	10	0.19147	T	0.46	.	6.8718	0.24125	0.0:0.1088:0.0:0.8912	.	234	Q96D09	GASP2_HUMAN	P	234	ENSP00000437872:S234P;ENSP00000437394:S234P;ENSP00000339057:S234P	ENSP00000339057:S234P	S	+	1	0	GPRASP2	101857153	0.689000	0.27690	0.052000	0.19188	0.002000	0.02628	0.707000	0.25704	0.815000	0.34398	0.486000	0.48141	TCT	.	.		0.532	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437	
NRK	203447	hgsc.bcm.edu	37	X	105153617	105153617	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:105153617T>C	ENST00000243300.9	+	13	2287	c.1984T>C	c.(1984-1986)Ttg>Ctg	p.L662L	NRK_ENST00000428173.2_Silent_p.L663L	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	662					activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						ACTTGGTCCGTTGCAAACCCT	0.453										HNSCC(51;0.14)																											p.L662L		Atlas-SNP	.											.	NRK	321	.	0			c.T1984C						.						37.0	34.0	35.0					X																	105153617		1884	4089	5973	SO:0001819	synonymous_variant	203447	exon13			GGTCCGTTGCAAA	BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.1984T>C	chrX.hg19:g.105153617T>C		73.0	0.0		100.0	4.0	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Silent	SNP	ENST00000243300.9	hg19																																																																																				.	.		0.453	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465	
TBC1D8B	54885	hgsc.bcm.edu	37	X	106116905	106116905	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:106116905A>G	ENST00000357242.5	+	21	3247	c.3073A>G	c.(3073-3075)Agg>Ggg	p.R1025G	TBC1D8B_ENST00000276175.3_Missense_Mutation_p.R1019G	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	1025							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|liver(4)|lung(15)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CCTTTTACTCAGGATGGAAGA	0.413																																					p.R1025G		Atlas-SNP	.											.	TBC1D8B	181	.	0			c.A3073G						.						135.0	131.0	132.0					X																	106116905		2203	4300	6503	SO:0001583	missense	54885	exon21			TTACTCAGGATGG	AK123957	CCDS14522.1, CCDS14523.1	Xq22.3	2013-01-10			ENSG00000133138	ENSG00000133138		"""EF-hand domain containing"""	24715	protein-coding gene	gene with protein product						8889548	Standard	NM_017752		Approved	FLJ20298, RP11-321G1.1	uc004emo.3	Q0IIM8	OTTHUMG00000022152	ENST00000357242.5:c.3073A>G	chrX.hg19:g.106116905A>G	ENSP00000349781:p.Arg1025Gly	94.0	0.0		112.0	5.0	NM_017752	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Missense_Mutation	SNP	ENST00000357242.5	hg19	CCDS14522.1	.	.	.	.	.	.	.	.	.	.	A	10.21	1.287530	0.23478	.	.	ENSG00000133138	ENST00000357242;ENST00000276175	T;T	0.09350	2.99;2.99	5.72	4.51	0.55191	.	0.310822	0.31976	N	0.006768	T	0.14485	0.0350	M	0.68317	2.08	0.35764	D	0.820377	B	0.26147	0.143	B	0.29524	0.103	T	0.08106	-1.0738	10	0.62326	D	0.03	-4.3801	10.1722	0.42917	0.6919:0.3081:0.0:0.0	.	1025	Q0IIM8	TBC8B_HUMAN	G	1025;1019	ENSP00000349781:R1025G;ENSP00000276175:R1019G	ENSP00000276175:R1019G	R	+	1	2	TBC1D8B	106003561	1.000000	0.71417	0.999000	0.59377	0.119000	0.20118	2.883000	0.48554	1.917000	0.55516	0.481000	0.45027	AGG	.	.		0.413	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2	NM_017752	
GUCY2F	2986	hgsc.bcm.edu	37	X	108691369	108691369	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:108691369T>C	ENST00000218006.2	-	6	1789	c.1498A>G	c.(1498-1500)Atc>Gtc	p.I500V		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	500					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						GGTCCTTTGATCAACTGGATT	0.423																																					p.I500V		Atlas-SNP	.											.	GUCY2F	178	.	0			c.A1498G						.						135.0	115.0	121.0					X																	108691369		2203	4300	6503	SO:0001583	missense	2986	exon6			CTTTGATCAACTG	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"""guanylate cyclase 2D-like, membrane (retina-specific)"""	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.1498A>G	chrX.hg19:g.108691369T>C	ENSP00000218006:p.Ile500Val	45.0	0.0		52.0	5.0	NM_001522	Q9UJF1	Missense_Mutation	SNP	ENST00000218006.2	hg19	CCDS14545.1	.	.	.	.	.	.	.	.	.	.	T	1.509	-0.550103	0.03996	.	.	ENSG00000101890	ENST00000218006	T	0.77620	-1.11	4.38	3.23	0.37069	.	0.187646	0.46145	D	0.000310	T	0.39860	0.1094	N	0.00554	-1.385	0.34113	D	0.663265	B	0.06786	0.001	B	0.09377	0.004	T	0.33007	-0.9885	10	0.16420	T	0.52	.	5.1422	0.14965	0.0:0.2326:0.0:0.7674	.	500	P51841	GUC2F_HUMAN	V	500	ENSP00000218006:I500V	ENSP00000218006:I500V	I	-	1	0	GUCY2F	108578025	0.994000	0.37717	1.000000	0.80357	0.982000	0.71751	0.993000	0.29680	0.803000	0.34113	0.486000	0.48141	ATC	.	.		0.423	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522	
DCX	1641	hgsc.bcm.edu	37	X	110574142	110574142	+	Intron	SNP	G	G	T	rs371447966		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:110574142G>T	ENST00000338081.3	-	5	1346				DCX_ENST00000356915.2_Missense_Mutation_p.N312K|DCX_ENST00000371993.2_Intron|DCX_ENST00000496551.1_5'UTR|DCX_ENST00000488120.1_Intron|DCX_ENST00000356220.3_Missense_Mutation_p.N312K	NM_000555.3	NP_000546.2	O43602	DCX_HUMAN	doublecortin						axon extension (GO:0048675)|axon guidance (GO:0007411)|brain development (GO:0007420)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neuron migration (GO:0001764)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuron projection (GO:0043005)	microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|skin(6)|upper_aerodigestive_tract(1)	41						CGTCTTGGTCGTTACCTGAGT	0.522																																					p.N312K		Atlas-SNP	.											.	DCX	158	.	0			c.C936A						.						322.0	256.0	279.0					X																	110574142		2203	4300	6503	SO:0001627	intron_variant	1641	exon5			TTGGTCGTTACCT	AF040254	CCDS14556.1, CCDS14557.1, CCDS14558.1	Xq22.3-q23	2008-08-01	2008-08-01		ENSG00000077279	ENSG00000077279			2714	protein-coding gene	gene with protein product	"""doublecortex"""	300121	"""doublecortex; lissencephaly, X-linked (doublecortin)"""			9489699, 9489700	Standard	NM_178151		Approved	SCLH, DC, LISX, DBCN, XLIS	uc004epd.3	O43602	OTTHUMG00000022204	ENST00000338081.3:c.1174+4C>A	chrX.hg19:g.110574142G>T		87.0	0.0		109.0	72.0	NM_001195553	A6NFY6|A9Z1V8|D3DUY8|D3DUY9|D3DUZ0|O43911|Q5JYZ5	Missense_Mutation	SNP	ENST00000338081.3	hg19	CCDS14556.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.65|14.65	2.600082|2.600082	0.46318|0.46318	.|.	.|.	ENSG00000077279|ENSG00000077279	ENST00000356915;ENST00000356220|ENST00000358070	T;T|.	0.21543|.	2.0;2.0|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.256890|.	0.31797|.	N|.	0.007046|.	T|T	0.40670|0.40670	0.1126|0.1126	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	D|D	1|1	P|.	0.35401|.	0.499|.	B|.	0.31442|.	0.13|.	T|T	0.30238|0.30238	-0.9985|-0.9985	10|5	0.06236|.	T|.	0.91|.	.|.	11.7176|11.7176	0.51663|0.51663	0.0827:0.0:0.9173:0.0|0.0827:0.0:0.9173:0.0	.|.	381|.	B4DM53|.	.|.	K|K	312|385	ENSP00000349385:N312K;ENSP00000348553:N312K|.	ENSP00000348553:N312K|.	N|T	-|-	3|2	2|0	DCX|DCX	110460798|110460798	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.209000|4.209000	0.58493|0.58493	2.238000|2.238000	0.73509|0.73509	0.594000|0.594000	0.82650|0.82650	AAC|ACG	.	.		0.522	DCX-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357058.1	NM_178153	
MAP7D3	79649	hgsc.bcm.edu	37	X	135328496	135328496	+	Silent	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:135328496A>G	ENST00000316077.9	-	2	295	c.75T>C	c.(73-75)gcT>gcC	p.A25A	MAP7D3_ENST00000370661.1_Silent_p.A25A|MAP7D3_ENST00000370663.5_Silent_p.A7A	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	25					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					CGTTTGCTGCAGCAACTAAAA	0.388																																					p.A25A		Atlas-SNP	.											.	MAP7D3	102	.	0			c.T75C						.						61.0	55.0	57.0					X																	135328496		2044	4173	6217	SO:0001819	synonymous_variant	79649	exon2			TGCTGCAGCAACT	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.75T>C	chrX.hg19:g.135328496A>G		122.0	0.0		143.0	6.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Silent	SNP	ENST00000316077.9	hg19	CCDS44004.1																																																																																			.	.		0.388	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2		
GABRQ	55879	hgsc.bcm.edu	37	X	151815555	151815555	+	Silent	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:151815555T>C	ENST00000370306.2	+	4	473	c.453T>C	c.(451-453)gcT>gcC	p.A151A		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	151					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|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)	GCAAGGATGCTTTCGTGCATG	0.537																																					p.A151A		Atlas-SNP	.											.	GABRQ	131	.	0			c.T453C						.						289.0	200.0	230.0					X																	151815555		2203	4300	6503	SO:0001819	synonymous_variant	55879	exon4			GGATGCTTTCGTG	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	14454	protein-coding gene	gene with protein product	"""GABA(A) receptor, theta"""	300349	"""gamma-aminobutyric acid (GABA) receptor, theta"""			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.453T>C	chrX.hg19:g.151815555T>C		120.0	0.0		98.0	4.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Silent	SNP	ENST00000370306.2	hg19	CCDS14707.1																																																																																			.	.		0.537	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558	
PNCK	139728	hgsc.bcm.edu	37	X	152937342	152937342	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:152937342T>C	ENST00000370150.1	-	5	585	c.407A>G	c.(406-408)gAc>gGc	p.D136G	PNCK_ENST00000447676.2_Missense_Mutation_p.D219G|PNCK_ENST00000370145.4_Missense_Mutation_p.D153G|PNCK_ENST00000370142.1_Missense_Mutation_p.D136G|PNCK_ENST00000340888.3_Missense_Mutation_p.D136G|PNCK_ENST00000475172.1_5'UTR|PNCK_ENST00000393831.2_Missense_Mutation_p.D136G			Q6P2M8	KCC1B_HUMAN	pregnancy up-regulated nonubiquitous CaM kinase	136	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|lung(3)|skin(1)	6	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CACCTTGAGGTCCCGGTGCAC	0.657																																					p.D219G		Atlas-SNP	.											.	PNCK	70	.	0			c.A656G						.						21.0	21.0	21.0					X																	152937342		2203	4292	6495	SO:0001583	missense	139728	exon5			TTGAGGTCCCGGT	BC033746	CCDS35503.2, CCDS48189.1	Xq28	2013-10-14	2013-10-14		ENSG00000130822	ENSG00000130822			13415	protein-coding gene	gene with protein product		300680	"""pregnancy upregulated non-ubiquitously expressed CaM kinase"", ""pregnancy up-regulated non-ubiquitously expressed CaM kinase"""			12477932	Standard	NM_001039582		Approved	MGC45419, CaMK1b	uc011myu.2	Q6P2M8	OTTHUMG00000024216	ENST00000370150.1:c.407A>G	chrX.hg19:g.152937342T>C	ENSP00000359169:p.Asp136Gly	132.0	0.0		134.0	8.0	NM_001039582	B4DJR8|B4E1A6|B7WPG0|D3DWU7|Q8N4R0	Missense_Mutation	SNP	ENST00000370150.1	hg19		.	.	.	.	.	.	.	.	.	.	t	23.5	4.428324	0.83667	.	.	ENSG00000130822	ENST00000340888;ENST00000370150;ENST00000393831;ENST00000370142;ENST00000370145;ENST00000447676;ENST00000439087;ENST00000422811	D;D;D;D;D;D;D;D	0.93019	-3.15;-3.15;-3.15;-3.15;-3.15;-3.15;-3.15;-3.15	5.01	5.01	0.66863	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000017	D	0.97901	0.9310	H	0.98133	4.155	0.80722	D	1	D;D;D;D	0.89917	1.0;0.996;0.992;0.992	D;P;D;D	0.87578	0.998;0.863;0.916;0.916	D	0.98715	1.0706	10	0.87932	D	0	-26.4021	12.7717	0.57426	0.0:0.0:0.0:1.0	.	163;219;153;136	B4DJG4;Q6P2M8-5;B4E1A6;Q6P2M8	.;.;.;KCC1B_HUMAN	G	136;136;136;136;153;219;136;136	ENSP00000340586:D136G;ENSP00000359169:D136G;ENSP00000377417:D136G;ENSP00000359161:D136G;ENSP00000359164:D153G;ENSP00000405950:D219G;ENSP00000415770:D136G;ENSP00000391772:D136G	ENSP00000340586:D136G	D	-	2	0	PNCK	152590536	1.000000	0.71417	0.998000	0.56505	0.914000	0.54420	6.153000	0.71819	1.653000	0.50694	0.430000	0.28490	GAC	.	.		0.657	PNCK-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000061044.2	NM_198452	
L1CAM	3897	hgsc.bcm.edu	37	X	153128287	153128287	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:153128287A>G	ENST00000370060.1	-	29	3794	c.3605T>C	c.(3604-3606)cTg>cCg	p.L1202P	L1CAM_ENST00000361981.3_Missense_Mutation_p.L1193P|L1CAM_ENST00000361699.4_Missense_Mutation_p.L1198P|L1CAM_ENST00000370057.3_Missense_Mutation_p.L1202P|L1CAM_ENST00000543994.1_Missense_Mutation_p.L1204P|L1CAM_ENST00000538883.1_Missense_Mutation_p.L1200P|L1CAM_ENST00000370055.1_Missense_Mutation_p.L1193P	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	1202					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)					GTCACTGCCCAGGGGCTTGAT	0.592																																					p.L1202P		Atlas-SNP	.											.	L1CAM	189	.	0			c.T3605C						.						74.0	55.0	61.0					X																	153128287		2203	4300	6503	SO:0001583	missense	3897	exon28			CTGCCCAGGGGCT	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.3605T>C	chrX.hg19:g.153128287A>G	ENSP00000359077:p.Leu1202Pro	63.0	0.0		72.0	5.0	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	hg19	CCDS14733.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.428003	0.43122	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000370058;ENST00000361699	D;D;D;D;D;D;D;D	0.86097	-2.07;-2.07;-2.07;-2.07;-2.07;-2.07;-2.07;-2.07	4.6	4.6	0.57074	.	0.000000	0.42053	D	0.000762	D	0.87740	0.6253	L	0.40543	1.245	0.80722	D	1	D;P;D	0.76494	0.999;0.86;0.999	D;P;D	0.77004	0.921;0.535;0.989	D	0.86471	0.1785	10	0.36615	T	0.2	.	12.0976	0.53763	1.0:0.0:0.0:0.0	.	1193;1198;1202	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	P	1202;1204;1202;1200;1193;1193;98;1198	ENSP00000359077:L1202P;ENSP00000438430:L1204P;ENSP00000359074:L1202P;ENSP00000439645:L1200P;ENSP00000354712:L1193P;ENSP00000359072:L1193P;ENSP00000359075:L98P;ENSP00000355380:L1198P	ENSP00000355380:L1198P	L	-	2	0	L1CAM	152781481	0.169000	0.23002	1.000000	0.80357	0.786000	0.44442	0.772000	0.26647	1.697000	0.51169	0.430000	0.28490	CTG	.	.		0.592	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003	
ATP6AP1	537	hgsc.bcm.edu	37	X	153664091	153664091	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:153664091T>C	ENST00000369762.2	+	10	1328	c.1267T>C	c.(1267-1269)Tcc>Ccc	p.S423P	GDI1_ENST00000447750.2_5'Flank	NM_001183.4	NP_001174.2	Q15904	VAS1_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 1	423					ATP hydrolysis coupled proton transport (GO:0015991)|establishment of organelle localization (GO:0051656)|pH reduction (GO:0045851)|positive regulation of bone resorption (GO:0045780)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoclast development (GO:2001206)|proton transport (GO:0015992)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuole (GO:0005773)	ATP binding (GO:0005524)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(5)	14	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)					CAGCTTCTTCTCCCCCGGCAT	0.562																																					p.S423P		Atlas-SNP	.											.	ATP6AP1	46	.	0			c.T1267C						.						191.0	180.0	184.0					X																	153664091		2203	4300	6503	SO:0001583	missense	537	exon10			TTCTTCTCCCCCG	D16469	CCDS35451.1	Xq28	2010-03-10	2003-08-28	2003-08-29	ENSG00000071553	ENSG00000071553			868	protein-coding gene	gene with protein product		300197	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump), subunit 1"""	ATP6S1, ATP6IP1		8733135, 8281148	Standard	NM_001183		Approved	ORF, XAP-3, VATPS1, 16A, Ac45, XAP3, CF2	uc004flf.1	Q15904	OTTHUMG00000033291	ENST00000369762.2:c.1267T>C	chrX.hg19:g.153664091T>C	ENSP00000358777:p.Ser423Pro	98.0	0.0		104.0	5.0	NM_001183	A6ZKI4|Q8NBT4|Q9H0C7	Missense_Mutation	SNP	ENST00000369762.2	hg19	CCDS35451.1	.	.	.	.	.	.	.	.	.	.	T	19.03	3.747755	0.69533	.	.	ENSG00000071553	ENST00000369762;ENST00000445849	.	.	.	5.4	5.4	0.78164	.	0.161766	0.56097	D	0.000028	T	0.79003	0.4373	M	0.79693	2.465	0.50632	D	0.999889	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.81799	-0.0767	9	0.72032	D	0.01	-30.5053	12.2595	0.54642	0.0:0.0:0.0:1.0	.	383;423	B3KR70;Q15904	.;VAS1_HUMAN	P	423;247	.	ENSP00000358777:S423P	S	+	1	0	ATP6AP1	153317285	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	0.885000	0.28227	1.799000	0.52666	0.486000	0.48141	TCC	.	.		0.562	ATP6AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081639.4	NM_001183	
TBL1Y	90665	hgsc.bcm.edu	37	Y	6938816	6938816	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrY:6938816T>C	ENST00000383032.1	+	10	1293	c.646T>C	c.(646-648)Tcc>Ccc	p.S216P	TBL1Y_ENST00000346432.3_Missense_Mutation_p.S216P|TBL1Y_ENST00000355162.2_Missense_Mutation_p.S216P	NM_033284.1	NP_150600.1	Q9BQ87	TBL1Y_HUMAN	transducin (beta)-like 1, Y-linked	216					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				kidney(1)|large_intestine(4)|lung(2)|skin(1)	8						CAACGGGGGCTCCACCCAGCT	0.478																																					p.S216P		Atlas-SNP	.											.	TBL1Y	15	.	0			c.T646C						.																																			SO:0001583	missense	90665	exon9			GGGGGCTCCACCC	AF332220	CCDS14779.1	Yp11.2	2013-01-10	2009-12-17		ENSG00000092377	ENSG00000092377		"""WD repeat domain containing"""	18502	protein-coding gene	gene with protein product		400033					Standard	NM_033284		Approved	TBL1	uc004frd.3	Q9BQ87	OTTHUMG00000035299	ENST00000383032.1:c.646T>C	chrY.hg19:g.6938816T>C	ENSP00000372499:p.Ser216Pro	122.0	0.0		95.0	5.0	NM_134258	A1L4B3	Missense_Mutation	SNP	ENST00000383032.1	hg19	CCDS14779.1																																																																																			.	.		0.478	TBL1Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085360.1	NM_033284	
CERS3	204219	hgsc.bcm.edu	37	15	101009634	101009634	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:101009634delA	ENST00000394113.1	-	12	1484	c.794delT	c.(793-795)ttcfs	p.F265fs	CERS3_ENST00000538112.2_Frame_Shift_Del_p.F265fs|CERS3_ENST00000284382.4_Frame_Shift_Del_p.F265fs|CERS3_ENST00000560944.1_Intron			Q8IU89	CERS3_HUMAN	ceramide synthase 3	265	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|keratinocyte differentiation (GO:0030216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										GGAGAAGATGAAAAACAGGGT	0.448																																					p.F265fs		Atlas-INDEL	.											.	.	.	.	0			c.795delC						.						113.0	110.0	111.0					15																	101009634		2203	4300	6503	SO:0001589	frameshift_variant	204219	exon11			.		CCDS10384.1	15q26.3	2012-11-19	2011-07-08	2011-07-08	ENSG00000154227	ENSG00000154227		"""Homeoboxes / CERS class"""	23752	protein-coding gene	gene with protein product		615276	"""LAG1 longevity assurance homolog 3 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 3"""	LASS3			Standard	NM_178842		Approved	MGC27091	uc002bwb.3	Q8IU89	OTTHUMG00000172568	ENST00000394113.1:c.794delT	chr15.hg19:g.101009634delA	ENSP00000377672:p.Phe265fs	151.0	0.0		138.0	10.0	NM_178842	Q8NE64|Q8NEN6	Frame_Shift_Del	DEL	ENST00000394113.1	hg19	CCDS10384.1																																																																																			.	.		0.448	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313594.4	NM_178842	
PEAR1	375033	hgsc.bcm.edu	37	1	156883056	156883056	+	Frame_Shift_Del	DEL	C	C	-	rs147826153		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:156883056delC	ENST00000338302.3	+	20	2718	c.2493delC	c.(2491-2493)aacfs	p.N831fs	PEAR1_ENST00000292357.7_Frame_Shift_Del_p.N831fs			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	831	Pro-rich.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GCTCCCCAAACCCCCCACCCC	0.607																																					p.N831fs		Atlas-INDEL	.											.	PEAR1	118	.	0			c.2492delA						.						103.0	102.0	103.0					1																	156883056		2203	4300	6503	SO:0001589	frameshift_variant	375033	exon19			.	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.2493delC	chr1.hg19:g.156883056delC	ENSP00000344465:p.Asn831fs	91.0	0.0		212.0	14.0	NM_001080471	Q8TEK2	Frame_Shift_Del	DEL	ENST00000338302.3	hg19	CCDS30892.1																																																																																			.	.		0.607	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
DLEU2	8847	hgsc.bcm.edu	37	13	50623292	50623292	+	RNA	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:50623292delT	ENST00000607334.1	-	0	45				MIR16-1_ENST00000385271.1_RNA	NR_029485.1				deleted in lymphocytic leukemia 2 (non-protein coding)																		GGCCTGCACCTTTTCAAAATC	0.318																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.						51.0	50.0	50.0					13																	50623292		1567	3582	5149			406948	.			.	Y15228		13q14	2014-07-18	2008-08-13		ENSG00000231607	ENSG00000231607		"""-"""	13748	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 22"", ""long intergenic non-protein coding RNA 22"", ""mir-15a-16-1 cluster host gene (non-protein coding)"""	605766	"""ret finger protein 2 opposite strand"", ""deleted in lymphocytic leukemia, 2"""	DLB2, BCMSUN, RFP2OS		9395242, 11072235	Standard	NR_002612		Approved	LEU2, TRIM13OS, NCRNA00022, LINC00022, MIR15AHG	uc001vdo.1		OTTHUMG00000016927		chr13.hg19:g.50623292delT		218.0	0.0		152.0	11.0	.		RNA	DEL	ENST00000607334.1	hg19																																																																																				.	.		0.318	DLEU2-202	KNOWN	basic	miRNA	processed_transcript		NR_002612	
QRICH2	84074	hgsc.bcm.edu	37	17	74274145	74274145	+	Frame_Shift_Del	DEL	C	C	-	rs200636552		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:74274145delC	ENST00000262765.5	-	15	4723	c.4544delG	c.(4543-4545)ggcfs	p.G1515fs		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	1515										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						CTTGGTGGAGCCCCCGAAGTG	0.642																																					p.G1515fs		Atlas-INDEL	.											.	QRICH2	143	.	0			c.4545delC						.						84.0	86.0	85.0					17																	74274145		2203	4300	6503	SO:0001589	frameshift_variant	84074	exon15			.	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.4544delG	chr17.hg19:g.74274145delC	ENSP00000262765:p.Gly1515fs	139.0	0.0		166.0	10.0	NM_032134	A2RRE1|Q96LM3	Frame_Shift_Del	DEL	ENST00000262765.5	hg19	CCDS32741.1																																																																																			.	.		0.642	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
SLC26A4	5172	hgsc.bcm.edu	37	7	107340574	107340574	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:107340574delT	ENST00000265715.3	+	15	1885	c.1661delT	c.(1660-1662)attfs	p.I554fs	SLC26A4_ENST00000541474.1_Frame_Shift_Del_p.I115fs|SLC26A4_ENST00000544569.1_Frame_Shift_Del_p.I141fs|SLC26A4_ENST00000543100.1_Frame_Shift_Del_p.I123fs|SLC26A4_ENST00000480841.1_3'UTR	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	554	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						TCCAGTCCTATTTTCTATGGC	0.318									Pendred syndrome																												p.I554fs		Atlas-INDEL	.											.	SLC26A4	117	.	0			c.1660delA						.						116.0	120.0	119.0					7																	107340574		2202	4299	6501	SO:0001589	frameshift_variant	5172	exon15	Familial Cancer Database	Goiter-Deafness syndrome	.	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"""Solute carriers"""	8818	protein-coding gene	gene with protein product	"""pendrin"""	605646	"""solute carrier family 26, member 4"""	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.1661delT	chr7.hg19:g.107340574delT	ENSP00000265715:p.Ile554fs	136.0	0.0		197.0	12.0	NM_000441	B7Z266|O43170	Frame_Shift_Del	DEL	ENST00000265715.3	hg19	CCDS5746.1																																																																																			.	.		0.318	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441	
GJA8	2703	hgsc.bcm.edu	37	1	147380686	147380686	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:147380686delA	ENST00000369235.1	+	1	604	c.604delA	c.(604-606)aaafs	p.K202fs	GJA8_ENST00000240986.4_Frame_Shift_Del_p.K202fs			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	202					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					GCCCACGGAGAAAACCATCTT	0.602																																					p.E201fs	Melanoma(76;1255 1795 8195 52096)	Atlas-INDEL	.											.	GJA8	108	.	0			c.603delG						.						119.0	102.0	108.0					1																	147380686		2203	4300	6503	SO:0001589	frameshift_variant	2703	exon2			.	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"""Ion channels / Gap junction proteins (connexins)"""	4281	protein-coding gene	gene with protein product	"""connexin 50"""	600897	"""gap junction protein, alpha 8, 50kD (connexin 50)"", ""gap junction protein, alpha 8, 50kDa (connexin 50)"""	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.604delA	chr1.hg19:g.147380686delA	ENSP00000358238:p.Lys202fs	89.0	0.0		148.0	10.0	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Frame_Shift_Del	DEL	ENST00000369235.1	hg19	CCDS30834.1																																																																																			.	.		0.602	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267	
SUCO	51430	hgsc.bcm.edu	37	1	172558537	172558537	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:172558537delC	ENST00000263688.3	+	18	2515	c.2296delC	c.(2296-2298)cccfs	p.P766fs	SUCO_ENST00000608151.1_Frame_Shift_Del_p.P918fs|SUCO_ENST00000367723.4_Frame_Shift_Del_p.P917fs|SUCO_ENST00000610051.1_Intron	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	766					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											ACCAGTGATTCCCCAAGAGAG	0.358																																					p.I765fs		Atlas-INDEL	.											.	.	.	.	0			c.2295delT						.						62.0	62.0	62.0					1																	172558537		2195	4291	6486	SO:0001589	frameshift_variant	51430	exon18			.	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"""SUN-like protein 1"", ""osteopotentia"""		"""chromosome 1 open reading frame 9"""	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.2296delC	chr1.hg19:g.172558537delC	ENSP00000263688:p.Pro766fs	76.0	0.0		138.0	10.0	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Frame_Shift_Del	DEL	ENST00000263688.3	hg19	CCDS1303.1																																																																																			.	.		0.358	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227	
HOXA4	3201	hgsc.bcm.edu	37	7	27170333	27170333	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:27170333delA	ENST00000360046.5	-	1	85	c.20delT	c.(19-21)ttgfs	p.L7fs	HOXA4_ENST00000428284.2_Frame_Shift_Del_p.L7fs|HOXA-AS2_ENST00000521159.1_RNA|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS2_ENST00000521687.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS2_ENST00000517550.1_RNA|HOXA3_ENST00000521401.1_Intron	NM_002141.4	NP_002132.3	Q00056	HXA4_HUMAN	homeobox A4	7					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)	12						GGAGTTTATCAAAAACGAGCT	0.582																																					p.L7fs		Atlas-INDEL	.											.	HOXA4	21	.	0			c.21delG						.						16.0	16.0	16.0					7																	27170333		2201	4291	6492	SO:0001589	frameshift_variant	3201	exon1			.		CCDS5405.1	7p15.2	2011-06-20	2005-12-22		ENSG00000197576	ENSG00000197576		"""Homeoboxes / ANTP class : HOXL subclass"""	5105	protein-coding gene	gene with protein product		142953	"""homeo box A4"""	HOX1D, HOX1		1973146, 1358459	Standard	NM_002141		Approved		uc003sym.4	Q00056	OTTHUMG00000023213	ENST00000360046.5:c.20delT	chr7.hg19:g.27170333delA	ENSP00000353151:p.Leu7fs	170.0	0.0		213.0	14.0	NM_002141	A4D180|O43366	Frame_Shift_Del	DEL	ENST00000360046.5	hg19	CCDS5405.1																																																																																			.	.		0.582	HOXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059534.4		
MDN1	23195	hgsc.bcm.edu	37	6	90504517	90504517	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:90504517delA	ENST00000369393.3	-	3	448	c.333delT	c.(331-333)tttfs	p.F111fs	MDN1_ENST00000428876.1_Frame_Shift_Del_p.F111fs			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	111					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		ATCTCAGGGCAAACCTTCAAA	0.383																																					p.A112fs		Atlas-INDEL	.											.	MDN1	478	.	0			c.334delG						.						51.0	49.0	50.0					6																	90504517		2203	4300	6503	SO:0001589	frameshift_variant	23195	exon3			.	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.333delT	chr6.hg19:g.90504517delA	ENSP00000358400:p.Phe111fs	94.0	0.0		156.0	10.0	NM_014611	O15019|Q5T794	Frame_Shift_Del	DEL	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.383	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
SNRNP200	23020	hgsc.bcm.edu	37	2	96958714	96958714	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:96958714delT	ENST00000323853.5	-	16	2233	c.2156delA	c.(2155-2157)aatfs	p.N719fs	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	719	Helicase C-terminal 1. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						GCAAACCTGATTTTTTCCAGC	0.368																																					p.N719fs		Atlas-INDEL	.											.	SNRNP200	195	.	0			c.2157delT						.						113.0	102.0	106.0					2																	96958714		2203	4300	6503	SO:0001589	frameshift_variant	23020	exon16			.	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 200 KD"""	601664	"""activating signal cointegrator 1 complex subunit 3-like 1"", ""retinitis pigmentosa 33 (autosomal dominant)"""	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.2156delA	chr2.hg19:g.96958714delT	ENSP00000317123:p.Asn719fs	160.0	0.0		175.0	13.0	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Frame_Shift_Del	DEL	ENST00000323853.5	hg19	CCDS2020.1																																																																																			.	.		0.368	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014	
CEP44	80817	hgsc.bcm.edu	37	4	175224892	175224892	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:175224892delA	ENST00000503780.1	+	5	690	c.276delA	c.(274-276)acafs	p.T92fs	CEP44_ENST00000296519.4_Frame_Shift_Del_p.T92fs|CEP44_ENST00000457424.2_Frame_Shift_Del_p.T92fs|CEP44_ENST00000426172.1_Frame_Shift_Del_p.T92fs	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	92						centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)				endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						CAATTTTGACAAAAAAGCAGT	0.313																																					p.T92fs		Atlas-INDEL	.											.	CEP44	35	.	0			c.275delC						.						63.0	66.0	65.0					4																	175224892		2202	4299	6501	SO:0001589	frameshift_variant	80817	exon5			.	AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"""KIAA1712"""	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.276delA	chr4.hg19:g.175224892delA	ENSP00000423153:p.Thr92fs	182.0	0.0		178.0	11.0	NM_001040157	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Frame_Shift_Del	DEL	ENST00000503780.1	hg19	CCDS34106.1																																																																																			.	.		0.313	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633	
OGT	8473	hgsc.bcm.edu	37	X	70781722	70781722	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:70781722delT	ENST00000373719.3	+	15	2166	c.1949delT	c.(1948-1950)cttfs	p.L650fs	OGT_ENST00000373701.3_Frame_Shift_Del_p.L640fs	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	650					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)					CGAAATGAGCTTTTTGCTCTC	0.408																																					p.L650fs		Atlas-INDEL	.											.	OGT	207	.	0			c.1948delC						.						68.0	59.0	62.0					X																	70781722		2203	4300	6503	SO:0001589	frameshift_variant	8473	exon15			.	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.1949delT	chrX.hg19:g.70781722delT	ENSP00000362824:p.Leu650fs	173.0	0.0		146.0	10.0	NM_181672	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Frame_Shift_Del	DEL	ENST00000373719.3	hg19	CCDS14414.1																																																																																			.	.		0.408	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672	
CR1	1378	hgsc.bcm.edu	37	1	207700165	207700165	+	Frame_Shift_Del	DEL	T	T	-	rs3866235		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:207700165delT	ENST00000367049.4	+	6	954	c.954delT	c.(952-954)cctfs	p.P318fs	CR1_ENST00000400960.2_Frame_Shift_Del_p.P318fs|CR1_ENST00000367053.1_Frame_Shift_Del_p.P318fs|CR1_ENST00000367050.4_Intron|CR1_ENST00000367052.1_Frame_Shift_Del_p.P318fs|CR1_ENST00000367051.1_Intron	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	318	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						ACTTTTCACCTGGGCAGGAAG	0.572																																					p.P318fs		Atlas-INDEL	.											.	CR1	354	.	0			c.953delC						.						69.0	108.0	98.0					1																	207700165		1396	4008	5404	SO:0001589	frameshift_variant	1378	exon6			.	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.954delT	chr1.hg19:g.207700165delT	ENSP00000356016:p.Pro318fs	5.0	0.0		17.0	11.0	NM_000573	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Frame_Shift_Del	DEL	ENST00000367049.4	hg19	CCDS44308.1																																																																																			.	.		0.572	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
MAP7D3	79649	hgsc.bcm.edu	37	X	135328464	135328464	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:135328464delT	ENST00000316077.9	-	2	327	c.107delA	c.(106-108)aagfs	p.K36fs	MAP7D3_ENST00000370661.1_Frame_Shift_Del_p.K36fs|MAP7D3_ENST00000370663.5_Frame_Shift_Del_p.K18fs	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	36					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					CACATCTTGCTTCCTCCTTTC	0.383																																					p.K36fs		Atlas-INDEL	.											.	MAP7D3	102	.	0			c.108delG						.						89.0	80.0	83.0					X																	135328464		1986	4153	6139	SO:0001589	frameshift_variant	79649	exon2			.	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.107delA	chrX.hg19:g.135328464delT	ENSP00000318086:p.Lys36fs	140.0	0.0		158.0	10.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Frame_Shift_Del	DEL	ENST00000316077.9	hg19	CCDS44004.1																																																																																			.	.		0.383	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2		
SDPR	8436	hgsc.bcm.edu	37	2	192701068	192701068	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:192701068delT	ENST00000304141.4	-	2	1188	c.859delA	c.(859-861)agcfs	p.S288fs		NM_004657.5	NP_004648.1			serum deprivation response											NS(1)|central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(3)	23			OV - Ovarian serous cystadenocarcinoma(117;0.0647)			AAGGGGGAGCTTTTTCCTGAG	0.463																																					p.S287fs		Atlas-INDEL	.											.	SDPR	67	.	0			c.860delG						.						134.0	151.0	145.0					2																	192701068		2203	4300	6503	SO:0001589	frameshift_variant	8436	exon2			.	AF085481	CCDS2313.1	2q32-q33	2011-04-20	2009-09-18		ENSG00000168497	ENSG00000168497			10690	protein-coding gene	gene with protein product	"""phosphatidylserine binding protein"""	606728	"""serum deprivation response (phosphatidylserine-binding protein)"", ""serum deprivation response (phosphatidylserine binding protein)"""			10191091, 8241023	Standard	NM_004657		Approved	SDR, PS-p68, cavin-2, CAVIN2	uc002utb.3	O95810	OTTHUMG00000154309	ENST00000304141.4:c.859delA	chr2.hg19:g.192701068delT	ENSP00000305675:p.Ser288fs	170.0	0.0		209.0	13.0	NM_004657		Frame_Shift_Del	DEL	ENST00000304141.4	hg19	CCDS2313.1																																																																																			.	.		0.463	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657	
ELF5	2001	hgsc.bcm.edu	37	11	34511593	34511593	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:34511593delA	ENST00000312319.2	-	4	628	c.399delT	c.(397-399)tttfs	p.F133fs	ELF5_ENST00000257832.2_Frame_Shift_Del_p.F123fs|ELF5_ENST00000528709.1_5'UTR|ELF5_ENST00000429939.2_Intron	NM_001243081.1|NM_198381.1	NP_001230010.1|NP_938195.1	Q9UKW6	ELF5_HUMAN	E74-like factor 5 (ets domain transcription factor)	133					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|ectoderm development (GO:0007398)|mammary gland epithelial cell differentiation (GO:0060644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|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)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			large_intestine(4)|skin(1)	5		Acute lymphoblastic leukemia(5;0.0087)|all_hematologic(20;0.0384)				CAGCGTCATTAAAAAAGGAGT	0.488																																					p.N134fs	Melanoma(61;202 1660 4348 21594)	Atlas-INDEL	.											.	ELF5	21	.	0			c.400delA						.						242.0	235.0	237.0					11																	34511593		2202	4298	6500	SO:0001589	frameshift_variant	2001	exon4			.	AF049703	CCDS7892.1, CCDS7893.1, CCDS58129.1, CCDS73273.1	11p13-p12	2008-05-14			ENSG00000135374	ENSG00000135374			3320	protein-coding gene	gene with protein product		605169				9840936	Standard	NM_001422		Approved		uc001mvp.2	Q9UKW6	OTTHUMG00000166451	ENST00000312319.2:c.399delT	chr11.hg19:g.34511593delA	ENSP00000311010:p.Phe133fs	97.0	0.0		156.0	10.0	NM_198381	A6XAE6|A8K452|O95175|Q8N2K9|Q96QY3|Q9UKW5	Frame_Shift_Del	DEL	ENST00000312319.2	hg19	CCDS7892.1																																																																																			.	.		0.488	ELF5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389845.1	NM_198381	
SLC39A8	64116	hgsc.bcm.edu	37	4	103226251	103226251	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:103226251delG	ENST00000394833.2	-	4	1046	c.570delC	c.(568-570)cccfs	p.P190fs	SLC39A8_ENST00000510255.1_5'UTR|SLC39A8_ENST00000356736.4_Frame_Shift_Del_p.P190fs|SLC39A8_ENST00000424970.2_Frame_Shift_Del_p.P190fs	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	190					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)			large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		TGTCGACTTTGGGATCAAATC	0.333																																					p.K191fs		Atlas-INDEL	.											.	SLC39A8	24	.	0			c.571delA						.						64.0	63.0	63.0					4																	103226251		2203	4300	6503	SO:0001589	frameshift_variant	64116	exon4			.		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"""Solute carriers"""	20862	protein-coding gene	gene with protein product		608732	"""solute carrier family 39 (metal ion transporter), member 8"""			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.570delC	chr4.hg19:g.103226251delG	ENSP00000378310:p.Pro190fs	276.0	0.0		129.0	10.0	NM_022154	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Frame_Shift_Del	DEL	ENST00000394833.2	hg19	CCDS3656.1																																																																																			.	.		0.333	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154	
AGBL1	123624	hgsc.bcm.edu	37	15	87531281	87531281	+	Frame_Shift_Del	DEL	A	A	-	rs1006030	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:87531281delA	ENST00000441037.2	+	23	3242	c.3147delA	c.(3145-3147)acafs	p.T1049fs	AGBL1_ENST00000389298.3_Frame_Shift_Del_p.T780fs|AGBL1_ENST00000421325.2_Frame_Shift_Del_p.T1049fs|RP11-133L19.1_ENST00000558587.1_RNA	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	1049			Missing (in FECD8; enriched in the nucleus, decreased TCF4-binding). {ECO:0000269|PubMed:24094747}.		C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						ttgccattacaaactttttca	0.403																																					p.T1049fs		Atlas-INDEL	.											.	AGBL1	151	.	0			c.3146delC						.						274.0	256.0	261.0					15																	87531281		1860	4087	5947	SO:0001589	frameshift_variant	123624	exon23			.	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.3147delA	chr15.hg19:g.87531281delA	ENSP00000413001:p.Thr1049fs	180.0	0.0		138.0	11.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Frame_Shift_Del	DEL	ENST00000441037.2	hg19	CCDS58398.1																																																																																			.	.		0.403	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
GRB14	2888	hgsc.bcm.edu	37	2	165476321	165476321	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:165476321delT	ENST00000263915.3	-	2	738	c.200delA	c.(199-201)aagfs	p.K68fs		NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	68					blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.K67M(1)		breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						AAGATCTTTCTTTTTTCTCCT	0.368																																					p.K67fs		Atlas-INDEL	.											.	GRB14	73	.	1	Substitution - Missense(1)	ovary(1)	c.201delG						.						134.0	138.0	137.0					2																	165476321		2203	4300	6503	SO:0001589	frameshift_variant	2888	exon2			.		CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.200delA	chr2.hg19:g.165476321delT	ENSP00000263915:p.Lys68fs	271.0	0.0		253.0	16.0	NM_004490	B7Z7F9|Q7Z6I1	Frame_Shift_Del	DEL	ENST00000263915.3	hg19	CCDS2222.1																																																																																			.	.		0.368	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2		
SIGLEC7	27036	hgsc.bcm.edu	37	19	51650558	51650558	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:51650558delG	ENST00000317643.6	+	6	1274	c.1205delG	c.(1204-1206)aggfs	p.R402fs	SIGLEC7_ENST00000600577.1_Intron|SIGLEC7_ENST00000305628.7_Frame_Shift_Del_p.R309fs	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	402					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		AACACCATCAGGGGCTCAGCC	0.557																																					p.R402fs		Atlas-INDEL	.											.	SIGLEC7	74	.	0			c.1204delA						.						123.0	96.0	105.0					19																	51650558		2203	4300	6503	SO:0001589	frameshift_variant	27036	exon6			.	AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10876	protein-coding gene	gene with protein product		604410	"""sialic acid binding Ig-like lectin 19, pseudogene"", ""sialic acid binding Ig-like lectin, pseudogene 2"""	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.1205delG	chr19.hg19:g.51650558delG	ENSP00000323328:p.Arg402fs	118.0	0.0		121.0	10.0	NM_014385	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Frame_Shift_Del	DEL	ENST00000317643.6	hg19	CCDS12826.1																																																																																			.	.		0.557	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543	
USP14	9097	hgsc.bcm.edu	37	18	210016	210016	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:210016delT	ENST00000261601.7	+	14	1301	c.1210delT	c.(1210-1212)tttfs	p.F404fs	USP14_ENST00000582707.1_Frame_Shift_Del_p.F369fs|USP14_ENST00000383589.2_Frame_Shift_Del_p.F358fs|USP14_ENST00000400266.3_Frame_Shift_Del_p.F393fs	NM_005151.3	NP_005142.1	P54578	UBP14_HUMAN	ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase)	404	USP.				negative regulation of endopeptidase activity (GO:0010951)|protein deubiquitination (GO:0016579)|regulation of chemotaxis (GO:0050920)|regulation of proteasomal protein catabolic process (GO:0061136)|synaptic transmission (GO:0007268)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)|synapse (GO:0045202)	cysteine-type endopeptidase activity (GO:0004197)|endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)|tRNA guanylyltransferase activity (GO:0008193)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(2)	11		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				GTATGAACCCTTTTCTTTTGC	0.279																																					p.P403fs		Atlas-INDEL	.											.	USP14	41	.	0			c.1209delC						.						120.0	119.0	119.0					18																	210016		2203	4297	6500	SO:0001589	frameshift_variant	9097	exon14			.	U30888	CCDS32780.1, CCDS32781.1	18p11.32	2006-10-06	2005-08-08			ENSG00000101557		"""Ubiquitin-specific peptidases"""	12612	protein-coding gene	gene with protein product		607274	"""ubiquitin specific protease 14 (tRNA-guanine transglycosylase)"""			12838346	Standard	NM_001037334		Approved	TGT	uc002kkf.1	P54578		ENST00000261601.7:c.1210delT	chr18.hg19:g.210016delT	ENSP00000261601:p.Phe404fs	161.0	0.0		180.0	13.0	NM_005151	J3QRZ5|Q53XY5	Frame_Shift_Del	DEL	ENST00000261601.7	hg19	CCDS32780.1																																																																																			.	.		0.279	USP14-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440305.3	NM_005151	
JAK1	3716	hgsc.bcm.edu	37	1	65310468	65310468	+	Frame_Shift_Del	DEL	G	G	-	rs548872770		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:65310468delG	ENST00000342505.4	-	16	2468	c.2220delC	c.(2218-2220)cccfs	p.P740fs	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	740	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)	TGGGGATGCCGGGGTCACTGA	0.577			Mis		ALL																																p.G741fs		Atlas-INDEL	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.2221delG						.						92.0	108.0	103.0					1																	65310468		2124	4232	6356	SO:0001589	frameshift_variant	3716	exon16			.	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.2220delC	chr1.hg19:g.65310468delG	ENSP00000343204:p.Pro740fs	116.0	0.0		187.0	13.0	NM_002227	Q59GQ2|Q9UD26	Frame_Shift_Del	DEL	ENST00000342505.4	hg19	CCDS41346.1																																																																																			.	.		0.577	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
GPR115	221393	hgsc.bcm.edu	37	6	47680293	47680293	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:47680293delA	ENST00000283303.2	+	5	759	c.501delA	c.(499-501)ttafs	p.L167fs	GPR115_ENST00000371220.1_Frame_Shift_Del_p.L224fs|GPR115_ENST00000327753.3_Frame_Shift_Del_p.L167fs|RN7SKP116_ENST00000516902.1_RNA	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	167					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						TGGAGTTATTAAAAAATATTT	0.303																																					p.L167X	GBM(22;431 510 9010 26644 32828)	Atlas-INDEL	.											.	GPR115	140	.	0			c.500delT						.						61.0	66.0	64.0					6																	47680293		2203	4299	6502	SO:0001589	frameshift_variant	221393	exon5			.	AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"""-"", ""GPCR / Class B : Orphans"""	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.501delA	chr6.hg19:g.47680293delA	ENSP00000283303:p.Leu167fs	133.0	0.0		176.0	13.0	NM_153838	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Frame_Shift_Del	DEL	ENST00000283303.2	hg19	CCDS4922.2																																																																																			.	.		0.303	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838	
IL20RA	53832	hgsc.bcm.edu	37	6	137322699	137322699	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:137322699delT	ENST00000316649.5	-	7	1893	c.1658delA	c.(1657-1659)aacfs	p.N553fs	IL20RA_ENST00000541547.1_Frame_Shift_Del_p.N504fs|RP11-204P2.3_ENST00000458017.1_RNA|IL20RA_ENST00000367748.1_Frame_Shift_Del_p.N442fs	NM_001278722.1|NM_014432.2	NP_001265651.1|NP_055247	Q9UHF4	I20RA_HUMAN	interleukin 20 receptor, alpha	553					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of bone resorption (GO:0045124)	integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)		TTGGCATCAGTTTTCCATCTG	0.453																																					p.N553fs		Atlas-INDEL	.											.	IL20RA	54	.	0			c.1659delC						.						163.0	159.0	161.0					6																	137322699		2203	4300	6503	SO:0001589	frameshift_variant	53832	exon7			.	AF184971	CCDS5181.1, CCDS64535.1, CCDS64536.1	6q23.3	2008-02-05			ENSG00000016402	ENSG00000016402		"""Interleukins and interleukin receptors"""	6003	protein-coding gene	gene with protein product		605620				10875937, 11163236	Standard	NM_001278724		Approved	ZCYTOR7, IL-20R1	uc003qhj.3	Q9UHF4	OTTHUMG00000015654	ENST00000316649.5:c.1658delA	chr6.hg19:g.137322699delT	ENSP00000314976:p.Asn553fs	194.0	0.0		225.0	14.0	NM_014432	B4DLR5|F5H675|Q14CW2|Q6UWA9|Q96SH8	Frame_Shift_Del	DEL	ENST00000316649.5	hg19	CCDS5181.1																																																																																			.	.		0.453	IL20RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042393.1	NM_014432	
RAG1	5896	hgsc.bcm.edu	37	11	36594873	36594873	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:36594873delC	ENST00000299440.5	+	2	131	c.19delC	c.(19-21)cccfs	p.P7fs		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	7	Interaction with importin alpha-1.				adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				CTCTTTCCCACCCACCTTGGG	0.403									Familial Hemophagocytic Lymphohistiocytosis																												p.P6fs	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-INDEL	.											.	RAG1	151	.	0			c.18delA						.						64.0	65.0	65.0					11																	36594873		2202	4298	6500	SO:0001589	frameshift_variant	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	.	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"""RING-type (C3HC4) zinc fingers"""	9831	protein-coding gene	gene with protein product	"""recombination activating protein 1"", ""RING finger protein 74"", ""V(D)J recombination-activating protein 1"""	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.19delC	chr11.hg19:g.36594873delC	ENSP00000299440:p.Pro7fs	133.0	0.0		183.0	11.0	NM_000448	E9PPC4|Q8IY72|Q8NER2	Frame_Shift_Del	DEL	ENST00000299440.5	hg19	CCDS7902.1																																																																																			.	.		0.403	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448	
SELENBP1	8991	hgsc.bcm.edu	37	1	151339214	151339214	+	Frame_Shift_Del	DEL	G	G	-	rs375401678		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:151339214delG	ENST00000368868.5	-	6	739	c.648delC	c.(646-648)cccfs	p.P216fs	SELENBP1_ENST00000435071.1_Frame_Shift_Del_p.P152fs|SELENBP1_ENST00000473693.1_5'Flank|SELENBP1_ENST00000426705.2_Frame_Shift_Del_p.P258fs|SELENBP1_ENST00000447402.3_Frame_Shift_Del_p.P154fs	NM_003944.3	NP_003935.2	Q13228	SBP1_HUMAN	selenium binding protein 1	216					protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	selenium binding (GO:0008430)	p.P216P(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|urinary_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CCACATCAGCGGGGTTGAAGC	0.572																																					p.A259fs		Atlas-INDEL	.											.	SELENBP1	44	.	1	Substitution - coding silent(1)	lung(1)	c.775delG						.						175.0	153.0	160.0					1																	151339214		2203	4300	6503	SO:0001589	frameshift_variant	8991	exon6			.	U29091	CCDS995.1, CCDS58027.1, CCDS60266.1	1q21.3	2014-05-19			ENSG00000143416	ENSG00000143416			10719	protein-coding gene	gene with protein product		604188				9027582	Standard	NM_003944		Approved	hSP56, hSBP, LPSB	uc010pcy.3	Q13228	OTTHUMG00000012498	ENST00000368868.5:c.648delC	chr1.hg19:g.151339214delG	ENSP00000357861:p.Pro216fs	88.0	0.0		163.0	10.0	NM_001258289	A6NML9|A6PVW9|B2RDR3|B4DKP6|B4E1F3|Q49AQ8|Q96GX7	Frame_Shift_Del	DEL	ENST00000368868.5	hg19	CCDS995.1																																																																																			.	.		0.572	SELENBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034904.4		
DIAPH2	1730	hgsc.bcm.edu	37	X	96396689	96396689	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:96396689delA	ENST00000324765.8	+	22	2962	c.2615delA	c.(2614-2616)caafs	p.Q872fs	DIAPH2_ENST00000373049.4_Frame_Shift_Del_p.Q872fs|DIAPH2_ENST00000355827.4_Frame_Shift_Del_p.Q872fs|DIAPH2_ENST00000373061.3_Frame_Shift_Del_p.Q872fs|DIAPH2_ENST00000373054.4_Frame_Shift_Del_p.Q868fs			O60879	DIAP2_HUMAN	diaphanous-related formin 2	872	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						TCAGCGGATCAAAAAACAACC	0.313																																					p.Q872fs		Atlas-INDEL	.											.	DIAPH2	148	.	0			c.2614delC						.						64.0	57.0	59.0					X																	96396689		2203	4300	6503	SO:0001589	frameshift_variant	1730	exon22			.	Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202			2877	protein-coding gene	gene with protein product		300108	"""diaphanous (Drosophila, homolog) 2"", ""diaphanous homolog 2 (Drosophila)"""			9360932	Standard	NM_006729		Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.2615delA	chrX.hg19:g.96396689delA	ENSP00000321348:p.Gln872fs	158.0	0.0		148.0	11.0	NM_007309	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Frame_Shift_Del	DEL	ENST00000324765.8	hg19	CCDS14467.1																																																																																			.	.		0.313	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309	
POTEC	388468	hgsc.bcm.edu	37	18	14542924	14542924	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:14542924delC	ENST00000358970.5	-	1	221	c.222delG	c.(220-222)gggfs	p.G74fs	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	74										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						TCGTGCCGCTCCCCCTGCAGC	0.567																																					p.S75fs		Atlas-INDEL	.											.	POTEC	129	.	0			c.223delA						.						45.0	56.0	53.0					18																	14542924		692	1591	2283	SO:0001589	frameshift_variant	388468	exon1			.	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.222delG	chr18.hg19:g.14542924delC	ENSP00000351856:p.Gly74fs	422.0	0.0		461.0	29.0	NM_001137671		Frame_Shift_Del	DEL	ENST00000358970.5	hg19	CCDS45835.1																																																																																			.	.		0.567	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
CDCA4	55038	hgsc.bcm.edu	37	14	105477749	105477749	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:105477749delT	ENST00000336219.3	-	2	673	c.518delA	c.(517-519)aacfs	p.N173fs	CDCA4_ENST00000392590.3_Frame_Shift_Del_p.N173fs	NM_017955.3	NP_060425.2	Q9BXL8	CDCA4_HUMAN	cell division cycle associated 4	173						nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	6		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.142)		GCAGCTGGGGTTTTTAGTCTC	0.562																																					p.N173fs		Atlas-INDEL	.											.	CDCA4	18	.	0			c.519delC						.						86.0	83.0	84.0					14																	105477749		2203	4300	6503	SO:0001589	frameshift_variant	55038	exon2			.	BG354577	CCDS9996.1	14q32.33	2014-02-14			ENSG00000170779	ENSG00000170779			14625	protein-coding gene	gene with protein product	"""hematopoietic progenitor protein"""	612270				12188893	Standard	NM_145701		Approved	FLJ20764, Hepp	uc001yqb.2	Q9BXL8	OTTHUMG00000170767	ENST00000336219.3:c.518delA	chr14.hg19:g.105477749delT	ENSP00000337226:p.Asn173fs	133.0	0.0		174.0	12.0	NM_017955	Q8TB18|Q9NWK7	Frame_Shift_Del	DEL	ENST00000336219.3	hg19	CCDS9996.1																																																																																			.	.		0.562	CDCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410311.1	NM_145701	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37505286	37505286	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:37505286delA	ENST00000602533.1	+	32	2978	c.2879delA	c.(2878-2880)caafs	p.Q960fs	ANKRD30A_ENST00000374660.1_Frame_Shift_Del_p.Q1079fs|ANKRD30A_ENST00000361713.1_Frame_Shift_Del_p.Q960fs			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1016					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						TTAGAGAACCAAAAAGTTAAA	0.313																																					p.Q960fs		Atlas-INDEL	.											.	ANKRD30A	448	.	0			c.2878delC						.						75.0	76.0	76.0					10																	37505286		1831	4079	5910	SO:0001589	frameshift_variant	91074	exon32			.	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.2879delA	chr10.hg19:g.37505286delA	ENSP00000473551:p.Gln960fs	325.0	0.0		339.0	22.0	NM_052997	Q5W025	Frame_Shift_Del	DEL	ENST00000602533.1	hg19																																																																																				.	.		0.313	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
CAAP1	79886	hgsc.bcm.edu	37	9	26886160	26886160	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:26886160delT	ENST00000333916.5	-	3	619	c.531delA	c.(529-531)aaafs	p.K177fs	CAAP1_ENST00000520187.1_Intron|CAAP1_ENST00000495958.1_Intron|CAAP1_ENST00000535437.1_Frame_Shift_Del_p.K32fs	NM_001167575.1|NM_024828.3	NP_001161047.1|NP_079104.3	Q9H8G2	CAAP1_HUMAN	caspase activity and apoptosis inhibitor 1	177					apoptotic process (GO:0006915)												CCTGGCATAGTTTTTTAATTT	0.294																																					p.L178fs		Atlas-INDEL	.											.	.	.	.	0			c.532delC						.						30.0	32.0	32.0					9																	26886160		2186	4269	6455	SO:0001589	frameshift_variant	79886	exon3			.	BC014658	CCDS6516.1	9p21.2	2012-04-20	2012-04-20	2012-04-20	ENSG00000120159	ENSG00000120159			25834	protein-coding gene	gene with protein product	"""conserved anti-apoptotic protein"""		"""chromosome 9 open reading frame 82"""	C9orf82		21980415	Standard	NM_024828		Approved	FLJ13657, CAAP	uc003zqc.3	Q9H8G2	OTTHUMG00000019706	ENST00000333916.5:c.531delA	chr9.hg19:g.26886160delT	ENSP00000369431:p.Lys177fs	194.0	0.0		197.0	12.0	NM_024828	B4DWT4|D3DRK4|Q5VY32|Q6IPE6|Q96C59	Frame_Shift_Del	DEL	ENST00000333916.5	hg19	CCDS6516.1																																																																																			.	.		0.294	CAAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051954.1	NM_024828	
VEZT	55591	hgsc.bcm.edu	37	12	95694123	95694123	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:95694123delA	ENST00000436874.1	+	12	2119	c.2014delA	c.(2014-2016)aaafs	p.K672fs	VEZT_ENST00000261219.6_Frame_Shift_Del_p.K624fs|VEZT_ENST00000356859.4_3'UTR	NM_017599.3	NP_060069.3	Q9HBM0	VEZA_HUMAN	vezatin, adherens junctions transmembrane protein	672					chordate embryonic development (GO:0043009)|single organismal cell-cell adhesion (GO:0016337)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stereocilia ankle link complex (GO:0002142)				endometrium(2)|kidney(3)|large_intestine(1)|lung(14)|ovary(2)|upper_aerodigestive_tract(1)	23						TCTAGAAGGTAAAAATAAAGA	0.358																																					p.G671fs		Atlas-INDEL	.											.	VEZT	106	.	0			c.2013delT						.						39.0	37.0	38.0					12																	95694123		1848	4093	5941	SO:0001589	frameshift_variant	55591	exon12			.	AF216644	CCDS44954.1	12q22	2011-02-15			ENSG00000028203	ENSG00000028203			18258	protein-coding gene	gene with protein product						11080149, 16199027, 21156161	Standard	NM_017599		Approved	DKFZP761C241	uc001tdz.2	Q9HBM0	OTTHUMG00000170182	ENST00000436874.1:c.2014delA	chr12.hg19:g.95694123delA	ENSP00000410083:p.Lys672fs	93.0	0.0		193.0	12.0	NM_017599	Q6P1Q3|Q9H2F4|Q9H2U5|Q9NT70|Q9NVW0|Q9UF91	Frame_Shift_Del	DEL	ENST00000436874.1	hg19	CCDS44954.1																																																																																			.	.		0.358	VEZT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407804.2	NM_017599	
WDFY3	23001	hgsc.bcm.edu	37	4	85614081	85614081	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:85614081delA	ENST00000295888.4	-	59	9413	c.9006delT	c.(9004-9006)tttfs	p.F3002fs	WDFY3_ENST00000322366.6_Frame_Shift_Del_p.F2985fs	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	3002	Interaction with ATG5.|Interaction with SQSTM1.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		CTAGATGATGAAAAAAGATCT	0.358																																					p.H3003fs		Atlas-INDEL	.											.	WDFY3	314	.	0			c.9007delC						.						116.0	112.0	113.0					4																	85614081		2203	4300	6503	SO:0001589	frameshift_variant	23001	exon59			.	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.9006delT	chr4.hg19:g.85614081delA	ENSP00000295888:p.Phe3002fs	103.0	0.0		164.0	10.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Frame_Shift_Del	DEL	ENST00000295888.4	hg19	CCDS3609.1																																																																																			.	.		0.358	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
NUP155	9631	hgsc.bcm.edu	37	5	37309279	37309279	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:37309279delT	ENST00000231498.3	-	24	2922	c.2719delA	c.(2719-2721)attfs	p.I907fs	NUP155_ENST00000513532.1_Frame_Shift_Del_p.I843fs|NUP155_ENST00000381843.2_Frame_Shift_Del_p.I848fs|NUP155_ENST00000502533.1_5'UTR	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	907					atrial cardiac muscle cell action potential (GO:0086014)|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 export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|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)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGATTGCTAATTTTTTGATAT	0.343																																					p.I907fs		Atlas-INDEL	.											.	NUP155	116	.	0			c.2720delT						.						159.0	152.0	154.0					5																	37309279		2203	4300	6503	SO:0001589	frameshift_variant	9631	exon24			.	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"""nucleoporin 155kD"""			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.2719delA	chr5.hg19:g.37309279delT	ENSP00000231498:p.Ile907fs	175.0	0.0		198.0	12.0	NM_153485	Q9UBE9|Q9UFL5	Frame_Shift_Del	DEL	ENST00000231498.3	hg19	CCDS3921.1																																																																																			.	.		0.343	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298	
POLR2B	5431	hgsc.bcm.edu	37	4	57877166	57877166	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:57877166delT	ENST00000381227.1	+	14	2113	c.1700delT	c.(1699-1701)attfs	p.I567fs	POLR2B_ENST00000441246.2_Frame_Shift_Del_p.I560fs|POLR2B_ENST00000510355.1_3'UTR|POLR2B_ENST00000431623.2_Frame_Shift_Del_p.I492fs|POLR2B_ENST00000314595.5_Frame_Shift_Del_p.I567fs			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	567					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)					GCAACCAAGATTTTTGTTAAT	0.333																																					p.I567fs		Atlas-INDEL	.											.	POLR2B	108	.	0			c.1699delA						.						108.0	104.0	105.0					4																	57877166		2203	4300	6503	SO:0001589	frameshift_variant	5431	exon13			.		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.1700delT	chr4.hg19:g.57877166delT	ENSP00000370625:p.Ile567fs	161.0	0.0		145.0	11.0	NM_000938	A8K1A8|Q8IZ61	Frame_Shift_Del	DEL	ENST00000381227.1	hg19	CCDS3511.1																																																																																			.	.		0.333	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938	
CLSPN	63967	hgsc.bcm.edu	37	1	36228077	36228077	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:36228077delT	ENST00000318121.3	-	5	807	c.750delA	c.(748-750)aaafs	p.K250fs	CLSPN_ENST00000520551.1_Frame_Shift_Del_p.K250fs|CLSPN_ENST00000251195.5_Frame_Shift_Del_p.K250fs|CLSPN_ENST00000373220.3_Frame_Shift_Del_p.K250fs	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	250					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AAGATGGTTCTTTTTTCTAAA	0.398																																					p.E251fs		Atlas-INDEL	.											.	CLSPN	248	.	0			c.751delG						.						87.0	83.0	84.0					1																	36228077		2203	4300	6503	SO:0001589	frameshift_variant	63967	exon5			.	AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"""claspin homolog (Xenopus laevis)"""			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.750delA	chr1.hg19:g.36228077delT	ENSP00000312995:p.Lys250fs	100.0	0.0		141.0	11.0	NM_001190481	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Frame_Shift_Del	DEL	ENST00000318121.3	hg19	CCDS396.1																																																																																			.	.		0.398	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111	
CDHR5	53841	hgsc.bcm.edu	37	11	618994	618994	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:618994delG	ENST00000358353.3	-	14	1887	c.1565delC	c.(1564-1566)ccgfs	p.P522fs	CDHR5_ENST00000397542.2_Frame_Shift_Del_p.P522fs|CDHR5_ENST00000349570.7_Intron|IRF7_ENST00000397570.1_5'Flank|IRF7_ENST00000397574.2_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	522					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						TTCTGCACCCGGGGGCCCCCC	0.677																																					p.P522fs		Atlas-INDEL	.											.	CDHR5	77	.	0			c.1566delG						.						55.0	72.0	66.0					11																	618994		2203	4299	6502	SO:0001589	frameshift_variant	53841	exon13			.	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.1565delC	chr11.hg19:g.618994delG	ENSP00000351118:p.Pro522fs	91.0	0.0		166.0	11.0	NM_021924	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Frame_Shift_Del	DEL	ENST00000358353.3	hg19	CCDS7707.1																																																																																			.	.		0.677	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
SCN9A	6335	hgsc.bcm.edu	37	2	167141203	167141203	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:167141203delA	ENST00000409435.1	-	11	1733	c.1734delT	c.(1732-1734)tttfs	p.F578fs	SCN9A_ENST00000375387.4_Frame_Shift_Del_p.F579fs|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Frame_Shift_Del_p.F579fs|SCN9A_ENST00000409672.1_Frame_Shift_Del_p.F578fs			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	578					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CATTGTCTCCAAAAATGCTGT	0.507																																					p.G579fs		Atlas-INDEL	.											SCN9A_ENST00000375387,right_upper_lobe,carcinoma,+1,1	SCN9A	296	.	0			c.1735delG						.						99.0	103.0	102.0					2																	167141203		2071	4227	6298	SO:0001589	frameshift_variant	6335	exon12			.	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1734delT	chr2.hg19:g.167141203delA	ENSP00000386330:p.Phe578fs	146.0	0.0		152.0	11.0	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Frame_Shift_Del	DEL	ENST00000409435.1	hg19	CCDS46441.1																																																																																			.	.		0.507	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
UBE2J1	51465	hgsc.bcm.edu	37	6	90048232	90048232	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:90048232delT	ENST00000435041.2	-	4	546	c.268delA	c.(268-270)atcfs	p.I90fs		NM_016021.2	NP_057105.2	Q9Y385	UB2J1_HUMAN	ubiquitin-conjugating enzyme E2, J1	90					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			NS(1)|breast(2)|kidney(1)|large_intestine(2)|lung(11)|stomach(1)	18		all_cancers(76;1.65e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;2.5e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0139)		CTCAAACAGATTTTCTTGCCC	0.333																																					p.I90fs		Atlas-INDEL	.											.	UBE2J1	28	.	0			c.269delT						.						94.0	94.0	94.0					6																	90048232		2203	4300	6503	SO:0001589	frameshift_variant	51465	exon4			.	AJ245898	CCDS5021.1	6q15	2014-01-28	2012-06-08		ENSG00000198833	ENSG00000198833		"""Ubiquitin-conjugating enzymes E2"""	17598	protein-coding gene	gene with protein product			"""ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)"""			10708578	Standard	NM_016021		Approved	HSPC153, CGI-76, NCUBE1, UBC6	uc003pnc.3	Q9Y385	OTTHUMG00000016337	ENST00000435041.2:c.268delA	chr6.hg19:g.90048232delT	ENSP00000451261:p.Ile90fs	145.0	0.0		195.0	13.0	NM_016021	A8K3F9|Q53F25|Q5W0N4|Q9BZ32|Q9NQL3|Q9NY66|Q9P011|Q9P0S0|Q9UF10	Frame_Shift_Del	DEL	ENST00000435041.2	hg19	CCDS5021.1																																																																																			.	.		0.333	UBE2J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043742.2	NM_016021	
NFYC	4802	hgsc.bcm.edu	37	1	41204559	41204559	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:41204559delC	ENST00000308733.5	+	1	50	c.44delC	c.(43-45)gccfs	p.A15fs	NFYC_ENST00000456393.2_Frame_Shift_Del_p.A15fs|NFYC_ENST00000440226.3_Frame_Shift_Del_p.A15fs|NFYC_ENST00000425457.2_Frame_Shift_Del_p.A15fs|NFYC_ENST00000372654.1_Frame_Shift_Del_p.A15fs|NFYC_ENST00000427410.2_Frame_Shift_Del_p.A15fs|NFYC_ENST00000372652.1_Frame_Shift_Del_p.A15fs|NFYC_ENST00000372653.1_Frame_Shift_Del_p.A15fs|NFYC_ENST00000372651.1_Frame_Shift_Del_p.A15fs|NFYC_ENST00000447388.3_Frame_Shift_Del_p.A15fs			Q13952	NFYC_HUMAN	nuclear transcription factor Y, gamma	15					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription, DNA-templated (GO:0045893)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(3)|lung(1)|prostate(1)|skin(2)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.72e-17)			AGCAGTGATGCCCAGCAAAGC	0.403																																					p.A15fs		Atlas-INDEL	.											.	NFYC	39	.	0			c.43delG						.						118.0	119.0	118.0					1																	41204559		2203	4300	6503	SO:0001589	frameshift_variant	4802	exon2			.	U78774	CCDS455.1, CCDS44120.1, CCDS44121.1, CCDS44122.1, CCDS44123.1	1p32	2008-11-11			ENSG00000066136	ENSG00000066136			7806	protein-coding gene	gene with protein product		605344				8921405, 9249075	Standard	NM_014223		Approved	CBF-C, NF-YC	uc009vwd.3	Q13952	OTTHUMG00000007729	ENST00000308733.5:c.44delC	chr1.hg19:g.41204559delC	ENSP00000312617:p.Ala15fs	96.0	0.0		194.0	12.0	NM_001142587	B4DUS6|B4DW63|D3DPV9|F8VWM3|Q59GY4|Q5T6K8|Q5T6K9|Q5T6L1|Q5TZR6|Q92869|Q9HBX1|Q9NXB5|Q9UM67|Q9UML0|Q9UMT7	Frame_Shift_Del	DEL	ENST00000308733.5	hg19																																																																																				.	.		0.403	NFYC-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000020802.1	NM_014223	
COL5A3	50509	hgsc.bcm.edu	37	19	10087955	10087955	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:10087955delC	ENST00000264828.3	-	44	3323	c.3238delG	c.(3238-3240)gatfs	p.D1080fs		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1080	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			GCACCCACATCCCCCTGCAGA	0.612																																					p.D1080fs		Atlas-INDEL	.											.	COL5A3	243	.	0			c.3239delA						.						114.0	87.0	96.0					19																	10087955		2203	4300	6503	SO:0001589	frameshift_variant	50509	exon44			.	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.3238delG	chr19.hg19:g.10087955delC	ENSP00000264828:p.Asp1080fs	115.0	0.0		129.0	10.0	NM_015719	Q9NZQ6	Frame_Shift_Del	DEL	ENST00000264828.3	hg19	CCDS12222.1																																																																																			.	.		0.612	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
PKN2	5586	hgsc.bcm.edu	37	1	89270151	89270151	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:89270151delT	ENST00000370521.3	+	9	1718	c.1359delT	c.(1357-1359)gatfs	p.D453fs	PKN2_ENST00000544045.1_Frame_Shift_Del_p.D127fs|PKN2_ENST00000370513.5_Intron|PKN2_ENST00000370505.3_Frame_Shift_Del_p.D296fs|PKN2_ENST00000316005.7_Frame_Shift_Del_p.D453fs	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	453	C2.|Necessary to rescue apical junction formation. {ECO:0000250}.				apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		GGTTAGAAGATTTTTTAGACA	0.343																																					p.D453fs		Atlas-INDEL	.											.	PKN2	109	.	0			c.1358delA						.						110.0	104.0	106.0					1																	89270151		1843	4088	5931	SO:0001589	frameshift_variant	5586	exon9			.	U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"""cardiolipin-activated protein kinase Pak2"""	602549	"""protein kinase C-like 2"""	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.1359delT	chr1.hg19:g.89270151delT	ENSP00000359552:p.Asp453fs	176.0	0.0		223.0	14.0	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Frame_Shift_Del	DEL	ENST00000370521.3	hg19	CCDS714.1																																																																																			.	.		0.343	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256	
ACAN	176	hgsc.bcm.edu	37	15	89386594	89386594	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:89386594delT	ENST00000561243.1	+	5	766	c.766delT	c.(766-768)tttfs	p.F256fs	ACAN_ENST00000439576.2_Frame_Shift_Del_p.F256fs|ACAN_ENST00000559004.1_Frame_Shift_Del_p.F256fs|ACAN_ENST00000352105.7_Frame_Shift_Del_p.F256fs|ACAN_ENST00000558207.1_Frame_Shift_Del_p.F256fs			P16112	PGCA_HUMAN	aggrecan	256	G1-B'.|Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			AGGTGAGGTCTTTTATGCAAC	0.602																																					p.V255fs		Atlas-INDEL	.											.	ACAN	220	.	0			c.765delC						.						32.0	35.0	34.0					15																	89386594		1974	4160	6134	SO:0001589	frameshift_variant	176	exon6			.	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.766delT	chr15.hg19:g.89386594delT	ENSP00000453342:p.Phe256fs	151.0	0.0		182.0	12.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Frame_Shift_Del	DEL	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.		0.602	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
BCL7A	605	hgsc.bcm.edu	37	12	122473237	122473237	+	Splice_Site	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:122473237delA	ENST00000261822.4	+	3	381	c.175delA	c.(175-177)aaa>aa	p.K59fs	BCL7A_ENST00000538010.1_Splice_Site_p.K59fs	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	59					negative regulation of transcription, DNA-templated (GO:0045892)					haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		TCCCCTGCAGAAAAACAAGAA	0.498			T	MYC	BNHL																																.	GBM(17;197 467 16477 23242 44349)	Atlas-INDEL	.		Dom	yes		12	12q24.1	605	B-cell CLL/lymphoma 7A		L	BCL7A,mouth,carcinoma,0,1	BCL7A	31	.	0			c.175-1A>-						.						79.0	73.0	75.0					12																	122473237		2203	4300	6503	SO:0001630	splice_region_variant	605	exon3			.	X89984	CCDS9226.1, CCDS53841.1	12q24.1	2008-07-03			ENSG00000110987	ENSG00000110987			1004	protein-coding gene	gene with protein product		601406		BCL7		8605326, 9931421	Standard	NM_020993		Approved		uc001ubo.3	Q4VC05	OTTHUMG00000168951	ENST00000261822.4:c.175-1A>-	chr12.hg19:g.122473237delA		187.0	0.0		216.0	13.0	NM_020993	B4DJN6|B7ZB21|Q13843|Q14CT7	Splice_Site	DEL	ENST00000261822.4	hg19	CCDS53841.1																																																																																			.	.		0.498	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1		Frame_Shift_Del
PNISR	25957	hgsc.bcm.edu	37	6	99848584	99848584	+	Frame_Shift_Del	DEL	T	T	-	rs201782750		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:99848584delT	ENST00000369239.5	-	12	2454	c.2250delA	c.(2248-2250)aaafs	p.K750fs	PNISR_ENST00000438806.1_Frame_Shift_Del_p.K750fs	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	750	Ser-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						AGCCTGAATGTTTTTTACTAT	0.383																																					p.H751fs		Atlas-INDEL	.											.,1	PNISR	74	.	0			c.2251delC						.						193.0	196.0	195.0					6																	99848584		2203	4300	6503	SO:0001589	frameshift_variant	25957	exon11			.	AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 111"", ""splicing factor, arginine/serine-rich 18"""	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.2250delA	chr6.hg19:g.99848584delT	ENSP00000358242:p.Lys750fs	146.0	0.0		241.0	16.0	NM_015491	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Frame_Shift_Del	DEL	ENST00000369239.5	hg19	CCDS5043.1																																																																																			.	.		0.383	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870	
COG2	22796	hgsc.bcm.edu	37	1	230800279	230800279	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:230800279delA	ENST00000366669.4	+	5	546	c.431delA	c.(430-432)gaafs	p.E144fs	COG2_ENST00000366668.3_Frame_Shift_Del_p.E144fs|COG2_ENST00000535166.1_Frame_Shift_Del_p.E28fs|COG2_ENST00000534989.1_Frame_Shift_Del_p.E85fs	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	114.0	0.0		183.0	13.0	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	
OR8K1	390157	hgsc.bcm.edu	37	11	56114060	56114060	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:56114060delT	ENST00000279783.2	+	1	640	c.546delT	c.(544-546)tatfs	p.Y182fs		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	182						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					TAATCAGCTATTTTTACTGTG	0.348										HNSCC(65;0.19)																											p.Y182fs		Atlas-INDEL	.											.	OR8K1	93	.	0			c.545delA						.						144.0	146.0	145.0					11																	56114060		2201	4296	6497	SO:0001589	frameshift_variant	390157	exon1			.	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"""GPCR / Class A : Olfactory receptors"""	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.546delT	chr11.hg19:g.56114060delT	ENSP00000279783:p.Tyr182fs	126.0	0.0		192.0	13.0	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Frame_Shift_Del	DEL	ENST00000279783.2	hg19	CCDS31528.1																																																																																			.	.		0.348	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907	
LRRC32	2615	hgsc.bcm.edu	37	11	76370772	76370772	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76370772delC	ENST00000407242.2	-	3	2107	c.1865delG	c.(1864-1866)ggafs	p.G622fs	AP001189.4_ENST00000447519.1_RNA|LRRC32_ENST00000260061.5_Frame_Shift_Del_p.G622fs|LRRC32_ENST00000464145.1_Intron|LRRC32_ENST00000404995.1_Frame_Shift_Del_p.G622fs	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	622					negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cytokine secretion (GO:0050710)|positive regulation of gene expression (GO:0010628)	integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(26)|upper_aerodigestive_tract(1)	31						GTTCTTCAGTCCCCCCTTCTC	0.622																																					p.G622fs		Atlas-INDEL	.											.	LRRC32	74	.	0			c.1866delA						.						145.0	132.0	136.0					11																	76370772		2200	4292	6492	SO:0001589	frameshift_variant	2615	exon3			.	Z24680	CCDS8245.1	11q13.5-q14	2008-02-05	2005-02-25	2005-02-25	ENSG00000137507	ENSG00000137507			4161	protein-coding gene	gene with protein product		137207	"""glycoprotein A repetitions predominant"""	D11S833E, GARP		8180135, 1543912	Standard	NM_005512		Approved		uc001oxq.4	Q14392	OTTHUMG00000133687	ENST00000407242.2:c.1865delG	chr11.hg19:g.76370772delC	ENSP00000384126:p.Gly622fs	93.0	0.0		137.0	12.0	NM_001128922	Q86V06	Frame_Shift_Del	DEL	ENST00000407242.2	hg19	CCDS8245.1																																																																																			.	.		0.622	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512	
NHLRC2	374354	hgsc.bcm.edu	37	10	115657964	115657964	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:115657964delA	ENST00000369301.3	+	6	1347	c.1135delA	c.(1135-1137)aaafs	p.K379fs		NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	379										breast(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15				Epithelial(162;0.017)|all cancers(201;0.0187)		ACTGCCAAAGAAAAAGTAAGT	0.428																																					p.K378fs		Atlas-INDEL	.											NHLRC2,colon,carcinoma,0,1	NHLRC2	56	.	0			c.1134delG						.						36.0	36.0	36.0					10																	115657964		2203	4300	6503	SO:0001589	frameshift_variant	374354	exon6			.	AK090631	CCDS7585.1	10q26.11	2006-03-31			ENSG00000196865	ENSG00000196865			24731	protein-coding gene	gene with protein product						12477932	Standard	NM_198514		Approved	FLJ25621, FLJ20147, FLJ33312, MGC45492, DKFZp779F115	uc001lax.2	Q8NBF2	OTTHUMG00000019078	ENST00000369301.3:c.1135delA	chr10.hg19:g.115657964delA	ENSP00000358307:p.Lys379fs	222.0	0.0		265.0	16.0	NM_198514	Q8N1H1|Q8N5A6	Frame_Shift_Del	DEL	ENST00000369301.3	hg19	CCDS7585.1																																																																																			.	.		0.428	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514	
ABCA5	23461	hgsc.bcm.edu	37	17	67255885	67255885	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:67255885delT	ENST00000392676.3	-	28	3757	c.3693delA	c.(3691-3693)aaafs	p.K1231fs	ABCA5_ENST00000392677.2_Frame_Shift_Del_p.K1232fs|ABCA5_ENST00000588877.1_Frame_Shift_Del_p.K1231fs			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	1231					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)	TGCCTCCATATTTTTTCTCAT	0.313																																					p.Y1232fs		Atlas-INDEL	.											.	ABCA5	162	.	0			c.3694delT						.						60.0	59.0	59.0					17																	67255885		2203	4299	6502	SO:0001589	frameshift_variant	23461	exon27			.	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.3693delA	chr17.hg19:g.67255885delT	ENSP00000376443:p.Lys1231fs	137.0	0.0		265.0	18.0	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Frame_Shift_Del	DEL	ENST00000392676.3	hg19	CCDS11685.1																																																																																			.	.		0.313	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	
CTGF	1490	hgsc.bcm.edu	37	6	132270568	132270568	+	Frame_Shift_Del	DEL	G	G	-	rs15960		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:132270568delG	ENST00000367976.3	-	5	1086	c.886delC	c.(886-888)cacfs	p.H296fs	RP11-69I8.3_ENST00000435287.1_RNA	NM_001901.2	NP_001892	P29279	CTGF_HUMAN	connective tissue growth factor	296	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.|Heparin-binding.				angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|chondrocyte proliferation (GO:0035988)|cytosolic calcium ion transport (GO:0060401)|DNA replication (GO:0006260)|epidermis development (GO:0008544)|extracellular matrix constituent secretion (GO:0070278)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of gene expression (GO:0010629)|organ senescence (GO:0010260)|ossification (GO:0001503)|positive regulation of cardiac muscle contraction (GO:0060452)|positive regulation of cell activation (GO:0050867)|positive regulation of cell death (GO:0010942)|positive regulation of cell differentiation (GO:0045597)|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 ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G0 to G1 transition (GO:0070318)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|regulation of cell growth (GO:0001558)|regulation of chondrocyte differentiation (GO:0032330)|response to amino acid (GO:0043200)|response to anoxia (GO:0034059)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to glucose (GO:0009749)|response to mineralocorticoid (GO:0051385)|response to peptide hormone (GO:0043434)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell cortex (GO:0005938)|cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|insulin-like growth factor binding (GO:0005520)			breast(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	13	Breast(56;0.0602)			GBM - Glioblastoma multiforme(226;0.015)|OV - Ovarian serous cystadenocarcinoma(155;0.0169)		GTGGTTCTGTGGGGGGTGCAG	0.532																																					p.H296fs	Esophageal Squamous(127;510 1660 12817 24400 38449)	Atlas-INDEL	.											.	CTGF	36	.	0			c.887delA						.						167.0	164.0	165.0					6																	132270568		2203	4300	6503	SO:0001589	frameshift_variant	1490	exon5			.	X78947	CCDS5151.1	6q23.2	2008-02-05			ENSG00000118523	ENSG00000118523			2500	protein-coding gene	gene with protein product		121009				1654338	Standard	NM_001901		Approved	IGFBP8, CCN2	uc003qcz.3	P29279	OTTHUMG00000015573	ENST00000367976.3:c.886delC	chr6.hg19:g.132270568delG	ENSP00000356954:p.His296fs	102.0	0.0		179.0	14.0	NM_001901	E1P578|Q6LCY0|Q96A79|Q96QX2|Q9UDL6	Frame_Shift_Del	DEL	ENST00000367976.3	hg19	CCDS5151.1																																																																																			.	.		0.532	CTGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042239.2	NM_001901	
TCERG1L	256536	hgsc.bcm.edu	37	10	132891517	132891517	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:132891517delT	ENST00000368642.4	-	12	1754	c.1669delA	c.(1669-1671)agafs	p.R557fs	RP11-462G8.3_ENST00000436942.1_RNA	NM_174937.3	NP_777597.2	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	557	FF 2.									cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	31		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		TGGTCCTTTCTTTTTTGAACA	0.418																																					p.R557fs		Atlas-INDEL	.											.	TCERG1L	91	.	0			c.1670delG						.						100.0	102.0	101.0					10																	132891517		2203	4300	6503	SO:0001589	frameshift_variant	256536	exon12			.	AK096269	CCDS7662.2	10q26.3	2006-04-12			ENSG00000176769	ENSG00000176769			23533	protein-coding gene	gene with protein product							Standard	NM_174937		Approved	FLJ38950	uc001lkp.3	Q5VWI1	OTTHUMG00000019276	ENST00000368642.4:c.1669delA	chr10.hg19:g.132891517delT	ENSP00000357631:p.Arg557fs	126.0	0.0		134.0	10.0	NM_174937	Q5VWI2|Q86XM8	Frame_Shift_Del	DEL	ENST00000368642.4	hg19	CCDS7662.2																																																																																			.	.		0.418	TCERG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091619.2	NM_174937	
LRFN4	78999	hgsc.bcm.edu	37	11	66627324	66627324	+	Frame_Shift_Del	DEL	G	G	-	rs142190580		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:66627324delG	ENST00000309602.4	+	2	1809	c.1566delG	c.(1564-1566)gtgfs	p.V522fs	PC_ENST00000393960.1_Intron|LRFN4_ENST00000393952.3_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	522						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						CCGTGGCCGTGGGGGGTGTGC	0.716																																					p.V522fs		Atlas-INDEL	.											.	LRFN4	25	.	0			c.1565delT						.						28.0	22.0	24.0					11																	66627324		2187	4280	6467	SO:0001589	frameshift_variant	78999	exon2			.	BC007718	CCDS8153.1	11q13.1	2013-02-11				ENSG00000173621		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	28456	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 6"""	612810				16495444, 16828986	Standard	NM_024036		Approved	MGC3103, SALM3., FIGLER6	uc001ojr.3	Q6PJG9		ENST00000309602.4:c.1566delG	chr11.hg19:g.66627324delG	ENSP00000312535:p.Val522fs	76.0	0.0		149.0	10.0	NM_024036	Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	Frame_Shift_Del	DEL	ENST00000309602.4	hg19	CCDS8153.1																																																																																			.	.		0.716	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036	
ABHD12B	145447	hgsc.bcm.edu	37	14	51368597	51368597	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:51368597delA	ENST00000337334.2	+	10	846	c.831delA	c.(829-831)agafs	p.R277fs	PYGL_ENST00000532462.1_Intron|ABHD12B_ENST00000395752.1_Frame_Shift_Del_p.R170fs|ABHD12B_ENST00000353130.1_Frame_Shift_Del_p.R200fs	NM_001206673.1	NP_001193602.1	Q7Z5M8	AB12B_HUMAN	abhydrolase domain containing 12B	277							hydrolase activity (GO:0016787)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)	10	all_epithelial(31;0.00481)|Breast(41;0.148)					ATGCCCTGAGAAAAGACAAAA	0.313																																					p.R277fs		Atlas-INDEL	.											.	ABHD12B	53	.	0			c.830delG						.						77.0	73.0	74.0					14																	51368597		2203	4296	6499	SO:0001589	frameshift_variant	145447	exon10			.	BG698443	CCDS9702.1, CCDS55916.1	14q21.3	2009-10-09	2007-04-03	2007-04-03	ENSG00000131969	ENSG00000131969		"""Abhydrolase domain containing"""	19837	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 29"""	C14orf29			Standard	NM_181814		Approved	BEM46L3	uc001wys.3	Q7Z5M8	OTTHUMG00000140286	ENST00000337334.2:c.831delA	chr14.hg19:g.51368597delA	ENSP00000336693:p.Arg277fs	85.0	0.0		113.0	11.0	NM_001206673	Q3KNR9|Q3KNS0|Q7Z5M6|Q7Z5M7|Q8N4D2	Frame_Shift_Del	DEL	ENST00000337334.2	hg19	CCDS55916.1																																																																																			.	.		0.313	ABHD12B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411030.1		
PCDH15	65217	hgsc.bcm.edu	37	10	55582820	55582820	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:55582820delT	ENST00000320301.6	-	33	5060	c.4666delA	c.(4666-4668)atafs	p.I1556fs	PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395430.1_Frame_Shift_Del_p.I1553fs|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000437009.1_Frame_Shift_Del_p.I1487fs|PCDH15_ENST00000395432.2_Frame_Shift_Del_p.I1516fs|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000395433.1_Frame_Shift_Del_p.I1533fs|PCDH15_ENST00000361849.3_Frame_Shift_Del_p.I1558fs	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1556					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TTGGCTTGTATTTTGGGTGAA	0.428										HNSCC(58;0.16)																											p.I1563fs		Atlas-INDEL	.											.	PCDH15	1715	.	0			c.4688delT						.						85.0	89.0	87.0					10																	55582820		2203	4299	6502	SO:0001589	frameshift_variant	65217	exon35			.	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4666delA	chr10.hg19:g.55582820delT	ENSP00000322604:p.Ile1556fs	164.0	0.0		180.0	11.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Frame_Shift_Del	DEL	ENST00000320301.6	hg19	CCDS7248.1																																																																																			.	.		0.428	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
TMEM237	65062	hgsc.bcm.edu	37	2	202503720	202503720	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:202503720delT	ENST00000409883.2	-	4	244	c.128delA	c.(127-129)aacfs	p.N43fs	TMEM237_ENST00000409444.2_Frame_Shift_Del_p.N35fs	NM_001044385.2	NP_001037850.1	Q96Q45	TM237_HUMAN	transmembrane protein 237	43					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						ACCTGGTGTGTTTTTTGTTCT	0.403																																					p.N43fs		Atlas-INDEL	.											.	TMEM237	21	.	0			c.129delC						.						125.0	107.0	113.0					2																	202503720		1833	4089	5922	SO:0001589	frameshift_variant	65062	exon3			.	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.128delA	chr2.hg19:g.202503720delT	ENSP00000386264:p.Asn43fs	224.0	0.0		220.0	16.0	NM_001044385	B4E1R8|B4E2R8|E9PAR8|E9PBF8|E9PG24|E9PGX0|Q53TS9|Q53TT2|Q7Z3B6|Q8IZ18|Q8NBF8|Q96CY1	Frame_Shift_Del	DEL	ENST00000409883.2	hg19	CCDS46489.1																																																																																			.	.		0.403	TMEM237-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335753.1	NM_152388	
LRRC58	116064	hgsc.bcm.edu	37	3	120054700	120054700	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:120054700delT	ENST00000295628.3	-	2	696	c.601delA	c.(601-603)atcfs	p.I201fs		NM_001099678.1	NP_001093148.1	Q96CX6	LRC58_HUMAN	leucine rich repeat containing 58	201										large_intestine(2)|lung(5)	7				GBM - Glioblastoma multiforme(114;0.147)		ATGCTTTGGATTTTGTTGTCA	0.343																																					p.I201fs		Atlas-INDEL	.											.	LRRC58	18	.	0			c.602delT						.						166.0	157.0	160.0					3																	120054700		1828	4097	5925	SO:0001589	frameshift_variant	116064	exon2			.	BC013757	CCDS46892.1	3q13.33	2006-01-06			ENSG00000163428	ENSG00000163428			26968	protein-coding gene	gene with protein product							Standard	NM_001099678		Approved		uc003edr.2	Q96CX6	OTTHUMG00000159407	ENST00000295628.3:c.601delA	chr3.hg19:g.120054700delT	ENSP00000295628:p.Ile201fs	127.0	0.0		156.0	12.0	NM_001099678		Frame_Shift_Del	DEL	ENST00000295628.3	hg19	CCDS46892.1																																																																																			.	.		0.343	LRRC58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355142.1	XM_057296	
LDLRAD1	388633	hgsc.bcm.edu	37	1	54476004	54476004	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:54476004delT	ENST00000371360.1	-	5	437	c.420delA	c.(418-420)aaafs	p.K140fs	LDLRAD1_ENST00000420619.1_Frame_Shift_Del_p.K101fs|LDLRAD1_ENST00000545928.1_Frame_Shift_Del_p.K97fs|LDLRAD1_ENST00000371362.3_Frame_Shift_Del_p.K51fs	NM_001010978.2	NP_001010978.2	Q5T700	LRAD1_HUMAN	low density lipoprotein receptor class A domain containing 1	140	LDL-receptor class A 2; atypical. {ECO:0000255|PROSITE-ProRule:PRU00124}.					integral component of membrane (GO:0016021)				large_intestine(3)|prostate(1)|skin(3)	7						TGCCATCACATTTTTGGTCTG	0.607																																					p.C141fs		Atlas-INDEL	.											.	LDLRAD1	22	.	0			c.421delT						.						74.0	72.0	73.0					1																	54476004		2203	4300	6503	SO:0001589	frameshift_variant	388633	exon5			.		CCDS30725.1, CCDS60145.1, CCDS60146.1, CCDS60147.1	1p32.3	2008-02-05	2005-10-07		ENSG00000203985	ENSG00000203985			32069	protein-coding gene	gene with protein product			"""low density lipoprotein receptor A domain containing 1"""				Standard	NM_001010978		Approved		uc001cwm.2	Q5T700	OTTHUMG00000008433	ENST00000371360.1:c.420delA	chr1.hg19:g.54476004delT	ENSP00000360411:p.Lys140fs	90.0	0.0		164.0	11.0	NM_001010978	A0PJY0|B7ZME3|Q5T6Z9	Frame_Shift_Del	DEL	ENST00000371360.1	hg19	CCDS30725.1																																																																																			.	.		0.607	LDLRAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023243.1	NM_001010978	
ABCA8	10351	hgsc.bcm.edu	37	17	66918423	66918423	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:66918423delT	ENST00000269080.2	-	11	1598	c.1461delA	c.(1459-1461)aaafs	p.K487fs	ABCA8_ENST00000586539.1_Frame_Shift_Del_p.K487fs|ABCA8_ENST00000430352.2_Frame_Shift_Del_p.K487fs	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	487	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					CTTTATATTCTTTTGTAACAT	0.244																																					p.E488fs		Atlas-INDEL	.											.	ABCA8	213	.	0			c.1462delG						.						37.0	40.0	39.0					17																	66918423		2187	4289	6476	SO:0001589	frameshift_variant	10351	exon11			.	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.1461delA	chr17.hg19:g.66918423delT	ENSP00000269080:p.Lys487fs	92.0	0.0		197.0	14.0	NM_007168	A1L3U3|C9JQE6|Q86WW0	Frame_Shift_Del	DEL	ENST00000269080.2	hg19	CCDS11680.1																																																																																			.	.		0.244	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
TTC39C	125488	hgsc.bcm.edu	37	18	21662914	21662914	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:21662914delT	ENST00000317571.3	+	6	1089	c.853delT	c.(853-855)tttfs	p.F286fs	RP11-403A21.3_ENST00000578443.1_RNA|TTC39C_ENST00000304621.6_Frame_Shift_Del_p.F225fs	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	286										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						AGTCCGCCCGTTTTTTGCCTT	0.413																																					p.P284fs		Atlas-INDEL	.											.	TTC39C	83	.	0			c.852delG						.						186.0	180.0	182.0					18																	21662914		2203	4300	6503	SO:0001589	frameshift_variant	125488	exon6			.	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"""Tetratricopeptide (TTC) repeat domain containing"""	26595	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 17"""	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.853delT	chr18.hg19:g.21662914delT	ENSP00000323645:p.Phe286fs	127.0	0.0		162.0	10.0	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Frame_Shift_Del	DEL	ENST00000317571.3	hg19	CCDS45839.1																																																																																			.	.		0.413	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211	
SEC14L1	6397	hgsc.bcm.edu	37	17	75189591	75189591	+	Frame_Shift_Del	DEL	A	A	-	rs34381783		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:75189591delA	ENST00000413679.2	+	6	737	c.434delA	c.(433-435)gaafs	p.E145fs	SEC14L1_ENST00000443798.4_Frame_Shift_Del_p.E145fs|SEC14L1_ENST00000591437.1_Frame_Shift_Del_p.E111fs|SEC14L1_ENST00000431431.2_Frame_Shift_Del_p.E111fs|SEC14L1_ENST00000392476.2_Frame_Shift_Del_p.E145fs|SEC14L1_ENST00000430767.4_Frame_Shift_Del_p.E145fs|SEC14L1_ENST00000436233.4_Frame_Shift_Del_p.E145fs|SEC14L1_ENST00000585618.1_Frame_Shift_Del_p.E145fs	NM_001143998.1|NM_001143999.1|NM_003003.3	NP_001137470|NP_001137471|NP_002994	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)	145	PRELI/MSF1. {ECO:0000255|PROSITE- ProRule:PRU00158}.				transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(2)	31						AGTACAGTGGAAAAAATTGCA	0.378																																					p.E145fs		Atlas-INDEL	.											.	SEC14L1	81	.	0			c.433delG						.						76.0	75.0	75.0					17																	75189591		2203	4300	6503	SO:0001589	frameshift_variant	6397	exon8			.	D67029	CCDS11752.1, CCDS42385.1, CCDS45789.1	17q25.2	2008-02-01	2001-11-28			ENSG00000129657			10698	protein-coding gene	gene with protein product		601504	"""SEC14 (S. cerevisiae)-like 1"""	SEC14L		8697811	Standard	NM_001143998		Approved	PRELID4A	uc002jto.3	Q92503		ENST00000413679.2:c.434delA	chr17.hg19:g.75189591delA	ENSP00000394716:p.Glu145fs	110.0	0.0		174.0	12.0	NM_001204408	A8K4E8|B4DDI5|D5G3K1|Q99780	Frame_Shift_Del	DEL	ENST00000413679.2	hg19	CCDS11752.1																																																																																			.	.		0.378	SEC14L1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000436240.1	NM_003003	
THOC3	84321	hgsc.bcm.edu	37	5	175394993	175394993	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:175394993delC	ENST00000265097.4	-	1	309	c.219delG	c.(217-219)gggfs	p.G73fs	THOC3_ENST00000514861.1_Intron|THOC3_ENST00000510300.1_5'Flank|THOC3_ENST00000513482.1_Frame_Shift_Del_p.G73fs	NM_032361.2	NP_115737.1	Q96J01	THOC3_HUMAN	THO complex 3	73					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(2)	4	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		TGTCGAAGGACCCCGAGGCTA	0.672																																					p.S74fs		Atlas-INDEL	.											.	THOC3	11	.	0			c.220delT						.						9.0	10.0	10.0					5																	175394993		2002	3986	5988	SO:0001589	frameshift_variant	84321	exon1			.	BC006849	CCDS4397.1	5q35.3	2013-02-11			ENSG00000051596	ENSG00000051596		"""WD repeat domain containing"", ""THO complex subunits"""	19072	protein-coding gene	gene with protein product		606929				11979277	Standard	NM_032361		Approved	TEX1, MGC5469	uc003mdg.5	Q96J01	OTTHUMG00000130658	ENST00000265097.4:c.219delG	chr5.hg19:g.175394993delC	ENSP00000265097:p.Gly73fs	83.0	0.0		169.0	13.0	NM_032361	Q6NZ53	Frame_Shift_Del	DEL	ENST00000265097.4	hg19	CCDS4397.1																																																																																			.	.		0.672	THOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253148.1		
DNMT3B	1789	hgsc.bcm.edu	37	20	31369189	31369189	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:31369189delG	ENST00000328111.2	+	3	494	c.173delG	c.(172-174)aggfs	p.R58fs	DNMT3B_ENST00000201963.3_Frame_Shift_Del_p.R70fs|DNMT3B_ENST00000348286.2_Frame_Shift_Del_p.R58fs|DNMT3B_ENST00000375623.4_Frame_Shift_Del_p.R58fs|DNMT3B_ENST00000443239.3_Frame_Shift_Del_p.R58fs|DNMT3B_ENST00000456297.2_Frame_Shift_Del_p.R58fs|DNMT3B_ENST00000344505.4_Frame_Shift_Del_p.R58fs|DNMT3B_ENST00000353855.2_Frame_Shift_Del_p.R58fs	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	58	Interaction with DNMT1 and DNMT3A.				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 on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CTCTCCAAGAGGGAGGTGTCC	0.552																																					p.R70fs		Atlas-INDEL	.											.	DNMT3B	196	.	0			c.208delA						.						141.0	111.0	121.0					20																	31369189		2203	4300	6503	SO:0001589	frameshift_variant	1789	exon3			.		CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.173delG	chr20.hg19:g.31369189delG	ENSP00000328547:p.Arg58fs	127.0	0.0		144.0	10.0	NM_175850	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Frame_Shift_Del	DEL	ENST00000328111.2	hg19	CCDS13205.1																																																																																			.	.		0.552	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892	
SRCAP	10847	hgsc.bcm.edu	37	16	30735727	30735727	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:30735727delA	ENST00000262518.4	+	25	5367	c.4982delA	c.(4981-4983)caafs	p.Q1661fs	SRCAP_ENST00000344771.4_Frame_Shift_Del_p.Q1503fs|SRCAP_ENST00000395059.2_Frame_Shift_Del_p.Q1599fs	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1661	Pro-rich.				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)			TCATCAACTCAAACTATGCTA	0.582																																					p.Q1661fs		Atlas-INDEL	.											SRCAP,NS,carcinoma,0,2	SRCAP	298	.	0			c.4981delC						.						143.0	147.0	146.0					16																	30735727		2197	4300	6497	SO:0001589	frameshift_variant	10847	exon25			.	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.4982delA	chr16.hg19:g.30735727delA	ENSP00000262518:p.Gln1661fs	116.0	0.0		163.0	10.0	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Frame_Shift_Del	DEL	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.		0.582	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
TENM4	26011	hgsc.bcm.edu	37	11	78614323	78614323	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:78614323delG	ENST00000278550.7	-	7	1201	c.739delC	c.(739-741)ctgfs	p.L247fs		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	247	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				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)										CTGGTCTCCAGGGGGATGTTG	0.721																																					p.L247fs		Atlas-INDEL	.											.	.	.	.	0			c.740delT						.						10.0	14.0	12.0					11																	78614323		689	1588	2277	SO:0001589	frameshift_variant	26011	exon7			.	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.739delC	chr11.hg19:g.78614323delG	ENSP00000278550:p.Leu247fs	94.0	0.0		165.0	10.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Frame_Shift_Del	DEL	ENST00000278550.7	hg19	CCDS44688.1																																																																																			.	.		0.721	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
TCEAL4	79921	hgsc.bcm.edu	37	X	102841728	102841728	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:102841728delA	ENST00000472745.1	+	3	677	c.125delA	c.(124-126)gaafs	p.E42fs	TCEAL4_ENST00000415568.2_Frame_Shift_Del_p.E42fs|TCEAL4_ENST00000472484.1_Frame_Shift_Del_p.E42fs|TCEAL4_ENST00000372629.4_Frame_Shift_Del_p.E185fs|TCEAL4_ENST00000468024.1_Frame_Shift_Del_p.E42fs|TCEAL4_ENST00000494801.1_Frame_Shift_Del_p.E42fs			Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	42	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						AAGAAGTTagaaaacgaggga	0.423																																					p.E42fs		Atlas-INDEL	.											.	TCEAL4	18	.	0			c.124delG						.						87.0	88.0	88.0					X																	102841728		2187	4286	6473	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.125delA	chrX.hg19:g.102841728delA	ENSP00000424314:p.Glu42fs	115.0	0.0		142.0	10.0	NM_001006935	Q8WY12|Q9H2H1|Q9H775	Frame_Shift_Del	DEL	ENST00000472745.1	hg19	CCDS14510.2																																																																																			.	.		0.423	TCEAL4-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252339.2	NM_024863	
RYR2	6262	hgsc.bcm.edu	37	1	237604620	237604620	+	Splice_Site	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:237604620delA	ENST00000366574.2	+	13	1324	c.1007delA	c.(1006-1008)gaa>ga	p.E336fs	RYR2_ENST00000360064.6_Splice_Site_p.E334fs|RYR2_ENST00000542537.1_Splice_Site_p.E320fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	336	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TCCCCTTAGGAAAAATTGGAT	0.358																																					p.E336fs		Atlas-INDEL	.											.	RYR2	1273	.	0			c.1006delG						.						111.0	106.0	107.0					1																	237604620		1830	4085	5915	SO:0001630	splice_region_variant	6262	exon13			.	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.1006-1A>-	chr1.hg19:g.237604620delA		100.0	0.0		152.0	10.0	NM_001035	Q15411|Q546N8|Q5T3P2	Frame_Shift_Del	DEL	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.358	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	Frame_Shift_Del
GRID2	2895	hgsc.bcm.edu	37	4	94690497	94690497	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:94690497delG	ENST00000282020.4	+	15	2755	c.2497delG	c.(2497-2499)gggfs	p.G833fs	GRID2_ENST00000510992.1_Frame_Shift_Del_p.G738fs	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	833					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		GAGCTTTGCAGGGGTCTTTTG	0.527																																					p.A832fs		Atlas-INDEL	.											.	GRID2	233	.	0			c.2496delA						.						114.0	124.0	121.0					4																	94690497		2203	4300	6503	SO:0001589	frameshift_variant	2895	exon15			.	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.2497delG	chr4.hg19:g.94690497delG	ENSP00000282020:p.Gly833fs	182.0	0.0		143.0	10.0	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Frame_Shift_Del	DEL	ENST00000282020.4	hg19	CCDS3637.1																																																																																			.	.		0.527	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2		
GNAI1	2770	hgsc.bcm.edu	37	7	79842146	79842146	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:79842146delA	ENST00000351004.3	+	7	1208	c.835delA	c.(835-837)aaafs	p.K280fs	GNAI1_ENST00000457358.2_Frame_Shift_Del_p.K228fs	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	280					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						AGAAAAAATCAAAAAGAGCCC	0.328																																					p.I278fs		Atlas-INDEL	.											.	GNAI1	44	.	0			c.834delC						.						66.0	74.0	71.0					7																	79842146		2203	4294	6497	SO:0001589	frameshift_variant	2770	exon7			.	AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"""Gi1 protein alpha subunit"""	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.835delA	chr7.hg19:g.79842146delA	ENSP00000343027:p.Lys280fs	183.0	0.0		246.0	15.0	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Frame_Shift_Del	DEL	ENST00000351004.3	hg19	CCDS5595.1																																																																																			.	.		0.328	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069	
TTN	7273	hgsc.bcm.edu	37	2	179554548	179554548	+	Frame_Shift_Del	DEL	G	G	-	rs186731979		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:179554548delG	ENST00000591111.1	-	120	31111	c.30887delC	c.(30886-30888)ccafs	p.P10296fs	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Frame_Shift_Del_p.P10613fs|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.P9369fs			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACCTTTAGCTGGGGGAGCTTC	0.373																																					p.P10613fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.31839delA						.						160.0	154.0	156.0					2																	179554548		1836	4086	5922	SO:0001589	frameshift_variant	7273	exon122			.	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.30887delC	chr2.hg19:g.179554548delG	ENSP00000465570:p.Pro10296fs	101.0	0.0		131.0	11.0	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																																																																																				.	.		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TAOK1	57551	hgsc.bcm.edu	37	17	27805327	27805327	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:27805327delG	ENST00000261716.3	+	6	930	c.411delG	c.(409-411)cagfs	p.Q137fs	TAOK1_ENST00000536202.1_Frame_Shift_Del_p.Q137fs	NM_020791.2	NP_065842.1	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	137	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|execution phase of apoptosis (GO:0097194)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of cytoskeleton organization (GO:0051493)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28			Colorectal(6;0.198)			GTGCTCTTCAGGGATTAGCCT	0.299																																					p.Q137fs		Atlas-INDEL	.											.	TAOK1	151	.	0			c.410delA						.						109.0	114.0	112.0					17																	27805327		2203	4290	6493	SO:0001589	frameshift_variant	57551	exon6			.	AB037782	CCDS32601.1, CCDS56024.1	17q11.2	2014-01-28				ENSG00000160551			29259	protein-coding gene	gene with protein product		610266				10718198, 14517247	Standard	NM_020791		Approved	KIAA1361, MARKK, PSK2, MAP3K16, FLJ14314, TAO1	uc002hdz.2	Q7L7X3		ENST00000261716.3:c.411delG	chr17.hg19:g.27805327delG	ENSP00000261716:p.Gln137fs	213.0	0.0		234.0	15.0	NM_025142	A2RUT8|B7ZLV6|Q96L75|Q9H2K7|Q9H7S5|Q9P2I6	Frame_Shift_Del	DEL	ENST00000261716.3	hg19	CCDS32601.1																																																																																			.	.		0.299	TAOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447790.1	NM_020791	
PPP4R1	9989	hgsc.bcm.edu	37	18	9557277	9557277	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:9557277delA	ENST00000400556.3	-	15	2205	c.2132delT	c.(2131-2133)ttafs	p.L711fs	PPP4R1_ENST00000400555.3_Frame_Shift_Del_p.L694fs	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	711					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						GAGGTCTTTTAAAAATCCATT	0.348																																					p.L711fs	Melanoma(188;1232 2082 5061 11948 35994)	Atlas-INDEL	.											.	PPP4R1	63	.	0			c.2133delA						.						157.0	152.0	154.0					18																	9557277		1821	4076	5897	SO:0001589	frameshift_variant	9989	exon15			.	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.2132delT	chr18.hg19:g.9557277delA	ENSP00000383402:p.Leu711fs	166.0	0.0		149.0	11.0	NM_001042388	Q99774|Q9UNQ7	Frame_Shift_Del	DEL	ENST00000400556.3	hg19	CCDS42412.1																																																																																			.	.		0.348	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134	
TCERG1	10915	hgsc.bcm.edu	37	5	145890008	145890008	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:145890008delA	ENST00000296702.5	+	22	3138	c.3100delA	c.(3100-3102)aaafs	p.K1035fs	TCERG1_ENST00000394421.2_Frame_Shift_Del_p.K1014fs	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	1035	FF 6.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTTCAGATCCAAAAAATTAAT	0.368																																					p.S1033fs		Atlas-INDEL	.											.	TCERG1	148	.	0			c.3099delC						.						48.0	52.0	51.0					5																	145890008		2203	4300	6503	SO:0001589	frameshift_variant	10915	exon22			.	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"""transcription factor CA150"", ""co-activator of 150 kDa"", ""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"", ""TATA box-binding protein-associated factor 2S"""	605409	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"""	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.3100delA	chr5.hg19:g.145890008delA	ENSP00000296702:p.Lys1035fs	69.0	0.0		119.0	10.0	NM_006706	Q2NKN2|Q59EA1	Frame_Shift_Del	DEL	ENST00000296702.5	hg19	CCDS4282.1																																																																																			.	.		0.368	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006	
CPSF1	29894	hgsc.bcm.edu	37	8	145619169	145619169	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:145619169delG	ENST00000349769.3	-	35	4038	c.3944delC	c.(3943-3945)ccgfs	p.P1315fs	CPSF1_ENST00000531727.1_5'UTR|MIR939_ENST00000401314.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	1315					gene expression (GO:0010467)|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)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	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;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CCCCCGGCACGGGGTCCTCCA	0.622																																					p.P1315fs	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-INDEL	.											.	CPSF1	92	.	0			c.3945delG						.						56.0	55.0	55.0					8																	145619169		2201	4300	6501	SO:0001589	frameshift_variant	29894	exon35			.	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.3944delC	chr8.hg19:g.145619169delG	ENSP00000339353:p.Pro1315fs	87.0	0.0		274.0	17.0	NM_013291	Q96AF0	Frame_Shift_Del	DEL	ENST00000349769.3	hg19	CCDS34966.1																																																																																			.	.		0.622	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
EXO1	9156	hgsc.bcm.edu	37	1	242042452	242042452	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:242042452delC	ENST00000366548.3	+	13	2509	c.1916delC	c.(1915-1917)tccfs	p.S639fs	EXO1_ENST00000348581.5_Frame_Shift_Del_p.S639fs|EXO1_ENST00000518483.1_Frame_Shift_Del_p.S639fs	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	639	Interaction with MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			AAGAGCGATTCCCCCACCTCT	0.488								Editing and processing nucleases																													p.S639fs		Atlas-INDEL	.											.	EXO1	103	.	0			c.1915delT						.						78.0	73.0	75.0					1																	242042452		2203	4300	6503	SO:0001589	frameshift_variant	9156	exon13			.	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"""rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"""	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.1916delC	chr1.hg19:g.242042452delC	ENSP00000355506:p.Ser639fs	136.0	0.0		226.0	17.0	NM_130398	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Frame_Shift_Del	DEL	ENST00000366548.3	hg19	CCDS1620.1																																																																																			.	.		0.488	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027	
MEAF6	64769	hgsc.bcm.edu	37	1	37961495	37961495	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:37961495delT	ENST00000296214.5	-	6	585	c.558delA	c.(556-558)aaafs	p.K186fs	MEAF6_ENST00000373073.4_Intron|MEAF6_ENST00000373075.2_Frame_Shift_Del_p.K196fs|MEAF6_ENST00000373074.1_Frame_Shift_Del_p.K164fs|MEAF6_ENST00000475828.1_5'UTR|MEAF6_ENST00000448519.2_3'UTR	NM_001270875.1	NP_001257804.1	Q9HAF1	EAF6_HUMAN	MYST/Esa1-associated factor 6	186					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(3)	7						CAGCTCGTGGTTTTTTGTTTA	0.378																																					p.P197fs		Atlas-INDEL	.											.	MEAF6	25	.	0			c.589delC						.						95.0	99.0	98.0					1																	37961495		2203	4300	6503	SO:0001589	frameshift_variant	64769	exon7			.	BC016328	CCDS418.1, CCDS59195.1, CCDS59196.1	1p35.3-p33	2011-08-12	2009-07-13	2009-07-13	ENSG00000163875	ENSG00000163875			25674	protein-coding gene	gene with protein product	"""Esa1p-associated factor 6 homolog (S. cerevisiae)"", ""centromere protein 28"""	611001	"""chromosome 1 open reading frame 149"""	C1orf149		8619474, 9110174, 12963728, 14966270, 16387653	Standard	NM_022756		Approved	NY-SAR-91, FLJ11730, Eaf6, CENP-28	uc001cbe.2	Q9HAF1	OTTHUMG00000004223	ENST00000296214.5:c.558delA	chr1.hg19:g.37961495delT	ENSP00000296214:p.Lys186fs	132.0	0.0		200.0	12.0	NM_022756	B1AK64|Q4F967|Q7Z311|Q86WE3	Frame_Shift_Del	DEL	ENST00000296214.5	hg19	CCDS59196.1																																																																																			.	.		0.378	MEAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012161.1	NM_022756	
USP14	9097	hgsc.bcm.edu	37	18	198083	198083	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:198083delA	ENST00000261601.7	+	9	803	c.712delA	c.(712-714)aaafs	p.K240fs	USP14_ENST00000582707.1_Frame_Shift_Del_p.K205fs|USP14_ENST00000383589.2_Frame_Shift_Del_p.K194fs|USP14_ENST00000400266.3_Frame_Shift_Del_p.K229fs	NM_005151.3	NP_005142.1	P54578	UBP14_HUMAN	ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase)	240	USP.				negative regulation of endopeptidase activity (GO:0010951)|protein deubiquitination (GO:0016579)|regulation of chemotaxis (GO:0050920)|regulation of proteasomal protein catabolic process (GO:0061136)|synaptic transmission (GO:0007268)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)|synapse (GO:0045202)	cysteine-type endopeptidase activity (GO:0004197)|endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)|tRNA guanylyltransferase activity (GO:0008193)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(2)	11		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				GACACCTTCTAAAAAGAAAAG	0.328																																					p.S237fs		Atlas-INDEL	.											.	USP14	41	.	0			c.711delT						.						66.0	68.0	68.0					18																	198083		2203	4300	6503	SO:0001589	frameshift_variant	9097	exon9			.	U30888	CCDS32780.1, CCDS32781.1	18p11.32	2006-10-06	2005-08-08			ENSG00000101557		"""Ubiquitin-specific peptidases"""	12612	protein-coding gene	gene with protein product		607274	"""ubiquitin specific protease 14 (tRNA-guanine transglycosylase)"""			12838346	Standard	NM_001037334		Approved	TGT	uc002kkf.1	P54578		ENST00000261601.7:c.712delA	chr18.hg19:g.198083delA	ENSP00000261601:p.Lys240fs	117.0	0.0		172.0	12.0	NM_005151	J3QRZ5|Q53XY5	Frame_Shift_Del	DEL	ENST00000261601.7	hg19	CCDS32780.1																																																																																			.	.		0.328	USP14-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440305.3	NM_005151	
OXCT1	5019	hgsc.bcm.edu	37	5	41862804	41862804	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:41862804delA	ENST00000196371.5	-	2	287	c.127delT	c.(127-129)tatfs	p.Y43fs		NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	43					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular response to acid chemical (GO:0071229)|cellular response to glucose stimulus (GO:0071333)|heart development (GO:0007507)|ketone body catabolic process (GO:0046952)|ketone catabolic process (GO:0042182)|positive regulation of insulin secretion (GO:0032024)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hormone (GO:0009725)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-oxoacid CoA-transferase activity (GO:0008260)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(2)	28					Succinic acid(DB00139)	GGATCTGTATAAAACTTGGTA	0.373																																					p.Y43fs		Atlas-INDEL	.											.	OXCT1	54	.	0			c.128delA						.						128.0	114.0	119.0					5																	41862804		2203	4300	6503	SO:0001589	frameshift_variant	5019	exon2			.	U62961	CCDS3937.1	5p13	2008-02-05		2004-05-12	ENSG00000083720	ENSG00000083720			8527	protein-coding gene	gene with protein product		601424	"""3-oxoacid CoA transferase"""	OXCT		8751852	Standard	NM_000436		Approved	SCOT	uc003jmn.3	P55809	OTTHUMG00000094783	ENST00000196371.5:c.127delT	chr5.hg19:g.41862804delA	ENSP00000196371:p.Tyr43fs	161.0	0.0		211.0	15.0	NM_000436	B2R5V2|B7Z528	Frame_Shift_Del	DEL	ENST00000196371.5	hg19	CCDS3937.1																																																																																			.	.		0.373	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211594.2	NM_000436	
ANGEL2	90806	hgsc.bcm.edu	37	1	213181561	213181561	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:213181561delA	ENST00000366962.3	-	3	787	c.633delT	c.(631-633)tttfs	p.F211fs	ANGEL2_ENST00000540642.1_Frame_Shift_Del_p.F85fs|ANGEL2_ENST00000544555.1_Frame_Shift_Del_p.F42fs|ANGEL2_ENST00000360506.2_Frame_Shift_Del_p.F42fs|ANGEL2_ENST00000535388.1_Frame_Shift_Del_p.F42fs	NM_144567.3	NP_653168.2	Q5VTE6	ANGE2_HUMAN	angel homolog 2 (Drosophila)	211										central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(1)	24				OV - Ovarian serous cystadenocarcinoma(81;0.00446)|all cancers(67;0.0169)|Epithelial(68;0.0921)|GBM - Glioblastoma multiforme(131;0.185)		CGTCTGCATCAAAATGTTTAA	0.398																																					p.D212fs		Atlas-INDEL	.											.	ANGEL2	45	.	0			c.634delG						.						35.0	37.0	37.0					1																	213181561		2203	4300	6503	SO:0001589	frameshift_variant	90806	exon3			.	AL079275	CCDS1512.1, CCDS73027.1	1q32.3	2014-06-17			ENSG00000174606	ENSG00000174606			30534	protein-coding gene	gene with protein product						11943475	Standard	XM_005273344		Approved	KIAA0759L, FLJ12793, Ccr4d	uc001hjz.3	Q5VTE6	OTTHUMG00000036927	ENST00000366962.3:c.633delT	chr1.hg19:g.213181561delA	ENSP00000355929:p.Phe211fs	126.0	0.0		219.0	14.0	NM_144567	B7Z2U4|D3DTA3|Q86X13|Q8NHH3	Frame_Shift_Del	DEL	ENST00000366962.3	hg19	CCDS1512.1																																																																																			.	.		0.398	ANGEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089693.1	NM_144567	
MRPL3	11222	hgsc.bcm.edu	37	3	131188575	131188575	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:131188575delT	ENST00000264995.3	-	8	928	c.781delA	c.(781-783)atgfs	p.M261fs	MRPL3_ENST00000425847.2_Frame_Shift_Del_p.M288fs	NM_007208.3	NP_009139.1	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	261			M -> T (in dbSNP:rs2291381).		translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						ATGTTTCCCATTTTTCCAGGC	0.348																																					p.M261fs		Atlas-INDEL	.											.,1	MRPL3	32	.	0			c.782delT						.						128.0	112.0	117.0					3																	131188575		2203	4300	6503	SO:0001589	frameshift_variant	11222	exon8			.	X06323	CCDS3071.1	3q21-q23	2012-09-13			ENSG00000114686	ENSG00000114686		"""Mitochondrial ribosomal proteins / large subunits"""	10379	protein-coding gene	gene with protein product		607118		RPML3		2891103	Standard	NM_007208		Approved	MRL3	uc003eoh.3	P09001	OTTHUMG00000159607	ENST00000264995.3:c.781delA	chr3.hg19:g.131188575delT	ENSP00000264995:p.Met261fs	119.0	0.0		153.0	10.0	NM_007208	Q6IBT2	Frame_Shift_Del	DEL	ENST00000264995.3	hg19	CCDS3071.1																																																																																			.	.		0.348	MRPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356471.3	NM_007208	
RASGRP1	10125	hgsc.bcm.edu	37	15	38810590	38810590	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:38810590delT	ENST00000310803.5	-	5	601	c.424delA	c.(424-426)atgfs	p.M142fs	RASGRP1_ENST00000558164.1_Frame_Shift_Del_p.M142fs|RASGRP1_ENST00000539159.1_Frame_Shift_Del_p.M94fs|RASGRP1_ENST00000450598.2_Frame_Shift_Del_p.M142fs|RASGRP1_ENST00000561180.1_Frame_Shift_Del_p.M193fs|RASGRP1_ENST00000559830.1_Frame_Shift_Del_p.M142fs	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	142	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		CTGGCGTCCATTTTAAACATG	0.433																																					p.M142fs		Atlas-INDEL	.											.	RASGRP1	50	.	0			c.425delT						.						87.0	77.0	80.0					15																	38810590		1878	4112	5990	SO:0001589	frameshift_variant	10125	exon5			.	AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"""EF-hand domain containing"""	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.424delA	chr15.hg19:g.38810590delT	ENSP00000310244:p.Met142fs	105.0	0.0		135.0	10.0	NM_001128602	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Frame_Shift_Del	DEL	ENST00000310803.5	hg19	CCDS45222.1																																																																																			.	.		0.433	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418223.1	NM_005739	
FAM208A	23272	hgsc.bcm.edu	37	3	56694990	56694990	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:56694990delT	ENST00000493960.2	-	10	1226	c.1216delA	c.(1216-1218)atcfs	p.I406fs	FAM208A_ENST00000355628.5_Frame_Shift_Del_p.I406fs|FAM208A_ENST00000431842.2_Frame_Shift_Del_p.I10fs	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	406							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						GCTGGAGGGATTTTCTGTTTC	0.303																																					p.I406fs		Atlas-INDEL	.											.	FAM208A	113	.	0			c.1217delT						.						111.0	111.0	111.0					3																	56694990		2202	4299	6501	SO:0001589	frameshift_variant	23272	exon10			.	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 63"""	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.1216delA	chr3.hg19:g.56694990delT	ENSP00000417509:p.Ile406fs	131.0	0.0		230.0	16.0	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Frame_Shift_Del	DEL	ENST00000493960.2	hg19	CCDS46853.1																																																																																			.	.		0.303	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
LARP7	51574	hgsc.bcm.edu	37	4	113567545	113567545	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:113567545delA	ENST00000344442.5	+	3	519	c.241delA	c.(241-243)aaafs	p.K82fs	MIR302B_ENST00000362188.1_RNA|MIR367_ENST00000362299.1_RNA|MIR302C_ENST00000362232.1_RNA|MIR302D_ENST00000362275.1_RNA|MIR302B_ENST00000505215.1_RNA|MIR302A_ENST00000385192.1_RNA|LARP7_ENST00000509061.1_Frame_Shift_Del_p.K89fs|MIR302B_ENST00000510655.1_RNA|LARP7_ENST00000324052.6_Frame_Shift_Del_p.K82fs|MIR302B_ENST00000509938.1_RNA	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	82	HTH La-type RNA-binding. {ECO:0000255|PROSITE-ProRule:PRU00332}.				RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		TAACAAAATGAAAAAATTGAC	0.289																																					p.M87fs		Atlas-INDEL	.											.,1	LARP7	54	.	0			c.261delG						.																																			SO:0001589	frameshift_variant	51574	exon5			.	AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"""La ribonucleoprotein domain containing"", ""RNA binding motif (RRM) containing"""	24912	protein-coding gene	gene with protein product	"""P-TEFb-interaction protein for 7SK stability"""	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.241delA	chr4.hg19:g.113567545delA	ENSP00000344950:p.Lys82fs	259.0	0.0		179.0	11.0	NM_001267039	B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	Frame_Shift_Del	DEL	ENST00000344442.5	hg19	CCDS3701.2																																																																																			.	.		0.289	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648	
PLAG1	5324	hgsc.bcm.edu	37	8	57078932	57078932	+	Frame_Shift_Del	DEL	G	G	-	rs144552372		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:57078932delG	ENST00000316981.3	-	5	1852	c.1373delC	c.(1372-1374)ccafs	p.P458fs	PLAG1_ENST00000429357.2_Frame_Shift_Del_p.P458fs|PLAG1_ENST00000423799.2_Frame_Shift_Del_p.P376fs	NM_001114634.1|NM_002655.2	NP_001108106.1|NP_002646.2	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1	458	Activates transcription; Inhibition of nuclear import due to lack of NLS and KPNA2 interaction.|Massively activates transcription.		P -> T (in dbSNP:rs35883156). {ECO:0000269|PubMed:9020842}.		gland morphogenesis (GO:0022612)|multicellular organism growth (GO:0035264)|negative regulation of gene expression (GO:0010629)|organ growth (GO:0035265)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		CTNNB1/PLAG1(60)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|FGFR1_ENST00000447712/PLAG1(28)|COL1A2/PLAG1(3)|CHCHD7/PLAG1(12)|TCEA1_ENST00000521604/PLAG1(3)	breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)			CTGTGTTTGTGGGGGGAGCTG	0.488			T	"""TCEA1, LIFR, CTNNB1, CHCHD7"""	salivary adenoma																																p.P458fs		Atlas-INDEL	.		Dom	yes		8	8q12	5324	pleiomorphic adenoma gene 1		E	.	PLAG1	123	.	0			c.1374delA						.						127.0	129.0	129.0					8																	57078932		2203	4300	6503	SO:0001589	frameshift_variant	5324	exon5			.	U65002	CCDS6165.1, CCDS47860.1	8q12	2010-07-30				ENSG00000181690		"""Zinc fingers, C2H2-type"""	9045	protein-coding gene	gene with protein product		603026				9268638	Standard	NM_002655		Approved	ZNF912	uc010lyi.3	Q6DJT9		ENST00000316981.3:c.1373delC	chr8.hg19:g.57078932delG	ENSP00000325546:p.Pro458fs	88.0	0.0		229.0	15.0	NM_002655	B4DLC2|Q59GH8|Q9Y4L2	Frame_Shift_Del	DEL	ENST00000316981.3	hg19	CCDS6165.1																																																																																			.	.		0.488	PLAG1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378212.1	NM_002655	
ANKRD17	26057	hgsc.bcm.edu	37	4	73957752	73957752	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:73957752delT	ENST00000358602.4	-	29	5709	c.5593delA	c.(5593-5595)accfs	p.T1865fs	ANKRD17_ENST00000509867.2_Frame_Shift_Del_p.T1752fs|ANKRD17_ENST00000330838.6_Frame_Shift_Del_p.T1614fs	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	1865					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTCTTAATGGTTTTGTGAGTG	0.433																																					p.T1865fs		Atlas-INDEL	.											.	ANKRD17	214	.	0			c.5594delC						.						175.0	183.0	180.0					4																	73957752		2203	4300	6503	SO:0001589	frameshift_variant	26057	exon29			.	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.5593delA	chr4.hg19:g.73957752delT	ENSP00000351416:p.Thr1865fs	189.0	0.0		197.0	14.0	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Frame_Shift_Del	DEL	ENST00000358602.4	hg19	CCDS34004.1																																																																																			.	.		0.433	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
SPATA2L	124044	hgsc.bcm.edu	37	16	89764134	89764134	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:89764134delC	ENST00000289805.5	-	3	951	c.883delG	c.(883-885)gccfs	p.A295fs	SPATA2L_ENST00000335360.7_Intron	NM_152339.3	NP_689552.2	Q8IUW3	SPA2L_HUMAN	spermatogenesis associated 2-like	295										breast(1)|cervix(1)|endometrium(1)|lung(2)|skin(1)	6		Lung NSC(15;0.00043)|all_lung(18;0.000665)|all_hematologic(23;0.0355)		BRCA - Breast invasive adenocarcinoma(80;0.0272)		TCCTCCAAGGCCCCATATGGT	0.672																																					p.A295fs		Atlas-INDEL	.											.	SPATA2L	16	.	0			c.884delC						.						22.0	24.0	23.0					16																	89764134		2193	4295	6488	SO:0001589	frameshift_variant	124044	exon3			.	AF070574	CCDS10985.1	16q24.3	2007-01-30	2007-01-30	2007-01-30	ENSG00000158792	ENSG00000158792			28393	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 76"""	C16orf76		8619474	Standard	NM_152339		Approved	MGC26885, tamo	uc002foj.3	Q8IUW3	OTTHUMG00000138047	ENST00000289805.5:c.883delG	chr16.hg19:g.89764134delC	ENSP00000289805:p.Ala295fs	92.0	0.0		138.0	10.0	NM_152339	D3DX85|Q8NHV3	Frame_Shift_Del	DEL	ENST00000289805.5	hg19	CCDS10985.1																																																																																			.	.		0.672	SPATA2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269923.1	NM_152339	
STYX	6815	hgsc.bcm.edu	37	14	53213189	53213189	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:53213189delA	ENST00000354586.4	+	3	429	c.136delA	c.(136-138)aaafs	p.K46fs	STYX_ENST00000442123.2_Frame_Shift_Del_p.K46fs|STYX_ENST00000556861.1_Intron	NM_145251.3	NP_660294.1	Q8WUJ0	STYX_HUMAN	serine/threonine/tyrosine interacting protein	46					MAPK export from nucleus (GO:0045204)|protein dephosphorylation (GO:0006470)|regulation of ERK1 and ERK2 cascade (GO:0070372)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5	Breast(41;0.176)					ATCTGCTATGAAAAGCAAGGT	0.294																																					p.M45fs		Atlas-INDEL	.											.	STYX	14	.	0			c.135delG						.						61.0	63.0	62.0					14																	53213189		2202	4298	6500	SO:0001589	frameshift_variant	6815	exon4			.		CCDS9711.1	14q22.1	2011-06-09	2001-11-29		ENSG00000198252	ENSG00000198252		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	11447	protein-coding gene	gene with protein product		615814	"""serine/threonine/tyrosine-interacting protein"""			7592916	Standard	NM_145251		Approved		uc010tqy.2	Q8WUJ0	OTTHUMG00000140306	ENST00000354586.4:c.136delA	chr14.hg19:g.53213189delA	ENSP00000346599:p.Lys46fs	180.0	0.0		203.0	14.0	NM_001130701	B9EJG0|Q99850	Frame_Shift_Del	DEL	ENST00000354586.4	hg19	CCDS9711.1																																																																																			.	.		0.294	STYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276902.1	NM_145251	
APBB3	10307	hgsc.bcm.edu	37	5	139936736	139936736	+	IGR	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:139936736delG	ENST00000357560.4	-	0	2218				SRA1_ENST00000336283.6_Frame_Shift_Del_p.P61fs|SRA1_ENST00000520427.1_5'UTR	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGCACCTCTGGGGGATCCAT	0.662																																					p.P101fs		Atlas-INDEL	.											.	SRA1	24	.	0			c.303delA						.						37.0	44.0	42.0					5																	139936736		2188	4283	6471	SO:0001628	intergenic_variant	10011	exon1			.	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504		chr5.hg19:g.139936736delG		103.0	0.0		189.0	15.0	NM_001253764	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Frame_Shift_Del	DEL	ENST00000357560.4	hg19	CCDS4229.1																																																																																			.	.		0.662	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
BEND3	57673	hgsc.bcm.edu	37	6	107389947	107389947	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:107389947delT	ENST00000369042.1	-	4	2638	c.2448delA	c.(2446-2448)aaafs	p.K816fs	BEND3_ENST00000429433.2_Frame_Shift_Del_p.K816fs			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	816	BEN 4. {ECO:0000255|PROSITE- ProRule:PRU00784}.									central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						GGATGTCGCATTTTTTCCTGT	0.577																																					p.C817fs		Atlas-Indel,Pindel	.											.	BEND3	70	.	0			c.2449delT						.						59.0	61.0	60.0					6																	107389947		2203	4299	6502	SO:0001589	frameshift_variant	57673	exon5			.	AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"""BEN domain containing"""	23040	protein-coding gene	gene with protein product			"""KIAA1553"""	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.2448delA	chr6.hg19:g.107389947delT	ENSP00000358038:p.Lys816fs	119.0	0.0		231.0	14.0	NM_001080450	A2RRH2|Q9HCL9	Frame_Shift_Del	DEL	ENST00000369042.1	hg19	CCDS34507.1																																																																																			.	.		0.577	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913	
ADAMTS19	171019	hgsc.bcm.edu	37	5	128994381	128994381	+	Frame_Shift_Del	DEL	A	A	-	rs552521438		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:128994381delA	ENST00000274487.4	+	15	2503	c.2358delA	c.(2356-2358)ggafs	p.G786fs	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	786	Cys-rich.					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)		ATGGCAATGGAAAATCATGCA	0.363																																					p.G786fs		Atlas-INDEL	.											.	ADAMTS19	216	.	0			c.2357delG						.						167.0	166.0	167.0					5																	128994381		2203	4300	6503	SO:0001589	frameshift_variant	171019	exon15			.	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.2358delA	chr5.hg19:g.128994381delA	ENSP00000274487:p.Gly786fs	78.0	0.0		164.0	10.0	NM_133638		Frame_Shift_Del	DEL	ENST00000274487.4	hg19	CCDS4146.1																																																																																			.	.		0.363	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638	
ZNF343	79175	hgsc.bcm.edu	37	20	2474194	2474194	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:2474194delG	ENST00000278772.4	-	4	635	c.148delC	c.(148-150)cagfs	p.Q50fs	RP4-734P14.4_ENST00000461548.1_Frame_Shift_Del_p.Q50fs|ZNF343_ENST00000358413.2_Frame_Shift_Del_p.Q50fs|ZNF343_ENST00000381253.1_Frame_Shift_Del_p.Q50fs	NM_001282495.1|NM_001282496.1|NM_024325.4	NP_001269424.1|NP_001269425.1|NP_077301.4	Q6P1L6	ZN343_HUMAN	zinc finger protein 343	50					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(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|skin(4)|upper_aerodigestive_tract(1)	25						TCCTTTTTCTGGGGGCAGTCA	0.478																																					p.Q50fs		Atlas-INDEL	.											.	ZNF343	47	.	0			c.149delA						.						59.0	65.0	63.0					20																	2474194		2203	4300	6503	SO:0001589	frameshift_variant	79175	exon4			.	AK096911	CCDS13028.1, CCDS74692.1, CCDS74693.1, CCDS74694.1	20p13	2013-01-08			ENSG00000088876	ENSG00000088876		"""Zinc fingers, C2H2-type"", ""-"""	16017	protein-coding gene	gene with protein product							Standard	NM_001282498		Approved	MGC10715	uc002wge.1	Q6P1L6	OTTHUMG00000031701	ENST00000278772.4:c.148delC	chr20.hg19:g.2474194delG	ENSP00000278772:p.Gln50fs	146.0	0.0		159.0	10.0	NM_024325	Q5JXU8|Q5JXU9|Q8N8F2|Q96EX8|Q96NA5|Q9BQB0	Frame_Shift_Del	DEL	ENST00000278772.4	hg19	CCDS13028.1																																																																																			.	.		0.478	ZNF343-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077617.1	NM_024325	
DLD	1738	hgsc.bcm.edu	37	7	107555996	107555996	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:107555996delT	ENST00000205402.5	+	9	1011	c.730delT	c.(730-732)tttfs	p.F244fs	DLD_ENST00000537148.1_Frame_Shift_Del_p.F145fs|DLD_ENST00000437604.2_Frame_Shift_Del_p.F196fs|DLD_ENST00000440410.1_Frame_Shift_Del_p.F221fs	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	244					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	AGCAGTTGAATTTTTAGGTCA	0.318																																					p.E243fs		Atlas-INDEL	.											.	DLD	72	.	0			c.729delA						.						118.0	119.0	118.0					7																	107555996		2203	4300	6503	SO:0001589	frameshift_variant	1738	exon9			.	AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"""E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"""	238331	"""dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"""	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.730delT	chr7.hg19:g.107555996delT	ENSP00000205402:p.Phe244fs	112.0	0.0		155.0	13.0	NM_000108	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Frame_Shift_Del	DEL	ENST00000205402.5	hg19	CCDS5749.1																																																																																			.	.		0.318	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108	
ALCAM	214	hgsc.bcm.edu	37	3	105243184	105243184	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:105243184delA	ENST00000306107.5	+	3	726	c.226delA	c.(226-228)aaafs	p.K76fs	ALCAM_ENST00000472644.2_Frame_Shift_Del_p.K76fs|ALCAM_ENST00000481337.1_3'UTR|ALCAM_ENST00000486979.2_Frame_Shift_Del_p.K25fs	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	76	Ig-like V-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						CTCTACAAAGAAAAGTGTGCA	0.353																																					p.K75fs		Atlas-INDEL	.											.	ALCAM	71	.	0			c.225delG						.						111.0	107.0	108.0					3																	105243184		2203	4300	6503	SO:0001589	frameshift_variant	214	exon3			.	AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	400	protein-coding gene	gene with protein product		601662	"""activated leucocyte cell adhesion molecule"""			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.226delA	chr3.hg19:g.105243184delA	ENSP00000305988:p.Lys76fs	97.0	0.0		159.0	10.0	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Frame_Shift_Del	DEL	ENST00000306107.5	hg19	CCDS33810.1																																																																																			.	.		0.353	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627	
KNTC1	9735	hgsc.bcm.edu	37	12	123014679	123014679	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:123014679delA	ENST00000333479.7	+	2	246	c.69delA	c.(67-69)agafs	p.R23fs	KNTC1_ENST00000450485.2_Frame_Shift_Del_p.R23fs	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	23					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		TCGGTTCAAGAAAAGAACATG	0.388																																					p.R23fs		Atlas-INDEL	.											.	KNTC1	182	.	0			c.68delG						.						126.0	130.0	128.0					12																	123014679		1863	4108	5971	SO:0001589	frameshift_variant	9735	exon2			.		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.69delA	chr12.hg19:g.123014679delA	ENSP00000328236:p.Arg23fs	103.0	0.0		154.0	10.0	NM_014708	A7E2C4|B3KSG2	Frame_Shift_Del	DEL	ENST00000333479.7	hg19	CCDS45002.1																																																																																			.	.		0.388	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
SMC1A	8243	hgsc.bcm.edu	37	X	53407993	53407993	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:53407993delG	ENST00000322213.4	-	23	3580	c.3453delC	c.(3451-3453)cccfs	p.P1151fs	SMC1A_ENST00000469129.1_5'Flank	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	1151	Ala/Asp-rich (DA-box).				DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						GGACGAAGAAGGGGGCTGGCT	0.622																																					p.F1152fs		Atlas-INDEL	.											.	SMC1A	112	.	0			c.3454delT						.						68.0	59.0	62.0					X																	53407993		2203	4300	6503	SO:0001589	frameshift_variant	8243	exon23			.	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"""Structural maintenance of chromosomes proteins"""	11111	protein-coding gene	gene with protein product		300040	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"""	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.3453delC	chrX.hg19:g.53407993delG	ENSP00000323421:p.Pro1151fs	125.0	0.0		125.0	10.0	NM_006306	O14995|Q16351|Q2M228	Frame_Shift_Del	DEL	ENST00000322213.4	hg19	CCDS14352.1																																																																																			.	.		0.622	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306	
DLGAP5	9787	hgsc.bcm.edu	37	14	55625371	55625371	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:55625371delT	ENST00000247191.2	-	14	1958	c.1742delA	c.(1741-1743)aatfs	p.N581fs	DLGAP5_ENST00000395425.2_Frame_Shift_Del_p.N581fs	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	581					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						TCTCATTGCATTTTTTATGGC	0.393																																					p.N581fs		Atlas-INDEL	.											.	DLGAP5	84	.	0			c.1743delT						.						116.0	103.0	107.0					14																	55625371		2202	4300	6502	SO:0001589	frameshift_variant	9787	exon14			.	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.1742delA	chr14.hg19:g.55625371delT	ENSP00000247191:p.Asn581fs	180.0	0.0		205.0	13.0	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Frame_Shift_Del	DEL	ENST00000247191.2	hg19	CCDS9723.1																																																																																			.	.		0.393	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750	
GZMA	3001	hgsc.bcm.edu	37	5	54403626	54403626	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:54403626delA	ENST00000274306.6	+	3	255	c.220delA	c.(220-222)aaafs	p.K74fs		NM_006144.3	NP_006135	P12544	GRAA_HUMAN	granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)	74	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|immune response (GO:0006955)|negative regulation of DNA binding (GO:0043392)|negative regulation of endodeoxyribonuclease activity (GO:0032078)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of apoptotic process (GO:0043065)|proteolysis involved in cellular protein catabolic process (GO:0051603)	extracellular region (GO:0005576)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	25		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				TCTCAGGAACAAAAGGTCCCA	0.378																																					p.N73fs		Atlas-INDEL	.											.	GZMA	60	.	0			c.219delC						.						105.0	101.0	103.0					5																	54403626		2203	4300	6503	SO:0001589	frameshift_variant	3001	exon3			.		CCDS3965.1	5q11-q12	2008-07-18			ENSG00000145649	ENSG00000145649			4708	protein-coding gene	gene with protein product	"""CTL tryptase"", ""Granzyme A (Cytotoxic T-lymphocyte-associated serine esterase-3; Hanukah factor serine protease)"""	140050		HFSP, CTLA3		3262682, 3533635	Standard	NM_006144		Approved		uc003jpm.3	P12544	OTTHUMG00000097011	ENST00000274306.6:c.220delA	chr5.hg19:g.54403626delA	ENSP00000274306:p.Lys74fs	85.0	0.0		163.0	10.0	NM_006144	A4PHN1|Q6IB36	Frame_Shift_Del	DEL	ENST00000274306.6	hg19	CCDS3965.1																																																																																			.	.		0.378	GZMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214100.2	NM_006144	
ZNF701	55762	hgsc.bcm.edu	37	19	53085947	53085947	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:53085947delA	ENST00000540331.1	+	5	1058	c.833delA	c.(832-834)gaafs	p.E278fs	CTD-3099C6.7_ENST00000599222.1_RNA|ZNF701_ENST00000391785.3_Frame_Shift_Del_p.E212fs|ZNF701_ENST00000301093.2_Frame_Shift_Del_p.E278fs	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	278					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(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		CACACAAGAGAAAAATCTTTC	0.348																																					p.E278fs	NSCLC(89;451 1475 9611 20673 52284)	Atlas-INDEL	.											.	ZNF701	44	.	0			c.832delG						.						57.0	60.0	59.0					19																	53085947		2203	4300	6503	SO:0001589	frameshift_variant	55762	exon5			.	AK001753	CCDS33092.1, CCDS54311.1	19q13.41	2013-01-08				ENSG00000167562		"""Zinc fingers, C2H2-type"", ""-"""	25597	protein-coding gene	gene with protein product							Standard	NM_018260		Approved	FLJ10891	uc021uyw.1	Q9NV72		ENST00000540331.1:c.833delA	chr19.hg19:g.53085947delA	ENSP00000444339:p.Glu278fs	91.0	0.0		125.0	10.0	NM_001172655	A2RRM8|B9EGF2|F5GZM6|Q66K42	Frame_Shift_Del	DEL	ENST00000540331.1	hg19	CCDS54311.1																																																																																			.	.		0.348	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260	
ADAMTS3	9508	hgsc.bcm.edu	37	4	73280611	73280611	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:73280611delT	ENST00000286657.4	-	4	618	c.582delA	c.(580-582)aaafs	p.K194fs		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	194					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)			GAATCCTTCCTTTTTCTTCCT	0.403																																					p.G195fs	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-INDEL	.											.	ADAMTS3	164	.	0			c.583delG						.						173.0	166.0	168.0					4																	73280611		2203	4300	6503	SO:0001589	frameshift_variant	9508	exon4			.	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.582delA	chr4.hg19:g.73280611delT	ENSP00000286657:p.Lys194fs	124.0	0.0		156.0	10.0	NM_014243	A1L3U9|Q9BXZ8	Frame_Shift_Del	DEL	ENST00000286657.4	hg19	CCDS3553.1																																																																																			.	.		0.403	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2		
PIEZO2	63895	hgsc.bcm.edu	37	18	10671532	10671532	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:10671532delT	ENST00000503781.3	-	52	8250	c.8251delA	c.(8251-8253)acafs	p.T2751fs	PIEZO2_ENST00000285141.4_Frame_Shift_Del_p.T543fs|PIEZO2_ENST00000538948.1_Frame_Shift_Del_p.T708fs|PIEZO2_ENST00000581680.1_5'Flank|PIEZO2_ENST00000580640.1_Frame_Shift_Del_p.T2776fs|PIEZO2_ENST00000302079.6_Frame_Shift_Del_p.T2688fs	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2751					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										TTTCAATTTGTTTTTTCTCTA	0.338																																					p.T2751fs		Atlas-INDEL	.											.	.	.	.	0			c.8252delC						.						110.0	98.0	102.0					18																	10671532		2203	4300	6503	SO:0001589	frameshift_variant	63895	exon52			.	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"""chromosome 18 open reading frame 30"", ""chromosome 18 open reading frame 58"", ""family with sequence similarity 38, member B"""	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.8251delA	chr18.hg19:g.10671532delT	ENSP00000421377:p.Thr2751fs	163.0	0.0		184.0	12.0	NM_022068	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Frame_Shift_Del	DEL	ENST00000503781.3	hg19																																																																																				.	.		0.338	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068	
IGSF9	57549	hgsc.bcm.edu	37	1	159900106	159900106	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:159900106delG	ENST00000368094.1	-	15	2134	c.1937delC	c.(1936-1938)ccafs	p.P646fs	IGSF9_ENST00000493195.1_5'UTR|IGSF9_ENST00000361509.3_Frame_Shift_Del_p.P630fs	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	646	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			GACCAGCTCTGGGGGATCCCA	0.667																																					p.P646fs		Atlas-INDEL	.											.	IGSF9	123	.	0			c.1938delA						.						83.0	90.0	87.0					1																	159900106		2203	4300	6503	SO:0001589	frameshift_variant	57549	exon15			.	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.1937delC	chr1.hg19:g.159900106delG	ENSP00000357073:p.Pro646fs	62.0	0.0		154.0	10.0	NM_001135050		Frame_Shift_Del	DEL	ENST00000368094.1	hg19	CCDS44254.1																																																																																			.	.		0.667	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789	
ITGAD	3681	hgsc.bcm.edu	37	16	31413551	31413551	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:31413551delG	ENST00000389202.2	+	6	592	c.543delG	c.(541-543)gagfs	p.E181fs	RP11-120K18.2_ENST00000567545.1_RNA	NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	181	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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						GCCAGTTTGAGGGCACTGACA	0.607																																					p.E181fs		Atlas-INDEL	.											.	ITGAD	154	.	0			c.542delA						.						95.0	88.0	90.0					16																	31413551		2197	4300	6497	SO:0001589	frameshift_variant	3681	exon6			.	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.543delG	chr16.hg19:g.31413551delG	ENSP00000373854:p.Glu181fs	143.0	0.0		144.0	10.0	NM_005353	Q15575|Q15576	Frame_Shift_Del	DEL	ENST00000389202.2	hg19	CCDS32438.1																																																																																			.	.		0.607	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
SIMC1	375484	hgsc.bcm.edu	37	5	175740835	175740835	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:175740835delC	ENST00000443967.1	+	7	2226	c.1819delC	c.(1819-1821)cccfs	p.P607fs	SIMC1_ENST00000332772.4_Frame_Shift_Del_p.P68fs|SIMC1_ENST00000341199.6_Frame_Shift_Del_p.P192fs|SIMC1_ENST00000430704.2_Frame_Shift_Del_p.P192fs			Q8NDZ2	SIMC1_HUMAN	SUMO-interacting motifs containing 1	607							SUMO polymer binding (GO:0032184)										TGACAAGCAGCCCCACAATGT	0.542																																					p.Q191fs		Atlas-INDEL	.											.	.	.	.	0			c.573delG						.						85.0	79.0	81.0					5																	175740835		2203	4300	6503	SO:0001589	frameshift_variant	375484	exon4			.	BC037298	CCDS4398.2	5q35.2	2013-08-14	2012-11-14	2012-11-14	ENSG00000170085	ENSG00000170085			24779	protein-coding gene	gene with protein product	"""oocyte maturation associated 1"", ""platform element for inhibition of autolytic degradation"""		"""chromosome 5 open reading frame 25"""	C5orf25		23086935, 23707407	Standard	NM_198567		Approved	FLJ44216, OOMA1, PLEIAD	uc003mds.4	Q8NDZ2	OTTHUMG00000130663	ENST00000443967.1:c.1819delC	chr5.hg19:g.175740835delC	ENSP00000406571:p.Pro607fs	113.0	0.0		171.0	11.0	NM_198567	J3KQQ8|Q6NXN8|Q6ZTU4|Q8IZ15	Frame_Shift_Del	DEL	ENST00000443967.1	hg19																																																																																				.	.		0.542	SIMC1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000253155.2	NM_198567	
METTL17	64745	hgsc.bcm.edu	37	14	21462740	21462740	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:21462740delT	ENST00000339374.6	+	8	969	c.736delT	c.(736-738)tttfs	p.F247fs	RP11-84C10.4_ENST00000557335.1_RNA|METTL17_ENST00000556670.2_Frame_Shift_Del_p.F247fs|METTL17_ENST00000382985.4_Frame_Shift_Del_p.F247fs	NM_001029991.1|NM_022734.2	NP_001025162.1|NP_073571.1	Q9H7H0	MET17_HUMAN	methyltransferase like 17	247					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	copper ion binding (GO:0005507)|methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20						TCCAGGTGTCTTTTTCAGACA	0.418																																					p.V245fs		Atlas-INDEL	.											METTL17,NS,carcinoma,0,1	METTL17	46	.	0			c.735delC						.						148.0	149.0	149.0					14																	21462740		2203	4300	6503	SO:0001589	frameshift_variant	64745	exon8			.	AK024512	CCDS9562.1, CCDS41913.1	14q11.2	2011-03-03	2011-03-02	2011-03-02	ENSG00000165792	ENSG00000165792			19280	protein-coding gene	gene with protein product			"""methyltransferase 11 domain containing 1"""	METT11D1		11278769	Standard	XM_006720235		Approved	FLJ20859	uc001vyn.3	Q9H7H0	OTTHUMG00000029610	ENST00000339374.6:c.736delT	chr14.hg19:g.21462740delT	ENSP00000343041:p.Phe247fs	162.0	0.0		172.0	11.0	NM_022734	Q9BSH1|Q9BZH2|Q9BZH3	Frame_Shift_Del	DEL	ENST00000339374.6	hg19	CCDS9562.1																																																																																			.	.		0.418	METTL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073804.4	NM_022734	
PSMB2	5690	hgsc.bcm.edu	37	1	36101937	36101937	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:36101937delT	ENST00000373237.3	-	2	599	c.188delA	c.(187-189)aacfs	p.N63fs		NM_002794.4	NP_002785.1	P49721	PSB2_HUMAN	proteasome (prosome, macropain) subunit, beta type, 2	63					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)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|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)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|large_intestine(2)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)			Bortezomib(DB00188)|Carfilzomib(DB08889)	AAGTTGCACGTTTTTCTGAAT	0.398																																					p.N63fs		Atlas-INDEL	.											.	PSMB2	9	.	0			c.189delC						.						139.0	132.0	134.0					1																	36101937		2202	4300	6502	SO:0001589	frameshift_variant	5690	exon2			.	D26599	CCDS394.1, CCDS72755.1	1p34.2	2008-02-05			ENSG00000126067	ENSG00000126067		"""Proteasome (prosome, macropain) subunits"""	9539	protein-coding gene	gene with protein product		602175				7918633	Standard	NM_002794		Approved	HC7-I	uc001bzf.2	P49721	OTTHUMG00000004169	ENST00000373237.3:c.188delA	chr1.hg19:g.36101937delT	ENSP00000362334:p.Asn63fs	170.0	0.0		344.0	26.0	NM_002794	D3DPS0|P31145|Q9BWZ9	Frame_Shift_Del	DEL	ENST00000373237.3	hg19	CCDS394.1																																																																																			.	.		0.398	PSMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012016.1	NM_002794	
ACPP	55	hgsc.bcm.edu	37	3	132075605	132075605	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:132075605delC	ENST00000336375.5	+	10	1134	c.1044delC	c.(1042-1044)agcfs	p.S348fs	ACPP_ENST00000475741.1_Frame_Shift_Del_p.S315fs|ACPP_ENST00000351273.7_Frame_Shift_Del_p.S348fs	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	348					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						CTGGCTGCAGCCCCAGCTGTC	0.557																																					p.S348fs		Atlas-INDEL	.											ACPP_ENST00000351273,NS,carcinoma,0,2	ACPP	118	.	0			c.1043delG						.						161.0	141.0	148.0					3																	132075605		2203	4300	6503	SO:0001589	frameshift_variant	55	exon10			.		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.1044delC	chr3.hg19:g.132075605delC	ENSP00000337471:p.Ser348fs	115.0	0.0		165.0	10.0	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Frame_Shift_Del	DEL	ENST00000336375.5	hg19	CCDS3073.1																																																																																			.	.		0.557	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099	
DHX35	60625	hgsc.bcm.edu	37	20	37650554	37650554	+	Frame_Shift_Del	DEL	C	C	-	rs142673637		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:37650554delC	ENST00000252011.3	+	16	1602	c.1569delC	c.(1567-1569)gtcfs	p.V523fs	DHX35_ENST00000373325.2_Frame_Shift_Del_p.V523fs|DHX35_ENST00000373323.4_Frame_Shift_Del_p.V492fs	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	523					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				TCTTTGTGGTCCCCCCAAACC	0.453																																					p.V523fs		Atlas-INDEL	.											.	DHX35	82	.	0			c.1568delT						.						143.0	137.0	139.0					20																	37650554		2203	4300	6503	SO:0001589	frameshift_variant	60625	exon16			.	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"""DEAH-boxes"""	15861	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"""	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.1569delC	chr20.hg19:g.37650554delC	ENSP00000252011:p.Val523fs	187.0	0.0		179.0	12.0	NM_021931	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Frame_Shift_Del	DEL	ENST00000252011.3	hg19	CCDS13310.1																																																																																			.	.		0.453	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931	
ZNF532	55205	hgsc.bcm.edu	37	18	56651255	56651255	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:56651255delC	ENST00000336078.4	+	11	4239	c.3463delC	c.(3463-3465)cccfs	p.P1155fs	ZNF532_ENST00000591808.1_Frame_Shift_Del_p.P1155fs|ZNF532_ENST00000591230.1_Frame_Shift_Del_p.P1155fs|ZNF532_ENST00000588956.1_3'UTR|ZNF532_ENST00000589288.1_Frame_Shift_Del_p.P1155fs|ZNF532_ENST00000591083.1_Frame_Shift_Del_p.P1155fs	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	1155					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						GTTCAGGCCTCCCCGAGGAGC	0.493																																					p.P1154fs		Atlas-INDEL	.											.	ZNF532	108	.	0			c.3462delT						.						77.0	78.0	78.0					18																	56651255		2203	4300	6503	SO:0001589	frameshift_variant	55205	exon11			.	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"""Zinc fingers, C2H2-type"""	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.3463delC	chr18.hg19:g.56651255delC	ENSP00000338217:p.Pro1155fs	223.0	0.0		253.0	16.0	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Frame_Shift_Del	DEL	ENST00000336078.4	hg19	CCDS11969.1																																																																																			.	.		0.493	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181	
LCE2D	353141	hgsc.bcm.edu	37	1	152636615	152636615	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	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	113.0	0.0		146.0	10.0	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	
MNDA	4332	hgsc.bcm.edu	37	1	158813107	158813107	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:158813107delA	ENST00000368141.4	+	3	565	c.304delA	c.(304-306)aaafs	p.K103fs		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	103					B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					AGCTCCAGTGAAAAAAATAAA	0.433																																					p.V101fs		Atlas-INDEL	.											.	MNDA	147	.	0			c.303delG						.						34.0	36.0	36.0					1																	158813107		2203	4299	6502	SO:0001589	frameshift_variant	4332	exon3			.	BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.304delA	chr1.hg19:g.158813107delA	ENSP00000357123:p.Lys103fs	75.0	0.0		116.0	12.0	NM_002432		Frame_Shift_Del	DEL	ENST00000368141.4	hg19	CCDS1177.1																																																																																			.	.		0.433	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432	
NAALAD2	10003	hgsc.bcm.edu	37	11	89883695	89883695	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:89883695delA	ENST00000534061.1	+	5	759	c.529delA	c.(529-531)aaafs	p.K177fs	NAALAD2_ENST00000321955.4_Frame_Shift_Del_p.K177fs|NAALAD2_ENST00000375944.3_Frame_Shift_Del_p.K177fs|NAALAD2_ENST00000525171.1_Frame_Shift_Del_p.K177fs	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	177					neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				AGACTTTTTCAAACTAGAAAG	0.299																																					p.F176fs		Atlas-INDEL	.											.	NAALAD2	113	.	0			c.528delC						.						87.0	93.0	91.0					11																	89883695		2201	4299	6500	SO:0001589	frameshift_variant	10003	exon5			.	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase III"""	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.529delA	chr11.hg19:g.89883695delA	ENSP00000432481:p.Lys177fs	136.0	0.0		166.0	11.0	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Frame_Shift_Del	DEL	ENST00000534061.1	hg19	CCDS8288.1																																																																																			.	.		0.299	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467	
SGSM2	9905	hgsc.bcm.edu	37	17	2282488	2282488	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:2282488delT	ENST00000426855.2	+	22	3098	c.2923delT	c.(2923-2925)tttfs	p.F976fs	RP1-59D14.5_ENST00000574290.1_RNA|SGSM2_ENST00000574563.1_Frame_Shift_Del_p.F976fs|SGSM2_ENST00000268989.3_Frame_Shift_Del_p.F1021fs|RP1-59D14.5_ENST00000573007.1_RNA	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	976					late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		CATCATCAAGTTTTTCAATGG	0.577																																					p.K1019fs		Atlas-INDEL	.											.	SGSM2	60	.	0			c.3057delG						.						189.0	149.0	163.0					17																	2282488		2203	4300	6503	SO:0001589	frameshift_variant	9905	exon23			.	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"""Small G protein signaling modulators"""	29026	protein-coding gene	gene with protein product		611418	"""RUN and TBC1 domain containing 1"""	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.2923delT	chr17.hg19:g.2282488delT	ENSP00000415107:p.Phe976fs	244.0	0.0		200.0	12.0	NM_014853	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Frame_Shift_Del	DEL	ENST00000426855.2	hg19	CCDS45570.1																																																																																			.	.		0.577	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853	
DDX60	55601	hgsc.bcm.edu	37	4	169223484	169223484	+	Frame_Shift_Del	DEL	A	A	-	rs34458540		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:169223484delA	ENST00000393743.3	-	6	981	c.690delT	c.(688-690)tttfs	p.F230fs		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	230					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		TTAAACTTCCAAAAAGAGGTG	0.279																																					p.G231fs		Atlas-INDEL	.											.	DDX60	304	.	0			c.691delG						.						39.0	39.0	39.0					4																	169223484		2197	4291	6488	SO:0001589	frameshift_variant	55601	exon6			.	AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.690delT	chr4.hg19:g.169223484delA	ENSP00000377344:p.Phe230fs	158.0	0.0		152.0	12.0	NM_017631	Q6PK35|Q9NVE3	Frame_Shift_Del	DEL	ENST00000393743.3	hg19	CCDS34097.1																																																																																			.	.		0.279	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631	
HSPG2	3339	hgsc.bcm.edu	37	1	22217107	22217107	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:22217107delG	ENST00000374695.3	-	4	404	c.325delC	c.(325-327)cgafs	p.R109fs		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	109	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GACACCTCTCGGAACTCTCTG	0.592																																					p.R109fs		Atlas-INDEL	.											HSPG2,leg,malignant_melanoma,0,1	HSPG2	311	.	0			c.326delG						.						101.0	104.0	103.0					1																	22217107		2203	4300	6503	SO:0001589	frameshift_variant	3339	exon4			.	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.325delC	chr1.hg19:g.22217107delG	ENSP00000363827:p.Arg109fs	105.0	0.0		174.0	11.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Frame_Shift_Del	DEL	ENST00000374695.3	hg19	CCDS30625.1																																																																																			.	.		0.592	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
KRT16	3868	hgsc.bcm.edu	37	17	39766478	39766478	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:39766478delG	ENST00000301653.4	-	7	1355	c.1291delC	c.(1291-1293)cagfs	p.Q432fs		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	432	Tail.				aging (GO:0007568)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|epidermis development (GO:0008544)|hair cycle (GO:0042633)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of cell migration (GO:0030336)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Breast(137;0.000307)				GATGCTTGCTGGGAGGAAAGG	0.617																																					p.Q431fs		Atlas-INDEL	.											.	KRT16	45	.	0			c.1292delA						.						39.0	41.0	40.0					17																	39766478		2203	4300	6503	SO:0001589	frameshift_variant	3868	exon7			.	S79867	CCDS11401.1	17q21.2	2013-01-16	2008-08-01		ENSG00000186832	ENSG00000186832		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6423	protein-coding gene	gene with protein product	"""focal non-epidermolytic palmoplantar keratoderma"""	148067				2451124, 16831889	Standard	NM_005557		Approved	NEPPK	uc002hxg.4	P08779	OTTHUMG00000133495	ENST00000301653.4:c.1291delC	chr17.hg19:g.39766478delG	ENSP00000301653:p.Gln432fs	187.0	0.0		173.0	11.0	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Frame_Shift_Del	DEL	ENST00000301653.4	hg19	CCDS11401.1																																																																																			.	.		0.617	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557	
PCIF1	63935	hgsc.bcm.edu	37	20	44569759	44569759	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:44569759delC	ENST00000372409.3	+	7	950	c.586delC	c.(586-588)cccfs	p.P197fs		NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	197					negative regulation of phosphatase activity (GO:0010923)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	20						AGAGGTGCTGCCCCCGCATCC	0.612																																					p.L195fs		Atlas-INDEL	.											.	PCIF1	51	.	0			c.585delG						.						50.0	46.0	48.0					20																	44569759		2203	4300	6503	SO:0001589	frameshift_variant	63935	exon7			.	AB050014	CCDS13388.1	20q13.12	2014-06-13	2008-04-29	2008-04-29	ENSG00000100982	ENSG00000100982			16200	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 121"""		"""chromosome 20 open reading frame 67"""	C20orf67		12565871, 15121856	Standard	NM_022104		Approved	bA465L10.1, PPP1R121	uc002xqs.3	Q9H4Z3	OTTHUMG00000032635	ENST00000372409.3:c.586delC	chr20.hg19:g.44569759delC	ENSP00000361486:p.Pro197fs	130.0	0.0		166.0	10.0	NM_022104	E1P5P1|Q54AB9|Q9NT85	Frame_Shift_Del	DEL	ENST00000372409.3	hg19	CCDS13388.1																																																																																			.	.		0.612	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104	
SCN4A	6329	hgsc.bcm.edu	37	17	62021202	62021202	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:62021202delC	ENST00000435607.1	-	22	3997	c.3921delG	c.(3919-3921)gggfs	p.G1307fs	SCN4A_ENST00000578147.1_Frame_Shift_Del_p.G1307fs	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1307					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)	AGATGTCTTTCCCCCCTAAGT	0.537																																					p.K1308fs		Atlas-INDEL	.											.	SCN4A	205	.	0			c.3922delA						.						68.0	70.0	69.0					17																	62021202		2139	4276	6415	SO:0001589	frameshift_variant	6329	exon22			.	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.3921delG	chr17.hg19:g.62021202delC	ENSP00000396320:p.Gly1307fs	176.0	0.0		251.0	17.0	NM_000334	Q15478|Q16447|Q7Z6B1	Frame_Shift_Del	DEL	ENST00000435607.1	hg19	CCDS45761.1																																																																																			.	.		0.537	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
PRKRIR	5612	hgsc.bcm.edu	37	11	76066662	76066662	+	Splice_Site	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76066662delT	ENST00000260045.3	-	4	460	c.355delA	c.(355-357)att>tt	p.I119fs	PRKRIR_ENST00000531878.1_5'UTR	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	119					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						TATCACTTACTTTTTTTCTGT	0.318																																					.		Atlas-INDEL	.											.	PRKRIR	65	.	0			c.355+1A>-						.						172.0	157.0	162.0					11																	76066662		2196	4291	6487	SO:0001630	splice_region_variant	5612	exon5			.	AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"""THAP (C2CH-type zinc finger) domain containing"""	9440	protein-coding gene	gene with protein product	"""THAP domain containing 12"""	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.355+1A>-	chr11.hg19:g.76066662delT		82.0	0.0		120.0	12.0	NM_004705	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Splice_Site	DEL	ENST00000260045.3	hg19	CCDS8243.1																																																																																			.	.		0.318	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705	Frame_Shift_Del
SRSF4	6429	hgsc.bcm.edu	37	1	29475675	29475675	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:29475675delT	ENST00000373795.4	-	6	966	c.732delA	c.(730-732)aaafs	p.K244fs	SRSF4_ENST00000546138.1_Frame_Shift_Del_p.R143fs|SRSF4_ENST00000466448.1_5'UTR|RP11-242O24.3_ENST00000413004.1_lincRNA	NM_005626.4	NP_005617.2	Q08170	SRSF4_HUMAN	serine/arginine-rich splicing factor 4	244	Arg/Ser-rich (RS domain).				gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|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)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(1)	27						TGCTTTTCTCTTTCTTgctcc	0.597																																					p.E245fs		Atlas-INDEL	.											.	SRSF4	44	.	0			c.733delG						.						66.0	77.0	73.0					1																	29475675		2202	4300	6502	SO:0001589	frameshift_variant	6429	exon6			.	BC002781	CCDS333.1	1p35.3	2013-02-12	2010-06-22	2010-06-22	ENSG00000116350	ENSG00000116350		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10786	protein-coding gene	gene with protein product	"""SR splicing factor 4"""	601940	"""splicing factor, arginine/serine-rich 4"""	SFRS4		8321209, 20516191	Standard	NM_005626		Approved	SRP75	uc001bro.3	Q08170	OTTHUMG00000003663	ENST00000373795.4:c.732delA	chr1.hg19:g.29475675delT	ENSP00000362900:p.Lys244fs	106.0	0.0		166.0	10.0	NM_005626	Q5VXP1|Q9BUA4|Q9UEB5	Frame_Shift_Del	DEL	ENST00000373795.4	hg19	CCDS333.1																																																																																			.	.		0.597	SRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010392.1	NM_005626	
N4BP1	9683	hgsc.bcm.edu	37	16	48596281	48596281	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:48596281delA	ENST00000262384.3	-	2	509	c.273delT	c.(271-273)tttfs	p.F91fs	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	91					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				CTGCCCCAACAAAAATGCAGT	0.418																																					p.V92fs		Atlas-INDEL	.											.	N4BP1	121	.	0			c.274delG						.						51.0	52.0	51.0					16																	48596281		1917	4121	6038	SO:0001589	frameshift_variant	9683	exon2			.	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.273delT	chr16.hg19:g.48596281delA	ENSP00000262384:p.Phe91fs	126.0	0.0		142.0	10.0	NM_153029	A7MD49|Q2YDX1	Frame_Shift_Del	DEL	ENST00000262384.3	hg19	CCDS45479.1																																																																																			.	.		0.418	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664	
PLCB4	5332	hgsc.bcm.edu	37	20	9352974	9352974	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:9352974delT	ENST00000378493.1	+	8	625	c.610delT	c.(610-612)tttfs	p.F204fs	PLCB4_ENST00000378501.2_Frame_Shift_Del_p.F204fs|PLCB4_ENST00000378473.3_Frame_Shift_Del_p.F204fs|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000334005.3_Frame_Shift_Del_p.F204fs|PLCB4_ENST00000278655.4_Frame_Shift_Del_p.F204fs|PLCB4_ENST00000414679.2_Frame_Shift_Del_p.F204fs			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	204					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						GCCCACAGCATTTTCTTATGA	0.363																																					p.A203fs		Atlas-INDEL	.											.	PLCB4	204	.	0			c.609delA						.						79.0	81.0	80.0					20																	9352974		2202	4300	6502	SO:0001589	frameshift_variant	5332	exon9			.		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.610delT	chr20.hg19:g.9352974delT	ENSP00000367754:p.Phe204fs	239.0	0.0		215.0	13.0	NM_182797	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Frame_Shift_Del	DEL	ENST00000378493.1	hg19	CCDS13105.1																																																																																			.	.		0.363	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2		
WDFY4	57705	hgsc.bcm.edu	37	10	50015979	50015979	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:50015979delC	ENST00000325239.5	+	27	4841	c.4814delC	c.(4813-4815)tccfs	p.S1605fs	WDFY4_ENST00000413659.2_Frame_Shift_Del_p.F1035fs	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1605						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						GTAATATCTTCCCCCCAGCTT	0.443																																					p.S1605fs		Atlas-INDEL	.											.	WDFY4	205	.	0			c.4813delT						.						114.0	107.0	109.0					10																	50015979		692	1591	2283	SO:0001589	frameshift_variant	57705	exon28			.	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.4814delC	chr10.hg19:g.50015979delC	ENSP00000320563:p.Ser1605fs	128.0	0.0		151.0	10.0	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Frame_Shift_Del	DEL	ENST00000325239.5	hg19	CCDS44385.1																																																																																			.	.		0.443	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
DOCK10	55619	hgsc.bcm.edu	37	2	225695297	225695297	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:225695297delT	ENST00000258390.7	-	27	3064	c.2997delA	c.(2995-2997)aaafs	p.K999fs	DOCK10_ENST00000409592.3_Frame_Shift_Del_p.K993fs	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	999					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GTGCCATCGATTTTAGGATAA	0.284																																					p.S1000fs		Atlas-INDEL	.											.	DOCK10	308	.	0			c.2998delT						.																																			SO:0001589	frameshift_variant	55619	exon27			.	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.2997delA	chr2.hg19:g.225695297delT	ENSP00000258390:p.Lys999fs	182.0	0.0		163.0	11.0	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Frame_Shift_Del	DEL	ENST00000258390.7	hg19	CCDS46528.1																																																																																			.	.		0.284	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
PLCG1	5335	hgsc.bcm.edu	37	20	39798114	39798114	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:39798114delC	ENST00000373271.1	+	23	3003	c.2598delC	c.(2596-2598)agcfs	p.S866fs	PLCG1_ENST00000244007.3_Frame_Shift_Del_p.S866fs|PLCG1_ENST00000373272.2_Frame_Shift_Del_p.S866fs	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	866					activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|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)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				ACGAGAACAGCCCCCTAGGGG	0.552																																					p.S866fs		Atlas-INDEL	.											.	PLCG1	111	.	0			c.2597delG						.						163.0	160.0	161.0					20																	39798114		2203	4300	6503	SO:0001589	frameshift_variant	5335	exon23			.	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"", ""SH2 domain containing"""	9065	protein-coding gene	gene with protein product		172420	"""phospholipase C, gamma 1 (formerly subtype 148)"""	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.2598delC	chr20.hg19:g.39798114delC	ENSP00000362368:p.Ser866fs	176.0	0.0		174.0	11.0	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Frame_Shift_Del	DEL	ENST00000373271.1	hg19	CCDS13314.1																																																																																			.	.		0.552	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811	
IL31RA	133396	hgsc.bcm.edu	37	5	55168109	55168109	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:55168109delA	ENST00000447346.2	+	4	349	c.284delA	c.(283-285)gaafs	p.E95fs	IL31RA_ENST00000490985.1_5'UTR|IL31RA_ENST00000354961.4_Frame_Shift_Del_p.E76fs|IL31RA_ENST00000396834.1_Frame_Shift_Del_p.E76fs|IL31RA_ENST00000297015.3_5'UTR|IL31RA_ENST00000359040.5_Frame_Shift_Del_p.E95fs|IL31RA_ENST00000396836.2_Frame_Shift_Del_p.E95fs	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	63	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				GCTTTTGGAGAAAAACATGAT	0.313																																					p.E95fs		Atlas-INDEL	.											.	IL31RA	84	.	0			c.283delG						.						53.0	57.0	55.0					5																	55168109		2203	4299	6502	SO:0001589	frameshift_variant	133396	exon4			.	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.284delA	chr5.hg19:g.55168109delA	ENSP00000415900:p.Glu95fs	106.0	0.0		164.0	11.0	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Frame_Shift_Del	DEL	ENST00000447346.2	hg19	CCDS3970.2																																																																																			.	.		0.313	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017	
SLC6A14	11254	hgsc.bcm.edu	37	X	115573885	115573885	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:115573885delT	ENST00000371900.4	+	4	465	c.377delT	c.(376-378)attfs	p.I126fs		NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	126					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)	CTGATCTCCATTTTTGTGACA	0.299																																					p.I126fs		Atlas-INDEL	.											.	SLC6A14	56	.	0			c.376delA						.						139.0	133.0	135.0					X																	115573885		2203	4299	6502	SO:0001589	frameshift_variant	11254	exon4			.	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.377delT	chrX.hg19:g.115573885delT	ENSP00000360967:p.Ile126fs	104.0	0.0		121.0	10.0	NM_007231	Q5H942	Frame_Shift_Del	DEL	ENST00000371900.4	hg19	CCDS14570.1																																																																																			.	.		0.299	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1		
ZNF334	55713	hgsc.bcm.edu	37	20	45131438	45131438	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:45131438delT	ENST00000347606.4	-	5	722	c.540delA	c.(538-540)aaafs	p.K180fs	ZNF334_ENST00000593880.1_Frame_Shift_Del_p.K203fs|ZNF334_ENST00000457685.2_Frame_Shift_Del_p.K142fs	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	180					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(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				TGTATCTGTATTTTTTCATTC	0.338																																					p.Y181fs		Atlas-INDEL	.											.	ZNF334	101	.	0			c.541delT						.						95.0	91.0	92.0					20																	45131438		2203	4300	6503	SO:0001589	frameshift_variant	55713	exon5			.	AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"""Zinc fingers, C2H2-type"", ""-"""	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.540delA	chr20.hg19:g.45131438delT	ENSP00000255129:p.Lys180fs	185.0	0.0		197.0	12.0	NM_018102	Q5T6U2|Q9NVW4	Frame_Shift_Del	DEL	ENST00000347606.4	hg19	CCDS33480.1																																																																																			.	.		0.338	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1		
SPON2	10417	hgsc.bcm.edu	37	4	1165676	1165676	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:1165676delG	ENST00000290902.5	-	2	516	c.184delC	c.(184-186)ctgfs	p.L62fs	SPON2_ENST00000431380.1_Frame_Shift_Del_p.L62fs	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	62	Spondin. {ECO:0000255|PROSITE- ProRule:PRU00364}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		GGGCGGAACAGGGGGTACTGC	0.672																																					p.L62fs		Atlas-INDEL	.											.	SPON2	22	.	0			c.185delT						.						55.0	76.0	69.0					4																	1165676		2189	4287	6476	SO:0001589	frameshift_variant	10417	exon2			.	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"""Mindin"", ""M-spondin"""	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.184delC	chr4.hg19:g.1165676delG	ENSP00000290902:p.Leu62fs	95.0	0.0		159.0	10.0	NM_012445	D3DVN9|Q4W5N4|Q9ULW1	Frame_Shift_Del	DEL	ENST00000290902.5	hg19	CCDS3347.1																																																																																			.	.		0.672	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2		
ZNF292	23036	hgsc.bcm.edu	37	6	87970974	87970974	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:87970974delA	ENST00000369577.3	+	8	7670	c.7627delA	c.(7627-7629)aaafs	p.K2544fs	ZNF292_ENST00000339907.4_Frame_Shift_Del_p.K2539fs	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	2544						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)		CTCACAAAATAAAAAAAGGAA	0.358																																					p.N2542fs		Atlas-INDEL	.											.	ZNF292	479	.	0			c.7626delT						.						42.0	41.0	41.0					6																	87970974		1820	4073	5893	SO:0001589	frameshift_variant	23036	exon8			.	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.7627delA	chr6.hg19:g.87970974delA	ENSP00000358590:p.Lys2544fs	76.0	0.0		100.0	11.0	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Frame_Shift_Del	DEL	ENST00000369577.3	hg19	CCDS47457.1																																																																																			.	.		0.358	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021	
MAML1	9794	hgsc.bcm.edu	37	5	179193024	179193024	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:179193024delC	ENST00000292599.3	+	2	1276	c.1013delC	c.(1012-1014)tccfs	p.S338fs	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGTACAGATTCCCCCAGCCTA	0.617																																					p.S338fs		Atlas-INDEL	.											.	MAML1	118	.	0			c.1012delT						.						31.0	34.0	33.0					5																	179193024		2203	4300	6503	SO:0001589	frameshift_variant	9794	exon2			.	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"""mastermind homolog"""	605424	"""mastermind (drosophila)-like 1"""			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.1013delC	chr5.hg19:g.179193024delC	ENSP00000292599:p.Ser338fs	69.0	0.0		144.0	10.0	NM_014757		Frame_Shift_Del	DEL	ENST00000292599.3	hg19	CCDS34315.1																																																																																			.	.		0.617	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757	
NASP	4678	hgsc.bcm.edu	37	1	46073055	46073055	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:46073055delA	ENST00000350030.3	+	6	559	c.472delA	c.(472-474)aaafs	p.K159fs	NASP_ENST00000537798.1_Frame_Shift_Del_p.K95fs|NASP_ENST00000372052.4_Intron|NASP_ENST00000402363.3_Frame_Shift_Del_p.K161fs|NASP_ENST00000351223.3_Intron	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	159	Glu-rich (acidic).			K -> T (in Ref. 3; BAD96536). {ECO:0000305}.	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)					AGAAGAAGCCAAAAAAACAGA	0.393																																					p.A157fs		Atlas-INDEL	.											.	NASP	77	.	0			c.471delC						.						55.0	56.0	56.0					1																	46073055		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.472delA	chr1.hg19:g.46073055delA	ENSP00000255120:p.Lys159fs	138.0	0.0		238.0	17.0	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	
COL5A1	1289	hgsc.bcm.edu	37	9	137593113	137593113	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:137593113delC	ENST00000371817.3	+	4	1002	c.588delC	c.(586-588)cacfs	p.H196fs	COL5A1_ENST00000464187.1_3'UTR	NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	196	Laminin G-like.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GCAGCGACCACCCCATGATCG	0.542																																					p.H196fs		Atlas-INDEL	.											.	COL5A1	323	.	0			c.587delA						.						169.0	124.0	139.0					9																	137593113		2203	4300	6503	SO:0001589	frameshift_variant	1289	exon4			.	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.588delC	chr9.hg19:g.137593113delC	ENSP00000360882:p.His196fs	178.0	0.0		192.0	13.0	NM_000093	Q15094|Q5SUX4	Frame_Shift_Del	DEL	ENST00000371817.3	hg19	CCDS6982.1																																																																																			.	.		0.542	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
PPA1	5464	hgsc.bcm.edu	37	10	71977640	71977640	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:71977640delT	ENST00000373232.3	-	4	324	c.225delA	c.(223-225)aaafs	p.K75fs	PPA1_ENST00000608321.1_Frame_Shift_Del_p.K75fs|PPA1_ENST00000495346.1_5'Flank	NM_021129.3	NP_066952.1	Q15181	IPYR_HUMAN	pyrophosphatase (inorganic) 1	75					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						GAAGTTTTCCTTTTTTCACAT	0.353																																					p.G76fs		Atlas-INDEL	.											.	PPA1	24	.	0			c.226delG						.						100.0	93.0	96.0					10																	71977640		2203	4300	6503	SO:0001589	frameshift_variant	5464	exon4			.	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.225delA	chr10.hg19:g.71977640delT	ENSP00000362329:p.Lys75fs	137.0	0.0		148.0	11.0	NM_021129	Q2M348|Q5SQT7|Q6P7P4|Q9UQJ5|Q9Y5B1	Frame_Shift_Del	DEL	ENST00000373232.3	hg19	CCDS7299.1																																																																																			.	.		0.353	PPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048490.2	NM_021129	
CCDC109B	55013	hgsc.bcm.edu	37	4	110605773	110605773	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:110605773delT	ENST00000394650.4	+	6	920	c.787delT	c.(787-789)tttfs	p.F264fs		NM_017918.4	NP_060388.2	Q9NWR8	MCUB_HUMAN	coiled-coil domain containing 109B	264					mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)	calcium channel complex (GO:0034704)|integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of membrane (GO:0031224)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium channel inhibitor activity (GO:0019855)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(1)	9				OV - Ovarian serous cystadenocarcinoma(123;6.65e-06)		TTCTATGGTCTTTTTTGCATA	0.423																																					p.V262fs		Atlas-INDEL	.											.	CCDC109B	47	.	0			c.786delC						.						189.0	175.0	180.0					4																	110605773		2203	4300	6503	SO:0001589	frameshift_variant	55013	exon6			.	BC002633	CCDS3683.2	4q25	2011-05-24			ENSG00000005059	ENSG00000005059			26076	protein-coding gene	gene with protein product						12477932	Standard	NM_017918		Approved	FLJ20647	uc011cfs.2	Q9NWR8	OTTHUMG00000161103	ENST00000394650.4:c.787delT	chr4.hg19:g.110605773delT	ENSP00000378145:p.Phe264fs	156.0	0.0		107.0	10.0	NM_017918	A8K4Y3|Q6IAC1	Frame_Shift_Del	DEL	ENST00000394650.4	hg19	CCDS3683.2																																																																																			.	.		0.423	CCDC109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254865.1	NM_017918	
TARS2	80222	hgsc.bcm.edu	37	1	150469064	150469064	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:150469064delG	ENST00000369064.3	+	8	915	c.881delG	c.(880-882)aggfs	p.R294fs	TARS2_ENST00000463555.1_Intron|TARS2_ENST00000438568.2_3'UTR|TARS2_ENST00000606933.1_Intron|TARS2_ENST00000369054.2_Intron	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	294					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	GAAGCATGGAGGGAGGAAGCA	0.542																																					p.R294fs		Atlas-INDEL	.											.	TARS2	91	.	0			c.880delA						.						131.0	125.0	127.0					1																	150469064		2203	4300	6503	SO:0001589	frameshift_variant	80222	exon8			.	BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"""Aminoacyl tRNA synthetases / Class II"""	30740	protein-coding gene	gene with protein product	"""threonine tRNA ligase 2, mitochondrial"""	612805	"""threonyl-tRNA synthetase-like 1"""	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.881delG	chr1.hg19:g.150469064delG	ENSP00000358060:p.Arg294fs	121.0	0.0		216.0	14.0	NM_025150	Q53GW7|Q96I50|Q9H9V2	Frame_Shift_Del	DEL	ENST00000369064.3	hg19	CCDS952.1																																																																																			.	.		0.542	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150	
TPP2	7174	hgsc.bcm.edu	37	13	103326668	103326668	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:103326668delC	ENST00000376065.4	+	27	3404	c.3368delC	c.(3367-3369)gccfs	p.A1123fs	TPP2_ENST00000466153.1_3'UTR|TPP2_ENST00000376052.3_Frame_Shift_Del_p.A1136fs	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	1123					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)			breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CTCGTAGATGCCCTTTGTAGG	0.413																																					p.A1123fs		Atlas-INDEL	.											.	TPP2	124	.	0			c.3367delG						.						103.0	95.0	98.0					13																	103326668		2203	4300	6503	SO:0001589	frameshift_variant	7174	exon27			.	M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.3368delC	chr13.hg19:g.103326668delC	ENSP00000365233:p.Ala1123fs	91.0	0.0		162.0	10.0	NM_003291	Q5VZU8	Frame_Shift_Del	DEL	ENST00000376065.4	hg19	CCDS9502.1																																																																																			.	.		0.413	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2		
MSI1	4440	hgsc.bcm.edu	37	12	120784098	120784098	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:120784098delG	ENST00000257552.2	-	13	975	c.887delC	c.(886-888)cctfs	p.P297fs		NM_002442.3	NP_002433.1	O43347	MSI1H_HUMAN	musashi RNA-binding protein 1	297					epithelial cell differentiation (GO:0030855)|nervous system development (GO:0007399)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			breast(4)|central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(5)|skin(2)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGAACCTGGAGGGGGAGCCAT	0.697																																					p.P296fs		Atlas-INDEL	.											.	MSI1	40	.	0			c.888delT						.						11.0	9.0	10.0					12																	120784098		2124	4206	6330	SO:0001589	frameshift_variant	4440	exon13			.	AB012851	CCDS9196.1	12q24	2013-07-16	2012-12-13					"""RNA binding motif (RRM) containing"""	7330	protein-coding gene	gene with protein product		603328	"""Musashi (Drosophila) homolog 1"", ""musashi homolog 1 (Drosophila)"""			9790759	Standard	NM_002442		Approved		uc001tye.2	O43347	OTTHUMG00000169344	ENST00000257552.2:c.887delC	chr12.hg19:g.120784098delG	ENSP00000257552:p.Pro297fs	64.0	0.0		151.0	11.0	NM_002442	Q96PU0|Q96PU1|Q96PU2|Q96PU3	Frame_Shift_Del	DEL	ENST00000257552.2	hg19	CCDS9196.1																																																																																			.	.		0.697	MSI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403629.1	NM_002442	
TCP11	6954	hgsc.bcm.edu	37	6	35096919	35096919	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:35096919delA	ENST00000512012.1	-	3	433	c.277delT	c.(277-279)tggfs	p.W93fs	TCP11_ENST00000412155.2_Frame_Shift_Del_p.W55fs|TCP11_ENST00000510465.1_5'UTR|TCP11_ENST00000311875.5_Frame_Shift_Del_p.W106fs|TCP11_ENST00000418521.2_Frame_Shift_Del_p.W30fs|TCP11_ENST00000244645.3_Frame_Shift_Del_p.W31fs|TCP11_ENST00000444780.2_Frame_Shift_Del_p.W101fs|TCP11_ENST00000373979.2_Frame_Shift_Del_p.W31fs|TCP11_ENST00000373974.4_Frame_Shift_Del_p.W60fs			Q8WWU5	TCP11_HUMAN	t-complex 11, testis-specific	93					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				breast(1)|kidney(5)|large_intestine(3)|lung(10)|ovary(3)|prostate(1)|skin(4)	27						AGATGGTCCCAAAAGGCATTG	0.428																																					p.W106fs		Atlas-INDEL	.											.	TCP11	94	.	0			c.317delG						.						159.0	133.0	142.0					6																	35096919		2203	4300	6503	SO:0001589	frameshift_variant	6954	exon4			.		CCDS4799.1, CCDS47413.1, CCDS59015.1, CCDS59016.1, CCDS59017.1, CCDS59018.1	6p21.31	2012-09-20	2012-09-20		ENSG00000124678	ENSG00000124678			11658	protein-coding gene	gene with protein product	"""fertilization-promoting peptide receptor"""	186982	"""t-complex 11 (a murine tcp homolog)"", ""t-complex 11 homolog (mouse)"""	D6S230E		1427894, 11756566, 21597245	Standard	NM_001093728		Approved	KIAA0229, FPPR	uc003okd.2	Q8WWU5	OTTHUMG00000014560	ENST00000512012.1:c.277delT	chr6.hg19:g.35096919delA	ENSP00000425995:p.Trp93fs	135.0	0.0		181.0	12.0	NM_001093728	B2RCE9|B3KQ27|B7Z7B5|B7Z7G1|B7Z7H4|B7Z7S8|E7EP29|J3KNG1|Q8NF85|Q9NQZ9|Q9NR39	Frame_Shift_Del	DEL	ENST00000512012.1	hg19																																																																																				.	.		0.428	TCP11-014	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000370354.1	NM_001093728	
SLC43A3	29015	hgsc.bcm.edu	37	11	57193097	57193097	+	Frame_Shift_Del	DEL	C	C	-	rs571852590		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:57193097delC	ENST00000395123.2	-	4	535	c.231delG	c.(229-231)gggfs	p.G77fs	SLC43A3_ENST00000529554.1_Frame_Shift_Del_p.G77fs|SLC43A3_ENST00000352187.1_Frame_Shift_Del_p.G77fs|SLC43A3_ENST00000528098.1_5'UTR|SLC43A3_ENST00000395124.1_Frame_Shift_Del_p.G77fs|SLC43A3_ENST00000533524.1_Frame_Shift_Del_p.G90fs	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	77					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						TCATGAAGGACCCCAGGGTGA	0.522																																					p.S78fs		Atlas-INDEL	.											.	SLC43A3	54	.	0			c.232delT						.						116.0	104.0	108.0					11																	57193097		2201	4296	6497	SO:0001589	frameshift_variant	29015	exon4			.	AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"""Solute carriers"""	17466	protein-coding gene	gene with protein product	"""likely ortholog of mouse embryonic epithelial gene 1"""					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.231delG	chr11.hg19:g.57193097delC	ENSP00000378555:p.Gly77fs	134.0	0.0		155.0	13.0	NM_014096	B4DNR8|E7EQD2|Q9NSS4	Frame_Shift_Del	DEL	ENST00000395123.2	hg19	CCDS7956.1																																																																																			.	.		0.522	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611	
TRANK1	9881	hgsc.bcm.edu	37	3	36897154	36897154	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:36897154delA	ENST00000429976.2	-	12	4174	c.3927delT	c.(3925-3927)tttfs	p.F1309fs	TRANK1_ENST00000301807.6_Frame_Shift_Del_p.F759fs|TRANK1_ENST00000428977.2_Frame_Shift_Del_p.F759fs	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1309							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						AACCCTTTAGAAAAGATTTTA	0.433																																					p.L1310X		Atlas-INDEL	.											.	TRANK1	398	.	0			c.3928delC						.						118.0	116.0	117.0					3																	36897154		1829	4083	5912	SO:0001589	frameshift_variant	9881	exon12			.	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29011	protein-coding gene	gene with protein product	"""lupus brain antigen 1"", ""KIAA0342"""					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.3927delT	chr3.hg19:g.36897154delA	ENSP00000416168:p.Phe1309fs	118.0	0.0		170.0	12.0	NM_014831	Q8N8K0	Frame_Shift_Del	DEL	ENST00000429976.2	hg19	CCDS46789.2																																																																																			.	.		0.433	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
EIF4G2	1982	hgsc.bcm.edu	37	11	10822385	10822385	+	Intron	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:10822385delA	ENST00000526148.1	-	16	2050				EIF4G2_ENST00000525681.1_Intron|EIF4G2_ENST00000339995.5_Intron|RP11-685M7.5_ENST00000532365.1_RNA|EIF4G2_ENST00000396525.2_Intron|SNORD97_ENST00000459187.1_RNA	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2											NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		TGAGGTGTCTAAAAAACAAGC	0.378																																					.		Atlas-INDEL	.											.	EIF4G2	89	.	0			c.1540-2T>-						.						95.0	92.0	93.0					11																	10822385		2201	4294	6495	SO:0001627	intron_variant	1982	exon17			.	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.1540-3T>-	chr11.hg19:g.10822385delA		83.0	0.0		157.0	10.0	NM_001172705		Splice_Site	DEL	ENST00000526148.1	hg19	CCDS31428.1																																																																																			.	.		0.378	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418	
ADNP	23394	hgsc.bcm.edu	37	20	49508560	49508560	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:49508560delA	ENST00000396029.3	-	5	3258	c.2691delT	c.(2689-2691)tttfs	p.F897fs	ADNP_ENST00000371602.4_Frame_Shift_Del_p.F897fs|ADNP_ENST00000396032.3_Frame_Shift_Del_p.F897fs|ADNP_ENST00000349014.3_Frame_Shift_Del_p.F897fs	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	897					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						GTTCAACTTCAAAAACAGGGT	0.403																																					p.E898fs		Atlas-INDEL	.											.	ADNP	106	.	0			c.2692delG						.						143.0	144.0	144.0					20																	49508560		2203	4300	6503	SO:0001589	frameshift_variant	23394	exon5			.	AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"""Homeoboxes / ZF class"""	15766	protein-coding gene	gene with protein product	"""ADNP homeobox 1"""	611386	"""activity-dependent neuroprotector"""			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.2691delT	chr20.hg19:g.49508560delA	ENSP00000379346:p.Phe897fs	109.0	0.0		144.0	10.0	NM_015339	E1P5Y2|O94881|Q5BKU2|Q9UG34	Frame_Shift_Del	DEL	ENST00000396029.3	hg19	CCDS13433.1																																																																																			.	.		0.403	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442	
TLDC1	57707	hgsc.bcm.edu	37	16	84520325	84520325	+	Frame_Shift_Del	DEL	T	T	-	rs431389	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	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	151.0	0.0		156.0	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	
IKBIP	121457	hgsc.bcm.edu	37	12	99020228	99020228	+	Intron	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:99020228delA	ENST00000342502.2	-	2	709				IKBIP_ENST00000420861.1_Intron|IKBIP_ENST00000299157.4_Frame_Shift_Del_p.L205fs|IKBIP_ENST00000393042.3_Intron	NM_201612.2	NP_963906.1	Q70UQ0	IKIP_HUMAN	IKBKB interacting protein						response to X-ray (GO:0010165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	6						GCTATCTTCCAAATCTTTTAG	0.363																																					p.L205fs		Atlas-INDEL	.											.	IKBIP	46	.	0			c.615delG						.						143.0	136.0	139.0					12																	99020228		2203	4300	6503	SO:0001627	intron_variant	121457	exon3			.	AJ539425	CCDS9067.1, CCDS9068.1, CCDS41822.1	12q23.1	2010-02-17			ENSG00000166130	ENSG00000166130			26430	protein-coding gene	gene with protein product	"""I kappa B kinase interacting protein"""	609861				15389287	Standard	NM_153687		Approved	FLJ31051, IKIP	uc001tfx.4	Q70UQ0	OTTHUMG00000170213	ENST00000342502.2:c.297+7845T>-	chr12.hg19:g.99020228delA		97.0	0.0		165.0	10.0	NM_153687	Q6ZWH4|Q70UP9|Q86V91|Q96ND2	Frame_Shift_Del	DEL	ENST00000342502.2	hg19	CCDS9067.1																																																																																			.	.		0.363	IKBIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408003.2	NM_153687	
ZFHX4	79776	hgsc.bcm.edu	37	8	77775609	77775609	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:77775609delA	ENST00000521891.2	+	11	10107	c.9659delA	c.(9658-9660)gaafs	p.E3220fs	ZFHX4_ENST00000050961.6_Frame_Shift_Del_p.E3171fs|ZFHX4_ENST00000455469.2_Frame_Shift_Del_p.E3175fs|ZFHX4_ENST00000518282.1_Frame_Shift_Del_p.E3194fs	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3171					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAAAAAGAGGAAAAAATCTCA	0.403										HNSCC(33;0.089)																											p.E3220fs		Atlas-INDEL	.											.	ZFHX4	878	.	0			c.9658delG						.						130.0	126.0	128.0					8																	77775609		1864	4098	5962	SO:0001589	frameshift_variant	79776	exon11			.		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.9659delA	chr8.hg19:g.77775609delA	ENSP00000430497:p.Glu3220fs	67.0	0.0		246.0	15.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Frame_Shift_Del	DEL	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.		0.403	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
CDCA3	83461	hgsc.bcm.edu	37	12	6958537	6958537	+	Frame_Shift_Del	DEL	G	G	-	rs142590132		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:6958537delG	ENST00000538862.2	-	5	1502	c.601delC	c.(601-603)ctcfs	p.L201fs	CDCA3_ENST00000422785.3_Intron|USP5_ENST00000389231.5_5'Flank|CDCA3_ENST00000604599.1_5'Flank|CDCA3_ENST00000540683.1_Intron|CDCA3_ENST00000229265.6_Frame_Shift_Del_p.L176fs|CDCA3_ENST00000535406.1_Frame_Shift_Del_p.L201fs|USP5_ENST00000229268.8_5'Flank			Q99618	CDCA3_HUMAN	cell division cycle associated 3	201					mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|large_intestine(4)|lung(1)|stomach(1)	8						AGGATGGTGAGGGGGGATCTC	0.512																																					p.L201fs		Atlas-INDEL	.											.	CDCA3	17	.	0			c.602delT						.						164.0	158.0	160.0					12																	6958537		2203	4300	6503	SO:0001589	frameshift_variant	83461	exon5			.	BG354576	CCDS8565.1, CCDS73428.1	12p13.31	2010-07-20				ENSG00000111665			14624	protein-coding gene	gene with protein product	"""trigger of mitotic entry 1"""	607749				9074930, 12188893	Standard	XR_242988		Approved	TOME-1, GRCC8	uc001qrg.2	Q99618		ENST00000538862.2:c.601delC	chr12.hg19:g.6958537delG	ENSP00000442068:p.Leu201fs	247.0	0.0		200.0	13.0	NM_031299	A8K5V6|D3DUS6	Frame_Shift_Del	DEL	ENST00000538862.2	hg19	CCDS8565.1																																																																																			.	.		0.512	CDCA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401940.2	NM_031299	
HELLS	3070	hgsc.bcm.edu	37	10	96336531	96336531	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:96336531delA	ENST00000348459.5	+	10	1106	c.1001delA	c.(1000-1002)gaafs	p.E334fs	RP11-119K6.6_ENST00000432120.1_RNA|HELLS_ENST00000239026.6_3'UTR|HELLS_ENST00000371332.4_Frame_Shift_Del_p.E334fs|HELLS_ENST00000394045.1_Frame_Shift_Del_p.E334fs|HELLS_ENST00000394044.1_Intron|HELLS_ENST00000394036.1_3'UTR	NM_018063.3	NP_060533.2			helicase, lymphoid-specific											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		ACGTCATTTGAAATAGCCATG	0.348																																					p.E334fs		Atlas-INDEL	.											.	HELLS	63	.	0			c.1000delG						.						141.0	129.0	133.0					10																	96336531		2203	4300	6503	SO:0001589	frameshift_variant	3070	exon10			.	AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"""SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6"", ""proliferation-associated SNF2-like protein"""	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.1001delA	chr10.hg19:g.96336531delA	ENSP00000239027:p.Glu334fs	157.0	0.0		184.0	12.0	NM_018063		Frame_Shift_Del	DEL	ENST00000348459.5	hg19	CCDS7434.1																																																																																			.	.		0.348	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063	
GLO1	2739	hgsc.bcm.edu	37	6	38654690	38654690	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:38654690delA	ENST00000373365.4	-	2	231	c.145delT	c.(145-147)tatfs	p.Y49fs		NM_006708.2	NP_006699.2	Q04760	LGUL_HUMAN	glyoxalase I	49					carbohydrate metabolic process (GO:0005975)|glutathione metabolic process (GO:0006749)|methylglyoxal metabolic process (GO:0009438)|negative regulation of apoptotic process (GO:0043066)|osteoclast differentiation (GO:0030316)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	lactoylglutathione lyase activity (GO:0004462)|zinc ion binding (GO:0008270)			lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	6					Glutathione(DB00143)|Indomethacin(DB00328)	ACTCTAGTATAAAAATCCAGT	0.333																																					p.Y49fs		Atlas-INDEL	.											.	GLO1	12	.	0			c.146delA						.						68.0	74.0	72.0					6																	38654690		2203	4300	6503	SO:0001589	frameshift_variant	2739	exon2			.	L07837	CCDS4837.1	6p21.3-p21.1	2012-10-02			ENSG00000124767	ENSG00000124767	4.4.1.5		4323	protein-coding gene	gene with protein product	"""glyoxalase domain containing 1"""	138750				8449929, 7684374	Standard	NM_006708		Approved	GLOD1	uc003ooc.3	Q04760	OTTHUMG00000014636	ENST00000373365.4:c.145delT	chr6.hg19:g.38654690delA	ENSP00000362463:p.Tyr49fs	218.0	0.0		333.0	20.0	NM_006708	B2R6P7|B4DDV0|P78375|Q59EL0|Q5TZW3|Q96FC0|Q96J41	Frame_Shift_Del	DEL	ENST00000373365.4	hg19	CCDS4837.1																																																																																			.	.		0.333	GLO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040438.2	NM_006708	
WAC	51322	hgsc.bcm.edu	37	10	28908473	28908473	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:28908473delT	ENST00000354911.4	+	14	2043	c.1882delT	c.(1882-1884)tttfs	p.F628fs	WAC_ENST00000375646.1_Frame_Shift_Del_p.F476fs|WAC_ENST00000347934.4_Frame_Shift_Del_p.F525fs|WAC_ENST00000375664.4_Frame_Shift_Del_p.F583fs	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil	628					cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						CAGGATACTATTTTTGAGACA	0.284																																					p.L627fs		Atlas-INDEL	.											.	WAC	77	.	0			c.1881delA						.						40.0	42.0	41.0					10																	28908473		2200	4300	6500	SO:0001589	frameshift_variant	51322	exon14			.	AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"""WW domain-containing adaptor with coiled coil"""			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.1882delT	chr10.hg19:g.28908473delT	ENSP00000346986:p.Phe628fs	133.0	0.0		163.0	10.0	NM_016628	A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Frame_Shift_Del	DEL	ENST00000354911.4	hg19	CCDS7159.1																																																																																			.	.		0.284	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000047371.1	NM_100264	
SLITRK5	26050	hgsc.bcm.edu	37	13	88328344	88328344	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:88328344delA	ENST00000325089.6	+	2	920	c.701delA	c.(700-702)gaafs	p.E234fs	SLITRK5_ENST00000400028.3_Intron	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	234					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					CAGCTGGAGGAAAACCCTTGG	0.532																																					p.E234fs		Atlas-INDEL	.											.	SLITRK5	192	.	0			c.700delG						.						84.0	87.0	86.0					13																	88328344		2203	4300	6503	SO:0001589	frameshift_variant	26050	exon2			.	AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"""leucine rich repeat containing 11"""	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.701delA	chr13.hg19:g.88328344delA	ENSP00000366283:p.Glu234fs	98.0	0.0		189.0	12.0	NM_015567	B3KNB8|B4DSH5|Q5VT81	Frame_Shift_Del	DEL	ENST00000325089.6	hg19	CCDS9465.1																																																																																			.	.		0.532	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3		
CXorf30	645090	hgsc.bcm.edu	37	X	36379541	36379541	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:36379541delA	ENST00000378657.4	+	15	1934	c.1286delA	c.(1285-1287)gaafs	p.E429fs		NM_001098843.4	NP_001092313.2	A6PW82	CX030_HUMAN	chromosome X open reading frame 30	429										breast(1)|lung(2)|stomach(1)	4						TATATGATTGAAAAATCTTAT	0.284																																					p.E429fs		Atlas-INDEL	.											.	CXorf30	76	.	0			c.1285delG						.						46.0	39.0	41.0					X																	36379541		690	1544	2234	SO:0001589	frameshift_variant	645090	exon16			.		CCDS55396.1	Xp21.1	2014-08-07			ENSG00000205081	ENSG00000205081			27298	protein-coding gene	gene with protein product							Standard	NM_001098843		Approved		uc011mkc.3	A6PW82	OTTHUMG00000021353	ENST00000378657.4:c.1286delA	chrX.hg19:g.36379541delA	ENSP00000367926:p.Glu429fs	134.0	0.0		162.0	10.0	NM_001098843		Frame_Shift_Del	DEL	ENST00000378657.4	hg19	CCDS55396.1																																																																																			.	.		0.284	CXorf30-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NP_001092313	
GUSB	2990	hgsc.bcm.edu	37	7	65429409	65429409	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:65429409delT	ENST00000304895.4	-	11	1820	c.1690delA	c.(1690-1692)agtfs	p.S564fs	GUSB_ENST00000421103.1_Frame_Shift_Del_p.S418fs|GUSB_ENST00000345660.6_Frame_Shift_Del_p.S513fs	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	564					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						TCTAGCAGACTTTTCTGGTAC	0.413																																					p.S564fs		Atlas-INDEL	.											.	GUSB	52	.	0			c.1691delG						.						55.0	49.0	51.0					7																	65429409		2203	4299	6502	SO:0001589	frameshift_variant	2990	exon11			.	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.1690delA	chr7.hg19:g.65429409delT	ENSP00000302728:p.Ser564fs	122.0	0.0		155.0	11.0	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Frame_Shift_Del	DEL	ENST00000304895.4	hg19	CCDS5530.1																																																																																			.	.		0.413	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181	
FANCI	55215	hgsc.bcm.edu	37	15	89828374	89828374	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:89828374delT	ENST00000310775.7	+	18	1832	c.1746delT	c.(1744-1746)actfs	p.T582fs	FANCI_ENST00000300027.8_Frame_Shift_Del_p.T582fs	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	582					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					CCAATGAAACTTTTTGCCTTG	0.418								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.T582fs		Atlas-INDEL	.											.	FANCI	129	.	0			c.1745delC						.						220.0	188.0	199.0					15																	89828374		2200	4299	6499	SO:0001589	frameshift_variant	55215	exon18	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.1746delT	chr15.hg19:g.89828374delT	ENSP00000310842:p.Thr582fs	135.0	0.0		161.0	10.0	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Frame_Shift_Del	DEL	ENST00000310775.7	hg19	CCDS45346.1																																																																																			.	.		0.418	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
TSTD2	158427	hgsc.bcm.edu	37	9	100389705	100389705	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:100389705delT	ENST00000341170.4	-	2	522	c.140delA	c.(139-141)aagfs	p.K48fs	TSTD2_ENST00000354801.2_5'UTR	NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	48										large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						CGAGTATTTCTTTTTTGTACT	0.343																																					p.K47fs		Atlas-INDEL	.											.	TSTD2	42	.	0			c.141delG						.						177.0	163.0	167.0					9																	100389705		2203	4300	6503	SO:0001589	frameshift_variant	158427	exon2			.	AF258575	CCDS6727.2	9q22.33	2013-09-20	2009-08-12	2009-08-12	ENSG00000136925	ENSG00000136925			30087	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 97"""	C9orf97		12477932	Standard	NM_139246		Approved	PP4189	uc004axn.3	Q5T7W7	OTTHUMG00000020328	ENST00000341170.4:c.140delA	chr9.hg19:g.100389705delT	ENSP00000342499:p.Lys48fs	163.0	0.0		188.0	13.0	NM_139246	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	Frame_Shift_Del	DEL	ENST00000341170.4	hg19	CCDS6727.2																																																																																			.	.		0.343	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053325.4	NM_139246	
NPS	594857	hgsc.bcm.edu	37	10	129350732	129350732	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:129350732delA	ENST00000398023.1	+	3	119	c.99delA	c.(97-99)ggafs	p.G33fs		NM_001030013.1	NP_001025184.1	P0C0P6	NPS_HUMAN	neuropeptide S	33					neuropeptide signaling pathway (GO:0007218)|positive regulation of action potential (GO:0045760)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|visual learning (GO:0008542)	extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						AGGTGTCTGGAAAATCTGATT	0.393																																					p.G33fs		Atlas-INDEL	.											.	NPS	14	.	0			c.98delG						.						317.0	315.0	316.0					10																	129350732		1827	4092	5919	SO:0001589	frameshift_variant	594857	exon3			.	BC148465	CCDS41577.1	10q26.2	2013-02-26			ENSG00000214285	ENSG00000214285		"""Endogenous ligands"""	33940	protein-coding gene	gene with protein product	"""prepro-neuropeptide S"""	609513				18181564, 15312648	Standard	NM_001030013		Approved		uc001ljx.1	P0C0P6		ENST00000398023.1:c.99delA	chr10.hg19:g.129350732delA	ENSP00000381105:p.Gly33fs	128.0	0.0		118.0	10.0	NM_001030013		Frame_Shift_Del	DEL	ENST00000398023.1	hg19	CCDS41577.1																																																																																			.	.		0.393	NPS-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001030013	
AGAP4	119016	hgsc.bcm.edu	37	10	51363013	51363013	+	Intron	DEL	G	G	-	rs112991319		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:51363013delG	ENST00000602930.1	-	1	468				RP11-592B15.3_ENST00000432221.2_RNA	NM_001276343.1	NP_001263272.1	Q5SRD3	AGAP8_HUMAN							regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|lung(2)|ovary(2)	6						ACCGTTTCCTGAATTCAATGT	0.408																																					p.R354fs		Atlas-INDEL	.											.	PARG	46	.	0			c.1060delA						.						79.0	83.0	82.0					10																	51363013		233	1110	1343	SO:0001627	intron_variant	8505	exon3			.																												ENST00000602930.1:c.81+7840C>-	chr10.hg19:g.51363013delG		5.0	0.0		11.0	10.0	NM_003631		Frame_Shift_Del	DEL	ENST00000602930.1	hg19																																																																																				.	.		0.408	AGAP8-006	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000467541.1		
PRDM2	7799	hgsc.bcm.edu	37	1	14108857	14108857	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:14108857delA	ENST00000235372.7	+	8	5423	c.4567delA	c.(4567-4569)aaafs	p.K1523fs	PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000343137.4_Frame_Shift_Del_p.K1322fs|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000311066.5_Frame_Shift_Del_p.K1523fs|PRDM2_ENST00000413440.1_Frame_Shift_Del_p.K1322fs|PRDM2_ENST00000376048.5_Intron	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1523					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		TGCGGAGATTAAAATGCAAAG	0.522																																					p.I1522fs		Atlas-INDEL	.											.	PRDM2	147	.	0			c.4566delT						.						65.0	72.0	70.0					1																	14108857		2203	4300	6503	SO:0001589	frameshift_variant	7799	exon8			.	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.4567delA	chr1.hg19:g.14108857delA	ENSP00000235372:p.Lys1523fs	85.0	0.0		125.0	10.0	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Frame_Shift_Del	DEL	ENST00000235372.7	hg19	CCDS150.1																																																																																			.	.		0.522	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
MTRF1L	54516	hgsc.bcm.edu	37	6	153323592	153323592	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:153323592delC	ENST00000367233.5	-	1	228	c.229delG	c.(229-231)gagfs	p.E77fs	MTRF1L_ENST00000464135.1_5'UTR|MTRF1L_ENST00000367230.1_Frame_Shift_Del_p.E77fs|MTRF1L_ENST00000367231.5_Frame_Shift_Del_p.E77fs	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	77						mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		TCCCGCAGCTCCCGCTCCTTC	0.617																																					p.E77fs		Atlas-INDEL	.											.	MTRF1L	21	.	0			c.230delA						.						30.0	31.0	31.0					6																	153323592		2203	4300	6503	SO:0001589	frameshift_variant	54516	exon1			.	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.229delG	chr6.hg19:g.153323592delC	ENSP00000356202:p.Glu77fs	190.0	0.0		227.0	14.0	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Frame_Shift_Del	DEL	ENST00000367233.5	hg19	CCDS5243.1																																																																																			.	.		0.617	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041	
CYP39A1	51302	hgsc.bcm.edu	37	6	46604172	46604172	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:46604172delT	ENST00000275016.2	-	5	889	c.686delA	c.(685-687)aacfs	p.N229fs		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	229					bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						ATCTGGAATGTTTTTCTCAAA	0.274																																					p.N229fs		Atlas-INDEL	.											.	CYP39A1	41	.	0			c.687delC						.						50.0	52.0	51.0					6																	46604172		2202	4293	6495	SO:0001589	frameshift_variant	51302	exon5			.	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"""Cytochrome P450s"""	17449	protein-coding gene	gene with protein product		605994	"""cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"""			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.686delA	chr6.hg19:g.46604172delT	ENSP00000275016:p.Asn229fs	94.0	0.0		144.0	11.0	NM_016593	Q5VTT0|Q96FW5	Frame_Shift_Del	DEL	ENST00000275016.2	hg19	CCDS4916.1																																																																																			.	.		0.274	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1		
PYROXD1	79912	hgsc.bcm.edu	37	12	21620538	21620538	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:21620538delT	ENST00000240651.9	+	11	1294	c.1240delT	c.(1240-1242)tttfs	p.F415fs	PYROXD1_ENST00000538582.1_Frame_Shift_Del_p.F344fs	NM_024854.3	NP_079130.2	Q8WU10	PYRD1_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 1	415							oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|soft_tissue(1)	18						TGTGACAAAATTTTTTAACTA	0.358																																					p.K413fs		Atlas-INDEL	.											.	PYROXD1	38	.	0			c.1239delA						.						90.0	91.0	91.0					12																	21620538		2203	4300	6503	SO:0001589	frameshift_variant	79912	exon11			.	AL832441	CCDS31755.1	12p12.1	2014-02-12			ENSG00000121350	ENSG00000121350			26162	protein-coding gene	gene with protein product						12477932	Standard	NM_024854		Approved	DKFZp762G094, FLJ22028	uc001rew.3	Q8WU10	OTTHUMG00000169129	ENST00000240651.9:c.1240delT	chr12.hg19:g.21620538delT	ENSP00000240651:p.Phe415fs	243.0	0.0		209.0	13.0	NM_024854	A6NKI6|B3KWN8|Q9H6P1	Frame_Shift_Del	DEL	ENST00000240651.9	hg19	CCDS31755.1																																																																																			.	.		0.358	PYROXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402363.1	NM_024854	
SCIN	85477	hgsc.bcm.edu	37	7	12664770	12664770	+	Intron	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:12664770delA	ENST00000297029.5	+	6	993				SCIN_ENST00000445618.2_Intron|SCIN_ENST00000519209.1_Intron|SCIN_ENST00000473722.1_Intron	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin						actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		ATGGAAAGGTAAAAAATTCCA	0.348																																					.		Atlas-INDEL	.											.	SCIN	105	.	0			c.892+2A>-						.						49.0	48.0	48.0					7																	12664770		1841	4091	5932	SO:0001627	intron_variant	85477	exon6			.	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.892+3A>-	chr7.hg19:g.12664770delA		115.0	0.0		146.0	10.0	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Splice_Site	DEL	ENST00000297029.5	hg19	CCDS47545.1																																																																																			.	.		0.348	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128	
MYCL	4610	hgsc.bcm.edu	37	1	40366859	40366859	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:40366859delC	ENST00000372816.2	-	1	695	c.248delG	c.(247-249)ggcfs	p.G83fs	MYCL_ENST00000372815.1_Frame_Shift_Del_p.G113fs|MYCL_ENST00000429311.1_Frame_Shift_Del_p.G83fs|MYCL_ENST00000397332.2_Frame_Shift_Del_p.G113fs|RP1-118J21.5_ENST00000418255.1_RNA			P12524	MYCL_HUMAN	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived homolog	83						nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GTAGTTCCTGCCCCAGCCTTT	0.711																																					p.G113fs		Atlas-INDEL	.											.	MYCL1	36	.	0			c.339delC						.						26.0	25.0	26.0					1																	40366859		2200	4293	6493	SO:0001589	frameshift_variant	4610	exon2			.		CCDS30682.1, CCDS44117.1, CCDS44117.2, CCDS53300.1	1p34.3	2013-07-09	2013-07-09	2013-07-09	ENSG00000116990	ENSG00000116990		"""Basic helix-loop-helix proteins"""	7555	protein-coding gene	gene with protein product	"""l-myc protein"", ""myc-related gene from lung cancer"", ""oncogene lmyc"""	164850	"""v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived"""	MYCL1		8978772	Standard	NM_001033082		Approved	LMYC, bHLHe38	uc001cer.2	P12524	OTTHUMG00000009243	ENST00000372816.2:c.248delG	chr1.hg19:g.40366859delC	ENSP00000361903:p.Gly83fs	176.0	0.0		302.0	19.0	NM_005376	A2A2C9|B4DJH2|Q14897|Q5QPL0|Q5QPL1|Q9NUE9	Frame_Shift_Del	DEL	ENST00000372816.2	hg19	CCDS30682.1																																																																																			.	.		0.711	MYCL-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277004.1	NM_001033082	
IRAK4	51135	hgsc.bcm.edu	37	12	44180517	44180517	+	Stop_Codon_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:44180517delA	ENST00000448290.2	+	0	1453				IRAK4_ENST00000551736.1_Stop_Codon_Del|IRAK4_ENST00000440781.2_Stop_Codon_Del|IRAK4_ENST00000431837.1_Stop_Codon_Del	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4						cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)					all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		ACAGCTTCTTAAAACTTTATT	0.289																																					p.X461K		Atlas-INDEL	.											.	IRAK4	77	.	0			c.1381delT						.						57.0	63.0	61.0					12																	44180517		2202	4299	6501	SO:0001567	stop_retained_variant	51135	exon12			.	AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		Exception_encountered	chr12.hg19:g.44180517delA		127.0	0.0		145.0	10.0	NM_016123	Q69FE1|Q8TDF7|Q9Y589	Frame_Shift_Del	DEL	ENST00000448290.2	hg19	CCDS8744.1																																																																																			.	.		0.289	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1		
EIF4B	1975	hgsc.bcm.edu	37	12	53427592	53427592	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:53427592delC	ENST00000262056.9	+	9	1308	c.982delC	c.(982-984)cccfs	p.P329fs	EIF4B_ENST00000416762.3_Frame_Shift_Del_p.P290fs|RP11-983P16.4_ENST00000552905.1_RNA|EIF4B_ENST00000420463.3_Frame_Shift_Del_p.P329fs	NM_001417.4	NP_001408.2	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	329	Arg-rich.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation initiation factor activity (GO:0003743)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)	22						TAACTTAGGTCCCCCCCAAAG	0.423																																					p.G327fs		Atlas-INDEL	.											.	EIF4B	38	.	0			c.981delT						.						60.0	56.0	57.0					12																	53427592		1816	4081	5897	SO:0001589	frameshift_variant	1975	exon9			.	X55733	CCDS41788.1, CCDS73474.1	12q13.13	2013-02-12			ENSG00000063046	ENSG00000063046		"""RNA binding motif (RRM) containing"""	3285	protein-coding gene	gene with protein product		603928					Standard	XM_005268709		Approved		uc001sbh.4	P23588	OTTHUMG00000169570	ENST00000262056.9:c.982delC	chr12.hg19:g.53427592delC	ENSP00000262056:p.Pro329fs	328.0	0.0		389.0	26.0	NM_001417	Q4G0E3|Q53HQ2|Q6GPH5|Q6IB46|Q8WYK5	Frame_Shift_Del	DEL	ENST00000262056.9	hg19	CCDS41788.1																																																																																			.	.		0.423	EIF4B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404852.2	NM_001417	
MYO7A	4647	hgsc.bcm.edu	37	11	76917218	76917218	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76917218delA	ENST00000409709.3	+	41	5985	c.5713delA	c.(5713-5715)aaafs	p.K1905fs	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Frame_Shift_Del_p.K1856fs|MYO7A_ENST00000458637.2_Frame_Shift_Del_p.K1867fs	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1905	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GATTTTCCACAAAGTCTACTT	0.602																																					p.H1904fs		Atlas-INDEL	.											.	MYO7A	164	.	0			c.5712delC						.						79.0	90.0	87.0					11																	76917218		2009	4162	6171	SO:0001589	frameshift_variant	4647	exon41			.	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.5713delA	chr11.hg19:g.76917218delA	ENSP00000386331:p.Lys1905fs	88.0	0.0		127.0	10.0	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Frame_Shift_Del	DEL	ENST00000409709.3	hg19	CCDS53683.1																																																																																			.	.		0.602	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
BAIAP2	10458	hgsc.bcm.edu	37	17	79089623	79089623	+	Intron	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:79089623delC	ENST00000321300.6	+	14	1676				BAIAP2_ENST00000392411.3_Frame_Shift_Del_p.A452fs|BAIAP2_ENST00000435091.3_3'UTR|BAIAP2_ENST00000428708.2_Frame_Shift_Del_p.A530fs|BAIAP2_ENST00000575245.1_3'UTR	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2						actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GACAGGTCTGCCCCCCTCCTC	0.562																																					p.A530fs		Atlas-INDEL	.											.	BAIAP2	74	.	0			c.1588delG						.						79.0	82.0	81.0					17																	79089623		2203	4300	6503	SO:0001627	intron_variant	10458	exon14			.	AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698	ENST00000321300.6:c.1583+6C>-	chr17.hg19:g.79089623delC		83.0	0.0		131.0	11.0	NM_001144888	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Frame_Shift_Del	DEL	ENST00000321300.6	hg19	CCDS11775.1																																																																																			.	.		0.562	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1		
FLNB	2317	hgsc.bcm.edu	37	3	58107010	58107010	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:58107010delG	ENST00000295956.4	+	20	3071	c.2906delG	c.(2905-2907)aggfs	p.R969fs	FLNB_ENST00000490882.1_Frame_Shift_Del_p.R969fs|FLNB_ENST00000357272.4_Frame_Shift_Del_p.R969fs|FLNB_ENST00000429972.2_Frame_Shift_Del_p.R969fs|FLNB_ENST00000358537.3_Frame_Shift_Del_p.R969fs|FLNB_ENST00000493452.1_Frame_Shift_Del_p.R800fs|FLNB_ENST00000348383.5_Frame_Shift_Del_p.R969fs|FLNB_ENST00000419752.2_Frame_Shift_Del_p.R800fs	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	969					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		GTTGATACCAGGGGGGCAGGA	0.572																																					p.R969fs		Atlas-INDEL	.											.	FLNB	430	.	0			c.2905delA						.						135.0	126.0	129.0					3																	58107010		2203	4300	6503	SO:0001589	frameshift_variant	2317	exon20			.	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.2906delG	chr3.hg19:g.58107010delG	ENSP00000295956:p.Arg969fs	134.0	0.0		166.0	10.0	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Frame_Shift_Del	DEL	ENST00000295956.4	hg19	CCDS2885.1																																																																																			.	.		0.572	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
KDM4C	23081	hgsc.bcm.edu	37	9	6805725	6805725	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:6805725delA	ENST00000381309.3	+	3	836	c.271delA	c.(271-273)aaafs	p.K92fs	KDM4C_ENST00000535193.1_Frame_Shift_Del_p.K114fs|KDM4C_ENST00000489243.1_3'UTR|KDM4C_ENST00000381306.3_Frame_Shift_Del_p.K92fs|KDM4C_ENST00000536108.1_5'UTR|KDM4C_ENST00000543771.1_Frame_Shift_Del_p.K92fs|KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000401787.3_Frame_Shift_Del_p.K92fs	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	92					histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						CAACATCCAGAAAAAAGCGAT	0.423																																					p.Q112fs		Atlas-INDEL	.											.	KDM4C	186	.	0			c.336delG						.						124.0	118.0	120.0					9																	6805725		2203	4300	6503	SO:0001589	frameshift_variant	23081	exon3			.	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.271delA	chr9.hg19:g.6805725delA	ENSP00000370710:p.Lys92fs	193.0	0.0		199.0	12.0	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Frame_Shift_Del	DEL	ENST00000381309.3	hg19	CCDS6471.1																																																																																			.	.		0.423	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
PRKD1	5587	hgsc.bcm.edu	37	14	30095706	30095706	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:30095706delA	ENST00000331968.5	-	12	2011	c.1782delT	c.(1780-1782)tttfs	p.F594fs	PRKD1_ENST00000415220.2_Frame_Shift_Del_p.F602fs	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	594	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|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 histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		AAACAATTCCAAACTGTCCAG	0.323																																					p.G595fs		Atlas-INDEL	.											.	PRKD1	316	.	0			c.1783delG						.						56.0	58.0	57.0					14																	30095706		2203	4299	6502	SO:0001589	frameshift_variant	5587	exon12			.		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	9407	protein-coding gene	gene with protein product		605435	"""protein kinase C, mu"""	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.1782delT	chr14.hg19:g.30095706delA	ENSP00000333568:p.Phe594fs	193.0	0.0		193.0	12.0	NM_002742	A6NL64|B2RAF6	Frame_Shift_Del	DEL	ENST00000331968.5	hg19	CCDS9637.1																																																																																			.	.		0.323	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742	
JAG2	3714	hgsc.bcm.edu	37	14	105618518	105618518	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:105618518delC	ENST00000331782.3	-	6	1302	c.899delG	c.(898-900)ggcfs	p.G301fs	RP11-44N21.4_ENST00000548203.1_RNA|JAG2_ENST00000347004.2_Frame_Shift_Del_p.G301fs	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	301	EGF-like 2; atypical. {ECO:0000255|PROSITE-ProRule:PRU00076}.				auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|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)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		GAGCAGGCCGCCCCAGTTGGT	0.642																																					p.G300fs		Atlas-INDEL	.											.	JAG2	69	.	0			c.900delC						.						80.0	71.0	74.0					14																	105618518		2203	4300	6503	SO:0001589	frameshift_variant	3714	exon6			.	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.899delG	chr14.hg19:g.105618518delC	ENSP00000328169:p.Gly301fs	196.0	0.0		220.0	14.0	NM_145159	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Frame_Shift_Del	DEL	ENST00000331782.3	hg19	CCDS9998.1																																																																																			.	.		0.642	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
TBX18	9096	hgsc.bcm.edu	37	6	85446613	85446613	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:85446613delG	ENST00000369663.5	-	8	1951	c.1614delC	c.(1612-1614)cccfs	p.P538fs	TBX18_ENST00000606784.1_Intron	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	538					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		CAGCCAGTTTGGGGGATGTGG	0.502																																					p.K539fs		Atlas-INDEL	.											.	TBX18	131	.	0			c.1615delA						.						84.0	98.0	94.0					6																	85446613		2203	4300	6503	SO:0001589	frameshift_variant	9096	exon8			.	AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"""T-boxes"""	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.1614delC	chr6.hg19:g.85446613delG	ENSP00000358677:p.Pro538fs	127.0	0.0		191.0	12.0	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Frame_Shift_Del	DEL	ENST00000369663.5	hg19	CCDS34495.1																																																																																			.	.		0.502	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508	
FHAD1	114827	hgsc.bcm.edu	37	1	15692403	15692403	+	Frame_Shift_Del	DEL	C	C	-	rs373444389		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:15692403delC	ENST00000375998.4	+	22	3062	c.3062delC	c.(3061-3063)gccfs	p.A1021fs	FHAD1_ENST00000375999.3_Frame_Shift_Del_p.A1021fs|FHAD1_ENST00000358897.4_Frame_Shift_Del_p.A1021fs|FHAD1_ENST00000417793.1_Frame_Shift_Del_p.A985fs|FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000314740.8_Frame_Shift_Del_p.A274fs			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	1021										skin(1)|stomach(1)	2						CTTACCGAAGCCCACAGCAGA	0.453																																					p.A1021fs		Atlas-INDEL	.											.	FHAD1	78	.	0			c.3061delG						.						86.0	84.0	85.0					1																	15692403		692	1591	2283	SO:0001589	frameshift_variant	114827	exon23			.	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.3062delC	chr1.hg19:g.15692403delC	ENSP00000365166:p.Ala1021fs	89.0	0.0		216.0	13.0	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Frame_Shift_Del	DEL	ENST00000375998.4	hg19																																																																																				.	.		0.453	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
HSPA1B	3304	hgsc.bcm.edu	37	6	31796253	31796253	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:31796253delC	ENST00000375650.3	+	1	742	c.526delC	c.(526-528)cccfs	p.P176fs	HSPA1B_ENST00000545241.1_Frame_Shift_Del_p.P85fs	NM_005346.4	NP_005337.2	P08107	HSP71_HUMAN	heat shock 70kDa protein 1B	176					ATP catabolic process (GO:0006200)|cellular heat acclimation (GO:0070370)|cellular response to heat (GO:0034605)|gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of inclusion body assembly (GO:0090084)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of erythrocyte differentiation (GO:0045648)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)	aggresome (GO:0016235)|blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|inclusion body (GO:0016234)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|protein N-terminus binding (GO:0047485)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|virus receptor activity (GO:0001618)			breast(1)|large_intestine(1)|prostate(1)	3						CATCAACGAGCCCACGGCCGC	0.662																																					p.E175fs		Atlas-INDEL	.											.	HSPA1B	5	.	0			c.525delG						.						1.0	1.0	1.0					6																	31796253		5	12	17	SO:0001589	frameshift_variant	3304	exon1			.		CCDS34415.1	6p21.3	2011-09-02	2002-08-29		ENSG00000204388	ENSG00000204388		"""Heat shock proteins / HSP70"""	5233	protein-coding gene	gene with protein product		603012	"""heat shock 70kD protein 1B"""			1700760	Standard	NM_005346		Approved	HSP70-2	uc003nxk.2	P08107	OTTHUMG00000031202	ENST00000375650.3:c.526delC	chr6.hg19:g.31796253delC	ENSP00000364801:p.Pro176fs	117.0	0.0		153.0	10.0	NM_005346	B4E3B6|P19790|Q5JQI4|Q5SP17|Q9UQL9|Q9UQM0	Frame_Shift_Del	DEL	ENST00000375650.3	hg19	CCDS34415.1																																																																																			.	.		0.662	HSPA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076402.2		
CASC4	113201	hgsc.bcm.edu	37	15	44673029	44673029	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:44673029delC	ENST00000345795.2	+	8	1197	c.927delC	c.(925-927)aacfs	p.N309fs	CASC4_ENST00000299957.6_Frame_Shift_Del_p.N309fs|CASC4_ENST00000360824.3_3'UTR	NM_177974.2	NP_816929.1	Q6P4E1	CASC4_HUMAN	cancer susceptibility candidate 4	309						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(2)	17		all_cancers(109;1.69e-13)|all_epithelial(112;3.94e-11)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.027)		all cancers(107;2.91e-20)|GBM - Glioblastoma multiforme(94;1.57e-06)|COAD - Colon adenocarcinoma(120;0.217)|Colorectal(105;0.237)		ACAATGGAAACCCCGGTACTT	0.343																																					p.N309fs		Atlas-INDEL	.											.	CASC4	34	.	0			c.926delA						.						63.0	61.0	62.0					15																	44673029		2198	4298	6496	SO:0001589	frameshift_variant	113201	exon8			.	AF103804	CCDS10108.1, CCDS10109.1	15q15.1	2010-11-24			ENSG00000166734	ENSG00000166734			24892	protein-coding gene	gene with protein product						10497265	Standard	NM_138423		Approved	H63, DKFZp459F1927	uc001ztp.3	Q6P4E1	OTTHUMG00000131133	ENST00000345795.2:c.927delC	chr15.hg19:g.44673029delC	ENSP00000335063:p.Asn309fs	130.0	0.0		156.0	13.0	NM_138423	B4DPZ6|G5E934|Q6UY45|Q96EM1	Frame_Shift_Del	DEL	ENST00000345795.2	hg19	CCDS10109.1																																																																																			.	.		0.343	CASC4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253816.1	NM_138423	
DLK1	8788	hgsc.bcm.edu	37	14	101200644	101200644	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:101200644delT	ENST00000341267.4	+	5	805	c.563delT	c.(562-564)attfs	p.I188fs	DLK1_ENST00000331224.6_Frame_Shift_Del_p.I188fs	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	188	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|negative regulation of Notch signaling pathway (GO:0045746)|Notch signaling pathway (GO:0007219)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(16)|ovary(2)|prostate(1)|skin(1)	29		Melanoma(154;0.155)				TGCACTGACATTGGGGGCGAC	0.667																																					p.I188fs		Atlas-INDEL	.											.	DLK1	57	.	0			c.562delA						.						52.0	57.0	55.0					14																	101200644		2203	4300	6503	SO:0001589	frameshift_variant	8788	exon5			.	U15979	CCDS9963.1	14q32	2011-12-05	2001-12-03			ENSG00000185559			2907	protein-coding gene	gene with protein product		176290	"""delta-like homolog (Drosophila)"""			8095043, 7925474	Standard	NM_003836		Approved	FA1, pG2, Pref-1, ZOG, Delta1	uc001yhs.4	P80370		ENST00000341267.4:c.563delT	chr14.hg19:g.101200644delT	ENSP00000340292:p.Ile188fs	190.0	0.0		211.0	13.0	NM_003836	P15803|Q96DW5	Frame_Shift_Del	DEL	ENST00000341267.4	hg19	CCDS9963.1																																																																																			.	.		0.667	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1		
XPO1	7514	hgsc.bcm.edu	37	2	61719275	61719275	+	Frame_Shift_Del	DEL	T	T	-	rs3816341	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:61719275delT	ENST00000401558.2	-	16	2509	c.1782delA	c.(1780-1782)aaafs	p.K594fs	XPO1_ENST00000406957.1_Frame_Shift_Del_p.K594fs|XPO1_ENST00000404992.2_Frame_Shift_Del_p.K594fs	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	594	Necessary for HTLV-1 Rex-mediated mRNA export.				gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			GCCTGCGGCATTTTTGGGCTA	0.373			Mis		CLL																																p.C595fs		Atlas-INDEL	.	-'	Dom	yes		2	2p15	7514	"""exportin 1 (CRM1 homolog, yeast)"""		L	.	XPO1	108	.	0			c.1783delT						.						76.0	77.0	77.0					2																	61719275		2203	4300	6503	SO:0001589	frameshift_variant	7514	exon16			.	Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"""Exportins"""	12825	protein-coding gene	gene with protein product	"""chromosome region maintenance 1 homolog (yeast)"""	602559	"""exportin 1 (CRM1, yeast, homolog)"", ""exportin 1 (CRM1 homolog, yeast)"""			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.1782delA	chr2.hg19:g.61719275delT	ENSP00000384863:p.Lys594fs	138.0	0.0		146.0	10.0	NM_003400	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Frame_Shift_Del	DEL	ENST00000401558.2	hg19	CCDS33205.1																																																																																			.	.		0.373	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400	
FAM83B	222584	hgsc.bcm.edu	37	6	54735393	54735393	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:54735393delG	ENST00000306858.7	+	2	465	c.349delG	c.(349-351)gggfs	p.G118fs		NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	118										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)					CGGACTCTTAGGGGGCACCCA	0.433																																					p.L116fs		Atlas-INDEL	.											.	FAM83B	186	.	0			c.348delA						.						84.0	87.0	86.0					6																	54735393		2203	4300	6503	SO:0001589	frameshift_variant	222584	exon2			.	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.349delG	chr6.hg19:g.54735393delG	ENSP00000304078:p.Gly118fs	124.0	0.0		184.0	12.0	NM_001010872	Q2M1P3|Q96DQ2	Frame_Shift_Del	DEL	ENST00000306858.7	hg19	CCDS34479.1																																																																																			.	.		0.433	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
TIAM1	7074	hgsc.bcm.edu	37	21	32519299	32519299	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:32519299delC	ENST00000286827.3	-	21	3860	c.3389delG	c.(3388-3390)ggafs	p.G1130fs	TIAM1_ENST00000541036.1_Frame_Shift_Del_p.G1070fs	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1130	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CAGGAATGATCCCCCCAGAGA	0.507																																					p.G1130fs		Atlas-INDEL	.											.	TIAM1	522	.	0			c.3390delA						.						124.0	99.0	107.0					21																	32519299		2203	4300	6503	SO:0001589	frameshift_variant	7074	exon21			.		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.3389delG	chr21.hg19:g.32519299delC	ENSP00000286827:p.Gly1130fs	194.0	0.0		155.0	10.0	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Frame_Shift_Del	DEL	ENST00000286827.3	hg19	CCDS13609.1																																																																																			.	.		0.507	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
KCNG3	170850	hgsc.bcm.edu	37	2	42671493	42671493	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:42671493delA	ENST00000306078.1	-	2	1487	c.892delT	c.(892-894)tggfs	p.W298fs	KCNG3_ENST00000394973.4_Frame_Shift_Del_p.W287fs	NM_133329.5|NM_172344.2	NP_579875.1|NP_758847.1	Q8TAE7	KCNG3_HUMAN	potassium voltage-gated channel, subfamily G, member 3	298					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	6						TTAATCACCCAAAAAATCCTC	0.443																																					p.W298fs		Atlas-INDEL	.											.	KCNG3	19	.	0			c.893delG						.						100.0	94.0	96.0					2																	42671493		2203	4300	6503	SO:0001589	frameshift_variant	170850	exon2			.	AB070604	CCDS1809.1, CCDS42674.1	2p21	2011-07-05			ENSG00000171126	ENSG00000171126		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18306	protein-coding gene	gene with protein product		606767				11852086, 16382104	Standard	NM_133329		Approved	Kv6.3	uc002rsn.3	Q8TAE7	OTTHUMG00000128604	ENST00000306078.1:c.892delT	chr2.hg19:g.42671493delA	ENSP00000304127:p.Trp298fs	116.0	0.0		173.0	12.0	NM_133329	Q53SC1	Frame_Shift_Del	DEL	ENST00000306078.1	hg19	CCDS1809.1																																																																																			.	.		0.443	KCNG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250464.2	NM_172344	
AGXT2	64902	hgsc.bcm.edu	37	5	35025928	35025928	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:35025928delC	ENST00000231420.6	-	9	1103	c.903delG	c.(901-903)gggfs	p.G301fs		NM_031900.3	NP_114106.1	Q9BYV1	AGT2_HUMAN	alanine--glyoxylate aminotransferase 2	301					cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process, by transamination (GO:0019481)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity (GO:0047305)|alanine-glyoxylate transaminase activity (GO:0008453)|beta-alanine-pyruvate transaminase activity (GO:0016223)|pyridoxal phosphate binding (GO:0030170)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(18)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	41	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyruvic acid(DB00119)	CCTTTAGAAACCCCTTTGGGT	0.463																																					p.F302fs		Atlas-INDEL	.											.	AGXT2	89	.	0			c.904delT						.						88.0	84.0	85.0					5																	35025928		2203	4300	6503	SO:0001589	frameshift_variant	64902	exon9			.	AJ292204	CCDS3908.1	5p13	2010-05-07	2010-05-07		ENSG00000113492	ENSG00000113492	2.6.1.44		14412	protein-coding gene	gene with protein product	"""beta-alanine-pyruvate aminotransferase"", ""beta-ALAAT II"""	612471	"""alanine-glyoxylate aminotransferase 2"""			15240345	Standard	NM_031900		Approved	AGT2	uc003jjf.3	Q9BYV1	OTTHUMG00000090788	ENST00000231420.6:c.903delG	chr5.hg19:g.35025928delC	ENSP00000231420:p.Gly301fs	89.0	0.0		139.0	12.0	NM_031900	B7ZM47|E9PDL7|Q53FB4|Q53FY7|Q53G03|Q5W7Q1	Frame_Shift_Del	DEL	ENST00000231420.6	hg19	CCDS3908.1																																																																																			.	.		0.463	AGXT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207574.2	NM_031900	
ELMO1	9844	hgsc.bcm.edu	37	7	37252948	37252948	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:37252948delG	ENST00000310758.4	-	12	1593	c.946delC	c.(946-948)cagfs	p.Q316fs	ELMO1_ENST00000448602.1_Frame_Shift_Del_p.Q316fs|ELMO1_ENST00000442504.1_Frame_Shift_Del_p.Q316fs	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	316					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						ACCTGGTCCTGGGGGTCCATT	0.488																																					p.Q316fs		Atlas-INDEL	.											.	ELMO1	141	.	0			c.947delA						.						136.0	122.0	127.0					7																	37252948		2203	4300	6503	SO:0001589	frameshift_variant	9844	exon12			.	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.946delC	chr7.hg19:g.37252948delG	ENSP00000312185:p.Gln316fs	142.0	0.0		232.0	15.0	NM_014800	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Frame_Shift_Del	DEL	ENST00000310758.4	hg19	CCDS5449.1																																																																																			.	.		0.488	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442	
NCAPH2	29781	hgsc.bcm.edu	37	22	50957703	50957703	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:50957703delC	ENST00000420993.2	+	9	937	c.815delC	c.(814-816)gccfs	p.A272fs	NCAPH2_ENST00000299821.11_Frame_Shift_Del_p.A272fs|NCAPH2_ENST00000395698.3_Frame_Shift_Del_p.A272fs|NCAPH2_ENST00000395701.3_Frame_Shift_Del_p.A272fs	NM_001185011.1|NM_152299.3	NP_001171940.1|NP_689512.2	Q6IBW4	CNDH2_HUMAN	non-SMC condensin II complex, subunit H2	272					chromosome condensation (GO:0030261)|mitotic cell cycle (GO:0000278)	chromosome (GO:0005694)|membrane (GO:0016020)|nucleoplasm (GO:0005654)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|lung(10)|ovary(1)|prostate(2)|skin(3)|stomach(1)	24		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.212)		GAGGCCTCGGCCCCCAAGGCC	0.677																																					p.A272fs		Atlas-INDEL	.											.	NCAPH2	69	.	0			c.814delG						.						22.0	29.0	27.0					22																	50957703		2196	4296	6492	SO:0001589	frameshift_variant	29781	exon9			.	BC001937	CCDS14094.2, CCDS43038.1, CCDS54546.1	22q13.33	2008-02-04			ENSG00000025770	ENSG00000025770			25071	protein-coding gene	gene with protein product	"""kleisin beta"", ""CAP-H2 subunit of the condensin II complex"""	611230				10493829	Standard	NM_014551		Approved	384D8-2, hCAP-H2, CAP-H2	uc003blx.4	Q6IBW4	OTTHUMG00000150205	ENST00000420993.2:c.815delC	chr22.hg19:g.50957703delC	ENSP00000410088:p.Ala272fs	175.0	0.0		187.0	12.0	NM_152299	B7WPH1|O43788|Q13391|Q96C14|Q96GJ0|Q9BQ71|Q9BUT3|Q9BVD1	Frame_Shift_Del	DEL	ENST00000420993.2	hg19	CCDS14094.2																																																																																			.	.		0.677	NCAPH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317012.1	NM_152299	
RC3H2	54542	hgsc.bcm.edu	37	9	125652757	125652757	+	Frame_Shift_Del	DEL	G	G	-	rs10818759	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:125652757delG	ENST00000373670.1	-	3	1017	c.417delC	c.(415-417)aacfs	p.N139fs	RC3H2_ENST00000471874.2_Frame_Shift_Del_p.N139fs|RC3H2_ENST00000357244.2_Frame_Shift_Del_p.N139fs|RC3H2_ENST00000478216.1_5'UTR|RC3H2_ENST00000373665.2_Frame_Shift_Del_p.N139fs|RC3H2_ENST00000335387.5_Frame_Shift_Del_p.N139fs|RC3H2_ENST00000423239.2_Frame_Shift_Del_p.N139fs			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	139					B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						CCAGTTGACAGTTTACAAGTG	0.473																																					p.C140fs		Atlas-INDEL	.											.	RC3H2	150	.	0			c.418delT						.						99.0	99.0	99.0					9																	125652757		1941	4155	6096	SO:0001589	frameshift_variant	54542	exon4			.	AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCCH-type domain containing"""	21461	protein-coding gene	gene with protein product		615231	"""membrane associated DNA binding protein"", ""ring finger and CCCH-type zinc finger domains 2"""	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.417delC	chr9.hg19:g.125652757delG	ENSP00000362774:p.Asn139fs	137.0	0.0		173.0	11.0	NM_018835	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Frame_Shift_Del	DEL	ENST00000373670.1	hg19	CCDS43874.1																																																																																			.	.		0.473	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835	
ARHGAP33	115703	hgsc.bcm.edu	37	19	36278689	36278689	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:36278689delC	ENST00000007510.4	+	21	3366	c.3222delC	c.(3220-3222)ggcfs	p.G1074fs	AC002398.5_ENST00000433059.1_lincRNA|ARHGAP33_ENST00000314737.5_Frame_Shift_Del_p.G913fs|ARHGAP33_ENST00000378944.5_Frame_Shift_Del_p.G910fs			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	1074					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						GCTCTCTGGGCCCCCCTGCAC	0.662																																					p.G913fs		Atlas-INDEL	.											.	ARHGAP33	102	.	0			c.2738delG						.						26.0	30.0	29.0					19																	36278689		2200	4296	6496	SO:0001589	frameshift_variant	115703	exon21			.	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"""Rho GTPase activating proteins"""	23085	protein-coding gene	gene with protein product		614902	"""sorting nexin 26"""	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.3222delC	chr19.hg19:g.36278689delC	ENSP00000007510:p.Gly1074fs	136.0	0.0		157.0	10.0	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Frame_Shift_Del	DEL	ENST00000007510.4	hg19																																																																																				.	.		0.662	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948	
POTEF	728378	hgsc.bcm.edu	37	2	130865619	130865619	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:130865619delT	ENST00000409914.2	-	8	1488	c.1089delA	c.(1087-1089)aaafs	p.K363fs	POTEF_ENST00000361163.4_Frame_Shift_Del_p.K373fs|POTEF_ENST00000360967.5_Frame_Shift_Del_p.K363fs|AC018804.3_ENST00000433507.1_RNA|RNU6-1049P_ENST00000516414.1_RNA|POTEF_ENST00000357462.5_Frame_Shift_Del_p.K363fs	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	363					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						TTAGCATCTGTTTTTCTTTGT	0.308																																					p.Q364fs		Atlas-INDEL	.											.	POTEF	140	.	0			c.1090delC						.						2.0	3.0	3.0					2																	130865619		863	1896	2759	SO:0001589	frameshift_variant	728378	exon8			.	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.1089delA	chr2.hg19:g.130865619delT	ENSP00000386786:p.Lys363fs	238.0	0.0		247.0	17.0	NM_001099771	A6NC34	Frame_Shift_Del	DEL	ENST00000409914.2	hg19	CCDS46409.1																																																																																			.	.		0.308	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
VAPB	9217	hgsc.bcm.edu	37	20	57019177	57019177	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:57019177delC	ENST00000475243.1	+	6	956	c.618delC	c.(616-618)agcfs	p.S206fs	VAPB_ENST00000265619.2_3'UTR|VAPB_ENST00000395802.3_Frame_Shift_Del_p.P86fs	NM_004738.4	NP_004729.1	O95292	VAPB_HUMAN	VAMP (vesicle-associated membrane protein)-associated protein B and C	206					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|endoplasmic reticulum unfolded protein response (GO:0030968)|modulation by virus of host morphology or physiology (GO:0019048)|positive regulation of viral genome replication (GO:0045070)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-tubulin binding (GO:0048487)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|structural molecule activity (GO:0005198)			kidney(2)|lung(3)|prostate(1)	6	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)			AGAGCAACAGCCCCATTTCAG	0.507																																					p.S206fs		Atlas-INDEL	.											.	VAPB	21	.	0			c.617delG						.						244.0	219.0	227.0					20																	57019177		2203	4300	6503	SO:0001589	frameshift_variant	9217	exon6			.	AF086628	CCDS33498.1, CCDS56198.1	20q13	2014-09-17			ENSG00000124164	ENSG00000124164			12649	protein-coding gene	gene with protein product		605704				9920726	Standard	NM_004738		Approved	VAP-B, VAP-C, ALS8	uc002xza.3	O95292	OTTHUMG00000032840	ENST00000475243.1:c.618delC	chr20.hg19:g.57019177delC	ENSP00000417175:p.Ser206fs	159.0	0.0		174.0	12.0	NM_004738	A2A2F2|O95293|Q9P0H0	Frame_Shift_Del	DEL	ENST00000475243.1	hg19	CCDS33498.1																																																																																			.	.		0.507	VAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079875.2		
COL9A2	1298	hgsc.bcm.edu	37	1	40776921	40776921	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:40776921delG	ENST00000372748.3	-	11	653	c.557delC	c.(556-558)ccafs	p.P186fs		NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	186	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			CTGCAGCCCTGGGGGACCTTT	0.587																																					p.P186fs		Atlas-INDEL	.											.	COL9A2	63	.	0			c.558delA						.						77.0	78.0	78.0					1																	40776921		2203	4300	6503	SO:0001589	frameshift_variant	1298	exon11			.	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.557delC	chr1.hg19:g.40776921delG	ENSP00000361834:p.Pro186fs	77.0	0.0		147.0	11.0	NM_001852	B2RMP9	Frame_Shift_Del	DEL	ENST00000372748.3	hg19	CCDS450.1																																																																																			.	.		0.587	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852	
CNTNAP4	85445	hgsc.bcm.edu	37	16	76486452	76486452	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:76486452delT	ENST00000476707.1	+	7	1267	c.1128delT	c.(1126-1128)actfs	p.T376fs	CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000377504.4_Frame_Shift_Del_p.T324fs|CNTNAP4_ENST00000478060.1_Frame_Shift_Del_p.T300fs|CNTNAP4_ENST00000307431.8_Frame_Shift_Del_p.T372fs			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	373					cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						TGCCCGTGACTTTTCTGAGCT	0.408																																					p.T300fs		Atlas-INDEL	.											.	CNTNAP4	600	.	0			c.899delC						.						98.0	98.0	98.0					16																	76486452		2198	4300	6498	SO:0001589	frameshift_variant	85445	exon7			.	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.1128delT	chr16.hg19:g.76486452delT	ENSP00000417628:p.Thr376fs	138.0	0.0		127.0	10.0	NM_138994	E9PFZ6|Q86YZ7	Frame_Shift_Del	DEL	ENST00000476707.1	hg19																																																																																				.	.		0.408	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401	
ZFAND5	7763	hgsc.bcm.edu	37	9	74974352	74974352	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:74974352delT	ENST00000237937.3	-	4	906	c.349delA	c.(349-351)acafs	p.T117fs	ZFAND5_ENST00000376960.4_Frame_Shift_Del_p.T117fs|ZFAND5_ENST00000376962.5_Frame_Shift_Del_p.T117fs|ZFAND5_ENST00000343431.2_Frame_Shift_Del_p.T117fs|ZFAND5_ENST00000488164.1_5'UTR	NM_001102421.1|NM_001278243.1|NM_001278244.1|NM_001278245.1|NM_006007.2	NP_001095891.1|NP_001265172.1|NP_001265173.1|NP_001265174.1|NP_005998.1	O76080	ZFAN5_HUMAN	zinc finger, AN1-type domain 5	117					face development (GO:0060324)|fibroblast migration (GO:0010761)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|respiratory system process (GO:0003016)|skeletal system morphogenesis (GO:0048705)|smooth muscle tissue development (GO:0048745)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|kidney(2)|lung(2)|prostate(1)	6						GACACCTCTGTTTTCGGGGTA	0.418																																					p.T117fs		Atlas-INDEL	.											.	ZFAND5	14	.	0			c.350delC						.						89.0	87.0	87.0					9																	74974352		2203	4299	6502	SO:0001589	frameshift_variant	7763	exon5			.	AF062072	CCDS6642.1	9q13-q21	2008-05-02	2006-07-07	2006-07-07	ENSG00000107372	ENSG00000107372		"""Zinc fingers, AN1-type domain containing"""	13008	protein-coding gene	gene with protein product		604761	"""zinc finger protein 216"", ""zinc finger, A20 domain containing 2"""	ZNF216, ZA20D2		9758550	Standard	NM_001278243		Approved	ZFAND5A	uc004aiy.2	O76080	OTTHUMG00000020008	ENST00000237937.3:c.349delA	chr9.hg19:g.74974352delT	ENSP00000237937:p.Thr117fs	105.0	0.0		116.0	10.0	NM_001102420	A8K484	Frame_Shift_Del	DEL	ENST00000237937.3	hg19	CCDS6642.1																																																																																			.	.		0.418	ZFAND5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052644.1		
ZNF597	146434	hgsc.bcm.edu	37	16	3486565	3486565	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:3486565delA	ENST00000301744.4	-	4	1369	c.1134delT	c.(1132-1134)tttfs	p.F378fs		NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	378					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	13						AGTCCAAAGCAAAACTTTCCT	0.438																																					p.A379fs		Atlas-INDEL	.											.	ZNF597	41	.	0			c.1135delG						.						74.0	65.0	68.0					16																	3486565		2197	4299	6496	SO:0001589	frameshift_variant	146434	exon4			.	AK057633	CCDS10505.1	16p13.3	2013-01-08			ENSG00000167981	ENSG00000167981		"""Zinc fingers, C2H2-type"", ""-"""	26573	protein-coding gene	gene with protein product		614685				12477932	Standard	NM_152457		Approved	FLJ33071	uc002cvd.3	Q96LX8	OTTHUMG00000129359	ENST00000301744.4:c.1134delT	chr16.hg19:g.3486565delA	ENSP00000301744:p.Phe378fs	135.0	0.0		163.0	10.0	NM_152457		Frame_Shift_Del	DEL	ENST00000301744.4	hg19	CCDS10505.1																																																																																			.	.		0.438	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457	
SFMBT2	57713	hgsc.bcm.edu	37	10	7214583	7214583	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:7214583delG	ENST00000361972.4	-	18	2115	c.2025delC	c.(2023-2025)cccfs	p.P675fs	SFMBT2_ENST00000397167.1_Frame_Shift_Del_p.P675fs	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	675			P -> R (in dbSNP:rs3740212).		negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						TTTCCCCGATGGGGGGCTTGG	0.517																																					p.I676fs		Atlas-INDEL	.											.	SFMBT2	209	.	0			c.2026delA						.						48.0	58.0	54.0					10																	7214583		2203	4300	6503	SO:0001589	frameshift_variant	57713	exon18			.	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"""Sterile alpha motif (SAM) domain containing"""	20256	protein-coding gene	gene with protein product		615392	"""Scm-related gene containing four mbt domains 2"""			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.2025delC	chr10.hg19:g.7214583delG	ENSP00000355109:p.Pro675fs	203.0	0.0		217.0	17.0	NM_001029880	A7MD09|Q9HCF5	Frame_Shift_Del	DEL	ENST00000361972.4	hg19	CCDS31138.1																																																																																			.	.		0.517	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880	
CREB3L4	148327	hgsc.bcm.edu	37	1	153941909	153941909	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:153941909delC	ENST00000368607.3	+	4	787	c.521delC	c.(520-522)gccfs	p.A174fs	CREB3L4_ENST00000468845.1_3'UTR|CREB3L4_ENST00000405694.3_Frame_Shift_Del_p.A27fs|CREB3L4_ENST00000368600.3_Frame_Shift_Del_p.A154fs|SLC39A1_ENST00000310483.6_5'Flank|CREB3L4_ENST00000271889.4_Frame_Shift_Del_p.A174fs|CREB3L4_ENST00000368601.1_Frame_Shift_Del_p.A174fs|CREB3L4_ENST00000368603.1_Frame_Shift_Del_p.A174fs|RP11-422P24.10_ENST00000608147.1_RNA	NM_001255978.1|NM_001255980.1|NM_130898.3	NP_001242907.1|NP_001242909.1|NP_570968.1	Q8TEY5	CR3L4_HUMAN	cAMP responsive element binding protein 3-like 4	174					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|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)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(3)	13	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGCACCGTAGCCCCAGTGCCC	0.532																																					p.A174fs		Atlas-INDEL	.											.	CREB3L4	36	.	0			c.520delG						.						104.0	88.0	93.0					1																	153941909		2203	4300	6503	SO:0001589	frameshift_variant	148327	exon4			.	AF394167	CCDS1056.1, CCDS58029.1	1q21.2	2013-01-10			ENSG00000143578	ENSG00000143578		"""basic leucine zipper proteins"""	18854	protein-coding gene	gene with protein product		607138					Standard	NM_130898		Approved	AIbZIP, CREB4, CREB3, hJAL, ATCE1	uc001fdr.3	Q8TEY5	OTTHUMG00000037159	ENST00000368607.3:c.521delC	chr1.hg19:g.153941909delC	ENSP00000357596:p.Ala174fs	90.0	0.0		165.0	10.0	NM_001255978	D3DV62|Q5T4L0|Q86YW6	Frame_Shift_Del	DEL	ENST00000368607.3	hg19	CCDS1056.1																																																																																			.	.		0.532	CREB3L4-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090291.1	NM_130898	
EEA1	8411	hgsc.bcm.edu	37	12	93251072	93251072	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:93251072delT	ENST00000322349.8	-	5	609	c.345delA	c.(343-345)aaafs	p.K115fs	EEA1_ENST00000547833.1_5'Flank	NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	115					early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						GCCCTTGATATTTTTCTAATT	0.254																																					p.Y116fs		Atlas-INDEL	.											.	EEA1	104	.	0			c.346delT						.						29.0	29.0	29.0					12																	93251072		2200	4289	6489	SO:0001589	frameshift_variant	8411	exon5			.	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"""Zinc fingers, FYVE domain containing"""	3185	protein-coding gene	gene with protein product		605070	"""early endosome antigen 1, 162kD"""			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.345delA	chr12.hg19:g.93251072delT	ENSP00000317955:p.Lys115fs	209.0	0.0		276.0	20.0	NM_003566	Q14221	Frame_Shift_Del	DEL	ENST00000322349.8	hg19	CCDS31874.1																																																																																			.	.		0.254	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566	
TRMT10B	158234	hgsc.bcm.edu	37	9	37762657	37762657	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:37762657delA	ENST00000297994.3	+	3	335	c.270delA	c.(268-270)agafs	p.R90fs	TRMT10B_ENST00000377753.2_Intron|RP11-613M10.9_ENST00000540557.1_Intron|TRMT10B_ENST00000377754.2_Intron|TRMT10B_ENST00000537911.1_Frame_Shift_Del_p.R90fs	NM_144964.2	NP_659401.2	Q6PF06	TM10B_HUMAN	tRNA methyltransferase 10 homolog B (S. cerevisiae)	90							methyltransferase activity (GO:0008168)										AAGAACGAAGAAAAGCCAATC	0.343																																					p.R90fs		Atlas-INDEL	.											.	.	.	.	0			c.269delG						.						45.0	47.0	46.0					9																	37762657		1824	4082	5906	SO:0001589	frameshift_variant	158234	exon3			.	BC057774	CCDS43804.1, CCDS69598.1, CCDS69600.1, CCDS69601.1	9p13.1	2012-06-28	2012-06-28	2012-06-28	ENSG00000165275	ENSG00000165275			26454	protein-coding gene	gene with protein product			"""RNA (guanine-9-) methyltransferase domain containing 3"""	RG9MTD3		14702039	Standard	XM_005251373		Approved	FLJ31455, bA3J10.9	uc004aai.3	Q6PF06	OTTHUMG00000019933	ENST00000297994.3:c.270delA	chr9.hg19:g.37762657delA	ENSP00000297994:p.Arg90fs	190.0	0.0		158.0	10.0	NM_144964	B7Z216|B7Z3D3|Q05DJ4|Q5QP83|Q8NAG2|Q96N36	Frame_Shift_Del	DEL	ENST00000297994.3	hg19	CCDS43804.1																																																																																			.	.		0.343	TRMT10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052482.1	NM_144964	
PALM3	342979	hgsc.bcm.edu	37	19	14164636	14164636	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:14164636delG	ENST00000340790.4	-	6	1802	c.1803delC	c.(1801-1803)cccfs	p.P601fs		NM_001145028.1	NP_001138500.1	A6NDB9	PALM3_HUMAN	paralemmin 3	601					negative regulation of cytokine-mediated signaling pathway (GO:0001960)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)			endometrium(1)|kidney(2)|pancreas(1)|skin(1)	5						CATCCCCCAAGGGGCCTTGGC	0.672																																					p.L602fs		Atlas-INDEL	.											.	PALM3	26	.	0			c.1804delT						.						39.0	40.0	40.0					19																	14164636		692	1591	2283	SO:0001589	frameshift_variant	342979	exon6			.		CCDS46001.1	19p13.12	2010-04-15			ENSG00000187867	ENSG00000187867			33274	protein-coding gene	gene with protein product							Standard	NM_001145028		Approved		uc010xnk.1	A6NDB9		ENST00000340790.4:c.1803delC	chr19.hg19:g.14164636delG	ENSP00000344996:p.Pro601fs	95.0	0.0		140.0	11.0	NM_001145028		Frame_Shift_Del	DEL	ENST00000340790.4	hg19	CCDS46001.1																																																																																			.	.		0.672	PALM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458540.1	NM_001145028	
CTXN2	399697	hgsc.bcm.edu	37	15	48493577	48493577	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:48493577delA	ENST00000417307.2	+	2	452	c.80delA	c.(79-81)caafs	p.Q27fs	CTXN2_ENST00000541248.1_Frame_Shift_Del_p.Q27fs|RP11-605F22.1_ENST00000559875.1_RNA	NM_001145668.1	NP_001139140.1	P0C2S0	CTXN2_HUMAN	cortexin 2	27						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)	2						ACTCTGGAGCAAAAAACTGGC	0.408																																					p.Q27fs		Atlas-INDEL	.											.	CTXN2	8	.	0			c.79delC						.						289.0	226.0	245.0					15																	48493577		687	1588	2275	SO:0001589	frameshift_variant	399697	exon2			.	BK004876	CCDS45254.1	15q21.1	2013-09-20			ENSG00000233932	ENSG00000233932			31109	protein-coding gene	gene with protein product							Standard	NM_001145668		Approved		uc001zwm.1	P0C2S0	OTTHUMG00000172152	ENST00000417307.2:c.80delA	chr15.hg19:g.48493577delA	ENSP00000406145:p.Gln27fs	278.0	0.0		328.0	20.0	NM_001145668		Frame_Shift_Del	DEL	ENST00000417307.2	hg19	CCDS45254.1																																																																																			.	.		0.408	CTXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417125.1		
KDF1	126695	hgsc.bcm.edu	37	1	27278443	27278443	+	Frame_Shift_Del	DEL	G	G	-	rs535449942		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:27278443delG	ENST00000320567.5	-	2	517	c.429delC	c.(427-429)cccfs	p.P143fs		NM_152365.2	NP_689578.2	Q8NAX2	KDF1_HUMAN		143					developmental growth (GO:0048589)|establishment of skin barrier (GO:0061436)|keratinocyte development (GO:0003334)|limb epidermis development (GO:0060887)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|positive regulation of epidermal cell differentiation (GO:0045606)|regulation of epidermal cell division (GO:0010482)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		CCCGCCGGCTGGGGGGTGCAC	0.632																																					p.S144fs		Atlas-INDEL	.											.	C1orf172	38	.	0			c.430delA						.						24.0	27.0	26.0					1																	27278443		2203	4300	6503	SO:0001589	frameshift_variant	126695	exon2			.																												ENST00000320567.5:c.429delC	chr1.hg19:g.27278443delG	ENSP00000319179:p.Pro143fs	181.0	0.0		351.0	22.0	NM_152365	Q5QP32|Q8N0S7	Frame_Shift_Del	DEL	ENST00000320567.5	hg19	CCDS293.1																																																																																			.	.		0.632	C1orf172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012340.1		
TLR10	81793	hgsc.bcm.edu	37	4	38777029	38777029	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:38777029delA	ENST00000308973.4	-	4	788	c.183delT	c.(181-183)tttfs	p.F61fs	TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000508334.1_Frame_Shift_Del_p.F61fs|TLR10_ENST00000361424.2_Frame_Shift_Del_p.F61fs|TLR10_ENST00000506111.1_Frame_Shift_Del_p.F61fs	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	61					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						TCTGGAGTTGAAAAAGGAGGT	0.423																																					p.Q62fs		Atlas-INDEL	.											.	TLR10	87	.	0			c.184delC						.						73.0	70.0	71.0					4																	38777029		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.183delT	chr4.hg19:g.38777029delA	ENSP00000308925:p.Phe61fs	166.0	0.0		200.0	13.0	NM_030956	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Frame_Shift_Del	DEL	ENST00000308973.4	hg19	CCDS3445.1																																																																																			.	.		0.423	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
SLC30A3	7781	hgsc.bcm.edu	37	2	27480186	27480186	+	Frame_Shift_Del	DEL	G	G	-	rs148758588		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:27480186delG	ENST00000233535.4	-	5	965	c.613delC	c.(613-615)cacfs	p.H205fs	SLC30A3_ENST00000447008.2_Frame_Shift_Del_p.H200fs	NM_003459.4	NP_003450.2	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter), member 3	205					positive regulation of transport (GO:0051050)|regulation of sequestering of zinc ion (GO:0061088)|transmembrane transport (GO:0055085)|transport (GO:0006810)|zinc ion transmembrane transport (GO:0071577)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	zinc transporting ATPase activity (GO:0015633)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|pancreas(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCGTGGCTGTGGGGGGGCCCA	0.657																																					p.H205fs		Atlas-INDEL	.											.	SLC30A3	39	.	0			c.614delA						.						16.0	18.0	17.0					2																	27480186		2202	4299	6501	SO:0001589	frameshift_variant	7781	exon5			.	U76010	CCDS1743.1	2p23.3	2013-05-22			ENSG00000115194	ENSG00000115194		"""Solute carriers"""	11014	protein-coding gene	gene with protein product		602878		ZNT3		8962159	Standard	NM_003459		Approved		uc002rjj.3	Q99726	OTTHUMG00000128409	ENST00000233535.4:c.613delC	chr2.hg19:g.27480186delG	ENSP00000233535:p.His205fs	136.0	0.0		163.0	11.0	NM_003459	Q8TC03	Frame_Shift_Del	DEL	ENST00000233535.4	hg19	CCDS1743.1																																																																																			.	.		0.657	SLC30A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250189.2		
ARID1A	8289	hgsc.bcm.edu	37	1	27087916	27087916	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:27087916delA	ENST00000324856.7	+	6	2574	c.2203delA	c.(2203-2205)agcfs	p.S735fs	ARID1A_ENST00000457599.2_Frame_Shift_Del_p.S735fs|RN7SL501P_ENST00000578818.1_RNA|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.S352fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	735					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)		CCAGTCGGACAGCATCATGCA	0.537			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.D734fs		Atlas-Indel,Pindel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.2202delC						.						92.0	84.0	86.0					1																	27087916		2203	4300	6503	SO:0001589	frameshift_variant	8289	exon6			.	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.2203delA	chr1.hg19:g.27087916delA	ENSP00000320485:p.Ser735fs	326.0	0.0		505.0	34.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.537	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
COL9A3	1299	hgsc.bcm.edu	37	20	61450582	61450582	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:61450582delG	ENST00000343916.3	+	4	195	c.192delG	c.(190-192)aagfs	p.K64fs		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	64	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					AGGGACCAAAGGGGGCCCCAG	0.657																																					p.K64fs		Atlas-INDEL	.											.	COL9A3	70	.	0			c.191delA						.						22.0	32.0	29.0					20																	61450582		2197	4298	6495	SO:0001589	frameshift_variant	1299	exon4			.	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2219	protein-coding gene	gene with protein product	"""collagen type IX proteoglycan"""	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.192delG	chr20.hg19:g.61450582delG	ENSP00000341640:p.Lys64fs	180.0	0.0		199.0	13.0	NM_001853	Q13681|Q9H4G9|Q9UPE2	Frame_Shift_Del	DEL	ENST00000343916.3	hg19	CCDS13505.1																																																																																			.	.		0.657	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853	
WDR35	57539	hgsc.bcm.edu	37	2	20188946	20188946	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:20188946delA	ENST00000345530.3	-	2	237	c.122delT	c.(121-123)ttgfs	p.L41fs	AC079145.4_ENST00000416575.1_RNA|WDR35_ENST00000281405.4_Frame_Shift_Del_p.L41fs	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	41					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCTAATTTCAAAACTTTCAG	0.413																																					p.L41fs		Atlas-INDEL	.											.	WDR35	92	.	0			c.123delG						.						252.0	227.0	235.0					2																	20188946		2203	4300	6503	SO:0001589	frameshift_variant	57539	exon2			.	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.122delT	chr2.hg19:g.20188946delA	ENSP00000314444:p.Leu41fs	137.0	0.0		160.0	10.0	NM_020779	B3KVI5|Q4ZG01|Q8NE11	Frame_Shift_Del	DEL	ENST00000345530.3	hg19	CCDS33152.1																																																																																			.	.		0.413	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779	
BAZ2B	29994	hgsc.bcm.edu	37	2	160182380	160182380	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:160182380delT	ENST00000392783.2	-	35	6488	c.5993delA	c.(5992-5994)aagfs	p.K1998fs	BAZ2B_ENST00000392782.1_Frame_Shift_Del_p.K1962fs|BAZ2B_ENST00000343439.5_Frame_Shift_Del_p.K1898fs|BAZ2B_ENST00000355831.2_Frame_Shift_Del_p.K1964fs	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1998					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)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						CTCATTAGTCTTTTTTCCTTT	0.323																																					p.K1998fs		Atlas-INDEL	.											.	BAZ2B	196	.	0			c.5994delG						.						95.0	85.0	88.0					2																	160182380		1820	4079	5899	SO:0001589	frameshift_variant	29994	exon35			.	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"""Zinc fingers, PHD-type"""	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.5993delA	chr2.hg19:g.160182380delT	ENSP00000376534:p.Lys1998fs	133.0	0.0		173.0	13.0	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Frame_Shift_Del	DEL	ENST00000392783.2	hg19	CCDS2209.2																																																																																			.	.		0.323	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
KCNIP1	30820	hgsc.bcm.edu	37	5	170139893	170139893	+	Intron	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:170139893delA	ENST00000411494.1	+	2	94				KCNIP1_ENST00000434108.1_Intron|KCNIP1_ENST00000390656.4_Intron|KCNIP1_ENST00000328939.4_Intron|KCNIP1_ENST00000377360.4_Intron|KCNIP1_ENST00000520740.1_Intron			Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1						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)			TCAGAGAGGTAAAAAACAGTT	0.378																																					.		Atlas-INDEL	.											.	KCNIP1	66	.	0			c.94+2A>-						.						157.0	149.0	152.0					5																	170139893		2203	4300	6503	SO:0001627	intron_variant	30820	exon2			.	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.94+3A>-	chr5.hg19:g.170139893delA		107.0	0.0		174.0	12.0	NM_001034837	B7Z7B4|Q3YAD0|Q3YAD1|Q3YAD2|Q3YAD3|Q5U822	Splice_Site	DEL	ENST00000411494.1	hg19	CCDS34286.1																																																																																			.	.		0.378	KCNIP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371760.1		
CYC1	1537	hgsc.bcm.edu	37	8	145150814	145150814	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:145150814delG	ENST00000318911.4	+	2	281	c.208delG	c.(208-210)gggfs	p.G71fs		NM_001916.3	NP_001907	P08574	CY1_HUMAN	cytochrome c-1	71					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|response to glucagon (GO:0033762)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|respiratory chain (GO:0070469)	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity (GO:0045155)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)	15	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GCTGGCGGCAGGGGGTGCGGG	0.662											OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A69fs		Atlas-INDEL	.											.	CYC1	34	.	0			c.207delA						.						58.0	60.0	60.0					8																	145150814		2203	4299	6502	SO:0001589	frameshift_variant	1537	exon2			.	BC001006	CCDS6415.1	8q24	2011-07-04			ENSG00000179091	ENSG00000179091		"""Mitochondrial respiratory chain complex / Complex III"""	2579	protein-coding gene	gene with protein product		123980					Standard	NM_001916		Approved	UQCR4	uc003zaz.4	P08574	OTTHUMG00000165242	ENST00000318911.4:c.208delG	chr8.hg19:g.145150814delG	ENSP00000317159:p.Gly71fs	62.0	0.0	1692	239.0	15.0	NM_001916	Q5U062|Q6FHS7	Frame_Shift_Del	DEL	ENST00000318911.4	hg19	CCDS6415.1																																																																																			.	.		0.662	CYC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382895.1	NM_001916	
C17orf47	284083	hgsc.bcm.edu	37	17	56620577	56620577	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:56620577delG	ENST00000321691.3	-	1	1152	c.971delC	c.(970-972)ccafs	p.P324fs	RP11-112H10.4_ENST00000580769.1_RNA|SEPT4_ENST00000412945.3_5'Flank|RP11-112H10.4_ENST00000578022.1_RNA|SEPT4_ENST00000457347.2_5'Flank|RP11-112H10.4_ENST00000580589.1_RNA	NM_001038704.2	NP_001033793	Q8NEP4	CQ047_HUMAN	chromosome 17 open reading frame 47	324										NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	24	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCCTCGGATTGGGGTCCTCAC	0.532																																					p.P324fs		Atlas-INDEL	.											.	C17orf47	59	.	0			c.972delA						.						99.0	88.0	92.0					17																	56620577		2203	4300	6503	SO:0001589	frameshift_variant	284083	exon1			.		CCDS32691.1	17q23.2	2012-10-11			ENSG00000181013	ENSG00000181013			26844	protein-coding gene	gene with protein product							Standard	NM_001038704		Approved	FLJ40121	uc002iwq.2	Q8NEP4	OTTHUMG00000179244	ENST00000321691.3:c.971delC	chr17.hg19:g.56620577delG	ENSP00000354874:p.Pro324fs	163.0	0.0		178.0	11.0	NM_001038704	Q8N821	Frame_Shift_Del	DEL	ENST00000321691.3	hg19	CCDS32691.1																																																																																			.	.		0.532	C17orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445443.1	NM_001038704	
CC2D1A	54862	hgsc.bcm.edu	37	19	14031386	14031386	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:14031386delC	ENST00000318003.7	+	13	1614	c.1373delC	c.(1372-1374)gccfs	p.A458fs	CC2D1A_ENST00000589606.1_Frame_Shift_Del_p.A458fs	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	458					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)			AGCCCTGTGGCCCCCACAGCC	0.587																																					p.A458fs		Atlas-INDEL	.											.	CC2D1A	67	.	0			c.1372delG						.						35.0	49.0	45.0					19																	14031386		1930	4129	6059	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.1373delC	chr19.hg19:g.14031386delC	ENSP00000313601:p.Ala458fs	183.0	0.0		193.0	13.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Frame_Shift_Del	DEL	ENST00000318003.7	hg19	CCDS42512.1																																																																																			.	.		0.587	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
ACVR1	90	hgsc.bcm.edu	37	2	158622477	158622477	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:158622477delT	ENST00000263640.3	-	8	1451	c.1022delA	c.(1021-1023)aatfs	p.N341fs	ACVR1_ENST00000410057.2_Frame_Shift_Del_p.N341fs|ACVR1_ENST00000434821.1_Frame_Shift_Del_p.N341fs|ACVR1_ENST00000409283.2_Frame_Shift_Del_p.N341fs	NM_001105.4	NP_001096.1	Q04771	ACVR1_HUMAN	activin A receptor, type I	341	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|acute inflammatory response (GO:0002526)|atrial septum primum morphogenesis (GO:0003289)|BMP signaling pathway (GO:0030509)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to glucocorticoid stimulus (GO:0071385)|determination of left/right symmetry (GO:0007368)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion cell fate commitment (GO:0061445)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation with mouth forming second (GO:0001702)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|mesoderm formation (GO:0001707)|mitral valve morphogenesis (GO:0003183)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of signal transduction (GO:0009968)|neural crest cell migration (GO:0001755)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of bone mineralization (GO:0030501)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of ossification (GO:0030278)|regulation of skeletal muscle tissue development (GO:0048641)|smooth muscle cell differentiation (GO:0051145)|transforming growth factor beta receptor signaling pathway (GO:0007179)|urogenital system development (GO:0001655)	activin receptor complex (GO:0048179)|apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.N341I(1)		endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	19				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	AACCAGAATATTTTTGCTCTT	0.363																																					p.N341fs		Atlas-INDEL	.											.	ACVR1	52	.	1	Substitution - Missense(1)	large_intestine(1)	c.1023delT						.						90.0	90.0	90.0					2																	158622477		2203	4300	6503	SO:0001589	frameshift_variant	90	exon8			.		CCDS2206.1	2q23-q24	2008-06-13			ENSG00000115170	ENSG00000115170			171	protein-coding gene	gene with protein product		102576		ACVRLK2		8397373	Standard	NM_001105		Approved	SKR1, ALK2, ACVR1A	uc010fog.2	Q04771	OTTHUMG00000131967	ENST00000263640.3:c.1022delA	chr2.hg19:g.158622477delT	ENSP00000263640:p.Asn341fs	141.0	0.0		160.0	10.0	NM_001105		Frame_Shift_Del	DEL	ENST00000263640.3	hg19	CCDS2206.1																																																																																			.	.		0.363	ACVR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254927.1	NM_001105	
C11orf54	28970	hgsc.bcm.edu	37	11	93492928	93492928	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:93492928delC	ENST00000331239.4	+	8	857	c.678delC	c.(676-678)tgcfs	p.C226fs	C11orf54_ENST00000540113.1_Frame_Shift_Del_p.C207fs|C11orf54_ENST00000528099.1_Frame_Shift_Del_p.C226fs|C11orf54_ENST00000354421.3_Frame_Shift_Del_p.C226fs|C11orf54_ENST00000528288.1_Frame_Shift_Del_p.C176fs			Q9H0W9	CK054_HUMAN	chromosome 11 open reading frame 54	226					metabolic process (GO:0008152)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|large_intestine(1)|lung(5)	8		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TTTCTTCCTGCCCCTTGAACT	0.303																																					p.C176fs		Atlas-INDEL	.											.	C11orf54	23	.	0			c.527delG						.						126.0	137.0	133.0					11																	93492928		2201	4298	6499	SO:0001589	frameshift_variant	28970	exon7			.	AF092133	CCDS8294.1, CCDS66204.1, CCDS73365.1, CCDS73366.1	11q21	2012-08-09			ENSG00000182919	ENSG00000182919			30204	protein-coding gene	gene with protein product		615810				16522806	Standard	NM_014039		Approved	PTD012	uc001pef.3	Q9H0W9	OTTHUMG00000167452	ENST00000331239.4:c.678delC	chr11.hg19:g.93492928delC	ENSP00000331209:p.Cys226fs	102.0	0.0		165.0	11.0	NM_014039	A8K850|Q6FI88|Q6XYB0|Q96EI3|Q96IX1|Q9Y6B4	Frame_Shift_Del	DEL	ENST00000331239.4	hg19																																																																																				.	.		0.303	C11orf54-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394671.1	NM_014039	
TACSTD2	4070	hgsc.bcm.edu	37	1	59041883	59041883	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:59041883delC	ENST00000371225.2	-	1	1283	c.946delG	c.(946-948)gagfs	p.E316fs		NM_002353.2	NP_002344.2	P09758	TACD2_HUMAN	tumor-associated calcium signal transducer 2	316					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell motility (GO:2000146)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of stem cell differentiation (GO:2000738)|regulation of epithelial cell proliferation (GO:0050678)|ureteric bud morphogenesis (GO:0060675)|visual perception (GO:0007601)	basal plasma membrane (GO:0009925)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|nucleus (GO:0005634)	receptor activity (GO:0004872)					all_cancers(7;6.54e-05)					TTTCTCAACTCCCCCAGTTCC	0.612																																					p.E316fs		Atlas-INDEL	.											.	TACSTD2	6	.	0			c.947delA						.						71.0	67.0	68.0					1																	59041883		2203	4300	6503	SO:0001589	frameshift_variant	4070	exon1			.	X77753	CCDS609.1	1p32	2008-02-05			ENSG00000184292	ENSG00000184292			11530	protein-coding gene	gene with protein product		137290		M1S1		8382772, 11306819	Standard	NM_002353		Approved	TROP2, GA733-1, EGP-1	uc001cyz.4	P09758	OTTHUMG00000010067	ENST00000371225.2:c.946delG	chr1.hg19:g.59041883delC	ENSP00000360269:p.Glu316fs	64.0	0.0		121.0	10.0	NM_002353	Q15658|Q6FG48|Q7Z7Q4|Q96QD2	Frame_Shift_Del	DEL	ENST00000371225.2	hg19	CCDS609.1																																																																																			.	.		0.612	TACSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027818.1	NM_002353	
ROBO1	6091	hgsc.bcm.edu	37	3	78710322	78710322	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:78710322delA	ENST00000464233.1	-	16	2291	c.2178delT	c.(2176-2178)tttfs	p.F726fs	ROBO1_ENST00000467549.1_Frame_Shift_Del_p.F690fs|ROBO1_ENST00000495273.1_Frame_Shift_Del_p.F690fs|ROBO1_ENST00000436010.2_Frame_Shift_Del_p.F687fs	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	726	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TCCTCACTTCAAAAACTAACC	0.398																																					p.E727fs		Atlas-INDEL	.											.	ROBO1	833	.	0			c.2179delG						.						103.0	100.0	101.0					3																	78710322		1826	4092	5918	SO:0001589	frameshift_variant	6091	exon16			.	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10249	protein-coding gene	gene with protein product		602430	"""roundabout (axon guidance receptor, Drosophila) homolog 1"""			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.2178delT	chr3.hg19:g.78710322delA	ENSP00000420321:p.Phe726fs	127.0	0.0		165.0	10.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Frame_Shift_Del	DEL	ENST00000464233.1	hg19	CCDS54611.1																																																																																			.	.		0.398	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941	
FAM21A	387680	hgsc.bcm.edu	37	10	51829353	51829353	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:51829353delC	ENST00000282633.5	+	3	218	c.173delC	c.(172-174)accfs	p.T58fs	RP11-324H6.5_ENST00000456967.1_RNA|FAM21A_ENST00000351071.6_Frame_Shift_Del_p.T58fs|FAM21A_ENST00000314664.7_Frame_Shift_Del_p.T58fs|FAM21A_ENST00000492914.1_3'UTR	NM_001005751.1	NP_001005751.1	Q641Q2	FA21A_HUMAN	family with sequence similarity 21, member A	58					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)				breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	15						ATCTCTAGGACCCATGAAATC	0.368																																					p.T58fs		Atlas-INDEL	.											.	FAM21A	32	.	0			c.172delA						.						121.0	117.0	118.0					10																	51829353		1823	4080	5903	SO:0001589	frameshift_variant	387680	exon3			.	BC082258	CCDS41527.1	10q11.23	2014-06-19			ENSG00000099290	ENSG00000099290			23416	protein-coding gene	gene with protein product			"""family with sequence similarity 21, member B"""	FAM21B			Standard	XM_005269805		Approved	bA56A21.1, bA98I6.1, FLJ10824	uc001jjb.3	Q641Q2	OTTHUMG00000018225	ENST00000282633.5:c.173delC	chr10.hg19:g.51829353delC	ENSP00000282633:p.Thr58fs	187.0	0.0		191.0	12.0	NM_001005751	A2A3S2|A2A3U6|Q6DHY0	Frame_Shift_Del	DEL	ENST00000282633.5	hg19	CCDS41527.1																																																																																			.	.		0.368	FAM21A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276917.2	NM_001005751	
ABL2	27	hgsc.bcm.edu	37	1	179086622	179086622	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:179086622delC	ENST00000502732.1	-	8	1456	c.1253delG	c.(1252-1254)ggafs	p.G418fs	ABL2_ENST00000367623.4_Frame_Shift_Del_p.G397fs|ABL2_ENST00000512653.1_Frame_Shift_Del_p.G403fs|ABL2_ENST00000504405.1_Frame_Shift_Del_p.G382fs|ABL2_ENST00000511413.1_Frame_Shift_Del_p.G418fs|ABL2_ENST00000408940.3_Frame_Shift_Del_p.G382fs|ABL2_ENST00000344730.3_Frame_Shift_Del_p.G403fs|ABL2_ENST00000392043.3_Frame_Shift_Del_p.G397fs|ABL2_ENST00000507173.1_Frame_Shift_Del_p.G397fs	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	418	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	ATGGTTTTCTCCCACTAGGCA	0.428			T	ETV6	AML																																p.G418fs		Atlas-INDEL	.		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	.	ABL2	307	.	0			c.1254delA						.						118.0	105.0	110.0					1																	179086622		2203	4300	6503	SO:0001589	frameshift_variant	27	exon8			.	M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"""SH2 domain containing"""	77	protein-coding gene	gene with protein product	"""Abelson-related gene"""	164690	"""v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)"", ""v-abl Abelson murine leukemia viral oncogene homolog 2"", ""c-abl oncogene 2, non-receptor tyrosine kinase"""	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.1253delG	chr1.hg19:g.179086622delC	ENSP00000427562:p.Gly418fs	94.0	0.0		182.0	12.0	NM_007314	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Frame_Shift_Del	DEL	ENST00000502732.1	hg19	CCDS30947.1																																																																																			.	.		0.428	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158	
UTP20	27340	hgsc.bcm.edu	37	12	101746865	101746865	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:101746865delA	ENST00000261637.4	+	40	5239	c.5065delA	c.(5065-5067)aaafs	p.K1689fs		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1689					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CTTTGACCACAAAACTCTTGA	0.274																																					p.H1688fs		Atlas-INDEL	.											.	UTP20	222	.	0			c.5064delC						.						49.0	52.0	51.0					12																	101746865		2200	4293	6493	SO:0001589	frameshift_variant	27340	exon40			.	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.5065delA	chr12.hg19:g.101746865delA	ENSP00000261637:p.Lys1689fs	141.0	0.0		186.0	13.0	NM_014503	Q9H3H4	Frame_Shift_Del	DEL	ENST00000261637.4	hg19	CCDS9081.1																																																																																			.	.		0.274	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
SNRNP48	154007	hgsc.bcm.edu	37	6	7594353	7594353	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:7594353delT	ENST00000342415.5	+	3	351	c.292delT	c.(292-294)tttfs	p.F99fs		NM_152551.3	NP_689764.3	Q6IEG0	SNR48_HUMAN	small nuclear ribonucleoprotein 48kDa (U11/U12)	99					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)			kidney(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						TAATCCTGAGTTTTTCTATGA	0.234																																					p.E97fs		Atlas-INDEL	.											.	SNRNP48	32	.	0			c.291delG						.						23.0	24.0	24.0					6																	7594353		2134	4195	6329	SO:0001589	frameshift_variant	154007	exon3			.	AK056796	CCDS4502.1	6p24.3	2011-10-11	2008-10-29	2008-10-29	ENSG00000168566	ENSG00000168566			21368	protein-coding gene	gene with protein product	"""U11/U12 snRNP 48K"""		"""chromosome 6 open reading frame 151"""	C6orf151		15146077	Standard	XR_427825		Approved	FLJ32234, dJ512B11.2, dJ336K20B.1	uc003mxr.3	Q6IEG0	OTTHUMG00000014213	ENST00000342415.5:c.292delT	chr6.hg19:g.7594353delT	ENSP00000339834:p.Phe99fs	98.0	0.0		176.0	11.0	NM_152551	A8K8P4|Q14C91|Q5T339|Q5THM1|Q5THM2|Q96MK1	Frame_Shift_Del	DEL	ENST00000342415.5	hg19	CCDS4502.1																																																																																			.	.		0.234	SNRNP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039787.3	NM_152551	
FBXL13	222235	hgsc.bcm.edu	37	7	102665640	102665640	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:102665640delT	ENST00000313221.4	-	6	791	c.365delA	c.(364-366)aatfs	p.N122fs	FBXL13_ENST00000379308.3_Frame_Shift_Del_p.N122fs|FBXL13_ENST00000456695.1_Frame_Shift_Del_p.N122fs|FBXL13_ENST00000379305.3_Frame_Shift_Del_p.N122fs|FBXL13_ENST00000455112.2_Frame_Shift_Del_p.N122fs|FBXL13_ENST00000436908.1_Frame_Shift_Del_p.N122fs|FBXL13_ENST00000379306.3_Frame_Shift_Del_p.N122fs|FBXL13_ENST00000471074.1_5'UTR|FBXL13_ENST00000393772.2_Frame_Shift_Del_p.N122fs	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	122										NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						TATTAACCTATTTTTCCATTT	0.323																																					p.N122fs		Atlas-INDEL	.											.	FBXL13	65	.	0			c.366delT						.						44.0	42.0	43.0					7																	102665640		2201	4297	6498	SO:0001589	frameshift_variant	222235	exon6			.	BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			ENSG00000161040	ENSG00000161040		"""F-boxes / Leucine-rich repeats"""	21658	protein-coding gene	gene with protein product		609080					Standard	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	Q8NEE6	OTTHUMG00000157224	ENST00000313221.4:c.365delA	chr7.hg19:g.102665640delT	ENSP00000321927:p.Asn122fs	103.0	0.0		163.0	11.0	NM_145032	C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Frame_Shift_Del	DEL	ENST00000313221.4	hg19	CCDS5726.1																																																																																			.	.		0.323	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1	NM_145032	
PDCD11	22984	hgsc.bcm.edu	37	10	105205170	105205170	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:105205170delC	ENST00000369797.3	+	36	5574	c.5480delC	c.(5479-5481)gccfs	p.A1827fs		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1827					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)		CTGAGCTTGGCCCCCAAGAGA	0.547																																					p.A1827fs		Atlas-INDEL	.											.	PDCD11	160	.	0			c.5479delG						.						160.0	139.0	146.0					10																	105205170		2203	4300	6503	SO:0001589	frameshift_variant	22984	exon36			.	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.5480delC	chr10.hg19:g.105205170delC	ENSP00000358812:p.Ala1827fs	174.0	0.0		175.0	12.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Frame_Shift_Del	DEL	ENST00000369797.3	hg19	CCDS31276.1																																																																																			.	.		0.547	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
RPS3A	6189	hgsc.bcm.edu	37	4	152025347	152025347	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:152025347delA	ENST00000509736.1	+	3	319	c.225delA	c.(223-225)ggafs	p.G75fs	RPS3A_ENST00000506126.1_Frame_Shift_Del_p.G157fs|RPS3A_ENST00000514682.1_Frame_Shift_Del_p.G157fs|SNORD73A_ENST00000386062.1_RNA|RPS3A_ENST00000274065.4_Frame_Shift_Del_p.G194fs|SNORD73_ENST00000364394.1_RNA|RPS3A_ENST00000512690.1_Frame_Shift_Del_p.K192fs					ribosomal protein S3A											endometrium(1)|lung(1)|ovary(1)|pancreas(1)	4	all_hematologic(180;0.093)					ACAGCATTGGAAAAGACATAG	0.358																																					p.G194fs		Atlas-INDEL	.											.	RPS3A	11	.	0			c.581delG						.						52.0	54.0	53.0					4																	152025347		2203	4300	6503	SO:0001589	frameshift_variant	6189	exon5			.	X87373	CCDS3775.1	4q31.2-q31.3	2011-04-05			ENSG00000145425	ENSG00000145425		"""S ribosomal proteins"""	10421	protein-coding gene	gene with protein product		180478		MFTL		8647443, 1398113	Standard	NM_001006		Approved	S3A	uc003ilz.4	P61247	OTTHUMG00000161445	ENST00000509736.1:c.225delA	chr4.hg19:g.152025347delA	ENSP00000422994:p.Gly75fs	153.0	0.0		159.0	10.0	NM_001006		Frame_Shift_Del	DEL	ENST00000509736.1	hg19																																																																																				.	.		0.358	RPS3A-006	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000364962.2		
CTBP1	1487	hgsc.bcm.edu	37	4	1206096	1206096	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:1206096delG	ENST00000290921.6	-	9	1436	c.1255delC	c.(1255-1257)cacfs	p.H419fs	CTBP1_ENST00000382952.3_Frame_Shift_Del_p.H408fs	NM_001328.2	NP_001319.1	Q13363	CTBP1_HUMAN	C-terminal binding protein 1	419					Golgi organization (GO:0007030)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone deacetylation (GO:0031065)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of transcription by chromatin organization (GO:0034401)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.00818)	Colorectal(103;0.2)		GAAGGGGCGTGGGGCGGGTGG	0.701																																					p.H419fs		Atlas-INDEL	.											.	CTBP1	30	.	0			c.1256delA						.						10.0	11.0	11.0					4																	1206096		2152	4257	6409	SO:0001589	frameshift_variant	1487	exon9			.	U37408	CCDS3348.1, CCDS43203.1	4p16	2008-02-05			ENSG00000159692	ENSG00000159692			2494	protein-coding gene	gene with protein product	"""brefeldin A-ribosylated substrate"""	602618				9479502	Standard	XM_005272261		Approved	BARS	uc003gcv.1	Q13363	OTTHUMG00000089259	ENST00000290921.6:c.1255delC	chr4.hg19:g.1206096delG	ENSP00000290921:p.His419fs	177.0	0.0		180.0	11.0	NM_001328	Q4W5N3|Q7Z2Q5	Frame_Shift_Del	DEL	ENST00000290921.6	hg19	CCDS3348.1																																																																																			.	.		0.701	CTBP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000202938.1	NM_001328	
RASAL1	8437	hgsc.bcm.edu	37	12	113553545	113553545	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:113553545delC	ENST00000261729.5	-	11	1213	c.898delG	c.(898-900)gacfs	p.D300fs	RASAL1_ENST00000446861.3_Frame_Shift_Del_p.D300fs|RASAL1_ENST00000546530.1_Frame_Shift_Del_p.D300fs|RASAL1_ENST00000548055.1_Frame_Shift_Del_p.D300fs|RASAL1_ENST00000418411.2_5'UTR			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	300					intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						TGGCGGCAGTCCCCCAAGGTC	0.637																																					p.D300fs		Atlas-INDEL	.											.	RASAL1	89	.	0			c.899delA						.						56.0	62.0	60.0					12																	113553545		2203	4300	6503	SO:0001589	frameshift_variant	8437	exon11			.	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"""Pleckstrin homology (PH) domain containing"""	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.898delG	chr12.hg19:g.113553545delC	ENSP00000261729:p.Asp300fs	119.0	0.0		194.0	12.0	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Frame_Shift_Del	DEL	ENST00000261729.5	hg19	CCDS9165.1																																																																																			.	.		0.637	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658	
OR4X1	390113	hgsc.bcm.edu	37	11	48286313	48286313	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:48286313delG	ENST00000320048.1	+	1	901	c.901delG	c.(901-903)gggfs	p.G302fs		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	28						GAGATTTATTGGGGGAAAAGT	0.398																																					p.I300fs		Atlas-INDEL	.											.	OR4X1	75	.	0			c.900delT						.						35.0	35.0	35.0					11																	48286313		2201	4296	6497	SO:0001589	frameshift_variant	390113	exon1			.	AB065544	CCDS31487.1	11p11.2	2013-10-10	2013-10-10		ENSG00000176567	ENSG00000176567		"""GPCR / Class A : Olfactory receptors"""	14854	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily X, member 1"""				Standard	NM_001004726		Approved		uc010rht.2	Q8NH49	OTTHUMG00000165301	ENST00000320048.1:c.901delG	chr11.hg19:g.48286313delG	ENSP00000321506:p.Gly302fs	114.0	0.0		152.0	11.0	NM_001004726	Q6IF74	Frame_Shift_Del	DEL	ENST00000320048.1	hg19	CCDS31487.1																																																																																			.	.		0.398	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726	
TTN	7273	hgsc.bcm.edu	37	2	179429759	179429759	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:179429759delT	ENST00000591111.1	-	276	76401	c.76177delA	c.(76177-76179)atafs	p.I25393fs	TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.I18094fs|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000460472.2_Frame_Shift_Del_p.I17969fs|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000589042.1_Frame_Shift_Del_p.I27034fs|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.I18161fs|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.I24466fs|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25393	Fibronectin type-III 84. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)			AGTTTGGTTATTTTAATTGTT	0.413																																					p.I27034fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.81101delT						.						135.0	133.0	134.0					2																	179429759		1904	4115	6019	SO:0001589	frameshift_variant	7273	exon326			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.76177delA	chr2.hg19:g.179429759delT	ENSP00000465570:p.Ile25393fs	163.0	0.0		176.0	11.0	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																																																																																				.	.		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
HECTD1	25831	hgsc.bcm.edu	37	14	31617960	31617960	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:31617960delT	ENST00000399332.1	-	15	2951	c.2463delA	c.(2461-2463)aaafs	p.K821fs	HECTD1_ENST00000553700.1_Frame_Shift_Del_p.K821fs	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	821					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TAGATTTCAGTTTTCTGCCTC	0.323																																					p.L822X		Atlas-INDEL	.											.	HECTD1	159	.	0			c.2464delC						.						99.0	89.0	92.0					14																	31617960		1803	4065	5868	SO:0001589	frameshift_variant	25831	exon15			.	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.2463delA	chr14.hg19:g.31617960delT	ENSP00000382269:p.Lys821fs	189.0	0.0		178.0	11.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Frame_Shift_Del	DEL	ENST00000399332.1	hg19	CCDS41939.1																																																																																			.	.		0.323	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
BBX	56987	hgsc.bcm.edu	37	3	107497314	107497314	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:107497314delA	ENST00000325805.8	+	13	2438	c.2151delA	c.(2149-2151)agafs	p.R717fs	BBX_ENST00000473542.1_3'UTR|BBX_ENST00000402543.1_Frame_Shift_Del_p.R717fs|BBX_ENST00000416476.2_Frame_Shift_Del_p.E381fs|BBX_ENST00000406780.1_Frame_Shift_Del_p.R717fs|BBX_ENST00000415149.2_Frame_Shift_Del_p.R717fs			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	717	Lys-rich.				bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			CTGTCCCAAGAAAAAAGAAGA	0.428																																					p.R717fs		Atlas-INDEL	.											.	BBX	156	.	0			c.2150delG						.						101.0	98.0	99.0					3																	107497314		2203	4300	6503	SO:0001589	frameshift_variant	56987	exon13			.	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"""x 001 protein"""					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.2151delA	chr3.hg19:g.107497314delA	ENSP00000319974:p.Arg717fs	187.0	0.0		275.0	20.0	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Frame_Shift_Del	DEL	ENST00000325805.8	hg19	CCDS46881.1																																																																																			.	.		0.428	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235	
PRSS57	400668	hgsc.bcm.edu	37	19	687117	687117	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:687117delG	ENST00000329267.7	-	4	482	c.453delC	c.(451-453)cccfs	p.P151fs		NM_214710.3	NP_999875	Q6UWY2	PRS57_HUMAN	protease, serine, 57	151	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|lung(5)	6						TCCCCGCTGTGGGGGGCCTGG	0.682																																					p.T152fs		Atlas-INDEL	.											.	PRSS57	18	.	0			c.454delA						.																																			SO:0001589	frameshift_variant	400668	exon4			.	AY358594	CCDS12041.1	19p13.3	2012-03-26	2011-03-07	2011-03-07		ENSG00000185198		"""Serine peptidases / Serine peptidases"""	31397	protein-coding gene	gene with protein product			"""protease, serine-like 1"""	PRSSL1		12975309	Standard	NM_214710		Approved	UNQ782	uc002lpl.1	Q6UWY2		ENST00000329267.7:c.453delC	chr19.hg19:g.687117delG	ENSP00000327386:p.Pro151fs	155.0	0.0		175.0	11.0	NM_214710	B2RNW8	Frame_Shift_Del	DEL	ENST00000329267.7	hg19	CCDS12041.1																																																																																			.	.		0.682	PRSS57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452480.2	NM_214710	
TLR1	7096	hgsc.bcm.edu	37	4	38800352	38800352	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:38800352delT	ENST00000502213.2	-	3	330	c.101delA	c.(100-102)aacfs	p.N34fs	TLR1_ENST00000308979.2_Frame_Shift_Del_p.N34fs			Q15399	TLR1_HUMAN	toll-like receptor 1	34					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						GATGAGACCGTTTTTTGACCT	0.323																																					p.N34fs	GBM(5;216 373 40795 46382)	Atlas-INDEL	.											.	TLR1	70	.	0			c.102delC						.						63.0	68.0	67.0					4																	38800352		2197	4299	6496	SO:0001589	frameshift_variant	7096	exon4			.	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.101delA	chr4.hg19:g.38800352delT	ENSP00000421259:p.Asn34fs	127.0	0.0		151.0	11.0	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Frame_Shift_Del	DEL	ENST00000502213.2	hg19	CCDS33973.1																																																																																			.	.		0.323	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
PPOX	5498	hgsc.bcm.edu	37	1	161140706	161140706	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:161140706delC	ENST00000367999.4	+	12	1524	c.1258delC	c.(1258-1260)cccfs	p.P420fs	PPOX_ENST00000432542.2_Intron|PPOX_ENST00000495483.1_Intron|PPOX_ENST00000544598.1_Frame_Shift_Del_p.P128fs|PPOX_ENST00000352210.5_Frame_Shift_Del_p.P420fs|B4GALT3_ENST00000470882.1_5'Flank|PPOX_ENST00000535223.1_Intron	NM_001122764.1	NP_001116236.1	P50336	PPOX_HUMAN	protoporphyrinogen oxidase	420			P -> R (in VP). {ECO:0000269|PubMed:24073655}.		heme biosynthetic process (GO:0006783)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound biosynthetic process (GO:0006779)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of mitochondrial inner membrane (GO:0031304)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)	flavin adenine dinucleotide binding (GO:0050660)|oxygen-dependent protoporphyrinogen oxidase activity (GO:0004729)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(3)	15	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			GAACTGCATTCCCCAGTATAC	0.473																																					p.I419fs		Atlas-INDEL	.											.	PPOX	34	.	0			c.1257delT						.						132.0	133.0	133.0					1																	161140706		2203	4300	6503	SO:0001589	frameshift_variant	5498	exon12			.	BC002357	CCDS1221.1	1q22	2008-02-05			ENSG00000143224	ENSG00000143224	1.3.3.4		9280	protein-coding gene	gene with protein product		600923	"""variegate porphyria"""	VP		8575762, 10457135	Standard	NM_000309		Approved	PPO	uc001fyg.2	P50336	OTTHUMG00000034342	ENST00000367999.4:c.1258delC	chr1.hg19:g.161140706delC	ENSP00000356978:p.Pro420fs	87.0	0.0		120.0	10.0	NM_001122764	D3DVG0|Q5VTW8	Frame_Shift_Del	DEL	ENST00000367999.4	hg19	CCDS1221.1																																																																																			.	.		0.473	PPOX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082993.1	NM_000309	
LYPD1	116372	hgsc.bcm.edu	37	2	133403775	133403775	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:133403775delG	ENST00000397463.2	-	3	541	c.269delC	c.(268-270)ccafs	p.P90fs	GPR39_ENST00000329321.3_3'UTR|LYPD1_ENST00000345008.6_Frame_Shift_Del_p.P38fs|GPR39_ENST00000470071.1_3'UTR	NM_144586.5	NP_653187.3	Q8N2G4	LYPD1_HUMAN	LY6/PLAUR domain containing 1	90	UPAR/Ly6.					anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				lung(2)	2						CAGTTTCCCTGGGGAGCAGAA	0.572																																					p.P90fs		Atlas-INDEL	.											.	LYPD1	11	.	0			c.270delA						.						54.0	61.0	59.0					2																	133403775		2082	4208	6290	SO:0001589	frameshift_variant	116372	exon3			.	AK075487	CCDS42759.1, CCDS46416.1	2q21.2	2008-02-05		2005-08-30	ENSG00000150551	ENSG00000150551			28431	protein-coding gene	gene with protein product		610450		LYPDC1		12477932	Standard	NM_144586		Approved	MGC29643	uc002ttn.3	Q8N2G4	OTTHUMG00000153609	ENST00000397463.2:c.269delC	chr2.hg19:g.133403775delG	ENSP00000380605:p.Pro90fs	117.0	0.0		156.0	10.0	NM_144586	H7BXW6|Q6ZP52|Q6ZWI4|Q96AC2	Frame_Shift_Del	DEL	ENST00000397463.2	hg19	CCDS42759.1																																																																																			.	.		0.572	LYPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331821.1	NM_144586	
TCEB3	6924	hgsc.bcm.edu	37	1	24077422	24077422	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:24077422delG	ENST00000418390.2	+	4	676	c.405delG	c.(403-405)gagfs	p.E135fs	TCEB3_ENST00000487554.1_3'UTR|TCEB3_ENST00000609199.1_Frame_Shift_Del_p.E109fs	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	135					gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		AGGAGATGGAGGGGGACTACC	0.527																																					p.E135fs		Atlas-INDEL	.											.	TCEB3	61	.	0			c.404delA						.						47.0	52.0	51.0					1																	24077422		2203	4300	6503	SO:0001589	frameshift_variant	6924	exon4			.	L47345	CCDS239.2	1p36.1	2010-06-22	2002-08-29		ENSG00000011007	ENSG00000011007			11620	protein-coding gene	gene with protein product		600786	"""transcription elongation factor B (SIII), polypeptide 3 (110kD, elongin A)"""			8586449, 7660129	Standard	NM_003198		Approved	SIII, TCEB3A	uc001bho.3	Q14241	OTTHUMG00000002957	ENST00000418390.2:c.405delG	chr1.hg19:g.24077422delG	ENSP00000395574:p.Glu135fs	70.0	0.0		128.0	10.0	NM_003198	B2R7Q8|Q8IXH1	Frame_Shift_Del	DEL	ENST00000418390.2	hg19	CCDS239.2																																																																																			.	.		0.527	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198	
C3orf30	152405	hgsc.bcm.edu	37	3	118867142	118867142	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:118867142delA	ENST00000295622.1	+	2	1554	c.1514delA	c.(1513-1515)gaafs	p.E505fs	RP11-484M3.5_ENST00000490594.1_Intron|IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	505										NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		CAATACATGGAAAAACACCAC	0.333																																					p.E505fs		Atlas-INDEL	.											.	C3orf30	64	.	0			c.1513delG						.						66.0	70.0	69.0					3																	118867142		2203	4300	6503	SO:0001589	frameshift_variant	152405	exon2			.	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.1514delA	chr3.hg19:g.118867142delA	ENSP00000295622:p.Glu505fs	170.0	0.0		279.0	18.0	NM_152539	A1L4B7	Frame_Shift_Del	DEL	ENST00000295622.1	hg19	CCDS2984.1																																																																																			.	.		0.333	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
AQR	9716	hgsc.bcm.edu	37	15	35174733	35174733	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:35174733delT	ENST00000156471.5	-	27	3360	c.3135delA	c.(3133-3135)aaafs	p.K1045fs		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	1045					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		AGTCATGTCGTTTTAAGGCAG	0.358																																					p.R1046fs		Atlas-INDEL	.											.	AQR	139	.	0			c.3136delC						.						79.0	73.0	75.0					15																	35174733		1832	4088	5920	SO:0001589	frameshift_variant	9716	exon27			.	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 164"""	610548	"""aquarius homolog (mouse)"""			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.3135delA	chr15.hg19:g.35174733delT	ENSP00000156471:p.Lys1045fs	161.0	0.0		149.0	10.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Frame_Shift_Del	DEL	ENST00000156471.5	hg19	CCDS42013.1																																																																																			.	.		0.358	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691	
PKD2L1	9033	hgsc.bcm.edu	37	10	102054379	102054379	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:102054379delA	ENST00000318222.3	-	9	1954	c.1572delT	c.(1570-1572)tttfs	p.F524fs	PKD2L1_ENST00000338519.3_Frame_Shift_Del_p.F449fs|PKD2L1_ENST00000353274.3_Frame_Shift_Del_p.F524fs	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	524					cation transport (GO:0006812)|cellular response to acidic pH (GO:0071468)|detection of chemical stimulus involved in sensory perception of sour taste (GO:0001581)|detection of mechanical stimulus (GO:0050982)|potassium ion transmembrane transport (GO:0071805)|protein homotrimerization (GO:0070207)|sensory perception of sour taste (GO:0050915)|smoothened signaling pathway (GO:0007224)|sodium ion transmembrane transport (GO:0035725)	calcium channel complex (GO:0034704)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	alpha-actinin binding (GO:0051393)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-activated potassium channel activity (GO:0015269)|cation channel activity (GO:0005261)|cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|sodium channel activity (GO:0005272)|sour taste receptor activity (GO:0033040)			NS(2)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	43		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		CATTGTAGTCAAAGTCCCCGA	0.522																																					p.D525fs		Atlas-INDEL	.											.	PKD2L1	103	.	0			c.1573delG						.						172.0	160.0	164.0					10																	102054379		2203	4300	6503	SO:0001589	frameshift_variant	9033	exon9			.	AF094827	CCDS7492.1	10q24.31	2011-12-16			ENSG00000107593	ENSG00000107593		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9011	protein-coding gene	gene with protein product	"""transient receptor potential cation channel, subfamily P, member 3"""	604532		PKD2L, PKDL		9878261, 9748274	Standard	NM_016112		Approved	PCL, TRPP3	uc001kqx.1	Q9P0L9	OTTHUMG00000018910	ENST00000318222.3:c.1572delT	chr10.hg19:g.102054379delA	ENSP00000325296:p.Phe524fs	128.0	0.0		157.0	10.0	NM_016112	O75972|Q5W039|Q9UP35|Q9UPA2	Frame_Shift_Del	DEL	ENST00000318222.3	hg19	CCDS7492.1																																																																																			.	.		0.522	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049863.2	NM_016112	
ZNF678	339500	hgsc.bcm.edu	37	1	227843509	227843509	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:227843509delA	ENST00000343776.5	+	4	1903	c.1558delA	c.(1558-1560)aaafs	p.K521fs	ZNF678_ENST00000608949.1_Intron|ZNF678_ENST00000397097.3_Frame_Shift_Del_p.K576fs	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	521					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				TGACAAATGTAAAAAATGTGG	0.323																																					p.C574X		Atlas-INDEL	.											.	ZNF678	137	.	0			c.1722delT						.						40.0	44.0	43.0					1																	227843509		2202	4295	6497	SO:0001589	frameshift_variant	339500	exon4			.	BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"""Zinc fingers, C2H2-type"", ""-"""	28652	protein-coding gene	gene with protein product	"""hypothetical protein MGC42493"""					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.1558delA	chr1.hg19:g.227843509delA	ENSP00000344828:p.Lys521fs	120.0	0.0		189.0	12.0	NM_178549	Q8IVQ9	Frame_Shift_Del	DEL	ENST00000343776.5	hg19																																																																																				.	.		0.323	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549	
ALPK2	115701	hgsc.bcm.edu	37	18	56246440	56246440	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:56246440delT	ENST00000361673.3	-	4	1781	c.1568delA	c.(1567-1569)aagfs	p.K523fs	ALPK2_ENST00000587399.1_5'UTR	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	523						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCATAAGTCCTTTCCCCCCAC	0.522											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K523fs		Atlas-INDEL	.											.	ALPK2	487	.	0			c.1569delG						.						227.0	226.0	226.0					18																	56246440		2203	4300	6503	SO:0001589	frameshift_variant	115701	exon4			.	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.1568delA	chr18.hg19:g.56246440delT	ENSP00000354991:p.Lys523fs	105.0	0.0	1014	124.0	10.0	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Frame_Shift_Del	DEL	ENST00000361673.3	hg19	CCDS11966.2																																																																																			.	.		0.522	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
SORBS2	8470	hgsc.bcm.edu	37	4	186583322	186583322	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:186583322delG	ENST00000284776.7	-	5	539	c.30delC	c.(28-30)cccfs	p.P10fs	SORBS2_ENST00000431808.1_Frame_Shift_Del_p.P10fs|SORBS2_ENST00000449407.2_Frame_Shift_Del_p.P96fs|SORBS2_ENST00000355634.5_Frame_Shift_Del_p.P110fs|SORBS2_ENST00000319471.9_Frame_Shift_Del_p.P96fs|SORBS2_ENST00000393528.3_Frame_Shift_Del_p.P56fs|SORBS2_ENST00000448662.2_Frame_Shift_Del_p.P79fs|SORBS2_ENST00000437304.2_Frame_Shift_Del_p.P189fs	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	10					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)		AATATGCCGAGGGGGAAAACG	0.512																																					p.S190fs	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-INDEL	.											.	SORBS2	300	.	0			c.568delT						.						117.0	101.0	107.0					4																	186583322		2203	4300	6503	SO:0001589	frameshift_variant	8470	exon6			.		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.30delC	chr4.hg19:g.186583322delG	ENSP00000284776:p.Pro10fs	209.0	0.0		225.0	15.0	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																																																																																			.	.		0.512	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
VIL1	7429	hgsc.bcm.edu	37	2	219292980	219292980	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:219292980delG	ENST00000248444.5	+	6	575	c.487delG	c.(487-489)gggfs	p.G163fs	VIL1_ENST00000440053.1_Frame_Shift_Del_p.G163fs|VIL1_ENST00000392114.2_Intron	NM_007127.2	NP_009058.2	P09327	VILI_HUMAN	villin 1	163	Core.				actin filament capping (GO:0051693)|actin filament depolymerization (GO:0030042)|actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cytoplasmic actin-based contraction involved in cell motility (GO:0060327)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell migration (GO:0010634)|protein complex assembly (GO:0006461)|regulation of actin nucleation (GO:0051125)|regulation of cell shape (GO:0008360)|regulation of lamellipodium morphogenesis (GO:2000392)|regulation of wound healing (GO:0061041)|response to bacterium (GO:0009617)	actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|microvillus (GO:0005902)|ruffle (GO:0001726)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|identical protein binding (GO:0042802)|lysophosphatidic acid binding (GO:0035727)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTTCAACCGAGGGGATGTTTT	0.547																																					p.R162fs		Atlas-INDEL	.											.	VIL1	65	.	0			c.486delA						.						140.0	128.0	132.0					2																	219292980		2203	4300	6503	SO:0001589	frameshift_variant	7429	exon6			.	X12901	CCDS2417.1	2q35	2012-10-02			ENSG00000127831	ENSG00000127831			12690	protein-coding gene	gene with protein product		193040		VIL		2846586	Standard	NM_007127		Approved	D2S1471	uc002via.3	P09327	OTTHUMG00000133112	ENST00000248444.5:c.487delG	chr2.hg19:g.219292980delG	ENSP00000248444:p.Gly163fs	213.0	0.0		186.0	12.0	NM_007127	B2R9A7|Q53S11|Q96AC8	Frame_Shift_Del	DEL	ENST00000248444.5	hg19	CCDS2417.1																																																																																			.	.		0.547	VIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256778.3	NM_007127	
VCAM1	7412	hgsc.bcm.edu	37	1	101197977	101197977	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:101197977delC	ENST00000294728.2	+	7	1630	c.1529delC	c.(1528-1530)gccfs	p.A510fs	VCAM1_ENST00000347652.2_Frame_Shift_Del_p.A418fs|VCAM1_ENST00000370119.4_Frame_Shift_Del_p.A448fs|VCAM1_ENST00000370115.1_Frame_Shift_Del_p.A311fs	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	510					acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	TTTTCAGTTGCCCCCAGAGAT	0.483																																					p.A510fs		Atlas-INDEL	.											.	VCAM1	111	.	0			c.1528delG						.						84.0	86.0	86.0					1																	101197977		2203	4300	6503	SO:0001589	frameshift_variant	7412	exon7			.	M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	12663	protein-coding gene	gene with protein product		192225					Standard	NM_080682		Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.1529delC	chr1.hg19:g.101197977delC	ENSP00000294728:p.Ala510fs	57.0	0.0		101.0	11.0	NM_001078	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Frame_Shift_Del	DEL	ENST00000294728.2	hg19	CCDS773.1																																																																																			.	.		0.483	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078	
RPL18A	6142	hgsc.bcm.edu	37	19	17973742	17973742	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:17973742delC	ENST00000222247.5	+	4	425	c.344delC	c.(343-345)gccfs	p.A115fs	RPL18A_ENST00000599898.1_Frame_Shift_Del_p.A76fs|SNORA68_ENST00000384437.1_RNA|RPL18A_ENST00000600147.1_Frame_Shift_Del_p.A115fs|RPL18A_ENST00000599870.1_Frame_Shift_Del_p.A86fs	NM_000980.3	NP_000971.1	Q02543	RL18A_HUMAN	ribosomal protein L18a	115					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|upper_aerodigestive_tract(1)	5						GACATGGGTGCCCGGCACCGC	0.642																																					p.A115fs		Atlas-INDEL	.											.	RPL18A	15	.	0			c.343delG						.						29.0	30.0	30.0					19																	17973742		2203	4300	6503	SO:0001589	frameshift_variant	6142	exon4			.	AB007175	CCDS12367.1	19p13.11	2011-04-06			ENSG00000105640	ENSG00000105640		"""L ribosomal proteins"""	10311	protein-coding gene	gene with protein product	"""60S ribosomal protein L18a"", ""ribosomal protein L18a-like protein"""	604178				9582194	Standard	NM_000980		Approved	L18A	uc002nhp.3	Q02543		ENST00000222247.5:c.344delC	chr19.hg19:g.17973742delC	ENSP00000222247:p.Ala115fs	112.0	0.0		155.0	10.0	NM_000980		Frame_Shift_Del	DEL	ENST00000222247.5	hg19	CCDS12367.1																																																																																			.	.		0.642	RPL18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466679.1	NM_000980	
ABCA5	23461	hgsc.bcm.edu	37	17	67282042	67282042	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:67282042delA	ENST00000392676.3	-	17	2333	c.2269delT	c.(2269-2271)tcafs	p.S757fs	ABCA5_ENST00000392677.2_Frame_Shift_Del_p.S757fs|ABCA5_ENST00000588877.1_Frame_Shift_Del_p.S757fs			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	757					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)	GTAATACCTGAAAATTTGTCC	0.353																																					p.S757X		Atlas-INDEL	.											.	ABCA5	162	.	0			c.2270delC						.						144.0	142.0	143.0					17																	67282042		2203	4300	6503	SO:0001589	frameshift_variant	23461	exon16			.	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.2269delT	chr17.hg19:g.67282042delA	ENSP00000376443:p.Ser757fs	93.0	0.0		178.0	13.0	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Frame_Shift_Del	DEL	ENST00000392676.3	hg19	CCDS11685.1																																																																																			.	.		0.353	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	
ITGA6	3655	hgsc.bcm.edu	37	2	173355995	173355995	+	Frame_Shift_Del	DEL	G	G	-	rs377077160		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:173355995delG	ENST00000264106.6	+	23	3145	c.2942delG	c.(2941-2943)cggfs	p.R981fs	ITGA6_ENST00000375221.2_Frame_Shift_Del_p.R981fs|ITGA6_ENST00000409532.1_Frame_Shift_Del_p.R823fs|ITGA6_ENST00000343713.4_Frame_Shift_Del_p.R937fs|ITGA6_ENST00000409080.1_Frame_Shift_Del_p.R942fs|ITGA6_ENST00000264107.7_Frame_Shift_Del_p.R942fs|AC093818.1_ENST00000442417.1_RNA			P23229	ITA6_HUMAN	integrin, alpha 6	981					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			TGCCCGCTGCGGGGGCTGGAC	0.468																																					p.R942fs		Atlas-INDEL	.											.	ITGA6	171	.	0			c.2824delC						.						132.0	137.0	135.0					2																	173355995		2203	4300	6503	SO:0001589	frameshift_variant	3655	exon22			.		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"""CD molecules"", ""Integrins"""	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.2942delG	chr2.hg19:g.173355995delG	ENSP00000264106:p.Arg981fs	152.0	0.0		183.0	11.0	NM_000210	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Frame_Shift_Del	DEL	ENST00000264106.6	hg19																																																																																				.	.		0.468	ITGA6-201	KNOWN	basic	protein_coding	protein_coding			
DSEL	92126	hgsc.bcm.edu	37	18	65178866	65178866	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:65178866delA	ENST00000310045.7	-	2	4483	c.3010delT	c.(3010-3012)tacfs	p.Y1005fs	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	995					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				CTTGGATAGTAAACCAGGTGT	0.418																																					p.Y1004fs		Atlas-INDEL	.											.	DSEL	196	.	0			c.3011delA						.						63.0	67.0	66.0					18																	65178866		2203	4300	6503	SO:0001589	frameshift_variant	92126	exon2			.	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.3010delT	chr18.hg19:g.65178866delA	ENSP00000310565:p.Tyr1005fs	135.0	0.0		147.0	13.0	NM_032160	Q17RH1|Q6P5Z3	Frame_Shift_Del	DEL	ENST00000310045.7	hg19	CCDS11995.1																																																																																			.	.		0.418	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
KIAA1429	25962	hgsc.bcm.edu	37	8	95531264	95531264	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:95531264delT	ENST00000297591.5	-	9	2537	c.2462delA	c.(2461-2463)aatfs	p.N821fs	KIAA1429_ENST00000437199.1_Frame_Shift_Del_p.N821fs|KIAA1429_ENST00000421249.2_Frame_Shift_Del_p.N821fs	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	821					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			ACTTTGGAGATTTTTCTCCAG	0.363																																					p.N821fs		Atlas-INDEL	.											.	KIAA1429	176	.	0			c.2463delT						.						54.0	59.0	57.0					8																	95531264		2203	4300	6503	SO:0001589	frameshift_variant	25962	exon9			.	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.2462delA	chr8.hg19:g.95531264delT	ENSP00000297591:p.Asn821fs	51.0	0.0		160.0	10.0	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Frame_Shift_Del	DEL	ENST00000297591.5	hg19	CCDS34923.1																																																																																			.	.		0.363	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
AMFR	267	hgsc.bcm.edu	37	16	56441911	56441911	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:56441911delG	ENST00000290649.5	-	4	841	c.631delC	c.(631-633)cacfs	p.H211fs	RP11-413H22.2_ENST00000563090.1_RNA	NM_001144.5	NP_001135.3	Q9UKV5	AMFR_HUMAN	autocrine motility factor receptor, E3 ubiquitin protein ligase	211					aging (GO:0007568)|cellular component movement (GO:0006928)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|learning or memory (GO:0007611)|protein oligomerization (GO:0051259)|protein polyubiquitination (GO:0000209)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)	dendrite (GO:0030425)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	ligase activity (GO:0016874)|receptor activity (GO:0004872)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17						TGCATTCCGTGGGTGTAGCCG	0.557																																					p.H211fs	Pancreas(2;144 323 39528)	Atlas-INDEL	.											.	AMFR	40	.	0			c.632delA						.						78.0	74.0	76.0					16																	56441911		2198	4300	6498	SO:0001589	frameshift_variant	267	exon4			.	L35233	CCDS10758.1	16q21	2013-01-09	2012-02-23		ENSG00000159461	ENSG00000159461		"""RING-type (C3HC4) zinc fingers"""	463	protein-coding gene	gene with protein product		603243	"""autocrine motility factor receptor"""			1649192	Standard	NM_001144		Approved	RNF45, gp78	uc002eiy.4	Q9UKV5	OTTHUMG00000133239	ENST00000290649.5:c.631delC	chr16.hg19:g.56441911delG	ENSP00000290649:p.His211fs	196.0	0.0		196.0	12.0	NM_001144	P26442|Q8IZ70	Frame_Shift_Del	DEL	ENST00000290649.5	hg19	CCDS10758.1																																																																																			.	.		0.557	AMFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256978.2		
TRAPPC3L	100128327	hgsc.bcm.edu	37	6	116818135	116818135	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:116818135delT	ENST00000368602.3	-	5	623	c.528delA	c.(526-528)aaafs	p.K176fs	TRAPPC3L_ENST00000356128.4_Frame_Shift_Del_p.K92fs|RP11-259P20.1_ENST00000420595.2_RNA	NM_001139444.2	NP_001132916.1	Q5T215	TPC3L_HUMAN	trafficking protein particle complex 3-like	176					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)											TCCCTCTATATTTTTTCTCGT	0.378																																					p.Y177fs		Atlas-INDEL	.											.	BET3L	18	.	0			c.529delT						.						280.0	235.0	248.0					6																	116818135		692	1591	2283	SO:0001589	frameshift_variant	100128327	exon5			.	AK002042	CCDS47468.1	6q22.31	2013-05-01	2013-05-01	2013-05-01	ENSG00000173626	ENSG00000173626			21090	protein-coding gene	gene with protein product		614137	"""BET3 like (S. cerevisiae)"""	BET3L		21525244	Standard	NM_001139444		Approved	bA259P20.2, FLJ11180		Q5T215	OTTHUMG00000015440	ENST00000368602.3:c.528delA	chr6.hg19:g.116818135delT	ENSP00000357591:p.Lys176fs	145.0	0.0		207.0	14.0	NM_001139444	Q5T213|Q5T214	Frame_Shift_Del	DEL	ENST00000368602.3	hg19	CCDS47468.1																																																																																			.	.		0.378	TRAPPC3L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000101701.1	XM_166322	
BDP1	55814	hgsc.bcm.edu	37	5	70806693	70806693	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:70806693delA	ENST00000358731.4	+	17	4037	c.3774delA	c.(3772-3774)ggafs	p.G1258fs	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	1258	9 X 55 AA repeats of G-R-R-X-I-S-P-X-E-N- G-X-E-E-V-K-P-X-X-E-M-E-T-D-L-K-X-T-G-R- E-X-X-X-R-E-K-T-X-E-X-X-D-A-X-E-E-I-D-X- D-L-E-E-T.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		AAGAAACTGGAAAAAGAGACA	0.363																																					p.G1258fs		Atlas-INDEL	.											.	BDP1	204	.	0			c.3773delG						.						142.0	142.0	142.0					5																	70806693		1833	4081	5914	SO:0001589	frameshift_variant	55814	exon17			.	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.3774delA	chr5.hg19:g.70806693delA	ENSP00000351575:p.Gly1258fs	71.0	0.0		175.0	11.0	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Frame_Shift_Del	DEL	ENST00000358731.4	hg19	CCDS43328.1																																																																																			.	.		0.363	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
ZRANB1	54764	hgsc.bcm.edu	37	10	126670335	126670335	+	Frame_Shift_Del	DEL	T	T	-	rs367624249		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:126670335delT	ENST00000359653.4	+	6	1856	c.1485delT	c.(1483-1485)catfs	p.H495fs	ZRANB1_ENST00000471421.1_3'UTR	NM_017580.2	NP_060050.2	Q9UGI0	ZRAN1_HUMAN	zinc finger, RAN-binding domain containing 1	495	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding.				cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|positive regulation of Wnt signaling pathway (GO:0030177)|protein deubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0071947)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell morphogenesis (GO:0022604)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	23		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.113)|COAD - Colon adenocarcinoma(40;0.119)		TTGGTTTACATTTTTCCTTGA	0.368																																					p.H495fs		Atlas-INDEL	.											.	ZRANB1	60	.	0			c.1484delA						.						130.0	134.0	132.0					10																	126670335		2203	4300	6503	SO:0001589	frameshift_variant	54764	exon6			.	AJ252060	CCDS7642.1	10q26.12	2014-02-24			ENSG00000019995	ENSG00000019995		"""Zinc fingers, RAN-binding domain containing"", ""OTU domain containing"""	18224	protein-coding gene	gene with protein product		611749				11463333	Standard	NM_017580		Approved	TRABID	uc001lic.3	Q9UGI0	OTTHUMG00000019223	ENST00000359653.4:c.1485delT	chr10.hg19:g.126670335delT	ENSP00000352676:p.His495fs	145.0	0.0		179.0	11.0	NM_017580	B4DZ98|D3DRF4|Q5SQP6|Q69YK3	Frame_Shift_Del	DEL	ENST00000359653.4	hg19	CCDS7642.1																																																																																			.	.		0.368	ZRANB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050898.1	NM_017580	
AOX1	316	hgsc.bcm.edu	37	2	201485931	201485931	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:201485931delT	ENST00000374700.2	+	18	2204	c.1963delT	c.(1963-1965)tttfs	p.F656fs	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	656					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	CTCCTTCTGCTTTTTTACTGA	0.393																																					p.C654fs		Atlas-INDEL	.											.	AOX1	152	.	0			c.1962delC						.						156.0	149.0	152.0					2																	201485931		2203	4300	6503	SO:0001589	frameshift_variant	316	exon18			.	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.1963delT	chr2.hg19:g.201485931delT	ENSP00000363832:p.Phe656fs	169.0	0.0		186.0	12.0	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Frame_Shift_Del	DEL	ENST00000374700.2	hg19	CCDS33360.1																																																																																			.	.		0.393	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	
ADCY10	55811	hgsc.bcm.edu	37	1	167780125	167780125	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:167780125delT	ENST00000367851.4	-	32	4692	c.4508delA	c.(4507-4509)aatfs	p.N1503fs	ADCY10_ENST00000367848.1_Frame_Shift_Del_p.N1411fs|ADCY10_ENST00000545172.1_Frame_Shift_Del_p.N1350fs	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	1503					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						GCCAGTGGTATTTTGAGCCAC	0.428																																					p.N1503fs		Atlas-INDEL	.											.	ADCY10	175	.	0			c.4509delT						.						65.0	66.0	65.0					1																	167780125		2203	4300	6503	SO:0001589	frameshift_variant	55811	exon32			.	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"""Adenylate cyclases"""	21285	protein-coding gene	gene with protein product	"""soluble adenylyl cyclase"", ""Hypercalciuria, absorptive, 2"""	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.4508delA	chr1.hg19:g.167780125delT	ENSP00000356825:p.Asn1503fs	141.0	0.0		216.0	13.0	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Frame_Shift_Del	DEL	ENST00000367851.4	hg19	CCDS1265.1																																																																																			.	.		0.428	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417	
LRP12	29967	hgsc.bcm.edu	37	8	105503191	105503191	+	Frame_Shift_Del	DEL	C	C	-	rs370769936		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:105503191delC	ENST00000276654.5	-	7	2398	c.2290delG	c.(2290-2292)gtafs	p.V764fs	LRP12_ENST00000424843.2_Frame_Shift_Del_p.V745fs|LRP12_ENST00000518375.1_5'UTR	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	764					endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CTTCCACTTACCCCATTATCA	0.428																																					p.V764fs		Atlas-INDEL	.											.	LRP12	124	.	0			c.2291delT						.						116.0	114.0	115.0					8																	105503191		2203	4300	6503	SO:0001589	frameshift_variant	29967	exon7			.	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"""Low density lipoprotein receptors"""	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.2290delG	chr8.hg19:g.105503191delC	ENSP00000276654:p.Val764fs	24.0	0.0		182.0	11.0	NM_013437	A8K137|B4DRQ2	Frame_Shift_Del	DEL	ENST00000276654.5	hg19	CCDS6303.1																																																																																			.	.		0.428	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437	
MIR205HG	642587	hgsc.bcm.edu	37	1	209602687	209602687	+	lincRNA	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	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		68.0	0.0		162.0	10.0	NM_001104548		Frame_Shift_Del	DEL	ENST00000384891.1	hg19																																																																																				.	.		0.502	MIR205HG-202	KNOWN	basic	miRNA	lincRNA			
CAMSAP2	23271	hgsc.bcm.edu	37	1	200818368	200818368	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:200818368delA	ENST00000236925.4	+	12	2553	c.2504delA	c.(2503-2505)caafs	p.Q835fs	CAMSAP2_ENST00000358823.2_Frame_Shift_Del_p.Q824fs|CAMSAP2_ENST00000413307.2_Frame_Shift_Del_p.Q808fs			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	835					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										AAGGAATCACAAAAAACTGAT	0.428																																					p.Q824fs		Atlas-INDEL	.											.	.	.	.	0			c.2470delC						.						104.0	111.0	109.0					1																	200818368		2203	4298	6501	SO:0001589	frameshift_variant	23271	exon11			.	AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"""calmodulin regulated spectrin-associated protein 1-like 1"""	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.2504delA	chr1.hg19:g.200818368delA	ENSP00000236925:p.Gln835fs	100.0	0.0		197.0	12.0	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Frame_Shift_Del	DEL	ENST00000236925.4	hg19																																																																																				.	.		0.428	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459	
P2RY12	64805	hgsc.bcm.edu	37	3	151055960	151055960	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:151055960delC	ENST00000302632.3	-	3	973	c.674delG	c.(673-675)ggtfs	p.G225fs	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000491549.1_Intron|MED12L_ENST00000474524.1_Intron	NM_022788.4|NM_176876.2	NP_073625.1|NP_795345.1	Q9H244	P2Y12_HUMAN	purinergic receptor P2Y, G-protein coupled, 12	225					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell projection organization (GO:0030030)|G-protein coupled purinergic nucleotide receptor signaling pathway (GO:0035589)|G-protein coupled receptor signaling pathway (GO:0007186)|hemostasis (GO:0007599)|negative regulation of cell differentiation (GO:0045596)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of GTPase activity (GO:0043547)|positive regulation of ion transport (GO:0043270)|potassium ion transmembrane transport (GO:0071805)|protein kinase B signaling (GO:0043491)|regulation of calcium ion transport (GO:0051924)	basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	ADP receptor activity (GO:0001621)|G-protein coupled adenosine receptor activity (GO:0001609)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	17			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		Clopidogrel(DB00758)|Epoprostenol(DB01240)|Prasugrel(DB06209)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Treprostinil(DB00374)	TTTACCTACACCCCTCGTTCT	0.348																																					p.G225fs		Atlas-INDEL	.											.	P2RY12	36	.	0			c.675delT						.						73.0	75.0	75.0					3																	151055960		2203	4300	6503	SO:0001589	frameshift_variant	64805	exon3			.	AJ320495	CCDS3159.1	3q24-q25	2014-09-17			ENSG00000169313	ENSG00000169313		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	18124	protein-coding gene	gene with protein product		600515				11502873, 11104774	Standard	NM_022788		Approved	P2Y12, SP1999, HORK3	uc003eyw.1	Q9H244	OTTHUMG00000159863	ENST00000302632.3:c.674delG	chr3.hg19:g.151055960delC	ENSP00000307259:p.Gly225fs	109.0	0.0		166.0	13.0	NM_022788	D3DNJ5|Q546J7	Frame_Shift_Del	DEL	ENST00000302632.3	hg19	CCDS3159.1																																																																																			.	.		0.348	P2RY12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357796.1		
GABRA1	2554	hgsc.bcm.edu	37	5	161277851	161277851	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:161277851delG	ENST00000428797.2	+	3	390	c.35delG	c.(34-36)tggfs	p.W12fs	GABRA1_ENST00000420560.1_Frame_Shift_Del_p.W12fs|GABRA1_ENST00000437025.2_Frame_Shift_Del_p.W12fs|GABRA1_ENST00000393943.4_Frame_Shift_Del_p.W12fs|GABRA1_ENST00000444819.1_Frame_Shift_Del_p.W12fs|GABRA1_ENST00000023897.6_Frame_Shift_Del_p.W12fs	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	12					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	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;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|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)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	GACTGTCTTTGGGCCTGGATC	0.423																																					p.W12fs		Atlas-INDEL	.											.	GABRA1	132	.	0			c.34delT						.						111.0	106.0	107.0					5																	161277851		2203	4300	6503	SO:0001589	frameshift_variant	2554	exon2			.		CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4075	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 1"""	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.35delG	chr5.hg19:g.161277851delG	ENSP00000393097:p.Trp12fs	139.0	0.0		235.0	15.0	NM_001127644	D3DQK6|Q8N629	Frame_Shift_Del	DEL	ENST00000428797.2	hg19	CCDS4357.1																																																																																			.	.		0.423	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5	
AIM1L	55057	hgsc.bcm.edu	37	1	26670276	26670276	+	5'UTR	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:26670276delG	ENST00000308182.5	-	0	167				AIM1L_ENST00000527815.1_Frame_Shift_Del_p.P84fs			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like								carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		CTTCTCCGTTGGGGATGATCT	0.632																																					p.P958fs		Atlas-INDEL	.											.	AIM1L	98	.	0			c.2874delA						.																																			SO:0001623	5_prime_UTR_variant	55057	exon2			.			1p35	2010-07-14			ENSG00000176092	ENSG00000176092			17295	protein-coding gene	gene with protein product	"""beta-gamma crystallin domain containing 2"""						Standard	NM_001039775		Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490	ENST00000308182.5:c.-263C>-	chr1.hg19:g.26670276delG		105.0	0.0		154.0	10.0	NM_001039775	B2RNG3|Q5T137|Q5T150	Frame_Shift_Del	DEL	ENST00000308182.5	hg19																																																																																				.	.		0.632	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2	
NUP85	79902	hgsc.bcm.edu	37	17	73221299	73221299	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:73221299delG	ENST00000245544.4	+	8	770	c.699delG	c.(697-699)atgfs	p.M233fs	NUP85_ENST00000579324.1_Frame_Shift_Del_p.M121fs|NUP85_ENST00000541827.1_Frame_Shift_Del_p.M187fs|NUP85_ENST00000447371.2_Frame_Shift_Del_p.M65fs|NUP85_ENST00000579298.1_Intron|NUP85_ENST00000449421.2_3'UTR|NUP85_ENST00000540768.1_5'Flank	NM_024844.3	NP_079120.1	Q9BW27	NUP85_HUMAN	nucleoporin 85kDa	233					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|lamellipodium assembly (GO:0030032)|macrophage chemotaxis (GO:0048246)|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)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	16	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			GCCGAATCATGGGGGACCTGA	0.562																																					p.M233fs		Atlas-INDEL	.											.	NUP85	44	.	0			c.698delT						.						125.0	124.0	124.0					17																	73221299		2203	4300	6503	SO:0001589	frameshift_variant	79902	exon8			.	AF514995	CCDS32730.1	17q25	2006-11-29	2005-11-03	2005-11-03		ENSG00000125450			8734	protein-coding gene	gene with protein product		170285				8124707	Standard	XM_005257690		Approved	NUP75, FLJ12549	uc002jng.1	Q9BW27		ENST00000245544.4:c.699delG	chr17.hg19:g.73221299delG	ENSP00000245544:p.Met233fs	93.0	0.0		150.0	10.0	NM_024844	B4DMQ3|B4DPW1|Q8NDI4|Q9H9U1	Frame_Shift_Del	DEL	ENST00000245544.4	hg19	CCDS32730.1																																																																																			.	.		0.562	NUP85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446619.1	NM_024844	
POLB	5423	hgsc.bcm.edu	37	8	42213041	42213041	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:42213041delA	ENST00000265421.4	+	7	548	c.378delA	c.(376-378)agafs	p.R126fs	POLB_ENST00000538005.1_5'UTR	NM_002690.2	NP_002681.1	P06746	DPOLB_HUMAN	polymerase (DNA directed), beta	126					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neuron apoptotic process (GO:0051402)|pyrimidine dimer repair (GO:0006290)|response to ethanol (GO:0045471)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|enzyme binding (GO:0019899)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(1)	16	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	CAGATCTCAGAAAAAATGAAG	0.303								DNA polymerases (catalytic subunits)																													p.R126fs		Atlas-INDEL	.											.	POLB	60	.	0			c.377delG						.						65.0	69.0	67.0					8																	42213041		2203	4298	6501	SO:0001589	frameshift_variant	5423	exon7			.		CCDS6129.1	8p12-p11	2012-10-02			ENSG00000070501	ENSG00000070501	2.7.7.7	"""DNA polymerases"""	9174	protein-coding gene	gene with protein product		174760					Standard	NM_002690		Approved		uc003xoz.2	P06746	OTTHUMG00000164093	ENST00000265421.4:c.378delA	chr8.hg19:g.42213041delA	ENSP00000265421:p.Arg126fs	264.0	0.0		158.0	10.0	NM_002690	B2RC78|Q3KP48|Q6FI34	Frame_Shift_Del	DEL	ENST00000265421.4	hg19	CCDS6129.1																																																																																			.	.		0.303	POLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377242.1	NM_002690	
POLR3A	11128	hgsc.bcm.edu	37	10	79745906	79745906	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:79745906delT	ENST00000372371.3	-	22	3050	c.2913delA	c.(2911-2913)aaafs	p.K971fs		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	971					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			CCTTAATGAATTTTTTTATTT	0.358																																					p.F972fs		Atlas-INDEL	.											.	POLR3A	104	.	0			c.2914delT						.						117.0	120.0	119.0					10																	79745906		2203	4300	6503	SO:0001589	frameshift_variant	11128	exon22			.	AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"""RNA polymerase subunits"""	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.2913delA	chr10.hg19:g.79745906delT	ENSP00000361446:p.Lys971fs	97.0	0.0		160.0	10.0	NM_007055	Q8IW34|Q8TCW5	Frame_Shift_Del	DEL	ENST00000372371.3	hg19	CCDS7354.1																																																																																			.	.		0.358	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055	
TRAPPC8	22878	hgsc.bcm.edu	37	18	29429604	29429604	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:29429604delT	ENST00000283351.4	-	25	3995	c.3660delA	c.(3658-3660)aaafs	p.K1220fs	TRAPPC8_ENST00000582539.1_Frame_Shift_Del_p.K1166fs	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	1220					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CTGTTGACTGTTTTTCTGTAT	0.358																																					p.Q1221fs		Atlas-INDEL	.											.	TRAPPC8	126	.	0			c.3661delC						.						124.0	111.0	116.0					18																	29429604		2203	4300	6503	SO:0001589	frameshift_variant	22878	exon25			.	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"""Trafficking protein particle complex"""	29169	protein-coding gene	gene with protein product	"""general sporulation gene 1 homolog (S. cerevisiae)"""	614136	"""KIAA1012"""	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.3660delA	chr18.hg19:g.29429604delT	ENSP00000283351:p.Lys1220fs	146.0	0.0		159.0	10.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Frame_Shift_Del	DEL	ENST00000283351.4	hg19	CCDS11901.1																																																																																			.	.		0.358	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939	
OR6C68	403284	hgsc.bcm.edu	37	12	55886489	55886489	+	Frame_Shift_Del	DEL	T	T	-	rs7304753	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:55886489delT	ENST00000548615.1	+	1	328	c.328delT	c.(328-330)tttfs	p.F111fs	RP11-110A12.2_ENST00000556750.1_RNA|OR6C68_ENST00000379662.1_Frame_Shift_Del_p.F116fs|RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA	NM_001005519.2	NP_001005519.2	A6NDL8	O6C68_HUMAN	olfactory receptor, family 6, subfamily C, member 68	111						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(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15						GGTAACTGAATTTTTTCTTTT	0.373																																					p.E109fs		Atlas-INDEL	.											.	OR6C68	36	.	0			c.327delA						.						163.0	153.0	156.0					12																	55886489		2203	4300	6503	SO:0001589	frameshift_variant	403284	exon1			.		CCDS31826.1, CCDS31826.2	12q13.2	2013-09-23			ENSG00000205327	ENSG00000205327		"""GPCR / Class A : Olfactory receptors"""	31297	protein-coding gene	gene with protein product							Standard	NM_001005519		Approved		uc031qhq.1	A6NDL8	OTTHUMG00000169958	ENST00000548615.1:c.328delT	chr12.hg19:g.55886489delT	ENSP00000448811:p.Phe111fs	145.0	0.0		153.0	11.0	NM_001005519		Frame_Shift_Del	DEL	ENST00000548615.1	hg19	CCDS31826.2																																																																																			.	.		0.373	OR6C68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406677.1		
ASIC2	40	hgsc.bcm.edu	37	17	31439005	31439005	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:31439005delC	ENST00000359872.6	-	2	1397	c.636delG	c.(634-636)gggfs	p.G212fs	RP11-40A13.1_ENST00000584688.1_RNA|ASIC2_ENST00000448983.1_5'UTR|ASIC2_ENST00000225823.2_Frame_Shift_Del_p.G263fs	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2	212					central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	CGTTGCCTGTCCCCCCCTTGA	0.552																																					p.T264fs		Atlas-INDEL	.											.,2	.	.	.	0			c.790delA						.						146.0	120.0	129.0					17																	31439005		2203	4300	6503	SO:0001589	frameshift_variant	40	exon2			.	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	99	protein-coding gene	gene with protein product	"""degenerin"""	601784	"""amiloride-sensitive cation channel 1, neuronal"""	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.636delG	chr17.hg19:g.31439005delC	ENSP00000352934:p.Gly212fs	146.0	0.0		153.0	10.0	NM_183377	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Frame_Shift_Del	DEL	ENST00000359872.6	hg19	CCDS42296.1																																																																																			.	.		0.552	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094	
ITGB2	3689	hgsc.bcm.edu	37	21	46309403	46309403	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:46309403delC	ENST00000397850.2	-	14	2117	c.1665delG	c.(1663-1665)gggfs	p.G555fs	ITGB2_ENST00000397854.3_Frame_Shift_Del_p.G498fs|ITGB2_ENST00000397852.1_Frame_Shift_Del_p.G555fs|ITGB2_ENST00000302347.5_Frame_Shift_Del_p.G555fs|ITGB2_ENST00000397857.1_Frame_Shift_Del_p.G555fs|ITGB2_ENST00000355153.4_Frame_Shift_Del_p.G555fs			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	555	Cysteine-rich tandem repeats.				apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	AGAAGCAGAGCCCCCTCCCTG	0.697																																					p.L556fs		Atlas-INDEL	.											.	ITGB2	107	.	0			c.1666delC						.						24.0	20.0	22.0					21																	46309403		2160	4257	6417	SO:0001589	frameshift_variant	3689	exon13			.	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"""CD molecules"", ""Complement system"", ""Integrins"""	6155	protein-coding gene	gene with protein product		600065	"""integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"""	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.1665delG	chr21.hg19:g.46309403delC	ENSP00000380948:p.Gly555fs	134.0	0.0		166.0	10.0	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Frame_Shift_Del	DEL	ENST00000397850.2	hg19	CCDS13716.1																																																																																			.	.		0.697	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
DDX4	54514	hgsc.bcm.edu	37	5	55110940	55110940	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:55110940delT	ENST00000505374.1	+	20	2019	c.1927delT	c.(1927-1929)tttfs	p.F644fs	DDX4_ENST00000511853.1_Frame_Shift_Del_p.F495fs|DDX4_ENST00000353507.5_Frame_Shift_Del_p.F610fs|DDX4_ENST00000514278.2_Frame_Shift_Del_p.F624fs|DDX4_ENST00000354991.5_Frame_Shift_Del_p.F610fs	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	644	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				AGCAATTTCCTTTTTTGATCT	0.358																																					p.S642fs		Atlas-INDEL	.											.	DDX4	194	.	0			c.1926delC						.						178.0	173.0	175.0					5																	55110940		2203	4300	6503	SO:0001589	frameshift_variant	54514	exon20			.	AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"""DEAD-boxes"""	18700	protein-coding gene	gene with protein product		605281	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"""			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.1927delT	chr5.hg19:g.55110940delT	ENSP00000424838:p.Phe644fs	295.0	0.0		466.0	29.0	NM_024415	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Frame_Shift_Del	DEL	ENST00000505374.1	hg19	CCDS3969.1																																																																																			.	.		0.358	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33536901	33536901	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:33536901delA	ENST00000290943.6	+	6	862	c.766delA	c.(766-768)aaafs	p.K256fs		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	256										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						TTTGGAACATAAAAATAAGAT	0.244																																					p.H255fs		Atlas-INDEL	.											.	ANKRD18B	46	.	0			c.765delT						.																																			SO:0001589	frameshift_variant	441459	exon6			.			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.766delA	chr9.hg19:g.33536901delA	ENSP00000290943:p.Lys256fs	167.0	0.0		199.0	13.0	NM_001244752		Frame_Shift_Del	DEL	ENST00000290943.6	hg19																																																																																				.	.		0.244	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
ANKAR	150709	hgsc.bcm.edu	37	2	190569839	190569839	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:190569839delA	ENST00000520309.1	+	8	1887	c.1799delA	c.(1798-1800)gaafs	p.E600fs	ANKAR_ENST00000281412.6_Frame_Shift_Del_p.E364fs|ANKAR_ENST00000438402.2_Frame_Shift_Del_p.E600fs|ANKAR_ENST00000313581.4_Frame_Shift_Del_p.E600fs|ANKAR_ENST00000431575.2_Frame_Shift_Del_p.E529fs	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	600						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)			ACGCTTTCTGAAAAAAGAGGC	0.443																																					p.E600fs		Atlas-INDEL	.											.	ANKAR	184	.	0			c.1798delG						.						158.0	145.0	149.0					2																	190569839		2203	4300	6503	SO:0001589	frameshift_variant	150709	exon8			.	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.1799delA	chr2.hg19:g.190569839delA	ENSP00000427882:p.Glu600fs	144.0	0.0		152.0	10.0	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Frame_Shift_Del	DEL	ENST00000520309.1	hg19	CCDS33351.2																																																																																			.	.		0.443	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708	
IFNG	3458	hgsc.bcm.edu	37	12	68551987	68551987	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:68551987delA	ENST00000229135.3	-	2	298	c.167delT	c.(166-168)ttgfs	p.L56fs	IFNG-AS1_ENST00000536914.1_RNA	NM_000619.2	NP_000610.2	P01579	IFNG_HUMAN	interferon, gamma	56					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell cycle arrest (GO:0007050)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to interleukin-18 (GO:0071351)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|extrinsic apoptotic signaling pathway (GO:0097191)|humoral immune response (GO:0006959)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-17 production (GO:0032700)|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 myelination (GO:0031642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil apoptotic process (GO:0001781)|neutrophil chemotaxis (GO:0030593)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity (GO:0060550)|positive regulation of fructose 1,6-bisphosphate metabolic process (GO:0060552)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|regulation of insulin secretion (GO:0050796)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of the force of heart contraction (GO:0002026)|response to drug (GO:0042493)|response to virus (GO:0009615)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|interferon-gamma receptor binding (GO:0005133)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000829)	Glucosamine(DB01296)|Olsalazine(DB01250)	CCAATTCTTCAAAATGCCTAA	0.338																																					p.L56fs		Atlas-INDEL	.											.	IFNG	38	.	0			c.168delG						.						97.0	98.0	98.0					12																	68551987		2203	4300	6503	SO:0001589	frameshift_variant	3458	exon2			.		CCDS8980.1	12q14	2007-10-17			ENSG00000111537	ENSG00000111537		"""Interferons"""	5438	protein-coding gene	gene with protein product		147570					Standard	NM_000619		Approved		uc001stw.1	P01579	OTTHUMG00000169113	ENST00000229135.3:c.167delT	chr12.hg19:g.68551987delA	ENSP00000229135:p.Leu56fs	106.0	0.0		76.0	11.0	NM_000619	B5BU88|Q53ZV4	Frame_Shift_Del	DEL	ENST00000229135.3	hg19	CCDS8980.1																																																																																			.	.		0.338	IFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402301.1		
SLIT3	6586	hgsc.bcm.edu	37	5	168127640	168127640	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:168127640delG	ENST00000519560.1	-	27	3308	c.2889delC	c.(2887-2889)cccfs	p.P963fs	SLIT3_ENST00000332966.8_Frame_Shift_Del_p.P970fs|SLIT3_ENST00000404867.3_Frame_Shift_Del_p.P963fs	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	963	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CATGCTGACAGGGGTTCTGGA	0.572																																					p.C971fs	Ovarian(29;311 847 10864 17279 24903)	Atlas-INDEL	.											.	SLIT3	224	.	0			c.2911delT						.						111.0	93.0	99.0					5																	168127640		2203	4300	6503	SO:0001589	frameshift_variant	6586	exon27			.	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.2889delC	chr5.hg19:g.168127640delG	ENSP00000430333:p.Pro963fs	140.0	0.0		273.0	18.0	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Frame_Shift_Del	DEL	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.		0.572	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
CRELD2	79174	hgsc.bcm.edu	37	22	50319089	50319089	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:50319089delA	ENST00000328268.4	+	9	967	c.893delA	c.(892-894)gaafs	p.E298fs	CRELD2_ENST00000403427.3_Frame_Shift_Del_p.E270fs|CRELD2_ENST00000407217.3_Frame_Shift_Del_p.E266fs|CRELD2_ENST00000404488.3_Frame_Shift_Del_p.E347fs	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2	298	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		TCACTAGCAGAAAAAACCTGT	0.438																																					p.E347fs		Atlas-INDEL	.											.	CRELD2	57	.	0			c.1039delG						.						107.0	108.0	108.0					22																	50319089		2203	4300	6503	SO:0001589	frameshift_variant	79174	exon10			.	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.893delA	chr22.hg19:g.50319089delA	ENSP00000332223:p.Glu298fs	123.0	0.0		137.0	10.0	NM_001135101	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Frame_Shift_Del	DEL	ENST00000328268.4	hg19	CCDS14082.1																																																																																			.	.		0.438	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324	
MRPS18B	28973	hgsc.bcm.edu	37	6	30587360	30587360	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:30587360delA	ENST00000259873.4	+	2	326	c.169delA	c.(169-171)aaafs	p.K57fs	MRPS18B_ENST00000472229.1_3'UTR|PPP1R10_ENST00000484449.1_5'Flank|MRPS18B_ENST00000506373.2_Frame_Shift_Del_p.K57fs|PPP1R10_ENST00000376511.2_5'Flank	NM_014046.3	NP_054765.1	Q9Y676	RT18B_HUMAN	mitochondrial ribosomal protein S18B	57					translation (GO:0006412)	cell junction (GO:0030054)|mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|skin(2)	13						TGAGCCCTGGAAATATCTGGA	0.488																																					p.W56X		Atlas-INDEL	.											.	MRPS18B	22	.	0			c.168delG						.						65.0	78.0	74.0					6																	30587360		1508	2709	4217	SO:0001589	frameshift_variant	28973	exon2			.	AF100761	CCDS4682.1	6p21	2012-09-13			ENSG00000204568	ENSG00000204568		"""Mitochondrial ribosomal proteins / small subunits"""	14516	protein-coding gene	gene with protein product		611982				11279123	Standard	NM_014046		Approved	MRPS18-2, PTD017, C6orf14, HSPC183	uc003nqo.2	Q9Y676	OTTHUMG00000031268	ENST00000259873.4:c.169delA	chr6.hg19:g.30587360delA	ENSP00000259873:p.Lys57fs	102.0	0.0		151.0	10.0	NM_014046	A6NDQ0|Q659G4|Q9BS27	Frame_Shift_Del	DEL	ENST00000259873.4	hg19	CCDS4682.1																																																																																			.	.		0.488	MRPS18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076584.2		
RYR2	6262	hgsc.bcm.edu	37	1	237957192	237957192	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:237957192delA	ENST00000366574.2	+	95	14125	c.13808delA	c.(13807-13809)gaafs	p.E4603fs	RYR2_ENST00000360064.6_Frame_Shift_Del_p.E4609fs|RYR2_ENST00000542537.1_Frame_Shift_Del_p.E4587fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4603					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTTAAGCGAGAAAAGGAAGTG	0.348																																					p.E4603fs		Atlas-INDEL	.											.	RYR2	1273	.	0			c.13807delG						.						62.0	58.0	59.0					1																	237957192		1808	4071	5879	SO:0001589	frameshift_variant	6262	exon95			.	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.13808delA	chr1.hg19:g.237957192delA	ENSP00000355533:p.Glu4603fs	114.0	0.0		200.0	12.0	NM_001035	Q15411|Q546N8|Q5T3P2	Frame_Shift_Del	DEL	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.348	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
TOX4	9878	hgsc.bcm.edu	37	14	21957371	21957371	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:21957371delA	ENST00000405508.1	+	6	895	c.619delA	c.(619-621)aaafs	p.K208fs	TOX4_ENST00000262709.3_Frame_Shift_Del_p.K208fs|TOX4_ENST00000448790.2_Frame_Shift_Del_p.K185fs			O94842	TOX4_HUMAN	TOX high mobility group box family member 4	208						chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)			large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)		GGAAGCAGGGAAAAAGCAGAA	0.418																																					p.G206fs		Atlas-INDEL	.											.	TOX4	50	.	0			c.618delG						.						91.0	100.0	97.0					14																	21957371		2203	4300	6503	SO:0001589	frameshift_variant	9878	exon5			.	AB018280	CCDS32043.1	14q11.2	2007-03-20	2007-03-20	2007-03-20	ENSG00000092203	ENSG00000092203			20161	protein-coding gene	gene with protein product		614032	"""chromosome 14 open reading frame 92"", ""KIAA0737"""	C14orf92, KIAA0737			Standard	NM_014828		Approved	LCP1	uc001waz.3	O94842	OTTHUMG00000150278	ENST00000405508.1:c.619delA	chr14.hg19:g.21957371delA	ENSP00000385102:p.Lys208fs	111.0	0.0		120.0	11.0	NM_014828	B4DPY8|B4DSM0|E7EV69	Frame_Shift_Del	DEL	ENST00000405508.1	hg19	CCDS32043.1																																																																																			.	.		0.418	TOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317287.2	NM_014828	
NDST3	9348	hgsc.bcm.edu	37	4	118975821	118975821	+	Frame_Shift_Del	DEL	T	T	-	rs35086179		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:118975821delT	ENST00000296499.5	+	2	1159	c.756delT	c.(754-756)gctfs	p.A252fs	NDST3_ENST00000433996.2_Frame_Shift_Del_p.A252fs	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	252	Heparan sulfate N-deacetylase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						CTAAAGGTGCTTTTTATGCCA	0.393																																					p.A252fs		Atlas-INDEL	.											.	NDST3	107	.	0			c.755delC						.						130.0	126.0	127.0					4																	118975821		2203	4299	6502	SO:0001589	frameshift_variant	9348	exon2			.	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"""Sulfotransferases, membrane-bound"""	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.756delT	chr4.hg19:g.118975821delT	ENSP00000296499:p.Ala252fs	173.0	0.0		180.0	11.0	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Frame_Shift_Del	DEL	ENST00000296499.5	hg19	CCDS3708.1																																																																																			.	.		0.393	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784	
C4orf45	152940	hgsc.bcm.edu	37	4	159894380	159894380	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:159894380delT	ENST00000434826.2	-	2	232	c.148delA	c.(148-150)actfs	p.T50fs	C4orf45_ENST00000508011.1_5'UTR	NM_152543.2	NP_689756.2	Q96LM5	CD045_HUMAN	chromosome 4 open reading frame 45	50										large_intestine(2)|lung(3)	5						AGATCTCCAGTTTTTTCTAAC	0.388																																					p.T50fs		Atlas-INDEL	.											.	C4orf45	8	.	0			c.149delC						.						97.0	83.0	87.0					4																	159894380		1824	4088	5912	SO:0001589	frameshift_variant	152940	exon2			.		CCDS47156.1	4q32.1	2012-03-02			ENSG00000164123	ENSG00000164123			26342	protein-coding gene	gene with protein product							Standard	NM_152543		Approved	FLJ25371	uc003iqf.1	Q96LM5	OTTHUMG00000161988	ENST00000434826.2:c.148delA	chr4.hg19:g.159894380delT	ENSP00000412215:p.Thr50fs	136.0	0.0		134.0	10.0	NM_152543	A8MPU3|C9J0T8	Frame_Shift_Del	DEL	ENST00000434826.2	hg19	CCDS47156.1																																																																																			.	.		0.388	C4orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366636.1	NM_152543	
TREX1	11277	hgsc.bcm.edu	37	3	48508447	48508447	+	Frame_Shift_Del	DEL	C	C	-	rs78762691		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:48508447delC	ENST00000422277.2	+	1	1219	c.558delC	c.(556-558)ttcfs	p.F186fs	TREX1_ENST00000436480.2_Frame_Shift_Del_p.F131fs|TREX1_ENST00000444177.1_Frame_Shift_Del_p.F121fs|TREX1_ENST00000433541.1_5'UTR|SHISA5_ENST00000465449.1_5'Flank|TREX1_ENST00000456089.1_Intron|TREX1_ENST00000296443.9_Frame_Shift_Del_p.F131fs|TREX1_ENST00000492235.1_3'UTR	NM_016381.4	NP_057465.1	Q9NSU2	TREX1_HUMAN	three prime repair exonuclease 1	186					cell death (GO:0008219)|cellular response to interferon-beta (GO:0035458)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|innate immune response (GO:0045087)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	endoplasmic reticulum membrane (GO:0005789)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|3'-5'-exodeoxyribonuclease activity (GO:0008296)|adenyl deoxyribonucleotide binding (GO:0032558)|double-stranded DNA binding (GO:0003690)|exodeoxyribonuclease III activity (GO:0008853)|metal ion binding (GO:0046872)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein homodimerization activity (GO:0042803)|single-stranded DNA binding (GO:0003697)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|skin(3)	9				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GCTACGACTTCCCCCTGCTCC	0.607																																					p.F186fs		Atlas-INDEL	.											.	TREX1	17	.	0			c.557delT						.						72.0	70.0	71.0					3																	48508447		2203	4300	6503	SO:0001589	frameshift_variant	11277	exon1			.	AF151105	CCDS2769.1, CCDS59451.1	3p21.31	2014-09-17			ENSG00000213689	ENSG00000213689			12269	protein-coding gene	gene with protein product		606609	"""Aicardi-Goutieres syndrome 1"""	AGS1		10391904, 10393201, 16845398	Standard	NM_033629		Approved	DRN3	uc010hka.4	Q9NSU2	OTTHUMG00000156205	ENST00000422277.2:c.558delC	chr3.hg19:g.48508447delC	ENSP00000390478:p.Phe186fs	111.0	0.0		152.0	10.0	NM_016381	B2RCN9|Q8TEU2|Q9BPW1|Q9Y4X2	Frame_Shift_Del	DEL	ENST00000422277.2	hg19	CCDS43086.1																																																																																			.	.		0.607	TREX1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_016381	
OR10A3	26496	hgsc.bcm.edu	37	11	7960747	7960747	+	Frame_Shift_Del	DEL	A	A	-	rs35194212		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:7960747delA	ENST00000360759.3	-	1	394	c.321delT	c.(319-321)tttfs	p.F107fs		NM_001003745.1	NP_001003745.1	P58181	O10A3_HUMAN	olfactory receptor, family 10, subfamily A, member 3	107					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)	21				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CAGTCCCACCAAAAAGAAGGA	0.443																																					p.G108fs		Atlas-INDEL	.											.	OR10A3	54	.	0			c.322delG						.						94.0	87.0	89.0					11																	7960747		2201	4296	6497	SO:0001589	frameshift_variant	26496	exon1			.	BK004404	CCDS31421.1	11p15.4	2012-08-09			ENSG00000170683	ENSG00000170683		"""GPCR / Class A : Olfactory receptors"""	8162	protein-coding gene	gene with protein product						1370859	Standard	NM_001003745		Approved	HTPCRX12, HSHTPCRX12	uc010rbi.2	P58181	OTTHUMG00000165672	ENST00000360759.3:c.321delT	chr11.hg19:g.7960747delA	ENSP00000353988:p.Phe107fs	87.0	0.0		161.0	13.0	NM_001003745	B9EH39|Q6IF58|Q96R11	Frame_Shift_Del	DEL	ENST00000360759.3	hg19	CCDS31421.1																																																																																			.	.		0.443	OR10A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385704.1	NM_001003745	
C17orf85	55421	hgsc.bcm.edu	37	17	3716454	3716454	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:3716454delC	ENST00000389005.4	-	13	1774	c.1747delG	c.(1747-1749)gctfs	p.A583fs	C17orf85_ENST00000158149.3_Frame_Shift_Del_p.A303fs	NM_001114118.2	NP_001107590.1	Q53F19	CQ085_HUMAN	chromosome 17 open reading frame 85	583							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A303fs*2(1)		endometrium(2)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (3;0.0725)		TTAATCAGAGCCCCCCATGCC	0.507																																					p.A583fs		Atlas-INDEL	.											.	C17orf85	66	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1748delC						.						139.0	139.0	139.0					17																	3716454		2203	4300	6503	SO:0001589	frameshift_variant	55421	exon13			.		CCDS45578.1	17p13.2	2012-10-23			ENSG00000074356	ENSG00000074356			24612	protein-coding gene	gene with protein product	"""ELG protein"""					11412301	Standard	NM_001114118		Approved	HSA277841, ELG	uc010ckl.2	Q53F19	OTTHUMG00000177672	ENST00000389005.4:c.1747delG	chr17.hg19:g.3716454delC	ENSP00000373657:p.Ala583fs	206.0	0.0		151.0	13.0	NM_001114118	B3KWG7|Q7L406|Q96FK1|Q9NXZ4	Frame_Shift_Del	DEL	ENST00000389005.4	hg19	CCDS45578.1																																																																																			.	.		0.507	C17orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438385.1	NM_018553	
SYVN1	84447	hgsc.bcm.edu	37	11	64897763	64897763	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:64897763delG	ENST00000377190.3	-	12	1288	c.1194delC	c.(1192-1194)cccfs	p.P398fs	SYVN1_ENST00000526060.1_Frame_Shift_Del_p.P398fs|SYVN1_ENST00000307289.6_Frame_Shift_Del_p.P347fs|SYVN1_ENST00000294256.8_Frame_Shift_Del_p.P398fs|SYVN1_ENST00000526121.1_5'Flank	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	398	Pro-rich.				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)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						CTCCTGAGCTGGGGGGAGGCG	0.642																																					p.S399fs		Atlas-INDEL	.											.	SYVN1	55	.	0			c.1195delA						.						11.0	14.0	13.0					11																	64897763		2195	4280	6475	SO:0001589	frameshift_variant	84447	exon12			.	AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"""RING-type (C3HC4) zinc fingers"""	20738	protein-coding gene	gene with protein product	"""HMG-coA reductase degradation 1 homolog (S. cerevisiae)"""	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.1194delC	chr11.hg19:g.64897763delG	ENSP00000366395:p.Pro398fs	107.0	0.0		153.0	10.0	NM_032431	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Frame_Shift_Del	DEL	ENST00000377190.3	hg19	CCDS31605.1																																																																																			.	.		0.642	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431	
HTATIP2	10553	hgsc.bcm.edu	37	11	20398242	20398242	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:20398242delT	ENST00000451739.2	+	3	861	c.420delT	c.(418-420)aatfs	p.N140fs	HTATIP2_ENST00000443524.2_Frame_Shift_Del_p.N140fs|HTATIP2_ENST00000531058.1_Intron|HTATIP2_ENST00000421577.2_Frame_Shift_Del_p.N140fs|HTATIP2_ENST00000419348.2_Frame_Shift_Del_p.N174fs	NM_001098522.1	NP_001091992.1			HIV-1 Tat interactive protein 2, 30kDa											large_intestine(2)|lung(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	8						AATCAAGCAATTTTTTATATC	0.358																																					p.N174fs		Atlas-INDEL	.											HTATIP2_ENST00000419348,NS,carcinoma,0,3	HTATIP2	30	.	0			c.521delA						.						86.0	89.0	88.0					11																	20398242		2203	4300	6503	SO:0001589	frameshift_variant	10553	exon4			.	AF039103	CCDS7852.1, CCDS44553.1, CCDS53613.1	11p15.1	2011-09-14	2002-08-29		ENSG00000109854	ENSG00000109854	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	16637	protein-coding gene	gene with protein product	"""Tat-interacting protein (30kD)"", ""short chain dehydrogenase/reductase family 44U, member 1"""	605628	"""HIV-1 Tat interactive protein 2, 30 kDa"""			9482853, 9174052, 19027726	Standard	NM_006410		Approved	TIP30, CC3, FLJ26963, SDR44U1	uc001mpx.2	Q9BUP3	OTTHUMG00000166015	ENST00000451739.2:c.420delT	chr11.hg19:g.20398242delT	ENSP00000394259:p.Asn140fs	127.0	0.0		167.0	13.0	NM_001098520		Frame_Shift_Del	DEL	ENST00000451739.2	hg19	CCDS7852.1																																																																																			.	.		0.358	HTATIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387445.2	NM_001098521	
SALL4	57167	hgsc.bcm.edu	37	20	50408744	50408744	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:50408744delT	ENST00000217086.4	-	2	389	c.278delA	c.(277-279)aatfs	p.N93fs	SALL4_ENST00000483130.1_5'UTR|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Frame_Shift_Del_p.N93fs	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	93					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTTAGTGCAATTTTTCTTATG	0.522																																					p.N93fs		Atlas-INDEL	.											.	SALL4	168	.	0			c.279delT						.						62.0	64.0	63.0					20																	50408744		2203	4300	6503	SO:0001589	frameshift_variant	57167	exon2			.	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.278delA	chr20.hg19:g.50408744delT	ENSP00000217086:p.Asn93fs	73.0	0.0		103.0	10.0	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Frame_Shift_Del	DEL	ENST00000217086.4	hg19	CCDS13438.1																																																																																			.	.		0.522	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
DNAH14	127602	hgsc.bcm.edu	37	1	225230572	225230572	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:225230572delA	ENST00000445597.2	+	11	1581	c.1581delA	c.(1579-1581)agafs	p.R527fs	DNAH14_ENST00000439375.2_Frame_Shift_Del_p.R508fs|DNAH14_ENST00000430092.1_Frame_Shift_Del_p.R508fs			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	527					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						AGGATTTGAGAAAAACATATG	0.338																																					p.R508fs		Atlas-INDEL	.											.	DNAH14	300	.	0			c.1523delG						.						59.0	47.0	51.0					1																	225230572		692	1591	2283	SO:0001589	frameshift_variant	127602	exon13			.	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.1581delA	chr1.hg19:g.225230572delA	ENSP00000409472:p.Arg527fs	154.0	0.0		314.0	20.0	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Frame_Shift_Del	DEL	ENST00000445597.2	hg19																																																																																				.	.		0.338	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
RPS4Y2	140032	hgsc.bcm.edu	37	Y	22921883	22921883	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrY:22921883delA	ENST00000288666.5	+	3	211	c.211delA	c.(211-213)aaafs	p.K71fs		NM_001039567.2	NP_001034656.1	Q8TD47	RS4Y2_HUMAN	ribosomal protein S4, Y-linked 2	71	S4 RNA-binding.				translation (GO:0006412)	ribosome (GO:0005840)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			lung(2)	2						ACACTTCCTCAAAATTGATGG	0.418																																					p.L70fs		Atlas-INDEL	.											.	RPS4Y2	3	.	0			c.210delC						.																																			SO:0001589	frameshift_variant	140032	exon3			.	AF497481	CCDS44028.1	Yq11.223	2006-02-22	2006-02-22	2006-02-22	ENSG00000157828	ENSG00000157828		"""S ribosomal proteins"""	18501	protein-coding gene	gene with protein product		400030	"""ribosomal protein S4, Y-linked 2 pseudogene"""	RPS4Y2P		12815422	Standard	NM_001039567		Approved		uc011nbb.2	Q8TD47	OTTHUMG00000036540	ENST00000288666.5:c.211delA	chrY.hg19:g.22921883delA	ENSP00000288666:p.Lys71fs	143.0	0.0		166.0	10.0	NM_001039567	A6NIR6	Frame_Shift_Del	DEL	ENST00000288666.5	hg19	CCDS44028.1																																																																																			.	.		0.418	RPS4Y2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088873.1		
WDR64	128025	hgsc.bcm.edu	37	1	241936138	241936138	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:241936138delA	ENST00000366552.2	+	19	2512	c.2305delA	c.(2305-2307)aaafs	p.K770fs	WDR64_ENST00000437684.2_Intron	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	770										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GCCAATGGACAAAAAACACCC	0.478																																					p.D768fs		Atlas-INDEL	.											.	WDR64	234	.	0			c.2304delC						.						108.0	106.0	107.0					1																	241936138		692	1591	2283	SO:0001589	frameshift_variant	128025	exon19			.	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"""WD repeat domain containing"""	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.2305delA	chr1.hg19:g.241936138delA	ENSP00000355510:p.Lys770fs	110.0	0.0		164.0	12.0	NM_144625	B1ANT0|Q7Z573|Q96LY9	Frame_Shift_Del	DEL	ENST00000366552.2	hg19																																																																																				.	.		0.478	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625	
COL3A1	1281	hgsc.bcm.edu	37	2	189852856	189852856	+	Frame_Shift_Del	DEL	C	C	-	rs374532486		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:189852856delC	ENST00000304636.3	+	6	748	c.578delC	c.(577-579)tccfs	p.S193fs	COL3A1_ENST00000317840.5_Frame_Shift_Del_p.S193fs	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	193	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	CATCCTGGTTCCCCTGTAAGT	0.398																																					p.S193fs		Atlas-INDEL	.											.	COL3A1	292	.	0			c.577delT						.						103.0	106.0	105.0					2																	189852856		2203	4300	6503	SO:0001589	frameshift_variant	1281	exon6			.	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.578delC	chr2.hg19:g.189852856delC	ENSP00000304408:p.Ser193fs	276.0	0.0		321.0	20.0	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Frame_Shift_Del	DEL	ENST00000304636.3	hg19	CCDS2297.1																																																																																			.	.		0.398	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
ARHGEF5	7984	hgsc.bcm.edu	37	7	144075858	144075858	+	Frame_Shift_Del	DEL	C	C	-	rs201067947		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:144075858delC	ENST00000056217.5	+	14	4709	c.4535delC	c.(4534-4536)tccfs	p.S1512fs	ARHGEF5_ENST00000471847.2_Frame_Shift_Del_p.S434fs	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	1512					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)|myeloid dendritic cell chemotaxis (GO:0002408)|positive regulation of podosome assembly (GO:0071803)|regulation of Rho GTPase activity (GO:0032319)		GTP binding (GO:0005525)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Melanoma(164;0.14)					TCCAAAGACTCCCCCCAGGTA	0.557																																					p.S1512fs		Atlas-INDEL	.											.	ARHGEF5	73	.	0			c.4534delT						.						161.0	156.0	158.0					7																	144075858		2203	4300	6503	SO:0001589	frameshift_variant	7984	exon14			.	U02082	CCDS34771.1	7q35	2012-09-20			ENSG00000050327	ENSG00000050327		"""Rho guanine nucleotide exchange factors"""	13209	protein-coding gene	gene with protein product	"""transforming immortalized mammary oncogene"", ""guanine nucleotide regulatory protein TIM"""	600888				8134109, 7656213	Standard	NM_005435		Approved	TIM, TIM1, GEF5, P60	uc003wel.3	Q12774	OTTHUMG00000158004	ENST00000056217.5:c.4535delC	chr7.hg19:g.144075858delC	ENSP00000056217:p.Ser1512fs	158.0	0.0		227.0	14.0	NM_005435	A6NNJ2|Q6ZML7	Frame_Shift_Del	DEL	ENST00000056217.5	hg19	CCDS34771.1																																																																																			.	.		0.557	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435	
KCNQ5	56479	hgsc.bcm.edu	37	6	73787525	73787525	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:73787525delT	ENST00000370398.1	+	5	942	c.833delT	c.(832-834)attfs	p.I278fs	KCNQ5_ENST00000403813.2_Frame_Shift_Del_p.I278fs|KCNQ5_ENST00000370392.1_Frame_Shift_Del_p.I278fs|KCNQ5_ENST00000355635.3_Frame_Shift_Del_p.I278fs|KCNQ5_ENST00000402622.2_Frame_Shift_Del_p.I278fs|KCNQ5_ENST00000355194.4_Frame_Shift_Del_p.I278fs|KCNQ5_ENST00000414165.2_Frame_Shift_Del_p.I278fs|KCNQ5_ENST00000342056.2_Frame_Shift_Del_p.I278fs	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	278					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	TTGGTTCTTATTTTTTCGTCT	0.338																																					p.I278fs	GBM(142;1375 1859 14391 23261 44706)	Atlas-INDEL	.											.	KCNQ5	153	.	0			c.832delA						.						143.0	121.0	128.0					6																	73787525		2203	4300	6503	SO:0001589	frameshift_variant	56479	exon5			.	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.833delT	chr6.hg19:g.73787525delT	ENSP00000359425:p.Ile278fs	114.0	0.0		183.0	11.0	NM_001160132	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Frame_Shift_Del	DEL	ENST00000370398.1	hg19	CCDS4976.1																																																																																			.	.		0.338	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842	
CAV2	858	hgsc.bcm.edu	37	7	116140387	116140387	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:116140387delC	ENST00000222693.4	+	2	616	c.224delC	c.(223-225)gccfs	p.A75fs	AC002066.1_ENST00000446355.2_RNA|CAV2_ENST00000343213.2_Intron|CAV2_ENST00000393480.2_Frame_Shift_Del_p.A75fs|CAV2_ENST00000462876.1_3'UTR	NM_001206747.1|NM_001206748.1|NM_001233.4	NP_001193676.1|NP_001193677.1|NP_001224.1	P51636	CAV2_HUMAN	caveolin 2	75					caveola assembly (GO:0070836)|endoplasmic reticulum organization (GO:0007029)|mitochondrion organization (GO:0007005)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of endothelial cell proliferation (GO:0001938)|protein oligomerization (GO:0051259)|regulation of mitosis (GO:0007088)|skeletal muscle fiber development (GO:0048741)|synaptic transmission (GO:0007268)|vesicle docking (GO:0048278)|vesicle fusion (GO:0006906)|vesicle organization (GO:0016050)	acrosomal membrane (GO:0002080)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lipid particle (GO:0005811)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	D1 dopamine receptor binding (GO:0031748)|protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(1)|skin(1)	3	all_epithelial(6;1.53e-06)|Lung NSC(10;0.00592)|all_lung(10;0.00642)		STAD - Stomach adenocarcinoma(10;0.00878)			TGCAGCCATGCCCTCTTTGAA	0.552																																					p.A75fs		Atlas-INDEL	.											.	CAV2	10	.	0			c.223delG						.						180.0	147.0	158.0					7																	116140387		2203	4300	6503	SO:0001589	frameshift_variant	858	exon2			.	AF035752	CCDS5765.1, CCDS5766.1	7q31	2006-02-09			ENSG00000105971	ENSG00000105971			1528	protein-coding gene	gene with protein product		601048				8552590, 10087206	Standard	NM_001233		Approved	CAV	uc003vid.3	P51636	OTTHUMG00000023414	ENST00000222693.4:c.224delC	chr7.hg19:g.116140387delC	ENSP00000222693:p.Ala75fs	101.0	0.0		157.0	11.0	NM_001233	A4D0U2|Q9UGM7	Frame_Shift_Del	DEL	ENST00000222693.4	hg19	CCDS5766.1																																																																																			.	.		0.552	CAV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059735.4	NM_001233	
HOXA9	3205	hgsc.bcm.edu	37	7	27204507	27204507	+	Frame_Shift_Del	DEL	G	G	-	rs370679767		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:27204507delG	ENST00000343483.6	-	1	642	c.570delC	c.(568-570)cccfs	p.P190fs	RP1-170O19.20_ENST00000470747.4_Frame_Shift_Del_p.P30fs|RP1-170O19.20_ENST00000465941.1_Intron|HOXA9_ENST00000497089.1_Intron|HOXA9_ENST00000396345.1_3'UTR	NM_152739.3	NP_689952.1	P31269	HXA9_HUMAN	homeobox A9	190					endothelial cell activation (GO:0042118)|multicellular organismal development (GO:0007275)|negative regulation of myeloid cell differentiation (GO:0045638)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)	p.P190P(1)		central_nervous_system(1)|endometrium(1)|lung(5)|prostate(1)	8						TGGGATCGATGGGGGGCTTGT	0.587			T	"""NUP98, MSI2"""	AML*																																p.I191fs		Atlas-INDEL	.		Dom	yes		7	7p15-p14.2	3205	homeo box A9		L	.	HOXA9	20	.	1	Substitution - coding silent(1)	central_nervous_system(1)	c.571delA						.						45.0	52.0	50.0					7																	27204507		2203	4300	6503	SO:0001589	frameshift_variant	3205	exon1			.		CCDS5409.1	7p15.2	2011-06-20	2005-12-22		ENSG00000078399	ENSG00000078399		"""Homeoboxes / ANTP class : HOXL subclass"""	5109	protein-coding gene	gene with protein product		142956	"""homeo box A9"""	HOX1G, HOX1		1973146, 1358459	Standard	NM_152739		Approved		uc003syt.3	P31269	OTTHUMG00000023220	ENST00000343483.6:c.570delC	chr7.hg19:g.27204507delG	ENSP00000343619:p.Pro190fs	88.0	0.0		157.0	11.0	NM_152739	O43369|O43429|Q99820	Frame_Shift_Del	DEL	ENST00000343483.6	hg19	CCDS5409.1																																																																																			.	.		0.587	HOXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358706.2		
OR4A5	81318	hgsc.bcm.edu	37	11	51411652	51411652	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:51411652delA	ENST00000319760.6	-	1	796	c.744delT	c.(742-744)tttfs	p.F248fs		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				TACAGGGTACAAAAAAGAGGA	0.408																																					p.V249fs		Atlas-INDEL	.											.	OR4A5	116	.	0			c.745delG						.						55.0	54.0	54.0					11																	51411652		2201	4296	6497	SO:0001589	frameshift_variant	81318	exon1			.	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.744delT	chr11.hg19:g.51411652delA	ENSP00000367664:p.Phe248fs	86.0	0.0		143.0	13.0	NM_001005272	Q6IF84	Frame_Shift_Del	DEL	ENST00000319760.6	hg19	CCDS31497.1																																																																																			.	.		0.408	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
PMS1	5378	hgsc.bcm.edu	37	2	190719511	190719511	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:190719511delA	ENST00000441310.2	+	9	1746	c.1513delA	c.(1513-1515)aaafs	p.K505fs	PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000418224.3_Frame_Shift_Del_p.K329fs|PMS1_ENST00000432292.3_Frame_Shift_Del_p.K329fs|PMS1_ENST00000447232.2_Frame_Shift_Del_p.K505fs|PMS1_ENST00000409823.3_Frame_Shift_Del_p.K466fs	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	505					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)			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)			AAATATACTTAAAAATTCAGT	0.353			"""Mis, N"""			"""colorectal, endometrial, ovarian"""		Direct reversal of damage;Mismatch excision repair (MMR)																													p.L504fs		Atlas-INDEL	.	yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	.	PMS1	78	.	0			c.1512delT						.						35.0	40.0	38.0					2																	190719511		2191	4289	6480	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.1513delA	chr2.hg19:g.190719511delA	ENSP00000406490:p.Lys505fs	145.0	0.0		162.0	11.0	NM_001128144	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Frame_Shift_Del	DEL	ENST00000441310.2	hg19	CCDS2302.1																																																																																			.	.		0.353	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2		
TOP3A	7156	hgsc.bcm.edu	37	17	18217965	18217965	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:18217965delT	ENST00000321105.5	-	1	342	c.128delA	c.(127-129)aacfs	p.N43fs	SMCR8_ENST00000406438.3_5'Flank|TOP3A_ENST00000582230.1_5'UTR|TOP3A_ENST00000542570.1_5'UTR	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	43	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						GGCCGCGTCGTTTTTTTCGGC	0.652																																					p.N43fs		Atlas-INDEL	.											.	TOP3A	85	.	0			c.129delC						.						53.0	42.0	46.0					17																	18217965		2203	4300	6503	SO:0001589	frameshift_variant	7156	exon1			.	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 7"""	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.128delA	chr17.hg19:g.18217965delT	ENSP00000321636:p.Asn43fs	132.0	0.0		156.0	13.0	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Frame_Shift_Del	DEL	ENST00000321105.5	hg19	CCDS11194.1																																																																																			.	.		0.652	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2		
UGT1A1	54658	hgsc.bcm.edu	37	2	234668947	234668947	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:234668947delC	ENST00000608383.1	+	1	14	c.14delC	c.(13-15)tccfs	p.S5fs	UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A3_ENST00000482026.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A8_ENST00000305208.5_Frame_Shift_Del_p.S5fs|UGT1A1_ENST00000360418.3_Frame_Shift_Del_p.S5fs|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000609767.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A6_ENST00000406651.1_Intron			P22309	UD11_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A1	5					acute-phase response (GO:0006953)|bilirubin conjugation (GO:0006789)|biphenyl catabolic process (GO:0070980)|cellular glucuronidation (GO:0052695)|cellular response to ethanol (GO:0071361)|cellular response to glucocorticoid stimulus (GO:0071385)|digestion (GO:0007586)|drug metabolic process (GO:0017144)|estrogen metabolic process (GO:0008210)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|heme catabolic process (GO:0042167)|heterocycle metabolic process (GO:0046483)|liver development (GO:0001889)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of steroid metabolic process (GO:0045939)|organ regeneration (GO:0031100)|porphyrin-containing compound metabolic process (GO:0006778)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	cytochrome complex (GO:0070069)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(2)|endometrium(7)|large_intestine(5)|lung(9)|skin(4)|urinary_tract(2)	30		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Abacavir(DB01048)|Acetaminophen(DB00316)|Adenine(DB00173)|Atorvastatin(DB01076)|Axitinib(DB06626)|Diclofenac(DB00586)|Dolutegravir(DB08930)|Eltrombopag(DB06210)|Erlotinib(DB00530)|Estradiol(DB00783)|Etoposide(DB00773)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indacaterol(DB05039)|Indomethacin(DB00328)|Irinotecan(DB00762)|Losartan(DB00678)|Lovastatin(DB00227)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naltrexone(DB00704)|Naproxen(DB00788)|Nilotinib(DB04868)|Pazopanib(DB06589)|Propofol(DB00818)|Raltegravir(DB06817)|Regorafenib(DB08896)|Rifampicin(DB01045)|Simvastatin(DB00641)|Sorafenib(DB00398)|Suprofen(DB00870)|Testosterone Propionate(DB01420)	GCTGTGGAGTCCCAGGGCGGA	0.542											OREG0003837	type=REGULATORY REGION|Gene=UGT1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.S5fs		Atlas-INDEL	.											.	UGT1A1	81	.	0			c.13delT						.						31.0	30.0	30.0					2																	234668947		2203	4300	6503	SO:0001589	frameshift_variant	54658	exon1			.	M57899	CCDS2510.1	2q37.1	2014-09-17	2005-07-20		ENSG00000242366	ENSG00000242366	2.4.1.17	"""UDP glucuronosyltransferases"""	12530	other	complex locus constituent		191740	"""UDP glycosyltransferase 1 family, polypeptide A1"""	UGT1, GNT1		9295054, 9535849	Standard	NM_000463		Approved	UGT1A		P22309	OTTHUMG00000059117	ENST00000608383.1:c.14delC	chr2.hg19:g.234668947delC	ENSP00000476741:p.Ser5fs	135.0	0.0	2375	159.0	10.0	NM_000463	A6NJC3|B8K286	Frame_Shift_Del	DEL	ENST00000608383.1	hg19	CCDS2510.1																																																																																			.	.		0.542	UGT1A1-203	KNOWN	basic|CCDS	protein_coding	protein_coding			
ERG	2078	hgsc.bcm.edu	37	21	39755389	39755389	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:39755389delC	ENST00000417133.2	-	12	1582	c.1397delG	c.(1396-1398)ggtfs	p.G466fs	ERG_ENST00000398907.1_Frame_Shift_Del_p.G436fs|ERG_ENST00000398905.1_Frame_Shift_Del_p.G435fs|ERG_ENST00000398910.1_Frame_Shift_Del_p.G443fs|ERG_ENST00000288319.7_Frame_Shift_Del_p.G459fs|ERG_ENST00000398897.1_Frame_Shift_Del_p.G343fs|ERG_ENST00000398911.1_Frame_Shift_Del_p.G442fs|ERG_ENST00000442448.1_Frame_Shift_Del_p.G442fs|ERG_ENST00000453032.2_Frame_Shift_Del_p.G367fs|ERG_ENST00000398919.2_Frame_Shift_Del_p.G466fs	NM_001136154.1|NM_001243432.1	NP_001129626.1|NP_001230361.1	Q12809	KCNH2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog	0					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)		EWSR1/ERG(178)|NDRG1/ERG(5)|TMPRSS2/ERG(3582)|FUS/ERG(167)|SLC45A3/ERG(50)	lung(2)|ovary(1)|skin(1)	4		Prostate(19;3.6e-06)			Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GGGGTATATACCCCCAGTTGG	0.537			T	"""EWSR1, TMPRSS2, ELF4, FUS, HERPUD1, NDRG1"""	"""Ewing sarcoma, prostate, AML"""																																p.G466fs	Esophageal Squamous(130;336 1700 3010 3083 40589)	Atlas-INDEL	.		Dom	yes		21	21q22.3	2078	v-ets erythroblastosis virus E26 oncogene like (avian)		"""M, E, L"""	.	ERG	78	.	0			c.1398delT						.						34.0	35.0	35.0					21																	39755389		2203	4300	6503	SO:0001589	frameshift_variant	2078	exon12			.		CCDS13657.1, CCDS13658.1, CCDS46648.1, CCDS46649.1, CCDS58789.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157554	ENSG00000157554			3446	protein-coding gene	gene with protein product	"""v-ets avian erythroblastosis virus E26 oncogene related"", ""transcriptional regulator ERG (transforming protein ERG)"", ""v-ets erythroblastosis virus E26 oncogene like"", ""TMPRSS2-ERG prostate cancer specific"""	165080	"""v-ets avian erythroblastosis virus E26 oncogene related"""			3274086	Standard	NM_001136154		Approved	erg-3, p55	uc002yxa.3	P11308	OTTHUMG00000090767	ENST00000417133.2:c.1397delG	chr21.hg19:g.39755389delC	ENSP00000414150:p.Gly466fs	145.0	0.0		156.0	14.0	NM_001136154	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Frame_Shift_Del	DEL	ENST00000417133.2	hg19	CCDS46648.1																																																																																			.	.		0.537	ERG-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207532.2	NM_182918	
CCDC47	57003	hgsc.bcm.edu	37	17	61831827	61831827	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:61831827delA	ENST00000225726.5	-	9	1382	c.1000delT	c.(1000-1002)tcafs	p.S334fs	CCDC47_ENST00000582252.1_Frame_Shift_Del_p.S334fs|CCDC47_ENST00000403162.3_Frame_Shift_Del_p.S334fs|RP11-51F16.8_ENST00000580553.1_5'Flank	NM_020198.2	NP_064583.2	Q96A33	CCD47_HUMAN	coiled-coil domain containing 47	334					calcium ion homeostasis (GO:0055074)|ER overload response (GO:0006983)|osteoblast differentiation (GO:0001649)|post-embryonic development (GO:0009791)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	18						AACTGGTCTGAAAAATGAACA	0.303																																					p.S334X		Atlas-INDEL	.											.	CCDC47	34	.	0			c.1001delC						.						49.0	51.0	51.0					17																	61831827		2203	4300	6503	SO:0001589	frameshift_variant	57003	exon9			.	AF226054	CCDS11643.1	17q23.3	2005-12-19				ENSG00000108588			24856	protein-coding gene	gene with protein product						12477932	Standard	NM_020198		Approved	GK001	uc002jbs.4	Q96A33		ENST00000225726.5:c.1000delT	chr17.hg19:g.61831827delA	ENSP00000225726:p.Ser334fs	243.0	0.0		326.0	20.0	NM_020198	B2RAS8|D3DU20|Q96D00|Q96JZ7|Q9H3E4|Q9NRG3	Frame_Shift_Del	DEL	ENST00000225726.5	hg19	CCDS11643.1																																																																																			.	.		0.303	CCDC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444016.2	NM_020198	
DOK4	55715	hgsc.bcm.edu	37	16	57507902	57507902	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:57507902delC	ENST00000340099.4	-	7	1020	c.649delG	c.(649-651)gagfs	p.E217fs	DOK4_ENST00000569548.1_Frame_Shift_Del_p.E217fs|DOK4_ENST00000566936.1_Frame_Shift_Del_p.E217fs|DOK4_ENST00000561918.1_5'Flank	NM_018110.3	NP_060580.2	Q8TEW6	DOK4_HUMAN	docking protein 4	217	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				MAPK cascade (GO:0000165)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)		receptor signaling protein activity (GO:0005057)			kidney(1)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(2)	6						TAAATCTGCTCCCCCTCTTGT	0.597																																					p.E217fs		Atlas-INDEL	.											.	DOK4	19	.	0			c.650delA						.						101.0	90.0	94.0					16																	57507902		2198	4300	6498	SO:0001589	frameshift_variant	55715	exon7			.	BC003541	CCDS10783.1	16q13	2013-01-10			ENSG00000125170	ENSG00000125170		"""Pleckstrin homology (PH) domain containing"""	19868	protein-coding gene	gene with protein product		608333				10493829	Standard	NM_018110		Approved	FLJ10488	uc002elv.4	Q8TEW6	OTTHUMG00000133460	ENST00000340099.4:c.649delG	chr16.hg19:g.57507902delC	ENSP00000344277:p.Glu217fs	155.0	0.0		159.0	11.0	NM_018110	O75209|Q9BTP2|Q9NVV3	Frame_Shift_Del	DEL	ENST00000340099.4	hg19	CCDS10783.1																																																																																			.	.		0.597	DOK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257335.3		
PRR16	51334	hgsc.bcm.edu	37	5	120022115	120022115	+	Frame_Shift_Del	DEL	A	A	-	rs35167981		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:120022115delA	ENST00000407149.2	+	2	835	c.626delA	c.(625-627)gaafs	p.E209fs	PRR16_ENST00000446965.1_Frame_Shift_Del_p.E139fs|PRR16_ENST00000379551.2_Frame_Shift_Del_p.E186fs|PRR16_ENST00000505123.1_Frame_Shift_Del_p.E139fs			Q569H4	LARGN_HUMAN	proline rich 16	209	Pro-rich.				positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)					endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		CGGTTTAATGAAAAAGTACAG	0.483																																					p.E186fs		Atlas-INDEL	.											.	PRR16	71	.	0			c.556delG						.						74.0	75.0	75.0					5																	120022115		2203	4300	6503	SO:0001589	frameshift_variant	51334	exon3			.	AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.626delA	chr5.hg19:g.120022115delA	ENSP00000385118:p.Glu209fs	107.0	0.0		167.0	11.0	NM_016644	D3DSZ0|Q8IXY1|Q9NYI5	Frame_Shift_Del	DEL	ENST00000407149.2	hg19																																																																																				.	.		0.483	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644	
LHX1	3975	hgsc.bcm.edu	37	17	35300095	35300095	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:35300095delC	ENST00000254457.5	+	5	2299	c.888delC	c.(886-888)ttcfs	p.F296fs	RP11-445F12.2_ENST00000607336.1_RNA	NM_005568.3	NP_005559.2	P48742	LHX1_HUMAN	LIM homeobox 1	296					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell signaling (GO:0007267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|cerebellum development (GO:0021549)|cervix development (GO:0060067)|comma-shaped body morphogenesis (GO:0072049)|dorsal/ventral pattern formation (GO:0009953)|ectoderm formation (GO:0001705)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|embryonic viscerocranium morphogenesis (GO:0048703)|endoderm formation (GO:0001706)|epithelium development (GO:0060429)|forebrain regionalization (GO:0021871)|gastrulation with mouth forming second (GO:0001702)|head development (GO:0060322)|horizontal cell localization (GO:0035852)|kidney development (GO:0001822)|lateral motor column neuron migration (GO:0097477)|mesonephric duct development (GO:0072177)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerulus development (GO:0072224)|metanephric part of ureteric bud development (GO:0035502)|metanephric renal vesicle morphogenesis (GO:0072283)|metanephric S-shaped body morphogenesis (GO:0072284)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct elongation (GO:0035849)|nephric duct morphogenesis (GO:0072178)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|oviduct development (GO:0060066)|oviduct epithelium development (GO:0035846)|paramesonephric duct development (GO:0061205)|pattern specification process (GO:0007389)|positive regulation of anterior head development (GO:2000744)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primitive streak formation (GO:0090009)|pronephros development (GO:0048793)|regulation of gene expression (GO:0010468)|renal vesicle morphogenesis (GO:0072077)|retina layer formation (GO:0010842)|S-shaped body morphogenesis (GO:0072050)|somite rostral/caudal axis specification (GO:0032525)|spinal cord association neuron differentiation (GO:0021527)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)|uterine epithelium development (GO:0035847)|uterus development (GO:0060065)|vagina development (GO:0060068)|ventral spinal cord development (GO:0021517)	nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Breast(25;0.00607)				ACGACTTCTTCCCGCAAGGCC	0.731																																					p.F296fs		Atlas-INDEL	.											.	LHX1	48	.	0			c.887delT						.						15.0	17.0	16.0					17																	35300095		2199	4296	6495	SO:0001589	frameshift_variant	3975	exon5			.	U14755	CCDS11316.1	17q12	2014-04-11			ENSG00000132130	ENSG00000273706		"""Homeoboxes / LIM class"""	6593	protein-coding gene	gene with protein product		601999				9212161	Standard	NM_005568		Approved	LIM-1, LIM1	uc002hnh.2	P48742	OTTHUMG00000188456	ENST00000254457.5:c.888delC	chr17.hg19:g.35300095delC	ENSP00000254457:p.Phe296fs	119.0	0.0		153.0	10.0	NM_005568	Q3MIW0	Frame_Shift_Del	DEL	ENST00000254457.5	hg19	CCDS11316.1																																																																																			.	.		0.731	LHX1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256704.3	NM_005568	
KMT2C	58508	hgsc.bcm.edu	37	7	151848557	151848557	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:151848557delT	ENST00000262189.6	-	50	12854	c.12636delA	c.(12634-12636)aaafs	p.K4212fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.K4269fs|KMT2C_ENST00000485241.1_5'Flank	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4212					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)										CTTTGAAAGATTTCCGCACAC	0.448																																					p.S4213fs		Atlas-INDEL	.											.	MLL3	1564	.	0			c.12637delT						.						104.0	88.0	94.0					7																	151848557		2203	4300	6503	SO:0001589	frameshift_variant	58508	exon50			.	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.12636delA	chr7.hg19:g.151848557delT	ENSP00000262189:p.Lys4212fs	92.0	0.0		157.0	11.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.		0.448	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
TENM4	26011	hgsc.bcm.edu	37	11	78423720	78423720	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:78423720delG	ENST00000278550.7	-	26	4323	c.3861delC	c.(3859-3861)cccfs	p.P1287fs		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1287					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)										CCCCACTCATGGGGTCTGTGG	0.502																																					p.M1288X		Atlas-INDEL	.											.	.	.	.	0			c.3862delA						.						54.0	55.0	55.0					11																	78423720		1887	4099	5986	SO:0001589	frameshift_variant	26011	exon26			.	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.3861delC	chr11.hg19:g.78423720delG	ENSP00000278550:p.Pro1287fs	77.0	0.0		148.0	10.0	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Frame_Shift_Del	DEL	ENST00000278550.7	hg19	CCDS44688.1																																																																																			.	.		0.502	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
SMAD3	4088	hgsc.bcm.edu	37	15	67482771	67482771	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:67482771delC	ENST00000327367.4	+	9	1485	c.1175delC	c.(1174-1176)accfs	p.T392fs	SMAD3_ENST00000439724.3_Frame_Shift_Del_p.T348fs|SMAD3_ENST00000540846.2_Frame_Shift_Del_p.T287fs|SMAD3_ENST00000537194.2_Frame_Shift_Del_p.T197fs	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	392	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				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)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|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 wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|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 beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		GTGACCAGTACCCCCTGCTGG	0.532																																					p.T392fs		Atlas-INDEL	.											.	SMAD3	119	.	0			c.1174delA						.						62.0	59.0	60.0					15																	67482771		2201	4299	6500	SO:0001589	frameshift_variant	4088	exon9			.	BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"""SMADs"""	6769	protein-coding gene	gene with protein product		603109	"""MAD, mothers against decapentaplegic homolog 3 (Drosophila)"", ""SMAD, mothers against DPP homolog 3 (Drosophila)"""	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.1175delC	chr15.hg19:g.67482771delC	ENSP00000332973:p.Thr392fs	133.0	0.0		147.0	10.0	NM_005902	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Frame_Shift_Del	DEL	ENST00000327367.4	hg19	CCDS10222.1																																																																																			.	.		0.532	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902	
SOS1	6654	hgsc.bcm.edu	37	2	39262357	39262357	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:39262357delA	ENST00000426016.1	-	9	1156	c.1070delT	c.(1069-1071)ttgfs	p.L357fs	SOS1_ENST00000428721.2_Frame_Shift_Del_p.L300fs|SOS1_ENST00000402219.2_Frame_Shift_Del_p.L357fs|SOS1_ENST00000395038.2_Frame_Shift_Del_p.L357fs			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	357	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				TCTTACCTTCAAAAGTTCAAA	0.353									Noonan syndrome																												p.L357fs		Atlas-INDEL	.											.	SOS1	134	.	0			c.1071delG						.						43.0	46.0	45.0					2																	39262357		2203	4300	6503	SO:0001589	frameshift_variant	6654	exon8	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	.	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11187	protein-coding gene	gene with protein product		182530	"""gingival fibromatosis, hereditary, 1"""	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.1070delT	chr2.hg19:g.39262357delA	ENSP00000387784:p.Leu357fs	163.0	0.0		173.0	11.0	NM_005633	A8K2G3|B4DXG2	Frame_Shift_Del	DEL	ENST00000426016.1	hg19	CCDS1802.1																																																																																			.	.		0.353	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633	
HDAC6	10013	hgsc.bcm.edu	37	X	48661166	48661166	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:48661166delC	ENST00000334136.5	+	2	245	c.67delC	c.(67-69)cccfs	p.P24fs	HDAC6_ENST00000469223.1_Intron|HDAC6_ENST00000376619.2_Frame_Shift_Del_p.P24fs|HDAC6_ENST00000413163.2_Intron|HDAC6_ENST00000444343.2_Frame_Shift_Del_p.P38fs			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	24					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)	CCCCCAGTCGCCCCCTCAGGA	0.622																																					p.S22fs	Pancreas(112;205 1675 2305 8976 15959)	Atlas-INDEL	.											.	HDAC6	111	.	0			c.66delG						.						46.0	38.0	41.0					X																	48661166		2200	4300	6500	SO:0001589	frameshift_variant	10013	exon2			.	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.67delC	chrX.hg19:g.48661166delC	ENSP00000334061:p.Pro24fs	123.0	0.0		147.0	10.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Frame_Shift_Del	DEL	ENST00000334136.5	hg19	CCDS14306.1																																																																																			.	.		0.622	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044	
HSPG2	3339	hgsc.bcm.edu	37	1	22178628	22178628	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:22178628delG	ENST00000374695.3	-	53	6902	c.6823delC	c.(6823-6825)cagfs	p.Q2275fs	HSPG2_ENST00000430507.1_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2275	Ig-like C2-type 8.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CATGTGACCTGGGCGTGGGCC	0.652																																					p.Q2275fs		Atlas-INDEL	.											.	HSPG2	311	.	0			c.6824delA						.						49.0	48.0	48.0					1																	22178628		2203	4299	6502	SO:0001589	frameshift_variant	3339	exon53			.	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6823delC	chr1.hg19:g.22178628delG	ENSP00000363827:p.Gln2275fs	114.0	0.0		243.0	15.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Frame_Shift_Del	DEL	ENST00000374695.3	hg19	CCDS30625.1																																																																																			.	.		0.652	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
UGGT2	55757	hgsc.bcm.edu	37	13	96684195	96684195	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:96684195delT	ENST00000376747.3	-	2	259	c.189delA	c.(187-189)aaafs	p.K63fs	UGGT2_ENST00000376714.3_Frame_Shift_Del_p.K63fs|UGGT2_ENST00000376712.4_Frame_Shift_Del_p.K63fs|UGGT2_ENST00000397618.3_Frame_Shift_Del_p.K63fs	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	63					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						ACTGCCAAAATTTTTCATTAC	0.269																																					p.F64fs		Atlas-INDEL	.											.	UGGT2	127	.	0			c.190delT						.						54.0	57.0	56.0					13																	96684195		2199	4279	6478	SO:0001589	frameshift_variant	55757	exon2			.	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"""UDP-glucose:glycoprotein glucosyltransferase 2"""	605898	"""UDP-glucose ceramide glucosyltransferase-like 2"""	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.189delA	chr13.hg19:g.96684195delT	ENSP00000365938:p.Lys63fs	140.0	0.0		203.0	13.0	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Frame_Shift_Del	DEL	ENST00000376747.3	hg19	CCDS9480.1																																																																																			.	.		0.269	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
PTTG1	9232	hgsc.bcm.edu	37	5	159851311	159851311	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:159851311delA	ENST00000393964.1	+	3	747	c.344delA	c.(343-345)gaafs	p.E115fs	PTTG1_ENST00000352433.5_Frame_Shift_Del_p.E115fs|PTTG1_ENST00000520452.1_Frame_Shift_Del_p.E115fs|PTTG1_ENST00000519287.1_3'UTR	NM_001282382.1	NP_001269311.1	O95997	PTTG1_HUMAN	pituitary tumor-transforming 1	115					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|DNA repair (GO:0006281)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of endopeptidase activity (GO:0010951)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(1)|lung(4)	6	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.00219)|Epithelial(171;0.00348)|all cancers(165;0.0104)		CCAGAAATAGAAAAATTCTTT	0.383																																					p.E115fs		Atlas-INDEL	.											.	PTTG1	15	.	0			c.343delG						.						112.0	118.0	116.0					5																	159851311		2203	4300	6503	SO:0001589	frameshift_variant	9232	exon4			.	AF062649	CCDS4353.1	5q35.1	2014-08-04			ENSG00000164611	ENSG00000164611			9690	protein-coding gene	gene with protein product	"""ESP1-associated protein 1"", ""tumor-transforming protein 1"""	604147		TUTR1		9811450, 9892021	Standard	NM_004219		Approved	PTTG, HPTTG, EAP1, securin	uc003lyj.3	O95997	OTTHUMG00000130328	ENST00000393964.1:c.344delA	chr5.hg19:g.159851311delA	ENSP00000377536:p.Glu115fs	104.0	0.0		173.0	11.0	NM_004219		Frame_Shift_Del	DEL	ENST00000393964.1	hg19	CCDS4353.1																																																																																			.	.		0.383	PTTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252677.1	NM_004219	
HECTD4	283450	hgsc.bcm.edu	37	12	112622648	112622648	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:112622648delC	ENST00000430131.2	-	60	10001	c.8856delG	c.(8854-8856)gggfs	p.G2952fs	HECTD4_ENST00000377560.5_Frame_Shift_Del_p.G3202fs|HECTD4_ENST00000550722.1_Frame_Shift_Del_p.G3228fs			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2952					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)										TCACGCCCAGCCCCTGTGGGT	0.682																																					p.L3241fs		Atlas-INDEL	.											.	.	.	.	0			c.9721delC						.						72.0	87.0	82.0					12																	112622648		2196	4278	6474	SO:0001589	frameshift_variant	283450	exon61			.	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.8856delG	chr12.hg19:g.112622648delC	ENSP00000404379:p.Gly2952fs	84.0	0.0		183.0	11.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Frame_Shift_Del	DEL	ENST00000430131.2	hg19																																																																																				.	.		0.682	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
ZFP41	286128	hgsc.bcm.edu	37	8	144332034	144332034	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:144332034delA	ENST00000330701.4	+	2	390	c.21delA	c.(19-21)agafs	p.R7fs	ZFP41_ENST00000520584.1_Frame_Shift_Del_p.R7fs|ZFP41_ENST00000522452.1_Frame_Shift_Del_p.R7fs	NM_173832.4	NP_776193.1	Q8N8Y5	ZFP41_HUMAN	ZFP41 zinc finger protein	7					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|lung(4)|ovary(1)	8	all_cancers(97;1.01e-10)|all_epithelial(106;4.6e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			CTGCAGGCAGAAAAAAGAAGA	0.587																																					p.R7fs		Atlas-INDEL	.											.	ZFP41	25	.	0			c.20delG						.						24.0	27.0	26.0					8																	144332034		2201	4299	6500	SO:0001589	frameshift_variant	286128	exon2			.		CCDS6397.1	8q24.3	2013-01-08	2012-11-27		ENSG00000181638	ENSG00000181638		"""Zinc fingers, C2H2-type"""	26786	protein-coding gene	gene with protein product			"""zinc finger protein 41 homolog (mouse)"""			11214971	Standard	NM_173832		Approved	FLJ38705, FLJ00028, ZNF753	uc003yxw.4	Q8N8Y5	OTTHUMG00000164951	ENST00000330701.4:c.21delA	chr8.hg19:g.144332034delA	ENSP00000327427:p.Arg7fs	47.0	0.0		198.0	13.0	NM_173832	D3DWJ5	Frame_Shift_Del	DEL	ENST00000330701.4	hg19	CCDS6397.1																																																																																			.	.		0.587	ZFP41-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381114.2	NM_173832	
MIA3	375056	hgsc.bcm.edu	37	1	222824154	222824154	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:222824154delA	ENST00000344922.5	+	11	3843	c.3818delA	c.(3817-3819)gaafs	p.E1273fs	MIA3_ENST00000344441.6_Frame_Shift_Del_p.E1273fs|MIA3_ENST00000344507.1_Intron|MIA3_ENST00000340535.7_Frame_Shift_Del_p.E151fs	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1273					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		AAGACACTTGAAAAAAATCAG	0.303																																					p.E1273fs		Atlas-INDEL	.											.	MIA3	167	.	0			c.3817delG						.						53.0	52.0	53.0					1																	222824154		1800	4067	5867	SO:0001589	frameshift_variant	375056	exon11			.		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.3818delA	chr1.hg19:g.222824154delA	ENSP00000340900:p.Glu1273fs	143.0	0.0		250.0	17.0	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Frame_Shift_Del	DEL	ENST00000344922.5	hg19	CCDS41470.1																																																																																			.	.		0.303	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
AP1S2	8905	hgsc.bcm.edu	37	X	15864073	15864073	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:15864073delC	ENST00000329235.2	-	3	484	c.241delG	c.(241-243)gaafs	p.E81fs	AP1S2_ENST00000479184.1_5'Flank|AP1S2_ENST00000421527.2_Frame_Shift_Del_p.E123fs|AP1S2_ENST00000545766.1_Frame_Shift_Del_p.E123fs|AP1S2_ENST00000380291.1_Frame_Shift_Del_p.E81fs	NM_001272071.1|NM_003916.3	NP_001259000.1|NP_003907.3	P56377	AP1S2_HUMAN	adaptor-related protein complex 1, sigma 2 subunit	81					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|coated pit (GO:0005905)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)	protein transporter activity (GO:0008565)			large_intestine(1)	1	Hepatocellular(33;0.183)					TGAATTATTTCCAGGGTAATT	0.323																																					p.E81fs		Atlas-INDEL	.											.	AP1S2	9	.	0			c.242delA						.						84.0	87.0	86.0					X																	15864073		2203	4292	6495	SO:0001589	frameshift_variant	8905	exon3			.	AB015320	CCDS14173.1, CCDS75958.1	Xp22	2014-01-31			ENSG00000182287	ENSG00000182287			560	protein-coding gene	gene with protein product		300629	"""mental retardation, X-linked 59"", ""mental retardation, X-linked, syndromic 5"", ""Pettigrew X-linked mental retardation syndrome"""	MRX59, MRXS5, PGS		9733768, 17186471, 23756445	Standard	NM_003916		Approved	SIGMA1B	uc010nex.4	P56377	OTTHUMG00000021186	ENST00000329235.2:c.241delG	chrX.hg19:g.15864073delC	ENSP00000328789:p.Glu81fs	130.0	0.0		165.0	10.0	NM_001272071	B4DSU4|O95326|Q9H2N6	Frame_Shift_Del	DEL	ENST00000329235.2	hg19	CCDS14173.1																																																																																			.	.		0.323	AP1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055893.1	NM_003916	
ZC3H6	376940	hgsc.bcm.edu	37	2	113089974	113089974	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:113089974delC	ENST00000409871.1	+	12	3880	c.3479delC	c.(3478-3480)accfs	p.T1160fs	AC115115.2_ENST00000607612.1_RNA|ZC3H6_ENST00000343936.4_Frame_Shift_Del_p.T1160fs	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	1160							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						GGGAGCCCGACCCCAGATAAT	0.473																																					p.T1160fs		Atlas-INDEL	.											.	ZC3H6	93	.	0			c.3478delA						.						50.0	59.0	56.0					2																	113089974		1908	4119	6027	SO:0001589	frameshift_variant	376940	exon12			.	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"""Zinc fingers, CCCH-type domain containing"""	24762	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 6"""	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.3479delC	chr2.hg19:g.113089974delC	ENSP00000386764:p.Thr1160fs	112.0	0.0		166.0	11.0	NM_198581	A9JR71|Q6ZW96	Frame_Shift_Del	DEL	ENST00000409871.1	hg19	CCDS46393.1																																																																																			.	.		0.473	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581	
ST5	6764	hgsc.bcm.edu	37	11	8736195	8736195	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:8736195delT	ENST00000534127.1	-	10	2289	c.1904delA	c.(1903-1905)aagfs	p.K635fs	ST5_ENST00000313726.6_Frame_Shift_Del_p.K635fs|ST5_ENST00000526757.1_Frame_Shift_Del_p.K215fs|ST5_ENST00000530991.1_Frame_Shift_Del_p.K107fs|ST5_ENST00000530438.1_Frame_Shift_Del_p.K215fs|ST5_ENST00000526099.1_Frame_Shift_Del_p.K148fs|ST5_ENST00000357665.1_Frame_Shift_Del_p.K635fs|RPL27A_ENST00000531102.1_Intron	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	635					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		CATAGACAACTTTTTTAATCT	0.468																																					p.K635fs		Atlas-INDEL	.											.	ST5	85	.	0			c.1905delG						.						258.0	231.0	240.0					11																	8736195		2201	4296	6497	SO:0001589	frameshift_variant	6764	exon7			.	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"""DENN/MADD domain containing"""	11350	protein-coding gene	gene with protein product	"""DENN/MADD domain containing 2B"""	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.1904delA	chr11.hg19:g.8736195delT	ENSP00000433528:p.Lys635fs	134.0	0.0		186.0	15.0	NM_213618	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Frame_Shift_Del	DEL	ENST00000534127.1	hg19	CCDS7791.1																																																																																			.	.		0.468	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418	
SMCHD1	23347	hgsc.bcm.edu	37	18	2722560	2722560	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:2722560delT	ENST00000320876.6	+	20	2840	c.2502delT	c.(2500-2502)cctfs	p.P834fs	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Frame_Shift_Del_p.P834fs	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	834					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TGGATCTTCCTTTTCGTGTTG	0.368																																					p.P834fs		Atlas-INDEL	.											.	SMCHD1	88	.	0			c.2501delC						.						183.0	165.0	171.0					18																	2722560		1816	4080	5896	SO:0001589	frameshift_variant	23347	exon20			.	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.2502delT	chr18.hg19:g.2722560delT	ENSP00000326603:p.Pro834fs	149.0	0.0		162.0	10.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Frame_Shift_Del	DEL	ENST00000320876.6	hg19	CCDS45822.1																																																																																			.	.		0.368	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
CLSTN2	64084	hgsc.bcm.edu	37	3	140178605	140178605	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:140178605delA	ENST00000458420.3	+	7	1406	c.1216delA	c.(1216-1218)aaafs	p.K406fs	RP11-68L1.1_ENST00000483759.2_RNA|RP11-68L1.2_ENST00000503357.1_RNA	NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	406					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						CAACTCAGACAAAACCGGTGA	0.567										HNSCC(16;0.037)																											p.D405fs	GBM(45;858 913 3709 36904 37282)	Atlas-INDEL	.											.	CLSTN2	190	.	0			c.1215delC						.						75.0	68.0	70.0					3																	140178605		2203	4300	6503	SO:0001589	frameshift_variant	64084	exon7			.	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"""Cadherins / Cadherin-related"""	17448	protein-coding gene	gene with protein product	"""cadherin-related family member 13"""	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.1216delA	chr3.hg19:g.140178605delA	ENSP00000402460:p.Lys406fs	102.0	0.0		211.0	15.0	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Frame_Shift_Del	DEL	ENST00000458420.3	hg19	CCDS3112.1																																																																																			.	.		0.567	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	
VPS26A	9559	hgsc.bcm.edu	37	10	70928313	70928313	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:70928313delA	ENST00000373382.1	+	9	1449	c.796delA	c.(796-798)aaafs	p.K267fs	VPS26A_ENST00000395098.1_Intron|VPS26A_ENST00000489794.1_Intron|VPS26A_ENST00000263559.6_Frame_Shift_Del_p.K267fs|VPS26A_ENST00000546041.1_Frame_Shift_Del_p.K250fs|VPS26A_ENST00000541711.1_Frame_Shift_Del_p.K156fs|VPS26A_ENST00000490696.1_3'UTR			O75436	VP26A_HUMAN	vacuolar protein sorting 26 homolog A (S. pombe)	267					retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|vesicle (GO:0031982)	protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)	8						AGATGTGAACAAAAAATTTTC	0.368																																					p.N265fs	Colon(90;545 1358 4729 6702 16773)	Atlas-INDEL	.											.	VPS26A	24	.	0			c.795delC						.						93.0	98.0	96.0					10																	70928313		2203	4300	6503	SO:0001589	frameshift_variant	9559	exon8			.	AF054179	CCDS7286.1, CCDS41536.1	10q21.1	2007-01-12	2007-01-12	2005-10-11	ENSG00000122958	ENSG00000122958			12711	protein-coding gene	gene with protein product		605506	"""vacuolar protein sorting 26 (yeast homolog)"", ""vacuolar protein sorting 26 (yeast)"", ""vacuolar protein sorting 26 homolog A (yeast)"""	VPS26		1638986, 9653160	Standard	NM_004896		Approved	Hbeta58, PEP8A	uc001jpb.3	O75436	OTTHUMG00000018376	ENST00000373382.1:c.796delA	chr10.hg19:g.70928313delA	ENSP00000362480:p.Lys267fs	142.0	0.0		168.0	13.0	NM_004896	A8MZ56|B2RDD3|Q8TBH4|Q9H982	Frame_Shift_Del	DEL	ENST00000373382.1	hg19	CCDS7286.1																																																																																			.	.		0.368	VPS26A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048403.1	NM_004896	
KCNMA1	3778	hgsc.bcm.edu	37	10	78799310	78799310	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:78799310delC	ENST00000286628.8	-	15	1834	c.1835delG	c.(1834-1836)ggtfs	p.G612fs	KCNMA1_ENST00000354353.5_Frame_Shift_Del_p.G612fs|KCNMA1_ENST00000372440.1_Frame_Shift_Del_p.G612fs|KCNMA1_ENST00000286627.5_Frame_Shift_Del_p.G612fs|KCNMA1_ENST00000404771.3_Frame_Shift_Del_p.G612fs|KCNMA1_ENST00000406533.3_Frame_Shift_Del_p.G612fs|KCNMA1_ENST00000404857.1_Frame_Shift_Del_p.G612fs|KCNMA1_ENST00000372443.1_Frame_Shift_Del_p.G612fs	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	612					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	GAAGGACAGACCCACGAAGGC	0.453																																					p.G612fs		Atlas-INDEL	.											.	KCNMA1	370	.	0			c.1836delT						.						228.0	192.0	204.0					10																	78799310		2203	4300	6503	SO:0001589	frameshift_variant	3778	exon15			.	U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6284	protein-coding gene	gene with protein product	"""BK channel alpha subunit"""	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.1835delG	chr10.hg19:g.78799310delC	ENSP00000286628:p.Gly612fs	117.0	0.0		157.0	10.0	NM_002247	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Frame_Shift_Del	DEL	ENST00000286628.8	hg19																																																																																				.	.		0.453	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247	
YIF1B	90522	hgsc.bcm.edu	37	19	38796095	38796095	+	Frame_Shift_Del	DEL	G	G	-	rs536877708		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:38796095delG	ENST00000339413.6	-	8	887	c.842delC	c.(841-843)ccgfs	p.P281fs	YIF1B_ENST00000592246.1_Frame_Shift_Del_p.P215fs|YIF1B_ENST00000392124.3_Frame_Shift_Del_p.P250fs|YIF1B_ENST00000592694.1_Frame_Shift_Del_p.P250fs|YIF1B_ENST00000337679.8_3'UTR|YIF1B_ENST00000591784.1_Frame_Shift_Del_p.P250fs|YIF1B_ENST00000329420.8_Frame_Shift_Del_p.P266fs	NM_001039672.2|NM_001039673.2	NP_001034761.1|NP_001034762.1	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B (S. cerevisiae)	281						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)	10	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CCCACGCACCGGGACCCCCTC	0.642																																					p.P281fs		Atlas-INDEL	.											.	YIF1B	47	.	0			c.843delG						.						15.0	17.0	17.0					19																	38796095		2196	4288	6484	SO:0001589	frameshift_variant	90522	exon8			.	AL833382	CCDS12512.1, CCDS33010.1, CCDS46066.1, CCDS46067.1	19q13.2	2008-02-05							30511	protein-coding gene	gene with protein product						12975309	Standard	NM_001039672		Approved	FinGER8	uc002ohz.2	Q5BJH7		ENST00000339413.6:c.842delC	chr19.hg19:g.38796095delG	ENSP00000343435:p.Pro281fs	161.0	0.0		162.0	10.0	NM_001039672	H7BXS8|Q5JPC2|Q8WY70|Q96C02|Q96IC4	Frame_Shift_Del	DEL	ENST00000339413.6	hg19	CCDS33010.1																																																																																			.	.		0.642	YIF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460511.1	NM_033557	
P2RX3	5024	hgsc.bcm.edu	37	11	57118235	57118235	+	Splice_Site	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:57118235delG	ENST00000263314.2	+	8	739		c.e8-1			NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3						behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)			endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						CGTTTCTTCAGGGGGGAGTTC	0.607																																					.		Atlas-INDEL	.											.	P2RX3	55	.	0			c.706-2G>-						.						65.0	57.0	59.0					11																	57118235		2201	4296	6497	SO:0001630	splice_region_variant	5024	exon8			.	Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.706-1G>-	chr11.hg19:g.57118235delG		145.0	0.0		195.0	14.0	NM_002559	Q6DK37|Q9UQB6	Splice_Site	DEL	ENST00000263314.2	hg19	CCDS7953.1																																																																																			.	.		0.607	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559	Intron
UTP11L	51118	hgsc.bcm.edu	37	1	38483393	38483393	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:38483393delA	ENST00000373014.4	+	3	240	c.179delA	c.(178-180)gaafs	p.E60fs	UTP11L_ENST00000537711.1_Frame_Shift_Del_p.E60fs|UTP11L_ENST00000488453.1_3'UTR	NM_016037.3	NP_057121.2	Q9Y3A2	UTP11_HUMAN	UTP11-like, U3 small nucleolar ribonucleoprotein (yeast)	60					nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleolus (GO:0005730)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				AAGGCTCTTGAAAAAAATCCA	0.378																																					p.E60fs		Atlas-INDEL	.											.	UTP11L	17	.	0			c.178delG						.						74.0	84.0	81.0					1																	38483393		2201	4300	6501	SO:0001589	frameshift_variant	51118	exon3			.	AF151852	CCDS429.1	1p34.3	2014-03-06	2014-03-06		ENSG00000183520	ENSG00000183520			24329	protein-coding gene	gene with protein product		609440				11860508, 10810093	Standard	NM_016037		Approved	CGI-94	uc001ccn.4	Q9Y3A2	OTTHUMG00000004435	ENST00000373014.4:c.179delA	chr1.hg19:g.38483393delA	ENSP00000362105:p.Glu60fs	160.0	0.0		262.0	16.0	NM_016037	A8K785|B4DJC6|D3DPT7|Q5VT93|Q9BS98|Q9NS31	Frame_Shift_Del	DEL	ENST00000373014.4	hg19	CCDS429.1																																																																																			.	.		0.378	UTP11L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012962.1	NM_016037	
HEATR5B	54497	hgsc.bcm.edu	37	2	37234290	37234290	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:37234290delT	ENST00000233099.5	-	29	4775	c.4680delA	c.(4678-4680)aaafs	p.K1560fs	HEATR5B_ENST00000354531.2_Frame_Shift_Del_p.K1560fs	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1560						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				ATGTAGAACGTTTTTGTAAAC	0.428																																					p.R1561fs		Atlas-INDEL	.											.	HEATR5B	185	.	0			c.4681delC						.						143.0	131.0	135.0					2																	37234290		2203	4300	6503	SO:0001589	frameshift_variant	54497	exon29			.	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.4680delA	chr2.hg19:g.37234290delT	ENSP00000233099:p.Lys1560fs	119.0	0.0		152.0	12.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Frame_Shift_Del	DEL	ENST00000233099.5	hg19	CCDS33181.1																																																																																			.	.		0.428	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
SMC1B	27127	hgsc.bcm.edu	37	22	45798221	45798221	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:45798221delT	ENST00000357450.4	-	5	845	c.846delA	c.(844-846)aaafs	p.K282fs	SMC1B_ENST00000404354.3_Frame_Shift_Del_p.K282fs	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	282					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)		ACTTTAATTCTTTTTCTGTTT	0.299																																					p.E283fs		Atlas-INDEL	.											SMC1B,NS,carcinoma,0,1	SMC1B	215	.	0			c.847delG						.						124.0	105.0	111.0					22																	45798221		1811	4069	5880	SO:0001589	frameshift_variant	27127	exon5			.	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.846delA	chr22.hg19:g.45798221delT	ENSP00000350036:p.Lys282fs	149.0	0.0		192.0	12.0	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Frame_Shift_Del	DEL	ENST00000357450.4	hg19	CCDS43027.1																																																																																			.	.		0.299	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
UGT2B7	7364	hgsc.bcm.edu	37	4	69962593	69962593	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:69962593delT	ENST00000508661.1	+	1	382	c.355delT	c.(355-357)tttfs	p.F119fs	UGT2B7_ENST00000305231.7_Frame_Shift_Del_p.F119fs|UGT2B7_ENST00000509763.1_Intron			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	119					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CATGTCAATATTTGGTGACAT	0.313																																					p.I118fs		Atlas-INDEL	.											.	UGT2B7	79	.	0			c.354delA						.						49.0	49.0	49.0					4																	69962593		2185	4294	6479	SO:0001589	frameshift_variant	7364	exon1			.	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.355delT	chr4.hg19:g.69962593delT	ENSP00000427659:p.Phe119fs	132.0	0.0		164.0	10.0	NM_001074	B2R810|Q6GTW0	Frame_Shift_Del	DEL	ENST00000508661.1	hg19																																																																																				.	.		0.313	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074	
MAP7D3	79649	hgsc.bcm.edu	37	X	135313838	135313838	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:135313838delG	ENST00000316077.9	-	8	1498	c.1278delC	c.(1276-1278)cccfs	p.P426fs	MAP7D3_ENST00000370661.1_Frame_Shift_Del_p.P391fs|MAP7D3_ENST00000495432.1_5'Flank|MAP7D3_ENST00000370663.5_Frame_Shift_Del_p.P408fs	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	426					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					CACTCTCCTTGGGGGCTACTT	0.602																																					p.K427fs		Atlas-INDEL	.											.	MAP7D3	102	.	0			c.1279delA						.						88.0	82.0	84.0					X																	135313838		1938	4115	6053	SO:0001589	frameshift_variant	79649	exon8			.	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.1278delC	chrX.hg19:g.135313838delG	ENSP00000318086:p.Pro426fs	141.0	0.0		142.0	10.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Frame_Shift_Del	DEL	ENST00000316077.9	hg19	CCDS44004.1																																																																																			.	.		0.602	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2		
C2orf71	388939	hgsc.bcm.edu	37	2	29293880	29293880	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:29293880delG	ENST00000331664.5	-	1	3247	c.3248delC	c.(3247-3249)cctfs	p.P1083fs		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1083	Pro-rich.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						AATCGAGAAAGGGGGGCTTGC	0.602																																					p.P1083fs		Atlas-INDEL	.											.	C2orf71	146	.	0			c.3249delT						.						57.0	65.0	63.0					2																	29293880		1891	4089	5980	SO:0001589	frameshift_variant	388939	exon1			.		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3248delC	chr2.hg19:g.29293880delG	ENSP00000332809:p.Pro1083fs	57.0	0.0		102.0	10.0	NM_001029883		Frame_Shift_Del	DEL	ENST00000331664.5	hg19	CCDS42669.1																																																																																			.	.		0.602	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
SOX6	55553	hgsc.bcm.edu	37	11	16208476	16208476	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:16208476delT	ENST00000352083.6	-	5	638	c.561delA	c.(559-561)aaafs	p.K187fs	SOX6_ENST00000528429.1_Frame_Shift_Del_p.K187fs|SOX6_ENST00000316399.6_Frame_Shift_Del_p.K187fs|SOX6_ENST00000527619.1_Frame_Shift_Del_p.K190fs|SOX6_ENST00000528252.1_Frame_Shift_Del_p.K187fs|SOX6_ENST00000396356.3_Frame_Shift_Del_p.K187fs			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	187					astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	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)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						GCTGCCGTTCTTTTTCTGCCA	0.473																																					p.E201fs		Atlas-INDEL	.											.	SOX6	149	.	0			c.601delG						.						118.0	119.0	119.0					11																	16208476		2200	4294	6494	SO:0001589	frameshift_variant	55553	exon5			.	AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"""SRY (sex determining region Y)-boxes"""	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.561delA	chr11.hg19:g.16208476delT	ENSP00000339876:p.Lys187fs	114.0	0.0		175.0	11.0	NM_001145819	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Frame_Shift_Del	DEL	ENST00000352083.6	hg19																																																																																				.	.		0.473	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326	
KIAA2026	158358	hgsc.bcm.edu	37	9	5954073	5954073	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:5954073delT	ENST00000399933.3	-	4	2234	c.2235delA	c.(2233-2235)aaafs	p.K745fs	KIAA2026_ENST00000381461.2_Frame_Shift_Del_p.K745fs	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	745	Lys-rich.									breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		TTGTGATTGCTTTTTTAGAGA	0.308																																					p.A746fs		Atlas-INDEL	.											.	KIAA2026	231	.	0			c.2236delG						.						164.0	145.0	151.0					9																	5954073		1798	4061	5859	SO:0001589	frameshift_variant	158358	exon4			.	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.2235delA	chr9.hg19:g.5954073delT	ENSP00000382815:p.Lys745fs	138.0	0.0		135.0	10.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Frame_Shift_Del	DEL	ENST00000399933.3	hg19																																																																																				.	.		0.308	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969	
TLK1	9874	hgsc.bcm.edu	37	2	171862754	171862754	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:171862754delT	ENST00000431350.2	-	18	2211	c.1807delA	c.(1807-1809)atcfs	p.I603fs	TLK1_ENST00000434911.2_Frame_Shift_Del_p.I507fs|TLK1_ENST00000442919.2_Frame_Shift_Del_p.I555fs|TLK1_ENST00000521943.1_Frame_Shift_Del_p.I555fs|TLK1_ENST00000360843.3_Frame_Shift_Del_p.I624fs			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	603	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						GTGATTTTGATTTCACCACAT	0.353																																					p.I603fs		Atlas-INDEL	.											.	TLK1	134	.	0			c.1808delT						.						126.0	118.0	121.0					2																	171862754		2203	4300	6503	SO:0001589	frameshift_variant	9874	exon18			.	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.1807delA	chr2.hg19:g.171862754delT	ENSP00000411099:p.Ile603fs	174.0	0.0		195.0	12.0	NM_012290	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Frame_Shift_Del	DEL	ENST00000431350.2	hg19	CCDS2241.1																																																																																			.	.		0.353	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290	
CRELD1	78987	hgsc.bcm.edu	37	3	9976237	9976237	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:9976237delC	ENST00000383811.3	+	1	714	c.115delC	c.(115-117)cccfs	p.P41fs	CRELD1_ENST00000397170.3_Frame_Shift_Del_p.P41fs|CRELD1_ENST00000326434.5_Frame_Shift_Del_p.P41fs|CRELD1_ENST00000452070.1_Frame_Shift_Del_p.P41fs|RP11-1020A11.1_ENST00000602411.1_RNA	NM_015513.4	NP_056328	Q96HD1	CREL1_HUMAN	cysteine-rich with EGF-like domains 1	41	Pro-rich.				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						CCAGTCTTCTCCCCCGCCTCA	0.627																																					p.S38fs		Atlas-INDEL	.											.	CRELD1	48	.	0			c.114delT						.						55.0	45.0	48.0					3																	9976237		2203	4300	6503	SO:0001589	frameshift_variant	78987	exon2			.	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.115delC	chr3.hg19:g.9976237delC	ENSP00000373322:p.Pro41fs	139.0	0.0		167.0	11.0	NM_001077415	A8MX90|B2RAA9|Q6I9X5|Q8NFT4|Q9Y409	Frame_Shift_Del	DEL	ENST00000383811.3	hg19	CCDS2593.1																																																																																			.	.		0.627	CRELD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250533.1	NM_015513	
PABPC4	8761	hgsc.bcm.edu	37	1	40028016	40028016	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:40028016delG	ENST00000372857.3	-	13	2485	c.1693delC	c.(1693-1695)cagfs	p.Q565fs	PABPC4_ENST00000372856.3_Frame_Shift_Del_p.Q552fs|RP11-69E11.8_ENST00000415255.1_RNA|PABPC4_ENST00000372858.3_Frame_Shift_Del_p.Q581fs|PABPC4_ENST00000372862.3_Frame_Shift_Del_p.Q536fs	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	565	PABC. {ECO:0000255|PROSITE- ProRule:PRU00641}.				blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TTCTGTTCCTGGGGGGGTGCT	0.602																																					p.Q581fs		Atlas-INDEL	.											.	PABPC4	56	.	0			c.1742delA						.						50.0	54.0	53.0					1																	40028016		2203	4300	6503	SO:0001589	frameshift_variant	8761	exon13			.	U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"""RNA binding motif (RRM) containing"""	8557	protein-coding gene	gene with protein product		603407	"""poly(A)-binding protein, cytoplasmic 4 (inducible form)"""			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.1693delC	chr1.hg19:g.40028016delG	ENSP00000361948:p.Gln565fs	135.0	0.0		248.0	16.0	NM_001135653	B1ANQ8|Q4VC03|Q6P0N3	Frame_Shift_Del	DEL	ENST00000372857.3	hg19	CCDS438.1																																																																																			.	.		0.602	PABPC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025220.1	NM_001135653	
BBS9	27241	hgsc.bcm.edu	37	7	33217199	33217199	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:33217199delA	ENST00000242067.6	+	5	959	c.438delA	c.(436-438)gtafs	p.V146fs	RNA5SP229_ENST00000410809.1_RNA|BBS9_ENST00000396127.2_Frame_Shift_Del_p.V146fs|BBS9_ENST00000425508.2_Frame_Shift_Del_p.V101fs|BBS9_ENST00000355070.2_Frame_Shift_Del_p.V146fs|BBS9_ENST00000354265.4_Frame_Shift_Del_p.V146fs|BBS9_ENST00000350941.3_Frame_Shift_Del_p.V146fs	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	146					cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			TTGGTGGTGTAAAAGGTAATT	0.343									Bardet-Biedl syndrome																												p.V146fs		Atlas-INDEL	.											.	BBS9	194	.	0			c.437delT						.						151.0	141.0	145.0					7																	33217199		2203	4300	6503	SO:0001589	frameshift_variant	27241	exon5	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	.		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507			30000	protein-coding gene	gene with protein product	"""parathyroid hormone responsive B1 gene"""	607968				16380913, 10221542	Standard	XM_005249701		Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.438delA	chr7.hg19:g.33217199delA	ENSP00000242067:p.Val146fs	75.0	0.0		99.0	11.0	NM_014451	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Frame_Shift_Del	DEL	ENST00000242067.6	hg19	CCDS43566.1																																																																																			.	.		0.343	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1		
LUZP4	51213	hgsc.bcm.edu	37	X	114536631	114536631	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:114536631delA	ENST00000371920.3	+	2	173	c.166delA	c.(166-168)aaafs	p.K57fs	LUZP4_ENST00000451986.2_Frame_Shift_Del_p.V13fs	NM_016383.3	NP_057467.1	Q9P127	LUZP4_HUMAN	leucine zipper protein 4	57						nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	14						GAACCATAGTAAAAAGGAATC	0.348																																					p.S55fs		Atlas-INDEL	.											.	LUZP4	51	.	0			c.165delT						.						145.0	136.0	139.0					X																	114536631		2203	4300	6503	SO:0001589	frameshift_variant	51213	exon2			.	AF124430	CCDS14567.1	Xq24	2009-03-25			ENSG00000102021	ENSG00000102021			24971	protein-coding gene	gene with protein product	"""cancer/testis antigen 28"""	300616				12032826, 11051238	Standard	XM_005268343		Approved	HOM-TES-85, CT-8, CT28	uc004eqa.3	Q9P127	OTTHUMG00000022234	ENST00000371920.3:c.166delA	chrX.hg19:g.114536631delA	ENSP00000360988:p.Lys57fs	184.0	0.0		185.0	12.0	NM_016383	B3KSD6	Frame_Shift_Del	DEL	ENST00000371920.3	hg19	CCDS14567.1																																																																																			.	.		0.348	LUZP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057972.1	NM_016383	
SECISBP2L	9728	hgsc.bcm.edu	37	15	49293086	49293086	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:49293086delT	ENST00000559471.1	-	15	2499	c.2236delA	c.(2236-2238)atcfs	p.I746fs	SECISBP2L_ENST00000261847.3_Frame_Shift_Del_p.I701fs|SECISBP2L_ENST00000559122.1_5'UTR	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	746							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						TTTGACTGGATTTTTTCACAG	0.343																																					p.I746fs		Atlas-INDEL	.											.	SECISBP2L	118	.	0			c.2237delT						.						92.0	87.0	89.0					15																	49293086		2196	4295	6491	SO:0001589	frameshift_variant	9728	exon15			.	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.2236delA	chr15.hg19:g.49293086delT	ENSP00000453854:p.Ile746fs	193.0	0.0		214.0	14.0	NM_001193489	Q8N767	Frame_Shift_Del	DEL	ENST00000559471.1	hg19	CCDS53942.1																																																																																			.	.		0.343	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701	
ANKRD26	22852	hgsc.bcm.edu	37	10	27303455	27303455	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:27303455delT	ENST00000376087.4	-	31	4857	c.4692delA	c.(4690-4692)aaafs	p.K1564fs	ANKRD26_ENST00000436985.2_Frame_Shift_Del_p.K1580fs|ANKRD26_ENST00000376070.3_Frame_Shift_Del_p.K1121fs	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1563					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						ATTTTCTAACTTTTAATTCTT	0.274																																					p.V1565fs		Atlas-INDEL	.											.	ANKRD26	179	.	0			c.4693delG						.						42.0	40.0	41.0					10																	27303455		1779	4038	5817	SO:0001589	frameshift_variant	22852	exon31			.	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.4692delA	chr10.hg19:g.27303455delT	ENSP00000365255:p.Lys1564fs	146.0	0.0		152.0	10.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Frame_Shift_Del	DEL	ENST00000376087.4	hg19	CCDS41499.1																																																																																			.	.		0.274	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		
THBS2	7058	hgsc.bcm.edu	37	6	169646335	169646336	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:169646335_169646336delCA	ENST00000366787.3	-	5	899_900	c.650_651delTG	c.(649-651)gtgfs	p.V217fs		NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	217	Heparin-binding. {ECO:0000255}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.V217A(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		GAATATCTTCCACAGAGTTTTC	0.406																																					p.217_218del	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-INDEL	.											.	THBS2	230	.	1	Substitution - Missense(1)	lung(1)	c.651_652del						.																																			SO:0001589	frameshift_variant	7058	exon5			.		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.650_651delTG	chr6.hg19:g.169646337_169646338delCA	ENSP00000355751:p.Val217fs	87.0	0.0		111.0	17.0	NM_003247	A6H8N1|A7E232|Q5RI52	Frame_Shift_Del	DEL	ENST00000366787.3	hg19	CCDS34574.1																																																																																			.	.		0.406	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
CACNA1F	778	hgsc.bcm.edu	37	X	49066137	49066137	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:49066137delT	ENST00000376265.2	-	41	4867	c.4806delA	c.(4804-4806)aaafs	p.K1602fs	CACNA1F_ENST00000376251.1_Frame_Shift_Del_p.K1537fs|CACNA1F_ENST00000323022.5_Frame_Shift_Del_p.K1591fs	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1602					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CTAGTAGCCCTTTTTCTTTCC	0.587																																					p.G1603fs		Atlas-INDEL	.											.	CACNA1F	218	.	0			c.4807delG						.						87.0	66.0	73.0					X																	49066137		2203	4300	6503	SO:0001589	frameshift_variant	778	exon41			.	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1393	protein-coding gene	gene with protein product		300110	"""Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"""	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.4806delA	chrX.hg19:g.49066137delT	ENSP00000365441:p.Lys1602fs	92.0	0.0		123.0	11.0	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Frame_Shift_Del	DEL	ENST00000376265.2	hg19	CCDS35253.1																																																																																			.	.		0.587	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
CES3	23491	hgsc.bcm.edu	37	16	66995238	66995238	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:66995238delG	ENST00000303334.4	+	1	99	c.28delG	c.(28-30)gggfs	p.G10fs	RP11-361L15.4_ENST00000566869.1_RNA|CES3_ENST00000394037.1_Frame_Shift_Del_p.G10fs	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3	10						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		AGTGGAGTCCGGGGTCCTGGT	0.582											OREG0023869	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S9fs		Atlas-INDEL	.											.	CES3	56	.	0			c.27delC						.						101.0	88.0	92.0					16																	66995238		2200	4300	6500	SO:0001589	frameshift_variant	23491	exon1			.	AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828		"""Carboxylesterases"""	1865	protein-coding gene	gene with protein product	"""esterase 31"", ""brain carboxylesterase BR3"""	605279	"""carboxylesterase 3 (brain)"""			10518925, 14581373, 15100172, 20931200	Standard	NM_001185176		Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000303334.4:c.28delG	chr16.hg19:g.66995238delG	ENSP00000304782:p.Gly10fs	162.0	0.0	1096	191.0	12.0	NM_024922	B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Frame_Shift_Del	DEL	ENST00000303334.4	hg19	CCDS10826.1																																																																																			.	.		0.582	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922	
VPS29	51699	hgsc.bcm.edu	37	12	110933940	110933940	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:110933940delT	ENST00000549578.1	-	2	137	c.72delA	c.(70-72)aaafs	p.K24fs	VPS29_ENST00000552130.2_5'UTR|SNORD50_ENST00000365465.1_RNA|VPS29_ENST00000549970.1_5'UTR|VPS29_ENST00000447578.2_5'UTR|VPS29_ENST00000551655.1_5'Flank|VPS29_ENST00000360579.7_Frame_Shift_Del_p.K28fs|VPS29_ENST00000546588.1_Frame_Shift_Del_p.K56fs	NM_016226.3	NP_057310.1	Q9UBQ0	VPS29_HUMAN	vacuolar protein sorting 29 homolog (S. cerevisiae)	24					protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphoserine phosphatase activity (GO:0004647)			kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						GCACCAGGAGTTTTTTGAATT	0.423																																					p.L29fs		Atlas-INDEL	.											.	VPS29	10	.	0			c.85delC						.						140.0	126.0	130.0					12																	110933940		1864	4101	5965	SO:0001589	frameshift_variant	51699	exon3			.	AF193795	CCDS41832.1, CCDS53832.1, CCDS73525.1	12q24	2006-12-19	2006-12-19			ENSG00000111237			14340	protein-coding gene	gene with protein product		606932	"""vacuolar protein sorting 29 (yeast homolog)"", ""vacuolar protein sorting 29 (yeast)"""			11062004	Standard	NM_001282151		Approved	PEP11, DC7, DC15	uc001tqx.3	Q9UBQ0	OTTHUMG00000169527	ENST00000549578.1:c.72delA	chr12.hg19:g.110933940delT	ENSP00000447058:p.Lys24fs	103.0	0.0		144.0	11.0	NM_057180	Q502Y5|Q6FIF8|Q6IAH3|Q9H0W0|Q9NRP1|Q9NRU7	Frame_Shift_Del	DEL	ENST00000549578.1	hg19	CCDS41832.1																																																																																			.	.		0.423	VPS29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404623.1		
ELF1	1997	hgsc.bcm.edu	37	13	41523943	41523943	+	Splice_Site	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr13:41523943delT	ENST00000239882.3	-	5	842	c.528delA	c.(526-528)aaa>aa	p.K176fs	ELF1_ENST00000442101.1_Splice_Site_p.K152fs|ELF1_ENST00000498824.1_5'UTR	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	176					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		CCCACCTACCTTTTTTCCTCT	0.423																																					p.G177fs		Atlas-INDEL	.											.	ELF1	65	.	0			c.529delG						.						197.0	194.0	195.0					13																	41523943		2203	4300	6503	SO:0001630	splice_region_variant	1997	exon5			.	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.529+1A>-	chr13.hg19:g.41523943delT		245.0	0.0		169.0	13.0	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Frame_Shift_Del	DEL	ENST00000239882.3	hg19	CCDS9374.1																																																																																			.	.		0.423	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	Frame_Shift_Del
ADAM9	8754	hgsc.bcm.edu	37	8	38880753	38880753	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:38880753delG	ENST00000487273.2	+	9	901	c.823delG	c.(823-825)gggfs	p.G276fs		NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	276	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			CAACATAGTTGGGGGTGCTGG	0.423																																					p.V274fs		Atlas-INDEL	.											.	ADAM9	66	.	0			c.822delT						.						153.0	139.0	144.0					8																	38880753		2203	4300	6503	SO:0001589	frameshift_variant	8754	exon9			.	U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"""ADAM metallopeptidase domain containing"""	216	protein-coding gene	gene with protein product	"""meltrin gamma"""	602713	"""a disintegrin and metalloproteinase domain 9 (meltrin gamma)"", ""cone rod dystrophy 9"""	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.823delG	chr8.hg19:g.38880753delG	ENSP00000419446:p.Gly276fs	196.0	0.0		157.0	10.0	NM_003816	B7ZLN7|Q10718|Q8NFM6	Frame_Shift_Del	DEL	ENST00000487273.2	hg19	CCDS6112.1																																																																																			.	.		0.423	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2		
TBX10	347853	hgsc.bcm.edu	37	11	67402373	67402373	+	Frame_Shift_Del	DEL	G	G	-	rs144542807		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:67402373delG	ENST00000335385.3	-	3	378	c.291delC	c.(289-291)cccfs	p.P97fs		NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	97					anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|lung(4)|ovary(1)	7						TCACCTGGAAGGGGGGGAACA	0.677																																					p.F98fs		Atlas-INDEL	.											.	TBX10	25	.	0			c.292delT						.						50.0	49.0	49.0					11																	67402373		2200	4294	6494	SO:0001589	frameshift_variant	347853	exon3			.	AH006177	CCDS31621.1	11q13.2	2005-10-11	2004-10-05		ENSG00000167800	ENSG00000167800		"""T-boxes"""	11593	protein-coding gene	gene with protein product		604648	"""T-box 7"""	TBX7		9545502	Standard	NM_005995		Approved	TBX13	uc001omp.3	O75333	OTTHUMG00000167291	ENST00000335385.3:c.291delC	chr11.hg19:g.67402373delG	ENSP00000335191:p.Pro97fs	109.0	0.0		188.0	16.0	NM_005995	Q14D64|Q86XS3	Frame_Shift_Del	DEL	ENST00000335385.3	hg19	CCDS31621.1																																																																																			.	.		0.677	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394034.1	NM_005995	
TSKU	25987	hgsc.bcm.edu	37	11	76507185	76507185	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76507185delC	ENST00000527881.1	+	2	1551	c.525delC	c.(523-525)cacfs	p.H175fs	TSKU_ENST00000333090.4_Frame_Shift_Del_p.H175fs			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	175					anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)				NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					TCGTGCCCCACCCCACGAGGG	0.672																																					p.H175fs		Atlas-INDEL	.											.	TSKU	26	.	0			c.524delA						.						63.0	72.0	69.0					11																	76507185		2200	4292	6492	SO:0001589	frameshift_variant	25987	exon2			.	AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"""leucine rich repeat containing 54"", ""tsukushin"", ""tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"""	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.525delC	chr11.hg19:g.76507185delC	ENSP00000434847:p.His175fs	102.0	0.0		159.0	10.0	NM_015516	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	Frame_Shift_Del	DEL	ENST00000527881.1	hg19	CCDS8246.1																																																																																			.	.		0.672	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516	
ASPM	259266	hgsc.bcm.edu	37	1	197102505	197102505	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:197102505delT	ENST00000367409.4	-	6	2650	c.2394delA	c.(2392-2394)aaafs	p.K798fs	ASPM_ENST00000367408.1_Frame_Shift_Del_p.K48fs|ASPM_ENST00000294732.7_Frame_Shift_Del_p.K798fs	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	798					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						GGTGTCTATCTTTTCGAACAA	0.353																																					p.D799fs		Atlas-INDEL	.											.	ASPM	444	.	0			c.2395delG						.						66.0	66.0	66.0					1																	197102505		2203	4300	6503	SO:0001589	frameshift_variant	259266	exon6			.	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.2394delA	chr1.hg19:g.197102505delT	ENSP00000356379:p.Lys798fs	100.0	0.0		179.0	11.0	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Frame_Shift_Del	DEL	ENST00000367409.4	hg19	CCDS1389.1																																																																																			.	.		0.353	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
GALNT16	57452	hgsc.bcm.edu	37	14	69795179	69795179	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:69795179delC	ENST00000337827.4	+	6	908	c.581delC	c.(580-582)tccfs	p.S194fs	GALNT16_ENST00000448469.3_Frame_Shift_Del_p.S194fs|GALNT16_ENST00000553669.1_Frame_Shift_Del_p.S194fs	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	Q8N428	GLT16_HUMAN	polypeptide N-acetylgalactosaminyltransferase 16	194	Catalytic subdomain A.				protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										CTGATCCGGTCCCGAGTGCGT	0.632																																					p.S194fs		Atlas-INDEL	.											.	GALNT16	8	.	0			c.580delT						.						97.0	88.0	91.0					14																	69795179		2203	4300	6503	SO:0001589	frameshift_variant	57452	exon6			.	AB032956	CCDS32107.1	14q24.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000100626	ENSG00000100626	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	23233	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 16"""	615132	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16"""	GALNTL1		10574461, 22186971	Standard	NM_020692		Approved	KIAA1130, GalNAc-T16	uc010aqu.2	Q8N428	OTTHUMG00000171231	ENST00000337827.4:c.581delC	chr14.hg19:g.69795179delC	ENSP00000336729:p.Ser194fs	76.0	0.0		103.0	10.0	NM_001168368	Q4KMG3|Q58A55|Q9ULT9	Frame_Shift_Del	DEL	ENST00000337827.4	hg19	CCDS32107.1																																																																																			.	.		0.632	GALNT16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412434.1	NM_001168368	
SF3B1	23451	hgsc.bcm.edu	37	2	198285793	198285793	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:198285793delG	ENST00000335508.6	-	3	351	c.260delC	c.(259-261)cctfs	p.P87fs	SF3B1_ENST00000487698.1_Frame_Shift_Del_p.P87fs|SF3B1_ENST00000409915.4_Frame_Shift_Del_p.P87fs|SF3B1_ENST00000414963.2_Frame_Shift_Del_p.P87fs	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	87					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CAATGCCACAGGGGCATGATA	0.388			Mis		myelodysplastic syndrome																																p.P87fs		Atlas-INDEL	.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	.	SF3B1	1038	.	0			c.261delT						.						157.0	162.0	160.0					2																	198285793		2203	4300	6503	SO:0001589	frameshift_variant	23451	exon3			.	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.260delC	chr2.hg19:g.198285793delG	ENSP00000335321:p.Pro87fs	151.0	0.0		153.0	10.0	NM_001005526	E9PCH3	Frame_Shift_Del	DEL	ENST00000335508.6	hg19	CCDS33356.1																																																																																			.	.		0.388	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
DUSP12	11266	hgsc.bcm.edu	37	1	161726728	161726728	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:161726728delA	ENST00000367943.4	+	6	1046	c.1014delA	c.(1012-1014)ggafs	p.G338fs		NM_007240.1	NP_009171.1	Q9UNI6	DUS12_HUMAN	dual specificity phosphatase 12	338					cellular protein modification process (GO:0006464)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of glucokinase activity (GO:0033133)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|lung(1)	5	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			CACAAACAGGAAAAATATGAA	0.358																																					p.G338fs		Atlas-INDEL	.											.	DUSP12	20	.	0			c.1013delG						.						49.0	49.0	49.0					1																	161726728		2203	4300	6503	SO:0001589	frameshift_variant	11266	exon6			.	AF119226	CCDS1234.1	1q21-q22	2011-06-09			ENSG00000081721	ENSG00000081721		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	3067	protein-coding gene	gene with protein product	"""serine/threonine specific protein phosphatase"", ""YVH1 protein-tyrosine phosphatase (S. cerevisiae) ortholog"""	604835				10446167	Standard	XM_005244862		Approved	YVH1, DUSP1	uc001gbo.3	Q9UNI6	OTTHUMG00000034540	ENST00000367943.4:c.1014delA	chr1.hg19:g.161726728delA	ENSP00000356920:p.Gly338fs	76.0	0.0		140.0	10.0	NM_007240	Q5VXA8	Frame_Shift_Del	DEL	ENST00000367943.4	hg19	CCDS1234.1																																																																																			.	.		0.358	DUSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083588.1	NM_007240	
RBPMS2	348093	hgsc.bcm.edu	37	15	65040685	65040685	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:65040685delG	ENST00000300069.4	-	6	767	c.500delC	c.(499-501)ccafs	p.P167fs	RBPMS2_ENST00000560606.1_Frame_Shift_Del_p.P56fs	NM_194272.1	NP_919248.1	Q6ZRY4	RBPS2_HUMAN	RNA binding protein with multiple splicing 2	167							nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)			breast(1)|large_intestine(3)|lung(3)|prostate(1)	8						GGAGATGGCTGGGGTCAGCTC	0.617																																					p.P167fs		Atlas-INDEL	.											.	RBPMS2	14	.	0			c.501delA						.						83.0	72.0	76.0					15																	65040685		2202	4299	6501	SO:0001589	frameshift_variant	348093	exon6			.	AY369207	CCDS32271.1	15q22.31	2014-05-15			ENSG00000166831	ENSG00000166831		"""RNA binding motif (RRM) containing"""	19098	protein-coding gene	gene with protein product							Standard	NM_194272		Approved		uc002anq.3	Q6ZRY4	OTTHUMG00000172423	ENST00000300069.4:c.500delC	chr15.hg19:g.65040685delG	ENSP00000300069:p.Pro167fs	124.0	0.0		149.0	10.0	NM_194272	A2RRG0	Frame_Shift_Del	DEL	ENST00000300069.4	hg19	CCDS32271.1																																																																																			.	.		0.617	RBPMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418466.1		
WIBG	84305	hgsc.bcm.edu	37	12	56296053	56296053	+	Frame_Shift_Del	DEL	G	G	-	rs201814214		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56296053delG	ENST00000408946.2	-	3	369	c.218delC	c.(217-219)ccafs	p.P73fs	WIBG_ENST00000557259.1_3'UTR|WIBG_ENST00000302533.6_5'UTR|WIBG_ENST00000398213.4_Frame_Shift_Del_p.P72fs|WIBG_ENST00000547925.1_3'UTR	NM_032345.2	NP_115721.1	Q9BRP8	WIBG_HUMAN	within bgcn homolog (Drosophila)	73					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|exon-exon junction complex (GO:0035145)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						AGGCCTGGATGGGGTGACAGG	0.522																																					p.P73fs		Atlas-INDEL	.											.	WIBG	11	.	0			c.219delA						.						60.0	57.0	58.0					12																	56296053		1905	4131	6036	SO:0001589	frameshift_variant	84305	exon3			.	BC014976	CCDS41795.1, CCDS44916.1	12q13.2	2008-02-05				ENSG00000170473			30258	protein-coding gene	gene with protein product						12438415, 12483225	Standard	NM_032345		Approved	PYM	uc001sif.1	Q9BRP8	OTTHUMG00000170220	ENST00000408946.2:c.218delC	chr12.hg19:g.56296053delG	ENSP00000386156:p.Pro73fs	100.0	0.0		139.0	11.0	NM_032345	B6ZDM5|Q8IXJ8|Q8N8E7	Frame_Shift_Del	DEL	ENST00000408946.2	hg19	CCDS41795.1																																																																																			.	.		0.522	WIBG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408079.1	NM_032345	
DUT	1854	hgsc.bcm.edu	37	15	48634251	48634251	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:48634251delT	ENST00000331200.3	+	7	828	c.735delT	c.(733-735)ggtfs	p.G245fs	DUT_ENST00000455976.2_Frame_Shift_Del_p.G157fs|DUT_ENST00000559540.1_3'UTR|DUT_ENST00000559416.1_Frame_Shift_Del_p.G160fs|DUT_ENST00000558813.1_Frame_Shift_Del_p.G134fs	NM_001025248.1|NM_001025249.1	NP_001020419.1|NP_001020420.1	P33316	DUT_HUMAN	deoxyuridine triphosphatase	245					DNA replication (GO:0006260)|dUMP biosynthetic process (GO:0006226)|dUTP catabolic process (GO:0046081)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotrimerization (GO:0070207)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of protein heterodimerization activity (GO:0043497)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dUTP diphosphatase activity (GO:0004170)|poly(A) RNA binding (GO:0044822)|pyrimidine deoxyribonucleotide binding (GO:0032556)|receptor inhibitor activity (GO:0030547)			kidney(2)	2		all_lung(180;0.00265)		all cancers(107;2.66e-09)|GBM - Glioblastoma multiforme(94;6.76e-07)		GTTCAGGAGGTTTTGGTTCCA	0.358								Modulation of nucleotide pools																													p.G245fs		Atlas-INDEL	.											.	DUT	9	.	0			c.734delG						.						77.0	82.0	80.0					15																	48634251		2198	4297	6495	SO:0001589	frameshift_variant	1854	exon7			.	M89913	CCDS32231.1, CCDS45255.1, CCDS45256.1	15q21.1	2010-06-24	2007-12-17		ENSG00000128951	ENSG00000128951	3.6.1.23		3078	protein-coding gene	gene with protein product		601266	"""dUTP pyrophosphatase"""			1325640, 9070952	Standard	XM_005254211		Approved	dUTPase	uc001zws.3	P33316		ENST00000331200.3:c.735delT	chr15.hg19:g.48634251delT	ENSP00000370376:p.Gly245fs	165.0	0.0		198.0	12.0	NM_001025248	A8K650|B4DPR5|O14785|Q16708|Q16860|Q6FHN1|Q6NSA3|Q96Q81	Frame_Shift_Del	DEL	ENST00000331200.3	hg19	CCDS32231.1																																																																																			.	.		0.358	DUT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000417142.2		
ARHGAP20	57569	hgsc.bcm.edu	37	11	110454273	110454273	+	Splice_Site	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:110454273delT	ENST00000260283.4	-	14	1888	c.1604delA	c.(1603-1605)aag>ag	p.K535fs	ARHGAP20_ENST00000357139.3_Splice_Site_p.K509fs|ARHGAP20_ENST00000529591.1_Splice_Site_p.K78fs|ARHGAP20_ENST00000533353.1_Splice_Site_p.K509fs|ARHGAP20_ENST00000527598.1_Splice_Site_p.K499fs|ARHGAP20_ENST00000528829.1_Splice_Site_p.K499fs|ARHGAP20_ENST00000524756.1_Splice_Site_p.K512fs	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	535	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)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		CTTCATTACCTTTTTTGTAAA	0.368																																					p.K535fs		Atlas-INDEL	.											.	ARHGAP20	150	.	0			c.1605delG						.						80.0	76.0	77.0					11																	110454273		2201	4298	6499	SO:0001630	splice_region_variant	57569	exon14			.	AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"""Rho GTPase activating proteins"""	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.1605+1A>-	chr11.hg19:g.110454273delT		90.0	0.0		141.0	10.0	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Frame_Shift_Del	DEL	ENST00000260283.4	hg19	CCDS31673.1																																																																																			.	.		0.368	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809	Frame_Shift_Del
OR2T11	127077	hgsc.bcm.edu	37	1	248790265	248790265	+	Frame_Shift_Del	DEL	G	G	-	rs537122223		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:248790265delG	ENST00000330803.2	-	1	226	c.165delC	c.(163-165)cccfs	p.P55fs		NM_001001964.1	NP_001001964.1	Q8NH01	O2T11_HUMAN	olfactory receptor, family 2, subfamily T, member 11 (gene/pseudogene)	55						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(5)|lung(20)|skin(2)	28	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)			GAAAGTACATGGGGGTGTGGA	0.468																																					p.M56fs		Atlas-INDEL	.											.,1	OR2T11	64	.	0			c.166delA						.						65.0	72.0	70.0					1																	248790265		2052	4235	6287	SO:0001589	frameshift_variant	127077	exon1			.	BK004476	CCDS31122.1	1q44	2013-10-10	2013-10-10		ENSG00000183130	ENSG00000183130		"""GPCR / Class A : Olfactory receptors"""	19574	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 11"""				Standard	NM_001001964		Approved	OR2T11Q	uc001ier.1	Q8NH01	OTTHUMG00000040384	ENST00000330803.2:c.165delC	chr1.hg19:g.248790265delG	ENSP00000328934:p.Pro55fs	102.0	0.0		196.0	12.0	NM_001001964	Q6IEY6	Frame_Shift_Del	DEL	ENST00000330803.2	hg19	CCDS31122.1																																																																																			.	.		0.468	OR2T11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097134.1	NM_001001964	
AHDC1	27245	hgsc.bcm.edu	37	1	27875231	27875231	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:27875231delA	ENST00000247087.5	-	5	3992	c.3396delT	c.(3394-3396)tttfs	p.F1132fs	AHDC1_ENST00000374011.2_Frame_Shift_Del_p.F1132fs			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1132							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		CGTGGCAGTCAAAACTGGGAT	0.587																																					p.D1133fs		Atlas-INDEL	.											.	AHDC1	98	.	0			c.3397delG						.						81.0	80.0	80.0					1																	27875231		2203	4299	6502	SO:0001589	frameshift_variant	27245	exon6			.	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.3396delT	chr1.hg19:g.27875231delA	ENSP00000247087:p.Phe1132fs	88.0	0.0		154.0	10.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Frame_Shift_Del	DEL	ENST00000247087.5	hg19	CCDS30652.1																																																																																			.	.		0.587	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3		
LRRC8B	23507	hgsc.bcm.edu	37	1	90049043	90049043	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:90049043delT	ENST00000330947.2	+	5	1194	c.834delT	c.(832-834)tatfs	p.Y278fs	RP5-1007M22.2_ENST00000443562.1_RNA|LRRC8B_ENST00000358200.4_Frame_Shift_Del_p.Y278fs|LRRC8B_ENST00000439853.1_Frame_Shift_Del_p.Y278fs	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	278					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	26		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		ATGTTCCATATTTTTTAACCC	0.373																																					p.Y278fs		Atlas-INDEL	.											.	LRRC8B	49	.	0			c.833delA						.						121.0	118.0	119.0					1																	90049043		2203	4300	6503	SO:0001589	frameshift_variant	23507	exon5			.	AF385436	CCDS724.1	1p22.2	2008-02-05			ENSG00000197147	ENSG00000197147			30692	protein-coding gene	gene with protein product	"""T cell activation leucine repeat rich protein"""	612888				9039502	Standard	NM_015350		Approved	TA-LRRP, KIAA0231	uc001dni.3	Q6P9F7	OTTHUMG00000010129	ENST00000330947.2:c.834delT	chr1.hg19:g.90049043delT	ENSP00000332674:p.Tyr278fs	113.0	0.0		178.0	11.0	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Frame_Shift_Del	DEL	ENST00000330947.2	hg19	CCDS724.1																																																																																			.	.		0.373	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33881513	33881513	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:33881513delA	ENST00000504830.1	-	2	535	c.200delT	c.(199-201)ttgfs	p.L67fs	ADAMTS12_ENST00000352040.3_Frame_Shift_Del_p.L67fs|ADAMTS12_ENST00000515401.1_Frame_Shift_Del_p.L67fs	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	67					cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						GCCATATGACAAAAAATGCCC	0.483										HNSCC(64;0.19)																											p.L67fs		Atlas-INDEL	.											.,2	ADAMTS12	464	.	0			c.201delG						.						124.0	126.0	125.0					5																	33881513		2203	4300	6503	SO:0001589	frameshift_variant	81792	exon2			.	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.200delT	chr5.hg19:g.33881513delA	ENSP00000422554:p.Leu67fs	122.0	0.0		143.0	10.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Frame_Shift_Del	DEL	ENST00000504830.1	hg19	CCDS34140.1																																																																																			.	.		0.483	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
PNPT1	87178	hgsc.bcm.edu	37	2	55907883	55907883	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:55907883delG	ENST00000447944.2	-	7	615	c.529delC	c.(529-531)ctcfs	p.L177fs		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	177					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)			GATAATGAGAGGGCTACGGAA	0.284																																					p.L177fs		Atlas-INDEL	.											.	PNPT1	68	.	0			c.530delT						.						48.0	53.0	51.0					2																	55907883		2202	4300	6502	SO:0001589	frameshift_variant	87178	exon7			.	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.529delC	chr2.hg19:g.55907883delG	ENSP00000400646:p.Leu177fs	139.0	0.0		180.0	11.0	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	
CACNA1E	777	hgsc.bcm.edu	37	1	181701779	181701779	+	Frame_Shift_Del	DEL	G	G	-	rs556292815	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:181701779delG	ENST00000367573.2	+	20	2557	c.2557delG	c.(2557-2559)gggfs	p.G854fs	CACNA1E_ENST00000360108.3_Frame_Shift_Del_p.G835fs|CACNA1E_ENST00000367567.4_Frame_Shift_Del_p.G461fs|CACNA1E_ENST00000358338.5_Frame_Shift_Del_p.G786fs|CACNA1E_ENST00000367570.1_Frame_Shift_Del_p.G854fs|CACNA1E_ENST00000526775.1_Frame_Shift_Del_p.G835fs|CACNA1E_ENST00000357570.5_Frame_Shift_Del_p.G805fs	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	854					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CATCAGCCGTGGGGGGTCCCT	0.682																																					p.R852fs		Atlas-INDEL	.											.	CACNA1E	778	.	0			c.2556delT						.						11.0	14.0	13.0					1																	181701779		1882	4083	5965	SO:0001589	frameshift_variant	777	exon20			.	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.2557delG	chr1.hg19:g.181701779delG	ENSP00000356545:p.Gly854fs	153.0	0.0		249.0	15.0	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Frame_Shift_Del	DEL	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.		0.682	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
TIGD6	81789	hgsc.bcm.edu	37	5	149375707	149375707	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:149375707delT	ENST00000296736.3	-	2	979	c.205delA	c.(205-207)aggfs	p.R69fs	TIGD6_ENST00000515406.2_Frame_Shift_Del_p.R69fs	NM_030953.3	NP_112215.1	Q17RP2	TIGD6_HUMAN	tigger transposable element derived 6	69	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.					nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|stomach(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CTCCTCATCCTTTTCCGCTGG	0.433																																					p.R69fs		Atlas-INDEL	.											.	TIGD6	29	.	0			c.206delG						.						111.0	112.0	112.0					5																	149375707		2203	4300	6503	SO:0001589	frameshift_variant	81789	exon2			.	AK056604	CCDS4301.1	5q33.1	2008-02-05			ENSG00000164296	ENSG00000164296			18332	protein-coding gene	gene with protein product						11230166	Standard	NM_030953		Approved	DKFZp761E2110	uc003lrj.3	Q17RP2	OTTHUMG00000130045	ENST00000296736.3:c.205delA	chr5.hg19:g.149375707delT	ENSP00000296736:p.Arg69fs	63.0	0.0		143.0	13.0	NM_001243253	B3KTZ8|Q96MQ4|Q9H0X7	Frame_Shift_Del	DEL	ENST00000296736.3	hg19	CCDS4301.1																																																																																			.	.		0.433	TIGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252324.1	NM_030953	
VWC2L	402117	hgsc.bcm.edu	37	2	215279116	215279116	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:215279116delT	ENST00000312504.5	+	2	1001	c.199delT	c.(199-201)tttfs	p.F68fs	AC107218.3_ENST00000437883.1_RNA|VWC2L_ENST00000427124.1_Frame_Shift_Del_p.F68fs|AC107218.3_ENST00000412896.1_RNA	NM_001080500.2	NP_001073969.1	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain containing protein 2-like	68	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)				breast(1)|endometrium(1)|large_intestine(3)|lung(10)|prostate(1)	16						GGGAGAACGATTTTTCCCTGG	0.458																																					p.R66fs		Atlas-INDEL	.											.	VWC2L	40	.	0			c.198delA						.						118.0	124.0	122.0					2																	215279116		1961	4149	6110	SO:0001589	frameshift_variant	402117	exon2			.	AB374231	CCDS46509.1	2q34-q35	2011-01-25	2011-01-25		ENSG00000174453	ENSG00000174453			37203	protein-coding gene	gene with protein product			"""von Willebrand factor C domain-containing protein 2-like"""				Standard	NM_001080500		Approved		uc002vet.2	B2RUY7	OTTHUMG00000154811	ENST00000312504.5:c.199delT	chr2.hg19:g.215279116delT	ENSP00000308976:p.Phe68fs	121.0	0.0		115.0	10.0	NM_001080500	A6NC69|B2RUW7|B7X8X1	Frame_Shift_Del	DEL	ENST00000312504.5	hg19	CCDS46509.1																																																																																			.	.		0.458	VWC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337175.1	NM_001080500	
TAX1BP1	8887	hgsc.bcm.edu	37	7	27827096	27827096	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:27827096delA	ENST00000396319.2	+	8	1000	c.912delA	c.(910-912)ttafs	p.L304fs	TAX1BP1_ENST00000265393.6_Frame_Shift_Del_p.L304fs|TAX1BP1_ENST00000543117.1_Frame_Shift_Del_p.L304fs|TAX1BP1_ENST00000433216.2_Frame_Shift_Del_p.L147fs|TAX1BP1_ENST00000409980.1_Frame_Shift_Del_p.L304fs	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	304					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			TCCAGACTTTAAAAAATTTAG	0.343																																					p.L304X		Atlas-INDEL	.											.	TAX1BP1	71	.	0			c.911delT						.						72.0	77.0	75.0					7																	27827096		2203	4300	6503	SO:0001589	frameshift_variant	8887	exon8			.	U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.912delA	chr7.hg19:g.27827096delA	ENSP00000379612:p.Leu304fs	116.0	0.0		171.0	14.0	NM_001206901	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Frame_Shift_Del	DEL	ENST00000396319.2	hg19	CCDS5415.1																																																																																			.	.		0.343	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024	
AGO4	192670	hgsc.bcm.edu	37	1	36306817	36306817	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:36306817delC	ENST00000373210.3	+	14	2021	c.1776delC	c.(1774-1776)cacfs	p.H592fs		NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	592	Piwi. {ECO:0000255|HAMAP-Rule:MF_03033}.				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)|mRNA catabolic process (GO:0006402)|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)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)										ATGTCACACACCCCCCAGCAG	0.557																																					p.H592fs		Atlas-INDEL	.											.	.	.	.	0			c.1775delA						.						47.0	45.0	46.0					1																	36306817		2203	4300	6503	SO:0001589	frameshift_variant	192670	exon14			.	AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"""Argonaute/PIWI family"""	18424	protein-coding gene	gene with protein product	"""argonaute 4"""	607356	"""eukaryotic translation initiation factor 2C, 4"""	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.1776delC	chr1.hg19:g.36306817delC	ENSP00000362306:p.His592fs	113.0	0.0		154.0	10.0	NM_017629	A7MD27	Frame_Shift_Del	DEL	ENST00000373210.3	hg19	CCDS397.1																																																																																			.	.		0.557	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629	
ZBTB21	49854	hgsc.bcm.edu	37	21	43414014	43414014	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:43414014delT	ENST00000310826.5	-	3	374	c.191delA	c.(190-192)aatfs	p.N64fs	ZBTB21_ENST00000398505.3_Frame_Shift_Del_p.N64fs|ZBTB21_ENST00000398511.3_Frame_Shift_Del_p.N64fs|ZBTB21_ENST00000465968.1_Intron|ZBTB21_ENST00000398499.1_Frame_Shift_Del_p.N64fs	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	64	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.|Mediates homodimerization.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										TTGTGACTCATTTTCCTTATT	0.383																																					p.N64fs		Atlas-INDEL	.											.	.	.	.	0			c.192delT						.						72.0	67.0	69.0					21																	43414014		2203	4300	6503	SO:0001589	frameshift_variant	49854	exon3			.	AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13083	protein-coding gene	gene with protein product			"""zinc finger protein 295"""	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.191delA	chr21.hg19:g.43414014delT	ENSP00000308759:p.Asn64fs	174.0	0.0		160.0	12.0	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Frame_Shift_Del	DEL	ENST00000310826.5	hg19	CCDS13678.1																																																																																			.	.		0.383	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727	
ATP7A	538	hgsc.bcm.edu	37	X	77245318	77245318	+	Frame_Shift_Del	DEL	A	A	-	rs398123133		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:77245318delA	ENST00000341514.6	+	4	1355	c.1200delA	c.(1198-1200)tcafs	p.S400fs	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Frame_Shift_Del_p.S400fs	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	400	HMA 4. {ECO:0000255|PROSITE- ProRule:PRU00280}.				blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	GTGTCATATCAAAAAAGCCAG	0.423																																					p.S400X		Atlas-INDEL	.											.	ATP7A	248	.	0			c.1199delC						.						140.0	130.0	134.0					X																	77245318		2203	4296	6499	SO:0001589	frameshift_variant	538	exon4			.	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"""ATPases / P-type"""	869	protein-coding gene	gene with protein product	"""copper pump 1"", ""copper-transporting ATPase 1"""	300011	"""Menkes syndrome"""	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.1200delA	chrX.hg19:g.77245318delA	ENSP00000345728:p.Ser400fs	143.0	0.0		186.0	12.0	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Frame_Shift_Del	DEL	ENST00000341514.6	hg19	CCDS35339.1																																																																																			.	.		0.423	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052	
RABL2B	11158	hgsc.bcm.edu	37	22	51207957	51207957	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:51207957delT	ENST00000395598.3	-	7	641	c.430delA	c.(430-432)agcfs	p.S144fs	RABL2B_ENST00000395593.3_Frame_Shift_Del_p.S144fs|RABL2B_ENST00000435118.1_Frame_Shift_Del_p.S144fs|RABL2B_ENST00000395591.1_Frame_Shift_Del_p.S81fs|RABL2B_ENST00000465063.1_5'UTR|RABL2B_ENST00000354869.3_Frame_Shift_Del_p.S145fs|RABL2B_ENST00000395595.3_Frame_Shift_Del_p.S145fs	NM_001003789.1|NM_001130919.1|NM_001130922.1|NM_007081.2	NP_001003789.1|NP_001124391.1|NP_001124394.1|NP_009012.1	Q9UNT1	RBL2B_HUMAN	RAB, member of RAS oncogene family-like 2B	144					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)			lung(1)	1		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.0539)|LUAD - Lung adenocarcinoma(64;0.247)		AAATTGAAGCTTTTTTGGGTC	0.512																																					p.S145fs	GBM(148;358 1894 4987 13698 40400)	Atlas-INDEL	.											.	RABL2B	8	.	0			c.434delG						.						67.0	76.0	73.0					22																	51207957		2203	4297	6500	SO:0001589	frameshift_variant	11158	exon8			.		CCDS14102.1, CCDS33683.1, CCDS46738.1	22q13.33	2014-05-09			ENSG00000079974	ENSG00000079974		"""RAB, member RAS oncogene"""	9800	protein-coding gene	gene with protein product		605413				10444334	Standard	NM_001130919		Approved		uc011asg.1	Q9UNT1	OTTHUMG00000150156	ENST00000395598.3:c.430delA	chr22.hg19:g.51207957delT	ENSP00000378962:p.Ser144fs	388.0	0.0		438.0	28.0	NM_001130920	Q5TZT8|Q96C33	Frame_Shift_Del	DEL	ENST00000395598.3	hg19	CCDS14102.1																																																																																			.	.		0.512	RABL2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316606.1	NM_001003789	
RBMS3	27303	hgsc.bcm.edu	37	3	29628669	29628669	+	Frame_Shift_Del	DEL	A	A	-	rs199714122		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:29628669delA	ENST00000383767.2	+	4	708	c.372delA	c.(370-372)gcafs	p.A124fs	RBMS3_ENST00000452462.1_Frame_Shift_Del_p.A124fs|RBMS3_ENST00000383766.2_Frame_Shift_Del_p.A123fs|RBMS3_ENST00000396583.3_Frame_Shift_Del_p.A124fs|RBMS3_ENST00000273139.9_Frame_Shift_Del_p.A124fs|RBMS3_ENST00000434693.2_Frame_Shift_Del_p.A123fs|RBMS3_ENST00000445033.1_Frame_Shift_Del_p.A124fs|RBMS3_ENST00000456853.1_Frame_Shift_Del_p.A124fs			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	124	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				CTCTCAAGGCAAATGGCGTGC	0.408																																					p.A124fs		Atlas-INDEL	.											.	RBMS3	62	.	0			c.371delC						.						133.0	137.0	135.0					3																	29628669		2203	4300	6503	SO:0001589	frameshift_variant	27303	exon4			.	AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"""RNA binding motif (RRM) containing"""	13427	protein-coding gene	gene with protein product	"""RNA-binding protein"""	605786	"""RNA binding motif, single stranded interacting protein"""			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.372delA	chr3.hg19:g.29628669delA	ENSP00000373277:p.Ala124fs	91.0	0.0		143.0	10.0	NM_001177712	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Frame_Shift_Del	DEL	ENST00000383767.2	hg19	CCDS33724.1																																																																																			.	.		0.408	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792	
PRAME	23532	hgsc.bcm.edu	37	22	22892453	22892453	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:22892453delA	ENST00000398741.1	-	5	954	c.648delT	c.(646-648)tttfs	p.F216fs	PRAME_ENST00000402697.1_Frame_Shift_Del_p.F216fs|PRAME_ENST00000539862.1_Frame_Shift_Del_p.F200fs|PRAME_ENST00000405655.3_Frame_Shift_Del_p.F216fs|PRAME_ENST00000398743.2_Frame_Shift_Del_p.F216fs|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000424204.2_Frame_Shift_Del_p.F200fs|PRAME_ENST00000543184.1_Frame_Shift_Del_p.F216fs	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	216					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		TGGGCATTGCAAAAATCTTCA	0.438																																					p.A217fs	Melanoma(73;1707 1838 15168 27201)	Atlas-INDEL	.											.	PRAME	78	.	0			c.649delG						.						119.0	118.0	119.0					22																	22892453		2203	4300	6503	SO:0001589	frameshift_variant	23532	exon5			.	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"""-"""	9336	protein-coding gene	gene with protein product	"""cancer/testis antigen 130"""	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.648delT	chr22.hg19:g.22892453delA	ENSP00000381726:p.Phe216fs	169.0	0.0		145.0	10.0	NM_206954	B2R6Y7|O43481|Q8IXN8	Frame_Shift_Del	DEL	ENST00000398741.1	hg19	CCDS13801.1																																																																																			.	.		0.438	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953	
OR52E8	390079	hgsc.bcm.edu	37	11	5878820	5878820	+	Frame_Shift_Del	DEL	A	A	-	rs374161114		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:5878820delA	ENST00000537935.1	-	1	144	c.113delT	c.(112-114)ttcfs	p.F39fs	TRIM5_ENST00000380027.1_Intron	NM_001005168.1	NP_001005168.1	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E, member 8	39						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)|large_intestine(3)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATACACAAAGAAAAAAGGGAC	0.468																																					p.F38fs		Atlas-INDEL	.											.	OR52E8	54	.	0			c.114delC						.						110.0	132.0	124.0					11																	5878820		2144	4296	6440	SO:0001589	frameshift_variant	390079	exon1			.	BK004301	CCDS31400.1	11p15.4	2012-08-09	2003-12-15		ENSG00000183269	ENSG00000183269		"""GPCR / Class A : Olfactory receptors"""	15217	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily E, member 8 pseudogene"""				Standard	NM_001005168		Approved		uc010qzr.2	Q6IFG1	OTTHUMG00000168803	ENST00000537935.1:c.113delT	chr11.hg19:g.5878820delA	ENSP00000444054:p.Phe39fs	128.0	0.0		213.0	19.0	NM_001005168	B9EH38	Frame_Shift_Del	DEL	ENST00000537935.1	hg19	CCDS31400.1																																																																																			.	.		0.468	OR52E8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401145.1	NM_001005168	
RAP1GAP	5909	hgsc.bcm.edu	37	1	21936094	21936094	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:21936094delG	ENST00000374765.4	-	15	1245	c.1045delC	c.(1045-1047)ctcfs	p.L349fs	RAP1GAP_ENST00000290101.4_Frame_Shift_Del_p.L413fs|RAP1GAP_ENST00000542643.2_Frame_Shift_Del_p.L349fs|RAP1GAP_ENST00000374761.2_Frame_Shift_Del_p.L380fs|RAP1GAP_ENST00000374763.2_Frame_Shift_Del_p.L349fs	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	349	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		GGGTCCGGGAGGGGGGGTCCA	0.632																																					p.L413fs		Atlas-INDEL	.											.	RAP1GAP	119	.	0			c.1238delT						.						71.0	76.0	74.0					1																	21936094		2203	4300	6503	SO:0001589	frameshift_variant	5909	exon15			.	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"""RAP1, GTPase activating protein 1"""	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.1045delC	chr1.hg19:g.21936094delG	ENSP00000363897:p.Leu349fs	82.0	0.0		162.0	10.0	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Frame_Shift_Del	DEL	ENST00000374765.4	hg19	CCDS218.1																																																																																			.	.		0.632	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885	
MDN1	23195	hgsc.bcm.edu	37	6	90382309	90382309	+	Frame_Shift_Del	DEL	T	T	-	rs201481158		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:90382309delT	ENST00000369393.3	-	81	13702	c.13587delA	c.(13585-13587)aaafs	p.K4529fs	MDN1_ENST00000468568.1_5'Flank|RP1-122O8.7_ENST00000438877.1_RNA|MDN1_ENST00000428876.1_Frame_Shift_Del_p.K4529fs			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4529					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TCTCCTCTGCTTTTTCATTCT	0.393																																					p.A4530fs		Atlas-INDEL	.											.	MDN1	478	.	0			c.13588delG						.						108.0	112.0	110.0					6																	90382309		2203	4300	6503	SO:0001589	frameshift_variant	23195	exon81			.	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.13587delA	chr6.hg19:g.90382309delT	ENSP00000358400:p.Lys4529fs	149.0	0.0		193.0	12.0	NM_014611	O15019|Q5T794	Frame_Shift_Del	DEL	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.393	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
JAG1	182	hgsc.bcm.edu	37	20	10622493	10622493	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:10622493delC	ENST00000254958.5	-	22	3135	c.2620delG	c.(2620-2622)gccfs	p.A874fs	JAG1_ENST00000423891.2_Frame_Shift_Del_p.A715fs	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	874					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						TCCCATTTGGCCCCATCTGGT	0.532									Alagille Syndrome																												p.A874fs		Atlas-INDEL	.											.	JAG1	213	.	0			c.2621delC						.						214.0	186.0	195.0					20																	10622493		2203	4300	6503	SO:0001589	frameshift_variant	182	exon22	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	.	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.2620delG	chr20.hg19:g.10622493delC	ENSP00000254958:p.Ala874fs	187.0	0.0		188.0	13.0	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Frame_Shift_Del	DEL	ENST00000254958.5	hg19	CCDS13112.1																																																																																			.	.		0.532	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
RUFY1	80230	hgsc.bcm.edu	37	5	179023590	179023590	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:179023590delG	ENST00000319449.4	+	13	1551	c.1539delG	c.(1537-1539)cagfs	p.Q513fs	RUFY1_ENST00000393438.2_Frame_Shift_Del_p.Q405fs|RUFY1_ENST00000437570.2_Frame_Shift_Del_p.Q405fs|RUFY1_ENST00000377001.2_3'UTR|RP11-1379J22.2_ENST00000500262.1_RNA	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	513					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGGCGAGGCAGGGGGCTGAGG	0.607										HNSCC(44;0.11)																											p.Q513fs		Atlas-INDEL	.											.	RUFY1	101	.	0			c.1538delA						.						81.0	97.0	92.0					5																	179023590		2182	4267	6449	SO:0001589	frameshift_variant	80230	exon13			.	AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"""Zinc fingers, FYVE domain containing"""	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.1539delG	chr5.hg19:g.179023590delG	ENSP00000325594:p.Gln513fs	101.0	0.0		182.0	11.0	NM_025158	Q59FF3|Q71S93|Q9H6I3	Frame_Shift_Del	DEL	ENST00000319449.4	hg19	CCDS4445.2																																																																																			.	.		0.607	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451	
TREM1	54210	hgsc.bcm.edu	37	6	41250470	41250470	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:41250470delT	ENST00000244709.4	-	2	132	c.69delA	c.(67-69)aaafs	p.K23fs	TREM1_ENST00000591620.1_Frame_Shift_Del_p.K23fs|TREM1_ENST00000589614.1_Frame_Shift_Del_p.K23fs|TREM1_ENST00000334475.6_Frame_Shift_Del_p.K23fs	NM_018643.3	NP_061113.1	Q9NP99	TREM1_HUMAN	triggering receptor expressed on myeloid cells 1	23					blood coagulation (GO:0007596)|chemokine metabolic process (GO:0050755)|cytokine secretion involved in immune response (GO:0002374)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|neutrophil mediated killing of gram-negative bacterium (GO:0070945)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			NS(1)|breast(2)|endometrium(2)|large_intestine(5)|lung(5)|skin(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					CCTCAGTTAATTTAGTTGCAG	0.468																																					p.L24X		Atlas-INDEL	.											.	TREM1	38	.	0			c.70delT						.						93.0	101.0	98.0					6																	41250470		2203	4300	6503	SO:0001589	frameshift_variant	54210	exon2			.	AF196329	CCDS4854.1, CCDS56427.1, CCDS59499.1	6p21.1	2013-01-11			ENSG00000124731	ENSG00000124731		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	17760	protein-coding gene	gene with protein product		605085				11922939, 10799849	Standard	NM_018643		Approved	TREM-1, CD354	uc003oqf.2	Q9NP99	OTTHUMG00000014674	ENST00000244709.4:c.69delA	chr6.hg19:g.41250470delT	ENSP00000244709:p.Lys23fs	136.0	0.0		225.0	14.0	NM_001242590	B4DWG2|K7EJW1|Q53FL8|Q5T2C9|Q86YU1	Frame_Shift_Del	DEL	ENST00000244709.4	hg19	CCDS4854.1																																																																																			.	.		0.468	TREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040505.2	NM_018643	
SLC12A1	6557	hgsc.bcm.edu	37	15	48539132	48539132	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:48539132delC	ENST00000558405.1	+	11	1493	c.1479delC	c.(1477-1479)ggcfs	p.G493fs	SLC12A1_ENST00000396577.3_Frame_Shift_Del_p.G493fs|SLC12A1_ENST00000380993.3_Frame_Shift_Del_p.G493fs			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	493					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)	CAGGGTTCGGCCCCCTCATCA	0.498																																					p.G493fs		Atlas-INDEL	.											.	SLC12A1	243	.	0			c.1478delG						.						281.0	247.0	259.0					15																	48539132		2198	4297	6495	SO:0001589	frameshift_variant	6557	exon12			.		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.1479delC	chr15.hg19:g.48539132delC	ENSP00000453409:p.Gly493fs	100.0	0.0		135.0	10.0	NM_001184832	A8JYA2|E9PDW4	Frame_Shift_Del	DEL	ENST00000558405.1	hg19	CCDS10129.2																																																																																			.	.		0.498	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1		
MOCOS	55034	hgsc.bcm.edu	37	18	33800091	33800091	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:33800091delT	ENST00000261326.5	+	9	1892	c.1871delT	c.(1870-1872)gttfs	p.V624fs		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						CACAATGGTGTTTGCCTGAGT	0.517																																					p.V624fs		Atlas-INDEL	.											.	MOCOS	84	.	0			c.1870delG						.						150.0	131.0	138.0					18																	33800091		2203	4300	6503	SO:0001589	frameshift_variant	55034	exon9			.	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.1871delT	chr18.hg19:g.33800091delT	ENSP00000261326:p.Val624fs	121.0	0.0		135.0	10.0	NM_017947		Frame_Shift_Del	DEL	ENST00000261326.5	hg19	CCDS11919.1																																																																																			.	.		0.517	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1		
ZNF271	10778	hgsc.bcm.edu	37	18	32889977	32889977	+	RNA	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:32889977delG	ENST00000399070.3	+	0	4371					NR_024565.1|NR_024566.1		Q14591	ZN271_HUMAN	zinc finger protein 271						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(9)	12						tgtttggtttggggaaacctc	0.363																																					.		Atlas-INDEL	.											.	ZNF271	16	.	0			.						.																																					10778	.			.	X78930		18q12.2	2013-04-03			ENSG00000257267	ENSG00000257267		"""Zinc fingers, C2H2-type"""	13065	other	unknown		604754				7865130, 11777961	Standard	NR_024565		Approved	HZF7, ZNFEB	uc002kyp.4	Q14591	OTTHUMG00000132563		chr18.hg19:g.32889977delG		106.0	0.0		127.0	10.0	.	B3KN34|Q96T29|Q9BSX2|Q9UN33|Q9Y5B7	RNA	DEL	ENST00000399070.3	hg19																																																																																				.	.		0.363	ZNF271-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255767.2	NR_024565	
NIFK	84365	hgsc.bcm.edu	37	2	122485457	122485457	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:122485457delA	ENST00000285814.4	-	7	797	c.725delT	c.(724-726)ttgfs	p.L242fs	AC018737.1_ENST00000419902.1_RNA	NM_032390.4	NP_115766.3	Q9BYG3	MK67I_HUMAN		242	Interaction with MKI67.				negative regulation of phosphatase activity (GO:0010923)|protein complex assembly (GO:0006461)|rRNA metabolic process (GO:0016072)|rRNA transcription (GO:0009303)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|pancreas(1)|urinary_tract(1)	12						TCGCCTCTCCAAAAATGTTGG	0.338																																					p.L242fs		Atlas-INDEL	.											.	MKI67IP	27	.	0			c.726delG						.						68.0	67.0	67.0					2																	122485457		2203	4300	6503	SO:0001589	frameshift_variant	84365	exon7			.																												ENST00000285814.4:c.725delT	chr2.hg19:g.122485457delA	ENSP00000285814:p.Leu242fs	166.0	0.0		198.0	12.0	NM_032390	A8K788|Q8TB66|Q96ED4	Frame_Shift_Del	DEL	ENST00000285814.4	hg19	CCDS2135.1																																																																																			.	.		0.338	MKI67IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254239.2		
FILIP1	27145	hgsc.bcm.edu	37	6	76124598	76124598	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:76124598delT	ENST00000237172.7	-	2	421	c.91delA	c.(91-93)agtfs	p.S31fs	FILIP1_ENST00000393004.2_Frame_Shift_Del_p.S31fs	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	31										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						TCTGAGAGACTTTTTTCACCA	0.453																																					p.S31fs		Atlas-INDEL	.											.	FILIP1	173	.	0			c.92delG						.						181.0	174.0	177.0					6																	76124598		2203	4300	6503	SO:0001589	frameshift_variant	27145	exon2			.	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.91delA	chr6.hg19:g.76124598delT	ENSP00000237172:p.Ser31fs	133.0	0.0		192.0	13.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Frame_Shift_Del	DEL	ENST00000237172.7	hg19	CCDS4984.1																																																																																			.	.		0.453	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179	
BIRC2	329	hgsc.bcm.edu	37	11	102221110	102221110	+	Frame_Shift_Del	DEL	C	C	-	rs139349997		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:102221110delC	ENST00000227758.2	+	2	1924	c.525delC	c.(523-525)aacfs	p.N175fs	BIRC2_ENST00000530675.1_Frame_Shift_Del_p.N126fs|BIRC2_ENST00000532672.1_Frame_Shift_Del_p.N154fs|BIRC2_ENST00000527910.1_3'UTR	NM_001166.4|NM_001256163.1	NP_001157.1|NP_001243092.1	Q13490	BIRC2_HUMAN	baculoviral IAP repeat containing 2	175					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein K48-linked ubiquitination (GO:1902524)|positive regulation of protein K63-linked ubiquitination (GO:1902523)|positive regulation of protein monoubiquitination (GO:1902527)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle (GO:0051726)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription, DNA-templated (GO:0006355)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)		CGAGGACTAACCCCTACAGTT	0.423																																					p.N175fs		Atlas-INDEL	.											.	BIRC2	51	.	0			c.524delA						.						128.0	125.0	126.0					11																	102221110		2203	4299	6502	SO:0001589	frameshift_variant	329	exon2			.	L49431	CCDS8316.1, CCDS58169.1	11q22	2011-01-25	2011-01-25		ENSG00000110330	ENSG00000110330		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	590	protein-coding gene	gene with protein product	"""NFR2-TRAF signalling complex protein"", ""apoptosis inhibitor 1"""	601712	"""baculoviral IAP repeat-containing 2"""	API1		8552191, 8548810	Standard	NM_001166		Approved	cIAP1, hiap-2, MIHB, RNF48, c-IAP1	uc010ruq.3	Q13490	OTTHUMG00000167325	ENST00000227758.2:c.525delC	chr11.hg19:g.102221110delC	ENSP00000227758:p.Asn175fs	85.0	0.0		133.0	11.0	NM_001256163	B4E026|Q16516|Q4TTG0	Frame_Shift_Del	DEL	ENST00000227758.2	hg19	CCDS8316.1																																																																																			.	.		0.423	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166	
CHRNB4	1143	hgsc.bcm.edu	37	15	78921420	78921420	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:78921420delG	ENST00000261751.3	-	5	1338	c.1227delC	c.(1225-1227)cccfs	p.P409fs	RP11-335K5.2_ENST00000559120.1_RNA|CHRNB4_ENST00000560511.1_5'Flank|CHRNB4_ENST00000412074.2_Intron	NM_000750.3	NP_000741.1	P30926	ACHB4_HUMAN	cholinergic receptor, nicotinic, beta 4 (neuronal)	409					action potential (GO:0001508)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|regulation of neurotransmitter secretion (GO:0046928)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			endometrium(7)|kidney(1)|lung(13)|prostate(1)	22					Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)	AGAAATCCCTGGGGATAGCCA	0.577																																					p.R410fs		Atlas-INDEL	.											.	CHRNB4	59	.	0			c.1228delA						.						52.0	55.0	54.0					15																	78921420		2196	4293	6489	SO:0001589	frameshift_variant	1143	exon5			.	U48861	CCDS10306.1, CCDS58392.1	15q24	2012-02-11	2012-02-07		ENSG00000117971	ENSG00000117971		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1964	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 4 (neuronal)"""	118509	"""cholinergic receptor, nicotinic, beta polypeptide 4"""			2004777	Standard	NM_000750		Approved		uc002bed.1	P30926	OTTHUMG00000143860	ENST00000261751.3:c.1227delC	chr15.hg19:g.78921420delG	ENSP00000261751:p.Pro409fs	130.0	0.0		138.0	10.0	NM_000750	A4FTX5|E9PHE8|Q16607|Q4VBA5|Q8WXC8|Q9BQR4	Frame_Shift_Del	DEL	ENST00000261751.3	hg19	CCDS10306.1																																																																																			.	.		0.577	CHRNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290108.1		
CEP131	22994	hgsc.bcm.edu	37	17	79172711	79172711	+	Frame_Shift_Del	DEL	G	G	-	rs147729628	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:79172711delG	ENST00000269392.4	-	11	1500	c.1253delC	c.(1252-1254)ccafs	p.P418fs	AZI1_ENST00000450824.2_Frame_Shift_Del_p.P418fs|RP11-455O6.2_ENST00000571085.1_RNA|AZI1_ENST00000374782.3_Frame_Shift_Del_p.P418fs|AZI1_ENST00000575907.1_Frame_Shift_Del_p.P418fs|AZI1_ENST00000570482.2_5'Flank	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		418					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)	p.P418L(1)		breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CTGTGGTTCTGGGGATGAGTC	0.617																																					p.P418fs		Atlas-INDEL	.											.	AZI1	145	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.1254delA						.						77.0	57.0	64.0					17																	79172711		2181	4292	6473	SO:0001589	frameshift_variant	22994	exon11			.																												ENST00000269392.4:c.1253delC	chr17.hg19:g.79172711delG	ENSP00000269392:p.Pro418fs	78.0	0.0		130.0	10.0	NM_014984	A6NHI8|B2RN11|Q96F50	Frame_Shift_Del	DEL	ENST00000269392.4	hg19																																																																																				.	.		0.617	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
RORA	6095	hgsc.bcm.edu	37	15	60803793	60803793	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:60803793delT	ENST00000335670.6	-	5	552	c.452delA	c.(451-453)aagfs	p.K151fs	RORA_ENST00000261523.5_Frame_Shift_Del_p.K184fs|RORA_ENST00000309157.4_Frame_Shift_Del_p.K176fs|RP11-219B17.1_ENST00000501579.2_RNA|RORA_ENST00000449337.2_Frame_Shift_Del_p.K96fs|RP11-219B17.1_ENST00000558235.1_RNA|RP11-219B17.1_ENST00000559824.1_RNA|RP11-219B17.1_ENST00000559902.1_RNA|RP11-219B17.1_ENST00000558140.1_RNA|RORA_ENST00000560004.1_5'UTR	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	151	Hinge.				angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|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)|regulation of cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						GTCTCTCTGCTTTTTTGACAT	0.507																																					p.K184fs		Atlas-INDEL	.											.	RORA	114	.	0			c.552delG						.						51.0	47.0	48.0					15																	60803793		2203	4300	6503	SO:0001589	frameshift_variant	6095	exon6			.	U04897	CCDS10177.1, CCDS10178.1, CCDS10179.1, CCDS45271.1	15q21-q22	2013-01-16			ENSG00000069667	ENSG00000069667		"""Nuclear hormone receptors"""	10258	protein-coding gene	gene with protein product		600825				7926749	Standard	NM_134261		Approved	RZRA, ROR1, ROR2, ROR3, NR1F1	uc002agv.3	P35398	OTTHUMG00000132769	ENST00000335670.6:c.452delA	chr15.hg19:g.60803793delT	ENSP00000335087:p.Lys151fs	156.0	0.0		159.0	10.0	NM_134260	P35397|P35399|P45445|Q495X4|Q96H83	Frame_Shift_Del	DEL	ENST00000335670.6	hg19	CCDS10177.1																																																																																			.	.		0.507	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2		
PPIL6	285755	hgsc.bcm.edu	37	6	109757309	109757309	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:109757309delT	ENST00000521072.2	-	2	809	c.229delA	c.(229-231)aggfs	p.R77fs	PPIL6_ENST00000440797.2_Frame_Shift_Del_p.R77fs|PPIL6_ENST00000424445.2_Intron|AL109947.1_ENST00000459391.1_RNA	NM_173672.4	NP_775943.1	Q8IXY8	PPIL6_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 6	77					protein folding (GO:0006457)		peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.00684)|BRCA - Breast invasive adenocarcinoma(108;0.00889)|all cancers(137;0.0106)|OV - Ovarian serous cystadenocarcinoma(136;0.0259)		TCCTTTACCCTTTTTTTCTCC	0.338																																					p.R77fs		Atlas-INDEL	.											.	PPIL6	20	.	0			c.230delG						.						112.0	120.0	117.0					6																	109757309		2203	4300	6503	SO:0001589	frameshift_variant	285755	exon2			.		CCDS5074.1, CCDS47466.1, CCDS47466.2, CCDS69169.1	6q21	2009-11-18			ENSG00000185250	ENSG00000185250			21557	protein-coding gene	gene with protein product	"""radial spoke 12 homolog (Chlamydomonas)"""						Standard	NM_173672		Approved	bA425D10.6, MGC41939, dJ919F19.1, RSPH12	uc010kdp.3	Q8IXY8	OTTHUMG00000036593	ENST00000521072.2:c.229delA	chr6.hg19:g.109757309delT	ENSP00000427929:p.Arg77fs	198.0	0.0		286.0	18.0	NM_001111298	A9NIU0|A9NIU9|E7EX15	Frame_Shift_Del	DEL	ENST00000521072.2	hg19	CCDS5074.1																																																																																			.	.		0.338	PPIL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089003.4		
DCHS1	8642	hgsc.bcm.edu	37	11	6649903	6649903	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:6649903delC	ENST00000299441.3	-	13	5731	c.5320delG	c.(5320-5322)gccfs	p.A1774fs	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1774	Cadherin 17. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGATCAGAGGCCCGAAGCATG	0.572																																					p.A1774fs		Atlas-INDEL	.											.	DCHS1	277	.	0			c.5321delC						.						106.0	97.0	100.0					11																	6649903		2201	4296	6497	SO:0001589	frameshift_variant	8642	exon13			.	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.5320delG	chr11.hg19:g.6649903delC	ENSP00000299441:p.Ala1774fs	107.0	0.0		161.0	10.0	NM_003737	O15098	Frame_Shift_Del	DEL	ENST00000299441.3	hg19	CCDS7771.1																																																																																			.	.		0.572	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
PLXNC1	10154	hgsc.bcm.edu	37	12	94692436	94692436	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:94692436delT	ENST00000258526.4	+	27	4352	c.4103delT	c.(4102-4104)cttfs	p.L1368fs	PLXNC1_ENST00000545312.1_Frame_Shift_Del_p.L107fs|PLXNC1_ENST00000547057.1_Frame_Shift_Del_p.L415fs	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	1368					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						CTTGAAAAACTTTTTAGAAGC	0.348																																					p.L1368fs		Atlas-INDEL	.											.	PLXNC1	135	.	0			c.4102delC						.						74.0	75.0	75.0					12																	94692436		2203	4300	6503	SO:0001589	frameshift_variant	10154	exon27			.	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.4103delT	chr12.hg19:g.94692436delT	ENSP00000258526:p.Leu1368fs	120.0	0.0		165.0	11.0	NM_005761	Q59H25	Frame_Shift_Del	DEL	ENST00000258526.4	hg19	CCDS9049.1																																																																																			.	.		0.348	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
BOD1L1	259282	hgsc.bcm.edu	37	4	13602811	13602811	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:13602811delC	ENST00000040738.5	-	10	5848	c.5713delG	c.(5713-5715)gacfs	p.D1905fs		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1905						nucleus (GO:0005634)	DNA binding (GO:0003677)										ATCTGACTGTCCCCTTCTGCA	0.453																																					p.D1905fs		Atlas-INDEL	.											.	.	.	.	0			c.5714delA						.						132.0	132.0	132.0					4																	13602811		2203	4300	6503	SO:0001589	frameshift_variant	259282	exon10			.	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.5713delG	chr4.hg19:g.13602811delC	ENSP00000040738:p.Asp1905fs	153.0	0.0		149.0	10.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Frame_Shift_Del	DEL	ENST00000040738.5	hg19	CCDS3411.2																																																																																			.	.		0.453	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
SH2D3A	10045	hgsc.bcm.edu	37	19	6755180	6755180	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:6755180delG	ENST00000245908.6	-	5	912	c.643delC	c.(643-645)cggfs	p.R215fs	SH2D3A_ENST00000437152.3_Frame_Shift_Del_p.R93fs|SH2D3A_ENST00000599563.1_5'UTR	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	215					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						GAGGGTGTCCGGGGGGGCTTC	0.657																																					p.R215fs		Atlas-INDEL	.											.	SH2D3A	53	.	0			c.644delG						.						97.0	110.0	106.0					19																	6755180		2203	4300	6503	SO:0001589	frameshift_variant	10045	exon5			.	AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"""SH2 domain containing"""	16885	protein-coding gene	gene with protein product		604721	"""SH2 domain-containing 3A"""			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.643delC	chr19.hg19:g.6755180delG	ENSP00000245908:p.Arg215fs	127.0	0.0		168.0	11.0	NM_005490	A8K9R6|B4DRS7|Q9Y2X4	Frame_Shift_Del	DEL	ENST00000245908.6	hg19	CCDS12173.1																																																																																			.	.		0.657	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490	
N4BP2	55728	hgsc.bcm.edu	37	4	40123872	40123872	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:40123872delC	ENST00000261435.6	+	9	4557	c.4141delC	c.(4141-4143)cccfs	p.P1382fs		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1382					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						ATTGGCATTACCCCCTGAACT	0.413																																					p.L1380fs		Atlas-INDEL	.											.	N4BP2	166	.	0			c.4140delA						.						129.0	138.0	135.0					4																	40123872		2203	4300	6503	SO:0001589	frameshift_variant	55728	exon9			.	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.4141delC	chr4.hg19:g.40123872delC	ENSP00000261435:p.Pro1382fs	197.0	0.0		248.0	16.0	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Frame_Shift_Del	DEL	ENST00000261435.6	hg19	CCDS3457.1																																																																																			.	.		0.413	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
KALRN	8997	hgsc.bcm.edu	37	3	124210240	124210240	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:124210240delC	ENST00000240874.3	+	31	4809	c.4652delC	c.(4651-4653)accfs	p.T1551fs	KALRN_ENST00000360013.3_Frame_Shift_Del_p.T1551fs|KALRN_ENST00000460856.1_Frame_Shift_Del_p.T1542fs	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1551	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						TCTGGGCGCACCCCATCCTCA	0.542																																					p.T1551fs		Atlas-INDEL	.											.	KALRN	556	.	0			c.4651delA						.						84.0	75.0	78.0					3																	124210240		2203	4300	6503	SO:0001589	frameshift_variant	8997	exon31			.	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.4652delC	chr3.hg19:g.124210240delC	ENSP00000240874:p.Thr1551fs	68.0	0.0		151.0	10.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Frame_Shift_Del	DEL	ENST00000240874.3	hg19	CCDS3027.1																																																																																			.	.		0.542	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
TTLL11	158135	hgsc.bcm.edu	37	9	124736391	124736391	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:124736391delC	ENST00000321582.5	-	6	1835	c.1648delG	c.(1648-1650)gtgfs	p.V550fs	TTLL11_ENST00000474723.1_5'UTR	NM_001139442.1	NP_001132914.1	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	0					cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1)	18						TTTTCAAACACCCCTGGAGAA	0.493																																					p.V550fs		Atlas-INDEL	.											.	TTLL11	67	.	0			c.1649delT						.						138.0	123.0	128.0					9																	124736391		692	1591	2283	SO:0001589	frameshift_variant	158135	exon6			.	AF521886	CCDS6834.2, CCDS48012.1	9q34.11	2013-02-14	2005-07-28	2005-07-28	ENSG00000175764	ENSG00000175764		"""Tubulin tyrosine ligase-like family"""	18113	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 20"""	C9orf20		15890843	Standard	NM_001139442		Approved	bA244O19.1	uc011lyl.2	Q8NHH1	OTTHUMG00000020597	ENST00000321582.5:c.1648delG	chr9.hg19:g.124736391delC	ENSP00000321346:p.Val550fs	110.0	0.0		159.0	10.0	NM_001139442		Frame_Shift_Del	DEL	ENST00000321582.5	hg19	CCDS48012.1																																																																																			.	.		0.493	TTLL11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_088486	
STT3B	201595	hgsc.bcm.edu	37	3	31674442	31674442	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:31674442delC	ENST00000295770.2	+	15	2412	c.2203delC	c.(2203-2205)cccfs	p.P736fs		NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	736					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						TTTTCGTACACCCCCAGGTTT	0.363																																					p.T734fs		Atlas-INDEL	.											.	STT3B	52	.	0			c.2202delA						.						126.0	127.0	126.0					3																	31674442		2203	4300	6503	SO:0001589	frameshift_variant	201595	exon15			.	AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"""source of immunodominant MHC associated peptides"", ""dolichyl-diphosphooligosaccharide protein glycotransferase"""	608605	"""STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"""			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.2203delC	chr3.hg19:g.31674442delC	ENSP00000295770:p.Pro736fs	133.0	0.0		174.0	11.0	NM_178862	Q96JZ4|Q96KY7	Frame_Shift_Del	DEL	ENST00000295770.2	hg19	CCDS2650.1																																																																																			.	.		0.363	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862	
CCDC110	256309	hgsc.bcm.edu	37	4	186382237	186382237	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:186382237delT	ENST00000307588.3	-	5	389	c.314delA	c.(313-315)aatfs	p.N105fs	CCDC110_ENST00000507501.1_5'UTR|CCDC110_ENST00000510617.1_Frame_Shift_Del_p.N105fs|CCDC110_ENST00000393540.3_Intron	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	105						nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		AAACACCAGATTTTTTTCTGA	0.318																																					p.N105fs		Atlas-INDEL	.											.	CCDC110	78	.	0			c.315delT						.						141.0	137.0	138.0					4																	186382237		2203	4299	6502	SO:0001589	frameshift_variant	256309	exon5			.	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"""cancer/testis antigen 52"""	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.314delA	chr4.hg19:g.186382237delT	ENSP00000306776:p.Asn105fs	139.0	0.0		154.0	12.0	NM_152775	Q86YI9|Q8N7W0	Frame_Shift_Del	DEL	ENST00000307588.3	hg19	CCDS3843.1																																																																																			.	.		0.318	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775	
OR5M11	219487	hgsc.bcm.edu	37	11	56310222	56310222	+	Frame_Shift_Del	DEL	C	C	-	rs628524	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:56310222delC	ENST00000528616.2	-	1	535	c.512delG	c.(511-513)agtfs	p.S171fs		NM_001005245.1	NP_001005245.1	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M, member 11	171			S -> N (in dbSNP:rs628524). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)	18						GTTGATGACACTGGATCTACA	0.483																																					p.S171fs		Atlas-INDEL	.											.	OR5M11	60	.	0			c.513delT						.						45.0	47.0	47.0					11																	56310222		2092	4229	6321	SO:0001589	frameshift_variant	219487	exon1			.	AP002517	CCDS53629.1	11q11	2012-08-09				ENSG00000255223		"""GPCR / Class A : Olfactory receptors"""	15291	protein-coding gene	gene with protein product							Standard	NM_001005245		Approved	OR11-199	uc010rjl.2	Q96RB7		ENST00000528616.2:c.512delG	chr11.hg19:g.56310222delC	ENSP00000432417:p.Ser171fs	84.0	0.0		130.0	12.0	NM_001005245	B2RNL5|B2RNL7	Frame_Shift_Del	DEL	ENST00000528616.2	hg19	CCDS53629.1																																																																																			.	.		0.483	OR5M11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391608.1	NM_001005245	
C1QTNF3	114899	hgsc.bcm.edu	37	5	34035781	34035781	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:34035781delG	ENST00000231338.7	-	2	254	c.167delC	c.(166-168)cctfs	p.P56fs	RP11-1084J3.4_ENST00000382079.3_Frame_Shift_Del_p.P40fs|C1QTNF3_ENST00000382065.3_Frame_Shift_Del_p.P129fs|C1QTNF3_ENST00000513065.1_5'Flank	NM_030945.3	NP_112207.1	Q9BXJ4	C1QT3_HUMAN	C1q and tumor necrosis factor related protein 3	56	Collagen-like.				cellular triglyceride homeostasis (GO:0035356)|fat cell differentiation (GO:0045444)|negative regulation of gene expression (GO:0010629)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of cytokine secretion (GO:0050715)|protein trimerization (GO:0070206)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|prostate(3)|stomach(1)|urinary_tract(1)	17	all_lung(31;0.0207)					CGGTGGCCCAGGGGGGCCTTG	0.522																																					p.P129fs		Atlas-INDEL	.											.	C1QTNF3	31	.	0			c.387delT						.						42.0	45.0	44.0					5																	34035781		2203	4300	6503	SO:0001589	frameshift_variant	114899	exon2			.	AF329837	CCDS3904.1, CCDS34141.1	5p13	2009-05-20			ENSG00000082196	ENSG00000082196			14326	protein-coding gene	gene with protein product	"""cartonectin"""	612045				18421280	Standard	NM_030945		Approved	CTRP3, Cors, Corcs, 2310005P21Rik, Cors-26	uc003jio.3	Q9BXJ4	OTTHUMG00000090735	ENST00000231338.7:c.167delC	chr5.hg19:g.34035781delG	ENSP00000231338:p.Pro56fs	95.0	0.0		152.0	10.0	NM_181435	Q0VAN4|Q542Y2|Q6MZN1|Q96KY1	Frame_Shift_Del	DEL	ENST00000231338.7	hg19	CCDS3904.1																																																																																			.	.		0.522	C1QTNF3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207469.1	NM_030945	
VPS13D	55187	hgsc.bcm.edu	37	1	12433904	12433904	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:12433904delA	ENST00000358136.3	+	55	11038	c.10908delA	c.(10906-10908)ttafs	p.L3636fs	VPS13D_ENST00000356315.4_Frame_Shift_Del_p.L3611fs|VPS13D_ENST00000496628.1_3'UTR	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)		GAGTCATTTTAAAAAAGAAGG	0.468																																					p.L3636X		Atlas-INDEL	.											.	VPS13D	316	.	0			c.10907delT						.						37.0	38.0	38.0					1																	12433904		2203	4300	6503	SO:0001589	frameshift_variant	55187	exon55			.	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.10908delA	chr1.hg19:g.12433904delA	ENSP00000350854:p.Leu3636fs	191.0	0.0		268.0	17.0	NM_015378		Frame_Shift_Del	DEL	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.		0.468	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
MGAT4C	25834	hgsc.bcm.edu	37	12	86383211	86383211	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:86383211delA	ENST00000604798.1	-	6	1318	c.114delT	c.(112-114)tttfs	p.F38fs	MGAT4C_ENST00000549405.2_Frame_Shift_Del_p.F38fs|MGAT4C_ENST00000332156.1_Frame_Shift_Del_p.F38fs|MGAT4C_ENST00000552435.2_Frame_Shift_Del_p.F38fs|MGAT4C_ENST00000552808.2_Frame_Shift_Del_p.F38fs|MGAT4C_ENST00000548651.1_Frame_Shift_Del_p.F38fs|MGAT4C_ENST00000393205.2_Frame_Shift_Del_p.F67fs			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	38					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						ACAAGTTCATAAAAAGGAGAA	0.323																																					p.M39X		Atlas-INDEL	.											.	MGAT4C	110	.	0			c.115delA						.						86.0	75.0	79.0					12																	86383211		2203	4299	6502	SO:0001589	frameshift_variant	25834	exon5			.		CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	30871	protein-coding gene	gene with protein product		607385	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"""			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.114delT	chr12.hg19:g.86383211delA	ENSP00000474896:p.Phe38fs	205.0	0.0		179.0	11.0	NM_013244	B4DRH2|Q4G199|Q9UIU5	Frame_Shift_Del	DEL	ENST00000604798.1	hg19	CCDS9030.1																																																																																			.	.		0.323	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244	
MATN3	4148	hgsc.bcm.edu	37	2	20202988	20202988	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:20202988delC	ENST00000407540.3	-	3	912	c.850delG	c.(850-852)gaafs	p.E284fs	MATN3_ENST00000421259.2_Intron|AC079145.4_ENST00000416575.1_RNA	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	284	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTTGCCTTCCCCATCACTG	0.537																																					p.E284fs		Atlas-INDEL	.											.	MATN3	28	.	0			c.851delA						.						114.0	107.0	109.0					2																	20202988		2039	4196	6235	SO:0001589	frameshift_variant	4148	exon3			.	AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.850delG	chr2.hg19:g.20202988delC	ENSP00000383894:p.Glu284fs	144.0	0.0		137.0	10.0	NM_002381	B2CPU0|Q4ZG02	Frame_Shift_Del	DEL	ENST00000407540.3	hg19	CCDS46226.1																																																																																			.	.		0.537	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381	
CEP85L	387119	hgsc.bcm.edu	37	6	118803074	118803074	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:118803074delT	ENST00000368491.3	-	8	2234	c.1613delA	c.(1612-1614)aatfs	p.N538fs	CEP85L_ENST00000368488.5_Frame_Shift_Del_p.N541fs	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	538						centrosome (GO:0005813)|cytoplasm (GO:0005737)											TAAATTCTTATTTTTTTCTTC	0.313																																					p.N541fs		Atlas-Indel,Pindel	.											.	CEP85L	26	.	0			c.1623delT						.						69.0	61.0	63.0					6																	118803074		1789	4061	5850	SO:0001589	frameshift_variant	387119	exon9			.	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.1613delA	chr6.hg19:g.118803074delT	ENSP00000357477:p.Asn538fs	75.0	0.0		120.0	12.0	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Frame_Shift_Del	DEL	ENST00000368491.3	hg19	CCDS43498.1																																																																																			.	.		0.313	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475	
ZSCAN25	221785	hgsc.bcm.edu	37	7	99219096	99219096	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:99219096delG	ENST00000394152.2	+	5	815	c.488delG	c.(487-489)tggfs	p.W163fs	ZSCAN25_ENST00000334715.3_Frame_Shift_Del_p.W163fs|ZSCAN25_ENST00000262941.6_Frame_Shift_Del_p.W163fs|ZSCAN25_ENST00000466948.1_Intron	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	163					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)										AAGCCTGAATGGGGGATGCCC	0.622																																					p.W163fs		Atlas-INDEL	.											.	.	.	.	0			c.487delT						.						65.0	61.0	63.0					7																	99219096		2203	4300	6503	SO:0001589	frameshift_variant	221785	exon5			.	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"""-"", ""Zinc fingers, C2H2-type"""	21961	protein-coding gene	gene with protein product			"""zinc finger protein 498"""	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.488delG	chr7.hg19:g.99219096delG	ENSP00000377708:p.Trp163fs	120.0	0.0		159.0	10.0	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Frame_Shift_Del	DEL	ENST00000394152.2	hg19	CCDS5671.2																																																																																			.	.		0.622	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115	
DDX23	9416	hgsc.bcm.edu	37	12	49224336	49224336	+	Frame_Shift_Del	DEL	G	G	-	rs146973565	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:49224336delG	ENST00000308025.3	-	17	2458	c.2379delC	c.(2377-2379)cccfs	p.P793fs		NM_004818.2	NP_004809.2	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	793	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)	p.P793P(1)		NS(1)|cervix(1)|kidney(4)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(3)	36						TGGCTAGTTCGGGGGGACAGG	0.562																																					p.E794fs		Atlas-Indel,Pindel	.											DDX23,NS,carcinoma,0,1	DDX23	82	.	1	Substitution - coding silent(1)	lung(1)	c.2380delG						.						114.0	101.0	105.0					12																	49224336		2203	4300	6503	SO:0001589	frameshift_variant	9416	exon17			.	AF026402	CCDS8770.1	12q13.11	2013-07-16				ENSG00000174243		"""DEAD-boxes"""	17347	protein-coding gene	gene with protein product		612172	"""PRP28 homolog, yeast"""			9409622, 9539711	Standard	NM_004818		Approved	prp28, U5-100K, PRPF28, SNRNP100	uc001rsm.3	Q9BUQ8		ENST00000308025.3:c.2379delC	chr12.hg19:g.49224336delG	ENSP00000310723:p.Pro793fs	203.0	0.0		262.0	18.0	NM_004818	B2R600|B4DH15|O43188	Frame_Shift_Del	DEL	ENST00000308025.3	hg19	CCDS8770.1																																																																																			.	.		0.562	DDX23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408897.2	NM_004818	
C19orf12	83636	hgsc.bcm.edu	37	19	30193879	30193879	+	Frame_Shift_Del	DEL	C	C	-	rs398122409		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:30193879delC	ENST00000392278.2	-	3	325	c.199delG	c.(199-201)gctfs	p.A67fs	C19orf12_ENST00000392275.1_5'UTR|C19orf12_ENST00000392276.1_5'UTR|C19orf12_ENST00000323670.9_Frame_Shift_Del_p.A56fs|C19orf12_ENST00000592153.1_Frame_Shift_Del_p.A56fs	NM_001031726.3	NP_001026896.2	Q9NSK7	CS012_HUMAN	chromosome 19 open reading frame 12	67					cell death (GO:0008219)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)						Ovarian(5;0.000567)|Breast(6;0.0203)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0435)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.183)			CCCCCGACAGCCCCCCCTAGA	0.527																																					p.A67fs		Atlas-INDEL	.											.	C19orf12	16	.	0			c.200delC						.						58.0	66.0	63.0					19																	30193879		2203	4300	6503	SO:0001589	frameshift_variant	83636	exon3			.	AK057185	CCDS12418.2, CCDS42542.1, CCDS59373.1, CCDS74325.1	19q13.11	2013-07-24			ENSG00000131943	ENSG00000131943			25443	protein-coding gene	gene with protein product	"""neurodegeneration with brain iron accumulation 4"""	614297	"""spastic paraplegia 43 (autosomal recessive)"""	SPG43		21981780, 23857908	Standard	NM_031448		Approved	MGC10922, DKFZP762D096, NBIA4	uc002nsj.3	Q9NSK7	OTTHUMG00000149838	ENST00000392278.2:c.199delG	chr19.hg19:g.30193879delC	ENSP00000376103:p.Ala67fs	188.0	0.0		195.0	16.0	NM_001031726	B3KQ16|Q0D2Q0|Q6P4C5|Q9BSL7	Frame_Shift_Del	DEL	ENST00000392278.2	hg19	CCDS42542.1																																																																																			.	.		0.527	C19orf12-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313509.2	NM_031448	
SPATA31A4	642629	hgsc.bcm.edu	37	9	41321778	41321778	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:41321778delA	ENST00000429767.1	-	4	3554	c.3526delT	c.(3526-3528)tcafs	p.S1176fs	SPATA31A4_ENST00000603746.1_5'Flank|RP11-95K23.3_ENST00000440883.1_RNA			Q4VX67	S31A4_HUMAN	SPATA31 subfamily A, member 4	1176					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TTTTTCTTTGAAAAAATCCAC	0.448																																					p.S1190X		Atlas-INDEL	.											.	SPATA31A4	2	.	0			c.3569delC						.						1.0	1.0	1.0					9																	41321778		1	1	2	SO:0001589	frameshift_variant	642629	exon4			.			9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000234214				32004	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A4"""	FAM75A4		20850414	Standard			Approved	OTTHUMG00000066731	uc004abt.4	Q4VX67	OTTHUMG00000066731	ENST00000429767.1:c.3526delT	chr9.hg19:g.41321778delA	ENSP00000411237:p.Ser1176fs	273.0	0.0		227.0	14.0	NM_001242613		Frame_Shift_Del	DEL	ENST00000429767.1	hg19																																																																																				.	.		0.448	SPATA31A4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001242613	
PIN4	5303	hgsc.bcm.edu	37	X	71401650	71401650	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:71401650delA	ENST00000373669.2	+	1	122	c.90delA	c.(88-90)ggafs	p.G30fs	PIN4_ENST00000218432.5_Frame_Shift_Del_p.G30fs|PIN4_ENST00000423432.2_Frame_Shift_Del_p.G30fs	NM_006223.3	NP_006214.2	Q9Y237	PIN4_HUMAN	protein (peptidylprolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)	5	Necessary for association with the pre- rRNP complexes.				protein folding (GO:0006457)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|preribosome (GO:0030684)|spindle (GO:0005819)	bent DNA binding (GO:0003681)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(2)	3	Renal(35;0.156)					CGCCCAAAGGAAAAAGTGGTT	0.557																																					p.G30fs		Atlas-INDEL	.											.	PIN4	8	.	0			c.89delG						.						42.0	35.0	38.0					X																	71401650		2203	4300	6503	SO:0001589	frameshift_variant	5303	exon1			.	AB009690	CCDS14417.1, CCDS55447.1	Xq13.1	2008-02-05	2006-01-12		ENSG00000102309	ENSG00000102309			8992	protein-coding gene	gene with protein product		300252	"""protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)"""			16522211, 17875217	Standard	NM_006223		Approved	PAR14, PAR17, EPVH	uc004eam.3	Q9Y237	OTTHUMG00000021811	ENST00000373669.2:c.90delA	chrX.hg19:g.71401650delA	ENSP00000362773:p.Gly30fs	152.0	0.0		180.0	11.0	NM_001170747	A8E0G6|B3KXM0|F5H1P5|Q0D2H3|Q3MHV0|Q52M21|Q5HYW6|Q6IRW4	Frame_Shift_Del	DEL	ENST00000373669.2	hg19	CCDS14417.1																																																																																			.	.		0.557	PIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057175.2	NM_006223	
ANKRD50	57182	hgsc.bcm.edu	37	4	125591535	125591535	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:125591535delA	ENST00000504087.1	-	4	3934	c.2897delT	c.(2896-2898)ttafs	p.L966fs	ANKRD50_ENST00000515641.1_Frame_Shift_Del_p.L787fs	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	966										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						ACCATTTTCTAAAAAATATTC	0.428																																					p.L966fs		Atlas-INDEL	.											.	ANKRD50	136	.	0			c.2898delA						.						65.0	60.0	62.0					4																	125591535		2203	4300	6503	SO:0001589	frameshift_variant	57182	exon4			.	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.2897delT	chr4.hg19:g.125591535delA	ENSP00000425658:p.Leu966fs	159.0	0.0		178.0	15.0	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Frame_Shift_Del	DEL	ENST00000504087.1	hg19	CCDS34060.1																																																																																			.	.		0.428	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
NCBP1	4686	hgsc.bcm.edu	37	9	100410326	100410326	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:100410326delA	ENST00000375147.3	+	8	974	c.718delA	c.(718-720)aaafs	p.K241fs		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	241					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 cleavage (GO:0006379)|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 mRNA 3'-end processing (GO:0031442)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|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)|mitochondrion (GO:0005739)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA cap binding (GO:0000339)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)	19		Acute lymphoblastic leukemia(62;0.158)				TCAGAAATTGAAAAAGGATCG	0.378																																					p.L239fs	Ovarian(36;879 898 2893 44212 50307)	Atlas-INDEL	.											.	NCBP1	64	.	0			c.717delG						.						63.0	56.0	59.0					9																	100410326		2203	4300	6503	SO:0001589	frameshift_variant	4686	exon8			.	BC001450	CCDS6728.1	9q34.1	2010-01-26	2002-08-29		ENSG00000136937	ENSG00000136937			7658	protein-coding gene	gene with protein product		600469	"""nuclear cap binding protein subunit 1, 80kD"""	NCBP		7937105, 8812508	Standard	NM_002486		Approved	CBP80, Sto1	uc004axq.3	Q09161	OTTHUMG00000020332	ENST00000375147.3:c.718delA	chr9.hg19:g.100410326delA	ENSP00000364289:p.Lys241fs	167.0	0.0		146.0	11.0	NM_002486	B2R718|Q59G76|Q5T1V0|Q5T7X2	Frame_Shift_Del	DEL	ENST00000375147.3	hg19	CCDS6728.1																																																																																			.	.		0.378	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486	
ADD2	119	hgsc.bcm.edu	37	2	70890579	70890579	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:70890579delT	ENST00000264436.4	-	16	2603	c.2159delA	c.(2158-2160)aagfs	p.K721fs	ADD2_ENST00000407644.2_Frame_Shift_Del_p.K721fs	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	721	Interaction with calmodulin. {ECO:0000255}.				actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						TTTCTCCTTCTTTTTGCTCTT	0.547																																					p.K720fs		Atlas-INDEL	.											.	ADD2	261	.	0			c.2160delG						.						157.0	153.0	155.0					2																	70890579		2203	4300	6503	SO:0001589	frameshift_variant	119	exon16			.	X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.2159delA	chr2.hg19:g.70890579delT	ENSP00000264436:p.Lys721fs	107.0	0.0		120.0	11.0	NM_001617	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Frame_Shift_Del	DEL	ENST00000264436.4	hg19	CCDS1906.1																																																																																			.	.		0.547	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617	
TRIM66	9866	hgsc.bcm.edu	37	11	8642705	8642705	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:8642705delG	ENST00000299550.6	-	15	3085	c.2891delC	c.(2890-2892)ccafs	p.P964fs	TRIM66_ENST00000402157.2_Frame_Shift_Del_p.P993fs	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	964						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						TATTGGGGCTGGGGGGCCCTT	0.572																																					p.P964fs		Atlas-INDEL	.											.	TRIM66	45	.	0			c.2892delA						.						48.0	51.0	50.0					11																	8642705		692	1591	2283	SO:0001589	frameshift_variant	9866	exon15			.	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.2891delC	chr11.hg19:g.8642705delG	ENSP00000299550:p.Pro964fs	118.0	0.0		207.0	13.0	NM_014818	Q9BQQ4	Frame_Shift_Del	DEL	ENST00000299550.6	hg19																																																																																				.	.		0.572	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
MYOF	26509	hgsc.bcm.edu	37	10	95157188	95157188	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:95157188delT	ENST00000359263.4	-	14	1246	c.1247delA	c.(1246-1248)aatfs	p.N416fs	MYOF_ENST00000371502.4_Frame_Shift_Del_p.N416fs|MYOF_ENST00000371501.4_Frame_Shift_Del_p.N416fs|MYOF_ENST00000358334.5_Frame_Shift_Del_p.N416fs|MYOF_ENST00000371489.1_Frame_Shift_Del_p.N416fs	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	416	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TGGGTTTGCATTTTTCTCAAT	0.294																																					p.N416fs		Atlas-INDEL	.											.	MYOF	177	.	0			c.1248delT						.						139.0	128.0	132.0					10																	95157188		1812	4076	5888	SO:0001589	frameshift_variant	26509	exon14			.	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"""fer-1-like family member 3"""	604603	"""fer-1 (C.elegans)-like 3 (myoferlin)"", ""fer-1-like 3, myoferlin (C. elegans)"""	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.1247delA	chr10.hg19:g.95157188delT	ENSP00000352208:p.Asn416fs	126.0	0.0		156.0	10.0	NM_133337	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Frame_Shift_Del	DEL	ENST00000359263.4	hg19	CCDS41551.1																																																																																			.	.		0.294	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
SNX2	6643	hgsc.bcm.edu	37	5	122137589	122137589	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:122137589delT	ENST00000379516.2	+	4	524	c.416delT	c.(415-417)attfs	p.I139fs	SNX2_ENST00000510372.1_3'UTR|SNX2_ENST00000514949.1_Frame_Shift_Del_p.I22fs	NM_003100.2	NP_003091.2	O60749	SNX2_HUMAN	sorting nexin 2	139					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)|skin(1)	19		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		AATGGAGACATTTTTGACATA	0.239																																					p.I139fs		Atlas-INDEL	.											.	SNX2	42	.	0			c.415delA						.						72.0	82.0	78.0					5																	122137589		2174	4287	6461	SO:0001589	frameshift_variant	6643	exon4			.	AF043453	CCDS34217.1, CCDS64234.1	5q23.2	2011-05-03			ENSG00000205302	ENSG00000205302		"""Sorting nexins"""	11173	protein-coding gene	gene with protein product		605929				9819414	Standard	NM_003100		Approved		uc003kte.4	O60749	OTTHUMG00000163020	ENST00000379516.2:c.416delT	chr5.hg19:g.122137589delT	ENSP00000368831:p.Ile139fs	154.0	0.0		316.0	19.0	NM_003100	B3KN44|B4DEK4|B7Z408|O43650|P82862|Q53XK8|Q597H6|Q9BTS8	Frame_Shift_Del	DEL	ENST00000379516.2	hg19	CCDS34217.1																																																																																			.	.		0.239	SNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371392.1	NM_003100	
SPRY1	10252	hgsc.bcm.edu	37	4	124323707	124323707	+	3'UTR	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:124323707delT	ENST00000394339.2	+	0	1301				SPRY1_ENST00000339241.1_3'UTR	NM_001258039.1|NM_005841.2	NP_001244968.1|NP_005832.1	O43609	SPY1_HUMAN	sprouty homolog 1, antagonist of FGF signaling (Drosophila)						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						ACCATCATGATTTTTGGAGGT	0.433																																					p.X320C		Atlas-INDEL	.											.	SPRY1	28	.	0			c.960delA						.						64.0	68.0	67.0					4																	124323707		2173	4277	6450	SO:0001624	3_prime_UTR_variant	10252	exon3			.	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.*1T>-	chr4.hg19:g.124323707delT		148.0	0.0		168.0	13.0	NM_001258038	D3DNX6|Q6PNE0	Frame_Shift_Del	DEL	ENST00000394339.2	hg19	CCDS3731.1																																																																																			.	.		0.433	SPRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256711.1		
PLA2R1	22925	hgsc.bcm.edu	37	2	160806244	160806244	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:160806244delA	ENST00000283243.7	-	25	3790	c.3584delT	c.(3583-3585)ttcfs	p.F1195fs	PLA2R1_ENST00000392771.1_Frame_Shift_Del_p.F1195fs	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	1195	C-type lectin 7. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						CCAAAAAGTGAAAGAAGATTT	0.502																																					p.F1195fs		Atlas-INDEL	.											.	PLA2R1	153	.	0			c.3585delC						.						93.0	89.0	90.0					2																	160806244		2203	4300	6503	SO:0001589	frameshift_variant	22925	exon25			.	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"""C-type lectin domain containing"""	9042	protein-coding gene	gene with protein product		604939	"""phospholipase A2 receptor 1, 180kD"""			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.3584delT	chr2.hg19:g.160806244delA	ENSP00000283243:p.Phe1195fs	129.0	0.0		135.0	10.0	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Frame_Shift_Del	DEL	ENST00000283243.7	hg19	CCDS33309.1																																																																																			.	.		0.502	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		
NNT	23530	hgsc.bcm.edu	37	5	43644296	43644296	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:43644296delA	ENST00000264663.5	+	8	1188	c.967delA	c.(967-969)aaafs	p.K324fs	NNT_ENST00000344920.4_Frame_Shift_Del_p.K324fs|NNT_ENST00000512996.2_Frame_Shift_Del_p.K193fs	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	324					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					TTTATTAGGTAAAAAAGCTCC	0.328																																					p.G322fs		Atlas-INDEL	.											.	NNT	92	.	0			c.966delT						.						52.0	58.0	56.0					5																	43644296		2203	4300	6503	SO:0001589	frameshift_variant	23530	exon8			.	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.967delA	chr5.hg19:g.43644296delA	ENSP00000264663:p.Lys324fs	109.0	0.0		178.0	11.0	NM_182977	Q16796|Q2TB60|Q8N3V4	Frame_Shift_Del	DEL	ENST00000264663.5	hg19	CCDS3949.1																																																																																			.	.		0.328	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977	
KMT2E	55904	hgsc.bcm.edu	37	7	104715257	104715257	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:104715257delA	ENST00000311117.3	+	8	1269	c.724delA	c.(724-726)aaafs	p.K243fs	KMT2E_ENST00000476671.1_Frame_Shift_Del_p.K243fs|KMT2E_ENST00000257745.4_Frame_Shift_Del_p.K243fs|KMT2E_ENST00000334914.7_5'UTR|KMT2E_ENST00000334877.4_Frame_Shift_Del_p.K243fs	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	243					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)										TTCAAAATGTAAAAAGGTACG	0.353																																					p.C241X		Atlas-INDEL	.											.	MLL5	173	.	0			c.723delT						.						49.0	50.0	50.0					7																	104715257		2202	4300	6502	SO:0001589	frameshift_variant	55904	exon8			.	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.724delA	chr7.hg19:g.104715257delA	ENSP00000312379:p.Lys243fs	130.0	0.0		167.0	12.0	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																																																																																			.	.		0.353	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1		
ZNF286B	729288	hgsc.bcm.edu	37	17	18566149	18566149	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:18566149delT	ENST00000545289.1	-	5	920	c.670delA	c.(670-672)agcfs	p.S224fs	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	224					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						TGTTTCAAGCTTTTTTCAAGT	0.348																																					p.S224fs		Atlas-INDEL	.											.	ZNF286B	75	.	0			c.671delG						.						8.0	7.0	7.0					17																	18566149		683	1545	2228	SO:0001589	frameshift_variant	729288	exon5			.		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"""Zinc fingers, C2H2-type"""	33241	protein-coding gene	gene with protein product	"""zinc finger protein 590"""		"""zinc finger protein 286-like"", ""zinc finger 286C pseudogene"""	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.670delA	chr17.hg19:g.18566149delT	ENSP00000461413:p.Ser224fs	233.0	0.0		220.0	14.0	NM_001145045		Frame_Shift_Del	DEL	ENST00000545289.1	hg19	CCDS58523.1																																																																																			.	.		0.348	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
ANTXR2	118429	hgsc.bcm.edu	37	4	80957125	80957125	+	Splice_Site	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:80957125delC	ENST00000307333.7	-	8	700		c.e8+1		ANTXR2_ENST00000346652.6_Intron|ANTXR2_ENST00000404191.1_Splice_Site|ANTXR2_ENST00000403729.2_Splice_Site|ANTXR2_ENST00000295465.4_Splice_Site	NM_001145794.1	NP_001139266.1	P58335	ANTR2_HUMAN	anthrax toxin receptor 2						reproductive process (GO:0022414)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	13						TAAACACTTACCCCCCACACA	0.299									Juvenile Hyaline Fibromatosis																												.		Atlas-INDEL	.											.	ANTXR2	97	.	0			c.697+2G>-	GRCh37	CS033827	ANTXR2	S		.						26.0	25.0	26.0					4																	80957125		1784	4032	5816	SO:0001630	splice_region_variant	118429	exon9	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	.	AY040326	CCDS47085.1, CCDS47086.1, CCDS68733.1	4q21.3	2004-01-15			ENSG00000163297	ENSG00000163297			21732	protein-coding gene	gene with protein product	"""capillary morphogenesis protein 2"""	608041				11683410, 12700348	Standard	NM_058172		Approved	CMG2, CMG-2, FLJ31074	uc003hlz.4	P58335	OTTHUMG00000151982	ENST00000307333.7:c.697+1G>-	chr4.hg19:g.80957125delC		159.0	0.0		213.0	13.0	NM_058172	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	Splice_Site	DEL	ENST00000307333.7	hg19	CCDS47086.1																																																																																			.	.		0.299	ANTXR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324663.1	NM_058172	Intron
CCDC170	80129	hgsc.bcm.edu	37	6	151907220	151907220	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:151907220delA	ENST00000239374.7	+	7	1388	c.1289delA	c.(1288-1290)caafs	p.Q430fs	CCDC170_ENST00000367290.5_Frame_Shift_Del_p.Q430fs	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	430																	TTTGAGAAACAAAAAGTAATG	0.408																																					p.Q430fs		Atlas-INDEL	.											.	.	.	.	0			c.1288delC						.						54.0	53.0	53.0					6																	151907220		1863	4113	5976	SO:0001589	frameshift_variant	80129	exon7			.	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1289delA	chr6.hg19:g.151907220delA	ENSP00000239374:p.Gln430fs	73.0	0.0		145.0	12.0	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Frame_Shift_Del	DEL	ENST00000239374.7	hg19	CCDS43515.1																																																																																			.	.		0.408	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059	
DNAJC22	79962	hgsc.bcm.edu	37	12	49743396	49743396	+	Frame_Shift_Del	DEL	G	G	-	rs148896963		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:49743396delG	ENST00000549441.2	+	3	1945	c.741delG	c.(739-741)atgfs	p.M247fs	DNAJC22_ENST00000395069.3_Frame_Shift_Del_p.M247fs			Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	247						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(1)|ovary(1)|pancreas(1)	10						GGCTACTGATGGGGGAGACTG	0.532																																					p.M247fs		Atlas-INDEL	.											.	DNAJC22	29	.	0			c.740delT						.						116.0	120.0	119.0					12																	49743396		2203	4300	6503	SO:0001589	frameshift_variant	79962	exon2			.	AK055747	CCDS8785.1	12q13.12	2011-09-02		2008-07-08	ENSG00000178401	ENSG00000178401		"""Heat shock proteins / DNAJ (HSP40)"""	25802	protein-coding gene	gene with protein product	"""wurst homolog (Drosophila)"""					17558392	Standard	NM_024902		Approved	wus, FLJ13236	uc001rua.3	Q8N4W6		ENST00000549441.2:c.741delG	chr12.hg19:g.49743396delG	ENSP00000446830:p.Met247fs	135.0	0.0		155.0	10.0	NM_024902	B3KP54	Frame_Shift_Del	DEL	ENST00000549441.2	hg19	CCDS8785.1																																																																																			.	.		0.532	DNAJC22-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404302.2	NM_024902	
TPR	7175	hgsc.bcm.edu	37	1	186340145	186340145	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:186340145delT	ENST00000367478.4	-	3	583	c.287delA	c.(286-288)aacfs	p.N96fs	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	96	Necessary for interaction with HSF1.				carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|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)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		AAGTTCTTTGTTTTTCTCAGT	0.328			T	NTRK1	papillary thyroid																																p.N96fs		Atlas-INDEL	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.288delC						.						196.0	178.0	184.0					1																	186340145		1831	4082	5913	SO:0001589	frameshift_variant	7175	exon3			.	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.287delA	chr1.hg19:g.186340145delT	ENSP00000356448:p.Asn96fs	125.0	0.0		174.0	11.0	NM_003292	Q15655|Q5SWY0|Q99968	Frame_Shift_Del	DEL	ENST00000367478.4	hg19	CCDS41446.1																																																																																			.	.		0.328	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
PIEZO1	9780	hgsc.bcm.edu	37	16	88793481	88793481	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:88793481delC	ENST00000301015.9	-	24	3667	c.3421delG	c.(3421-3423)gagfs	p.E1141fs		NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1141					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						GGGTTGGGCTCCCCCCGCAGC	0.697																																					p.E1141fs		Atlas-INDEL	.											.	PIEZO1	79	.	0			c.3422delA						.						24.0	35.0	32.0					16																	88793481		691	1589	2280	SO:0001589	frameshift_variant	9780	exon24			.	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.3421delG	chr16.hg19:g.88793481delC	ENSP00000301015:p.Glu1141fs	136.0	0.0		158.0	10.0	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Frame_Shift_Del	DEL	ENST00000301015.9	hg19	CCDS54058.1																																																																																			.	.		0.697	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
CACNB4	785	hgsc.bcm.edu	37	2	152709963	152709963	+	Splice_Site	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:152709963delG	ENST00000539935.1	-	12	1182	c.1115delC	c.(1114-1116)cca>ca	p.P372fs	CACNB4_ENST00000201943.5_Splice_Site_p.P372fs|CACNB4_ENST00000397327.2_Splice_Site_p.P325fs|CACNB4_ENST00000534999.1_Splice_Site_p.P338fs|CACNB4_ENST00000360283.6_Splice_Site_p.P339fs|CACNB4_ENST00000427385.1_Splice_Site_p.P354fs	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	372					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CATACTTACTGGGGGGCATTG	0.358																																					p.P372fs		Atlas-INDEL	.											CACNB4_ENST00000539935,NS,carcinoma,0,2	CACNB4	108	.	0			c.1116delA						.						74.0	69.0	71.0					2																	152709963		1853	4095	5948	SO:0001630	splice_region_variant	785	exon12			.	AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"""Calcium channel subunits"""	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.1116+1C>-	chr2.hg19:g.152709963delG		89.0	0.0		115.0	10.0	NM_001145798	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Frame_Shift_Del	DEL	ENST00000539935.1	hg19	CCDS46426.1																																																																																			.	.		0.358	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3	Frame_Shift_Del
EYS	346007	hgsc.bcm.edu	37	6	64574091	64574091	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:64574091delG	ENST00000370621.3	-	36	7742	c.7216delC	c.(7216-7218)ctcfs	p.L2406fs	EYS_ENST00000370616.2_Frame_Shift_Del_p.L2406fs|EYS_ENST00000503581.1_Frame_Shift_Del_p.L2406fs			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2406	EGF-like 23. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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						TCAGTGCAGAGGGGTCCAGAC	0.448																																					p.L2406fs		Atlas-INDEL	.											.	EYS	527	.	0			c.7217delT						.						107.0	89.0	94.0					6																	64574091		692	1591	2283	SO:0001589	frameshift_variant	346007	exon36			.		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.7216delC	chr6.hg19:g.64574091delG	ENSP00000359655:p.Leu2406fs	97.0	0.0		184.0	12.0	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																																																																																				.	.		0.448	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
KCNH5	27133	hgsc.bcm.edu	37	14	63174612	63174612	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:63174612delT	ENST00000322893.7	-	11	2849	c.2581delA	c.(2581-2583)acafs	p.T861fs	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	861					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CAAGAATCTGTTTTTCTTAGT	0.478																																					p.T861fs		Atlas-INDEL	.											.	KCNH5	320	.	0			c.2582delC						.						159.0	142.0	148.0					14																	63174612		2203	4300	6503	SO:0001589	frameshift_variant	27133	exon11			.	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2581delA	chr14.hg19:g.63174612delT	ENSP00000321427:p.Thr861fs	193.0	0.0		183.0	14.0	NM_139318	C9JP98	Frame_Shift_Del	DEL	ENST00000322893.7	hg19	CCDS9756.1																																																																																			.	.		0.478	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
BCAR1	9564	hgsc.bcm.edu	37	16	75269533	75269533	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:75269533delC	ENST00000162330.5	-	5	1390	c.1264delG	c.(1264-1266)gcafs	p.A422fs	BCAR1_ENST00000546196.1_Frame_Shift_Del_p.A393fs|BCAR1_ENST00000393422.2_Frame_Shift_Del_p.A440fs|BCAR1_ENST00000542031.2_Frame_Shift_Del_p.A420fs|BCAR1_ENST00000393420.6_Frame_Shift_Del_p.A440fs|BCAR1_ENST00000535626.2_Frame_Shift_Del_p.A274fs|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000420641.3_Frame_Shift_Del_p.A440fs|BCAR1_ENST00000538440.2_Frame_Shift_Del_p.A422fs|BCAR1_ENST00000418647.3_Frame_Shift_Del_p.A468fs	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	422	Ser-rich.				actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		TTGCCCTCTGCCGGGGCTTCA	0.687																																					p.A468fs		Atlas-INDEL	.											.	BCAR1	184	.	0			c.1403delC						.						19.0	25.0	23.0					16																	75269533		2197	4298	6495	SO:0001589	frameshift_variant	9564	exon6			.	AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"""Cas scaffolding proteins"""	971	protein-coding gene	gene with protein product	"""Crk-associated substrate"", ""Cas scaffolding protein family member 1"""	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.1264delG	chr16.hg19:g.75269533delC	ENSP00000162330:p.Ala422fs	133.0	0.0		151.0	11.0	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Frame_Shift_Del	DEL	ENST00000162330.5	hg19	CCDS10915.1																																																																																			.	.		0.687	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567	
ERBB4	2066	hgsc.bcm.edu	37	2	212248737	212248737	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:212248737delT	ENST00000342788.4	-	28	3840	c.3530delA	c.(3529-3531)aatfs	p.N1177fs	ERBB4_ENST00000436443.1_Frame_Shift_Del_p.N1161fs|ERBB4_ENST00000402597.1_Frame_Shift_Del_p.N1167fs	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1177					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	AAGGTCTCCATTTTTTCTCCG	0.403										TSP Lung(8;0.080)																											p.N1177fs		Atlas-INDEL	.											ERBB4,NS,carcinoma,0,2	ERBB4	480	.	0			c.3531delT						.						111.0	113.0	112.0					2																	212248737		2203	4300	6503	SO:0001589	frameshift_variant	2066	exon28			.	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.3530delA	chr2.hg19:g.212248737delT	ENSP00000342235:p.Asn1177fs	108.0	0.0		113.0	11.0	NM_005235	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Frame_Shift_Del	DEL	ENST00000342788.4	hg19	CCDS2394.1																																																																																			.	.		0.403	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	
SAMM50	25813	hgsc.bcm.edu	37	22	44379821	44379821	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:44379821delT	ENST00000350028.4	+	12	1173	c.1016delT	c.(1015-1017)cttfs	p.L339fs	SAMM50_ENST00000396202.3_Frame_Shift_Del_p.L129fs	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	339					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)				AGGTTTTACCTTGGGGGACCC	0.552																																					p.L339fs		Atlas-INDEL	.											.	SAMM50	30	.	0			c.1015delC						.						171.0	156.0	161.0					22																	44379821		2203	4300	6503	SO:0001589	frameshift_variant	25813	exon12			.	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.1016delT	chr22.hg19:g.44379821delT	ENSP00000345445:p.Leu339fs	134.0	0.0		160.0	10.0	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Frame_Shift_Del	DEL	ENST00000350028.4	hg19	CCDS14055.1																																																																																			.	.		0.552	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380	
MYH7	4625	hgsc.bcm.edu	37	14	23888507	23888507	+	Intron	DEL	G	G	-	rs111467750		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:23888507delG	ENST00000355349.3	-	29	4016				MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta						adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CAGCTCACCTGGGGAAGCACC	0.592																																					.		Atlas-INDEL	.											.	MYH7	349	.	0			c.3854-2C>-						.						82.0	81.0	81.0					14																	23888507		2203	4300	6503	SO:0001627	intron_variant	4625	exon30			.	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"""Myosins / Myosin superfamily : Class II"""	7577	protein-coding gene	gene with protein product		160760	"""myopathy, distal 1"", ""myosin, heavy polypeptide 7, cardiac muscle, beta"""	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.3854-3C>-	chr14.hg19:g.23888507delG		84.0	0.0		126.0	10.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Splice_Site	DEL	ENST00000355349.3	hg19	CCDS9601.1																																																																																			.	.		0.592	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	
CTAGE5	4253	hgsc.bcm.edu	37	14	39788448	39788448	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:39788448delA	ENST00000280083.3	+	18	1810	c.1496delA	c.(1495-1497)gaafs	p.E499fs	CTAGE5_ENST00000556148.1_Frame_Shift_Del_p.E424fs|CTAGE5_ENST00000553352.1_Frame_Shift_Del_p.E470fs|CTAGE5_ENST00000348007.3_Frame_Shift_Del_p.E499fs|CTAGE5_ENST00000396165.4_Frame_Shift_Del_p.E470fs|CTAGE5_ENST00000396158.2_Frame_Shift_Del_p.E504fs|CTAGE5_ENST00000341502.5_Frame_Shift_Del_p.E499fs|CTAGE5_ENST00000557038.1_Frame_Shift_Del_p.E419fs|CTAGE5_ENST00000341749.3_Frame_Shift_Del_p.E487fs|RP11-407N17.3_ENST00000603904.1_Frame_Shift_Del_p.E470fs|RP11-407N17.3_ENST00000553728.1_Frame_Shift_Del_p.E1034fs			O15320	CTGE5_HUMAN	CTAGE family, member 5	499					positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		GAACTTTTAGAAAAAGATCCT	0.308																																					p.E504fs		Atlas-INDEL	.											CTAGE5,colon,carcinoma,0,1	CTAGE5	75	.	0			c.1510delG						.						83.0	84.0	83.0					14																	39788448		2203	4300	6503	SO:0001589	frameshift_variant	4253	exon18			.	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.1496delA	chr14.hg19:g.39788448delA	ENSP00000280083:p.Glu499fs	70.0	0.0		114.0	10.0	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Frame_Shift_Del	DEL	ENST00000280083.3	hg19	CCDS9674.1																																																																																			.	.		0.308	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
CTSA	5476	hgsc.bcm.edu	37	20	44521908	44521908	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:44521908delC	ENST00000372459.2	+	6	843	c.650delC	c.(649-651)tccfs	p.S217fs	CTSA_ENST00000354880.5_Frame_Shift_Del_p.S218fs|CTSA_ENST00000191018.5_Frame_Shift_Del_p.S217fs|RP3-337O18.9_ENST00000607703.1_RNA|NEURL2_ENST00000372518.4_5'Flank|CTSA_ENST00000372484.3_Frame_Shift_Del_p.S235fs			P10619	PPGB_HUMAN	cathepsin A	217					glycosphingolipid metabolic process (GO:0006687)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|enzyme activator activity (GO:0008047)|serine-type carboxypeptidase activity (GO:0004185)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				AATGACAACTCCCTGGTCTAC	0.552																																					p.S235fs		Atlas-INDEL	.											CTSA,NS,carcinoma,0,1	CTSA	52	.	0			c.703delT						.						143.0	122.0	129.0					20																	44521908		2203	4300	6503	SO:0001589	frameshift_variant	5476	exon7			.	M22960	CCDS13385.2, CCDS46609.1, CCDS54467.1	20q13.12	2012-02-10	2006-12-05	2006-12-05	ENSG00000064601	ENSG00000064601	3.4.16.5	"""Cathepsins"""	9251	protein-coding gene	gene with protein product	"""carboxypeptidase C"", ""lysosomal protective protein"", ""carboxypeptidase-L"", ""carboxypeptidase Y-like kininase"", ""deamidase"", ""lysosomal carboxypeptidase A"", ""urinary kininase"""	613111	"""protective protein for beta-galactosidase (galactosialidosis)"""	GSL, PPGB		2071143	Standard	NM_000308		Approved		uc002xqh.3	P10619	OTTHUMG00000033078	ENST00000372459.2:c.650delC	chr20.hg19:g.44521908delC	ENSP00000361537:p.Ser217fs	157.0	0.0		155.0	10.0	NM_000308	B2R798|Q561W6|Q5JZH1|Q96KJ2|Q9BR08|Q9BW68	Frame_Shift_Del	DEL	ENST00000372459.2	hg19	CCDS46609.1																																																																																			.	.		0.552	CTSA-012	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471297.2	NM_000308	
GPR107	57720	hgsc.bcm.edu	37	9	132863470	132863470	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:132863470delA	ENST00000372406.1	+	12	1606	c.1099delA	c.(1099-1101)aaafs	p.K368fs	GPR107_ENST00000372410.3_Frame_Shift_Del_p.K368fs|GPR107_ENST00000347136.6_Frame_Shift_Del_p.K368fs	NM_001136557.1	NP_001130029.1	Q5VW38	GP107_HUMAN	G protein-coupled receptor 107	368						integral component of membrane (GO:0016021)				endometrium(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	11		Ovarian(14;0.000531)				TGATAAAGACAAAAAGATCTT	0.458																																					p.D366fs		Atlas-INDEL	.											.	GPR107	30	.	0			c.1098delC						.						182.0	174.0	177.0					9																	132863470		2203	4300	6503	SO:0001589	frameshift_variant	57720	exon12			.	AF376725	CCDS35162.1, CCDS48041.1, CCDS48042.1	9q34.2	2014-01-30			ENSG00000148358	ENSG00000148358		"""GPCR / Unclassified : 7TM orphan receptors"""	17830	protein-coding gene	gene with protein product							Standard	NM_020960		Approved	KIAA1624, RP11-88G17, FLJ20998, LUSTR1	uc004bzd.2	Q5VW38	OTTHUMG00000020804	ENST00000372406.1:c.1099delA	chr9.hg19:g.132863470delA	ENSP00000361483:p.Lys368fs	184.0	0.0		190.0	12.0	NM_001136557	A6NJ53|Q2TB81|Q5JPA3|Q5VW39|Q96T26|Q9H658|Q9HCE8	Frame_Shift_Del	DEL	ENST00000372406.1	hg19	CCDS48041.1																																																																																			.	.		0.458	GPR107-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054643.2		
CDH11	1009	hgsc.bcm.edu	37	16	64981570	64981570	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:64981570delC	ENST00000268603.4	-	13	2942	c.2327delG	c.(2326-2328)ggafs	p.G776fs	CDH11_ENST00000394156.3_3'UTR|CDH11_ENST00000566827.1_Frame_Shift_Del_p.G650fs	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	776					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		AAAACGAGGTCCCCAGTTCTG	0.453			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.G776fs		Atlas-INDEL	.		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	.	CDH11	260	.	0			c.2328delA						.						77.0	79.0	78.0					16																	64981570		2203	4300	6503	SO:0001589	frameshift_variant	1009	exon13			.	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.2327delG	chr16.hg19:g.64981570delC	ENSP00000268603:p.Gly776fs	178.0	0.0		153.0	13.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Frame_Shift_Del	DEL	ENST00000268603.4	hg19	CCDS10803.1																																																																																			.	.		0.453	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
CRTAC1	55118	hgsc.bcm.edu	37	10	99640100	99640100	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:99640100delG	ENST00000370597.3	-	14	2080	c.1725delC	c.(1723-1725)cccfs	p.P575fs	CRTAC1_ENST00000298819.4_Frame_Shift_Del_p.P561fs|CRTAC1_ENST00000370591.2_Frame_Shift_Del_p.P575fs|CRTAC1_ENST00000468549.1_5'Flank	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	575	EGF-like.					extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		TGACACATACGGGCTTGTCTC	0.577																																					p.V576fs		Atlas-INDEL	.											.	CRTAC1	86	.	0			c.1726delG						.						145.0	111.0	122.0					10																	99640100		2203	4300	6503	SO:0001589	frameshift_variant	55118	exon14			.	AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.1725delC	chr10.hg19:g.99640100delG	ENSP00000359629:p.Pro575fs	144.0	0.0		152.0	10.0	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Frame_Shift_Del	DEL	ENST00000370597.3	hg19	CCDS31266.1																																																																																			.	.		0.577	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058	
CHDH	55349	hgsc.bcm.edu	37	3	53852175	53852175	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:53852175delT	ENST00000315251.6	-	9	1851	c.1414delA	c.(1414-1416)attfs	p.I472fs		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	472					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)	TGTGCAAAAATTTCTCTGGTG	0.517																																					p.I472fs		Atlas-INDEL	.											.	CHDH	34	.	0			c.1415delT						.						48.0	47.0	47.0					3																	53852175		2203	4300	6503	SO:0001589	frameshift_variant	55349	exon9			.	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.1414delA	chr3.hg19:g.53852175delT	ENSP00000319851:p.Ile472fs	105.0	0.0		155.0	11.0	NM_018397	Q9NY17	Frame_Shift_Del	DEL	ENST00000315251.6	hg19	CCDS2873.1																																																																																			.	.		0.517	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
RPP14	11102	hgsc.bcm.edu	37	3	58296091	58296091	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:58296091delT	ENST00000445193.3	+	2	446	c.35delT	c.(34-36)gttfs	p.V12fs	RPP14_ENST00000477305.1_Intron|RPP14_ENST00000466547.1_Frame_Shift_Del_p.V12fs|RPP14_ENST00000295959.5_Frame_Shift_Del_p.V12fs	NM_001098783.2	NP_001092253.1	O95059	RPP14_HUMAN	ribonuclease P/MRP 14kDa subunit	12					tRNA processing (GO:0008033)	nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)|RNA binding (GO:0003723)			large_intestine(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(55;0.000187)|KIRC - Kidney renal clear cell carcinoma(10;0.0102)|Kidney(10;0.0118)|OV - Ovarian serous cystadenocarcinoma(275;0.191)		GAAAGAGTAGTTTACAAAAAC	0.398																																					p.V12fs		Atlas-INDEL	.											.	RPP14	6	.	0			c.34delG						.						119.0	115.0	116.0					3																	58296091		2203	4300	6503	SO:0001589	frameshift_variant	11102	exon2			.	AF001175	CCDS2888.1	3p21.2	2012-05-21	2007-06-26		ENSG00000163684	ENSG00000163684			30327	protein-coding gene	gene with protein product		606112	"""ribonuclease P 14kDa subunit"""			10024167, 11929972	Standard	NM_001098783		Approved	P14	uc031sah.1	O95059	OTTHUMG00000159152	ENST00000445193.3:c.35delT	chr3.hg19:g.58296091delT	ENSP00000412894:p.Val12fs	117.0	0.0		157.0	10.0	NM_007042	Q53X97	Frame_Shift_Del	DEL	ENST00000445193.3	hg19	CCDS2888.1																																																																																			.	.		0.398	RPP14-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353527.2	NM_007042	
SENP6	26054	hgsc.bcm.edu	37	6	76331286	76331286	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:76331286delA	ENST00000447266.2	+	2	569	c.91delA	c.(91-93)aaafs	p.K31fs	SENP6_ENST00000370010.2_Frame_Shift_Del_p.K31fs|SENP6_ENST00000370014.3_Frame_Shift_Del_p.K31fs|SENP6_ENST00000327284.8_Frame_Shift_Del_p.K31fs	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	31					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)				TGGAGGTTTTAAAAATAATTG	0.289																																					p.F30fs		Atlas-INDEL	.											.	SENP6	189	.	0			c.90delT						.						99.0	99.0	99.0					6																	76331286		1786	4060	5846	SO:0001589	frameshift_variant	26054	exon2			.		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.91delA	chr6.hg19:g.76331286delA	ENSP00000402527:p.Lys31fs	157.0	0.0		256.0	16.0	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Frame_Shift_Del	DEL	ENST00000447266.2	hg19	CCDS47454.1																																																																																			.	.		0.289	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571	
TTLL7	79739	hgsc.bcm.edu	37	1	84386998	84386998	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:84386998delT	ENST00000260505.8	-	11	1599	c.1222delA	c.(1222-1224)aggfs	p.R408fs	TTLL7_ENST00000477524.1_5'UTR	NM_024686.4	NP_078962.4	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7	408					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			kidney(1)|large_intestine(8)|lung(15)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		GGTAAGAGCCTTTTAATTGAA	0.408																																					p.R408fs		Atlas-INDEL	.											.	TTLL7	93	.	0			c.1223delG						.						83.0	84.0	84.0					1																	84386998		2203	4299	6502	SO:0001589	frameshift_variant	79739	exon11			.	AY170843	CCDS690.2	1p31.1	2013-02-14			ENSG00000137941	ENSG00000137941		"""Tubulin tyrosine ligase-like family"""	26242	protein-coding gene	gene with protein product						15890843	Standard	XM_005271208		Approved	FLJ23033	uc001djc.3	Q6ZT98	OTTHUMG00000009932	ENST00000260505.8:c.1222delA	chr1.hg19:g.84386998delT	ENSP00000260505:p.Arg408fs	91.0	0.0		189.0	12.0	NM_024686	Q5TAX8|Q5TAX9|Q6P990|Q86YS1|Q9H5U4	Frame_Shift_Del	DEL	ENST00000260505.8	hg19	CCDS690.2																																																																																			.	.		0.408	TTLL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027498.1	NM_024686	
CNOT3	4849	hgsc.bcm.edu	37	19	54647778	54647778	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:54647778delA	ENST00000406403.1	+	5	1898	c.295delA	c.(295-297)aaafs	p.K99fs	CNOT3_ENST00000358389.3_5'UTR|CNOT3_ENST00000221232.5_Frame_Shift_Del_p.K99fs			O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	99					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(7)|urinary_tract(3)	28	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					ACGAGAGACCAAAACCAAAGC	0.557																																					p.T98fs		Atlas-INDEL	.											.	CNOT3	133	.	0			c.294delC						.						86.0	84.0	84.0					19																	54647778		2203	4300	6503	SO:0001589	frameshift_variant	4849	exon6			.	AF180474	CCDS12880.1	19q13.4	2011-02-14			ENSG00000088038	ENSG00000088038			7879	protein-coding gene	gene with protein product	"""NOT3 (negative regulator of transcription 3, yeast) homolog"""	604910		NOT3		10637334, 9734811	Standard	NM_014516		Approved	NOT3H, KIAA0691, LENG2	uc002qdj.2	O75175	OTTHUMG00000066468	ENST00000406403.1:c.295delA	chr19.hg19:g.54647778delA	ENSP00000383954:p.Lys99fs	107.0	0.0		122.0	10.0	NM_014516	Q9NZN7|Q9UF76	Frame_Shift_Del	DEL	ENST00000406403.1	hg19	CCDS12880.1																																																																																			.	.		0.557	CNOT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142130.3	NM_014516	
TMEM27	57393	hgsc.bcm.edu	37	X	15682878	15682878	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:15682878delA	ENST00000380342.3	-	1	276	c.21delT	c.(19-21)tttfs	p.F7fs		NM_020665.4	NP_065716.1	Q9HBJ8	TMM27_HUMAN	transmembrane protein 27	7					positive regulation of amino acid transport (GO:0051957)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of SNARE complex assembly (GO:0035543)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)			endometrium(3)|lung(4)|ovary(1)	8	Hepatocellular(33;0.183)					CAGTCACCAGAAAAAAGAGCA	0.398																																					p.L8fs		Atlas-INDEL	.											.	TMEM27	21	.	0			c.22delC						.						53.0	48.0	50.0					X																	15682878		2203	4299	6502	SO:0001589	frameshift_variant	57393	exon1			.	AF229179	CCDS14170.1	Xp22	2012-04-13			ENSG00000147003	ENSG00000147003			29437	protein-coding gene	gene with protein product	"""collectrin"""	300631				11278314	Standard	NM_020665		Approved	NX17	uc004cxc.2	Q9HBJ8	OTTHUMG00000021181	ENST00000380342.3:c.21delT	chrX.hg19:g.15682878delA	ENSP00000369699:p.Phe7fs	133.0	0.0		149.0	11.0	NM_020665	B2R9M1|Q6UW07	Frame_Shift_Del	DEL	ENST00000380342.3	hg19	CCDS14170.1																																																																																			.	.		0.398	TMEM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055879.1	NM_020665	
EYA4	2070	hgsc.bcm.edu	37	6	133783807	133783807	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:133783807delA	ENST00000367895.5	+	9	1093	c.629delA	c.(628-630)caafs	p.Q210fs	EYA4_ENST00000452339.2_Frame_Shift_Del_p.Q156fs|EYA4_ENST00000355286.6_Frame_Shift_Del_p.Q187fs|EYA4_ENST00000355167.3_Frame_Shift_Del_p.Q210fs|EYA4_ENST00000431403.2_Frame_Shift_Del_p.Q210fs|EYA4_ENST00000531901.1_Frame_Shift_Del_p.Q210fs|EYA4_ENST00000525849.1_Frame_Shift_Del_p.Q187fs|EYA4_ENST00000430974.2_Frame_Shift_Del_p.Q156fs	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	210					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA repair (GO:0006281)|inner ear development (GO:0048839)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|skin(1)	48	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		GGACTTTCCCAAACTCAGTCC	0.453																																					p.Q210fs	Melanoma(57;398 1237 3528 4702 7415)	Atlas-INDEL	.											.	EYA4	196	.	0			c.628delC						.						94.0	88.0	90.0					6																	133783807		2203	4300	6503	SO:0001589	frameshift_variant	2070	exon9			.	Y17114	CCDS5165.1, CCDS5166.1, CCDS43506.1, CCDS75521.1, CCDS75523.1	6q23	2014-09-17	2014-06-19		ENSG00000112319	ENSG00000112319		"""Protein tyrosine phosphatases / Asp-based PTPs"""	3522	protein-coding gene	gene with protein product		603550	"""eyes absent (Drosophila) homolog 4"", ""eyes absent homolog 4 (Drosophila)"""	DFNA10, CMD1J		9887327, 11159937	Standard	NM_004100		Approved		uc003qed.4	O95677	OTTHUMG00000015602	ENST00000367895.5:c.629delA	chr6.hg19:g.133783807delA	ENSP00000356870:p.Gln210fs	99.0	0.0		116.0	10.0	NM_172105	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Frame_Shift_Del	DEL	ENST00000367895.5	hg19	CCDS5165.1																																																																																			.	.		0.453	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100	
MIR1179	100302235	hgsc.bcm.edu	37	15	89151344	89151344	+	RNA	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:89151344delA	ENST00000408703.1	+	0	7					NR_031590.1				microRNA 1179																		TATTGGCTGGAAAGGAAGAAG	0.373																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.						222.0	198.0	205.0					15																	89151344		1566	3581	5147			100302235	.			.			15	2011-09-12		2008-12-18	ENSG00000221630	ENSG00000221630		"""ncRNAs / Micro RNAs"""	35260	non-coding RNA	RNA, micro				MIRN1179			Standard	NR_031590		Approved	hsa-mir-1179	uc021suc.1				chr15.hg19:g.89151344delA		129.0	0.0		165.0	10.0	.		RNA	DEL	ENST00000408703.1	hg19																																																																																				.	.		0.373	MIR1179-201	KNOWN	basic	miRNA	miRNA		NR_031590	
ACAD8	27034	hgsc.bcm.edu	37	11	134132519	134132519	+	Intron	DEL	A	A	-	rs377191168		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:134132519delA	ENST00000281182.4	+	10	1301				ACAD8_ENST00000374752.4_Intron|ACAD8_ENST00000537423.1_Intron	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8						branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	TCTAGAAGGTAAAAATTGCCA	0.577											OREG0021549	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.	GBM(65;238 1125 33403 41853 48889)	Atlas-INDEL	.											.	ACAD8	33	.	0			c.1195+2A>-						.						41.0	41.0	41.0					11																	134132519		2201	4297	6498	SO:0001627	intron_variant	27034	exon10			.	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"""acyl-Coenzyme A dehydrogenase family, member 8"""			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.1195+3A>-	chr11.hg19:g.134132519delA		58.0	0.0	1608	127.0	10.0	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Splice_Site	DEL	ENST00000281182.4	hg19	CCDS8498.1																																																																																			.	.		0.577	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384	
EML6	400954	hgsc.bcm.edu	37	2	55189708	55189708	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:55189708delA	ENST00000356458.6	+	35	5538	c.5018delA	c.(5017-5019)gaafs	p.E1673fs	EML6_ENST00000490828.1_3'UTR	NM_001039753.2	NP_001034842.2	Q6ZMW3	EMAL6_HUMAN	echinoderm microtubule associated protein like 6	1673						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(6)	7						GAAGTTGGTGAAAAAAATGCT	0.433																																					p.E1673fs		Atlas-Indel,Pindel	.											.	EML6	85	.	0			c.5017delG						.						115.0	108.0	110.0					2																	55189708		692	1591	2283	SO:0001589	frameshift_variant	400954	exon35			.		CCDS46286.1	2p16.1	2013-01-10			ENSG00000214595	ENSG00000214595		"""WD repeat domain containing"""	35412	protein-coding gene	gene with protein product							Standard	NM_001039753		Approved	FLJ42562	uc002ryb.4	Q6ZMW3	OTTHUMG00000152035	ENST00000356458.6:c.5018delA	chr2.hg19:g.55189708delA	ENSP00000348842:p.Glu1673fs	106.0	0.0		128.0	14.0	NM_001039753	A8MUB5|B6ZDG7	Frame_Shift_Del	DEL	ENST00000356458.6	hg19	CCDS46286.1																																																																																			.	.		0.433	EML6-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324997.3	XM_001725002	
AMPD3	272	hgsc.bcm.edu	37	11	10524339	10524339	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:10524339delT	ENST00000396554.3	+	13	2282	c.1941delT	c.(1939-1941)agtfs	p.S647fs	AMPD3_ENST00000530864.1_3'UTR|AMPD3_ENST00000444303.2_Frame_Shift_Del_p.S479fs	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	638					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		GCAACAACAGTTTGTTCCTCG	0.478																																					p.S647fs		Atlas-INDEL	.											.	AMPD3	68	.	0			c.1940delG						.						216.0	203.0	207.0					11																	10524339		2201	4294	6495	SO:0001589	frameshift_variant	272	exon13			.	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"""erythrocyte-specific AMP deaminase"""	102772	"""adenosine monophosphate deaminase (isoform E)"""			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.1941delT	chr11.hg19:g.10524339delT	ENSP00000379802:p.Ser647fs	141.0	0.0		152.0	10.0	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Frame_Shift_Del	DEL	ENST00000396554.3	hg19	CCDS7802.1																																																																																			.	.		0.478	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480	
SOGA3	387104	hgsc.bcm.edu	37	6	127834044	127834044	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:127834044delT	ENST00000525778.1	-	4	2222	c.1477delA	c.(1477-1479)atgfs	p.M493fs	SOGA3_ENST00000465909.2_Frame_Shift_Del_p.M493fs|SOGA3_ENST00000481848.2_Frame_Shift_Del_p.M493fs|SOGA3_ENST00000368268.2_Frame_Shift_Del_p.M493fs|SOGA3_ENST00000556132.1_Frame_Shift_Del_p.M493fs			Q5TF21	SOGA3_HUMAN	SOGA family member 3	493					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											ACCTCTTTCATTTTTTCCAGT	0.308																																					p.M493fs		Atlas-INDEL	.											.	.	.	.	0			c.1478delT						.						124.0	108.0	113.0					6																	127834044		1812	4070	5882	SO:0001589	frameshift_variant	387104	exon4			.	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1477delA	chr6.hg19:g.127834044delT	ENSP00000434570:p.Met493fs	172.0	0.0		245.0	16.0	NM_001012279		Frame_Shift_Del	DEL	ENST00000525778.1	hg19	CCDS43505.1																																																																																			.	.		0.308	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279	
HK3	3101	hgsc.bcm.edu	37	5	176309024	176309024	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:176309024delC	ENST00000292432.5	-	16	2249	c.2158delG	c.(2158-2160)gacfs	p.D721fs		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	721	Catalytic.|Hexokinase type-2 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGCCATCGTCCCCAAAGGCG	0.647																																					p.D720fs		Atlas-INDEL	.											.	HK3	210	.	0			c.2159delA						.						82.0	81.0	81.0					5																	176309024		2203	4300	6503	SO:0001589	frameshift_variant	3101	exon16			.		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.2158delG	chr5.hg19:g.176309024delC	ENSP00000292432:p.Asp721fs	97.0	0.0		193.0	15.0	NM_002115	Q8N1E7	Frame_Shift_Del	DEL	ENST00000292432.5	hg19	CCDS4407.1																																																																																			.	.		0.647	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
ACSM3	6296	hgsc.bcm.edu	37	16	20808252	20808252	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:20808252delA	ENST00000289416.5	+	14	2194	c.1719delA	c.(1717-1719)acafs	p.T573fs	ACSM3_ENST00000450120.2_Frame_Shift_Del_p.T565fs|ERI2_ENST00000564349.1_3'UTR|ERI2_ENST00000569729.1_3'UTR|ERI2_ENST00000357967.4_3'UTR|ERI2_ENST00000300005.3_Intron|ACSM3_ENST00000567387.1_3'UTR	NM_005622.3	NP_005613.2	Q53FZ2	ACSM3_HUMAN	acyl-CoA synthetase medium-chain family member 3	573					cholesterol homeostasis (GO:0042632)|fatty acid biosynthetic process (GO:0006633)|regulation of blood pressure (GO:0008217)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	21						GTGGGAAGACAAAAAGAAATG	0.323																																					p.T573fs		Atlas-INDEL	.											.	ACSM3	113	.	0			c.1718delC						.						79.0	85.0	83.0					16																	20808252		2201	4300	6501	SO:0001589	frameshift_variant	6296	exon14			.	D16350	CCDS10589.1, CCDS45435.1	16p13.11	2006-02-08	2005-09-08	2005-09-08	ENSG00000005187	ENSG00000005187		"""Acyl-CoA synthetase family"""	10522	protein-coding gene	gene with protein product		145505	"""SA (rat hypertension-associated) homolog"", ""SA hypertension-associated homolog (rat)"""	SAH		7843754, 7907320, 11470804	Standard	NM_005622		Approved	SA	uc002dhr.3	Q53FZ2	OTTHUMG00000131552	ENST00000289416.5:c.1719delA	chr16.hg19:g.20808252delA	ENSP00000289416:p.Thr573fs	209.0	0.0		205.0	13.0	NM_005622	O60363|Q13732|Q15425|Q7KYM6|Q9BUA2	Frame_Shift_Del	DEL	ENST00000289416.5	hg19	CCDS10589.1																																																																																			.	.		0.323	ACSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254414.2	NM_005622	
TRH	7200	hgsc.bcm.edu	37	3	129695643	129695643	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:129695643delG	ENST00000302649.3	+	3	840	c.313delG	c.(313-315)gggfs	p.G106fs	TRH_ENST00000507066.1_Frame_Shift_Del_p.G102fs	NM_007117.3	NP_009048.1	P20396	TRH_HUMAN	thyrotropin-releasing hormone	106					adult walking behavior (GO:0007628)|cell-cell signaling (GO:0007267)|eating behavior (GO:0042755)|histamine metabolic process (GO:0001692)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of feeding behavior (GO:2000252)|negative regulation of glutamate secretion (GO:0014050)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of insulin secretion (GO:0032024)|response to cold (GO:0009409)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	thyrotropin-releasing hormone activity (GO:0008437)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)	14						agaggaagaagggggggCTGT	0.567																																					p.E104fs	Esophageal Squamous(60;321 1330 17401 41911)	Atlas-INDEL	.											.	TRH	30	.	0			c.312delA						.						52.0	49.0	50.0					3																	129695643		2203	4300	6503	SO:0001589	frameshift_variant	7200	exon3			.		CCDS3066.1	3q13.3-q21	2013-02-28				ENSG00000170893		"""Endogenous ligands"""	12298	protein-coding gene	gene with protein product	"""prothyroliberin"""	613879				2126343, 1900134	Standard	NM_007117		Approved		uc003enc.4	P20396		ENST00000302649.3:c.313delG	chr3.hg19:g.129695643delG	ENSP00000303452:p.Gly106fs	70.0	0.0		142.0	10.0	NM_007117	B2R8R1|Q2TB83	Frame_Shift_Del	DEL	ENST00000302649.3	hg19	CCDS3066.1																																																																																			.	.		0.567	TRH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356592.1	NM_007117	
STK25	10494	hgsc.bcm.edu	37	2	242440926	242440926	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:242440926delG	ENST00000316586.4	-	3	577	c.228delC	c.(226-228)cccfs	p.P76fs	STK25_ENST00000478403.1_5'Flank|STK25_ENST00000405883.3_Intron|STK25_ENST00000405585.1_Intron|STK25_ENST00000401869.1_Frame_Shift_Del_p.P76fs|STK25_ENST00000535007.1_5'UTR|STK25_ENST00000543554.1_5'UTR|STK25_ENST00000403346.3_Frame_Shift_Del_p.P76fs	NM_001271977.1|NM_001271978.1|NM_001282308.1	NP_001258906.1|NP_001258907.1|NP_001269237.1	O00506	STK25_HUMAN	serine/threonine kinase 25	76	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				establishment or maintenance of cell polarity (GO:0007163)|Golgi localization (GO:0051645)|positive regulation of axonogenesis (GO:0050772)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	10		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		GGGTGATGTAGGGGCTGTCGC	0.602																																					p.Y77fs	NSCLC(99;1100 1566 7679 28647 48345)	Atlas-INDEL	.											.	STK25	32	.	0			c.229delT						.						128.0	101.0	110.0					2																	242440926		2203	4300	6503	SO:0001589	frameshift_variant	10494	exon3			.	D63780	CCDS2549.1, CCDS63199.1, CCDS63200.1	2q37.3	2010-06-25	2010-06-25		ENSG00000115694	ENSG00000115694			11404	protein-coding gene	gene with protein product		602255	"""serine/threonine kinase 25 (Ste20, yeast homolog)"""			8887545, 9160885, 15037601	Standard	NM_001271977		Approved	SOK1, YSK1	uc002wbp.4	O00506	OTTHUMG00000133408	ENST00000316586.4:c.228delC	chr2.hg19:g.242440926delG	ENSP00000325748:p.Pro76fs	98.0	0.0		119.0	10.0	NM_001271977	A8K6Z3|A8K7D2|B7Z9K1|Q15522|Q5BJF1	Frame_Shift_Del	DEL	ENST00000316586.4	hg19	CCDS2549.1																																																																																			.	.		0.602	STK25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257265.4	NM_006374	
BOD1L1	259282	hgsc.bcm.edu	37	4	13601642	13601642	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:13601642delG	ENST00000040738.5	-	10	7017	c.6882delC	c.(6880-6882)tccfs	p.S2294fs		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2294						nucleus (GO:0005634)	DNA binding (GO:0003677)										AGGTGCTTGTGGAAATCATGG	0.552																																					p.T2295fs		Atlas-INDEL	.											.	.	.	.	0			c.6883delA						.						61.0	52.0	55.0					4																	13601642		2203	4300	6503	SO:0001589	frameshift_variant	259282	exon10			.	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.6882delC	chr4.hg19:g.13601642delG	ENSP00000040738:p.Ser2294fs	169.0	0.0		179.0	11.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Frame_Shift_Del	DEL	ENST00000040738.5	hg19	CCDS3411.2																																																																																			.	.		0.552	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
ARL3	403	hgsc.bcm.edu	37	10	104449670	104449670	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:104449670delT	ENST00000260746.5	-	4	426	c.295delA	c.(295-297)agafs	p.R99fs		NM_004311.3	NP_004302.1	P36405	ARL3_HUMAN	ADP-ribosylation factor-like 3	99					cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|intraciliary transport (GO:0042073)|kidney development (GO:0001822)|photoreceptor cell development (GO:0042461)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)|spindle microtubule (GO:0005876)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			large_intestine(2)	2		Colorectal(252;0.122)		Epithelial(162;4.88e-09)|all cancers(201;1.29e-07)|BRCA - Breast invasive adenocarcinoma(275;0.22)		TCTTCAAATCTTTTTCTGTCT	0.313																																					p.R99fs		Atlas-INDEL	.											.	ARL3	13	.	0			c.296delG						.						50.0	55.0	54.0					10																	104449670		2203	4298	6501	SO:0001589	frameshift_variant	403	exon4			.	U07151	CCDS7538.1	10q23.3	2014-05-09			ENSG00000138175	ENSG00000138175		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	694	protein-coding gene	gene with protein product		604695				8034651, 10072593	Standard	NM_004311		Approved	ARFL3	uc001kwa.3	P36405	OTTHUMG00000018965	ENST00000260746.5:c.295delA	chr10.hg19:g.104449670delT	ENSP00000260746:p.Arg99fs	147.0	0.0		157.0	10.0	NM_004311	B2R6C7|Q53X83|Q5JSM2	Frame_Shift_Del	DEL	ENST00000260746.5	hg19	CCDS7538.1																																																																																			.	.		0.313	ARL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050088.2	NM_004311	
TTC3	7267	hgsc.bcm.edu	37	21	38555184	38555184	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:38555184delA	ENST00000399017.2	+	36	7473	c.4726delA	c.(4726-4728)aaafs	p.K1576fs	TTC3_ENST00000355666.1_Frame_Shift_Del_p.K1576fs|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Frame_Shift_Del_p.K1576fs	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1576	Arg/Lys-rich (basic).				negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				ACTGAAGAAGAAAATTAAAAA	0.279																																					p.K1575fs	Ovarian(38;194 1649 35661)	Atlas-INDEL	.											.	TTC3	182	.	0			c.4725delG						.						20.0	23.0	22.0					21																	38555184		2169	4271	6440	SO:0001589	frameshift_variant	7267	exon36			.	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.4726delA	chr21.hg19:g.38555184delA	ENSP00000381981:p.Lys1576fs	178.0	0.0		209.0	13.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Frame_Shift_Del	DEL	ENST00000399017.2	hg19	CCDS13651.1																																																																																			.	.		0.279	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
RBM12B	389677	hgsc.bcm.edu	37	8	94746023	94746023	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:94746023delA	ENST00000399300.2	-	3	2829	c.2616delT	c.(2614-2616)tttfs	p.F872fs	RBM12B_ENST00000520961.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA|RBM12B_ENST00000517700.1_Frame_Shift_Del_p.F752fs	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	872							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			GCGGGCTCCTAAAATCCTCAC	0.488																																					p.R873fs		Atlas-INDEL	.											.	RBM12B	78	.	0			c.2617delA						.						114.0	117.0	116.0					8																	94746023		1806	4077	5883	SO:0001589	frameshift_variant	389677	exon3			.		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"""RNA binding motif (RRM) containing"""	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.2616delT	chr8.hg19:g.94746023delA	ENSP00000382239:p.Phe872fs	54.0	0.0		163.0	10.0	NM_203390	A8MYB5	Frame_Shift_Del	DEL	ENST00000399300.2	hg19	CCDS43755.1																																																																																			.	.		0.488	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390	
LRRFIP1	9208	hgsc.bcm.edu	37	2	238666189	238666189	+	Intron	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:238666189delG	ENST00000392000.4	+	9	864				LRRFIP1_ENST00000289175.6_Intron|LRRFIP1_ENST00000308482.9_Frame_Shift_Del_p.G408fs|LRRFIP1_ENST00000244815.5_Intron	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1						innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		CAAAAAGATAGGGGTAGGATT	0.423																																					p.I407fs		Atlas-INDEL	.											.	LRRFIP1	171	.	0			c.1221delA						.						46.0	44.0	45.0					2																	238666189		1566	3573	5139	SO:0001627	intron_variant	9208	exon17			.	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"""GC-binding factor 2"""	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.747+1359G>-	chr2.hg19:g.238666189delG		248.0	0.0		240.0	16.0	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Frame_Shift_Del	DEL	ENST00000392000.4	hg19	CCDS46552.1																																																																																			.	.		0.423	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
ZCCHC9	84240	hgsc.bcm.edu	37	5	80608475	80608475	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:80608475delT	ENST00000254037.2	+	5	3965	c.810delT	c.(808-810)aatfs	p.N270fs	ZCCHC9_ENST00000380199.5_Frame_Shift_Del_p.N270fs|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000407610.3_Frame_Shift_Del_p.N270fs|ZCCHC9_ENST00000438268.2_Frame_Shift_Del_p.N270fs			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	270					negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		AAGTTGTTAATTTTTGATAAC	0.418																																					p.N270fs		Atlas-INDEL	.											.	ZCCHC9	26	.	0			c.809delA						.						81.0	78.0	79.0					5																	80608475		2203	4300	6503	SO:0001589	frameshift_variant	84240	exon6			.	BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732		"""Zinc fingers, CCHC domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25424	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 41"""					12477932	Standard	NM_032280		Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.810delT	chr5.hg19:g.80608475delT	ENSP00000254037:p.Asn270fs	105.0	0.0		212.0	13.0	NM_001131036	B2RAE7|Q9H027	Frame_Shift_Del	DEL	ENST00000254037.2	hg19	CCDS4054.1																																																																																			.	.		0.418	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280	
MYO10	4651	hgsc.bcm.edu	37	5	16762178	16762178	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:16762178delA	ENST00000513610.1	-	16	2086	c.1632delT	c.(1630-1632)tttfs	p.F544fs		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	544	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						GCTTCACTCCAAAATTGTTAA	0.313																																					p.G545fs		Atlas-INDEL	.											.	MYO10	198	.	0			c.1633delG						.						41.0	37.0	38.0					5																	16762178		1813	4065	5878	SO:0001589	frameshift_variant	4651	exon16			.	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.1632delT	chr5.hg19:g.16762178delA	ENSP00000421280:p.Phe544fs	101.0	0.0		192.0	13.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Frame_Shift_Del	DEL	ENST00000513610.1	hg19	CCDS54834.1																																																																																			.	.		0.313	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
CFL2	1073	hgsc.bcm.edu	37	14	35182277	35182277	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:35182277delT	ENST00000341223.3	-	3	528	c.377delA	c.(376-378)aagfs	p.K127fs	CFL2_ENST00000555765.1_Frame_Shift_Del_p.K110fs|CFL2_ENST00000298159.6_Frame_Shift_Del_p.K127fs|CFL2_ENST00000556161.1_Frame_Shift_Del_p.K110fs	NM_001243645.1|NM_021914.7	NP_001230574.1|NP_068733.1	Q9Y281	COF2_HUMAN	cofilin 2 (muscle)	127	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				actin filament depolymerization (GO:0030042)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of actin filament depolymerization (GO:0030836)|regulation of dendritic spine morphogenesis (GO:0061001)|sarcomere organization (GO:0045214)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|nucleus (GO:0005634)				breast(3)|endometrium(2)|lung(3)	8	Breast(36;0.0361)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;6.07e-06)|Lung(238;2.23e-05)|Epithelial(34;0.0387)|all cancers(34;0.0814)	GBM - Glioblastoma multiforme(112;0.0424)		TGTAAATTTCTTTTTAATGGC	0.264																																					p.K126fs		Atlas-INDEL	.											.	CFL2	22	.	0			c.378delG						.						23.0	21.0	22.0					14																	35182277		2196	4281	6477	SO:0001589	frameshift_variant	1073	exon3			.	AF087867	CCDS9649.1, CCDS9650.1, CCDS58311.1	14q13.2	2014-09-17			ENSG00000165410	ENSG00000165410			1875	protein-coding gene	gene with protein product	"""nemaline myopathy type 7"""	601443				8800436	Standard	NM_138638		Approved	NEM7	uc001wsh.3	Q9Y281	OTTHUMG00000029536	ENST00000341223.3:c.377delA	chr14.hg19:g.35182277delT	ENSP00000340635:p.Lys127fs	146.0	0.0		195.0	12.0	NM_021914	G3V5P4	Frame_Shift_Del	DEL	ENST00000341223.3	hg19	CCDS9650.1																																																																																			.	.		0.264	CFL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276639.1	NM_138638	
PUS7L	83448	hgsc.bcm.edu	37	12	44124292	44124292	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:44124292delT	ENST00000416848.2	-	9	2481	c.1993delA	c.(1993-1995)acgfs	p.T665fs	PUS7L_ENST00000431332.3_Frame_Shift_Del_p.T352fs|PUS7L_ENST00000344862.5_Frame_Shift_Del_p.T665fs|PUS7L_ENST00000551923.1_Frame_Shift_Del_p.T665fs	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	665					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)		GAACCTTTCGTTTTGACATCA	0.363																																					p.T665fs		Atlas-INDEL	.											PUS7L,colon,carcinoma,+1,1	PUS7L	73	.	0			c.1994delC						.						153.0	140.0	144.0					12																	44124292		2203	4300	6503	SO:0001589	frameshift_variant	83448	exon9			.	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.1993delA	chr12.hg19:g.44124292delT	ENSP00000415899:p.Thr665fs	226.0	0.0		243.0	15.0	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Frame_Shift_Del	DEL	ENST00000416848.2	hg19	CCDS8743.1																																																																																			.	.		0.363	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292	
KRT20	54474	hgsc.bcm.edu	37	17	39041106	39041106	+	Frame_Shift_Del	DEL	G	G	-	rs547778667		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:39041106delG	ENST00000167588.3	-	1	373	c.332delC	c.(331-333)ccgfs	p.P111fs		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	111	Linker 1.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)	p.P111Q(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				ACCAGCCCTCGGGGCGTTGGT	0.498																																					p.P111fs		Atlas-INDEL	.											.	KRT20	38	.	1	Substitution - Missense(1)	lung(1)	c.333delG						.						98.0	92.0	94.0					17																	39041106		2203	4300	6503	SO:0001589	frameshift_variant	54474	exon1			.	BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.332delC	chr17.hg19:g.39041106delG	ENSP00000167588:p.Pro111fs	172.0	0.0		157.0	10.0	NM_019010	B2R6W7	Frame_Shift_Del	DEL	ENST00000167588.3	hg19	CCDS11379.1																																																																																			.	.		0.498	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2		
DDX60L	91351	hgsc.bcm.edu	37	4	169348237	169348237	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:169348237delT	ENST00000511577.1	-	14	2161	c.1914delA	c.(1912-1914)aaafs	p.K638fs	DDX60L_ENST00000260184.7_Frame_Shift_Del_p.K638fs|DDX60L_ENST00000505890.1_Frame_Shift_Del_p.K638fs			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	638							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		CTCGGCAATGTTTTTTCCATG	0.338																																					p.H639fs		Atlas-INDEL	.											.	DDX60L	116	.	0			c.1915delC						.						64.0	57.0	59.0					4																	169348237		1846	4095	5941	SO:0001589	frameshift_variant	91351	exon14			.	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.1914delA	chr4.hg19:g.169348237delT	ENSP00000422423:p.Lys638fs	153.0	0.0		135.0	10.0	NM_001012967	Q96ND6	Frame_Shift_Del	DEL	ENST00000511577.1	hg19																																																																																				.	.		0.338	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
PDE2A	5138	hgsc.bcm.edu	37	11	72342169	72342169	+	Intron	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:72342169delG	ENST00000334456.5	-	2	390				PDE2A_ENST00000376450.3_Intron|PDE2A_ENST00000540380.1_Intron|PDE2A_ENST00000444035.2_Intron|PDE2A_ENST00000540345.1_Intron|PDE2A_ENST00000544570.1_Intron|PDE2A_ENST00000418754.2_Intron	NM_002599.4	NP_002590.1	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated						blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to drug (GO:0035690)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to mechanical stimulus (GO:0071260)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP catabolic process (GO:0046069)|cGMP-mediated signaling (GO:0019934)|establishment of endothelial barrier (GO:0061028)|metabolic process (GO:0008152)|monocyte differentiation (GO:0030224)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vascular permeability (GO:0043116)|positive regulation of inflammatory response (GO:0050729)|positive regulation of vascular permeability (GO:0043117)|protein targeting to mitochondrion (GO:0006626)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel activity (GO:0005262)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|drug binding (GO:0008144)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	36			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Caffeine(DB00201)|Tofisopam(DB08811)	TCCTTTGCAAGGGGGTCCAGG	0.652																																					p.L12fs		Atlas-INDEL	.											.	PDE2A	156	.	0			c.35delT						.																																			SO:0001627	intron_variant	5138	exon2			.	U67733	CCDS8216.1, CCDS44670.1, CCDS53678.1, CCDS73345.1	11q13.1-q14.1	2008-05-14			ENSG00000186642	ENSG00000186642	3.1.4.17	"""Phosphodiesterases"""	8777	protein-coding gene	gene with protein product		602658				9210593	Standard	NM_002599		Approved		uc010rrc.2	O00408	OTTHUMG00000102045	ENST00000334456.5:c.144+11128C>-	chr11.hg19:g.72342169delG		122.0	0.0		149.0	10.0	NM_001243784	B2R646|B3KRV5|E9PGI1|F6W5Z0|Q5J791|Q5J792|Q5J793|Q6ZMR1	Frame_Shift_Del	DEL	ENST00000334456.5	hg19	CCDS8216.1																																																																																			.	.		0.652	PDE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219839.2	NM_002599	
MARK3	4140	hgsc.bcm.edu	37	14	103934485	103934485	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:103934485delT	ENST00000429436.2	+	12	1736	c.1226delT	c.(1225-1227)gttfs	p.V409fs	MARK3_ENST00000216288.7_Frame_Shift_Del_p.V393fs|MARK3_ENST00000303622.9_Frame_Shift_Del_p.V409fs|MARK3_ENST00000561071.1_Intron|MARK3_ENST00000440884.3_Frame_Shift_Del_p.V330fs|MARK3_ENST00000416682.2_Frame_Shift_Del_p.V432fs|MARK3_ENST00000335102.5_Frame_Shift_Del_p.V432fs|MARK3_ENST00000553942.1_Frame_Shift_Del_p.V409fs	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	409						plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			CAGAGAAGTGTTTTTTCAAGC	0.478																																					p.V409fs		Atlas-INDEL	.											.	MARK3	86	.	0			c.1225delG						.						128.0	116.0	120.0					14																	103934485		1962	4159	6121	SO:0001589	frameshift_variant	4140	exon12			.	M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.1226delT	chr14.hg19:g.103934485delT	ENSP00000411397:p.Val409fs	157.0	0.0		179.0	11.0	NM_001128919	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Frame_Shift_Del	DEL	ENST00000429436.2	hg19	CCDS45165.1																																																																																			.	.		0.478	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918	
MTHFD1L	25902	hgsc.bcm.edu	37	6	151198808	151198808	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:151198808delT	ENST00000367321.3	+	3	625	c.351delT	c.(349-351)aatfs	p.N117fs	MTHFD1L_ENST00000367307.4_Frame_Shift_Del_p.N117fs	NM_001242767.1|NM_001242768.1|NM_015440.4	NP_001229696.1|NP_001229697.1|NP_056255.2	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	117	Methylenetetrahydrofolate dehydrogenase and cyclohydrolase.				folic acid-containing compound biosynthetic process (GO:0009396)|folic acid-containing compound metabolic process (GO:0006760)|formate metabolic process (GO:0015942)|one-carbon metabolic process (GO:0006730)|oxidation-reduction process (GO:0055114)|tetrahydrofolate interconversion (GO:0035999)|tetrahydrofolate metabolic process (GO:0046653)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	29		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		TCAACCAGAATTTGGCTGAGG	0.353																																					p.N117fs		Atlas-INDEL	.											.	MTHFD1L	75	.	0			c.350delA						.						119.0	116.0	117.0					6																	151198808		2203	4300	6503	SO:0001589	frameshift_variant	25902	exon3			.	BC017477	CCDS5228.1, CCDS56457.1, CCDS75535.1, CCDS75536.1	6q25.1	2010-07-19	2004-12-13	2004-12-14	ENSG00000120254	ENSG00000120254	6.3.4.3		21055	protein-coding gene	gene with protein product	"""10-formyl-THF synthetase"", ""mitochondrial C1-tetrahydrofolate synthase"", ""monofunctional C1-tetrahydrofolate synthase, mitochondrial"""	611427	"""formyltetrahydrofolate synthetase domain containing 1"""	FTHFSDC1		18804703	Standard	NM_015440		Approved	DKFZP586G1517, FLJ21145	uc021zgs.1	Q6UB35	OTTHUMG00000015828	ENST00000367321.3:c.351delT	chr6.hg19:g.151198808delT	ENSP00000356290:p.Asn117fs	117.0	0.0		154.0	11.0	NM_001242767	Q2TBF3|Q8WVW0|Q96HG8|Q9H789|Q9UFU8	Frame_Shift_Del	DEL	ENST00000367321.3	hg19	CCDS5228.1																																																																																			.	.		0.353	MTHFD1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042699.1	NM_015440	
MYH7	4625	hgsc.bcm.edu	37	14	23894966	23894966	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:23894966delC	ENST00000355349.3	-	20	2386	c.2224delG	c.(2224-2226)gcafs	p.A742fs		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	742	Myosin motor.		A -> E (in CMH1). {ECO:0000269|PubMed:16199542}.		adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		AGCTTCTCTGCCCCCTTCCTG	0.517																																					p.A742fs		Atlas-INDEL	.											.	MYH7	349	.	0			c.2225delC						.						121.0	102.0	109.0					14																	23894966		2203	4300	6503	SO:0001589	frameshift_variant	4625	exon20			.	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"""Myosins / Myosin superfamily : Class II"""	7577	protein-coding gene	gene with protein product		160760	"""myopathy, distal 1"", ""myosin, heavy polypeptide 7, cardiac muscle, beta"""	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.2224delG	chr14.hg19:g.23894966delC	ENSP00000347507:p.Ala742fs	118.0	0.0		164.0	11.0	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Frame_Shift_Del	DEL	ENST00000355349.3	hg19	CCDS9601.1																																																																																			.	.		0.517	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	
CCDC67	159989	hgsc.bcm.edu	37	11	93104240	93104240	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:93104240delA	ENST00000298050.3	+	7	683	c.583delA	c.(583-585)aaafs	p.K196fs		NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	196					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)	cytoplasm (GO:0005737)|deuterosome (GO:0098536)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				ACTAAATGGTAAAAAACAGTG	0.333																																					p.G194fs		Atlas-INDEL	.											.,1	CCDC67	57	.	0			c.582delT						.						58.0	55.0	56.0					11																	93104240		1821	4083	5904	SO:0001589	frameshift_variant	159989	exon7			.	AK058122	CCDS44707.1	11q21	2014-02-20				ENSG00000165325			26344	protein-coding gene	gene with protein product						24240477	Standard	NM_181645		Approved	FLJ25393	uc001pdq.3	Q05D60		ENST00000298050.3:c.583delA	chr11.hg19:g.93104240delA	ENSP00000298050:p.Lys196fs	152.0	0.0		241.0	16.0	NM_181645	Q8NEF1|Q96LL7	Frame_Shift_Del	DEL	ENST00000298050.3	hg19	CCDS44707.1																																																																																			.	.		0.333	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645	
HINT3	135114	hgsc.bcm.edu	37	6	126278229	126278229	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:126278229delG	ENST00000229633.5	+	1	303	c.106delG	c.(106-108)ggcfs	p.G36fs		NM_138571.4	NP_612638.3	Q9NQE9	HINT3_HUMAN	histidine triad nucleotide binding protein 3	36			G -> A (2.5-fold increase in affinity for indolepropinoic acyl-adenylate and cytosine; 2-fold decrease in hypoxanthine affinity; nearly no change in affinity for adenine, guanine and uracil; dbSNP:rs2295005). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17870088, ECO:0000269|Ref.1}.			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)		TGAAGCCGCTGGCAAGTCACC	0.672											OREG0017649	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A35fs		Atlas-INDEL	.											.	HINT3	14	.	0			c.105delT						.						27.0	21.0	23.0					6																	126278229		1869	3644	5513	SO:0001589	frameshift_variant	135114	exon1			.	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.106delG	chr6.hg19:g.126278229delG	ENSP00000229633:p.Gly36fs	111.0	0.0	1548	184.0	12.0	NM_138571	B3KQ91|Q8N0Y9	Frame_Shift_Del	DEL	ENST00000229633.5	hg19	CCDS5133.1																																																																																			.	.		0.672	HINT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042090.1	NM_138571	
SHPRH	257218	hgsc.bcm.edu	37	6	146254194	146254194	+	Splice_Site	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:146254194delT	ENST00000367505.2	-	14	3375	c.3111delA	c.(3109-3111)aaa>aa	p.K1037fs	SHPRH_ENST00000367503.3_Splice_Site_p.K1046fs|SHPRH_ENST00000438092.2_Splice_Site_p.K1046fs|SHPRH_ENST00000275233.7_Splice_Site_p.K1037fs			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1037					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)		ACCTTCTACCTTTAATAATAT	0.373																																					p.G1047fs		Atlas-INDEL	.											.	SHPRH	169	.	0			c.3139delG						.						93.0	87.0	89.0					6																	146254194		1845	4093	5938	SO:0001630	splice_region_variant	257218	exon14			.	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.3112+1A>-	chr6.hg19:g.146254194delT		85.0	0.0		125.0	10.0	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Frame_Shift_Del	DEL	ENST00000367505.2	hg19	CCDS43513.2																																																																																			.	.		0.373	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	Frame_Shift_Del
MRC1	4360	hgsc.bcm.edu	37	10	17917243	17917243	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:17917243delA	ENST00000331429.2	+	17	2631	c.2528delA	c.(2527-2529)gaafs	p.E843fs																	breast(1)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						AGTGAAAGTGAAAAGAAGTTT	0.333																																					p.E843fs		Atlas-INDEL	.											.	MRC1	13	.	0			c.2527delG						.						1.0	1.0	1.0					10																	17917243		34	89	123	SO:0001589	frameshift_variant	4360	exon17			.																												ENST00000331429.2:c.2528delA	chr10.hg19:g.17917243delA	ENSP00000332124:p.Glu843fs	138.0	0.0		175.0	11.0	NM_002438		Frame_Shift_Del	DEL	ENST00000331429.2	hg19																																																																																				.	.		0.333	MRC1L1-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047054.1		
SMARCD2	6603	hgsc.bcm.edu	37	17	61914354	61914354	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:61914354delA	ENST00000448276.2	-	4	760	c.495delT	c.(493-495)tttfs	p.F165fs	RN7SL805P_ENST00000581353.1_RNA|SMARCD2_ENST00000323347.10_Frame_Shift_Del_p.F117fs|SMARCD2_ENST00000225742.9_Frame_Shift_Del_p.F90fs	NM_001098426.1	NP_001091896.1	Q92925	SMRD2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	165					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)	8						GCTTCCGCTCAAAAGCCAAGA	0.552																																					p.E166fs		Atlas-INDEL	.											.	SMARCD2	29	.	0			c.496delG						.						88.0	89.0	89.0					17																	61914354		2017	4194	6211	SO:0001589	frameshift_variant	6603	exon4			.	U66618	CCDS45756.1	17q23.3	2014-07-16			ENSG00000108604	ENSG00000108604			11107	protein-coding gene	gene with protein product	"""mammalian chromatin remodeling complex BRG1-associated factor 60B"", ""Swp73-like protein"", ""chromatin remodeling complex BAF60B subunit"", ""SWI/SNF complex 60 kDa subunit B"""	601736				8804307, 9693044	Standard	NM_001098426		Approved	BAF60B, Rsc6p, CRACD2, PRO2451	uc010deb.1	Q92925	OTTHUMG00000179045	ENST00000448276.2:c.495delT	chr17.hg19:g.61914354delA	ENSP00000392617:p.Phe165fs	77.0	0.0		132.0	10.0	NM_001098426	A5PLL5|A6NNQ7|B4DV56|B4E1R6|Q7L2I6|Q9UHZ1	Frame_Shift_Del	DEL	ENST00000448276.2	hg19	CCDS45756.1																																																																																			.	.		0.552	SMARCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444544.1	NM_001098426	
PTPN23	25930	hgsc.bcm.edu	37	3	47454399	47454399	+	Frame_Shift_Del	DEL	G	G	-	rs6789730	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:47454399delG	ENST00000265562.4	+	25	4712	c.4635delG	c.(4633-4635)ccgfs	p.P1547fs	PTPN23_ENST00000431726.1_Frame_Shift_Del_p.P1421fs	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1547	Pro-rich.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTTCCTCCCCGCCCCCCCTTT	0.697																																					p.P1545fs		Atlas-INDEL	.											.	PTPN23	85	.	0			c.4634delC						.						21.0	23.0	22.0					3																	47454399		2195	4291	6486	SO:0001589	frameshift_variant	25930	exon25			.	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.4635delG	chr3.hg19:g.47454399delG	ENSP00000265562:p.Pro1547fs	182.0	0.0		328.0	22.0	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Frame_Shift_Del	DEL	ENST00000265562.4	hg19	CCDS2754.1																																																																																			.	.		0.697	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466	
SSX4	6759	hgsc.bcm.edu	37	X	48244046	48244046	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:48244046delA	ENST00000376886.2	+	3	276	c.113delA	c.(112-114)gaafs	p.E38fs	SSX4_ENST00000375517.3_Frame_Shift_Del_p.E38fs	NM_005636.3	NP_005627.1	O60224	SSX4_HUMAN	synovial sarcoma, X breakpoint 4	38	KRAB-related. {ECO:0000255|PROSITE- ProRule:PRU00120}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)		SS18/SSX4(12)	lung(1)	1						AAAGAGTGGGAAAAGATGAAA	0.383			T	SS18	synovial sarcoma																																p.E38fs		Atlas-INDEL	.		Dom	yes		X	Xp11.23	6759	"""synovial sarcoma, X breakpoint 4"""		M	.	SSX4B	9	.	0			c.112delG						.						8.0	4.0	6.0					X																	48244046		1829	3342	5171	SO:0001589	frameshift_variant	548313	exon3			.		CCDS35240.1, CCDS43934.1	Xp11.23	2009-06-17			ENSG00000204645	ENSG00000268009			11338	protein-coding gene	gene with protein product		300326					Standard	NM_005636		Approved	CT5.4		O60224	OTTHUMG00000022698	ENST00000376886.2:c.113delA	chrX.hg19:g.48244046delA	ENSP00000366083:p.Glu38fs	308.0	0.0		319.0	20.0	NM_001034832	A8MYD4|B2RPE3|Q3SYD4|Q5JQZ0|Q9UJU9	Frame_Shift_Del	DEL	ENST00000376886.2	hg19	CCDS35240.1																																																																																			.	.		0.383	SSX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058902.2		
CCDC7	79741	hgsc.bcm.edu	37	10	32832279	32832279	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:32832279delA	ENST00000362006.5	+	13	1588	c.1045delA	c.(1045-1047)aaafs	p.K350fs	CCDC7_ENST00000277657.6_Frame_Shift_Del_p.K350fs	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	350										NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				AACAGTGAAGAAAAAAGACAA	0.264																																					p.K348fs		Atlas-INDEL	.											.	CCDC7	47	.	0			c.1044delG						.						30.0	31.0	30.0					10																	32832279		2186	4267	6453	SO:0001589	frameshift_variant	221016	exon13			.	BC022020	CCDS7173.1	10p11.23	2013-12-13			ENSG00000216937	ENSG00000216937			26533	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 68"""	C10orf68		12477932	Standard	NM_024688		Approved	FLJ32762, FLJ13031	uc001iwk.3	Q96M83	OTTHUMG00000150517	ENST00000362006.5:c.1045delA	chr10.hg19:g.32832279delA	ENSP00000355078:p.Lys350fs	126.0	0.0		230.0	17.0	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Frame_Shift_Del	DEL	ENST00000362006.5	hg19	CCDS7173.1																																																																																			.	.		0.264	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023	
ATF3	467	hgsc.bcm.edu	37	1	212788594	212788594	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:212788594delA	ENST00000341491.4	+	2	496	c.231delA	c.(229-231)acafs	p.T77fs	ATF3_ENST00000336937.4_Frame_Shift_Del_p.T48fs|RN7SL512P_ENST00000578962.1_RNA|ATF3_ENST00000366987.2_Frame_Shift_Del_p.T77fs|ATF3_ENST00000366985.1_Frame_Shift_Del_p.T20fs|ATF3_ENST00000492118.1_Intron|ATF3_ENST00000366983.1_Frame_Shift_Del_p.T77fs	NM_001040619.2|NM_001206488.2|NM_001674.3	NP_001035709.1|NP_001193417.2|NP_001665.1	P18847	ATF3_HUMAN	activating transcription factor 3	77					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)|gluconeogenesis (GO:0006094)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|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 regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6				OV - Ovarian serous cystadenocarcinoma(81;0.00628)|all cancers(67;0.0097)|GBM - Glioblastoma multiforme(131;0.0388)|Epithelial(68;0.0933)	Pseudoephedrine(DB00852)	TGTCCATCACAAAAGCCGAGG	0.552																																					p.T77fs		Atlas-INDEL	.											.	ATF3	22	.	0			c.230delC						.						42.0	44.0	43.0					1																	212788594		2203	4300	6503	SO:0001589	frameshift_variant	467	exon2			.	L19871	CCDS1506.1, CCDS41464.1, CCDS55688.1, CCDS58059.1	1q32.3	2013-01-10			ENSG00000162772	ENSG00000162772		"""basic leucine zipper proteins"""	785	protein-coding gene	gene with protein product		603148				7515060	Standard	NM_001674		Approved		uc021pit.1	P18847	OTTHUMG00000036747	ENST00000341491.4:c.231delA	chr1.hg19:g.212788594delA	ENSP00000344352:p.Thr77fs	89.0	0.0		147.0	14.0	NM_001030287	Q5VTZ2|Q6ICQ9|Q7Z566|Q8WYM6	Frame_Shift_Del	DEL	ENST00000341491.4	hg19	CCDS1506.1																																																																																			.	.		0.552	ATF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089296.1	NM_001674	
ACRC	93953	hgsc.bcm.edu	37	X	70800684	70800684	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:70800684delA	ENST00000373695.1	+	1	550	c.13delA	c.(13-15)aaafs	p.K6fs	ACRC_ENST00000373696.3_Frame_Shift_Del_p.K6fs			Q96QF7	ACRC_HUMAN	acidic repeat containing	6						nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|endometrium(15)|kidney(4)|large_intestine(4)|lung(20)|ovary(5)|prostate(1)|skin(2)|stomach(1)	54	Renal(35;0.156)					GGATGGGTGCAAAAAAGAGCT	0.468																																					p.C4X		Atlas-INDEL	.											.	ACRC	110	.	0			c.12delC						.						143.0	130.0	134.0					X																	70800684		2203	4299	6502	SO:0001589	frameshift_variant	93953	exon2			.	AJ311392	CCDS35326.1	Xq13.1	2010-08-05			ENSG00000147174	ENSG00000147174			15805	protein-coding gene	gene with protein product		300369					Standard	NM_052957		Approved		uc004eae.2	Q96QF7	OTTHUMG00000033327	ENST00000373695.1:c.13delA	chrX.hg19:g.70800684delA	ENSP00000362799:p.Lys6fs	215.0	0.0		238.0	17.0	NM_052957	B9EG62	Frame_Shift_Del	DEL	ENST00000373695.1	hg19	CCDS35326.1																																																																																			.	.		0.468	ACRC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081856.1		
TOP2B	7155	hgsc.bcm.edu	37	3	25679663	25679663	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:25679663delT	ENST00000264331.4	-	5	533	c.534delA	c.(532-534)aaafs	p.K178fs	TOP2B_ENST00000435706.2_Frame_Shift_Del_p.K173fs	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	178					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	TACCTGTAACTTTTTTCTCAT	0.313																																					p.V174fs		Atlas-INDEL	.											.	TOP2B	98	.	0			c.520delG						.						70.0	62.0	65.0					3																	25679663		1788	4049	5837	SO:0001589	frameshift_variant	7155	exon5			.	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"""topoisomerase (DNA) II beta (180kD)"""			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.534delA	chr3.hg19:g.25679663delT	ENSP00000264331:p.Lys178fs	192.0	0.0		275.0	20.0	NM_001068	Q13600|Q9UMG8|Q9UQP8	Frame_Shift_Del	DEL	ENST00000264331.4	hg19																																																																																				.	.		0.313	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			
ZCWPW2	152098	hgsc.bcm.edu	37	3	28557110	28557110	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:28557110delG	ENST00000383768.2	+	8	970	c.782delG	c.(781-783)aggfs	p.R261fs	ZCWPW2_ENST00000421010.1_Frame_Shift_Del_p.R261fs			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	261							zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						AAGGAGAACAGGGGTATGTGA	0.318																																					p.R261fs		Atlas-INDEL	.											.	ZCWPW2	49	.	0			c.781delA						.						46.0	48.0	47.0					3																	28557110		2203	4296	6499	SO:0001589	frameshift_variant	152098	exon7			.	BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.782delG	chr3.hg19:g.28557110delG	ENSP00000373278:p.Arg261fs	126.0	0.0		200.0	12.0	NM_001040432		Frame_Shift_Del	DEL	ENST00000383768.2	hg19	CCDS33723.1																																																																																			.	.		0.318	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384	
FAM65B	9750	hgsc.bcm.edu	37	6	24806664	24806664	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:24806664delT	ENST00000259698.4	-	23	3319	c.3144delA	c.(3142-3144)aaafs	p.K1048fs	FAM65B_ENST00000538035.1_Frame_Shift_Del_p.K1027fs	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	1048					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						CTCGAGGAAATTTGTCCAATT	0.378																																					p.F1049fs		Atlas-INDEL	.											.	FAM65B	134	.	0			c.3145delT						.						152.0	129.0	136.0					6																	24806664		692	1591	2283	SO:0001589	frameshift_variant	9750	exon23			.	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"""myogenesis-related and NCAM-associated protein homolog (chicken)"""	611410	"""chromosome 6 open reading frame 32"""	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.3144delA	chr6.hg19:g.24806664delT	ENSP00000259698:p.Lys1048fs	81.0	0.0		106.0	12.0	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Frame_Shift_Del	DEL	ENST00000259698.4	hg19	CCDS47383.1																																																																																			.	.		0.378	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2		
SDAD1	55153	hgsc.bcm.edu	37	4	76895289	76895289	+	Intron	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:76895289delG	ENST00000356260.5	-	7	697				SDAD1_ENST00000395711.4_Intron|SDAD1_ENST00000513089.1_5'Flank	NM_018115.2	NP_060585.2	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1						actin cytoskeleton organization (GO:0030036)|protein transport (GO:0015031)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal large subunit export from nucleus (GO:0000055)	nucleolus (GO:0005730)				breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	19			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			CATCATTCCTGGGGGAAGACA	0.383																																					.		Atlas-INDEL	.											.	SDAD1	47	.	0			c.579-2C>-						.						167.0	145.0	152.0					4																	76895289		2203	4300	6503	SO:0001627	intron_variant	55153	exon8			.	AF132198	CCDS3573.2, CCDS75147.1	4q21.21	2010-11-24			ENSG00000198301	ENSG00000198301			25537	protein-coding gene	gene with protein product						11483580	Standard	NM_001288984		Approved	FLJ10498	uc003hje.4	Q9NVU7	OTTHUMG00000130111	ENST00000356260.5:c.579-3C>-	chr4.hg19:g.76895289delG		175.0	0.0		140.0	10.0	NM_018115	Q32Q11|Q68D52|Q7Z5U4|Q9H831|Q9H9P6	Splice_Site	DEL	ENST00000356260.5	hg19	CCDS3573.2																																																																																			.	.		0.383	SDAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252418.3	NM_018115	
SLC35F3	148641	hgsc.bcm.edu	37	1	234041422	234041422	+	Frame_Shift_Del	DEL	G	G	-	rs57010808	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:234041422delG	ENST00000366618.3	+	2	346	c.201delG	c.(199-201)ccgfs	p.P67fs		NM_173508.2	NP_775779.1	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	408					thiamine transport (GO:0015888)	integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|urinary_tract(1)	32	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			CCAGCGGGCCGGTGGGGCTCA	0.622																																					p.P67fs		Atlas-INDEL	.											.	SLC35F3	81	.	0			c.200delC						.						69.0	69.0	69.0					1																	234041422		2203	4300	6503	SO:0001589	frameshift_variant	148641	exon2			.		CCDS1600.1, CCDS73050.1	1q42.3	2013-05-22			ENSG00000183780	ENSG00000183780		"""Solute carriers"""	23616	protein-coding gene	gene with protein product							Standard	XM_005273070		Approved	FLJ37712	uc001hvy.1	Q8IY50	OTTHUMG00000037929	ENST00000366618.3:c.201delG	chr1.hg19:g.234041422delG	ENSP00000355577:p.Pro67fs	90.0	0.0		159.0	11.0	NM_173508	Q5TDD6|Q8N9C9	Frame_Shift_Del	DEL	ENST00000366618.3	hg19	CCDS1600.1																																																																																			.	.		0.622	SLC35F3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092579.2	NM_173508	
TTC37	9652	hgsc.bcm.edu	37	5	94856440	94856440	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:94856440delT	ENST00000358746.2	-	20	2392	c.2094delA	c.(2092-2094)aaafs	p.K698fs	RNU6-308P_ENST00000390957.1_RNA	NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	698						cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						ATTCCAGTGCTTTTTCTATGT	0.289																																					p.A699fs		Atlas-INDEL	.											.	TTC37	128	.	0			c.2095delG						.						63.0	65.0	64.0					5																	94856440		2203	4297	6500	SO:0001589	frameshift_variant	9652	exon20			.	AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"""Tetratricopeptide (TTC) repeat domain containing"""	23639	protein-coding gene	gene with protein product		614589	"""KIAA0372"""	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.2094delA	chr5.hg19:g.94856440delT	ENSP00000351596:p.Lys698fs	113.0	0.0		237.0	16.0	NM_014639	O15077|Q6PJI3	Frame_Shift_Del	DEL	ENST00000358746.2	hg19	CCDS4072.1																																																																																			.	.		0.289	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639	
APOBEC3B	9582	hgsc.bcm.edu	37	22	39381926	39381926	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:39381926delC	ENST00000333467.3	+	3	329	c.284delC	c.(283-285)accfs	p.T95fs	APOBEC3B_ENST00000407298.3_Frame_Shift_Del_p.T95fs|APOBEC3B_ENST00000402182.3_Frame_Shift_Del_p.T95fs	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	95	CMP/dCMP deaminase zinc-binding 1.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|negative regulation of transposition (GO:0010529)	nucleus (GO:0005634)	deoxycytidine deaminase activity (GO:0047844)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	13	Melanoma(58;0.04)					GTATCCTGGACCCCCTGCCCG	0.562																																					p.T95fs		Atlas-INDEL	.											.	APOBEC3B	32	.	0			c.283delA						.						136.0	128.0	131.0					22																	39381926		2202	4297	6499	SO:0001589	frameshift_variant	9582	exon3			.	AK024854	CCDS13982.1, CCDS58807.1	22q13.1-q13.2	2008-05-15			ENSG00000179750	ENSG00000179750		"""Apolipoprotein B mRNA editing enzymes"""	17352	protein-coding gene	gene with protein product	"""phorbolin 3"""	607110				11863358, 10469298	Standard	NM_004900		Approved	PHRBNL, FLJ21201	uc003awo.2	Q9UH17	OTTHUMG00000151085	ENST00000333467.3:c.284delC	chr22.hg19:g.39381926delC	ENSP00000327459:p.Thr95fs	126.0	0.0		127.0	10.0	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Frame_Shift_Del	DEL	ENST00000333467.3	hg19	CCDS13982.1																																																																																			.	.		0.562	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900	
IFNL3	282617	hgsc.bcm.edu	37	19	39734707	39734707	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:39734707delC	ENST00000413851.2	-	3	387	c.349delG	c.(349-351)gatfs	p.D117fs		NM_172139.2	NP_742151.2	Q8IZI9	IFNL3_HUMAN	interferon, lambda 3	117					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|negative regulation of viral genome replication (GO:0045071)|positive regulation of immune response (GO:0050778)	extracellular space (GO:0005615)											TCCAAGACATCCCCCAGGGCT	0.662																																					p.D117fs		Atlas-INDEL	.											.	.	.	.	0			c.350delA						.						61.0	66.0	64.0					19																	39734707		2203	4300	6503	SO:0001589	frameshift_variant	282617	exon3			.	AY129149	CCDS12530.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000197110	ENSG00000197110		"""Interferons"""	18365	protein-coding gene	gene with protein product		607402	"""interleukin 28B"", ""interleukin 28B (interferon, lambda 3)"""	IL28B			Standard	NM_172139		Approved	IL-28B, IL28C	uc010xut.2	Q8IZI9	OTTHUMG00000182805	ENST00000413851.2:c.349delG	chr19.hg19:g.39734707delC	ENSP00000409000:p.Asp117fs	108.0	0.0		161.0	10.0	NM_172139	A2BDE1|Q6VN56|Q7Z4J3|Q8IWL6	Frame_Shift_Del	DEL	ENST00000413851.2	hg19	CCDS12530.1																																																																																			.	.		0.662	IFNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463832.1	NM_172139	
RBM33	155435	hgsc.bcm.edu	37	7	155511123	155511123	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:155511123delC	ENST00000401878.3	+	9	1444	c.1246delC	c.(1246-1248)cccfs	p.P416fs	RBM33_ENST00000486747.1_3'UTR	NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	416	Pro-rich.						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)		TGCCGTGGGACCCCAGAGATT	0.483																																					p.G415fs		Atlas-INDEL	.											.	RBM33	157	.	0			c.1245delA						.						81.0	85.0	84.0					7																	155511123		1880	4130	6010	SO:0001589	frameshift_variant	155435	exon9			.	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.1246delC	chr7.hg19:g.155511123delC	ENSP00000384160:p.Pro416fs	129.0	0.0		166.0	10.0	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Frame_Shift_Del	DEL	ENST00000401878.3	hg19	CCDS5941.2																																																																																			.	.		0.483	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408	
ZHX2	22882	hgsc.bcm.edu	37	8	123965336	123965336	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:123965336delC	ENST00000314393.4	+	3	2421	c.1586delC	c.(1585-1587)gccfs	p.A529fs		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	529					mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			CCAGACTTTGCCCCCCAGAAG	0.517																																					p.A529fs	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-INDEL	.											.	ZHX2	106	.	0			c.1585delG						.						61.0	56.0	57.0					8																	123965336		2203	4300	6503	SO:0001589	frameshift_variant	22882	exon3			.	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1586delC	chr8.hg19:g.123965336delC	ENSP00000314709:p.Ala529fs	69.0	0.0		257.0	18.0	NM_014943		Frame_Shift_Del	DEL	ENST00000314393.4	hg19	CCDS6336.1																																																																																			.	.		0.517	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
AHDC1	27245	hgsc.bcm.edu	37	1	27876439	27876439	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:27876439delC	ENST00000247087.5	-	5	2784	c.2188delG	c.(2188-2190)gagfs	p.E730fs	AHDC1_ENST00000374011.2_Frame_Shift_Del_p.E730fs			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	730	Gly-rich.						DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GCGTCTACCTCCCCCCGGCCC	0.662																																					p.E730fs		Atlas-INDEL	.											.	AHDC1	98	.	0			c.2189delA						.						36.0	34.0	34.0					1																	27876439		2203	4300	6503	SO:0001589	frameshift_variant	27245	exon6			.	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.2188delG	chr1.hg19:g.27876439delC	ENSP00000247087:p.Glu730fs	195.0	0.0		348.0	22.0	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Frame_Shift_Del	DEL	ENST00000247087.5	hg19	CCDS30652.1																																																																																			.	.		0.662	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3		
SLC4A4	8671	hgsc.bcm.edu	37	4	72432766	72432766	+	3'UTR	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:72432766delA	ENST00000264485.5	+	0	3359				SLC4A4_ENST00000340595.3_3'UTR|SLC4A4_ENST00000351898.6_3'UTR|SLC4A4_ENST00000425175.1_Frame_Shift_Del_p.K1049fs	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4						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)	TCATGCTGATAAAATTCCTTT	0.358																																					p.D1048fs		Atlas-INDEL	.											SLC4A4_ENST00000425175,NS,carcinoma,0,1	SLC4A4	269	.	0			c.3144delT						.						147.0	134.0	139.0					4																	72432766		2203	4300	6503	SO:0001624	3_prime_UTR_variant	8671	exon24			.	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.*2A>-	chr4.hg19:g.72432766delA		124.0	0.0		100.0	10.0	NM_001134742	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Frame_Shift_Del	DEL	ENST00000264485.5	hg19	CCDS43236.1																																																																																			.	.		0.358	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759	
VIPR1	7433	hgsc.bcm.edu	37	3	42573788	42573788	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:42573788delC	ENST00000325123.4	+	10	1086	c.973delC	c.(973-975)cccfs	p.P326fs	VIPR1-AS1_ENST00000593621.1_RNA|VIPR1-AS1_ENST00000602176.1_RNA|VIPR1_ENST00000433647.1_Frame_Shift_Del_p.P285fs|VIPR1-AS1_ENST00000608869.1_RNA|VIPR1_ENST00000543411.1_Frame_Shift_Del_p.P278fs|VIPR1_ENST00000438259.2_Frame_Shift_Del_p.P116fs|VIPR1-AS1_ENST00000452639.3_RNA|VIPR1-AS1_ENST00000596630.1_RNA|VIPR1-AS1_ENST00000598837.1_RNA|VIPR1-AS1_ENST00000600342.1_RNA|VIPR1-AS1_ENST00000610022.1_RNA|VIPR1-AS1_ENST00000601312.1_RNA|VIPR1-AS1_ENST00000593611.1_RNA	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	326					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		GAAACTGCGGCCCCCAGATAT	0.557																																					p.R324fs		Atlas-INDEL	.											.	VIPR1	45	.	0			c.972delG						.						143.0	134.0	137.0					3																	42573788		2203	4300	6503	SO:0001589	frameshift_variant	7433	exon10			.	AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12694	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 1"""	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.973delC	chr3.hg19:g.42573788delC	ENSP00000327246:p.Pro326fs	135.0	0.0		215.0	14.0	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Frame_Shift_Del	DEL	ENST00000325123.4	hg19	CCDS2698.1																																																																																			.	.		0.557	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624	
SMARCA1	6594	hgsc.bcm.edu	37	X	128640085	128640085	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:128640085delA	ENST00000371122.4	-	8	1199	c.1070delT	c.(1069-1071)ttafs	p.L358fs	SMARCA1_ENST00000371121.3_Frame_Shift_Del_p.L358fs|SMARCA1_ENST00000478420.1_5'Flank|SMARCA1_ENST00000371123.1_Frame_Shift_Del_p.L358fs	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	358	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						ATCAGGCAATAAAAAGTTGAG	0.363																																					p.L357fs		Atlas-INDEL	.											.	SMARCA1	126	.	0			c.1071delA						.						190.0	179.0	183.0					X																	128640085		2203	4300	6503	SO:0001589	frameshift_variant	6594	exon8			.	M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.1070delT	chrX.hg19:g.128640085delA	ENSP00000360163:p.Leu358fs	128.0	0.0		142.0	11.0	NM_139035	Q5JV41|Q5JV42	Frame_Shift_Del	DEL	ENST00000371122.4	hg19	CCDS14612.1																																																																																			.	.		0.363	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069	
C14orf93	60686	hgsc.bcm.edu	37	14	23457145	23457145	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:23457145delT	ENST00000299088.6	-	6	1593	c.1164delA	c.(1162-1164)aaafs	p.K388fs	RP11-298I3.4_ENST00000555294.1_RNA|C14orf93_ENST00000397377.1_Frame_Shift_Del_p.K208fs|C14orf93_ENST00000341470.4_Frame_Shift_Del_p.K388fs|C14orf93_ENST00000397382.4_Frame_Shift_Del_p.K388fs|RP11-298I3.4_ENST00000556503.1_RNA|C14orf93_ENST00000406429.2_Frame_Shift_Del_p.K388fs|RP11-298I3.4_ENST00000557615.1_RNA|C14orf93_ENST00000397379.3_Frame_Shift_Del_p.K388fs	NM_001130708.1|NM_021944.2	NP_001124180.1|NP_068763.2	Q9H972	CN093_HUMAN	chromosome 14 open reading frame 93	388						extracellular region (GO:0005576)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	17	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)		TCTTCTCCTCTTTTTCCTTCA	0.507																																					p.E389fs		Atlas-INDEL	.											.	C14orf93	33	.	0			c.1165delG						.						108.0	105.0	106.0					14																	23457145		2203	4300	6503	SO:0001589	frameshift_variant	60686	exon6			.	AK023026	CCDS9583.1, CCDS61399.1, CCDS61400.1	14q11.1	2012-09-25			ENSG00000100802	ENSG00000100802			20162	protein-coding gene	gene with protein product							Standard	XM_005267971		Approved	FLJ12154	uc001wih.3	Q9H972	OTTHUMG00000028712	ENST00000299088.6:c.1164delA	chr14.hg19:g.23457145delT	ENSP00000299088:p.Lys388fs	115.0	0.0		148.0	11.0	NM_021944	B7WP03|D3DS38|D3DS39|Q86SE6|Q96CF7|Q9HA68	Frame_Shift_Del	DEL	ENST00000299088.6	hg19	CCDS9583.1																																																																																			.	.		0.507	C14orf93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071688.5	NM_021944	
SEC62	7095	hgsc.bcm.edu	37	3	169700648	169700648	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:169700648delA	ENST00000337002.4	+	4	463	c.405delA	c.(403-405)acafs	p.T135fs	SEC62-AS1_ENST00000479626.1_RNA|SEC62_ENST00000480708.1_Frame_Shift_Del_p.T135fs	NM_003262.3	NP_003253.1	Q99442	SEC62_HUMAN	SEC62 homolog (S. cerevisiae)	135					cotranslational protein targeting to membrane (GO:0006613)|posttranslational protein targeting to membrane (GO:0006620)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.E138fs*9(1)		NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	9						atgagaagacaaaaaaagaaa	0.254																																					p.T135fs		Atlas-INDEL	.											.,1	SEC62	27	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.404delC						.						17.0	19.0	19.0					3																	169700648		2082	4215	6297	SO:0001589	frameshift_variant	7095	exon4			.	D87127	CCDS3210.1	3q26.2	2008-04-22	2008-04-22	2008-04-22	ENSG00000008952	ENSG00000008952			11846	protein-coding gene	gene with protein product		602173	"""translocation protein 1"""	TLOC1		9020021, 10799540	Standard	NM_003262		Approved	Dtrp1, HTP1	uc003fgh.3	Q99442	OTTHUMG00000158753	ENST00000337002.4:c.405delA	chr3.hg19:g.169700648delA	ENSP00000337688:p.Thr135fs	68.0	0.0		126.0	10.0	NM_003262	D3DNQ0|O00682|O00729	Frame_Shift_Del	DEL	ENST00000337002.4	hg19	CCDS3210.1																																																																																			.	.		0.254	SEC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352043.1		
SEC24A	10802	hgsc.bcm.edu	37	5	134059335	134059335	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:134059335delT	ENST00000398844.2	+	22	3430	c.3142delT	c.(3142-3144)tttfs	p.F1049fs		NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	1049					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCAGAGACCATTTTTCCCAAT	0.373																																					p.P1047fs		Atlas-INDEL	.											.	SEC24A	77	.	0			c.3141delA						.						157.0	146.0	149.0					5																	134059335		1835	4081	5916	SO:0001589	frameshift_variant	10802	exon22			.	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"""SEC24 (S. cerevisiae) related gene family, member A"", ""SEC24 family, member A (S. cerevisiae)"""			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.3142delT	chr5.hg19:g.134059335delT	ENSP00000381823:p.Phe1049fs	99.0	0.0		177.0	11.0	NM_021982	A8MVW3|Q8WUV2|Q96GP7	Frame_Shift_Del	DEL	ENST00000398844.2	hg19	CCDS43363.1																																																																																			.	.		0.373	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1		
KMT2E	55904	hgsc.bcm.edu	37	7	104745930	104745930	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:104745930delA	ENST00000311117.3	+	18	2786	c.2241delA	c.(2239-2241)ggafs	p.G747fs	KMT2E_ENST00000257745.4_Frame_Shift_Del_p.G747fs|KMT2E_ENST00000334914.7_5'UTR|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000334877.4_Frame_Shift_Del_p.G747fs	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	66.0	0.0		120.0	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		
FAM151A	338094	hgsc.bcm.edu	37	1	55078303	55078303	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:55078303delG	ENST00000302250.2	-	5	816	c.656delC	c.(655-657)ccafs	p.P219fs	FAM151A_ENST00000371304.2_Frame_Shift_Del_p.P219fs|ACOT11_ENST00000371316.3_Intron	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	219						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	12						CGTCCTGTTTGGGGACGTGGA	0.572																																					p.P219fs		Atlas-INDEL	.											.	FAM151A	58	.	0			c.657delA						.						128.0	108.0	115.0					1																	55078303		2203	4300	6503	SO:0001589	frameshift_variant	338094	exon5			.	AK091901	CCDS594.1	1p32.3	2008-02-05	2007-12-18	2007-12-18	ENSG00000162391	ENSG00000162391			25032	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 179"""	C1orf179		17273976	Standard	NM_176782		Approved	MGC27169	uc001cxn.3	Q8WW52	OTTHUMG00000009888	ENST00000302250.2:c.656delC	chr1.hg19:g.55078303delG	ENSP00000306888:p.Pro219fs	101.0	0.0		156.0	10.0	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Frame_Shift_Del	DEL	ENST00000302250.2	hg19	CCDS594.1																																																																																			.	.		0.572	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782	
MYO15A	51168	hgsc.bcm.edu	37	17	18077149	18077149	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:18077149delC	ENST00000205890.5	+	65	10743	c.10405delC	c.(10405-10407)cccfs	p.P3469fs	RP11-258F1.1_ENST00000583062.1_RNA|MYO15A_ENST00000418233.3_Frame_Shift_Del_p.P733fs|RP11-258F1.1_ENST00000577847.1_RNA|MYO15A_ENST00000451725.2_Intron	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3469	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					GACCCAGCGGCCCACGGCCAA	0.662																																					p.R3468fs		Atlas-INDEL	.											.	MYO15A	268	.	0			c.10404delG						.						40.0	44.0	43.0					17																	18077149		1958	4137	6095	SO:0001589	frameshift_variant	51168	exon64			.	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.10405delC	chr17.hg19:g.18077149delC	ENSP00000205890:p.Pro3469fs	214.0	0.0		228.0	14.0	NM_016239	B4DFC7	Frame_Shift_Del	DEL	ENST00000205890.5	hg19	CCDS42271.1																																																																																			.	.		0.662	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
ZMYM4	9202	hgsc.bcm.edu	37	1	35835675	35835675	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:35835675delA	ENST00000314607.6	+	6	966	c.886delA	c.(886-888)aaafs	p.K296fs	ZMYM4_ENST00000482131.1_3'UTR|ZMYM4_ENST00000373297.2_Frame_Shift_Del_p.K296fs	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	296					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GGGGGAACTGAAAATTAGTGC	0.343																																					p.L295fs		Atlas-INDEL	.											.	ZMYM4	143	.	0			c.885delG						.						76.0	76.0	76.0					1																	35835675		2203	4300	6503	SO:0001589	frameshift_variant	9202	exon6			.	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"""Zinc fingers, MYM type"""	13055	protein-coding gene	gene with protein product		613568	"""zinc finger protein 262"""	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.886delA	chr1.hg19:g.35835675delA	ENSP00000322915:p.Lys296fs	102.0	0.0		161.0	12.0	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Frame_Shift_Del	DEL	ENST00000314607.6	hg19	CCDS389.1																																																																																			.	.		0.343	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095	
CLK4	57396	hgsc.bcm.edu	37	5	178032333	178032333	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:178032333delG	ENST00000316308.4	-	11	1353	c.1185delC	c.(1183-1185)cccfs	p.P395fs		NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	395	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|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)	all cancers(165;0.235)		GTTGTGGTATGGGTCCTAATA	0.343																																					p.I396fs		Atlas-INDEL	.											.	CLK4	103	.	0			c.1186delA						.						163.0	147.0	153.0					5																	178032333		2203	4299	6502	SO:0001589	frameshift_variant	57396	exon11			.	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"""CDC-like kinases"""	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.1185delC	chr5.hg19:g.178032333delG	ENSP00000316948:p.Pro395fs	120.0	0.0		214.0	13.0	NM_020666		Frame_Shift_Del	DEL	ENST00000316308.4	hg19	CCDS4437.1																																																																																			.	.		0.343	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2		
FAT2	2196	hgsc.bcm.edu	37	5	150924388	150924388	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:150924388delC	ENST00000261800.5	-	9	6312	c.6300delG	c.(6298-6300)gggfs	p.G2100fs		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2100	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCCCATTTGTCCCCAAGTCCT	0.443																																					p.T2101fs		Atlas-INDEL	.											.	FAT2	465	.	0			c.6301delA						.						123.0	127.0	126.0					5																	150924388		2203	4300	6503	SO:0001589	frameshift_variant	2196	exon9			.	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.6300delG	chr5.hg19:g.150924388delC	ENSP00000261800:p.Gly2100fs	110.0	0.0		208.0	14.0	NM_001447	O75091|Q9NSR7	Frame_Shift_Del	DEL	ENST00000261800.5	hg19	CCDS4317.1																																																																																			.	.		0.443	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
SOS1	6654	hgsc.bcm.edu	37	2	39262585	39262585	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:39262585delA	ENST00000426016.1	-	8	1007	c.921delT	c.(919-921)tttfs	p.F307fs	SOS1_ENST00000428721.2_Frame_Shift_Del_p.F250fs|SOS1_ENST00000402219.2_Frame_Shift_Del_p.F307fs|SOS1_ENST00000395038.2_Frame_Shift_Del_p.F307fs			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	307	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				AACGATCATGAAAACCAGGTC	0.333									Noonan syndrome																												p.H308fs		Atlas-INDEL	.											.	SOS1	134	.	0			c.922delC						.						75.0	78.0	77.0					2																	39262585		2203	4300	6503	SO:0001589	frameshift_variant	6654	exon7	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	.	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11187	protein-coding gene	gene with protein product		182530	"""gingival fibromatosis, hereditary, 1"""	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.921delT	chr2.hg19:g.39262585delA	ENSP00000387784:p.Phe307fs	177.0	0.0		165.0	11.0	NM_005633	A8K2G3|B4DXG2	Frame_Shift_Del	DEL	ENST00000426016.1	hg19	CCDS1802.1																																																																																			.	.		0.333	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633	
SYTL3	94120	hgsc.bcm.edu	37	6	159103969	159103969	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:159103969delA	ENST00000297239.9	+	5	536	c.342delA	c.(340-342)atafs	p.I114fs	SYTL3_ENST00000367081.3_5'UTR|SYTL3_ENST00000360448.3_Frame_Shift_Del_p.I114fs			Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	114	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	calcium-dependent phospholipid binding (GO:0005544)			endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|urinary_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		ATGTCAAAATAAAAACTGGAG	0.348																																					p.I114fs		Atlas-INDEL	.											.	SYTL3	49	.	0			c.341delT						.						56.0	57.0	57.0					6																	159103969		2203	4300	6503	SO:0001589	frameshift_variant	94120	exon7			.	AK055750	CCDS34563.1, CCDS56458.1	6q25.3	2008-07-04			ENSG00000164674	ENSG00000164674			15587	protein-coding gene	gene with protein product						11773082	Standard	NM_001242384		Approved	SLP3, exophilin-6	uc003qrp.3	Q4VX76	OTTHUMG00000015916	ENST00000297239.9:c.342delA	chr6.hg19:g.159103969delA	ENSP00000297239:p.Ile114fs	154.0	0.0		176.0	14.0	NM_001009991	Q496J4|Q496J6|Q5U3B9	Frame_Shift_Del	DEL	ENST00000297239.9	hg19	CCDS56458.1																																																																																			.	.		0.348	SYTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042876.1		
SPEG	10290	hgsc.bcm.edu	37	2	220354172	220354172	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:220354172delC	ENST00000312358.7	+	36	8564	c.8432delC	c.(8431-8433)gccfs	p.A2811fs	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2811	Pro-rich.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GCTCCTGCTGCCCCCACACCC	0.672																																					p.A2811fs		Atlas-INDEL	.											.	SPEG	272	.	0			c.8431delG						.						29.0	31.0	31.0					2																	220354172		1885	4089	5974	SO:0001589	frameshift_variant	10290	exon36			.	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.8432delC	chr2.hg19:g.220354172delC	ENSP00000311684:p.Ala2811fs	154.0	0.0		205.0	13.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Frame_Shift_Del	DEL	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.		0.672	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
TRUB1	142940	hgsc.bcm.edu	37	10	116698055	116698055	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:116698055delA	ENST00000298746.3	+	1	104	c.43delA	c.(43-45)aaafs	p.K15fs		NM_139169.4	NP_631908.1	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase family member 1	15					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(2)|kidney(2)|large_intestine(1)|lung(5)|urinary_tract(2)	12		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)		GCCGTCTTTGAAAACAGACAC	0.602																																					p.L14fs		Atlas-INDEL	.											.	TRUB1	30	.	0			c.42delG						.						48.0	47.0	48.0					10																	116698055		2203	4300	6503	SO:0001589	frameshift_variant	142940	exon1			.	AF448144	CCDS7591.1	10q25.3	2013-09-02	2013-09-02		ENSG00000165832	ENSG00000165832			16060	protein-coding gene	gene with protein product		610726	"""TruB pseudouridine (psi) synthase homolog 1 (E. coli)"""			12736709	Standard	NM_139169		Approved	PUS4	uc001lcd.3	Q8WWH5	OTTHUMG00000019094	ENST00000298746.3:c.43delA	chr10.hg19:g.116698055delA	ENSP00000298746:p.Lys15fs	175.0	0.0		186.0	14.0	NM_139169	B2R716|Q53ES2	Frame_Shift_Del	DEL	ENST00000298746.3	hg19	CCDS7591.1																																																																																			.	.		0.602	TRUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050504.1	NM_139169	
CPSF6	11052	hgsc.bcm.edu	37	12	69650513	69650513	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:69650513delA	ENST00000435070.2	+	4	521	c.411delA	c.(409-411)tcafs	p.S137fs	CPSF6_ENST00000551516.1_Intron|CPSF6_ENST00000456847.3_Frame_Shift_Del_p.S137fs|CPSF6_ENST00000266679.8_Frame_Shift_Del_p.S137fs	NM_007007.2	NP_008938.2	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6, 68kDa	137	Necessary for interaction with NUDT21/CPSF5.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(7)|lung(8)	16	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			AAGCATCTTCAAAAAAGTTAA	0.348																																					p.S137X		Atlas-INDEL	.											.	CPSF6	96	.	0			c.410delC						.						124.0	125.0	125.0					12																	69650513		2203	4300	6503	SO:0001589	frameshift_variant	11052	exon4			.	X67336	CCDS8988.1, CCDS73494.1	12q15	2013-06-18	2002-08-29			ENSG00000111605		"""RNA binding motif (RRM) containing"""	13871	protein-coding gene	gene with protein product	"""cleavage factor Im complex 68 kDa subunit"""	604979	"""cleavage and polyadenylation specific factor 6, 68kD subunit"""			9659921, 17267687	Standard	NM_007007		Approved	CFIM, HPBRII-4, HPBRII-7, CFIM68	uc001sut.4	Q16630		ENST00000435070.2:c.411delA	chr12.hg19:g.69650513delA	ENSP00000391774:p.Ser137fs	178.0	0.0		194.0	13.0	NM_007007	A8K7K9|Q53ES1|Q9BSJ7|Q9BW18	Frame_Shift_Del	DEL	ENST00000435070.2	hg19	CCDS8988.1																																																																																			.	.		0.348	CPSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403609.1	NM_007007	
IMMP1L	196294	hgsc.bcm.edu	37	11	31477911	31477911	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:31477911delT	ENST00000278200.1	-	5	412	c.217delA	c.(217-219)agcfs	p.S73fs	IMMP1L_ENST00000533642.1_Intron|IMMP1L_ENST00000528161.1_5'UTR|IMMP1L_ENST00000534812.1_Intron|IMMP1L_ENST00000532287.1_Frame_Shift_Del_p.S73fs|IMMP1L_ENST00000526776.1_Intron	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	73					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	serine-type peptidase activity (GO:0008236)			breast(1)|cervix(1)|large_intestine(1)|lung(4)	7	Lung SC(675;0.225)					TCACTTGGGCTTTTTGCAATC	0.348																																					p.S73fs		Atlas-INDEL	.											.	IMMP1L	16	.	0			c.218delG						.						57.0	54.0	55.0					11																	31477911		2202	4295	6497	SO:0001589	frameshift_variant	196294	exon5			.		CCDS7874.1	11p13	2014-07-30			ENSG00000148950	ENSG00000148950			26317	protein-coding gene	gene with protein product		612323					Standard	NM_144981		Approved	FLJ25059	uc001msy.1	Q96LU5	OTTHUMG00000166226	ENST00000278200.1:c.217delA	chr11.hg19:g.31477911delT	ENSP00000278200:p.Ser73fs	133.0	0.0		161.0	12.0	NM_144981	D3DQZ7|Q96SH9	Frame_Shift_Del	DEL	ENST00000278200.1	hg19	CCDS7874.1																																																																																			.	.		0.348	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981	
NR4A2	4929	hgsc.bcm.edu	37	2	157186374	157186374	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:157186374delG	ENST00000339562.4	-	3	687	c.325delC	c.(325-327)cagfs	p.Q109fs	NR4A2_ENST00000409108.2_Frame_Shift_Del_p.Q109fs|NR4A2_ENST00000409572.1_Frame_Shift_Del_p.Q109fs|NR4A2_ENST00000426264.1_Frame_Shift_Del_p.Q46fs|NR4A2_ENST00000539077.1_Frame_Shift_Del_p.Q120fs|NR4A2_ENST00000429376.1_Frame_Shift_Del_p.Q46fs	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	109	Gln-rich.				adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.Q109fs*3(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						TCCTCAGACTGGGGGGGCAGG	0.602																																					p.Q109fs		Atlas-INDEL	.											.,2	NR4A2	82	.	1	Insertion - Frameshift(1)	ovary(1)	c.326delA						.						83.0	83.0	83.0					2																	157186374		2203	4300	6503	SO:0001589	frameshift_variant	4929	exon3			.	X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"""Nuclear hormone receptors"""	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.325delC	chr2.hg19:g.157186374delG	ENSP00000344479:p.Gln109fs	143.0	0.0		172.0	11.0	NM_006186	Q16311|Q53RZ2|Q6NXU0	Frame_Shift_Del	DEL	ENST00000339562.4	hg19	CCDS2201.1																																																																																			.	.		0.602	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2		
KRT7	3855	hgsc.bcm.edu	37	12	52639299	52639299	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:52639299delG	ENST00000331817.5	+	7	1271	c.1088delG	c.(1087-1089)cggfs	p.R363fs	KRT7_ENST00000552322.1_3'UTR|RP3-416H24.1_ENST00000546686.1_RNA	NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	363	Coil 2.|Rod.				viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	GCCCTGCAGCGGGGCAAGCAG	0.647																																					p.R363fs		Atlas-INDEL	.											.	KRT7	48	.	0			c.1087delC						.						47.0	48.0	48.0					12																	52639299		2203	4300	6503	SO:0001589	frameshift_variant	3855	exon7			.		CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6445	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 7"", ""cytokeratin 7"", ""sarcolectin"", ""keratin, 55K type II cytoskeletal"""	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.1088delG	chr12.hg19:g.52639299delG	ENSP00000329243:p.Arg363fs	106.0	0.0		127.0	13.0	NM_005556	Q92676|Q9BUD8|Q9Y3R7	Frame_Shift_Del	DEL	ENST00000331817.5	hg19	CCDS8822.1																																																																																			.	.		0.647	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556	
EIF4G1	1981	hgsc.bcm.edu	37	3	184040193	184040193	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:184040193delA	ENST00000346169.2	+	11	1834	c.1563delA	c.(1561-1563)ctafs	p.L521fs	EIF4G1_ENST00000424196.1_Frame_Shift_Del_p.L528fs|EIF4G1_ENST00000392537.2_Frame_Shift_Del_p.L434fs|EIF4G1_ENST00000382330.3_Frame_Shift_Del_p.L528fs|EIF4G1_ENST00000342981.4_Frame_Shift_Del_p.L521fs|EIF4G1_ENST00000434061.2_Frame_Shift_Del_p.L325fs|EIF4G1_ENST00000414031.1_Frame_Shift_Del_p.L481fs|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000427845.1_Frame_Shift_Del_p.L434fs|EIF4G1_ENST00000435046.2_Frame_Shift_Del_p.L325fs|EIF4G1_ENST00000350481.5_Frame_Shift_Del_p.L357fs|EIF4G1_ENST00000319274.6_Frame_Shift_Del_p.L521fs|EIF4G1_ENST00000352767.3_Frame_Shift_Del_p.L528fs|EIF4G1_ENST00000441154.1_Frame_Shift_Del_p.L357fs|EIF4G1_ENST00000411531.1_Frame_Shift_Del_p.L481fs	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	521					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TTAAGGAGCTAAATAAGAAGG	0.433																																					p.L528fs		Atlas-INDEL	.											.	EIF4G1	151	.	0			c.1583delT						.						63.0	60.0	61.0					3																	184040193		2203	4300	6503	SO:0001589	frameshift_variant	1981	exon11			.	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.1563delA	chr3.hg19:g.184040193delA	ENSP00000316879:p.Leu521fs	114.0	0.0		183.0	16.0	NM_001194947	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Frame_Shift_Del	DEL	ENST00000346169.2	hg19	CCDS3259.1																																																																																			.	.		0.433	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
SLC1A4	6509	hgsc.bcm.edu	37	2	65237733	65237733	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:65237733delC	ENST00000234256.3	+	4	879	c.636delC	c.(634-636)atcfs	p.I212fs	SLC1A4_ENST00000493121.1_3'UTR|SLC1A4_ENST00000531327.1_5'UTR	NM_003038.4	NP_003029.2	P43007	SATT_HUMAN	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	212					amino acid transport (GO:0006865)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cognition (GO:0050890)|glutamine transport (GO:0006868)|hydroxyproline transport (GO:0034589)|ion transport (GO:0006811)|L-alanine transport (GO:0015808)|L-cystine transport (GO:0015811)|L-serine transport (GO:0015825)|proline transmembrane transport (GO:0035524)|proline transport (GO:0015824)|synaptic transmission, glutamatergic (GO:0035249)|threonine transport (GO:0015826)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|centrosome (GO:0005813)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament (GO:0005882)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|L-alanine transmembrane transporter activity (GO:0015180)|L-cystine transmembrane transporter activity (GO:0015184)|L-glutamine transmembrane transporter activity (GO:0015186)|L-hydroxyproline transmembrane transporter activity (GO:0034590)|L-proline transmembrane transporter activity (GO:0015193)|L-serine transmembrane transporter activity (GO:0015194)|L-threonine transmembrane transporter activity (GO:0015195)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|urinary_tract(1)	13					L-Alanine(DB00160)	TCCTGCAGATCCCCATAGGCA	0.448																																					p.I212fs		Atlas-INDEL	.											.	SLC1A4	33	.	0			c.635delT						.						161.0	153.0	155.0					2																	65237733		2203	4300	6503	SO:0001589	frameshift_variant	6509	exon4			.		CCDS1879.1, CCDS54362.1	2p15-p13	2013-05-22			ENSG00000115902	ENSG00000115902		"""Solute carriers"""	10942	protein-coding gene	gene with protein product	"""alanine/serine/cysteine/threonine transporter"""	600229				7896285, 8910405	Standard	NM_003038		Approved	SATT, ASCT1	uc010yqa.2	P43007	OTTHUMG00000129537	ENST00000234256.3:c.636delC	chr2.hg19:g.65237733delC	ENSP00000234256:p.Ile212fs	161.0	0.0		164.0	10.0	NM_003038	B7Z3C0|D6W5F0	Frame_Shift_Del	DEL	ENST00000234256.3	hg19	CCDS1879.1																																																																																			.	.		0.448	SLC1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251726.2	NM_003038	
XPOT	11260	hgsc.bcm.edu	37	12	64827209	64827209	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:64827209delT	ENST00000332707.5	+	19	2807	c.2278delT	c.(2278-2280)tttfs	p.F760fs		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	760	Necessary for tRNA-binding, cytoplasmic localization and nuclear export.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		GGTATCCCCGTTTTTACAACA	0.363																																					p.P759fs		Atlas-INDEL	.											.	XPOT	105	.	0			c.2277delG						.						133.0	131.0	132.0					12																	64827209		2203	4300	6503	SO:0001589	frameshift_variant	11260	exon19			.	AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"""Exportins"""	12826	protein-coding gene	gene with protein product		603180	"""exportin, tRNA (nuclear export receptor for tRNAs)"""			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.2278delT	chr12.hg19:g.64827209delT	ENSP00000327821:p.Phe760fs	128.0	0.0		138.0	12.0	NM_007235	A6NLH1|O43784|Q8WUG2|Q9BVS7	Frame_Shift_Del	DEL	ENST00000332707.5	hg19	CCDS31852.1																																																																																			.	.		0.363	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235	
URGCP	55665	hgsc.bcm.edu	37	7	43916637	43916637	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:43916637delT	ENST00000453200.1	-	6	2918	c.2425delA	c.(2425-2427)acgfs	p.T809fs	URGCP_ENST00000443736.1_Frame_Shift_Del_p.T766fs|URGCP_ENST00000497914.1_5'UTR|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000447717.3_Frame_Shift_Del_p.T766fs|URGCP_ENST00000223341.7_Frame_Shift_Del_p.T766fs|URGCP_ENST00000402306.3_Frame_Shift_Del_p.T800fs|URGCP_ENST00000336086.6_Frame_Shift_Del_p.T766fs			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	809	VLIG-type G.				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						ATGTGCCCCGTTTTTTCTAAC	0.502																																					p.T809fs		Atlas-INDEL	.											.	URGCP	170	.	0			c.2426delC						.						112.0	107.0	109.0					7																	43916637		1955	4143	6098	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.2425delA	chr7.hg19:g.43916637delT	ENSP00000396918:p.Thr809fs	103.0	0.0		196.0	12.0	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Frame_Shift_Del	DEL	ENST00000453200.1	hg19	CCDS47578.1																																																																																			.	.		0.502	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664	
TSPAN19	144448	hgsc.bcm.edu	37	12	85411267	85411267	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:85411267delA	ENST00000532498.2	-	7	642	c.562delT	c.(562-564)tgtfs	p.C188fs	TSPAN19_ENST00000547403.2_5'Flank	NM_001100917.1	NP_001094387.1	P0C672	TSN19_HUMAN	tetraspanin 19	188						integral component of membrane (GO:0016021)				ovary(1)	1						GGCTCATCACAAAACCATTTT	0.328																																					p.C188fs		Atlas-INDEL	.											.	TSPAN19	23	.	0			c.563delG						.						92.0	87.0	88.0					12																	85411267		1843	4092	5935	SO:0001589	frameshift_variant	144448	exon7			.		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.562delT	chr12.hg19:g.85411267delA	ENSP00000433816:p.Cys188fs	123.0	0.0		139.0	11.0	NM_001100917		Frame_Shift_Del	DEL	ENST00000532498.2	hg19	CCDS44949.1																																																																																			.	.		0.328	TSPAN19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388240.2	NM_001100917	
GPN3	51184	hgsc.bcm.edu	37	12	110895351	110895351	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:110895351delA	ENST00000228827.3	-	4	476	c.414delT	c.(412-414)tttfs	p.F138fs	GPN3_ENST00000543199.1_Frame_Shift_Del_p.F177fs|GPN3_ENST00000552180.1_5'Flank|GPN3_ENST00000537466.2_Frame_Shift_Del_p.F148fs	NM_016301.3	NP_057385.3			GPN-loop GTPase 3											endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|urinary_tract(1)	8						AATCAACAAGAAAAACTCCAC	0.403																																					p.L178fs		Atlas-INDEL	.											.	GPN3	37	.	0			c.532delC						.						56.0	52.0	53.0					12																	110895351		2203	4300	6503	SO:0001589	frameshift_variant	51184	exon4			.	BC008416	CCDS9147.1, CCDS53830.1, CCDS53831.1	12q24.11	2012-12-18	2008-04-30	2008-04-30	ENSG00000111231	ENSG00000111231		"""GPN-loop GTPases"""	30186	protein-coding gene	gene with protein product			"""ATP binding domain 1 family, member C"""	ATPBD1C		12975309	Standard	NM_016301		Approved	MGC14560	uc021rdu.1	Q9UHW5	OTTHUMG00000169524	ENST00000228827.3:c.414delT	chr12.hg19:g.110895351delA	ENSP00000228827:p.Phe138fs	129.0	0.0		194.0	13.0	NM_001164372		Frame_Shift_Del	DEL	ENST00000228827.3	hg19	CCDS9147.1																																																																																			.	.		0.403	GPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404607.1	NM_016301	
TAF1B	9014	hgsc.bcm.edu	37	2	9994472	9994472	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:9994472delT	ENST00000263663.5	+	5	509	c.321delT	c.(319-321)aatfs	p.N107fs	TAF1B_ENST00000396242.3_5'UTR|TAF1B_ENST00000402170.1_3'UTR	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	107	N-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)					TTTTACATAATTTTTGGAAGC	0.423																																					p.N107fs		Atlas-INDEL	.											.	TAF1B	62	.	0			c.320delA						.						135.0	129.0	131.0					2																	9994472		2203	4300	6503	SO:0001589	frameshift_variant	9014	exon5			.	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.321delT	chr2.hg19:g.9994472delT	ENSP00000263663:p.Asn107fs	151.0	0.0		163.0	10.0	NM_005680	B4DI42|F8WD72|Q15574|Q8WVC3	Frame_Shift_Del	DEL	ENST00000263663.5	hg19	CCDS33143.1																																																																																			.	.		0.423	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680	
PCNXL4	64430	hgsc.bcm.edu	37	14	60592492	60592492	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:60592492delT	ENST00000406854.1	+	10	3772	c.3218delT	c.(3217-3219)attfs	p.I1073fs	PCNXL4_ENST00000317623.4_Frame_Shift_Del_p.I839fs|PCNXL4_ENST00000406949.1_Frame_Shift_Del_p.I839fs|PCNXL4_ENST00000535349.1_Frame_Shift_Del_p.I280fs|PCNXL4_ENST00000404681.2_Frame_Shift_Del_p.I1073fs			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	1073						integral component of membrane (GO:0016021)											AAGGAAGCAATTTTACAAGAA	0.323																																					p.I839fs		Atlas-INDEL	.											.	.	.	.	0			c.2515delA						.						67.0	70.0	69.0					14																	60592492		2203	4300	6503	SO:0001589	frameshift_variant	64430	exon9			.	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.3218delT	chr14.hg19:g.60592492delT	ENSP00000384801:p.Ile1073fs	98.0	0.0		115.0	10.0	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Frame_Shift_Del	DEL	ENST00000406854.1	hg19																																																																																				.	.		0.323	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
IFT80	57560	hgsc.bcm.edu	37	3	160037585	160037585	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:160037585delT	ENST00000326448.7	-	9	1352	c.920delA	c.(919-921)aatfs	p.N307fs	IFT80_ENST00000483465.1_Frame_Shift_Del_p.N170fs|IFT80_ENST00000496589.1_Frame_Shift_Del_p.N170fs|RP11-432B6.3_ENST00000483754.1_Frame_Shift_Del_p.N478fs	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	307					bone morphogenesis (GO:0060349)|chondrocyte differentiation (GO:0002062)|cilium assembly (GO:0042384)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|osteoblast differentiation (GO:0001649)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(12)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TACTTGAAAATTTTTCCACTC	0.378																																					p.N307fs		Atlas-INDEL	.											.	IFT80	68	.	0			c.921delT						.						129.0	127.0	128.0					3																	160037585		2203	4300	6503	SO:0001589	frameshift_variant	57560	exon9			.	AB037795	CCDS3188.1, CCDS54668.1	3q25.33	2014-07-03	2014-07-03	2005-11-02	ENSG00000068885	ENSG00000068885		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29262	protein-coding gene	gene with protein product		611177	"""WD repeat domain 56"", ""intraflagellar transport 80 homolog (Chlamydomonas)"""	WDR56		10718198	Standard	NM_020800		Approved	KIAA1374	uc021xgq.1	Q9P2H3	OTTHUMG00000158953	ENST00000326448.7:c.920delA	chr3.hg19:g.160037585delT	ENSP00000312778:p.Asn307fs	127.0	0.0		162.0	10.0	NM_020800	B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	Frame_Shift_Del	DEL	ENST00000326448.7	hg19	CCDS3188.1																																																																																			.	.		0.378	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	NM_020800	
SYNE2	23224	hgsc.bcm.edu	37	14	64593150	64593150	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:64593150delC	ENST00000344113.4	+	72	13872	c.13660delC	c.(13660-13662)cccfs	p.P4554fs	SYNE2_ENST00000554584.1_Frame_Shift_Del_p.P4505fs|SYNE2_ENST00000555002.1_Frame_Shift_Del_p.P1188fs|SYNE2_ENST00000357395.3_Frame_Shift_Del_p.P939fs|SYNE2_ENST00000358025.3_Frame_Shift_Del_p.P4554fs|SYNE2_ENST00000394768.2_Frame_Shift_Del_p.P939fs|ESR2_ENST00000542956.1_Intron	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4554					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GCTGGAGATGCCCAGACTTTA	0.498																																					p.M4553fs		Atlas-INDEL	.											.	SYNE2	577	.	0			c.13659delG						.						95.0	92.0	93.0					14																	64593150		2203	4300	6503	SO:0001589	frameshift_variant	23224	exon72			.	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.13660delC	chr14.hg19:g.64593150delC	ENSP00000341781:p.Pro4554fs	165.0	0.0		201.0	13.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Frame_Shift_Del	DEL	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.498	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
EFHB	151651	hgsc.bcm.edu	37	3	19924173	19924173	+	Frame_Shift_Del	DEL	G	G	-	rs370616437		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:19924173delG	ENST00000295824.9	-	12	2358	c.2197delC	c.(2197-2199)cgafs	p.R733fs	EFHB_ENST00000344838.4_Frame_Shift_Del_p.R603fs	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	733							calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						CGACGAATTCGGGGAGCAGGA	0.423																																					p.R733fs		Atlas-INDEL	.											EFHB_ENST00000295824,NS,carcinoma,0,4	EFHB	186	.	0			c.2198delG						.						97.0	80.0	85.0					3																	19924173		2203	4300	6503	SO:0001589	frameshift_variant	151651	exon12			.	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"""EF-hand domain containing"""	26330	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 21"""					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.2197delC	chr3.hg19:g.19924173delG	ENSP00000295824:p.Arg733fs	91.0	0.0		144.0	10.0	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Frame_Shift_Del	DEL	ENST00000295824.9	hg19	CCDS33715.2																																																																																			.	.		0.423	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	
L3MBTL3	84456	hgsc.bcm.edu	37	6	130425608	130425608	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:130425608delA	ENST00000529410.1	+	21	2253	c.1774delA	c.(1774-1776)aaafs	p.K592fs	L3MBTL3_ENST00000361794.2_Frame_Shift_Del_p.K592fs|L3MBTL3_ENST00000526019.1_Frame_Shift_Del_p.K567fs|L3MBTL3_ENST00000533560.1_Frame_Shift_Del_p.K567fs|L3MBTL3_ENST00000368139.2_Frame_Shift_Del_p.K567fs|L3MBTL3_ENST00000368136.2_Frame_Shift_Del_p.K592fs			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	592					chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		CAATTTGAATAAAGACCGTAT	0.373																																					p.N591fs		Atlas-INDEL	.											.	L3MBTL3	99	.	0			c.1773delT						.						96.0	98.0	97.0					6																	130425608		2202	4300	6502	SO:0001589	frameshift_variant	84456	exon19			.	AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"""Sterile alpha motif (SAM) domain containing"""	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.1774delA	chr6.hg19:g.130425608delA	ENSP00000431962:p.Lys592fs	156.0	0.0		194.0	13.0	NM_032438	Q4VXE1|Q5VUM9|Q6P9B5	Frame_Shift_Del	DEL	ENST00000529410.1	hg19	CCDS34537.1																																																																																			.	.		0.373	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042195.2	XM_027074	
UBE3D	90025	hgsc.bcm.edu	37	6	83733743	83733743	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:83733743delA	ENST00000369747.3	-	6	804	c.682delT	c.(682-684)tatfs	p.Y228fs		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	228					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)										TCTGTCATATAAAACTTGGTG	0.284																																					p.Y228fs		Atlas-INDEL	.											.	.	.	.	0			c.683delA						.						38.0	43.0	41.0					6																	83733743		2199	4279	6478	SO:0001589	frameshift_variant	90025	exon6			.	AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"""UBCH10 binding protein with a hect-like domain"""	612495	"""chromosome 6 open reading frame 157"", ""ubiquitin-conjugating enzyme E2C binding protein"""	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.682delT	chr6.hg19:g.83733743delA	ENSP00000358762:p.Tyr228fs	147.0	0.0		215.0	15.0	NM_198920	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Frame_Shift_Del	DEL	ENST00000369747.3	hg19	CCDS34491.1																																																																																			.	.		0.284	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920	
PLEKHO1	51177	hgsc.bcm.edu	37	1	150131502	150131502	+	Frame_Shift_Del	DEL	C	C	-	rs587674656		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:150131502delC	ENST00000369124.4	+	6	1292	c.1014delC	c.(1012-1014)gacfs	p.D338fs	PLEKHO1_ENST00000025469.6_Frame_Shift_Del_p.D304fs|PLEKHO1_ENST00000369126.1_Frame_Shift_Del_p.D155fs	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	338	Negative regulator of AP-1 activity.					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)			AGGCCAAGGACCCCCCTCGGT	0.607																																					p.D338fs		Atlas-INDEL	.											.	PLEKHO1	37	.	0			c.1013delA						.						52.0	57.0	56.0					1																	150131502		2203	4300	6503	SO:0001589	frameshift_variant	51177	exon6			.	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.1014delC	chr1.hg19:g.150131502delC	ENSP00000358120:p.Asp338fs	126.0	0.0		233.0	16.0	NM_016274	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Frame_Shift_Del	DEL	ENST00000369124.4	hg19	CCDS945.1																																																																																			.	.		0.607	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274	
TMPRSS15	5651	hgsc.bcm.edu	37	21	19725327	19725327	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:19725327delA	ENST00000284885.3	-	10	1097	c.1064delT	c.(1063-1065)ttcfs	p.F355fs		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	355	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CTGGACCCAGAAACAAAAGCC	0.333																																					p.F355fs		Atlas-INDEL	.											.	TMPRSS15	189	.	0			c.1065delC						.						80.0	85.0	83.0					21																	19725327		2203	4299	6502	SO:0001589	frameshift_variant	5651	exon10			.		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1064delT	chr21.hg19:g.19725327delA	ENSP00000284885:p.Phe355fs	176.0	0.0		176.0	11.0	NM_002772	Q2NKL7	Frame_Shift_Del	DEL	ENST00000284885.3	hg19	CCDS13571.1																																																																																			.	.		0.333	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266867	41266867	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:41266867delA	ENST00000349496.5	+	5	818	c.538delA	c.(538-540)aaafs	p.K181fs	CTNNB1_ENST00000396185.3_Frame_Shift_Del_p.K181fs|CTNNB1_ENST00000396183.3_Frame_Shift_Del_p.K181fs|CTNNB1_ENST00000453024.1_Frame_Shift_Del_p.K174fs|CTNNB1_ENST00000405570.1_Frame_Shift_Del_p.K181fs	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	181					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)		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)		TCAGCTTTCTAAAAAGGAAGC	0.418		15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												p.S179fs	Colon(6;3 56 14213 18255)	Atlas-INDEL	.		Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	.	CTNNB1	4904	.	0			c.537delT						.						65.0	67.0	66.0					3																	41266867		2203	4300	6503	SO:0001589	frameshift_variant	1499	exon5	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	.	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.538delA	chr3.hg19:g.41266867delA	ENSP00000344456:p.Lys181fs	122.0	0.0		182.0	12.0	NM_001098210	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Frame_Shift_Del	DEL	ENST00000349496.5	hg19	CCDS2694.1																																																																																			.	.		0.418	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
MYH11	4629	hgsc.bcm.edu	37	16	15876271	15876271	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:15876271delT	ENST00000300036.5	-	6	806	c.697delA	c.(697-699)acafs	p.T233fs	MYH11_ENST00000576790.2_Frame_Shift_Del_p.T233fs|MYH11_ENST00000452625.2_Frame_Shift_Del_p.T240fs|MYH11_ENST00000396324.3_Frame_Shift_Del_p.T240fs	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	233	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TTCTTCACTGTTTTGGCGTTG	0.463			T	CBFB	AML																																p.T240fs		Atlas-INDEL	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.719delC						.						171.0	155.0	160.0					16																	15876271		2197	4300	6497	SO:0001589	frameshift_variant	4629	exon7			.	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.697delA	chr16.hg19:g.15876271delT	ENSP00000300036:p.Thr233fs	146.0	0.0		142.0	11.0	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Frame_Shift_Del	DEL	ENST00000300036.5	hg19	CCDS10565.1																																																																																			.	.		0.463	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
STT3B	201595	hgsc.bcm.edu	37	3	31656646	31656646	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:31656646delT	ENST00000295770.2	+	6	1136	c.927delT	c.(925-927)cctfs	p.P309fs	STT3B_ENST00000453168.1_3'UTR	NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	309					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						TGCAGATACCTTTTGTGGGAT	0.338																																					p.P309fs		Atlas-INDEL	.											.	STT3B	52	.	0			c.926delC						.						105.0	100.0	102.0					3																	31656646		2203	4299	6502	SO:0001589	frameshift_variant	201595	exon6			.	AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"""source of immunodominant MHC associated peptides"", ""dolichyl-diphosphooligosaccharide protein glycotransferase"""	608605	"""STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"""			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.927delT	chr3.hg19:g.31656646delT	ENSP00000295770:p.Pro309fs	130.0	0.0		155.0	12.0	NM_178862	Q96JZ4|Q96KY7	Frame_Shift_Del	DEL	ENST00000295770.2	hg19	CCDS2650.1																																																																																			.	.		0.338	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862	
SLC9A6	10479	hgsc.bcm.edu	37	X	135080706	135080706	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:135080706delT	ENST00000370698.3	+	4	608	c.573delT	c.(571-573)tgtfs	p.C191fs	SLC9A6_ENST00000370701.1_Frame_Shift_Del_p.C171fs|SLC9A6_ENST00000370695.4_Frame_Shift_Del_p.C223fs	NM_006359.2	NP_006350.1	Q92581	SL9A6_HUMAN	solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6	191					axon extension (GO:0048675)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|dendrite extension (GO:0097484)|dendritic spine development (GO:0060996)|ion transport (GO:0006811)|neuron projection morphogenesis (GO:0048812)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon terminus (GO:0043679)|axonal spine (GO:0044308)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)	sodium:proton antiporter activity (GO:0015385)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(18)|ovary(2)|upper_aerodigestive_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CAATTTCTTGTTTCGTTATTG	0.274																																					p.C223fs		Atlas-INDEL	.											.	SLC9A6	64	.	0			c.668delG						.						65.0	66.0	66.0					X																	135080706		2202	4290	6492	SO:0001589	frameshift_variant	10479	exon4			.	AF030409	CCDS14654.1, CCDS44003.1, CCDS55504.1	Xq26.3	2013-05-22	2012-03-22		ENSG00000198689	ENSG00000198689		"""Solute carriers"""	11079	protein-coding gene	gene with protein product		300231	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 6"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 6"""			9507001	Standard	NM_001042537		Approved	NHE6, KIAA0267	uc004ezk.3	Q92581	OTTHUMG00000022498	ENST00000370698.3:c.573delT	chrX.hg19:g.135080706delT	ENSP00000359732:p.Cys191fs	138.0	0.0		154.0	11.0	NM_001042537	A6NIQ9|A8K160|B4DU30|B7ZAE0|Q3ZCW7|Q5JPP8|Q5JPP9|Q86VS0	Frame_Shift_Del	DEL	ENST00000370698.3	hg19	CCDS14654.1																																																																																			.	.		0.274	SLC9A6-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058450.1	NM_006359	
TTF2	8458	hgsc.bcm.edu	37	1	117618310	117618310	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:117618310delC	ENST00000369466.4	+	5	1148	c.1104delC	c.(1102-1104)agcfs	p.S368fs		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	368					ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		AGCCTGGGAGCCCCCTACTCT	0.527																																					p.S368fs		Atlas-INDEL	.											.	TTF2	92	.	0			c.1103delG						.			6,4260		2,2,2129	67.0	61.0	63.0			0.6	0.0	1		63	17,8237		7,3,4117	no	frameshift	TTF2	NM_003594.3		9,5,6246	A1A1,A1R,RR		0.206,0.1406,0.1837			117618310	23,12497	2203	4300	6503	SO:0001589	frameshift_variant	8458	exon5			.	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 6"""	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.1104delC	chr1.hg19:g.117618310delC	ENSP00000358478:p.Ser368fs	191.0	0.0		382.0	23.0	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Frame_Shift_Del	DEL	ENST00000369466.4	hg19	CCDS892.1																																																																																			.	.		0.527	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3		
SLCO1B1	10599	hgsc.bcm.edu	37	12	21375253	21375253	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	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	165.0	0.0		140.0	10.0	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	
SLC37A1	54020	hgsc.bcm.edu	37	21	43945906	43945906	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr21:43945906delT	ENST00000352133.2	+	3	1059	c.77delT	c.(76-78)attfs	p.I26fs	SLC37A1_ENST00000398341.3_Frame_Shift_Del_p.I26fs			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	26					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						TTCATTTTTATTTTGACATTT	0.378																																					p.I26fs		Atlas-INDEL	.											.	SLC37A1	48	.	0			c.76delA						.						155.0	136.0	143.0					21																	43945906		2203	4300	6503	SO:0001589	frameshift_variant	54020	exon4			.	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.77delT	chr21.hg19:g.43945906delT	ENSP00000344648:p.Ile26fs	169.0	0.0		161.0	11.0	NM_018964	D3DSJ7|Q9HAQ1	Frame_Shift_Del	DEL	ENST00000352133.2	hg19	CCDS13689.1																																																																																			.	.		0.378	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		
CUEDC1	404093	hgsc.bcm.edu	37	17	55945607	55945607	+	Intron	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:55945607delG	ENST00000577830.1	-	8	1354				CUEDC1_ENST00000407144.2_Intron|CUEDC1_ENST00000577840.1_Intron|CUEDC1_ENST00000360238.2_Intron|CUEDC1_ENST00000578357.1_Intron	NM_001271875.1	NP_001258804.1	Q9NWM3	CUED1_HUMAN	CUE domain containing 1											endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12						CCGGGTGGCTGGGGGCAGAGA	0.562																																					.		Atlas-INDEL	.											.	CUEDC1	37	.	0			c.941-2C>-						.						89.0	75.0	80.0					17																	55945607		2203	4300	6503	SO:0001627	intron_variant	404093	exon9			.	AK000746	CCDS11599.1	17q23.2	2004-03-16				ENSG00000180891			31350	protein-coding gene	gene with protein product							Standard	NM_001271875		Approved		uc002ive.2	Q9NWM3		ENST00000577830.1:c.941-3C>-	chr17.hg19:g.55945607delG		117.0	0.0		145.0	10.0	NM_001271875	D3DTZ2|Q9NWD0	Splice_Site	DEL	ENST00000577830.1	hg19	CCDS11599.1																																																																																			.	.		0.562	CUEDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443305.1	NM_017949	
FIGNL1	63979	hgsc.bcm.edu	37	7	50514614	50514614	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:50514614delT	ENST00000419119.1	-	2	1925	c.372delA	c.(370-372)aaafs	p.K124fs	FIGNL1_ENST00000395556.2_Frame_Shift_Del_p.K124fs|FIGNL1_ENST00000433017.1_Frame_Shift_Del_p.K124fs|FIGNL1_ENST00000356889.4_Frame_Shift_Del_p.K124fs|FIGNL1_ENST00000435566.1_3'UTR			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	124					ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				AGTCTTTGAATTTTTTGCCAG	0.388																																					p.F125fs		Atlas-Indel,Pindel	.											.	FIGNL1	73	.	0			c.373delT						.						95.0	96.0	96.0					7																	50514614		2203	4300	6503	SO:0001589	frameshift_variant	63979	exon4			.	AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436		"""ATPases / AAA-type"""	13286	protein-coding gene	gene with protein product		615383					Standard	XM_005271783		Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.372delA	chr7.hg19:g.50514614delT	ENSP00000410811:p.Lys124fs	102.0	0.0		157.0	10.0	NM_022116	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Frame_Shift_Del	DEL	ENST00000419119.1	hg19	CCDS5510.1																																																																																			.	.		0.388	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762	
ANKLE2	23141	hgsc.bcm.edu	37	12	133312071	133312071	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:133312071delT	ENST00000357997.5	-	9	1710	c.1621delA	c.(1621-1623)actfs	p.T541fs	ANKLE2_ENST00000542374.1_5'Flank|ANKLE2_ENST00000337516.5_Frame_Shift_Del_p.T541fs|ANKLE2_ENST00000539605.1_Frame_Shift_Del_p.T479fs	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	541					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		CGAGGTGGAGTTTTCCAGAGC	0.522																																					p.T541fs		Atlas-INDEL	.											.	ANKLE2	76	.	0			c.1622delC						.						123.0	126.0	125.0					12																	133312071		1979	4169	6148	SO:0001589	frameshift_variant	23141	exon9			.	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"""Ankyrin repeat domain containing"""	29101	protein-coding gene	gene with protein product	"""LEM domain containing 7"""		"""KIAA0692"""	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.1621delA	chr12.hg19:g.133312071delT	ENSP00000350686:p.Thr541fs	118.0	0.0		178.0	11.0	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Frame_Shift_Del	DEL	ENST00000357997.5	hg19	CCDS41869.1																																																																																			.	.		0.522	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1		
PHF20	51230	hgsc.bcm.edu	37	20	34526859	34526859	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:34526859delT	ENST00000374012.3	+	16	2670	c.2541delT	c.(2539-2541)tatfs	p.Y848fs	PHF20_ENST00000439301.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	848					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					CCCGCGCCTATTACCCTGCCG	0.632																																					p.Y847fs		Atlas-INDEL	.											.	PHF20	94	.	0			c.2540delA						.						48.0	44.0	45.0					20																	34526859		2203	4300	6503	SO:0001589	frameshift_variant	51230	exon16			.	AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	16098	protein-coding gene	gene with protein product	"""tudor domain containing 20A"""	610335	"""chromosome 20 open reading frame 104"""	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.2541delT	chr20.hg19:g.34526859delT	ENSP00000363124:p.Tyr848fs	101.0	0.0		128.0	10.0	NM_016436	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Frame_Shift_Del	DEL	ENST00000374012.3	hg19	CCDS13268.1																																																																																			.	.		0.632	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436	
CSNK1A1	1452	hgsc.bcm.edu	37	5	148889476	148889476	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:148889476delT	ENST00000377843.2	-	7	1195	c.716delA	c.(715-717)aagfs	p.K240fs	CSNK1A1_ENST00000606299.1_5'UTR|CSNK1A1_ENST00000515435.1_Frame_Shift_Del_p.K179fs|CSNK1A1_ENST00000261798.5_Frame_Shift_Del_p.K240fs|CSNK1A1_ENST00000504676.1_Frame_Shift_Del_p.K151fs|CSNK1A1_ENST00000606719.1_Frame_Shift_Del_p.K37fs|CSNK1A1_ENST00000515768.1_Frame_Shift_Del_p.K268fs	NM_001025105.1|NM_001892.4	NP_001020276.1|NP_001883.4	P48729	KC1A_HUMAN	casein kinase 1, alpha 1	240	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(4)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		GGACATCTTCTTTTCACTAAT	0.333																																					p.K267fs	Colon(5;64 69 1309 10383)	Atlas-INDEL	.											.	CSNK1A1	63	.	0			c.801delG						.						111.0	107.0	109.0					5																	148889476		1973	4213	6186	SO:0001589	frameshift_variant	1452	exon8			.	AF119911	CCDS47303.1, CCDS47304.1, CCDS64291.1	5q32	2013-01-17			ENSG00000113712	ENSG00000113712			2451	protein-coding gene	gene with protein product	"""clock regulator kinase"""	600505				8050587	Standard	NM_001025105		Approved	CK1, CK1a, CK1alpha, CKIa, CKIalpha	uc003lqw.2	P48729	OTTHUMG00000163463	ENST00000377843.2:c.716delA	chr5.hg19:g.148889476delT	ENSP00000367074:p.Lys240fs	73.0	0.0		225.0	15.0	NM_001025105	D3DQG0|D3DQG1|Q4JJA0|Q5U046|Q5U047|Q6FGA2|Q71TU5|Q96HD2|Q9UDK3	Frame_Shift_Del	DEL	ENST00000377843.2	hg19	CCDS47303.1																																																																																			.	.		0.333	CSNK1A1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001892	
STT3B	201595	hgsc.bcm.edu	37	3	31665200	31665200	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:31665200delA	ENST00000295770.2	+	11	1783	c.1574delA	c.(1573-1575)gaafs	p.E525fs		NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	525					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						ACTGAACAGGAAAAAACTGAA	0.358																																					p.E525fs		Atlas-INDEL	.											.	STT3B	52	.	0			c.1573delG						.						166.0	144.0	152.0					3																	31665200		2203	4300	6503	SO:0001589	frameshift_variant	201595	exon11			.	AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"""source of immunodominant MHC associated peptides"", ""dolichyl-diphosphooligosaccharide protein glycotransferase"""	608605	"""STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"""			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.1574delA	chr3.hg19:g.31665200delA	ENSP00000295770:p.Glu525fs	133.0	0.0		156.0	10.0	NM_178862	Q96JZ4|Q96KY7	Frame_Shift_Del	DEL	ENST00000295770.2	hg19	CCDS2650.1																																																																																			.	.		0.358	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862	
NOVA2	4858	hgsc.bcm.edu	37	19	46464290	46464290	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:46464290delG	ENST00000263257.5	-	2	401	c.207delC	c.(205-207)tccfs	p.S69fs		NM_002516.2	NP_002507.1	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2	69	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of RNA metabolic process (GO:0051252)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(5)|lung(13)	21		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)		CTTTGGACTTGGAGAGCTTGA	0.652																																					p.K70fs		Atlas-INDEL	.											.	NOVA2	38	.	0			c.208delA						.						51.0	52.0	52.0					19																	46464290		2198	4296	6494	SO:0001589	frameshift_variant	4858	exon2			.	U70477	CCDS12679.1	19q13.3	2008-07-17				ENSG00000104967			7887	protein-coding gene	gene with protein product	"""neuro-oncological ventral antigen 3"""	601991		NOVA3		9344654, 10368286	Standard	NM_002516		Approved	ANOVA	uc002pdv.2	Q9UNW9		ENST00000263257.5:c.207delC	chr19.hg19:g.46464290delG	ENSP00000263257:p.Ser69fs	116.0	0.0		128.0	10.0	NM_002516	O43267|Q9UEA1	Frame_Shift_Del	DEL	ENST00000263257.5	hg19	CCDS12679.1																																																																																			.	.		0.652	NOVA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437210.2	NM_002516	
TULP1	7287	hgsc.bcm.edu	37	6	35473878	35473878	+	Frame_Shift_Del	DEL	G	G	-	rs201070350|rs62636292		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:35473878delG	ENST00000229771.6	-	10	980	c.901delC	c.(901-903)cagfs	p.Q301fs	TULP1_ENST00000322263.4_Frame_Shift_Del_p.Q248fs	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN	tubby like protein 1	301					dendrite development (GO:0016358)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|phagocytosis (GO:0006909)|photoreceptor cell maintenance (GO:0045494)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|retina development in camera-type eye (GO:0060041)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|synapse (GO:0045202)	actin filament binding (GO:0051015)|G-protein coupled photoreceptor activity (GO:0008020)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						GTGCGGCCCTGGGGGGCAGGC	0.667																																					p.Q301fs	GBM(55;1027 1091 11115 23439)	Atlas-INDEL	.											.	TULP1	51	.	0			c.902delA	GRCh37	CD004592	TULP1	D		.						39.0	45.0	43.0					6																	35473878		2202	4298	6500	SO:0001589	frameshift_variant	7287	exon10			.	U82468	CCDS4807.1, CCDS75436.1	6p21.3	2014-01-28			ENSG00000112041	ENSG00000112041			12423	protein-coding gene	gene with protein product		602280		RP14		9096357, 9521870	Standard	NM_003322		Approved	TUBL1, LCA15	uc003okv.4	O00294	OTTHUMG00000014575	ENST00000229771.6:c.901delC	chr6.hg19:g.35473878delG	ENSP00000229771:p.Gln301fs	36.0	0.0		83.0	11.0	NM_003322	O43536|Q5TGM5|Q8N571	Frame_Shift_Del	DEL	ENST00000229771.6	hg19	CCDS4807.1																																																																																			.	.		0.667	TULP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040307.2		
HAPLN1	1404	hgsc.bcm.edu	37	5	82948593	82948593	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:82948593delA	ENST00000274341.4	-	3	1001	c.151delT	c.(151-153)tcafs	p.S51fs	HAPLN1_ENST00000514416.1_Frame_Shift_Del_p.S51fs	NM_001884.3	NP_001875.1	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	51	Ig-like V-type.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|liver(1)|lung(15)|ovary(1)|prostate(1)|skin(1)	34		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)	Hyaluronan(DB08818)	CCTCTGTGTGAAAACACCTTG	0.373																																					p.S51fs		Atlas-INDEL	.											.	HAPLN1	79	.	0			c.152delC						.						56.0	56.0	56.0					5																	82948593		2203	4300	6503	SO:0001589	frameshift_variant	1404	exon3			.		CCDS4061.1	5q14.3	2013-01-11	2004-03-16	2004-03-17	ENSG00000145681	ENSG00000145681		"""Immunoglobulin superfamily / V-set domain containing"""	2380	protein-coding gene	gene with protein product	"""Cartilage link protein"", ""hyaluronan and proteoglycan link protein 1"""	115435	"""cartilage linking protein 1"""	CRTL1		2286376, 2320422	Standard	NM_001884		Approved		uc003kin.3	P10915	OTTHUMG00000119045	ENST00000274341.4:c.151delT	chr5.hg19:g.82948593delA	ENSP00000274341:p.Ser51fs	77.0	0.0		162.0	10.0	NM_001884	B2R9A9	Frame_Shift_Del	DEL	ENST00000274341.4	hg19	CCDS4061.1																																																																																			.	.		0.373	HAPLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239256.2	NM_001884	
KMT2A	4297	hgsc.bcm.edu	37	11	118347674	118347674	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:118347674delT	ENST00000389506.5	+	4	3311	c.3311delT	c.(3310-3312)attfs	p.I1104fs	KMT2A_ENST00000534358.1_Frame_Shift_Del_p.I1104fs|KMT2A_ENST00000354520.4_Frame_Shift_Del_p.I1104fs			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1104					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)										CGAGAAAAGATTTTGTCTTCC	0.478																																					p.I1104fs		Atlas-INDEL	.											.	MLL	548	.	0			c.3310delA						.						108.0	100.0	103.0					11																	118347674		2200	4296	6496	SO:0001589	frameshift_variant	4297	exon4			.	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.3311delT	chr11.hg19:g.118347674delT	ENSP00000374157:p.Ile1104fs	157.0	0.0		161.0	10.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Frame_Shift_Del	DEL	ENST00000389506.5	hg19	CCDS31686.1																																																																																			.	.		0.478	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
SEC24C	9632	hgsc.bcm.edu	37	10	75525560	75525560	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:75525560delC	ENST00000339365.2	+	11	1531	c.1369delC	c.(1369-1371)cccfs	p.P458fs	SEC24C_ENST00000411652.2_Frame_Shift_Del_p.P339fs|SEC24C_ENST00000546025.1_Intron|SEC24C_ENST00000345254.4_Frame_Shift_Del_p.P458fs|SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000535742.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	458					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					TCCCACAGTTCCCCCCCAGTA	0.507																																					p.V456fs		Atlas-INDEL	.											.,1	SEC24C	86	.	0			c.1368delT						.						195.0	176.0	182.0					10																	75525560		2203	4300	6503	SO:0001589	frameshift_variant	9632	exon11			.	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"""SEC24 (S. cerevisiae) related gene family, member C"", ""SEC24 family, member C (S. cerevisiae)"""			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.1369delC	chr10.hg19:g.75525560delC	ENSP00000343405:p.Pro458fs	184.0	0.0		173.0	12.0	NM_004922	B4DZT4|Q8WV25	Frame_Shift_Del	DEL	ENST00000339365.2	hg19	CCDS7332.1																																																																																			.	.		0.507	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1		
HECTD4	283450	hgsc.bcm.edu	37	12	112630422	112630422	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:112630422delG	ENST00000430131.2	-	58	9113	c.7968delC	c.(7966-7968)cccfs	p.P2656fs	HECTD4_ENST00000377560.5_Frame_Shift_Del_p.P2906fs|HECTD4_ENST00000550722.1_Frame_Shift_Del_p.P2932fs			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2656					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)										GGTCAGCGGTGGGGGGAGGTG	0.607																																					p.T2945fs		Atlas-INDEL	.											C12orf51_ENST00000377560,NS,carcinoma,0,2	.	.	.	0			c.8833delA						.						26.0	30.0	28.0					12																	112630422		2006	4160	6166	SO:0001589	frameshift_variant	283450	exon59			.	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.7968delC	chr12.hg19:g.112630422delG	ENSP00000404379:p.Pro2656fs	70.0	0.0		152.0	11.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Frame_Shift_Del	DEL	ENST00000430131.2	hg19																																																																																				.	.		0.607	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
RBBP8	5932	hgsc.bcm.edu	37	18	20573135	20573135	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:20573135delA	ENST00000399722.2	+	11	1696	c.1345delA	c.(1345-1347)aaafs	p.K449fs	RBBP8_ENST00000399725.2_Frame_Shift_Del_p.K449fs|RBBP8_ENST00000360790.5_Frame_Shift_Del_p.K449fs|RBBP8_ENST00000327155.5_Frame_Shift_Del_p.K449fs	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	449					blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			CAAAAGGAAGAAAACTGAGGA	0.403								Homologous recombination																													p.K448fs		Atlas-INDEL	.											.	RBBP8	138	.	0			c.1344delG						.						49.0	52.0	51.0					18																	20573135		2198	4298	6496	SO:0001589	frameshift_variant	5932	exon11			.	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"""CTBP-interacting protein"""	604124	"""retinoblastoma-binding protein 8"", ""Seckel syndrome 2"""	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.1345delA	chr18.hg19:g.20573135delA	ENSP00000382628:p.Lys449fs	150.0	0.0		136.0	10.0	NM_203292	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Frame_Shift_Del	DEL	ENST00000399722.2	hg19	CCDS11875.1																																																																																			.	.		0.403	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291	
ANKRD26	22852	hgsc.bcm.edu	37	10	27317833	27317833	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:27317833delT	ENST00000376087.4	-	27	4085	c.3920delA	c.(3919-3921)aagfs	p.K1307fs	ANKRD26_ENST00000436985.2_Frame_Shift_Del_p.K1323fs|ANKRD26_ENST00000376070.3_Frame_Shift_Del_p.K864fs	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1306					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						GTCCATTTGCTTTTTGACTGT	0.284																																					p.K1307fs		Atlas-INDEL	.											.	ANKRD26	179	.	0			c.3921delG						.						117.0	108.0	110.0					10																	27317833		1800	4060	5860	SO:0001589	frameshift_variant	22852	exon27			.	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.3920delA	chr10.hg19:g.27317833delT	ENSP00000365255:p.Lys1307fs	218.0	0.0		240.0	16.0	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Frame_Shift_Del	DEL	ENST00000376087.4	hg19	CCDS41499.1																																																																																			.	.		0.284	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		
EDA2R	60401	hgsc.bcm.edu	37	X	65822591	65822591	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:65822591delG	ENST00000374719.3	-	5	457	c.401delC	c.(400-402)cctfs	p.P134fs	EDA2R_ENST00000253392.5_Frame_Shift_Del_p.P134fs|EDA2R_ENST00000451436.2_Frame_Shift_Del_p.P40fs|EDA2R_ENST00000450752.1_Frame_Shift_Del_p.P134fs|EDA2R_ENST00000396050.1_Frame_Shift_Del_p.P134fs|EDA2R_ENST00000456230.2_Frame_Shift_Del_p.P134fs	NM_021783.3	NP_068555	Q9HAV5	TNR27_HUMAN	ectodysplasin A2 receptor	134					cell differentiation (GO:0030154)|embryo development (GO:0009790)|epidermis development (GO:0008544)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						GGCCTCCTGAGGGGGCACTGT	0.537																																					p.P134fs		Atlas-INDEL	.											.	EDA2R	30	.	0			c.402delT						.						50.0	35.0	40.0					X																	65822591		2203	4299	6502	SO:0001589	frameshift_variant	60401	exon4			.	AF298812	CCDS14386.1, CCDS56603.1	Xq11.1	2013-05-22			ENSG00000131080	ENSG00000131080		"""Tumor necrosis factor receptor superfamily"""	17756	protein-coding gene	gene with protein product		300276				11039935	Standard	NM_021783		Approved	XEDAR, EDA-A2R, EDAA2R, TNFRSF27	uc004dwt.2	Q9HAV5	OTTHUMG00000021736	ENST00000374719.3:c.401delC	chrX.hg19:g.65822591delG	ENSP00000363851:p.Pro134fs	109.0	0.0		155.0	12.0	NM_001242310	Q5VYX9|Q5VYY0|Q6UWM2|Q8IZA6	Frame_Shift_Del	DEL	ENST00000374719.3	hg19	CCDS14386.1																																																																																			.	.		0.537	EDA2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057002.1	NM_021783	
MUCL1	118430	hgsc.bcm.edu	37	12	55251994	55251994	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:55251994delG	ENST00000308796.6	+	4	287	c.241delG	c.(241-243)gggfs	p.G81fs	MUCL1_ENST00000547990.1_3'UTR|MUCL1_ENST00000546809.1_Frame_Shift_Del_p.G76fs	NM_058173.2	NP_477521.1	Q96DR8	MUCL1_HUMAN	mucin-like 1	81					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|membrane (GO:0016020)				breast(1)|kidney(1)|lung(1)	3						CAAATGGGTTGGGGATCTCCC	0.413																																					p.V80fs		Atlas-INDEL	.											.	MUCL1	11	.	0			c.240delT						.						172.0	163.0	166.0					12																	55251994		2203	4300	6503	SO:0001589	frameshift_variant	118430	exon4			.	AF414087	CCDS8885.1	12q13.2	2007-07-02							30588	protein-coding gene	gene with protein product	"""small breast epithelial mucin"""	610857				12019145	Standard	NM_058173		Approved	SBEM	uc001sgk.3	Q96DR8		ENST00000308796.6:c.241delG	chr12.hg19:g.55251994delG	ENSP00000311364:p.Gly81fs	179.0	0.0		196.0	12.0	NM_058173	Q0VG95|Q32ZB5	Frame_Shift_Del	DEL	ENST00000308796.6	hg19	CCDS8885.1																																																																																			.	.		0.413	MUCL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406062.1	NM_058173	
SMCR8	140775	hgsc.bcm.edu	37	17	18221365	18221365	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:18221365delC	ENST00000406438.3	+	1	2742	c.2262delC	c.(2260-2262)gtcfs	p.V754fs		NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	754						nucleus (GO:0005634)		p.V754V(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						CTATCTTTGTCCCCAGCTATG	0.532																																					p.V754fs		Atlas-INDEL	.											.	SMCR8	62	.	1	Substitution - coding silent(1)	lung(1)	c.2261delT						.						129.0	108.0	115.0					17																	18221365		2203	4300	6503	SO:0001589	frameshift_variant	140775	exon1			.	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.2262delC	chr17.hg19:g.18221365delC	ENSP00000385025:p.Val754fs	113.0	0.0		147.0	12.0	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Frame_Shift_Del	DEL	ENST00000406438.3	hg19	CCDS11195.2																																																																																			.	.		0.532	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
PYROXD1	79912	hgsc.bcm.edu	37	12	21605042	21605042	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:21605042delA	ENST00000240651.9	+	5	496	c.442delA	c.(442-444)aaafs	p.K148fs	PYROXD1_ENST00000545178.1_Intron|PYROXD1_ENST00000538582.1_Frame_Shift_Del_p.K77fs	NM_024854.3	NP_079130.2	Q8WU10	PYRD1_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 1	148							oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|soft_tissue(1)	18						TACTAAAGCTAAAAGAATAAT	0.264																																					p.A147fs		Atlas-INDEL	.											.	PYROXD1	38	.	0			c.441delT						.						31.0	34.0	33.0					12																	21605042		2197	4281	6478	SO:0001589	frameshift_variant	79912	exon5			.	AL832441	CCDS31755.1	12p12.1	2014-02-12			ENSG00000121350	ENSG00000121350			26162	protein-coding gene	gene with protein product						12477932	Standard	NM_024854		Approved	DKFZp762G094, FLJ22028	uc001rew.3	Q8WU10	OTTHUMG00000169129	ENST00000240651.9:c.442delA	chr12.hg19:g.21605042delA	ENSP00000240651:p.Lys148fs	230.0	0.0		156.0	11.0	NM_024854	A6NKI6|B3KWN8|Q9H6P1	Frame_Shift_Del	DEL	ENST00000240651.9	hg19	CCDS31755.1																																																																																			.	.		0.264	PYROXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402363.1	NM_024854	
TRIM46	80128	hgsc.bcm.edu	37	1	155156381	155156381	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:155156381delG	ENST00000334634.4	+	10	1995	c.1995delG	c.(1993-1995)tcgfs	p.S665fs	TRIM46_ENST00000392451.2_3'UTR|MUC1_ENST00000462215.1_5'Flank|RP11-201K10.3_ENST00000473363.2_Intron|TRIM46_ENST00000468878.1_3'UTR|TRIM46_ENST00000545012.1_Frame_Shift_Del_p.S539fs|TRIM46_ENST00000368382.1_Frame_Shift_Del_p.S642fs	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	665	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TGCTGGGGTCGGGGGCAAGCT	0.672																																					p.S665fs		Atlas-INDEL	.											.	TRIM46	79	.	0			c.1994delC						.						59.0	61.0	60.0					1																	155156381		2203	4300	6503	SO:0001589	frameshift_variant	80128	exon10			.		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19019	protein-coding gene	gene with protein product		600986	"""tripartite motif-containing 46"""				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.1995delG	chr1.hg19:g.155156381delG	ENSP00000334657:p.Ser665fs	78.0	0.0		133.0	11.0	NM_025058	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Frame_Shift_Del	DEL	ENST00000334634.4	hg19	CCDS1097.1																																																																																			.	.		0.672	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058	
NCKAP1	10787	hgsc.bcm.edu	37	2	183822266	183822266	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	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	162.0	0.0		152.0	10.0	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	
LIMK1	3984	hgsc.bcm.edu	37	7	73521482	73521482	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:73521482delG	ENST00000336180.2	+	8	1075	c.1024delG	c.(1024-1026)gggfs	p.G342fs	LIMK1_ENST00000418310.1_Frame_Shift_Del_p.G372fs|LIMK1_ENST00000538333.3_Frame_Shift_Del_p.G308fs	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	342	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	CCTCATCCACGGGGAGGTGCT	0.677																																					p.H341fs		Atlas-INDEL	.											LIMK1,NS,carcinoma,0,1	LIMK1	55	.	0			c.1023delC						.						49.0	48.0	49.0					7																	73521482		2203	4300	6503	SO:0001589	frameshift_variant	3984	exon8			.	D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.1024delG	chr7.hg19:g.73521482delG	ENSP00000336740:p.Gly342fs	151.0	0.0		169.0	11.0	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Frame_Shift_Del	DEL	ENST00000336180.2	hg19	CCDS5563.1																																																																																			.	.		0.677	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314	
WDR17	116966	hgsc.bcm.edu	37	4	177093632	177093632	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:177093632delA	ENST00000280190.4	+	26	3482	c.3326delA	c.(3325-3327)gaafs	p.E1109fs	WDR17_ENST00000508596.1_Frame_Shift_Del_p.E1070fs|WDR17_ENST00000393643.2_Frame_Shift_Del_p.E1085fs|WDR17_ENST00000507824.2_Frame_Shift_Del_p.E1084fs			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1109										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		CAAGAACCTGAAAAAGCCCTT	0.333																																					p.E1109fs		Atlas-INDEL	.											.	WDR17	198	.	0			c.3325delG						.						69.0	73.0	72.0					4																	177093632		2203	4300	6503	SO:0001589	frameshift_variant	116966	exon26			.	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"""WD repeat domain containing"""	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.3326delA	chr4.hg19:g.177093632delA	ENSP00000280190:p.Glu1109fs	204.0	0.0		195.0	15.0	NM_170710	E7EQX0|Q0QD35	Frame_Shift_Del	DEL	ENST00000280190.4	hg19	CCDS3825.1																																																																																			.	.		0.333	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		
PRICKLE2	166336	hgsc.bcm.edu	37	3	64085551	64085551	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:64085551delA	ENST00000295902.6	-	8	2296	c.1711delT	c.(1711-1713)tccfs	p.S571fs	PRICKLE2-AS1_ENST00000476308.1_RNA|PRICKLE2-AS1_ENST00000460946.1_RNA|RP11-129B22.1_ENST00000482609.1_RNA|PRICKLE2_ENST00000564377.1_Frame_Shift_Del_p.S627fs	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	571					establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		TCAGGCATGGAAAATCGGGAT	0.537																																					p.S571fs		Atlas-INDEL	.											.	PRICKLE2	88	.	0			c.1712delC						.						133.0	137.0	135.0					3																	64085551		2203	4300	6503	SO:0001589	frameshift_variant	166336	exon8			.	AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"""prickle-like 2 (Drosophila)"""			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.1711delT	chr3.hg19:g.64085551delA	ENSP00000295902:p.Ser571fs	99.0	0.0		137.0	10.0	NM_198859	Q0VF44	Frame_Shift_Del	DEL	ENST00000295902.6	hg19	CCDS2902.1																																																																																			.	.		0.537	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859	
FHOD3	80206	hgsc.bcm.edu	37	18	34205516	34205516	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:34205516delC	ENST00000359247.4	+	10	1000	c.1000delC	c.(1000-1002)cccfs	p.P335fs	FHOD3_ENST00000590592.1_Frame_Shift_Del_p.P335fs|FHOD3_ENST00000445677.1_Frame_Shift_Del_p.P335fs|FHOD3_ENST00000257209.4_Frame_Shift_Del_p.P335fs|FHOD3_ENST00000591635.1_Frame_Shift_Del_p.H8fs	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	335	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				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)		p.S336fs*138(1)		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)				CACGGAGCCACCCCCCAGTGG	0.677																																					p.P333fs		Atlas-INDEL	.											.	FHOD3	210	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.999delA						.						40.0	44.0	43.0					18																	34205516		2203	4299	6502	SO:0001589	frameshift_variant	80206	exon10			.	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.1000delC	chr18.hg19:g.34205516delC	ENSP00000352186:p.Pro335fs	105.0	0.0		144.0	10.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Frame_Shift_Del	DEL	ENST00000359247.4	hg19																																																																																				.	.		0.677	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114	
DNAH7	56171	hgsc.bcm.edu	37	2	196753679	196753679	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:196753679delA	ENST00000312428.6	-	32	5173	c.5073delT	c.(5071-5073)tttfs	p.F1691fs		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1691	AAA 2. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CTGGGCCATCAAAAATTAACC	0.368																																					p.D1692fs		Atlas-INDEL	.											.	DNAH7	512	.	0			c.5074delG						.						127.0	119.0	121.0					2																	196753679		1909	4135	6044	SO:0001589	frameshift_variant	56171	exon32			.	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.5073delT	chr2.hg19:g.196753679delA	ENSP00000311273:p.Phe1691fs	228.0	0.0		264.0	16.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Frame_Shift_Del	DEL	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.368	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
C1orf64	149563	hgsc.bcm.edu	37	1	16332618	16332618	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:16332618delC	ENST00000329454.2	+	2	355	c.287delC	c.(286-288)accfs	p.T96fs	RP11-5P18.5_ENST00000437156.1_RNA	NM_178840.2	NP_849162.1	Q8NEQ6	CA064_HUMAN	chromosome 1 open reading frame 64	96										breast(2)|endometrium(1)|lung(3)	6		Colorectal(325;0.000435)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;2.08e-05)|BRCA - Breast invasive adenocarcinoma(304;9.19e-05)|Kidney(64;0.000165)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0114)|READ - Rectum adenocarcinoma(331;0.0649)		ACTCGGGTGACCCCCATGGGT	0.652																																					p.T96fs		Atlas-INDEL	.											.	C1orf64	16	.	0			c.286delA						.						67.0	66.0	66.0					1																	16332618		2203	4300	6503	SO:0001589	frameshift_variant	149563	exon2			.	AK127425	CCDS166.1	1p36.13	2013-10-11			ENSG00000183888	ENSG00000183888			28339	protein-coding gene	gene with protein product	"""ER-related factor"""					22341523	Standard	NM_178840		Approved	MGC24047, ERRF	uc001axn.3	Q8NEQ6	OTTHUMG00000009523	ENST00000329454.2:c.287delC	chr1.hg19:g.16332618delC	ENSP00000332162:p.Thr96fs	104.0	0.0		148.0	10.0	NM_178840	B3KXI9	Frame_Shift_Del	DEL	ENST00000329454.2	hg19	CCDS166.1																																																																																			.	.		0.652	C1orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026317.1	NM_178840	
ZNF271	10778	hgsc.bcm.edu	37	18	32889109	32889109	+	RNA	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:32889109delA	ENST00000399070.3	+	0	3503					NR_024565.1|NR_024566.1		Q14591	ZN271_HUMAN	zinc finger protein 271						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(9)	12						CAGGATCTTTAAAAAAATTTT	0.303																																					.		Atlas-INDEL	.											.	ZNF271	16	.	0			.						.																																					10778	.			.	X78930		18q12.2	2013-04-03			ENSG00000257267	ENSG00000257267		"""Zinc fingers, C2H2-type"""	13065	other	unknown		604754				7865130, 11777961	Standard	NR_024565		Approved	HZF7, ZNFEB	uc002kyp.4	Q14591	OTTHUMG00000132563		chr18.hg19:g.32889109delA		175.0	0.0		179.0	11.0	.	B3KN34|Q96T29|Q9BSX2|Q9UN33|Q9Y5B7	RNA	DEL	ENST00000399070.3	hg19																																																																																				.	.		0.303	ZNF271-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255767.2	NR_024565	
ABCE1	6059	hgsc.bcm.edu	37	4	146033436	146033436	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:146033436delT	ENST00000296577.4	+	9	1271	c.756delT	c.(754-756)cgtfs	p.R252fs	ABCE1_ENST00000502803.1_Intron|OTUD4_ENST00000455611.2_Intron	NM_001040876.1|NM_002940.2	NP_001035809.1|NP_002931.2	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E (OABP), member 1	252	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				negative regulation of catalytic activity (GO:0043086)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|iron-sulfur cluster binding (GO:0051536)|ribonuclease inhibitor activity (GO:0008428)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|lung(5)|prostate(2)|skin(3)	18	all_hematologic(180;0.151)					TCAAGCAGCGTTTAAAGGCTG	0.313																																					p.R252fs		Atlas-INDEL	.											.	ABCE1	47	.	0			c.755delG						.						62.0	59.0	60.0					4																	146033436		2202	4300	6502	SO:0001589	frameshift_variant	6059	exon9			.	X74987	CCDS34071.1	4q31	2012-03-14			ENSG00000164163	ENSG00000164163		"""ATP binding cassette transporters / subfamily E"""	69	protein-coding gene	gene with protein product		601213		RNASEL1, RNASELI, RNS4I		7539425	Standard	NM_002940		Approved	RLI, OABP	uc003ijy.3	P61221	OTTHUMG00000161478	ENST00000296577.4:c.756delT	chr4.hg19:g.146033436delT	ENSP00000296577:p.Arg252fs	139.0	0.0		152.0	12.0	NM_002940	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Frame_Shift_Del	DEL	ENST00000296577.4	hg19	CCDS34071.1																																																																																			.	.		0.313	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940	
PRUNE2	158471	hgsc.bcm.edu	37	9	79318977	79318977	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:79318977delT	ENST00000376718.3	-	9	7675	c.7552delA	c.(7552-7554)acafs	p.T2518fs	PRUNE2_ENST00000428286.1_Frame_Shift_Del_p.T2159fs	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2518					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						GTAGGAATTGTTTTTTCTTCT	0.363																																					p.T2518fs		Atlas-INDEL	.											.	PRUNE2	331	.	0			c.7553delC						.						140.0	130.0	133.0					9																	79318977		1568	3582	5150	SO:0001589	frameshift_variant	158471	exon9			.	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.7552delA	chr9.hg19:g.79318977delT	ENSP00000365908:p.Thr2518fs	127.0	0.0		170.0	11.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Frame_Shift_Del	DEL	ENST00000376718.3	hg19	CCDS47982.1																																																																																			.	.		0.363	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
KIAA1598	57698	hgsc.bcm.edu	37	10	118728182	118728182	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:118728182delT	ENST00000355371.4	-	3	650	c.153delA	c.(151-153)aaafs	p.K51fs	KIAA1598_ENST00000497044.1_5'UTR|KIAA1598_ENST00000392901.4_5'UTR|KIAA1598_ENST00000392903.2_Frame_Shift_Del_p.K51fs|KIAA1598_ENST00000260777.10_Frame_Shift_Del_p.K51fs	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	51					axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)				endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		ATTCTTCCAGTTTTTTAACGG	0.313																																					p.L52fs		Atlas-INDEL	.											.	KIAA1598	74	.	0			c.154delC						.						132.0	118.0	123.0					10																	118728182		2200	4298	6498	SO:0001589	frameshift_variant	57698	exon3			.	BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164			29319	protein-coding gene	gene with protein product		611171				10997877, 17030985	Standard	NM_001127211		Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000355371.4:c.153delA	chr10.hg19:g.118728182delT	ENSP00000347532:p.Lys51fs	123.0	0.0		150.0	10.0	NM_001127211	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Frame_Shift_Del	DEL	ENST00000355371.4	hg19	CCDS44482.1																																																																																			.	.		0.313	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330	
ERAL1	26284	hgsc.bcm.edu	37	17	27182148	27182148	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:27182148delT	ENST00000254928.5	+	1	193	c.96delT	c.(94-96)cctfs	p.P32fs	ERAL1_ENST00000578001.1_3'UTR|FAM222B_ENST00000583953.1_5'Flank	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	115.0	0.0		175.0	11.0	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		
ELP3	55140	hgsc.bcm.edu	37	8	27995291	27995291	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:27995291delT	ENST00000256398.8	+	10	1360	c.983delT	c.(982-984)cttfs	p.L328fs	ELP3_ENST00000380353.4_Frame_Shift_Del_p.L236fs|ELP3_ENST00000537665.1_Frame_Shift_Del_p.L209fs|ELP3_ENST00000542181.1_Frame_Shift_Del_p.L199fs|ELP3_ENST00000524103.1_Frame_Shift_Del_p.L256fs|ELP3_ENST00000521015.1_Frame_Shift_Del_p.L314fs	NM_001284220.1|NM_001284226.1|NM_018091.5	NP_001271149.1|NP_001271155.1|NP_060561.3	Q9H9T3	ELP3_HUMAN	elongator acetyltransferase complex subunit 3	328					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	histone acetyltransferase activity (GO:0004402)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|phosphorylase kinase regulator activity (GO:0008607)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		GGGACCGGGCTTTATGAGCTT	0.483																																					p.L328fs		Atlas-INDEL	.											.	ELP3	36	.	0			c.982delC						.						111.0	110.0	110.0					8																	27995291		2203	4300	6503	SO:0001589	frameshift_variant	55140	exon10			.		CCDS6065.1, CCDS64860.1, CCDS64861.1, CCDS75717.1, CCDS75718.1	8p21.1	2012-08-14	2012-08-08		ENSG00000134014	ENSG00000134014		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Elongator acetyltransferase complex subunits"""	20696	protein-coding gene	gene with protein product		612722	"""elongation protein 3 homolog (S. cerevisiae)"""			11714725	Standard	NM_018091		Approved	FLJ10422, KAT9	uc003xgo.4	Q9H9T3	OTTHUMG00000102124	ENST00000256398.8:c.983delT	chr8.hg19:g.27995291delT	ENSP00000256398:p.Leu328fs	153.0	0.0		111.0	10.0	NM_018091	B4DE19|B4DIG1|E2QRI5|Q53G84|Q6AWB0|Q9BVF7|Q9NVZ1	Frame_Shift_Del	DEL	ENST00000256398.8	hg19	CCDS6065.1																																																																																			.	.		0.483	ELP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219963.2	NM_018091	
DNAH12	201625	hgsc.bcm.edu	37	3	57399487	57399487	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:57399487delA	ENST00000351747.2	-	39	6129	c.5949delT	c.(5947-5949)tttfs	p.F1983fs		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	1983	AAA 3. {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						GTCCACAGTCAAAAAACTGTC	0.294																																					p.D1984fs		Atlas-INDEL	.											.	DNAH12	182	.	0			c.5950delG						.						97.0	85.0	89.0					3																	57399487		692	1590	2282	SO:0001589	frameshift_variant	201625	exon39			.	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.5949delT	chr3.hg19:g.57399487delA	ENSP00000295937:p.Phe1983fs	192.0	0.0		270.0	20.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Frame_Shift_Del	DEL	ENST00000351747.2	hg19																																																																																				.	.		0.294	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
GDAP1L1	78997	hgsc.bcm.edu	37	20	42907863	42907863	+	Frame_Shift_Del	DEL	G	G	-	rs201609457		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:42907863delG	ENST00000342560.5	+	6	1115	c.1027delG	c.(1027-1029)gggfs	p.G343fs	GDAP1L1_ENST00000537864.1_Frame_Shift_Del_p.G151fs	NM_001256737.1|NM_024034.4	NP_001243666.1|NP_076939.3	Q96MZ0	GD1L1_HUMAN	ganglioside induced differentiation associated protein 1-like 1	343										endometrium(1)|large_intestine(5)|lung(10)|pancreas(1)|prostate(1)	18		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			ATCCTTCTTCGGGGCGTCCTT	0.587																																					p.F361fs		Atlas-INDEL	.											GDAP1L1,colon,carcinoma,0,1	GDAP1L1	36	.	0			c.1083delC						.						124.0	113.0	117.0					20																	42907863		2203	4300	6503	SO:0001589	frameshift_variant	78997	exon6			.		CCDS13328.1, CCDS74725.1, CCDS74726.1, CCDS74727.1	20q12	2012-02-09	2012-02-09		ENSG00000124194	ENSG00000124194			4213	protein-coding gene	gene with protein product							Standard	NM_024034		Approved		uc010zwl.3	Q96MZ0	OTTHUMG00000032530	ENST00000342560.5:c.1027delG	chr20.hg19:g.42907863delG	ENSP00000341782:p.Gly343fs	162.0	0.0		164.0	10.0	NM_001256737	B7Z621|Q5TE60|Q68CW7|Q9BQJ7|Q9BQV4|Q9BWJ4|Q9H3Y2|Q9H4G5	Frame_Shift_Del	DEL	ENST00000342560.5	hg19	CCDS13328.1																																																																																			.	.		0.587	GDAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079356.1	NM_024034	
PRUNE2	158471	hgsc.bcm.edu	37	9	79465566	79465566	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:79465566delC	ENST00000376718.3	-	3	280	c.157delG	c.(157-159)gttfs	p.V53fs	PRUNE2_ENST00000376713.3_Frame_Shift_Del_p.V53fs|PRUNE2_ENST00000428286.1_5'UTR	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	53					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						AAACACAGAACCCCTGGTGGA	0.403																																					p.V53fs		Atlas-INDEL	.											.	PRUNE2	331	.	0			c.158delT						.						102.0	106.0	105.0					9																	79465566		2203	4300	6503	SO:0001589	frameshift_variant	158471	exon3			.	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.157delG	chr9.hg19:g.79465566delC	ENSP00000365908:p.Val53fs	148.0	0.0		153.0	10.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Frame_Shift_Del	DEL	ENST00000376718.3	hg19	CCDS47982.1																																																																																			.	.		0.403	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
KIAA0355	9710	hgsc.bcm.edu	37	19	34832378	34832378	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:34832378delT	ENST00000299505.6	+	10	2412	c.1539delT	c.(1537-1539)gatfs	p.D513fs		NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	513										breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					AGATCTGTGATTTTGGCAACC	0.403																																					p.D513fs		Atlas-INDEL	.											.	KIAA0355	105	.	0			c.1538delA						.						76.0	79.0	78.0					19																	34832378		2203	4300	6503	SO:0001589	frameshift_variant	9710	exon10			.		CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.1539delT	chr19.hg19:g.34832378delT	ENSP00000299505:p.Asp513fs	152.0	0.0		178.0	12.0	NM_014686	Q2M3W4	Frame_Shift_Del	DEL	ENST00000299505.6	hg19	CCDS12436.1																																																																																			.	.		0.403	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686	
USP9X	8239	hgsc.bcm.edu	37	X	41069767	41069767	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:41069767delG	ENST00000324545.8	+	33	5654	c.5021delG	c.(5020-5022)tggfs	p.W1674fs	USP9X_ENST00000378308.2_Frame_Shift_Del_p.W1674fs	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1674	USP.				axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CTTAGGCTTTGGGGTGAGCCT	0.333																																					p.W1674fs	Ovarian(172;1807 2695 35459 49286)	Atlas-INDEL	.											.	USP9X	385	.	0			c.5020delT						.						113.0	107.0	109.0					X																	41069767		2164	4278	6442	SO:0001589	frameshift_variant	8239	exon33			.	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.5021delG	chrX.hg19:g.41069767delG	ENSP00000316357:p.Trp1674fs	145.0	0.0		148.0	11.0	NM_001039591	O75550|Q8WWT3|Q8WX12	Frame_Shift_Del	DEL	ENST00000324545.8	hg19	CCDS43930.1																																																																																			.	.		0.333	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652	
WDR64	128025	hgsc.bcm.edu	37	1	241875143	241875143	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:241875143delT	ENST00000366552.2	+	8	1191	c.984delT	c.(982-984)actfs	p.T328fs	WDR64_ENST00000437684.2_Frame_Shift_Del_p.T328fs	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	328										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GAGCCAACACTTTTTGCTACT	0.393																																					p.T328fs		Atlas-INDEL	.											.	WDR64	234	.	0			c.983delC						.						118.0	111.0	113.0					1																	241875143		2203	4300	6503	SO:0001589	frameshift_variant	128025	exon8			.	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"""WD repeat domain containing"""	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.984delT	chr1.hg19:g.241875143delT	ENSP00000355510:p.Thr328fs	92.0	0.0		194.0	15.0	NM_144625	B1ANT0|Q7Z573|Q96LY9	Frame_Shift_Del	DEL	ENST00000366552.2	hg19																																																																																				.	.		0.393	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625	
SNRPN	6638	hgsc.bcm.edu	37	15	25221497	25221497	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:25221497delG	ENST00000400100.1	+	9	1091	c.201delG	c.(199-201)ttgfs	p.L67fs	SNRPN_ENST00000554227.2_Frame_Shift_Del_p.L71fs|SNRPN_ENST00000400098.1_Frame_Shift_Del_p.L67fs|SNRPN_ENST00000444203.2_Frame_Shift_Del_p.L71fs|SNURF_ENST00000551312.2_Intron|SNURF_ENST00000338094.6_3'UTR|SNRPN_ENST00000577565.1_Frame_Shift_Del_p.L67fs|SNRPN_ENST00000400097.1_Frame_Shift_Del_p.L67fs|SNRPN_ENST00000346403.6_Frame_Shift_Del_p.L67fs|SNRPN_ENST00000390687.4_Frame_Shift_Del_p.L67fs	NM_022807.2	NP_073718.1	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N	67					response to hormone (GO:0009725)|RNA splicing (GO:0008380)	small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U2 snRNP (GO:0005686)	RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(14)|ovary(1)|skin(2)	24		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		AGCGGGTTTTGGGTCTGGTGT	0.453									Prader-Willi syndrome																												p.L67fs		Atlas-INDEL	.											.	SNRPN	58	.	0			c.200delT						.						94.0	99.0	97.0					15																	25221497		1909	4127	6036	SO:0001589	frameshift_variant	6638	exon9	Familial Cancer Database	Prader-Labhart-Willi syndrome	.	L80005	CCDS10017.1	15q11.2	2013-07-16			ENSG00000128739	ENSG00000128739			11164	protein-coding gene	gene with protein product	"""tissue-specific splicing protein"", ""SM protein N"", ""small nuclear ribonucleoprotein N"""	182279	"""Prader-Willi syndrome chromosome region"""	PWCR		1533223	Standard	NM_022805		Approved	SMN, SM-D, HCERN3, SNRNP-N, SNURF-SNRPN, RT-LI	uc001ywt.1	P63162	OTTHUMG00000129180	ENST00000400100.1:c.201delG	chr15.hg19:g.25221497delG	ENSP00000382972:p.Leu67fs	86.0	0.0		128.0	10.0	NM_022807	B3KVR1|P14648|P17135|Q0D2Q5	Frame_Shift_Del	DEL	ENST00000400100.1	hg19	CCDS10017.1																																																																																			.	.		0.453	SNRPN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413849.10	NM_003097	
SLFN12L	100506736	hgsc.bcm.edu	37	17	33806378	33806378	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:33806378delT	ENST00000260908.7	-	2	968	c.851delA	c.(850-852)aatfs	p.N284fs	SLFN12L_ENST00000449046.1_Frame_Shift_Del_p.N315fs|RP11-686D22.9_ENST00000587076.1_RNA|SLFN12L_ENST00000361112.4_Frame_Shift_Del_p.N313fs	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	284						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						CCCAATGGAATTTTTTGTTAC	0.353																																					p.N284fs		Atlas-INDEL	.											.	SLFN12L	140	.	0			c.852delT						.						126.0	104.0	110.0					17																	33806378		692	1591	2283	SO:0001589	frameshift_variant	100506736	exon2			.	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.851delA	chr17.hg19:g.33806378delT	ENSP00000437635:p.Asn284fs	140.0	0.0		157.0	10.0	NM_001195790	F5H6G3	Frame_Shift_Del	DEL	ENST00000260908.7	hg19	CCDS56026.1																																																																																			.	.		0.353	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206	
SNAPC1	6617	hgsc.bcm.edu	37	14	62245598	62245598	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:62245598delA	ENST00000216294.4	+	7	899	c.795delA	c.(793-795)atafs	p.I265fs	RP11-618G20.1_ENST00000555937.1_RNA	NM_003082.3	NP_003073.1	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex, polypeptide 1, 43kDa	265	SNAPC4-binding.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		TAGCGAAAATAAAATCAAAGG	0.284																																					p.I265fs	NSCLC(27;223 907 37180 39193 46568)	Atlas-INDEL	.											.	SNAPC1	32	.	0			c.794delT						.						76.0	81.0	79.0					14																	62245598		2203	4298	6501	SO:0001589	frameshift_variant	6617	exon7			.	Z47542	CCDS9755.1	14q22	2008-08-11	2002-08-29		ENSG00000023608	ENSG00000023608			11134	protein-coding gene	gene with protein product		600591	"""small nuclear RNA activating complex, polypeptide 1, 43kD"""			9644240	Standard	NM_003082		Approved	SNAP43, PTFgamma	uc001xft.3	Q16533	OTTHUMG00000140343	ENST00000216294.4:c.795delA	chr14.hg19:g.62245598delA	ENSP00000216294:p.Ile265fs	152.0	0.0		186.0	12.0	NM_003082		Frame_Shift_Del	DEL	ENST00000216294.4	hg19	CCDS9755.1																																																																																			.	.		0.284	SNAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276976.2	NM_003082	
C11orf30	56946	hgsc.bcm.edu	37	11	76257129	76257129	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76257129delC	ENST00000529032.1	+	19	3562	c.3562delC	c.(3562-3564)cccfs	p.P1188fs	C11orf30_ENST00000525919.1_Frame_Shift_Del_p.P1189fs|C11orf30_ENST00000524767.1_Frame_Shift_Del_p.P1203fs|C11orf30_ENST00000334736.3_Frame_Shift_Del_p.P1188fs|C11orf30_ENST00000524490.1_Frame_Shift_Del_p.P1090fs|C11orf30_ENST00000525038.1_Frame_Shift_Del_p.P1189fs|C11orf30_ENST00000343878.3_Intron|C11orf30_ENST00000533248.1_Frame_Shift_Del_p.P1097fs			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	1188					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						AGGATCATTACCCTCCACCCA	0.502																																					p.L1187fs		Atlas-INDEL	.											.	C11orf30	123	.	0			c.3561delA						.						89.0	89.0	89.0					11																	76257129		2200	4292	6492	SO:0001589	frameshift_variant	56946	exon20			.	AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.3562delC	chr11.hg19:g.76257129delC	ENSP00000432327:p.Pro1188fs	139.0	0.0		178.0	11.0	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Frame_Shift_Del	DEL	ENST00000529032.1	hg19	CCDS8244.1																																																																																			.	.		0.502	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193	
OBSCN	84033	hgsc.bcm.edu	37	1	228430955	228430955	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:228430955delA	ENST00000422127.1	+	10	3045	c.3001delA	c.(3001-3003)acgfs	p.T1001fs	OBSCN_ENST00000284548.11_Frame_Shift_Del_p.T1001fs|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Frame_Shift_Del_p.T1093fs	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1001	Ig-like 10.				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)				GGCCAGTGCCACGCTGAGCTG	0.612																																					p.A1092fs		Atlas-INDEL	.											.	OBSCN	2142	.	0			c.3276delC						.						27.0	27.0	27.0					1																	228430955		2014	4169	6183	SO:0001589	frameshift_variant	84033	exon11			.	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.3001delA	chr1.hg19:g.228430955delA	ENSP00000409493:p.Thr1001fs	112.0	0.0		216.0	13.0	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Frame_Shift_Del	DEL	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.		0.612	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
RBM43	375287	hgsc.bcm.edu	37	2	152107917	152107917	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:152107917delG	ENST00000331426.5	-	4	728	c.577delC	c.(577-579)cagfs	p.Q193fs		NM_198557.2	NP_940959.1	Q6ZSC3	RBM43_HUMAN	RNA binding motif protein 43	193							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)		AGATTCCTCTGGGGATTTTGT	0.418																																					p.Q193fs		Atlas-INDEL	.											.	RBM43	35	.	0			c.578delA						.						139.0	144.0	142.0					2																	152107917		2203	4300	6503	SO:0001589	frameshift_variant	375287	exon4			.	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.577delC	chr2.hg19:g.152107917delG	ENSP00000331211:p.Gln193fs	226.0	0.0		231.0	14.0	NM_198557	B2RMT5	Frame_Shift_Del	DEL	ENST00000331426.5	hg19	CCDS2191.1																																																																																			.	.		0.418	RBM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254816.2	NM_198557	
ATP2A2	488	hgsc.bcm.edu	37	12	110720572	110720572	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:110720572delT	ENST00000539276.2	+	3	300	c.191delT	c.(190-192)attfs	p.I64fs	ATP2A2_ENST00000395494.2_Frame_Shift_Del_p.I64fs|ATP2A2_ENST00000308664.6_Frame_Shift_Del_p.I64fs|ATP2A2_ENST00000552636.1_5'UTR			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	64					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						CTAGTTAGGATTTTATTACTG	0.323																																					p.I64fs		Atlas-INDEL	.											.	ATP2A2	78	.	0			c.190delA						.						113.0	109.0	111.0					12																	110720572		2203	4300	6503	SO:0001589	frameshift_variant	488	exon3			.		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"""ATPases / P-type"""	812	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 2"", ""calcium pump 2"""	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.191delT	chr12.hg19:g.110720572delT	ENSP00000440045:p.Ile64fs	104.0	0.0		156.0	11.0	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Frame_Shift_Del	DEL	ENST00000539276.2	hg19	CCDS9144.1																																																																																			.	.		0.323	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681	
KAT6A	7994	hgsc.bcm.edu	37	8	41832291	41832291	+	Frame_Shift_Del	DEL	A	A	-	rs141739124		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:41832291delA	ENST00000396930.3	-	9	1956	c.1413delT	c.(1411-1413)tttfs	p.F471fs	KAT6A_ENST00000406337.1_Frame_Shift_Del_p.F471fs|KAT6A_ENST00000265713.2_Frame_Shift_Del_p.F471fs|KAT6A_ENST00000485568.1_Frame_Shift_Del_p.F471fs	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	471	Interaction with PML.|Interaction with RUNX1-1.				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)										CCTGGCTCCCAAAAAGTCGCT	0.388																																					p.G472fs		Atlas-INDEL	.											.	.	.	.	0			c.1414delG						.						143.0	129.0	134.0					8																	41832291		2203	4300	6503	SO:0001589	frameshift_variant	7994	exon8			.	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.1413delT	chr8.hg19:g.41832291delA	ENSP00000380136:p.Phe471fs	215.0	0.0		182.0	12.0	NM_006766	Q76L81	Frame_Shift_Del	DEL	ENST00000396930.3	hg19	CCDS6124.1																																																																																			.	.		0.388	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
BPTF	2186	hgsc.bcm.edu	37	17	65955903	65955903	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:65955903delA	ENST00000321892.4	+	26	8612	c.8551delA	c.(8551-8553)aaafs	p.K2853fs	BPTF_ENST00000424123.3_Frame_Shift_Del_p.K2571fs|BPTF_ENST00000335221.5_Frame_Shift_Del_p.K2710fs|BPTF_ENST00000306378.6_Frame_Shift_Del_p.K2727fs			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2853	Poly-Lys.				anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			AAAGTCCAAGAAAAAGAAAAT	0.443																																					p.K2724fs		Atlas-INDEL	.											.	BPTF	415	.	0			c.8172delG						.						68.0	67.0	67.0					17																	65955903		2203	4300	6503	SO:0001589	frameshift_variant	2186	exon24			.	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.8551delA	chr17.hg19:g.65955903delA	ENSP00000315454:p.Lys2853fs	112.0	0.0		178.0	12.0	NM_182641	Q6NX67|Q7Z7D6|Q9UIG2	Frame_Shift_Del	DEL	ENST00000321892.4	hg19																																																																																				.	.		0.443	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
MED13	9969	hgsc.bcm.edu	37	17	60087940	60087940	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:60087940delA	ENST00000397786.2	-	9	2014	c.1938delT	c.(1936-1938)tttfs	p.F646fs		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	646					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TTTCCTGTCCAAAAGGTCCAA	0.348																																					p.G647fs		Atlas-INDEL	.											.	MED13	181	.	0			c.1939delG						.						68.0	62.0	64.0					17																	60087940		1840	4084	5924	SO:0001589	frameshift_variant	9969	exon9			.	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.1938delT	chr17.hg19:g.60087940delA	ENSP00000380888:p.Phe646fs	119.0	0.0		170.0	12.0	NM_005121	B2RU05|O60334	Frame_Shift_Del	DEL	ENST00000397786.2	hg19	CCDS42366.1																																																																																			.	.		0.348	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
ACCSL	390110	hgsc.bcm.edu	37	11	44077622	44077622	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:44077622delG	ENST00000378832.1	+	10	1228	c.1172delG	c.(1171-1173)tggfs	p.W391fs		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	391					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						CATGTGATCTGGGGTACCAGT	0.438																																					p.W391fs		Atlas-INDEL	.											.	ACCSL	57	.	0			c.1171delT						.						145.0	136.0	138.0					11																	44077622		1913	4127	6040	SO:0001589	frameshift_variant	390110	exon10			.		CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.1172delG	chr11.hg19:g.44077622delG	ENSP00000368109:p.Trp391fs	97.0	0.0		188.0	12.0	NM_001031854		Frame_Shift_Del	DEL	ENST00000378832.1	hg19	CCDS41636.1																																																																																			.	.		0.438	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854	
ASH1L	55870	hgsc.bcm.edu	37	1	155307895	155307895	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:155307895delT	ENST00000368346.3	-	27	9442	c.8803delA	c.(8803-8805)atcfs	p.I2935fs	ASH1L_ENST00000392403.3_Frame_Shift_Del_p.I2930fs			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2935					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TTTCCAGGGATTTTTTCAAGG	0.418																																					p.I2930fs		Atlas-INDEL	.											.	ASH1L	279	.	0			c.8789delT						.						99.0	92.0	94.0					1																	155307895		2203	4300	6503	SO:0001589	frameshift_variant	55870	exon27			.	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.8803delA	chr1.hg19:g.155307895delT	ENSP00000357330:p.Ile2935fs	102.0	0.0		165.0	10.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Frame_Shift_Del	DEL	ENST00000368346.3	hg19																																																																																				.	.		0.418	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
DGKZ	8525	hgsc.bcm.edu	37	11	46394213	46394213	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:46394213delG	ENST00000454345.1	+	13	1746	c.1621delG	c.(1621-1623)gggfs	p.G542fs	DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000532868.2_Frame_Shift_Del_p.G358fs|DGKZ_ENST00000395574.3_Frame_Shift_Del_p.G320fs|DGKZ_ENST00000343674.6_Frame_Shift_Del_p.G370fs|DGKZ_ENST00000421244.2_Frame_Shift_Del_p.G354fs|DGKZ_ENST00000527911.1_Frame_Shift_Del_p.G354fs|DGKZ_ENST00000318201.8_Frame_Shift_Del_p.G331fs|DGKZ_ENST00000456247.2_Frame_Shift_Del_p.G353fs|DGKZ_ENST00000528615.1_Frame_Shift_Del_p.G132fs	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	542	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.|Mediates interaction with RASGRP1.				blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)	p.G369R(1)|p.G541R(1)|p.G353R(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		CCTGGCGTGCGGGGGCGACGG	0.662																																					p.C540fs		Atlas-INDEL	.											.	DGKZ	199	.	3	Substitution - Missense(3)	lung(3)	c.1620delC						.						48.0	44.0	45.0					11																	46394213		2202	4299	6501	SO:0001589	frameshift_variant	8525	exon13			.	U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"""diacylglycerol kinase, zeta 104kDa"""			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.1621delG	chr11.hg19:g.46394213delG	ENSP00000412178:p.Gly542fs	51.0	0.0		132.0	10.0	NM_001105540	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Frame_Shift_Del	DEL	ENST00000454345.1	hg19	CCDS41640.1																																																																																			.	.		0.662	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540	
GATA1	2623	hgsc.bcm.edu	37	X	48650547	48650547	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:48650547delT	ENST00000376670.3	+	3	628	c.517delT	c.(517-519)tttfs	p.F173fs	GATA1_ENST00000376665.3_Frame_Shift_Del_p.F173fs	NM_002049.3	NP_002040.1	P15976	GATA1_HUMAN	GATA binding protein 1 (globin transcription factor 1)	173					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)	p.?(2)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(259)|large_intestine(8)|lung(9)|prostate(1)	283						CAGTACCTTCTTTTCTCCCAC	0.572			"""Mis, F"""		megakaryoblastic leukemia of Downs Syndrome																																p.F172fs	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	.	2	Unknown(2)	haematopoietic_and_lymphoid_tissue(2)	c.516delC						.						48.0	47.0	48.0					X																	48650547		2203	4300	6503	SO:0001589	frameshift_variant	2623	exon3			.	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.517delT	chrX.hg19:g.48650547delT	ENSP00000365858:p.Phe173fs	116.0	0.0		142.0	11.0	NM_002049	Q96GB8	Frame_Shift_Del	DEL	ENST00000376670.3	hg19	CCDS14305.1																																																																																			.	.		0.572	GATA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056517.1	NM_002049	
HMP19	51617	hgsc.bcm.edu	37	5	173473819	173473819	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:173473819delG	ENST00000303177.3	+	2	323	c.61delG	c.(61-63)ggcfs	p.G21fs	NSG2_ENST00000521585.1_Frame_Shift_Del_p.G21fs	NM_015980.4	NP_057064.1	Q9Y328	NSG2_HUMAN		21					clathrin coat assembly (GO:0048268)|dopamine receptor signaling pathway (GO:0007212)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.G21S(1)									AGTTGAGGATGGCTTCCAGAC	0.537																																					p.D20fs		Atlas-INDEL	.											.	HMP19	21	.	1	Substitution - Missense(1)	lung(1)	c.60delT						.						219.0	198.0	205.0					5																	173473819		2203	4300	6503	SO:0001589	frameshift_variant	0	exon2			.																												ENST00000303177.3:c.61delG	chr5.hg19:g.173473819delG	ENSP00000307722:p.Gly21fs	98.0	0.0		161.0	10.0	NM_015980	B2R5Y0|D3DQN0|Q9UHX8	Frame_Shift_Del	DEL	ENST00000303177.3	hg19	CCDS4391.1																																																																																			.	.		0.537	NSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252966.2		
ZNF184	7738	hgsc.bcm.edu	37	6	27420023	27420023	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:27420023delT	ENST00000211936.6	-	6	1599	c.1315delA	c.(1315-1317)actfs	p.T439fs	ZNF184_ENST00000377419.1_Frame_Shift_Del_p.T439fs	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	439					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(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						CCAGTATGAGTTTTTTGATGC	0.408																																					p.T439fs		Atlas-INDEL	.											.	ZNF184	89	.	0			c.1316delC						.						87.0	87.0	87.0					6																	27420023		2203	4300	6503	SO:0001589	frameshift_variant	7738	exon6			.	U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"""Zinc fingers, C2H2-type"", ""-"""	12975	protein-coding gene	gene with protein product		602277	"""zinc finger protein 184 (Kruppel-like)"""				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.1315delA	chr6.hg19:g.27420023delT	ENSP00000211936:p.Thr439fs	87.0	0.0		130.0	10.0	NM_007149	B2R715|O60792|Q8TBA9	Frame_Shift_Del	DEL	ENST00000211936.6	hg19	CCDS4624.1																																																																																			.	.		0.408	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149	
RANBP3L	202151	hgsc.bcm.edu	37	5	36270074	36270074	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:36270074delG	ENST00000296604.3	-	3	654	c.169delC	c.(169-171)ctgfs	p.L57fs	RANBP3L_ENST00000502994.1_Frame_Shift_Del_p.L57fs|RANBP3L_ENST00000515759.1_Frame_Shift_Del_p.L57fs	NM_145000.3	NP_659437.3	Q86VV4	RNB3L_HUMAN	RAN binding protein 3-like	57					intracellular transport (GO:0046907)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	16	all_lung(31;4.52e-05)		Epithelial(62;0.0543)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.149)|Colorectal(62;0.202)			GCTTCATACAGGGTGTCTTCT	0.388																																					p.L57fs		Atlas-INDEL	.											.	RANBP3L	41	.	0			c.170delT						.						178.0	195.0	189.0					5																	36270074		2203	4300	6503	SO:0001589	frameshift_variant	202151	exon3			.	BC047660	CCDS3918.1, CCDS54843.1	5p13.2	2008-02-05			ENSG00000164188	ENSG00000164188			26353	protein-coding gene	gene with protein product						12477932	Standard	NM_145000		Approved	FLJ25422	uc011cow.2	Q86VV4	OTTHUMG00000131110	ENST00000296604.3:c.169delC	chr5.hg19:g.36270074delG	ENSP00000296604:p.Leu57fs	116.0	0.0		172.0	11.0	NM_001161429	B7Z866|E9PGP9|Q96LK2	Frame_Shift_Del	DEL	ENST00000296604.3	hg19	CCDS3918.1																																																																																			.	.		0.388	RANBP3L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253773.2	NM_145000	
SYNE2	23224	hgsc.bcm.edu	37	14	64556329	64556329	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:64556329delA	ENST00000344113.4	+	59	11920	c.11708delA	c.(11707-11709)gaafs	p.E3903fs	SYNE2_ENST00000554584.1_Frame_Shift_Del_p.E3936fs|SYNE2_ENST00000555002.1_Frame_Shift_Del_p.E537fs|SYNE2_ENST00000357395.3_Frame_Shift_Del_p.E288fs|SYNE2_ENST00000358025.3_Frame_Shift_Del_p.E3903fs|SYNE2_ENST00000394768.2_Frame_Shift_Del_p.E288fs|ESR2_ENST00000542956.1_Intron	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3903					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AAATCAATGGAAAAAAGAGTT	0.284																																					p.E3903fs		Atlas-INDEL	.											SYNE2,NS,carcinoma,0,1	SYNE2	577	.	0			c.11707delG						.						32.0	34.0	33.0					14																	64556329		2194	4264	6458	SO:0001589	frameshift_variant	23224	exon59			.	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.11708delA	chr14.hg19:g.64556329delA	ENSP00000341781:p.Glu3903fs	185.0	0.0		211.0	13.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Frame_Shift_Del	DEL	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.284	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
PI4K2A	55361	hgsc.bcm.edu	37	10	99426199	99426199	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:99426199delT	ENST00000370631.3	+	7	1146	c.1089delT	c.(1087-1089)cctfs	p.P363fs	PI4K2A_ENST00000555577.1_Frame_Shift_Del_p.P333fs|PI4K2A_ENST00000370649.3_Frame_Shift_Del_p.P333fs	NM_018425.2	NP_060895.1	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	363	PI3K/PI4K.				basophil degranulation (GO:0002561)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endosome (GO:0005768)|exocytic vesicle (GO:0070382)|Golgi apparatus (GO:0005794)|growing cell tip (GO:0035838)|host cell presynaptic membrane (GO:0044231)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|AP-3 adaptor complex binding (GO:0035651)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)		TTTCAGATCCTTTTTACTGGG	0.478																																					p.P363fs		Atlas-INDEL	.											.	PI4K2A	57	.	0			c.1088delC						.						76.0	73.0	74.0					10																	99426199		2203	4300	6503	SO:0001589	frameshift_variant	55361	exon7			.	AF070611	CCDS7469.1	10q24	2011-02-09			ENSG00000155252	ENSG00000155252			30031	protein-coding gene	gene with protein product		609763				11244087, 11279162	Standard	NM_018425		Approved	PI4KII, DKFZP761G1923, PIK42A	uc001kog.1	Q9BTU6	OTTHUMG00000018863	ENST00000370631.3:c.1089delT	chr10.hg19:g.99426199delT	ENSP00000359665:p.Pro363fs	119.0	0.0		139.0	10.0	NM_018425	D3DR59|Q9NSG8	Frame_Shift_Del	DEL	ENST00000370631.3	hg19	CCDS7469.1																																																																																			.	.		0.478	PI4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049735.1	NM_018425	
XPO5	57510	hgsc.bcm.edu	37	6	43496599	43496599	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:43496599delG	ENST00000265351.7	-	24	2952	c.2742delC	c.(2740-2742)cccfs	p.P914fs	POLR1C_ENST00000304004.3_Intron	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	914					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			GTCCGAGGATGGGGGATACCA	0.473																																					p.I915fs		Atlas-INDEL	.											.	XPO5	79	.	0			c.2743delA						.						55.0	56.0	56.0					6																	43496599		1873	4104	5977	SO:0001589	frameshift_variant	57510	exon24			.	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"""Exportins"""	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.2742delC	chr6.hg19:g.43496599delG	ENSP00000265351:p.Pro914fs	106.0	0.0		156.0	11.0	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Frame_Shift_Del	DEL	ENST00000265351.7	hg19	CCDS47430.1																																																																																			.	.		0.473	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750	
MB21D2	151963	hgsc.bcm.edu	37	3	192516280	192516280	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:192516280delT	ENST00000392452.2	-	2	1691	c.1371delA	c.(1369-1371)aaafs	p.K457fs		NM_178496.3	NP_848591.2	Q8IYB1	M21D2_HUMAN	Mab-21 domain containing 2	457							protein complex binding (GO:0032403)			endometrium(3)|kidney(1)|large_intestine(4)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	31						GCTGCTGCAGTTTTTTTGCCA	0.512																																					p.L458fs		Atlas-INDEL	.											.	MB21D2	75	.	0			c.1372delC						.						108.0	113.0	111.0					3																	192516280		2203	4300	6503	SO:0001589	frameshift_variant	151963	exon2			.	AK056276	CCDS3302.2	3q28-q29	2011-02-23	2011-02-23	2011-02-23	ENSG00000180611	ENSG00000180611			30438	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 59"""	C3orf59		12477932	Standard	NM_178496		Approved		uc011bsp.2	Q8IYB1	OTTHUMG00000155768	ENST00000392452.2:c.1371delA	chr3.hg19:g.192516280delT	ENSP00000376246:p.Lys457fs	147.0	0.0		197.0	14.0	NM_178496	Q86VD8	Frame_Shift_Del	DEL	ENST00000392452.2	hg19	CCDS3302.2																																																																																			.	.		0.512	MB21D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341543.1	NM_178496	
HSPG2	3339	hgsc.bcm.edu	37	1	22168836	22168836	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:22168836delG	ENST00000374695.3	-	68	9027	c.8948delC	c.(8947-8949)cctfs	p.P2983fs		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2983	Ig-like C2-type 15.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TGAGTCGGCAGGGGAGACGAG	0.637																																					p.P2983fs		Atlas-INDEL	.											.	HSPG2	311	.	0			c.8949delT						.						29.0	27.0	28.0					1																	22168836		2203	4300	6503	SO:0001589	frameshift_variant	3339	exon68			.	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.8948delC	chr1.hg19:g.22168836delG	ENSP00000363827:p.Pro2983fs	113.0	0.0		174.0	11.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Frame_Shift_Del	DEL	ENST00000374695.3	hg19	CCDS30625.1																																																																																			.	.		0.637	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
OR52B6	340980	hgsc.bcm.edu	37	11	5602546	5602546	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:5602546delC	ENST00000345043.2	+	1	440	c.440delC	c.(439-441)tccfs	p.S147fs	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	147						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)		GCCATCTGCTCCCCCCTGCGA	0.507																																					p.S147fs		Atlas-INDEL	.											.	OR52B6	37	.	0			c.439delT						.						140.0	146.0	144.0					11																	5602546		2201	4297	6498	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.440delC	chr11.hg19:g.5602546delC	ENSP00000341581:p.Ser147fs	102.0	0.0		157.0	11.0	NM_001005162	Q6IFI7	Frame_Shift_Del	DEL	ENST00000345043.2	hg19	CCDS41611.1																																																																																			.	.		0.507	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162	
NT5DC2	64943	hgsc.bcm.edu	37	3	52562508	52562508	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:52562508delC	ENST00000307076.4	-	5	885	c.485delG	c.(484-486)ggtfs	p.G162fs	NT5DC2_ENST00000459839.1_Frame_Shift_Del_p.G174fs|NT5DC2_ENST00000490681.1_5'Flank|NT5DC2_ENST00000307092.4_Frame_Shift_Del_p.G103fs|NT5DC2_ENST00000422318.2_Frame_Shift_Del_p.G199fs	NM_022908.2	NP_075059.1	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2	162							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(1)|lung(3)|prostate(1)|stomach(1)	6				BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)		GTGCTGGGTACCCCCATACAG	0.577																																					p.G199fs		Atlas-INDEL	.											.	NT5DC2	35	.	0			c.597delT						.						105.0	94.0	98.0					3																	52562508		2203	4300	6503	SO:0001589	frameshift_variant	64943	exon5			.	AF131781	CCDS2858.1, CCDS46843.1	3p21.1	2006-02-03			ENSG00000168268	ENSG00000168268			25717	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_022908		Approved	FLJ12442	uc003den.3	Q9H857	OTTHUMG00000158626	ENST00000307076.4:c.485delG	chr3.hg19:g.52562508delC	ENSP00000302468:p.Gly162fs	250.0	0.0		406.0	26.0	NM_001134231	C9JTZ6|E9PAL9|O95888|Q96C80|Q9H9Z8	Frame_Shift_Del	DEL	ENST00000307076.4	hg19	CCDS2858.1																																																																																			.	.		0.577	NT5DC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000351509.1	NM_022908	
HLF	3131	hgsc.bcm.edu	37	17	53345191	53345191	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:53345191delG	ENST00000226067.5	+	2	668	c.195delG	c.(193-195)ctgfs	p.L65fs	HLF_ENST00000573945.1_5'UTR|HLF_ENST00000430986.2_5'UTR|HLF_ENST00000575345.1_5'UTR	NM_002126.4	NP_002117.1	Q16534	HLF_HUMAN	hepatic leukemia factor	65					multicellular organismal development (GO:0007275)|rhythmic process (GO:0048511)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|ovary(2)	3						CGGCATTCCTGGGGCCTACCT	0.483			T	TCF3	ALL																																p.L65fs		Atlas-INDEL	.		Dom	yes		17	17q22	3131	hepatic leukemia factor		L	.	HLF	39	.	0			c.194delT						.						91.0	91.0	91.0					17																	53345191		2203	4300	6503	SO:0001589	frameshift_variant	3131	exon2			.		CCDS11585.1	17q22	2011-05-19			ENSG00000108924	ENSG00000108924			4977	protein-coding gene	gene with protein product		142385				1386162	Standard	XM_005257269		Approved	MGC33822	uc002iug.1	Q16534		ENST00000226067.5:c.195delG	chr17.hg19:g.53345191delG	ENSP00000226067:p.Leu65fs	96.0	0.0		145.0	10.0	NM_002126	A8K1X8|Q6FHS9	Frame_Shift_Del	DEL	ENST00000226067.5	hg19	CCDS11585.1																																																																																			.	.		0.483	HLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439185.1	NM_002126	
BZRAP1	9256	hgsc.bcm.edu	37	17	56393388	56393388	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:56393388delA	ENST00000343736.4	-	16	2257	c.2094delT	c.(2092-2094)tttfs	p.F698fs	BZRAP1_ENST00000268893.6_Frame_Shift_Del_p.F638fs|BZRAP1_ENST00000355701.3_Frame_Shift_Del_p.F698fs			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	698	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCCTACCTTCAAAAAAGCCAT	0.502																																					p.E699fs		Atlas-INDEL	.											.	BZRAP1	287	.	0			c.2095delG						.						194.0	158.0	170.0					17																	56393388		2203	4300	6503	SO:0001589	frameshift_variant	9256	exon16			.	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.2094delT	chr17.hg19:g.56393388delA	ENSP00000345824:p.Phe698fs	174.0	0.0		260.0	19.0	NM_004758	O75111|Q8N5W3	Frame_Shift_Del	DEL	ENST00000343736.4	hg19	CCDS11605.1																																																																																			.	.		0.502	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
MCM9	254394	hgsc.bcm.edu	37	6	119238756	119238756	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:119238756delA	ENST00000316316.6	-	5	1160	c.874delT	c.(874-876)tggfs	p.W292fs	MCM9_ENST00000316068.3_Frame_Shift_Del_p.W292fs	NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	292					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)	MCM8-MCM9 complex (GO:0097362)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)		TAGTATTCCCAAAAATCTTCG	0.368																																					p.W292fs		Atlas-INDEL	.											.	MCM9	73	.	0			c.875delG						.						110.0	103.0	106.0					6																	119238756		2203	4300	6503	SO:0001589	frameshift_variant	254394	exon4			.	BC031658	CCDS5121.1, CCDS56447.1	6q22.31	2009-11-16	2007-04-04	2007-04-04	ENSG00000111877	ENSG00000111877			21484	protein-coding gene	gene with protein product		610098	"""minichromosome maintenance deficient domain containing 1"", ""chromosome 6 open reading frame 61"""	MCMDC1, C6orf61		16226853, 15850810, 16495042	Standard	NM_153255		Approved	MGC35304, dJ329L24.3, FLJ20170	uc021zeh.1	Q9NXL9	OTTHUMG00000015468	ENST00000316316.6:c.874delT	chr6.hg19:g.119238756delA	ENSP00000314505:p.Trp292fs	103.0	0.0		202.0	13.0	NM_017696	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Frame_Shift_Del	DEL	ENST00000316316.6	hg19	CCDS56447.1																																																																																			.	.		0.368	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255	
BUB1	699	hgsc.bcm.edu	37	2	111430402	111430402	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:111430402delA	ENST00000302759.6	-	4	376	c.258delT	c.(256-258)tttfs	p.F86fs	BUB1_ENST00000535254.1_Frame_Shift_Del_p.F66fs|BUB1_ENST00000409311.1_Frame_Shift_Del_p.F86fs	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	86	BUB1 N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00822}.|Necessary for kinetochore localization.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		ACAGAAACTCAAAAAATTGAT	0.478																																					p.E87fs		Atlas-INDEL	.											.	BUB1	91	.	0			c.259delG						.						101.0	104.0	103.0					2																	111430402		2203	4300	6503	SO:0001589	frameshift_variant	699	exon4			.	AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"""budding uninhibited by benzimidazoles 1 (yeast homolog)"", ""budding uninhibited by benzimidazoles 1 homolog (yeast)"""	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.258delT	chr2.hg19:g.111430402delA	ENSP00000302530:p.Phe86fs	124.0	0.0		123.0	10.0	NM_004336	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Frame_Shift_Del	DEL	ENST00000302759.6	hg19	CCDS33273.1																																																																																			.	.		0.478	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336	
FMN1	342184	hgsc.bcm.edu	37	15	33069072	33069072	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:33069072delT	ENST00000559047.1	-	17	4178	c.4179delA	c.(4177-4179)aaafs	p.K1393fs	FMN1_ENST00000561249.1_Frame_Shift_Del_p.K1295fs|FMN1_ENST00000334528.9_Frame_Shift_Del_p.K1170fs			Q68DA7	FMN1_HUMAN	formin 1	1393					actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TTGTCTCCACTTTCTTCTCTG	0.413																																					p.V1171fs		Atlas-INDEL	.											FMN1_ENST00000334528,brain,glioma,0,2	FMN1	174	.	0			c.3511delG						.						90.0	79.0	82.0					15																	33069072		1837	4093	5930	SO:0001589	frameshift_variant	342184	exon16			.	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.4179delA	chr15.hg19:g.33069072delT	ENSP00000454047:p.Lys1393fs	150.0	0.0		142.0	10.0	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Frame_Shift_Del	DEL	ENST00000559047.1	hg19																																																																																				.	.		0.413	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
ZNF80	7634	hgsc.bcm.edu	37	3	113955740	113955740	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:113955740delT	ENST00000482457.2	-	1	685	c.182delA	c.(181-183)aacfs	p.N61fs	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	61					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(1)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				AAGGAGGCTGTTTTTGTTAAA	0.473																																					p.N61fs	GBM(23;986 1114 21716)	Atlas-INDEL	.											.	ZNF80	75	.	0			c.183delC						.						120.0	104.0	109.0					3																	113955740		2203	4300	6503	SO:0001589	frameshift_variant	7634	exon1			.	X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"""Zinc fingers, C2H2-type"""	13155	protein-coding gene	gene with protein product		194553	"""zinc finger protein 80 (pT17)"""			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.182delA	chr3.hg19:g.113955740delT	ENSP00000417192:p.Asn61fs	84.0	0.0		136.0	11.0	NM_007136	Q6NSW4|Q6NT14	Frame_Shift_Del	DEL	ENST00000482457.2	hg19	CCDS2979.1																																																																																			.	.		0.473	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136	
LRBA	987	hgsc.bcm.edu	37	4	151829842	151829842	+	Frame_Shift_Del	DEL	A	A	-	rs373877713		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:151829842delA	ENST00000357115.3	-	10	1572	c.1329delT	c.(1327-1329)tttfs	p.F443fs	LRBA_ENST00000507224.1_Frame_Shift_Del_p.F443fs|LRBA_ENST00000535741.1_Frame_Shift_Del_p.F443fs|LRBA_ENST00000510413.1_Frame_Shift_Del_p.F443fs	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	443						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)					GTGAATGAACAAAAATTGAAG	0.388																																					p.V444fs		Atlas-INDEL	.											.	LRBA	253	.	0			c.1330delG						.						150.0	141.0	144.0					4																	151829842		2203	4300	6503	SO:0001589	frameshift_variant	987	exon10			.	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.1329delT	chr4.hg19:g.151829842delA	ENSP00000349629:p.Phe443fs	144.0	0.0		147.0	10.0	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Frame_Shift_Del	DEL	ENST00000357115.3	hg19	CCDS3773.1																																																																																			.	.		0.388	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1		
EZH1	2145	hgsc.bcm.edu	37	17	40860046	40860046	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:40860046delG	ENST00000428826.2	-	15	1711	c.1590delC	c.(1588-1590)cccfs	p.P530fs	EZH1_ENST00000590783.1_5'UTR|EZH1_ENST00000415827.2_Frame_Shift_Del_p.P521fs|EZH1_ENST00000590078.1_Frame_Shift_Del_p.P460fs|EZH1_ENST00000592743.1_Frame_Shift_Del_p.P530fs|EZH1_ENST00000435174.1_Frame_Shift_Del_p.P391fs|EZH1_ENST00000585893.1_Frame_Shift_Del_p.P490fs			Q92800	EZH1_HUMAN	enhancer of zeste 1 polycomb repressive complex 2 subunit	530	CXC. {ECO:0000255|PROSITE- ProRule:PRU00970}.|Cys-rich.				anatomical structure morphogenesis (GO:0009653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)			breast(1)|endometrium(4)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	27		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		TGCTGTCACAGGGGCGGTCTG	0.498																																					p.C531fs		Atlas-INDEL	.											.	EZH1	62	.	0			c.1591delT						.						149.0	137.0	141.0					17																	40860046		2203	4300	6503	SO:0001589	frameshift_variant	2145	exon15			.		CCDS32659.1	17q21.1-q21.3	2014-05-28	2014-05-28			ENSG00000108799		"""Chromatin-modifying enzymes / K-methyltransferases"""	3526	protein-coding gene	gene with protein product		601674	"""enhancer of zeste (Drosophila) homolog 1"", ""enhancer of zeste homolog 1 (Drosophila)"""			8921387	Standard	NM_001991		Approved	KIAA0388, KMT6B	uc002iaz.3	Q92800		ENST00000428826.2:c.1590delC	chr17.hg19:g.40860046delG	ENSP00000404658:p.Pro530fs	98.0	0.0		161.0	10.0	NM_001991	A6NCH6|B4DIJ1|B4DIZ7|B4DSS2|B4E3R7|O43287|Q14459|Q53XP3	Frame_Shift_Del	DEL	ENST00000428826.2	hg19	CCDS32659.1																																																																																			.	.		0.498	EZH1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452347.1	NM_001991	
ITGB4	3691	hgsc.bcm.edu	37	17	73746239	73746239	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:73746239delC	ENST00000200181.3	+	28	3551	c.3364delC	c.(3364-3366)cccfs	p.P1123fs	ITGB4_ENST00000339591.3_Frame_Shift_Del_p.P1123fs|ITGB4_ENST00000579662.1_Frame_Shift_Del_p.P1123fs|ITGB4_ENST00000450894.3_Frame_Shift_Del_p.P1123fs|ITGB4_ENST00000449880.2_Frame_Shift_Del_p.P1123fs	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1123					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			ATCACAGCCACCCCCTCACGG	0.612											OREG0024739	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P1121fs		Atlas-INDEL	.											.	ITGB4	165	.	0			c.3363delA						.						59.0	60.0	60.0					17																	73746239		2203	4300	6503	SO:0001589	frameshift_variant	3691	exon27			.		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.3364delC	chr17.hg19:g.73746239delC	ENSP00000200181:p.Pro1123fs	148.0	0.0	1147	171.0	11.0	NM_001005619	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Frame_Shift_Del	DEL	ENST00000200181.3	hg19	CCDS11727.1																																																																																			.	.		0.612	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
TGM3	7053	hgsc.bcm.edu	37	20	2291043	2291043	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:2291043delT	ENST00000381458.5	+	3	464	c.401delT	c.(400-402)cttfs	p.L134fs		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	134					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	TTCATACTGCTTTTTAACCCC	0.537																																					p.L134fs		Atlas-INDEL	.											.	TGM3	105	.	0			c.400delC						.						176.0	169.0	171.0					20																	2291043		2203	4300	6503	SO:0001589	frameshift_variant	7053	exon3			.	L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"""Transglutaminases"""	11779	protein-coding gene	gene with protein product	"""E polypeptide, protein-glutamine-gamma-glutamyltransferase"""	600238	"""transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"""			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.401delT	chr20.hg19:g.2291043delT	ENSP00000370867:p.Leu134fs	119.0	0.0		162.0	10.0	NM_003245	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Frame_Shift_Del	DEL	ENST00000381458.5	hg19	CCDS33435.1																																																																																			.	.		0.537	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245	
MRGPRG	386746	hgsc.bcm.edu	37	11	3239346	3239346	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:3239346delG	ENST00000332314.3	-	1	697	c.698delC	c.(697-699)ccgfs	p.P233fs	MRGPRG-AS1_ENST00000420873.2_RNA|MRGPRG-AS1_ENST00000434798.1_RNA	NM_001164377.1	NP_001157849.1	Q86SM5	MRGRG_HUMAN	MAS-related GPR, member G	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)										CGTGGCCAGCGGGGAAAACAC	0.667																																					p.P233fs		Atlas-INDEL	.											.	MRGPRG	6	.	0			c.699delG						.						39.0	48.0	46.0					11																	3239346		691	1587	2278	SO:0001589	frameshift_variant	386746	exon1			.	AY255583	CCDS44520.1	11p15.4	2012-08-21	2004-03-25		ENSG00000182170	ENSG00000182170		"""GPCR / Class A : Orphans"""	24829	protein-coding gene	gene with protein product		607234	"""G protein-coupled receptor 169"""	GPR169		12679517	Standard	NM_001164377		Approved	mrgG	uc001lxp.2	Q86SM5	OTTHUMG00000011709	ENST00000332314.3:c.698delC	chr11.hg19:g.3239346delG	ENSP00000330612:p.Pro233fs	93.0	0.0		221.0	14.0	NM_001164377		Frame_Shift_Del	DEL	ENST00000332314.3	hg19	CCDS44520.1																																																																																			.	.		0.667	MRGPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032347.1		
BCAS1	8537	hgsc.bcm.edu	37	20	52645367	52645367	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:52645367delA	ENST00000395961.3	-	4	453	c.287delT	c.(286-288)ttcfs	p.F96fs	BCAS1_ENST00000371435.2_Frame_Shift_Del_p.F96fs|BCAS1_ENST00000371440.3_Frame_Shift_Del_p.F96fs|BCAS1_ENST00000411563.1_5'UTR	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	96						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			GAGCATCAAGAAAAAACGAGA	0.522																																					p.F96fs		Atlas-INDEL	.											.	BCAS1	77	.	0			c.288delC						.						86.0	76.0	79.0					20																	52645367		2203	4300	6503	SO:0001589	frameshift_variant	8537	exon4			.	AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787			974	protein-coding gene	gene with protein product		602968				9671742	Standard	NM_003657		Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772	ENST00000395961.3:c.287delT	chr20.hg19:g.52645367delA	ENSP00000379290:p.Phe96fs	118.0	0.0		140.0	10.0	NM_003657	A0AVG5|Q68CZ3	Frame_Shift_Del	DEL	ENST00000395961.3	hg19	CCDS13444.1																																																																																			.	.		0.522	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657	
CNEP1R1	255919	hgsc.bcm.edu	37	16	50067341	50067341	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:50067341delT	ENST00000427478.2	+	4	259	c.205delT	c.(205-207)tttfs	p.F70fs	CNEP1R1_ENST00000562576.1_Frame_Shift_Del_p.F70fs|CNEP1R1_ENST00000565556.1_Frame_Shift_Del_p.F38fs|CNEP1R1_ENST00000458059.3_Frame_Shift_Del_p.F87fs	NM_001281789.1	NP_001268718.1	Q8N9A8	NEPR1_HUMAN	CTD nuclear envelope phosphatase 1 regulatory subunit 1	70					lipid metabolic process (GO:0006629)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of triglyceride biosynthetic process (GO:0010867)|protein localization to nucleus (GO:0034504)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|Nem1-Spo7 phosphatase complex (GO:0071595)|nuclear membrane (GO:0031965)											GAATCACCCATTTTTCACCAT	0.358																																					p.P85fs		Atlas-INDEL	.											.	.	.	.	0			c.255delA						.						124.0	106.0	112.0					16																	50067341		1855	4098	5953	SO:0001589	frameshift_variant	255919	exon5			.	AK095420	CCDS45480.1, CCDS61931.1	16q12.1	2012-02-01	2012-02-01	2012-02-01	ENSG00000205423	ENSG00000205423			26759	protein-coding gene	gene with protein product	"""nuclear envelope phosphatase 1-regulatory subunit 1"""		"""chromosome 16 open reading frame 69"", ""transmembrane protein 188"""	C16orf69, TMEM188		22134922	Standard	NM_153261		Approved	FLJ38101, NEP1-R1	uc002eft.3	Q8N9A8		ENST00000427478.2:c.205delT	chr16.hg19:g.50067341delT	ENSP00000394224:p.Phe70fs	148.0	0.0		173.0	11.0	NM_153261	Q4G1A9|Q5H9V0|Q8NE06	Frame_Shift_Del	DEL	ENST00000427478.2	hg19																																																																																				.	.		0.358	CNEP1R1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153261	
EMR2	30817	hgsc.bcm.edu	37	19	14884853	14884853	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:14884853delC	ENST00000315576.3	-	4	547	c.96delG	c.(94-96)tggfs	p.W32fs	EMR2_ENST00000353005.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000392965.3_Frame_Shift_Del_p.W32fs|EMR2_ENST00000353876.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000599423.1_5'UTR|EMR2_ENST00000392967.2_Frame_Shift_Del_p.W32fs|EMR2_ENST00000594294.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000601345.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000594076.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000595839.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000346057.1_Frame_Shift_Del_p.W32fs|EMR2_ENST00000596991.2_Frame_Shift_Del_p.W32fs|EMR2_ENST00000392964.3_5'Flank	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	32	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						CCTGAGGGCACCACCGGGCAC	0.592																																					p.C33fs		Atlas-INDEL	.											.	EMR2	99	.	0			c.97delT						.						117.0	110.0	112.0					19																	14884853		2203	4300	6503	SO:0001589	frameshift_variant	30817	exon3			.	AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	3337	protein-coding gene	gene with protein product		606100	"""egf-like module containing, mucin-like, hormone receptor-like sequence 2"""				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.96delG	chr19.hg19:g.14884853delC	ENSP00000319883:p.Trp32fs	144.0	0.0		178.0	12.0	NM_001271052	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Frame_Shift_Del	DEL	ENST00000315576.3	hg19	CCDS32935.1																																																																																			.	.		0.592	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2		
ZNF318	24149	hgsc.bcm.edu	37	6	43320194	43320194	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:43320194delT	ENST00000361428.2	-	5	2768	c.2691delA	c.(2689-2691)aaafs	p.K897fs	ZNF318_ENST00000318149.3_Frame_Shift_Del_p.K897fs	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	897					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			CATTCTTTAGTTTTTCCCTCT	0.433																																					p.L898X		Atlas-INDEL	.											.	ZNF318	175	.	0			c.2692delC						.						116.0	105.0	108.0					6																	43320194		2203	4300	6503	SO:0001589	frameshift_variant	24149	exon5			.	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"""Zinc fingers, C2H2-type"""	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.2691delA	chr6.hg19:g.43320194delT	ENSP00000354964:p.Lys897fs	118.0	0.0		182.0	13.0	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Frame_Shift_Del	DEL	ENST00000361428.2	hg19	CCDS4895.2																																																																																			.	.		0.433	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	
SALL2	6297	hgsc.bcm.edu	37	14	21991715	21991715	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:21991715delC	ENST00000327430.3	-	2	2441	c.2147delG	c.(2146-2148)ggcfs	p.G716fs	SALL2_ENST00000538754.1_Intron|SALL2_ENST00000317492.5_Intron|AE000658.22_ENST00000535893.1_RNA|SALL2_ENST00000450879.2_Frame_Shift_Del_p.G579fs	NM_005407.1	NP_005398.1	Q9Y467	SALL2_HUMAN	spalt-like transcription factor 2	716					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2)	43	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		GGGGATCTGGCCCCCCAGGTG	0.612																																					p.G716fs		Atlas-INDEL	.											.	SALL2	95	.	0			c.2148delC						.						65.0	60.0	61.0					14																	21991715		2203	4300	6503	SO:0001589	frameshift_variant	6297	exon2			.	AB002358	CCDS32045.1	14q11.1-q12.1	2013-10-17	2013-10-17		ENSG00000165821	ENSG00000165821		"""Zinc fingers, C2H2-type"""	10526	protein-coding gene	gene with protein product		602219	"""sal (Drosophila)-like 2"", ""sal-like 2 (Drosophila)"""			8975705	Standard	XM_005267983		Approved	KIAA0360, Hsal2, ZNF795	uc001wbe.3	Q9Y467	OTTHUMG00000168826	ENST00000327430.3:c.2147delG	chr14.hg19:g.21991715delC	ENSP00000333537:p.Gly716fs	86.0	0.0		115.0	11.0	NM_005407	B2RMX6|B9EGK8|Q8N656|Q9Y4G1	Frame_Shift_Del	DEL	ENST00000327430.3	hg19	CCDS32045.1																																																																																			.	.		0.612	SALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401242.1	NM_005407	
PSRC1	84722	hgsc.bcm.edu	37	1	109824582	109824582	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:109824582delG	ENST00000438534.2	-	4	316	c.178delC	c.(178-180)cagfs	p.Q60fs	PSRC1_ENST00000409138.2_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369903.2_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369904.3_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369907.3_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000409267.1_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369909.2_Frame_Shift_Del_p.Q60fs	NM_001005290.3	NP_001005290.1	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1	60					microtubule bundle formation (GO:0001578)|mitotic metaphase plate congression (GO:0007080)|negative regulation of cell growth (GO:0030308)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mitotic spindle organization (GO:0060236)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	microtubule binding (GO:0008017)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	7		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0286)|Lung(183;0.0658)|COAD - Colon adenocarcinoma(174;0.112)|Epithelial(280;0.188)|all cancers(265;0.213)		CTCACACCCTGGGGGGCAGGT	0.622																																					p.Q60fs		Atlas-INDEL	.											.	PSRC1	12	.	0			c.179delA						.						16.0	15.0	16.0					1																	109824582		2188	4287	6475	SO:0001589	frameshift_variant	84722	exon4			.		CCDS797.1, CCDS30791.1	1p13.3	2008-02-05			ENSG00000134222	ENSG00000134222			24472	protein-coding gene	gene with protein product	"""differential display and activated by p53"""	613126				12427559, 10618717	Standard	NM_001032291		Approved	DDA3	uc001dxd.3	Q6PGN9	OTTHUMG00000012000	ENST00000438534.2:c.178delC	chr1.hg19:g.109824582delG	ENSP00000413591:p.Gln60fs	74.0	0.0		165.0	11.0	NM_001032291	Q5T2Z3|Q6ZTI8|Q71MG3|Q9BV77	Frame_Shift_Del	DEL	ENST00000438534.2	hg19																																																																																				.	.		0.622	PSRC1-202	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335567.3	NM_032636	
TANC2	26115	hgsc.bcm.edu	37	17	61086972	61086972	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:61086972delA	ENST00000424789.2	+	1	56	c.52delA	c.(52-54)aaafs	p.K18fs	TANC2_ENST00000389520.4_Frame_Shift_Del_p.K18fs	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	18					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						ATCAAGTCGTAAAAACAGGTC	0.343																																					p.R17fs		Atlas-INDEL	.											.	TANC2	266	.	0			c.51delT						.						171.0	174.0	173.0					17																	61086972		1872	4109	5981	SO:0001589	frameshift_variant	26115	exon1			.	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30212	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.52delA	chr17.hg19:g.61086972delA	ENSP00000387593:p.Lys18fs	111.0	0.0		161.0	10.0	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Frame_Shift_Del	DEL	ENST00000424789.2	hg19	CCDS45754.1																																																																																			.	.		0.343	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1		
ZBTB11	27107	hgsc.bcm.edu	37	3	101371772	101371772	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:101371772delT	ENST00000312938.4	-	9	2900	c.2320delA	c.(2320-2322)agtfs	p.S774fs		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	774					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TCAAAGAAACTTTTTTCACAT	0.338																																					p.S774fs		Atlas-INDEL	.											.	ZBTB11	77	.	0			c.2321delG						.						103.0	96.0	99.0					3																	101371772		2203	4300	6503	SO:0001589	frameshift_variant	27107	exon9			.	U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.2320delA	chr3.hg19:g.101371772delT	ENSP00000326200:p.Ser774fs	115.0	0.0		189.0	12.0	NM_014415	Q2NKP9	Frame_Shift_Del	DEL	ENST00000312938.4	hg19	CCDS2943.1																																																																																			.	.		0.338	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415	
IGDCC3	9543	hgsc.bcm.edu	37	15	65623433	65623433	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:65623433delC	ENST00000327987.4	-	9	1767	c.1516delG	c.(1516-1518)gccfs	p.A506fs	IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	506	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GCTGAGCTGGCCCCCCTTGGT	0.597																																					p.A506fs		Atlas-INDEL	.											.	IGDCC3	82	.	0			c.1517delC						.						109.0	111.0	110.0					15																	65623433		2201	4299	6500	SO:0001589	frameshift_variant	9543	exon9			.	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9700	protein-coding gene	gene with protein product		604184	"""putative neuronal cell adhesion molecule"""	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.1516delG	chr15.hg19:g.65623433delC	ENSP00000332773:p.Ala506fs	151.0	0.0		168.0	15.0	NM_004884	O95215	Frame_Shift_Del	DEL	ENST00000327987.4	hg19	CCDS10205.1																																																																																			.	.		0.597	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884	
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24329517	24329517	+	IGR	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:24329517delA								AC096509.1 (24723 upstream) : AC004552.1 (37408 downstream)																							AGTATTTAGGAAAAACTGAAG	0.602																																					p.F639fs		Atlas-INDEL	.											.	.	.	.	0			c.1917delC						.						39.0	39.0	39.0					X																	24329517		1568	3581	5149	SO:0001628	intergenic_variant	170067	exon1			.																													chrX.hg19:g.24329517delA		144.0	0.0		210.0	13.0	NM_001136233		Frame_Shift_Del	DEL		hg19																																																																																				.	.	0	0.602								
GPR97	222487	hgsc.bcm.edu	37	16	57707239	57707239	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:57707239delA	ENST00000333493.4	+	2	226	c.65delA	c.(64-66)gaafs	p.E22fs	GPR97_ENST00000327655.6_5'UTR|GPR97_ENST00000450388.3_5'UTR	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	22					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TTAGGTCAGGAAAAGCCCACC	0.537																																					p.E22fs		Atlas-INDEL	.											.	GPR97	74	.	0			c.64delG						.						79.0	72.0	74.0					16																	57707239		2198	4300	6498	SO:0001589	frameshift_variant	222487	exon2			.	AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"""-"", ""GPCR / Class B : Orphans"""	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.65delA	chr16.hg19:g.57707239delA	ENSP00000332900:p.Glu22fs	168.0	0.0		165.0	11.0	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Frame_Shift_Del	DEL	ENST00000333493.4	hg19	CCDS10786.1																																																																																			.	.		0.537	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776	
MYH8	4626	hgsc.bcm.edu	37	17	10318665	10318665	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:10318665delG	ENST00000403437.2	-	8	779	c.685delC	c.(685-687)ctafs	p.L230fs	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	230	Myosin motor.				ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						GCCTCCAGTAGGGGATTGGCG	0.512									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.L229fs		Atlas-INDEL	.											.	MYH8	346	.	0			c.686delT						.						128.0	130.0	129.0					17																	10318665		2203	4300	6503	SO:0001589	frameshift_variant	4626	exon8	Familial Cancer Database	Carney Complex Variant	.		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.685delC	chr17.hg19:g.10318665delG	ENSP00000384330:p.Leu230fs	166.0	0.0		130.0	10.0	NM_002472	Q14910	Frame_Shift_Del	DEL	ENST00000403437.2	hg19	CCDS11153.1																																																																																			.	.		0.512	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
DCDC2	51473	hgsc.bcm.edu	37	6	24278359	24278359	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:24278359delT	ENST00000378454.3	-	7	1141	c.840delA	c.(838-840)aaafs	p.K280fs		NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	280					cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)					breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				TCACGTCTTCTTTTTTCCCTT	0.358																																					p.E281fs		Atlas-INDEL	.											DCDC2,colon,carcinoma,0,1	DCDC2	53	.	0			c.841delG						.						148.0	139.0	142.0					6																	24278359		2203	4300	6503	SO:0001589	frameshift_variant	51473	exon8			.	AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.840delA	chr6.hg19:g.24278359delT	ENSP00000367715:p.Lys280fs	148.0	0.0		230.0	16.0	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Frame_Shift_Del	DEL	ENST00000378454.3	hg19	CCDS4550.1																																																																																			.	.		0.358	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356	
PTPRS	5802	hgsc.bcm.edu	37	19	5231449	5231449	+	Frame_Shift_Del	DEL	G	G	-	rs376058028		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:5231449delG	ENST00000587303.1	-	13	2126	c.2027delC	c.(2026-2028)ccgfs	p.P676fs	PTPRS_ENST00000592099.1_Intron|PTPRS_ENST00000588552.1_Intron|PTPRS_ENST00000348075.2_Frame_Shift_Del_p.P663fs|PTPRS_ENST00000372412.4_Frame_Shift_Del_p.P677fs|PTPRS_ENST00000357368.4_Frame_Shift_Del_p.P676fs|PTPRS_ENST00000262963.6_Frame_Shift_Del_p.P672fs|PTPRS_ENST00000588012.1_Frame_Shift_Del_p.P663fs|PTPRS_ENST00000353284.2_Intron			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	676	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	AGTGGTGGTCGGGGGGATGCC	0.667																																					p.P676fs		Atlas-INDEL	.											.	PTPRS	169	.	0			c.2028delG						.						60.0	48.0	52.0					19																	5231449		2203	4300	6503	SO:0001589	frameshift_variant	5802	exon14			.	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.2027delC	chr19.hg19:g.5231449delG	ENSP00000467537:p.Pro676fs	89.0	0.0		102.0	10.0	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Frame_Shift_Del	DEL	ENST00000587303.1	hg19	CCDS45930.1																																																																																			.	.		0.667	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
RPS6KA6	27330	hgsc.bcm.edu	37	X	83374999	83374999	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:83374999delT	ENST00000262752.2	-	9	690	c.683delA	c.(682-684)aagfs	p.K229fs	RPS6KA6_ENST00000543399.1_Frame_Shift_Del_p.K229fs	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	229	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						GTAAGCCTTCTTTTCTTGATC	0.373																																					p.K228fs		Atlas-INDEL	.											.	RPS6KA6	116	.	0			c.684delG						.						95.0	82.0	86.0					X																	83374999		2203	4300	6503	SO:0001589	frameshift_variant	27330	exon9			.	AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"""ribosomal protein S6 kinase, 90kD, polypeptide 6"""			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.683delA	chrX.hg19:g.83374999delT	ENSP00000262752:p.Lys229fs	165.0	0.0		166.0	10.0	NM_014496	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Frame_Shift_Del	DEL	ENST00000262752.2	hg19	CCDS14451.1																																																																																			.	.		0.373	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496	
POLDIP3	84271	hgsc.bcm.edu	37	22	42981894	42981894	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:42981894delG	ENST00000252115.5	-	9	1273	c.1169delC	c.(1168-1170)cctfs	p.P390fs	POLDIP3_ENST00000339677.6_Intron|POLDIP3_ENST00000348657.2_Frame_Shift_Del_p.P361fs|POLDIP3_ENST00000491021.1_5'UTR|POLDIP3_ENST00000451060.2_3'UTR	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	390					poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	16						CACTTCGGCAGGGGGGTTGGA	0.572																																					p.P390fs	Ovarian(52;967 1128 5875 19997 42537)	Atlas-INDEL	.											.	POLDIP3	58	.	0			c.1170delT						.						70.0	63.0	65.0					22																	42981894		2203	4300	6503	SO:0001589	frameshift_variant	84271	exon9			.		CCDS14038.1, CCDS14039.1, CCDS74873.1	22q13.31	2013-02-12			ENSG00000100227	ENSG00000100227		"""RNA binding motif (RRM) containing"""	23782	protein-coding gene	gene with protein product		611520				12522211	Standard	NM_032311		Approved	PDIP46, KIAA1649	uc003bcu.3	Q9BY77	OTTHUMG00000150887	ENST00000252115.5:c.1169delC	chr22.hg19:g.42981894delG	ENSP00000252115:p.Pro390fs	130.0	0.0		121.0	10.0	NM_032311	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Frame_Shift_Del	DEL	ENST00000252115.5	hg19	CCDS14038.1																																																																																			.	.		0.572	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311	
FAM117B	150864	hgsc.bcm.edu	37	2	203621969	203621969	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:203621969delC	ENST00000392238.2	+	6	1138	c.1138delC	c.(1138-1140)cccfs	p.P381fs	FAM117B_ENST00000303116.6_Frame_Shift_Del_p.P137fs			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	381										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						TCGTGCTCCACCCCCCCTTGT	0.488																																					p.P379fs		Atlas-INDEL	.											.	FAM117B	73	.	0			c.1137delA						.						55.0	55.0	55.0					2																	203621969		2203	4300	6503	SO:0001589	frameshift_variant	150864	exon6			.	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.1138delC	chr2.hg19:g.203621969delC	ENSP00000376071:p.Pro381fs	222.0	0.0		295.0	19.0	NM_173511	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Frame_Shift_Del	DEL	ENST00000392238.2	hg19	CCDS33362.2																																																																																			.	.		0.488	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335888.3	NM_173511	
GDI2	2665	hgsc.bcm.edu	37	10	5836890	5836890	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:5836890delT	ENST00000380191.4	-	4	636	c.346delA	c.(346-348)atcfs	p.I116fs	GDI2_ENST00000380181.3_Intron|GDI2_ENST00000380132.4_Frame_Shift_Del_p.I120fs	NM_001115156.1|NM_001494.3	NP_001108628.1|NP_001485.2	P50395	GDIB_HUMAN	GDP dissociation inhibitor 2	116					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|Rab GDP-dissociation inhibitor activity (GO:0005093)|Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|large_intestine(1)|lung(6)|urinary_tract(1)	10						ACCTTGTAGATTTTTCCACCC	0.368																																					p.I116fs		Atlas-INDEL	.											.	GDI2	26	.	0			c.347delT						.						95.0	92.0	93.0					10																	5836890		2203	4300	6503	SO:0001589	frameshift_variant	2665	exon4			.	D13988	CCDS7071.1, CCDS44352.1	10p15	2010-03-16			ENSG00000057608	ENSG00000057608			4227	protein-coding gene	gene with protein product	"""rab GDP-dissociation"""	600767				9434952	Standard	NM_001494		Approved	RABGDIB	uc001iil.4	P50395	OTTHUMG00000017607	ENST00000380191.4:c.346delA	chr10.hg19:g.5836890delT	ENSP00000369538:p.Ile116fs	173.0	0.0		160.0	10.0	NM_001494	O43928|Q5SX88|Q9UQM6	Frame_Shift_Del	DEL	ENST00000380191.4	hg19	CCDS7071.1																																																																																			.	.		0.368	GDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046580.1	NM_001494	
SMC4	10051	hgsc.bcm.edu	37	3	160131299	160131299	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:160131299delA	ENST00000357388.3	+	8	1470	c.1019delA	c.(1018-1020)caafs	p.Q340fs	RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000462787.1_Frame_Shift_Del_p.Q340fs|SMC4_ENST00000360111.2_Frame_Shift_Del_p.Q340fs|SMC4_ENST00000469762.1_Frame_Shift_Del_p.Q315fs|SMC4_ENST00000344722.5_Frame_Shift_Del_p.Q340fs	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	340					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			ATGGAAACTCAAAAGGAAAAA	0.289																																					p.Q340fs		Atlas-INDEL	.											.	SMC4	135	.	0			c.1018delC						.						36.0	37.0	36.0					3																	160131299		2174	4267	6441	SO:0001589	frameshift_variant	10051	exon7			.	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"""Structural maintenance of chromosomes proteins"""	14013	protein-coding gene	gene with protein product		605575	"""SMC4 (structural maintenance of chromosomes 4, yeast)-like 1"", ""SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"""	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.1019delA	chr3.hg19:g.160131299delA	ENSP00000349961:p.Gln340fs	109.0	0.0		183.0	13.0	NM_005496	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Frame_Shift_Del	DEL	ENST00000357388.3	hg19	CCDS3189.1																																																																																			.	.		0.289	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1		
TRAF3IP1	26146	hgsc.bcm.edu	37	2	239237915	239237915	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:239237915delA	ENST00000373327.4	+	5	1069	c.847delA	c.(847-849)aaafs	p.K283fs	TRAF3IP1_ENST00000391994.2_Frame_Shift_Del_p.K283fs|TRAF3IP1_ENST00000391993.3_Frame_Shift_Del_p.K283fs	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	283	Abolishes microtubules-binding when missing.|DISC1-interaction domain.				cilium assembly (GO:0042384)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic heart tube development (GO:0035050)|intraciliary transport (GO:0042073)|negative regulation of defense response to virus (GO:0050687)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube patterning (GO:0021532)|post-anal tail morphogenesis (GO:0036342)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(2)	23		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)		acggagagtgaaaaacgggga	0.542																																					p.V282fs		Atlas-INDEL	.											TRAF3IP1,right_upper_lobe,carcinoma,0,1	TRAF3IP1	58	.	0			c.846delG						.						77.0	89.0	85.0					2																	239237915		2200	4299	6499	SO:0001589	frameshift_variant	26146	exon5			.	AF230877	CCDS33415.1, CCDS46557.1	2q37.3	2014-02-21			ENSG00000204104	ENSG00000204104		"""Intraflagellar transport homologs"""	17861	protein-coding gene	gene with protein product	"""microtubule interacting protein that associates with TRAF3"""	607380				10791955, 12935900	Standard	NM_015650		Approved	MIP-T3, DKFZP434F124, MIPT3, IFT54	uc002vye.3	Q8TDR0	OTTHUMG00000152872	ENST00000373327.4:c.847delA	chr2.hg19:g.239237915delA	ENSP00000362424:p.Lys283fs	100.0	0.0		152.0	12.0	NM_015650	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Frame_Shift_Del	DEL	ENST00000373327.4	hg19	CCDS33415.1																																																																																			.	.		0.542	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650	
SDCBP2	27111	hgsc.bcm.edu	37	20	1291473	1291473	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:1291473delG	ENST00000360779.3	-	8	968	c.795delC	c.(793-795)cccfs	p.P265fs	SDCBP2_ENST00000467129.1_5'UTR|SDCBP2_ENST00000381812.1_Frame_Shift_Del_p.P265fs|SDCBP2_ENST00000381808.3_Frame_Shift_Del_p.P180fs|SDCBP2_ENST00000339987.3_Frame_Shift_Del_p.P265fs	NM_080489.4	NP_536737.3	Q9H190	SDCB2_HUMAN	syndecan binding protein (syntenin) 2	265	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	7						AGATCACACTGGGGATGATGG	0.572																																					p.S266fs		Atlas-INDEL	.											.	SDCBP2	78	.	0			c.796delA						.						169.0	145.0	153.0					20																	1291473		2203	4300	6503	SO:0001589	frameshift_variant	27111	exon8			.	AF131809	CCDS13013.1, CCDS42848.1	20p13	2008-07-02			ENSG00000125775	ENSG00000125775			15756	protein-coding gene	gene with protein product						11152476	Standard	NM_080489		Approved	ST-2, SITAC18	uc021vzn.1	Q9H190	OTTHUMG00000031661	ENST00000360779.3:c.795delC	chr20.hg19:g.1291473delG	ENSP00000354013:p.Pro265fs	195.0	0.0		193.0	12.0	NM_080489	O95892|Q5W0X1|Q9BZ42|Q9H567|Q9NRY8	Frame_Shift_Del	DEL	ENST00000360779.3	hg19	CCDS42848.1																																																																																			.	.		0.572	SDCBP2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077513.2	NM_080489	
TRIM32	22954	hgsc.bcm.edu	37	9	119461528	119461528	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:119461528delG	ENST00000450136.1	+	2	1668	c.1507delG	c.(1507-1509)gggfs	p.G503fs	ASTN2_ENST00000361477.3_Intron|ASTN2_ENST00000313400.4_Intron|ASTN2_ENST00000373996.3_Intron|ASTN2_ENST00000361209.2_Intron|TRIM32_ENST00000373983.2_Frame_Shift_Del_p.G503fs	NM_001099679.1|NM_012210.3	NP_001093149.1|NP_036342.2	Q13049	TRI32_HUMAN	tripartite motif containing 32	503					fat cell differentiation (GO:0045444)|innate immune response (GO:0045087)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of proteolysis (GO:0045862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of type I interferon production (GO:0032479)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|striated muscle myosin thick filament (GO:0005863)	ligase activity (GO:0016874)|myosin binding (GO:0017022)|protein self-association (GO:0043621)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|translation initiation factor binding (GO:0031369)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	26						TCGAGGATCAGGGGTGGTCAA	0.522																																					p.S502fs	Esophageal Squamous(92;212 1916 19711 26951)	Atlas-INDEL	.											.	TRIM32	67	.	0			c.1506delA						.						84.0	70.0	75.0					9																	119461528		2203	4300	6503	SO:0001589	frameshift_variant	22954	exon2			.	U18543	CCDS6817.1	9q33.1	2014-09-17	2011-01-25		ENSG00000119401	ENSG00000119401		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16380	protein-coding gene	gene with protein product		602290	"""limb girdle muscular dystrophy 2H (autosomal recessive)"", ""tripartite motif-containing 32"""	LGMD2H		11331580, 7778269, 16606853	Standard	NM_001099679		Approved	HT2A, TATIP, BBS11	uc004bjx.2	Q13049	OTTHUMG00000021026	ENST00000450136.1:c.1507delG	chr9.hg19:g.119461528delG	ENSP00000408292:p.Gly503fs	161.0	0.0		171.0	11.0	NM_012210	Q9NQP8	Frame_Shift_Del	DEL	ENST00000450136.1	hg19	CCDS6817.1																																																																																			.	.		0.522	TRIM32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055466.2	NM_012210	
ANKRD12	23253	hgsc.bcm.edu	37	18	9257212	9257212	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:9257212delT	ENST00000262126.4	+	9	4187	c.3947delT	c.(3946-3948)attfs	p.I1316fs	ANKRD12_ENST00000400020.3_Frame_Shift_Del_p.I1293fs|ANKRD12_ENST00000383440.2_Frame_Shift_Del_p.I1293fs|RP11-888D10.4_ENST00000609701.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1316						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						CCTTCTGTCATTTGTGAACAT	0.403																																					p.I1316fs		Atlas-INDEL	.											.	ANKRD12	167	.	0			c.3946delA						.						133.0	126.0	128.0					18																	9257212		2203	4300	6503	SO:0001589	frameshift_variant	23253	exon9			.	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.3947delT	chr18.hg19:g.9257212delT	ENSP00000262126:p.Ile1316fs	142.0	0.0		134.0	10.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Frame_Shift_Del	DEL	ENST00000262126.4	hg19	CCDS11843.1																																																																																			.	.		0.403	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
MMP19	4327	hgsc.bcm.edu	37	12	56233389	56233389	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56233389delC	ENST00000322569.4	-	5	748	c.657delG	c.(655-657)gggfs	p.G219fs	MMP19_ENST00000547487.1_5'Flank|MMP19_ENST00000548629.1_Frame_Shift_Del_p.G196fs|MMP19_ENST00000409200.3_Intron|MMP19_ENST00000394182.1_5'Flank	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	219					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	AGTGCCCAAGCCCCAGAGCAT	0.612																																					p.L220fs		Atlas-INDEL	.											.	MMP19	61	.	0			c.658delC						.						73.0	59.0	64.0					12																	56233389		2203	4300	6503	SO:0001589	frameshift_variant	4327	exon5			.	X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"""matrix metalloproteinase 19"""	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.657delG	chr12.hg19:g.56233389delC	ENSP00000313437:p.Gly219fs	184.0	0.0		180.0	12.0	NM_002429	B4E030|O15278|O95606|Q99580	Frame_Shift_Del	DEL	ENST00000322569.4	hg19	CCDS8895.1																																																																																			.	.		0.612	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429	
LRRFIP2	9209	hgsc.bcm.edu	37	3	37149563	37149563	+	Splice_Site	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:37149563delC	ENST00000336686.4	-	13	795		c.e13+1		LRRFIP2_ENST00000421307.1_Splice_Site|LRRFIP2_ENST00000354379.4_Intron|LRRFIP2_ENST00000396428.2_Intron|LRRFIP2_ENST00000421276.2_Intron|LRRFIP2_ENST00000440230.1_Intron			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2						Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						AGACAGCTCACCCCTGGACTG	0.378																																					.		Atlas-INDEL	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.714+2G>-						.						88.0	84.0	85.0					3																	37149563		2203	4300	6503	SO:0001630	splice_region_variant	9209	exon15			.	AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.714+1G>-	chr3.hg19:g.37149563delC		110.0	0.0		154.0	10.0	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Splice_Site	DEL	ENST00000336686.4	hg19	CCDS2664.1																																																																																			.	.		0.378	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309	Intron
FIG4	9896	hgsc.bcm.edu	37	6	110098164	110098164	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:110098164delT	ENST00000230124.3	+	16	1914	c.1790delT	c.(1789-1791)gttfs	p.V597fs	FIG4_ENST00000441478.2_Frame_Shift_Del_p.V320fs	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	597					cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		TTCCTGGGAGTTTTCCATCCC	0.368																																					p.V597fs		Atlas-INDEL	.											.	FIG4	77	.	0			c.1789delG						.						61.0	66.0	64.0					6																	110098164		2203	4300	6503	SO:0001589	frameshift_variant	9896	exon16			.	D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"""KIAA0274"", ""FIG4 homolog (S. cerevisiae)"", ""FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"""	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.1790delT	chr6.hg19:g.110098164delT	ENSP00000230124:p.Val597fs	155.0	0.0		200.0	12.0	NM_014845	Q53H49|Q5TCS6	Frame_Shift_Del	DEL	ENST00000230124.3	hg19	CCDS5078.1																																																																																			.	.		0.368	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845	
SORCS2	57537	hgsc.bcm.edu	37	4	7716932	7716932	+	Frame_Shift_Del	DEL	T	T	-	rs6816604	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:7716932delT	ENST00000507866.2	+	17	2255	c.2146delT	c.(2146-2148)tccfs	p.S718fs	SORCS2_ENST00000329016.9_Frame_Shift_Del_p.S546fs	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	718					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						TGAGCGCTCCTCCTCCTCAGA	0.592																																					p.S715fs		Atlas-INDEL	.											.	SORCS2	98	.	0			c.2145delC						.						145.0	153.0	151.0					4																	7716932		2012	4155	6167	SO:0001589	frameshift_variant	57537	exon17			.	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.2146delT	chr4.hg19:g.7716932delT	ENSP00000422185:p.Ser718fs	153.0	0.0		150.0	11.0	NM_020777	Q9P2L7	Frame_Shift_Del	DEL	ENST00000507866.2	hg19	CCDS47008.1																																																																																			.	.		0.592	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777	
SUCO	51430	hgsc.bcm.edu	37	1	172571330	172571330	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:172571330delA	ENST00000263688.3	+	21	3364	c.3145delA	c.(3145-3147)aaafs	p.K1049fs	SUCO_ENST00000608151.1_Frame_Shift_Del_p.K1201fs|SUCO_ENST00000367723.4_Frame_Shift_Del_p.K1200fs|SUCO_ENST00000610051.1_Frame_Shift_Del_p.K678fs	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	1049					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											AAAACTTCCTAAAAGTAATCA	0.299																																					p.P1048fs		Atlas-INDEL	.											.	.	.	.	0			c.3144delT						.						78.0	72.0	74.0					1																	172571330		2201	4300	6501	SO:0001589	frameshift_variant	51430	exon21			.	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"""SUN-like protein 1"", ""osteopotentia"""		"""chromosome 1 open reading frame 9"""	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.3145delA	chr1.hg19:g.172571330delA	ENSP00000263688:p.Lys1049fs	84.0	0.0		159.0	12.0	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Frame_Shift_Del	DEL	ENST00000263688.3	hg19	CCDS1303.1																																																																																			.	.		0.299	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227	
POMT1	10585	hgsc.bcm.edu	37	9	134390827	134390827	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:134390827delC	ENST00000372228.3	+	13	1435	c.1256delC	c.(1255-1257)gccfs	p.A419fs	POMT1_ENST00000419118.2_Frame_Shift_Del_p.A245fs|POMT1_ENST00000423007.1_Frame_Shift_Del_p.A397fs|POMT1_ENST00000341012.7_Frame_Shift_Del_p.A343fs|POMT1_ENST00000404875.2_Frame_Shift_Del_p.A280fs|POMT1_ENST00000354713.4_Frame_Shift_Del_p.A367fs|POMT1_ENST00000485278.1_3'UTR|POMT1_ENST00000402686.3_Frame_Shift_Del_p.A397fs|RP11-334J6.6_ENST00000415423.1_RNA|POMT1_ENST00000541219.1_Frame_Shift_Del_p.A175fs	NM_007171.3	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1	419	MIR 2. {ECO:0000255|PROSITE- ProRule:PRU00131}.				carbohydrate metabolic process (GO:0005975)|extracellular matrix organization (GO:0030198)|mannosylation (GO:0097502)|multicellular organismal development (GO:0007275)|protein O-linked glycosylation (GO:0006493)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|sarcoplasmic reticulum (GO:0016529)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannosyltransferase activity (GO:0000030)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	31		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)		GATGTTGCAGCCCCCCTGAGC	0.507																																					p.A419fs		Atlas-INDEL	.											.	POMT1	59	.	0			c.1255delG						.						120.0	119.0	119.0					9																	134390827		2203	4300	6503	SO:0001589	frameshift_variant	10585	exon13			.	AF095136	CCDS6943.1, CCDS43894.1, CCDS43895.1, CCDS48045.1	9q34.1	2014-09-17			ENSG00000130714	ENSG00000130714	2.4.1.109	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	9202	protein-coding gene	gene with protein product	"""dolichyl-phosphate-mannose-protein mannosyltransferase"""	607423				10366449	Standard	NM_001077366		Approved	LGMD2K	uc004cav.3	Q9Y6A1	OTTHUMG00000020826	ENST00000372228.3:c.1256delC	chr9.hg19:g.134390827delC	ENSP00000361302:p.Ala419fs	137.0	0.0		156.0	11.0	NM_007171	B3KQG0|B4DIF0|Q5JT01|Q5JT06|Q5JT08|Q8NC91|Q8TCA9|Q9NX32|Q9NX82|Q9UNT2	Frame_Shift_Del	DEL	ENST00000372228.3	hg19	CCDS6943.1																																																																																			.	.		0.507	POMT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054737.1	NM_007171	
CSDE1	7812	hgsc.bcm.edu	37	1	115272999	115272999	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:115272999delT	ENST00000358528.4	-	12	1662	c.1236delA	c.(1234-1236)aaafs	p.K412fs	CSDE1_ENST00000339438.6_Frame_Shift_Del_p.K381fs|CSDE1_ENST00000534699.1_Frame_Shift_Del_p.K412fs|CSDE1_ENST00000261443.5_Frame_Shift_Del_p.K381fs|CSDE1_ENST00000369530.1_Frame_Shift_Del_p.K427fs|CSDE1_ENST00000530886.1_Frame_Shift_Del_p.K282fs|CSDE1_ENST00000438362.2_Frame_Shift_Del_p.K458fs|Y_RNA_ENST00000365030.1_RNA	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	412					male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-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)		CCTTGGGAAGTTTTTTAATCC	0.358																																					p.L459fs		Atlas-INDEL	.											.	CSDE1	145	.	0			c.1375delC						.						81.0	86.0	85.0					1																	115272999		2203	4300	6503	SO:0001589	frameshift_variant	7812	exon13			.		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"""upstream of NRAS"""	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.1236delA	chr1.hg19:g.115272999delT	ENSP00000351329:p.Lys412fs	72.0	0.0		116.0	10.0	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Frame_Shift_Del	DEL	ENST00000358528.4	hg19	CCDS30812.1																																																																																			.	.		0.358	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158	
PARP14	54625	hgsc.bcm.edu	37	3	122423544	122423544	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:122423544delT	ENST00000474629.2	+	8	3755	c.3489delT	c.(3487-3489)actfs	p.T1163fs		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1163	Macro 2. {ECO:0000255|PROSITE- ProRule:PRU00490}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		AGCTGAAAACTTTACAAGAGG	0.373																																					p.T1163fs		Atlas-INDEL	.											.	PARP14	242	.	0			c.3488delC						.						38.0	35.0	36.0					3																	122423544		1826	4068	5894	SO:0001589	frameshift_variant	54625	exon8			.	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.3489delT	chr3.hg19:g.122423544delT	ENSP00000418194:p.Thr1163fs	204.0	0.0		225.0	14.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Frame_Shift_Del	DEL	ENST00000474629.2	hg19	CCDS46894.1																																																																																			.	.		0.373	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
ACAN	176	hgsc.bcm.edu	37	15	89400592	89400592	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:89400592delA	ENST00000561243.1	+	11	4776	c.4776delA	c.(4774-4776)ggafs	p.G1592fs	ACAN_ENST00000439576.2_Frame_Shift_Del_p.G1592fs|ACAN_ENST00000559004.1_Frame_Shift_Del_p.G1592fs|ACAN_ENST00000352105.7_Frame_Shift_Del_p.G1592fs			P16112	PGCA_HUMAN	aggrecan	1626	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TGCCTTCTGGAAAAGAAGACT	0.532																																					p.G1592fs		Atlas-INDEL	.											.	ACAN	220	.	0			c.4775delG						.						101.0	106.0	105.0					15																	89400592		1886	4126	6012	SO:0001589	frameshift_variant	176	exon12			.	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.4776delA	chr15.hg19:g.89400592delA	ENSP00000453342:p.Gly1592fs	115.0	0.0		165.0	10.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Frame_Shift_Del	DEL	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.		0.532	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
IQCB1	9657	hgsc.bcm.edu	37	3	121527845	121527845	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:121527845delT	ENST00000310864.6	-	6	619	c.405delA	c.(403-405)aaafs	p.K135fs	IQCB1_ENST00000349820.6_Frame_Shift_Del_p.K135fs	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	135					cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)			NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		GTAATTCATCTTTTTCTTCAG	0.328																																					p.D136fs		Atlas-INDEL	.											IQCB1,NS,carcinoma,0,1	IQCB1	50	.	0			c.406delG						.						57.0	63.0	61.0					3																	121527845		2203	4300	6503	SO:0001589	frameshift_variant	9657	exon6			.	D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"""nephrocystin-5"""	609237	"""IQ calmodulin-binding motif containing 1"""			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.405delA	chr3.hg19:g.121527845delT	ENSP00000311505:p.Lys135fs	181.0	0.0		221.0	14.0	NM_001023571	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Frame_Shift_Del	DEL	ENST00000310864.6	hg19	CCDS33837.1																																																																																			.	.		0.328	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642	
HSPA2	3306	hgsc.bcm.edu	37	14	65008143	65008143	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:65008143delG	ENST00000394709.1	+	2	652	c.576delG	c.(574-576)gcgfs	p.A192fs	HSPA2_ENST00000554883.1_3'UTR|HSPA2_ENST00000247207.6_Frame_Shift_Del_p.A192fs|RP11-973N13.4_ENST00000554918.1_RNA			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	192					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		AGGGCTGCGCGGGCGGCGAGA	0.632																																					p.A192fs	Pancreas(136;1211 1835 24894 31984 38227)	Atlas-INDEL	.											HSPA2,NS,carcinoma,0,1	HSPA2	83	.	0			c.575delC						.						83.0	91.0	88.0					14																	65008143		2203	4300	6503	SO:0001589	frameshift_variant	3306	exon1			.	L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"""Heat shock proteins / HSP70"""	5235	protein-coding gene	gene with protein product		140560	"""heat shock 70kD protein 2"""				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311	ENST00000394709.1:c.576delG	chr14.hg19:g.65008143delG	ENSP00000378199:p.Ala192fs	133.0	0.0		162.0	10.0	NM_021979	Q15508|Q53XM3|Q9UE78	Frame_Shift_Del	DEL	ENST00000394709.1	hg19	CCDS9766.1																																																																																			.	.		0.632	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1		
AKAP9	10142	hgsc.bcm.edu	37	7	91726097	91726097	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:91726097delA	ENST00000359028.2	+	41	10061	c.9836delA	c.(9835-9837)caafs	p.Q3279fs	AKAP9_ENST00000356239.3_Frame_Shift_Del_p.Q3275fs|AKAP9_ENST00000358100.2_Frame_Shift_Del_p.Q3225fs			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3279					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GAATCCCAGCAAAAAATAGAA	0.383			T	BRAF	papillary thyroid																																p.Q3275fs		Atlas-INDEL	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	AKAP9_ENST00000356239,NS,carcinoma,0,2	AKAP9	788	.	0			c.9823delC						.						70.0	73.0	72.0					7																	91726097		2203	4300	6503	SO:0001589	frameshift_variant	10142	exon41			.	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.9836delA	chr7.hg19:g.91726097delA	ENSP00000351922:p.Gln3279fs	104.0	0.0		152.0	10.0	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Frame_Shift_Del	DEL	ENST00000359028.2	hg19																																																																																				.	.		0.383	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
ZFYVE16	9765	hgsc.bcm.edu	37	5	79732785	79732785	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:79732785delA	ENST00000338008.5	+	3	461	c.281delA	c.(280-282)gaafs	p.E94fs	ZFYVE16_ENST00000510158.1_Frame_Shift_Del_p.E94fs|ZFYVE16_ENST00000505560.1_Frame_Shift_Del_p.E94fs	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	94					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)		ATACAAAATGAAAAAAATGTA	0.378																																					p.E94fs	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-Indel,Pindel	.											ZFYVE16,colon,carcinoma,0,1	ZFYVE16	100	.	0			c.280delG						.						77.0	81.0	79.0					5																	79732785		2203	4300	6503	SO:0001589	frameshift_variant	9765	exon4			.	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.281delA	chr5.hg19:g.79732785delA	ENSP00000337159:p.Glu94fs	125.0	0.0		263.0	16.0	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Frame_Shift_Del	DEL	ENST00000338008.5	hg19	CCDS4050.1																																																																																			.	.		0.378	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733	
PSRC1	84722	hgsc.bcm.edu	37	1	109823047	109823047	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:109823047delG	ENST00000438534.2	-	6	1197	c.1059delC	c.(1057-1059)cccfs	p.P353fs	PSRC1_ENST00000409138.2_Frame_Shift_Del_p.P353fs|PSRC1_ENST00000369903.2_Frame_Shift_Del_p.P323fs|PSRC1_ENST00000369904.3_Frame_Shift_Del_p.Q290fs|PSRC1_ENST00000369907.3_Frame_Shift_Del_p.P323fs|PSRC1_ENST00000409267.1_Frame_Shift_Del_p.P323fs|PSRC1_ENST00000369909.2_Frame_Shift_Del_p.P323fs	NM_001005290.3	NP_001005290.1	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1	353	Pro/Ser-rich.				microtubule bundle formation (GO:0001578)|mitotic metaphase plate congression (GO:0007080)|negative regulation of cell growth (GO:0030308)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mitotic spindle organization (GO:0060236)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	microtubule binding (GO:0008017)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	7		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0286)|Lung(183;0.0658)|COAD - Colon adenocarcinoma(174;0.112)|Epithelial(280;0.188)|all cancers(265;0.213)		CCACTTTCCTGGGGGGCTGCA	0.547																																					p.R324fs		Atlas-INDEL	.											.	PSRC1	12	.	0			c.970delA						.						38.0	43.0	42.0					1																	109823047		2203	4300	6503	SO:0001589	frameshift_variant	84722	exon7			.		CCDS797.1, CCDS30791.1	1p13.3	2008-02-05			ENSG00000134222	ENSG00000134222			24472	protein-coding gene	gene with protein product	"""differential display and activated by p53"""	613126				12427559, 10618717	Standard	NM_001032291		Approved	DDA3	uc001dxd.3	Q6PGN9	OTTHUMG00000012000	ENST00000438534.2:c.1059delC	chr1.hg19:g.109823047delG	ENSP00000413591:p.Pro353fs	87.0	0.0		159.0	13.0	NM_001032291	Q5T2Z3|Q6ZTI8|Q71MG3|Q9BV77	Frame_Shift_Del	DEL	ENST00000438534.2	hg19																																																																																				.	.		0.547	PSRC1-202	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335567.3	NM_032636	
ERAP2	64167	hgsc.bcm.edu	37	5	96232481	96232481	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:96232481delA	ENST00000437043.3	+	9	2128	c.1417delA	c.(1417-1419)aaafs	p.K473fs	ERAP2_ENST00000515095.1_3'UTR|ERAP2_ENST00000379904.4_Frame_Shift_Del_p.K428fs|CTD-2260A17.2_ENST00000501338.1_Intron	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	473					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)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		GGGTGAGGAGAAATTCCAGAA	0.323																																					p.E472fs		Atlas-INDEL	.											.	ERAP2	77	.	0			c.1416delG						.						78.0	86.0	83.0					5																	96232481		2200	4299	6499	SO:0001589	frameshift_variant	64167	exon9			.	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"""leukocyte-derived arginine aminopeptidase"""	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.1417delA	chr5.hg19:g.96232481delA	ENSP00000400376:p.Lys473fs	119.0	0.0		171.0	11.0	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Frame_Shift_Del	DEL	ENST00000437043.3	hg19	CCDS4086.1																																																																																			.	.		0.323	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
SEL1L2	80343	hgsc.bcm.edu	37	20	13899678	13899678	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:13899678delT	ENST00000284951.5	-	4	449	c.375delA	c.(373-375)aaafs	p.K125fs	SEL1L2_ENST00000378072.5_Frame_Shift_Del_p.K125fs|SEL1L2_ENST00000486903.1_5'UTR			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	125						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						CTTCTTTTTGTTTTTGGCTTT	0.343																																					p.Q126fs		Atlas-INDEL	.											.	SEL1L2	103	.	0			c.376delC						.						167.0	151.0	156.0					20																	13899678		1823	4085	5908	SO:0001589	frameshift_variant	80343	exon4			.	AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"""chromosome 20 open reading frame 50"""	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.375delA	chr20.hg19:g.13899678delT	ENSP00000284951:p.Lys125fs	138.0	0.0		144.0	11.0	NM_001271539	B4DXX5	Frame_Shift_Del	DEL	ENST00000284951.5	hg19																																																																																				.	.		0.343	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229	
MUC4	4585	hgsc.bcm.edu	37	3	195511523	195511523	+	Frame_Shift_Del	DEL	C	C	-	rs142766505	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:195511523delC	ENST00000463781.3	-	2	7387	c.6928delG	c.(6928-6930)gctfs	p.A2310fs	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Frame_Shift_Del_p.A2310fs|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGAGGAAGCGTCGGTGACA	0.582																																					p.A2310fs		Atlas-INDEL	.											.	MUC4	1505	.	0			c.6929delC						.						4.0	5.0	5.0					3																	195511523		472	1216	1688	SO:0001589	frameshift_variant	4585	exon2			.	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6928delG	chr3.hg19:g.195511523delC	ENSP00000417498:p.Ala2310fs	66.0	0.0		127.0	11.0	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Frame_Shift_Del	DEL	ENST00000463781.3	hg19	CCDS54700.1																																																																																			.	.		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PCMTD1	115294	hgsc.bcm.edu	37	8	52773460	52773460	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:52773460delA	ENST00000360540.5	-	3	658	c.252delT	c.(250-252)tttfs	p.F84fs	PCMTD1_ENST00000519559.1_Intron|PCMTD1_ENST00000522514.1_Frame_Shift_Del_p.F84fs|PCMTD1_ENST00000544451.1_Intron|PCMTD1_ENST00000521344.1_Frame_Shift_Del_p.F84fs	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	84						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				CCAGGTTAAGAAAAGACAATC	0.338																																					p.L85fs		Atlas-INDEL	.											.	PCMTD1	73	.	0			c.253delC						.						87.0	83.0	85.0					8																	52773460		2203	4300	6503	SO:0001589	frameshift_variant	115294	exon2			.		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.252delT	chr8.hg19:g.52773460delA	ENSP00000353739:p.Phe84fs	93.0	0.0		202.0	15.0	NM_052937	Q96FK9	Frame_Shift_Del	DEL	ENST00000360540.5	hg19	CCDS6148.1																																																																																			.	.		0.338	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937	
MYH14	79784	hgsc.bcm.edu	37	19	50812903	50812903	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:50812903delC	ENST00000596571.1	+	40	5844	c.5844delC	c.(5842-5844)ggcfs	p.G1948fs	MYH14_ENST00000262269.8_Frame_Shift_Del_p.G1989fs|MYH14_ENST00000425460.1_Frame_Shift_Del_p.G1956fs|MYH14_ENST00000376970.2_Frame_Shift_Del_p.G1981fs|CTB-191K22.5_ENST00000595563.1_RNA|MYH14_ENST00000601313.1_Frame_Shift_Del_p.G1989fs|MYH14_ENST00000598205.1_Frame_Shift_Del_p.G1956fs|MYH14_ENST00000440075.2_Frame_Shift_Del_p.G1989fs			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1948					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)		ACAGACGCGGCCCCCTCACCT	0.642																																					p.G1989fs		Atlas-INDEL	.											.	MYH14	261	.	0			c.5966delG						.						22.0	23.0	23.0					19																	50812903		1975	4144	6119	SO:0001589	frameshift_variant	79784	exon43			.	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.5844delC	chr19.hg19:g.50812903delC	ENSP00000472819:p.Gly1948fs	154.0	0.0		141.0	10.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Frame_Shift_Del	DEL	ENST00000596571.1	hg19	CCDS59411.1																																																																																			.	.		0.642	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
SWT1	54823	hgsc.bcm.edu	37	1	185175808	185175808	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	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	109.0	0.0		176.0	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	
CHD2	1106	hgsc.bcm.edu	37	15	93540530	93540530	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr15:93540530delG	ENST00000394196.4	+	30	4850	c.3782delG	c.(3781-3783)tggfs	p.W1261fs	CHD2_ENST00000557381.1_Frame_Shift_Del_p.W1261fs	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1261					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GATGTAGAGTGGGGGGTGGAA	0.413																																					p.W1261fs		Atlas-INDEL	.											.	CHD2	280	.	0			c.3781delT						.						139.0	138.0	138.0					15																	93540530		2197	4298	6495	SO:0001589	frameshift_variant	1106	exon30			.	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.3782delG	chr15.hg19:g.93540530delG	ENSP00000377747:p.Trp1261fs	159.0	0.0		161.0	11.0	NM_001271	C6G482|Q96IP5	Frame_Shift_Del	DEL	ENST00000394196.4	hg19	CCDS10374.2																																																																																			.	.		0.413	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
FZD6	8323	hgsc.bcm.edu	37	8	104330820	104330820	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr8:104330820delT	ENST00000358755.4	+	3	497	c.180delT	c.(178-180)catfs	p.H60fs	FZD6_ENST00000540287.1_Intron|FZD6_ENST00000522566.1_Frame_Shift_Del_p.H60fs|FZD6_ENST00000523739.1_Frame_Shift_Del_p.H28fs	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	60	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			TTTAATAGCATTTTCTTCCTC	0.299																																					p.H60fs		Atlas-INDEL	.											.	FZD6	61	.	0			c.179delA						.						70.0	70.0	70.0					8																	104330820		2203	4300	6503	SO:0001589	frameshift_variant	8323	exon3			.	AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930		"""GPCR / Class F : Frizzled receptors"""	4044	protein-coding gene	gene with protein product		603409	"""frizzled (Drosophila) homolog 6"", ""frizzled homolog 6 (Drosophila)"", ""frizzled 6, seven transmembrane spanning receptor"", ""frizzled family receptor 6"""			9480858, 14747478	Standard	NM_003506		Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.180delT	chr8.hg19:g.104330820delT	ENSP00000351605:p.His60fs	98.0	0.0		299.0	18.0	NM_003506	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	Frame_Shift_Del	DEL	ENST00000358755.4	hg19	CCDS6298.1																																																																																			.	.		0.299	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380560.1	NM_003506	
R3HDML	140902	hgsc.bcm.edu	37	20	42979399	42979399	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:42979399delG	ENST00000217043.2	+	5	901	c.729delG	c.(727-729)aagfs	p.K243fs	RP5-881L22.5_ENST00000430481.2_RNA|RP5-881L22.5_ENST00000438702.1_RNA	NM_178491.2	NP_848586.1	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like	243						extracellular region (GO:0005576)	peptidase inhibitor activity (GO:0030414)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)	21		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			TGTGCTTCAAGGGGCTGAAAT	0.552																																					p.K243fs		Atlas-INDEL	.											.	R3HDML	33	.	0			c.728delA						.						159.0	139.0	146.0					20																	42979399		2203	4300	6503	SO:0001589	frameshift_variant	140902	exon5			.	BC107048	CCDS13329.1	20q13.12	2007-04-26	2005-09-02		ENSG00000101074	ENSG00000101074			16249	protein-coding gene	gene with protein product			"""R3H domain (binds single-stranded nucleic acids) containing-like"""				Standard	NM_178491		Approved	dJ881L22.3	uc002xls.2	Q9H3Y0	OTTHUMG00000032524	ENST00000217043.2:c.729delG	chr20.hg19:g.42979399delG	ENSP00000217043:p.Lys243fs	227.0	0.0		245.0	16.0	NM_178491		Frame_Shift_Del	DEL	ENST00000217043.2	hg19	CCDS13329.1																																																																																			.	.		0.552	R3HDML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079344.1	NM_178491	
PLOD2	5352	hgsc.bcm.edu	37	3	145804616	145804616	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:145804616delG	ENST00000360060.3	-	10	1262	c.1085delC	c.(1084-1086)ccafs	p.P362fs	PLOD2_ENST00000282903.5_Frame_Shift_Del_p.P362fs|PLOD2_ENST00000461497.1_5'Flank|PLOD2_ENST00000494950.1_Frame_Shift_Del_p.P307fs|RP11-274H2.2_ENST00000480247.1_RNA	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	362					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	ATTTTCTTCTGGTCCTACTAT	0.259																																					p.P362fs		Atlas-INDEL	.											.	PLOD2	81	.	0			c.1086delA						.						57.0	51.0	53.0					3																	145804616		2176	4274	6450	SO:0001589	frameshift_variant	5352	exon10			.	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"""lysyl hydroxlase 2"""	601865	"""procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"""			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.1085delC	chr3.hg19:g.145804616delG	ENSP00000353170:p.Pro362fs	114.0	0.0		159.0	10.0	NM_182943	B3KWS3|Q59ED2|Q8N170	Frame_Shift_Del	DEL	ENST00000360060.3	hg19	CCDS3131.1																																																																																			.	.		0.259	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935	
RALA	5898	hgsc.bcm.edu	37	7	39745787	39745787	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:39745787delA	ENST00000005257.2	+	5	944	c.564delA	c.(562-564)ggafs	p.G188fs	AC004837.5_ENST00000435766.1_RNA|RALA_ENST00000468201.1_3'UTR	NM_005402.3	NP_005393.2	P11233	RALA_HUMAN	v-ral simian leukemia viral oncogene homolog A (ras related)	188					actin cytoskeleton reorganization (GO:0031532)|chemotaxis (GO:0006935)|cytokinesis (GO:0000910)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|membrane raft localization (GO:0051665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of filopodium assembly (GO:0051491)|Ras protein signal transduction (GO:0007265)|regulation of exocytosis (GO:0017157)|signal transduction (GO:0007165)|viral process (GO:0016032)	cell surface (GO:0009986)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(9)|skin(3)	16						AAAAGAATGGAAAAAAGAAGA	0.308																																					p.G188fs		Atlas-INDEL	.											.	RALA	39	.	0			c.563delG						.						89.0	99.0	96.0					7																	39745787		2203	4296	6499	SO:0001589	frameshift_variant	5898	exon5			.		CCDS5460.1	7p22-p15	2014-05-09			ENSG00000006451	ENSG00000006451			9839	protein-coding gene	gene with protein product	"""RAS-like protein A"", ""Ras-related protein Ral-A"", ""Ras family small GTP binding protein RALA"", ""ras related GTP binding protein A"""	179550		RAL		3292391	Standard	NM_005402		Approved		uc003thd.3	P11233	OTTHUMG00000128775	ENST00000005257.2:c.564delA	chr7.hg19:g.39745787delA	ENSP00000005257:p.Gly188fs	228.0	0.0		330.0	23.0	NM_005402	A4D1W3	Frame_Shift_Del	DEL	ENST00000005257.2	hg19	CCDS5460.1																																																																																			.	.		0.308	RALA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250696.2	NM_005402	
PCYT1A	5130	hgsc.bcm.edu	37	3	195968954	195968954	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:195968954delA	ENST00000292823.2	-	8	745	c.573delT	c.(571-573)tttfs	p.F191fs	PCYT1A_ENST00000431016.1_Frame_Shift_Del_p.F191fs|PCYT1A_ENST00000419333.1_Frame_Shift_Del_p.F191fs	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	191			F -> L (in SMDCRD). {ECO:0000269|PubMed:24387990}.		CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)			cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	GTGTTGGAGCAAACATGCCTA	0.468																																					p.A192fs		Atlas-INDEL	.											.	PCYT1A	34	.	0			c.574delG						.						117.0	104.0	108.0					3																	195968954		2203	4300	6503	SO:0001589	frameshift_variant	5130	exon8			.	L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	2.7.7.15		8754	protein-coding gene	gene with protein product	"""phosphate cytidylyltransferase 1, choline, alpha isoform"""	123695	"""phosphate cytidylyltransferase 1, choline, alpha isoform"""	PCYT1		7918629	Standard	NM_005017		Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.573delT	chr3.hg19:g.195968954delA	ENSP00000292823:p.Phe191fs	82.0	0.0		132.0	10.0	NM_005017	A9LYK9|D3DXB1|Q86Y88	Frame_Shift_Del	DEL	ENST00000292823.2	hg19	CCDS3315.1																																																																																			.	.		0.468	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	NM_005017	
XRCC5	7520	hgsc.bcm.edu	37	2	217057430	217057430	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:217057430delA	ENST00000392133.3	+	20	2474	c.2013delA	c.(2011-2013)ttafs	p.L671fs	XRCC5_ENST00000392132.2_Frame_Shift_Del_p.L671fs			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	671					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to fatty acid (GO:0071398)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|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)|hematopoietic stem cell differentiation (GO:0060218)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of type I interferon production (GO:0032481)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	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)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|kidney(3)|large_intestine(8)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		TTAAACAATTAAATCATTTCT	0.338								Non-homologous end-joining																													p.L671X		Atlas-INDEL	.											.	XRCC5	64	.	0			c.2012delT						.						48.0	48.0	48.0					2																	217057430		2202	4300	6502	SO:0001589	frameshift_variant	7520	exon18			.	AF039597	CCDS2402.1	2q35	2008-07-31	2008-07-31		ENSG00000079246	ENSG00000079246			12833	protein-coding gene	gene with protein product	"""Ku autoantigen, 80kDa"""	194364	"""X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kD)"""			9636207, 9214634	Standard	NM_021141		Approved	KU80, KARP-1, Ku86, KUB2	uc002vfy.3	P13010	OTTHUMG00000133059	ENST00000392133.3:c.2013delA	chr2.hg19:g.217057430delA	ENSP00000375978:p.Leu671fs	205.0	0.0		280.0	21.0	NM_021141	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	Frame_Shift_Del	DEL	ENST00000392133.3	hg19	CCDS2402.1																																																																																			.	.		0.338	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256675.3	NM_021141	
SMG1	23049	hgsc.bcm.edu	37	16	18841357	18841357	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:18841357delA	ENST00000446231.2	-	53	9436	c.9024delT	c.(9022-9024)tttfs	p.F3008fs	SMG1_ENST00000389467.3_Frame_Shift_Del_p.F3008fs			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	3008					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						TATCATCATCAAAAAAATTAA	0.363																																					p.D3009fs		Atlas-INDEL	.											.	SMG1	401	.	0			c.9025delG						.						34.0	31.0	32.0					16																	18841357		1816	4073	5889	SO:0001589	frameshift_variant	23049	exon53			.	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.9024delT	chr16.hg19:g.18841357delA	ENSP00000402515:p.Phe3008fs	123.0	0.0		157.0	11.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Frame_Shift_Del	DEL	ENST00000446231.2	hg19	CCDS45430.1																																																																																			.	.		0.363	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
PAFAH1B2	5049	hgsc.bcm.edu	37	11	117038299	117038299	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:117038299delT	ENST00000527958.1	+	6	733	c.574delT	c.(574-576)tttfs	p.F192fs	PAFAH1B2_ENST00000529887.2_Intron|PAFAH1B2_ENST00000530272.1_Intron|PAFAH1B2_ENST00000526888.1_Intron|PAFAH1B2_ENST00000419197.2_Intron	NM_002572.3	NP_002563.1	P68402	PA1B2_HUMAN	platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa)	192					brain development (GO:0007420)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|positive regulation of macroautophagy (GO:0016239)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)			kidney(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;1.68e-05)|Epithelial(105;0.000162)|all cancers(92;0.00111)		CCACGACATGTTTGATTTTCT	0.532			T	IGH@	MLCLS																																p.M191fs		Atlas-INDEL	.		Dom	yes		11	11q23	5049	"""platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa"""		L	.	PAFAH1B2	19	.	0			c.573delG						.						84.0	69.0	74.0					11																	117038299		2201	4296	6497	SO:0001589	frameshift_variant	5049	exon6			.	D63390	CCDS8380.1, CCDS53713.1, CCDS53714.1, CCDS53715.1	11q23	2011-10-24	2010-02-10			ENSG00000168092			8575	protein-coding gene	gene with protein product	"""PAF-AH1b alpha 2 subunit"""	602508	"""platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa"", ""platelet-activating factor acetylhydrolase, isoform Ib, subunit 2 (30kDa)"""			9144386, 9693049	Standard	NM_002572		Approved		uc001pqe.2	P68402		ENST00000527958.1:c.574delT	chr11.hg19:g.117038299delT	ENSP00000435289:p.Phe192fs	123.0	0.0		171.0	11.0	NM_002572	A8DPS5|A8DPS6|A8DPS7|E9PEJ5|E9PLP3|O00687|Q29459|Q6IBR6	Frame_Shift_Del	DEL	ENST00000527958.1	hg19	CCDS8380.1																																																																																			.	.		0.532	PAFAH1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392826.1	NM_002572	
USP37	57695	hgsc.bcm.edu	37	2	219350428	219350428	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:219350428delC	ENST00000258399.3	-	16	2041	c.1629delG	c.(1627-1629)gggfs	p.G543fs	USP37_ENST00000418019.1_Frame_Shift_Del_p.G543fs|USP37_ENST00000475553.1_5'UTR|USP37_ENST00000415516.1_Frame_Shift_Del_p.G471fs|USP37_ENST00000454775.1_Frame_Shift_Del_p.G543fs	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	543	USP.				G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		GAGCACACTTCCCACCACACT	0.338																																					p.K544fs		Atlas-INDEL	.											.	USP37	76	.	0			c.1630delA						.						117.0	117.0	117.0					2																	219350428		2203	4300	6503	SO:0001589	frameshift_variant	57695	exon16			.	AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913		"""Ubiquitin-specific peptidases"""	20063	protein-coding gene	gene with protein product			"""ubiquitin specific protease 37"""			12838346	Standard	NM_020935		Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000258399.3:c.1629delG	chr2.hg19:g.219350428delC	ENSP00000258399:p.Gly543fs	160.0	0.0		179.0	11.0	NM_020935	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Frame_Shift_Del	DEL	ENST00000258399.3	hg19	CCDS2418.1																																																																																			.	.		0.338	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935	
USP21	27005	hgsc.bcm.edu	37	1	161134345	161134345	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:161134345delA	ENST00000289865.8	+	10	1548	c.1327delA	c.(1327-1329)aaafs	p.K443fs	PPOX_ENST00000432542.2_5'Flank|USP21_ENST00000368001.1_Frame_Shift_Del_p.K443fs|USP21_ENST00000493054.1_3'UTR|PPOX_ENST00000544598.1_5'Flank|PPOX_ENST00000352210.5_5'Flank|PPOX_ENST00000367999.4_5'Flank|USP21_ENST00000368002.3_Frame_Shift_Del_p.K443fs|PPOX_ENST00000535223.1_5'Flank	NM_012475.4	NP_036607.3	Q9UK80	UBP21_HUMAN	ubiquitin specific peptidase 21	443	USP.				histone deubiquitination (GO:0016578)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cysteine-type peptidase activity (GO:0008234)|metal ion binding (GO:0046872)|NEDD8-specific protease activity (GO:0019784)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|prostate(3)	29	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			ATGTCGGCAGAAAACTCGAAG	0.428																																					p.Q442fs		Atlas-INDEL	.											.	USP21	63	.	0			c.1326delG						.						102.0	89.0	94.0					1																	161134345		2203	4300	6503	SO:0001589	frameshift_variant	27005	exon11			.	AF177758	CCDS30920.1	1q22	2008-04-11	2005-08-08		ENSG00000143258	ENSG00000143258		"""Ubiquitin-specific peptidases"""	12620	protein-coding gene	gene with protein product		604729	"""ubiquitin specific protease 21"""	USP23		12838346, 10799498	Standard	XM_006711273		Approved	USP16	uc010pkd.2	Q9UK80	OTTHUMG00000033154	ENST00000289865.8:c.1327delA	chr1.hg19:g.161134345delA	ENSP00000289865:p.Lys443fs	157.0	0.0		236.0	15.0	NM_001014443	Q59H60|Q5BKT5|Q5VTW9|Q5VTX0|Q9BTV1|Q9HBS2|Q9NYN4	Frame_Shift_Del	DEL	ENST00000289865.8	hg19	CCDS30920.1																																																																																			.	.		0.428	USP21-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080801.1		
HMGN4	10473	hgsc.bcm.edu	37	6	26545644	26545644	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:26545644delA	ENST00000377575.2	+	2	387	c.210delA	c.(208-210)gcafs	p.A70fs		NM_006353.2	NP_006344.1	O00479	HMGN4_HUMAN	high mobility group nucleosomal binding domain 4	70						chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)			lung(2)|skin(1)	3						ACAACCCTGCAAAAAACCGAG	0.498																																					p.A70fs		Atlas-INDEL	.											.	HMGN4	4	.	0			c.209delC						.						92.0	105.0	100.0					6																	26545644		2203	4300	6503	SO:0001589	frameshift_variant	10473	exon2			.	U90549	CCDS4615.1	6p21.3	2011-07-01	2002-07-25	2002-07-26	ENSG00000182952	ENSG00000182952		"""High-mobility group / Canonical"""	4989	protein-coding gene	gene with protein product			"""high-mobility group (nonhistone chromosomal) protein 17-like 3"""	HMG17L3		9149941, 11410162	Standard	NM_006353		Approved	NHC	uc003nig.3	O00479	OTTHUMG00000014458	ENST00000377575.2:c.210delA	chr6.hg19:g.26545644delA	ENSP00000366798:p.Ala70fs	114.0	0.0		154.0	10.0	NM_006353	B2R4I6|Q53XL9	Frame_Shift_Del	DEL	ENST00000377575.2	hg19	CCDS4615.1																																																																																			.	.		0.498	HMGN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040123.2		
ARHGAP29	9411	hgsc.bcm.edu	37	1	94670628	94670628	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:94670628delT	ENST00000260526.6	-	7	868	c.686delA	c.(685-687)aagfs	p.K229fs	ARHGAP29_ENST00000370217.3_Frame_Shift_Del_p.K229fs	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	229					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		CAAGTTAAGCTTTTTTTCAAC	0.318																																					p.K229fs		Atlas-INDEL	.											.	ARHGAP29	132	.	0			c.687delG						.						84.0	84.0	84.0					1																	94670628		2202	4298	6500	SO:0001589	frameshift_variant	9411	exon7			.		CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"""Rho GTPase activating proteins"""	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.686delA	chr1.hg19:g.94670628delT	ENSP00000260526:p.Lys229fs	153.0	0.0		232.0	16.0	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Frame_Shift_Del	DEL	ENST00000260526.6	hg19	CCDS748.1																																																																																			.	.		0.318	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815	
ABCC9	10060	hgsc.bcm.edu	37	12	22001144	22001144	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:22001144delT	ENST00000261201.4	-	23	2805	c.2806delA	c.(2806-2808)actfs	p.T936fs	ABCC9_ENST00000345162.2_Frame_Shift_Del_p.T900fs|RP11-729I10.2_ENST00000539874.1_RNA|ABCC9_ENST00000261200.4_Frame_Shift_Del_p.T936fs	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	936					defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	CGTCGGAGAGTTTTCCTCTCT	0.413																																					p.T936fs		Atlas-INDEL	.											.	ABCC9	411	.	0			c.2807delC						.						133.0	121.0	125.0					12																	22001144		2203	4300	6503	SO:0001589	frameshift_variant	10060	exon23			.	AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"""ATP binding cassette transporters / subfamily C"""	60	protein-coding gene	gene with protein product	"""sulfonylurea receptor 2"""	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.2806delA	chr12.hg19:g.22001144delT	ENSP00000261201:p.Thr936fs	328.0	0.0		187.0	12.0	NM_005691	O60707	Frame_Shift_Del	DEL	ENST00000261201.4	hg19	CCDS8694.1																																																																																			.	.		0.413	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691	
ZNF205	7755	hgsc.bcm.edu	37	16	3163480	3163480	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:3163480delC	ENST00000382192.3	+	2	254	c.49delC	c.(49-51)cccfs	p.P18fs	ZNF205-AS1_ENST00000576943.1_RNA|ZNF205_ENST00000219091.4_Frame_Shift_Del_p.P18fs|RP11-473M20.14_ENST00000576490.1_RNA|RP11-473M20.14_ENST00000575139.1_RNA|ZNF205-AS1_ENST00000572691.1_RNA	NM_001278158.1|NM_003456.2	NP_001265087.1|NP_003447.2	O95201	ZN205_HUMAN	zinc finger protein 205	18					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hydrogen peroxide biosynthetic process (GO:0010729)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20						CAAGGAGACACCCCCGGAGGT	0.552																																					p.T16fs		Atlas-INDEL	.											.	ZNF205	42	.	0			c.48delA						.						68.0	68.0	68.0					16																	3163480		2197	4300	6497	SO:0001589	frameshift_variant	7755	exon2			.	AF060865	CCDS10494.2	16p13.3	2013-01-08			ENSG00000122386	ENSG00000122386		"""Zinc fingers, C2H2-type"", ""-"""	12996	protein-coding gene	gene with protein product		603436		ZNF210		9787081	Standard	NM_003456		Approved	Zfp13	uc002cub.3	O95201	OTTHUMG00000148676	ENST00000382192.3:c.49delC	chr16.hg19:g.3163480delC	ENSP00000371627:p.Pro18fs	119.0	0.0		162.0	10.0	NM_003456	A8MZK0|D3DUB4|Q9BU95	Frame_Shift_Del	DEL	ENST00000382192.3	hg19	CCDS10494.2																																																																																			.	.		0.552	ZNF205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309057.1	NM_003456	
C9orf156	51531	hgsc.bcm.edu	37	9	100672401	100672401	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:100672401delC	ENST00000375119.3	-	4	983	c.907delG	c.(907-909)gcafs	p.A303fs	C9orf156_ENST00000478126.1_5'UTR	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	303					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)				TGTGTCTCTGCCCTGCTTCCT	0.572																																					p.A303fs		Atlas-INDEL	.											.	C9orf156	35	.	0			c.908delC						.						114.0	97.0	102.0					9																	100672401		2203	4300	6503	SO:0001589	frameshift_variant	51531	exon4			.	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.907delG	chr9.hg19:g.100672401delC	ENSP00000364260:p.Ala303fs	141.0	0.0		181.0	12.0	NM_016481	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Frame_Shift_Del	DEL	ENST00000375119.3	hg19	CCDS6730.1																																																																																			.	.		0.572	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481	
CPSF6	11052	hgsc.bcm.edu	37	12	69652587	69652587	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:69652587delC	ENST00000435070.2	+	6	1022	c.912delC	c.(910-912)ggcfs	p.G304fs	CPSF6_ENST00000551516.1_Intron|CPSF6_ENST00000456847.3_Frame_Shift_Del_p.G231fs|CPSF6_ENST00000266679.8_Frame_Shift_Del_p.G341fs	NM_007007.2	NP_008938.2	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6, 68kDa	304	Pro-rich.				mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(7)|lung(8)	16	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			CAGGCTACGGCCCCCCTCCTG	0.632																																					p.G304fs		Atlas-INDEL	.											.	CPSF6	96	.	0			c.911delG						.						104.0	85.0	91.0					12																	69652587		2203	4300	6503	SO:0001589	frameshift_variant	11052	exon6			.	X67336	CCDS8988.1, CCDS73494.1	12q15	2013-06-18	2002-08-29			ENSG00000111605		"""RNA binding motif (RRM) containing"""	13871	protein-coding gene	gene with protein product	"""cleavage factor Im complex 68 kDa subunit"""	604979	"""cleavage and polyadenylation specific factor 6, 68kD subunit"""			9659921, 17267687	Standard	NM_007007		Approved	CFIM, HPBRII-4, HPBRII-7, CFIM68	uc001sut.4	Q16630		ENST00000435070.2:c.912delC	chr12.hg19:g.69652587delC	ENSP00000391774:p.Gly304fs	79.0	0.0		133.0	11.0	NM_007007	A8K7K9|Q53ES1|Q9BSJ7|Q9BW18	Frame_Shift_Del	DEL	ENST00000435070.2	hg19	CCDS8988.1																																																																																			.	.		0.632	CPSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403609.1	NM_007007	
L3MBTL2	83746	hgsc.bcm.edu	37	22	41620044	41620044	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr22:41620044delC	ENST00000216237.5	+	9	1121	c.963delC	c.(961-963)tacfs	p.Y321fs		NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	321					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GCATGAAGTACCCCTTTAGGC	0.602																																					p.Y321fs		Atlas-INDEL	.											.	L3MBTL2	61	.	0			c.962delA						.						111.0	71.0	85.0					22																	41620044		2203	4300	6503	SO:0001589	frameshift_variant	83746	exon9			.	AJ305226	CCDS14011.1	22q13.31-q13.33	2008-06-11			ENSG00000100395	ENSG00000100395			18594	protein-coding gene	gene with protein product		611865				11682070	Standard	NM_031488		Approved	H-l(3)mbt-l, DKFZP761I141, dJ756G23.3	uc003azo.3	Q969R5	OTTHUMG00000150942	ENST00000216237.5:c.963delC	chr22.hg19:g.41620044delC	ENSP00000216237:p.Tyr321fs	150.0	0.0		197.0	12.0	NM_031488	Q8TEN1|Q96SC4|Q9BQI2|Q9UGS4	Frame_Shift_Del	DEL	ENST00000216237.5	hg19	CCDS14011.1																																																																																			.	.		0.602	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	NM_031488	
RPE65	6121	hgsc.bcm.edu	37	1	68910348	68910348	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:68910348delA	ENST00000262340.5	-	5	414	c.361delT	c.(361-363)tctfs	p.S121fs		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	121					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						CGAAAGTAAGAAAAAAACCTG	0.368																																					p.S121fs		Atlas-INDEL	.											.	RPE65	87	.	0			c.362delC						.						50.0	53.0	52.0					1																	68910348		2201	4300	6501	SO:0001589	frameshift_variant	6121	exon5			.	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.361delT	chr1.hg19:g.68910348delA	ENSP00000262340:p.Ser121fs	80.0	0.0		169.0	13.0	NM_000329	A8K1L0|Q5T9U3	Frame_Shift_Del	DEL	ENST00000262340.5	hg19	CCDS643.1																																																																																			.	.		0.368	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329	
FANCM	57697	hgsc.bcm.edu	37	14	45645902	45645902	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:45645902delA	ENST00000267430.5	+	14	4030	c.3945delA	c.(3943-3945)gcafs	p.A1315fs	FANCM_ENST00000542564.2_Frame_Shift_Del_p.A1289fs	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1315					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						TGAGTGCAGCAAAAAATGAAG	0.323								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.A1315fs		Atlas-INDEL	.											.	FANCM	225	.	0			c.3944delC						.						75.0	74.0	74.0					14																	45645902		2202	4296	6498	SO:0001589	frameshift_variant	57697	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.3945delA	chr14.hg19:g.45645902delA	ENSP00000267430:p.Ala1315fs	183.0	0.0		172.0	12.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Frame_Shift_Del	DEL	ENST00000267430.5	hg19	CCDS32070.1																																																																																			.	.		0.323	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
EHMT2	10919	hgsc.bcm.edu	37	6	31864543	31864543	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:31864543delG	ENST00000375537.4	-	3	174	c.168delC	c.(166-168)cccfs	p.P56fs	EHMT2_ENST00000480912.1_5'Flank|C2_ENST00000469372.1_5'Flank|EHMT2_ENST00000375528.4_Frame_Shift_Del_p.P113fs|EHMT2_ENST00000395728.3_Frame_Shift_Del_p.P113fs|EHMT2_ENST00000375530.4_Frame_Shift_Del_p.P56fs	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	56					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						CCAGGGAGTCGGGGGTGGCCT	0.582																																					p.D57fs		Atlas-INDEL	.											.	EHMT2	45	.	0			c.169delG						.						55.0	65.0	62.0					6																	31864543		1509	2709	4218	SO:0001589	frameshift_variant	10919	exon3			.	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.168delC	chr6.hg19:g.31864543delG	ENSP00000364687:p.Pro56fs	97.0	0.0		161.0	10.0	NM_025256	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Frame_Shift_Del	DEL	ENST00000375537.4	hg19	CCDS4725.1																																																																																			.	.		0.582	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709	
CCDC69	26112	hgsc.bcm.edu	37	5	150563972	150563972	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:150563972delT	ENST00000355417.2	-	8	820	c.646delA	c.(646-648)attfs	p.I216fs	CCDC69_ENST00000521308.1_5'UTR	NM_015621.2	NP_056436.2	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	216										haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1)	9		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGGTCGTAATTTTTTCCTCC	0.488																																					p.I216fs		Atlas-INDEL	.											.	CCDC69	30	.	0			c.647delT						.						129.0	120.0	123.0					5																	150563972		2203	4300	6503	SO:0001589	frameshift_variant	26112	exon8			.		CCDS4312.1	5q33.1	2008-02-05			ENSG00000198624	ENSG00000198624			24487	protein-coding gene	gene with protein product						12477932	Standard	NM_015621		Approved	FLJ13705, DKFZP434C171	uc011dcq.3	A6NI79	OTTHUMG00000130127	ENST00000355417.2:c.646delA	chr5.hg19:g.150563972delT	ENSP00000347586:p.Ile216fs	139.0	0.0		231.0	14.0	NM_015621	A8K9X6	Frame_Shift_Del	DEL	ENST00000355417.2	hg19	CCDS4312.1																																																																																			.	.		0.488	CCDC69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252435.1	NM_015621	
MOB2	81532	hgsc.bcm.edu	37	11	1492622	1492622	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:1492622delC	ENST00000329957.6	-	4	582	c.393delG	c.(391-393)gggfs	p.G131fs	MOB2_ENST00000526462.1_5'UTR	NM_001172223.1	NP_001165694.1	Q70IA6	MOB2_HUMAN	MOB kinase activator 2	100					actin cytoskeleton organization (GO:0030036)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein phosphorylation (GO:0001934)	cytoplasm (GO:0005737)|neuron projection terminus (GO:0044306)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|kidney(2)|lung(1)	4						TGACCTTCTTCCCCCGCTCGT	0.597																																					p.K132fs		Atlas-INDEL	.											.	MOB2	23	.	0			c.394delA						.						116.0	130.0	125.0					11																	1492622		2163	4243	6406	SO:0001589	frameshift_variant	81532	exon4			.		CCDS53591.1	11p15.5	2011-09-28			ENSG00000182208	ENSG00000182208		"""MOB kinase activators"""	24904	protein-coding gene	gene with protein product	"""MOB2 Mps One Binder homolog (yeast)"""	611969				11223154, 15067004	Standard	NM_053005		Approved	HCCA2	uc010qwz.2	Q70IA6	OTTHUMG00000165545	ENST00000329957.6:c.393delG	chr11.hg19:g.1492622delC	ENSP00000328694:p.Gly131fs	132.0	0.0		177.0	12.0	NM_001172223	B4DKP3|Q96M67	Frame_Shift_Del	DEL	ENST00000329957.6	hg19	CCDS53591.1																																																																																			.	.		0.597	MOB2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000384770.1	NM_053005	
ITIH4	3700	hgsc.bcm.edu	37	3	52860860	52860860	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:52860860delC	ENST00000266041.4	-	4	562	c.466delG	c.(466-468)gtgfs	p.V156fs	ITIH4_ENST00000406595.1_Frame_Shift_Del_p.V156fs|ITIH4_ENST00000485816.1_Frame_Shift_Del_p.V156fs|ITIH4-AS1_ENST00000478366.1_RNA|RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4_ENST00000434759.3_Frame_Shift_Del_p.V68fs|ITIH4_ENST00000346281.5_Frame_Shift_Del_p.V156fs	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	156					acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		AGCTCGTACACCCCCAAACGC	0.592																																					p.V156fs		Atlas-INDEL	.											.	ITIH4	74	.	0			c.467delT						.						60.0	59.0	59.0					3																	52860860		2203	4300	6503	SO:0001589	frameshift_variant	3700	exon4			.	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"""plasma Kallikrein-sensitive glycoprotein"""	600564	"""inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"""	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.466delG	chr3.hg19:g.52860860delC	ENSP00000266041:p.Val156fs	143.0	0.0		196.0	12.0	NM_002218	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Frame_Shift_Del	DEL	ENST00000266041.4	hg19	CCDS2865.1																																																																																			.	.		0.592	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218	
TOR1B	27348	hgsc.bcm.edu	37	9	132571650	132571650	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:132571650delA	ENST00000259339.2	+	5	859	c.799delA	c.(799-801)aaafs	p.K267fs		NM_014506.1	NP_055321.1	O14657	TOR1B_HUMAN	torsin family 1, member B (torsin B)	267					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum organization (GO:0007029)|nuclear membrane organization (GO:0071763)|protein homooligomerization (GO:0051260)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)	12		Ovarian(14;0.0586)				ACTGATCGACAAAAACCTCAT	0.552																																					p.D266fs		Atlas-INDEL	.											.	TOR1B	20	.	0			c.798delC						.						99.0	83.0	89.0					9																	132571650		2203	4300	6503	SO:0001589	frameshift_variant	27348	exon5			.	AF007872	CCDS6929.1	9q34	2008-07-21			ENSG00000136816	ENSG00000136816			11995	protein-coding gene	gene with protein product		608050				9288096, 10644435	Standard	NM_014506		Approved	DQ1, MGC4386	uc004byk.1	O14657	OTTHUMG00000020795	ENST00000259339.2:c.799delA	chr9.hg19:g.132571650delA	ENSP00000259339:p.Lys267fs	146.0	0.0		177.0	17.0	NM_014506		Frame_Shift_Del	DEL	ENST00000259339.2	hg19	CCDS6929.1																																																																																			.	.		0.552	TOR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054615.1	NM_014506	
TPR	7175	hgsc.bcm.edu	37	1	186324639	186324639	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:186324639delT	ENST00000367478.4	-	17	2370	c.2074delA	c.(2074-2076)atafs	p.I692fs	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	692					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|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)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TCATTTTGTATTTTTTCATTT	0.318			T	NTRK1	papillary thyroid																																p.I692fs		Atlas-INDEL	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.2075delT						.						107.0	96.0	100.0					1																	186324639		1788	4066	5854	SO:0001589	frameshift_variant	7175	exon17			.	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.2074delA	chr1.hg19:g.186324639delT	ENSP00000356448:p.Ile692fs	87.0	0.0		196.0	12.0	NM_003292	Q15655|Q5SWY0|Q99968	Frame_Shift_Del	DEL	ENST00000367478.4	hg19	CCDS41446.1																																																																																			.	.		0.318	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
OR7A17	26333	hgsc.bcm.edu	37	19	14991635	14991635	+	Frame_Shift_Del	DEL	A	A	-	rs35659165		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:14991635delA	ENST00000327462.2	-	1	629	c.533delT	c.(532-534)ttcfs	p.F178fs		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	178						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12	Ovarian(108;0.203)					AAGTTCACAGAAAAAGTGGGG	0.483																																					p.F178fs		Atlas-INDEL	.											.	OR7A17	37	.	0			c.534delC						.						90.0	85.0	87.0					19																	14991635		2203	4300	6503	SO:0001589	frameshift_variant	26333	exon1			.	X64993	CCDS12319.1	19p13.12	2012-08-09				ENSG00000185385		"""GPCR / Class A : Olfactory receptors"""	8363	protein-coding gene	gene with protein product						1370859	Standard	NM_030901		Approved	HTPCRX19	uc010xob.2	O14581		ENST00000327462.2:c.533delT	chr19.hg19:g.14991635delA	ENSP00000328144:p.Phe178fs	127.0	0.0		155.0	10.0	NM_030901	Q6IFQ6|Q96R98	Frame_Shift_Del	DEL	ENST00000327462.2	hg19	CCDS12319.1																																																																																			.	.		0.483	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901	
HEATR6	63897	hgsc.bcm.edu	37	17	58124746	58124746	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:58124746delA	ENST00000184956.6	-	18	2709	c.2693delT	c.(2692-2694)ttcfs	p.F898fs	HEATR6_ENST00000585976.1_Frame_Shift_Del_p.F786fs	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	898							poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			CTCTTCCTGGAAACTTGGGTC	0.373																																					p.F898fs		Atlas-INDEL	.											.	HEATR6	98	.	0			c.2694delC						.						177.0	151.0	159.0					17																	58124746		2203	4300	6503	SO:0001589	frameshift_variant	63897	exon18			.	BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"""amplified in breast cancer 1"""					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.2693delT	chr17.hg19:g.58124746delA	ENSP00000184956:p.Phe898fs	151.0	0.0		210.0	13.0	NM_022070	B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Frame_Shift_Del	DEL	ENST00000184956.6	hg19	CCDS11623.1																																																																																			.	.		0.373	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070	
LRRC16A	55604	hgsc.bcm.edu	37	6	25619801	25619801	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:25619801delT	ENST00000329474.6	+	37	4474	c.4106delT	c.(4105-4107)attfs	p.I1369fs	LRRC16A_ENST00000476458.1_3'UTR	NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	1369					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						AAAGAGTTTATTTTTGTGTAA	0.483																																					p.I1369fs		Atlas-INDEL	.											.	LRRC16A	168	.	0			c.4105delA						.						94.0	96.0	96.0					6																	25619801		1923	4123	6046	SO:0001589	frameshift_variant	55604	exon37			.	AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"""capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"""	609593	"""leucine rich repeat containing 16"""	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.4106delT	chr6.hg19:g.25619801delT	ENSP00000331983:p.Ile1369fs	116.0	0.0		149.0	11.0	NM_017640	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Frame_Shift_Del	DEL	ENST00000329474.6	hg19	CCDS54973.1																																																																																			.	.		0.483	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
KHDRBS2	202559	hgsc.bcm.edu	37	6	62688078	62688078	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:62688078delG	ENST00000281156.4	-	4	654	c.376delC	c.(376-378)cacfs	p.H126fs		NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	126	KH. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) binding (GO:0008143)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|liver(1)|lung(13)|ovary(3)|prostate(3)|skin(12)|upper_aerodigestive_tract(2)|urinary_tract(1)	49				BRCA - Breast invasive adenocarcinoma(397;0.149)		TCACTCAAGTGGGCATATTTG	0.353																																					p.H126fs		Atlas-INDEL	.											.	KHDRBS2	103	.	0			c.377delA						.						123.0	109.0	114.0					6																	62688078		2203	4300	6503	SO:0001589	frameshift_variant	202559	exon4			.	BC034043	CCDS4963.1	6q11.1	2013-09-20			ENSG00000112232	ENSG00000112232			18114	protein-coding gene	gene with protein product	"""Sam68-like mammalian protein 1"""	610487					Standard	NM_152688		Approved	SLM1, SLM-1, MGC26664	uc003peg.2	Q5VWX1	OTTHUMG00000014936	ENST00000281156.4:c.376delC	chr6.hg19:g.62688078delG	ENSP00000281156:p.His126fs	144.0	0.0		163.0	10.0	NM_152688	A8K7M8|Q8N4I4|Q8TCZ4	Frame_Shift_Del	DEL	ENST00000281156.4	hg19	CCDS4963.1																																																																																			.	.		0.353	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	NM_152688	
SOBP	55084	hgsc.bcm.edu	37	6	107956410	107956410	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:107956410delA	ENST00000317357.5	+	6	3021	c.2362delA	c.(2362-2364)aaafs	p.K789fs	SOBP_ENST00000494935.1_3'UTR	NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)											endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		GGAGGCGGCCAAAAAGCTGAT	0.617																																					p.A787fs		Atlas-INDEL	.											.	SOBP	53	.	0			c.2361delC						.						42.0	52.0	49.0					6																	107956410		2006	4173	6179	SO:0001589	frameshift_variant	55084	exon6			.	AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320			29256	protein-coding gene	gene with protein product		613667					Standard	NM_018013		Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.2362delA	chr6.hg19:g.107956410delA	ENSP00000318900:p.Lys789fs	108.0	0.0		137.0	10.0	NM_018013		Frame_Shift_Del	DEL	ENST00000317357.5	hg19	CCDS43488.1																																																																																			.	.		0.617	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041693.2	NM_018013	
CAPN11	11131	hgsc.bcm.edu	37	6	44145022	44145022	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:44145022delG	ENST00000398776.1	+	12	1319	c.1281delG	c.(1279-1281)gagfs	p.E427fs	CAPN11_ENST00000542245.1_Frame_Shift_Del_p.E427fs	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	427	Domain III.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	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)			CTCTTCCTGAGGGGGATGACC	0.607																																					p.E427fs		Atlas-INDEL	.											.	CAPN11	66	.	0			c.1280delA						.						29.0	32.0	31.0					6																	44145022		2122	4241	6363	SO:0001589	frameshift_variant	11131	exon12			.	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"""EF-hand domain containing"""	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.1281delG	chr6.hg19:g.44145022delG	ENSP00000381758:p.Glu427fs	121.0	0.0		174.0	11.0	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Frame_Shift_Del	DEL	ENST00000398776.1	hg19	CCDS47436.1																																																																																			.	.		0.607	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3		
MYO7A	4647	hgsc.bcm.edu	37	11	76867058	76867058	+	Frame_Shift_Del	DEL	C	C	-	rs377214759		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:76867058delC	ENST00000409709.3	+	5	663	c.391delC	c.(391-393)cccfs	p.P132fs	MYO7A_ENST00000409893.1_Frame_Shift_Del_p.P132fs|MYO7A_ENST00000409619.2_Frame_Shift_Del_p.P121fs|MYO7A_ENST00000458637.2_Frame_Shift_Del_p.P132fs	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	132	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TGGGGAGATGCCCCCCCACAT	0.567																																					p.M130fs		Atlas-INDEL	.											.,1	MYO7A	164	.	0			c.390delG						.						49.0	52.0	51.0					11																	76867058		2076	4226	6302	SO:0001589	frameshift_variant	4647	exon5			.	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.391delC	chr11.hg19:g.76867058delC	ENSP00000386331:p.Pro132fs	92.0	0.0		139.0	11.0	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Frame_Shift_Del	DEL	ENST00000409709.3	hg19	CCDS53683.1																																																																																			.	.		0.567	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
AHNAK	79026	hgsc.bcm.edu	37	11	62288216	62288216	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:62288216delG	ENST00000378024.4	-	5	13947	c.13673delC	c.(13672-13674)cctfs	p.P4558fs	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4558					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)				GCCCACTTTAGGGCCTTTGAC	0.443																																					p.P4558fs		Atlas-INDEL	.											.	AHNAK	532	.	0			c.13674delT						.						82.0	80.0	81.0					11																	62288216		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.13673delC	chr11.hg19:g.62288216delG	ENSP00000367263:p.Pro4558fs	126.0	0.0		202.0	13.0	NM_001620	A1A586	Frame_Shift_Del	DEL	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.		0.443	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
PLA2G2F	64600	hgsc.bcm.edu	37	1	20465957	20465957	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:20465957delA	ENST00000375102.3	+	1	139	c.37delA	c.(37-39)aaafs	p.K15fs		NM_022819.3	NP_073730.3	Q9BZM2	PA2GF_HUMAN	phospholipase A2, group IIF	0					glycerophospholipid biosynthetic process (GO:0046474)|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)	cytosol (GO:0005829)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		CAAAGGGTTCAAAAAGAAGGT	0.592																																					p.F12fs		Atlas-INDEL	.											.	PLA2G2F	28	.	0			c.36delC						.						35.0	41.0	39.0					1																	20465957		1873	4103	5976	SO:0001589	frameshift_variant	64600	exon1			.	AL158172	CCDS204.2	1p35	2008-09-19			ENSG00000158786	ENSG00000158786	3.1.1.4		30040	protein-coding gene	gene with protein product						11112443	Standard	NM_022819		Approved		uc009vpp.1	Q9BZM2	OTTHUMG00000002704	ENST00000375102.3:c.37delA	chr1.hg19:g.20465957delA	ENSP00000364243:p.Lys15fs	87.0	0.0		146.0	10.0	NM_022819	Q5R385|Q8N217|Q9H506	Frame_Shift_Del	DEL	ENST00000375102.3	hg19	CCDS204.2																																																																																			.	.		0.592	PLA2G2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007687.1	NM_022819	
PTGR1	22949	hgsc.bcm.edu	37	9	114355220	114355220	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr9:114355220delC	ENST00000407693.2	-	4	457	c.195delG	c.(193-195)gggfs	p.G65fs	PTGR1_ENST00000538962.1_Frame_Shift_Del_p.G65fs|PTGR1_ENST00000309195.5_Frame_Shift_Del_p.G65fs|PTGR1_ENST00000238248.3_5'UTR	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	65					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						CCACTTGCTGCCCCATCATTG	0.368																																					p.Q66fs	Ovarian(200;132 2151 7551 19220 46064)	Atlas-INDEL	.											.	PTGR1	23	.	0			c.196delC						.						109.0	99.0	102.0					9																	114355220		2203	4300	6503	SO:0001589	frameshift_variant	22949	exon4			.	D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"""zinc binding alcohol dehydrogenase domain containing 3"""	601274	"""leukotriene B4 12-hydroxydehydrogenase"""	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.195delG	chr9.hg19:g.114355220delC	ENSP00000385763:p.Gly65fs	118.0	0.0		153.0	10.0	NM_001146108	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Frame_Shift_Del	DEL	ENST00000407693.2	hg19	CCDS6779.1																																																																																			.	.		0.368	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2		
SOX2	6657	hgsc.bcm.edu	37	3	181431499	181431499	+	3'UTR	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:181431499delA	ENST00000325404.1	+	0	1778					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)			GGAAGTTTGCAAAAGTCTTTA	0.368			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.*397A>-	chr3.hg19:g.181431499delA		117.0	0.0		146.0	10.0	.	Q14537	RNA	DEL	ENST00000325404.1	hg19	CCDS3239.1																																																																																			.	.		0.368	SOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350419.1	NM_003106	
FGA	2243	hgsc.bcm.edu	37	4	155507905	155507905	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:155507905delT	ENST00000302053.3	-	5	754	c.676delA	c.(676-678)atgfs	p.M226fs	FGA_ENST00000403106.3_Frame_Shift_Del_p.M226fs	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	226					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)	ACTGGTTTCATTTTTATCAGT	0.443																																					p.M226fs	NSCLC(143;340 1922 20892 22370 48145)	Atlas-INDEL	.											.	FGA	179	.	0			c.677delT						.						134.0	138.0	137.0					4																	155507905		2203	4300	6503	SO:0001589	frameshift_variant	2243	exon5			.		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.676delA	chr4.hg19:g.155507905delT	ENSP00000306361:p.Met226fs	147.0	0.0		154.0	13.0	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Frame_Shift_Del	DEL	ENST00000302053.3	hg19	CCDS3787.1																																																																																			.	.		0.443	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508	
SCN1A	6323	hgsc.bcm.edu	37	2	166852565	166852565	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:166852565delT	ENST00000303395.4	-	24	4538	c.4539delA	c.(4537-4539)aaafs	p.K1513fs	SCN1A_ENST00000423058.2_Frame_Shift_Del_p.K1513fs|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000409050.1_Frame_Shift_Del_p.K1485fs|SCN1A_ENST00000375405.3_Frame_Shift_Del_p.K1502fs			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1513					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)	TCGATCCTAATTTTTTCATTG	0.333																																					p.L1514X		Atlas-INDEL	.											SCN1A_ENST00000303395,caecum,carcinoma,0,2	SCN1A	641	.	0			c.4540delT						.						132.0	127.0	129.0					2																	166852565		2202	4300	6502	SO:0001589	frameshift_variant	6323	exon24			.	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.4539delA	chr2.hg19:g.166852565delT	ENSP00000303540:p.Lys1513fs	142.0	0.0		148.0	10.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Frame_Shift_Del	DEL	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.333	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
IMPG2	50939	hgsc.bcm.edu	37	3	101023118	101023118	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:101023118delA	ENST00000193391.7	-	3	560	c.373delT	c.(373-375)tggfs	p.W125fs		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	125					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	AGTCGATCCCAAAAAGTCCTG	0.403																																					p.W125fs		Atlas-INDEL	.											.	IMPG2	164	.	0			c.374delG						.						80.0	78.0	79.0					3																	101023118		2203	4300	6503	SO:0001589	frameshift_variant	50939	exon3			.	AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.373delT	chr3.hg19:g.101023118delA	ENSP00000193391:p.Trp125fs	134.0	0.0		151.0	11.0	NM_016247	A8MWT5|Q9UKD4|Q9UKK5	Frame_Shift_Del	DEL	ENST00000193391.7	hg19	CCDS2940.1																																																																																			.	.		0.403	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3		
BRAT1	221927	hgsc.bcm.edu	37	7	2583461	2583461	+	Frame_Shift_Del	DEL	C	C	-	rs531827528		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:2583461delC	ENST00000340611.4	-	5	822	c.566delG	c.(565-567)ggtfs	p.G189fs	BRAT1_ENST00000473879.1_5'Flank	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	189					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						GGGCCAGTCACCCCCCGGCAG	0.662																																					p.G189fs		Atlas-INDEL	.											.	BRAT1	57	.	0			c.567delT						.						46.0	55.0	52.0					7																	2583461		2203	4300	6503	SO:0001589	frameshift_variant	221927	exon5			.	BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"""BRCA1-associated protein required for ATM activation protein 1"""	614506	"""chromosome 7 open reading frame 27"""	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.566delG	chr7.hg19:g.2583461delC	ENSP00000339637:p.Gly189fs	116.0	0.0		163.0	10.0	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Frame_Shift_Del	DEL	ENST00000340611.4	hg19	CCDS5334.1																																																																																			.	.		0.662	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743	
LEPROT	54741	hgsc.bcm.edu	37	1	65897552	65897552	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:65897552delT	ENST00000371065.4	+	4	484	c.346delT	c.(346-348)tttfs	p.F117fs	LEPR_ENST00000371060.3_Intron|LEPR_ENST00000371059.3_Intron|LEPR_ENST00000344610.8_Intron|LEPR_ENST00000349533.6_Intron|LEPR_ENST00000406510.3_Intron	NM_001198681.1|NM_017526.4	NP_001185610.1|NP_059996.1	O15243	OBRG_HUMAN	leptin receptor overlapping transcript	117					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			kidney(1)|large_intestine(1)|lung(5)	7				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		AATTCAAGGGTTTTTCCTTAT	0.393																																					p.G124fs		Atlas-INDEL	.											.	LEPROT	16	.	0			c.372delG						.						136.0	131.0	132.0					1																	65897552		2203	4300	6503	SO:0001589	frameshift_variant	54741	exon5			.	Y12670	CCDS630.1, CCDS72801.1	1p31.2	2008-02-05			ENSG00000213625	ENSG00000213625			29477	protein-coding gene	gene with protein product	"""leptin receptor gene related protein"""	613461				9207021	Standard	NM_001198681		Approved	OBRGRP, OB-RGRP, VPS55, FLJ90360	uc001dcf.3	O15243	OTTHUMG00000009065	ENST00000371065.4:c.346delT	chr1.hg19:g.65897552delT	ENSP00000360104:p.Phe117fs	110.0	0.0		205.0	13.0	NM_001198681	Q6FHL5	Frame_Shift_Del	DEL	ENST00000371065.4	hg19	CCDS630.1																																																																																			.	.		0.393	LEPROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025132.4	NM_017526	
FLYWCH1	84256	hgsc.bcm.edu	37	16	2979748	2979748	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:2979748delC	ENST00000253928.9	+	3	467	c.62delC	c.(61-63)tccfs	p.S21fs	FLYWCH1_ENST00000399667.2_Frame_Shift_Del_p.S21fs|FLYWCH1_ENST00000416288.2_Frame_Shift_Del_p.S21fs			Q4VC44	FWCH1_HUMAN	FLYWCH-type zinc finger 1	21						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|lung(3)	4						CAGGAGCCATCCCCCAAGCCA	0.687																																					p.S21fs		Atlas-INDEL	.											.	FLYWCH1	27	.	0			c.61delT						.						42.0	49.0	47.0					16																	2979748		2198	4299	6497	SO:0001589	frameshift_variant	84256	exon3			.	AL136585	CCDS45390.1	16p13.3	2013-01-10	2007-06-21	2007-06-21	ENSG00000059122	ENSG00000059122		"""Zinc fingers"""	25404	protein-coding gene	gene with protein product						11230166, 10997877	Standard	XM_006720959		Approved	DKFZp761A132	uc002csc.3	Q4VC44		ENST00000253928.9:c.62delC	chr16.hg19:g.2979748delC	ENSP00000253928:p.Ser21fs	128.0	0.0		142.0	12.0	NM_020912	D3DUA1|Q6ZSQ1|Q8WV62|Q9BQG6|Q9BUS5|Q9HCM0	Frame_Shift_Del	DEL	ENST00000253928.9	hg19																																																																																				.	.		0.687	FLYWCH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000436479.1	NM_032296	
CCDC17	149483	hgsc.bcm.edu	37	1	46088658	46088658	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:46088658delC	ENST00000528266.1	-	4	772	c.625delG	c.(625-627)gccfs	p.A209fs	CCDC17_ENST00000464739.1_5'Flank|CCDC17_ENST00000343901.2_Frame_Shift_Del_p.A177fs|CCDC17_ENST00000421127.2_Frame_Shift_Del_p.A200fs|CCDC17_ENST00000445048.2_Intron			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	209										kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					TGAATGCGGGCCCCCAACACC	0.692																																					p.A209fs		Atlas-INDEL	.											.	CCDC17	54	.	0			c.626delC						.						24.0	29.0	28.0					1																	46088658		2203	4298	6501	SO:0001589	frameshift_variant	149483	exon4			.		CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.625delG	chr1.hg19:g.46088658delC	ENSP00000432172:p.Ala209fs	97.0	0.0		188.0	13.0	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Frame_Shift_Del	DEL	ENST00000528266.1	hg19	CCDS44131.2																																																																																			.	.		0.692	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500	
DOCK11	139818	hgsc.bcm.edu	37	X	117749649	117749649	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:117749649delA	ENST00000276202.7	+	30	3330	c.3267delA	c.(3265-3267)gcafs	p.A1089fs	DOCK11_ENST00000276204.6_Frame_Shift_Del_p.A1089fs	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1089					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TGGCATTTGCAAAACCTAAAC	0.363																																					p.A1089fs		Atlas-INDEL	.											.	DOCK11	185	.	0			c.3266delC						.						117.0	88.0	98.0					X																	117749649		2203	4300	6503	SO:0001589	frameshift_variant	139818	exon30			.	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"""Pleckstrin homology (PH) domain containing"""	23483	protein-coding gene	gene with protein product	"""zizimin2"""	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.3267delA	chrX.hg19:g.117749649delA	ENSP00000276202:p.Ala1089fs	162.0	0.0		200.0	13.0	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Frame_Shift_Del	DEL	ENST00000276202.7	hg19	CCDS35373.1																																																																																			.	.		0.363	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
CCDC83	220047	hgsc.bcm.edu	37	11	85622356	85622356	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:85622356delA	ENST00000342404.3	+	8	921	c.705delA	c.(703-705)ttafs	p.L235fs	CCDC83_ENST00000280245.4_Frame_Shift_Del_p.L235fs|CCDC83_ENST00000376067.1_Frame_Shift_Del_p.L136fs|CCDC83_ENST00000529676.2_3'UTR			Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	235										breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|skin(3)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				TTGAAGAATTAAAAAATGCTA	0.338																																					p.L235X		Atlas-INDEL	.											.	CCDC83	48	.	0			c.704delT						.						101.0	112.0	108.0					11																	85622356		2203	4299	6502	SO:0001589	frameshift_variant	220047	exon8			.	AK124113	CCDS8271.1, CCDS66196.1	11q14.1-q14.2	2014-01-21			ENSG00000150676	ENSG00000150676			28535	protein-coding gene	gene with protein product						12477932	Standard	XM_005273842		Approved	MGC34732, FLJ42119, CT148	uc001pbg.1	Q8IWF9	OTTHUMG00000166978	ENST00000342404.3:c.705delA	chr11.hg19:g.85622356delA	ENSP00000344512:p.Leu235fs	133.0	0.0		182.0	11.0	NM_173556	B2RA49|Q6X7T2|Q6ZVT5|Q8N9Y1	Frame_Shift_Del	DEL	ENST00000342404.3	hg19																																																																																				.	.		0.338	CCDC83-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392215.1	NM_173556	
LCA5	167691	hgsc.bcm.edu	37	6	80197095	80197095	+	Frame_Shift_Del	DEL	T	T	-	rs34176430		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:80197095delT	ENST00000392959.1	-	9	2331	c.1720delA	c.(1720-1722)agtfs	p.S575fs	LCA5_ENST00000369846.4_Frame_Shift_Del_p.S575fs	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	575					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)		AAAAAACTACTTTTTTGACTA	0.343																																					p.S574fs		Atlas-INDEL	.											.	LCA5	71	.	0			c.1721delG						.						65.0	69.0	68.0					6																	80197095		2203	4299	6502	SO:0001589	frameshift_variant	167691	exon8			.		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.1720delA	chr6.hg19:g.80197095delT	ENSP00000376686:p.Ser575fs	109.0	0.0		159.0	10.0	NM_001122769	E1P542|Q9BWX7	Frame_Shift_Del	DEL	ENST00000392959.1	hg19	CCDS4990.1																																																																																			.	.		0.343	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714	
IQSEC1	9922	hgsc.bcm.edu	37	3	12942773	12942773	+	Intron	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:12942773delC	ENST00000273221.4	-	13	3064					NM_014869.5	NP_055684.3	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1						actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CCTGCGGCAGCCCCTCTGGGG	0.701																																					p.L1019fs		Atlas-INDEL	.											.	IQSEC1	88	.	0			c.3055delC						.						1.0	2.0	1.0					3																	12942773		276	894	1170	SO:0001627	intron_variant	9922	exon15			.	BC010267	CCDS33703.1, CCDS74902.1	3p25.2	2011-09-23			ENSG00000144711	ENSG00000144711			29112	protein-coding gene	gene with protein product	"""brefeldin A-resistant ARF-GEF2"""	610166				9872452, 8619474	Standard	NM_001134382		Approved	KIAA0763, GEP100, BRAG2, ARF-GEP100	uc011auw.2	Q6DN90	OTTHUMG00000155398	ENST00000273221.4:c.2847+1499G>-	chr3.hg19:g.12942773delC		133.0	0.0		183.0	11.0	NM_001134382	O94863|Q96D85	Frame_Shift_Del	DEL	ENST00000273221.4	hg19	CCDS33703.1																																																																																			.	.		0.701	IQSEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339865.2	NM_014869	
DHX8	1659	hgsc.bcm.edu	37	17	41582118	41582118	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:41582118delA	ENST00000262415.3	+	12	1725	c.1653delA	c.(1651-1653)ggafs	p.G551fs	DHX8_ENST00000540306.1_Frame_Shift_Del_p.G551fs	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	551					ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		CCTCTTACGGAAAAAAGACCC	0.478																																					p.G551fs	NSCLC(56;1548 1661 49258 49987)	Atlas-INDEL	.											.	DHX8	98	.	0			c.1652delG						.						126.0	128.0	127.0					17																	41582118		2203	4300	6503	SO:0001589	frameshift_variant	1659	exon12			.	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"""DEAH-boxes"""	2749	protein-coding gene	gene with protein product		600396	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"""	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.1653delA	chr17.hg19:g.41582118delA	ENSP00000262415:p.Gly551fs	82.0	0.0		117.0	10.0	NM_004941		Frame_Shift_Del	DEL	ENST00000262415.3	hg19	CCDS11464.1																																																																																			.	.		0.478	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1		
LRCH3	84859	hgsc.bcm.edu	37	3	197566229	197566229	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:197566229delA	ENST00000425562.2	+	10	1289	c.1289delA	c.(1288-1290)caafs	p.Q430fs	LRCH3_ENST00000441090.2_Frame_Shift_Del_p.Q276fs|LRCH3_ENST00000414675.2_Frame_Shift_Del_p.Q402fs|LRCH3_ENST00000334859.4_Frame_Shift_Del_p.Q430fs|LRCH3_ENST00000536618.1_Frame_Shift_Del_p.Q25fs|LRCH3_ENST00000438796.2_Frame_Shift_Del_p.Q430fs			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	430						cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		AGGGAGTTTCAAAAAACAGAA	0.328																																					p.Q430fs		Atlas-INDEL	.											.	LRCH3	96	.	0			c.1288delC						.						52.0	53.0	53.0					3																	197566229		2203	4299	6502	SO:0001589	frameshift_variant	84859	exon10			.	AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.1289delA	chr3.hg19:g.197566229delA	ENSP00000393579:p.Gln430fs	96.0	0.0		155.0	11.0	NM_032773	B4E0T7|Q96FP9|Q9NT52	Frame_Shift_Del	DEL	ENST00000425562.2	hg19																																																																																				.	.		0.328	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773	
AEBP2	121536	hgsc.bcm.edu	37	12	19667647	19667647	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:19667647delA	ENST00000398864.3	+	7	1436	c.1410delA	c.(1408-1410)ttafs	p.L470fs	AEBP2_ENST00000360995.4_Frame_Shift_Del_p.L254fs|AEBP2_ENST00000541908.1_Frame_Shift_Del_p.L241fs|AEBP2_ENST00000266508.9_Frame_Shift_Del_p.L470fs	NM_001114176.1	NP_001107648.1	Q6ZN18	AEBP2_HUMAN	AE binding protein 2	470	Interaction with SUZ12.				chromatin modification (GO:0016568)	ESC/E(Z) complex (GO:0035098)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			ovary(1)	1	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)|Esophageal squamous(101;0.143)					GACATCAGTTAAAAACTAAAG	0.313																																					p.L470X		Atlas-INDEL	.											.	AEBP2	21	.	0			c.1409delT						.						81.0	77.0	78.0					12																	19667647		1828	4089	5917	SO:0001589	frameshift_variant	121536	exon7			.		CCDS44841.1, CCDS44842.1, CCDS58215.1	12p12.3	2012-10-02			ENSG00000139154	ENSG00000139154			24051	protein-coding gene	gene with protein product						10329662	Standard	NM_153207		Approved	MGC17922	uc001ref.2	Q6ZN18	OTTHUMG00000168906	ENST00000398864.3:c.1410delA	chr12.hg19:g.19667647delA	ENSP00000381840:p.Leu470fs	194.0	0.0		163.0	10.0	NM_001114176	Q59FS5|Q6ZN62|Q96BG3	Frame_Shift_Del	DEL	ENST00000398864.3	hg19	CCDS44841.1																																																																																			.	.		0.313	AEBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401575.1	NM_153207	
MARVELD3	91862	hgsc.bcm.edu	37	16	71674880	71674880	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:71674880delC	ENST00000299952.4	+	3	1226	c.1183delC	c.(1183-1185)cccfs	p.P395fs	MARVELD3_ENST00000565261.1_3'UTR|PHLPP2_ENST00000540628.1_3'UTR|MARVELD3_ENST00000561682.1_Intron	NM_001017967.3|NM_001271329.1	NP_001017967.2|NP_001258258.1	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	0					cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				CCGAGAACAGCCCGGAAGTTA	0.512																																					p.Q394fs		Atlas-INDEL	.											.	MARVELD3	63	.	0			c.1182delG						.						51.0	43.0	46.0					16																	71674880		2198	4300	6498	SO:0001589	frameshift_variant	91862	exon3			.	BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"""MARVEL (membrane-associating) domain containing 3"""	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000299952.4:c.1183delC	chr16.hg19:g.71674880delC	ENSP00000299952:p.Pro395fs	190.0	0.0		201.0	13.0	NM_001017967	A8K820|H3BQM5|Q96MJ4	Frame_Shift_Del	DEL	ENST00000299952.4	hg19	CCDS32478.1																																																																																			.	.		0.512	MARVELD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268990.1	NM_052858	
CDH10	1008	hgsc.bcm.edu	37	5	24487952	24487952	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr5:24487952delG	ENST00000264463.4	-	12	2694	c.2187delC	c.(2185-2187)cccfs	p.P729fs	CDH10_ENST00000502921.1_5'UTR	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	729					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)		GTGAGTCGTAGGGGGGTGCGG	0.463										HNSCC(23;0.051)																											p.Y730fs		Atlas-INDEL	.											.	CDH10	391	.	0			c.2188delT						.						105.0	108.0	107.0					5																	24487952		2203	4300	6503	SO:0001589	frameshift_variant	1008	exon12			.	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.2187delC	chr5.hg19:g.24487952delG	ENSP00000264463:p.Pro729fs	80.0	0.0		132.0	10.0	NM_006727	Q9ULB3	Frame_Shift_Del	DEL	ENST00000264463.4	hg19	CCDS3892.1																																																																																			.	.		0.463	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727	
PRDX2	7001	hgsc.bcm.edu	37	19	12911076	12911076	+	Frame_Shift_Del	DEL	G	G	-	rs1056648		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:12911076delG	ENST00000301522.2	-	4	423	c.295delC	c.(295-297)ctgfs	p.L99fs	PRDX2_ENST00000334482.5_Frame_Shift_Del_p.L99fs|CTD-2659N19.10_ENST00000585496.1_RNA	NM_005809.4	NP_005800.3	P32119	PRDX2_HUMAN	peroxiredoxin 2	99	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cellular response to oxidative stress (GO:0034599)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neuron apoptotic process (GO:0043524)|regulation of apoptotic process (GO:0042981)|removal of superoxide radicals (GO:0019430)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	antioxidant activity (GO:0016209)|thioredoxin peroxidase activity (GO:0008379)			endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4						GGGATGTTCAGGGGGCCCAAG	0.607																																					p.R99fs		Atlas-INDEL	.											.	PRDX2	20	.	0			c.296delG						.						62.0	67.0	65.0					19																	12911076		2203	4300	6503	SO:0001589	frameshift_variant	7001	exon4			.		CCDS12281.1	19p13.2	2008-07-17			ENSG00000167815	ENSG00000167815			9353	protein-coding gene	gene with protein product	"""thioredoxin-dependent peroxide reductase 1"", ""thiol-specific antioxidant 1"", ""natural killer-enhancing factor B"", ""thioredoxin peroxidase 1"", ""torin"""	600538		TDPX1		7607688	Standard	NM_005809		Approved	PRP, NKEFB, TSA, PRXII, PRX2, MGC4104	uc002mvd.4	P32119	OTTHUMG00000134285	ENST00000301522.2:c.295delC	chr19.hg19:g.12911076delG	ENSP00000301522:p.Leu99fs	251.0	0.0		227.0	15.0	NM_005809	A8K0C0|P31945|P32118|P35701|Q6FHG4|Q92763|Q9UC23	Frame_Shift_Del	DEL	ENST00000301522.2	hg19	CCDS12281.1																																																																																			.	.		0.607	PRDX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258950.2	NM_005809	
SEMG2	6407	hgsc.bcm.edu	37	20	43851552	43851552	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr20:43851552delA	ENST00000372769.3	+	2	1369	c.1279delA	c.(1279-1281)aaafs	p.K427fs		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	427	4 X 60 AA tandem repeats, type I.|Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				GGATGTACAGAAAGGTGTATC	0.383																																					p.Q426fs		Atlas-INDEL	.											.	SEMG2	92	.	0			c.1278delG						.						80.0	76.0	77.0					20																	43851552		2203	4300	6503	SO:0001589	frameshift_variant	6407	exon2			.		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"""Semenogelin 2"""	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.1279delA	chr20.hg19:g.43851552delA	ENSP00000361855:p.Lys427fs	107.0	0.0		158.0	10.0	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Frame_Shift_Del	DEL	ENST00000372769.3	hg19	CCDS13346.1																																																																																			.	.		0.383	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008	
NPY1R	4886	hgsc.bcm.edu	37	4	164246487	164246487	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:164246487delT	ENST00000296533.2	-	3	1654	c.1123delA	c.(1123-1125)atcfs	p.I375fs	NPY1R_ENST00000509586.1_Frame_Shift_Del_p.I132fs	NM_000909.5	NP_000900.1	P25929	NPY1R_HUMAN	neuropeptide Y receptor Y1	375					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose metabolic process (GO:0006006)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|regulation of blood pressure (GO:0008217)|regulation of multicellular organism growth (GO:0040014)|sensory perception of pain (GO:0019233)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			breast(1)|cervix(1)|large_intestine(4)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)	30	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				TTGTTGTTGATTTTTTTAAAT	0.378																																					p.I375fs		Atlas-INDEL	.											.	NPY1R	72	.	0			c.1124delT						.						138.0	140.0	139.0					4																	164246487		2203	4300	6503	SO:0001589	frameshift_variant	4886	exon3			.		CCDS34089.1	4q31.3-q32	2012-08-08				ENSG00000164128		"""GPCR / Class A : Neuropeptide receptors : Y"""	7956	protein-coding gene	gene with protein product		162641		NPYR		8095935	Standard	NM_000909		Approved		uc003iqm.2	P25929		ENST00000296533.2:c.1123delA	chr4.hg19:g.164246487delT	ENSP00000354652:p.Ile375fs	204.0	0.0		191.0	12.0	NM_000909	B2R6H5	Frame_Shift_Del	DEL	ENST00000296533.2	hg19	CCDS34089.1																																																																																			.	.		0.378	NPY1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364685.1		
PLK4	10733	hgsc.bcm.edu	37	4	128814719	128814719	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:128814719delA	ENST00000270861.5	+	12	2648	c.2374delA	c.(2374-2376)aaafs	p.K792fs	PLK4_ENST00000515069.1_Frame_Shift_Del_p.K714fs|RNU6-583P_ENST00000516012.1_RNA|PLK4_ENST00000513090.1_Frame_Shift_Del_p.K760fs|PLK4_ENST00000514379.1_Frame_Shift_Del_p.K751fs|PLK4_ENST00000507249.1_Frame_Shift_Del_p.K731fs	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	792					centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						AGAGGAAAGGAAAACTAGGAG	0.323																																					p.R791fs	Colon(135;508 1718 19061 31832 42879)	Atlas-INDEL	.											.	PLK4	65	.	0			c.2373delG						.						78.0	81.0	80.0					4																	128814719		2203	4300	6503	SO:0001589	frameshift_variant	10733	exon12			.	Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"""serine/threonine kinase 18"", ""polo-like kinase 4 (Drosophila)"""	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.2374delA	chr4.hg19:g.128814719delA	ENSP00000270861:p.Lys792fs	126.0	0.0		169.0	13.0	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Frame_Shift_Del	DEL	ENST00000270861.5	hg19	CCDS3735.1																																																																																			.	.		0.323	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3		
CNIH2	254263	hgsc.bcm.edu	37	11	66050215	66050215	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:66050215delA	ENST00000311445.6	+	3	420	c.162delA	c.(160-162)ttafs	p.L54fs	YIF1A_ENST00000526497.1_5'Flank|CNIH2_ENST00000528852.1_Frame_Shift_Del_p.L54fs|CNIH2_ENST00000530519.1_3'UTR	NM_182553.2	NP_872359.1	Q6PI25	CNIH2_HUMAN	cornichon family AMPA receptor auxiliary protein 2	54					intracellular signal transduction (GO:0035556)|localization within membrane (GO:0051668)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of membrane potential (GO:0042391)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	5						GCGAGCGTTTAAAAAACATCG	0.647											OREG0021100	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L54X		Atlas-INDEL	.											.	CNIH2	15	.	0			c.161delT						.						31.0	30.0	30.0					11																	66050215		2200	4294	6494	SO:0001589	frameshift_variant	254263	exon3			.	BC047953	CCDS8131.1	11q13.2	2013-08-28	2013-08-28		ENSG00000174871	ENSG00000174871			28744	protein-coding gene	gene with protein product		611288	"""cornichon homolog 2 (Drosophila)"""			12477932	Standard	NM_182553		Approved	MGC50896, Cnil, CNIH-2	uc001ohi.2	Q6PI25	OTTHUMG00000166919	ENST00000311445.6:c.162delA	chr11.hg19:g.66050215delA	ENSP00000310003:p.Leu54fs	107.0	0.0	1088	176.0	11.0	NM_182553		Frame_Shift_Del	DEL	ENST00000311445.6	hg19	CCDS8131.1																																																																																			.	.		0.647	CNIH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391892.1	NM_182553	
CDHR4	389118	hgsc.bcm.edu	37	3	49830724	49830724	+	Frame_Shift_Del	DEL	G	G	-	rs368005921		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr3:49830724delG	ENST00000412678.2	-	13	1652	c.1644delC	c.(1642-1644)cccfs	p.P548fs	CDHR4_ENST00000462108.1_5'Flank	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	548	Cadherin 3. {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)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						GCTCACACTCGGGGGCATGGT	0.572																																					p.E549fs		Atlas-INDEL	.											.	CDHR4	37	.	0			c.1645delG						.						55.0	58.0	57.0					3																	49830724		692	1591	2283	SO:0001589	frameshift_variant	389118	exon13			.		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"""Cadherins / Cadherin-related"""	34527	protein-coding gene	gene with protein product			"""cadherin-like 29"""	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.1644delC	chr3.hg19:g.49830724delG	ENSP00000391409:p.Pro548fs	52.0	0.0		107.0	10.0	NM_001007540	Q6UXT0	Frame_Shift_Del	DEL	ENST00000412678.2	hg19	CCDS46829.1																																																																																			.	.		0.572	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540	
MAGEC3	139081	hgsc.bcm.edu	37	X	140967163	140967163	+	Frame_Shift_Del	DEL	T	T	-	rs372869684		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:140967163delT	ENST00000298296.1	+	3	461	c.461delT	c.(460-462)cttfs	p.L154fs	MAGEC3_ENST00000536088.1_5'Flank|MAGEC3_ENST00000443323.2_5'Flank|MAGEC3_ENST00000448920.1_5'Flank	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	154										NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					GGCTACACCCTTTCCCTTCCT	0.567																																					p.L154fs		Atlas-INDEL	.											.	MAGEC3	228	.	0			c.460delC						.						38.0	33.0	35.0					X																	140967163		2067	4298	6365	SO:0001589	frameshift_variant	139081	exon3			.	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.461delT	chrX.hg19:g.140967163delT	ENSP00000298296:p.Leu154fs	175.0	0.0		193.0	12.0	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Frame_Shift_Del	DEL	ENST00000298296.1	hg19	CCDS14676.1																																																																																			.	.		0.567	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
KMT2B	9757	hgsc.bcm.edu	37	19	36223328	36223328	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr19:36223328delC	ENST00000222270.7	+	28	5878	c.5878delC	c.(5878-5880)cccfs	p.P1961fs	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Frame_Shift_Del_p.P1961fs	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1961					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)										GGAGCTGGCTCCCCCTGGCCC	0.647																																					p.A1959fs		Atlas-INDEL	.											.	MLL4	229	.	0			c.5877delT						.						31.0	37.0	35.0					19																	36223328		1984	4140	6124	SO:0001589	frameshift_variant	8085	exon28			.	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.5878delC	chr19.hg19:g.36223328delC	ENSP00000222270:p.Pro1961fs	160.0	0.0		166.0	10.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Frame_Shift_Del	DEL	ENST00000222270.7	hg19	CCDS46055.1																																																																																			.	.		0.647	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
PARPBP	55010	hgsc.bcm.edu	37	12	102589882	102589882	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:102589882delA	ENST00000358383.5	+	11	1598	c.1553delA	c.(1552-1554)gaafs	p.E518fs	PARPBP_ENST00000392911.2_Frame_Shift_Del_p.E437fs|PARPBP_ENST00000541394.1_Frame_Shift_Del_p.E595fs|PARPBP_ENST00000543784.1_3'UTR|PARPBP_ENST00000378128.3_3'UTR|PARPBP_ENST00000535811.1_3'UTR|PARPBP_ENST00000327680.2_Frame_Shift_Del_p.E437fs			Q9NWS1	PARI_HUMAN	PARP1 binding protein	518					DNA repair (GO:0006281)|negative regulation of double-strand break repair via homologous recombination (GO:2000042)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(8)|urinary_tract(2)	11						TTGGATGGTGAAAATATTCTC	0.323																																					p.E518fs		Atlas-INDEL	.											.	PARPBP	40	.	0			c.1552delG						.						62.0	63.0	63.0					12																	102589882		2203	4300	6503	SO:0001589	frameshift_variant	55010	exon11			.	AK000648	CCDS9090.1, CCDS9090.2	12q23.2	2013-03-14	2012-01-24	2012-01-24		ENSG00000185480			26074	protein-coding gene	gene with protein product	"""PARP-1 binding protein"""	613687	"""chromosome 12 open reading frame 48"""	C12orf48		20931645	Standard	NM_017915		Approved	FLJ20641, PARI	uc001tjf.3	Q9NWS1		ENST00000358383.5:c.1553delA	chr12.hg19:g.102589882delA	ENSP00000351153:p.Glu518fs	138.0	0.0		210.0	14.0	NM_017915	B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Frame_Shift_Del	DEL	ENST00000358383.5	hg19	CCDS9090.2																																																																																			.	.		0.323	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915	
NT5DC1	221294	hgsc.bcm.edu	37	6	116565118	116565118	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:116565118delA	ENST00000319550.4	+	12	1381	c.1299delA	c.(1297-1299)tcafs	p.S433fs	RP3-486I3.5_ENST00000457319.1_RNA	NM_152729.2	NP_689942.2	Q5TFE4	NT5D1_HUMAN	5'-nucleotidase domain containing 1	433							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			large_intestine(2)|lung(2)|prostate(2)|skin(1)|stomach(1)	8		all_cancers(87;0.00367)|all_epithelial(87;0.00449)|Colorectal(196;0.0469)		all cancers(137;0.0327)|OV - Ovarian serous cystadenocarcinoma(136;0.0445)|GBM - Glioblastoma multiforme(226;0.0719)|Epithelial(106;0.112)		CAAGCAATTCAAAAACAGCTG	0.358																																					p.S433X	Colon(128;1440 1664 38087 41475 42869)	Atlas-INDEL	.											.	NT5DC1	32	.	0			c.1298delC						.						53.0	54.0	54.0					6																	116565118		2202	4294	6496	SO:0001589	frameshift_variant	221294	exon12			.	BC015138	CCDS5104.1	6q22.31	2008-02-05	2006-01-27	2006-01-27	ENSG00000178425	ENSG00000178425			21556	protein-coding gene	gene with protein product			"""5'-nucleotidase, cytosolic II-like 1"""	NT5C2L1			Standard	NM_152729		Approved	dJ486I3.1, MGC24302	uc003pwj.3	Q5TFE4	OTTHUMG00000015428	ENST00000319550.4:c.1299delA	chr6.hg19:g.116565118delA	ENSP00000326858:p.Ser433fs	191.0	0.0		255.0	17.0	NM_152729	B2RND9|B3KR35|Q6XYD5	Frame_Shift_Del	DEL	ENST00000319550.4	hg19	CCDS5104.1																																																																																			.	.		0.358	NT5DC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041931.3	NM_152729	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10551340	10551340	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:10551340delA	ENST00000396560.2	+	7	1533	c.1306delA	c.(1306-1308)aaafs	p.K437fs	ATF7IP2_ENST00000324570.5_Frame_Shift_Del_p.K437fs|ATF7IP2_ENST00000356427.2_Frame_Shift_Del_p.K437fs|ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_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	140.0	0.0		139.0	10.0	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	
KDM2B	84678	hgsc.bcm.edu	37	12	122018773	122018773	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:122018773delG	ENST00000377071.4	-	1	116	c.44delC	c.(43-45)ccafs	p.P15fs	KDM2B_ENST00000538046.2_Frame_Shift_Del_p.P15fs|RP13-941N14.1_ENST00000541574.1_lincRNA|KDM2B_ENST00000377069.4_5'Flank|KDM2B_ENST00000536437.1_5'UTR	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	15					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						TCTTTTTCGTGGGGGGTGATC	0.483																																					p.P15fs		Atlas-INDEL	.											.	KDM2B	218	.	0			c.45delA						.						128.0	128.0	128.0					12																	122018773		1842	4084	5926	SO:0001589	frameshift_variant	84678	exon1			.	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.44delC	chr12.hg19:g.122018773delG	ENSP00000366271:p.Pro15fs	172.0	0.0		224.0	14.0	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Frame_Shift_Del	DEL	ENST00000377071.4	hg19	CCDS41850.1																																																																																			.	.		0.483	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
ANKRD12	23253	hgsc.bcm.edu	37	18	9279634	9279634	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr18:9279634delA	ENST00000262126.4	+	12	6235	c.5995delA	c.(5995-5997)aaafs	p.K1999fs	ANKRD12_ENST00000400020.3_Frame_Shift_Del_p.K1976fs|ANKRD12_ENST00000383440.2_Frame_Shift_Del_p.K1976fs|snoU13_ENST00000459594.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1999						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						TAAATTTGACAAATTAAAGGT	0.323																																					p.D1998fs		Atlas-INDEL	.											.	ANKRD12	167	.	0			c.5994delC						.						93.0	100.0	98.0					18																	9279634		2203	4299	6502	SO:0001589	frameshift_variant	23253	exon12			.	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5995delA	chr18.hg19:g.9279634delA	ENSP00000262126:p.Lys1999fs	173.0	0.0		216.0	14.0	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Frame_Shift_Del	DEL	ENST00000262126.4	hg19	CCDS11843.1																																																																																			.	.		0.323	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
HMGCS2	3158	hgsc.bcm.edu	37	1	120301762	120301762	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:120301762delT	ENST00000369406.3	-	4	878	c.829delA	c.(829-831)atcfs	p.I277fs	HMGCS2_ENST00000544913.2_Frame_Shift_Del_p.I235fs|HMGCS2_ENST00000476640.1_Intron	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	277					cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|ketone body biosynthetic process (GO:0046951)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxymethylglutaryl-CoA synthase activity (GO:0004421)	p.I277F(1)		NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		TGATTCTGGATTTTTTTACGG	0.478																																					p.I277fs		Atlas-Indel,Pindel	.											.	HMGCS2	58	.	1	Substitution - Missense(1)	NS(1)	c.830delT						.						131.0	131.0	131.0					1																	120301762		2203	4300	6503	SO:0001589	frameshift_variant	3158	exon4			.	BC044217	CCDS905.1, CCDS53353.1	1p13-p12	2014-09-17	2010-04-30		ENSG00000134240	ENSG00000134240			5008	protein-coding gene	gene with protein product		600234	"""3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)"""			7851882, 7893153	Standard	NM_005518		Approved		uc001eid.3	P54868	OTTHUMG00000012101	ENST00000369406.3:c.829delA	chr1.hg19:g.120301762delT	ENSP00000358414:p.Ile277fs	140.0	0.0		197.0	13.0	NM_005518	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Frame_Shift_Del	DEL	ENST00000369406.3	hg19	CCDS905.1																																																																																			.	.		0.478	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518	
IL9R	3581	hgsc.bcm.edu	37	X	155239775	155239775	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chrX:155239775delC	ENST00000244174.5	+	9	1446	c.1267delC	c.(1267-1269)cccfs	p.P424fs	IL9R_ENST00000424344.3_Frame_Shift_Del_p.P403fs|IL9R_ENST00000369423.2_3'UTR|IL9R_ENST00000540897.1_3'UTR	NM_002186.2	NP_002177.2	Q01113	IL9R_HUMAN	interleukin 9 receptor	424					cell proliferation (GO:0008283)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	interleukin-9 receptor activity (GO:0004919)			NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(12)|upper_aerodigestive_tract(1)	23	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TAGGCCGGCTCCCCCAGACTC	0.627																																					p.A422fs		Atlas-INDEL	.											.	IL9R	73	.	0			c.1266delT						.						14.0	22.0	19.0					X																	155239775		2190	4288	6478	SO:0001589	frameshift_variant	3581	exon9			.	M84747	CCDS14771.4, CCDS59180.1	Xq28 and Yq12	2008-02-05			ENSG00000124334	ENSG00000124334		"""Pseudoautosomal regions / PAR2"", ""Interleukins and interleukin receptors"", ""CD molecules"""	6030	protein-coding gene	gene with protein product		300007				1376929, 8666384	Standard	NM_002186		Approved	CD129	uc004fnv.1	Q01113	OTTHUMG00000022720	ENST00000244174.5:c.1267delC	chrX.hg19:g.155239775delC	ENSP00000244174:p.Pro424fs	114.0	0.0		157.0	10.0	NM_002186	B9ZVT0|Q14634|Q8WWU1|Q96TF0	Frame_Shift_Del	DEL	ENST00000244174.5	hg19	CCDS14771.4																																																																																			.	.		0.627	IL9R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058981.1	NM_002186	
DGKA	1606	hgsc.bcm.edu	37	12	56346858	56346858	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56346858delG	ENST00000331886.5	+	22	2431	c.1977delG	c.(1975-1977)ctgfs	p.L659fs	DGKA_ENST00000551156.1_Frame_Shift_Del_p.L659fs|DGKA_ENST00000394147.1_Frame_Shift_Del_p.L659fs|DGKA_ENST00000549079.2_3'UTR	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	659					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	TGGTTGGGCTGGAGGGTGCAA	0.502																																					p.L659fs		Atlas-INDEL	.											.	DGKA	70	.	0			c.1976delT						.						117.0	116.0	116.0					12																	56346858		2203	4300	6503	SO:0001589	frameshift_variant	1606	exon22			.	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"""EF-hand domain containing"""	2849	protein-coding gene	gene with protein product		125855	"""diacylglycerol kinase, alpha (80kD)"""	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.1977delG	chr12.hg19:g.56346858delG	ENSP00000328405:p.Leu659fs	180.0	0.0		149.0	10.0	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Frame_Shift_Del	DEL	ENST00000331886.5	hg19	CCDS8896.1																																																																																			.	.		0.502	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1		
TRAF3	7187	hgsc.bcm.edu	37	14	103371834	103371834	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:103371834delT	ENST00000560371.1	+	11	1637	c.1420delT	c.(1420-1422)tttfs	p.F475fs	TRAF3_ENST00000351691.5_Frame_Shift_Del_p.F450fs|TRAF3_ENST00000347662.4_Frame_Shift_Del_p.F450fs|TRAF3_ENST00000392745.2_Frame_Shift_Del_p.F475fs|TRAF3_ENST00000539721.1_Frame_Shift_Del_p.F392fs	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	475	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|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)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		CTTGTCGCTGTTTTTTGTCAT	0.517																																					p.L473fs		Atlas-INDEL	.											.	TRAF3	60	.	0			c.1419delG						.						229.0	203.0	212.0					14																	103371834		2203	4300	6503	SO:0001589	frameshift_variant	7187	exon12			.	U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.1420delT	chr14.hg19:g.103371834delT	ENSP00000454207:p.Phe475fs	154.0	0.0		177.0	11.0	NM_145725	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Frame_Shift_Del	DEL	ENST00000560371.1	hg19	CCDS9975.1																																																																																			.	.		0.517	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725	
KIAA1715	80856	hgsc.bcm.edu	37	2	176804341	176804341	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr2:176804341delG	ENST00000272748.4	-	10	998	c.751delC	c.(751-753)cgafs	p.R251fs	KIAA1715_ENST00000535310.1_Frame_Shift_Del_p.R176fs|KIAA1715_ENST00000544803.1_Frame_Shift_Del_p.R282fs	NM_030650.1	NP_085153.1	Q9C0E8	LNP_HUMAN	KIAA1715	251					blood coagulation (GO:0007596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|limb development (GO:0060173)|regulation of chondrocyte differentiation (GO:0032330)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)	20			OV - Ovarian serous cystadenocarcinoma(117;0.0793)			CCTCGTTCTCGGGGGAGAATA	0.323																																					p.R251fs		Atlas-INDEL	.											KIAA1715,caecum,carcinoma,-1,1	KIAA1715	61	.	0			c.752delG						.						85.0	83.0	84.0					2																	176804341		2203	4300	6503	SO:0001589	frameshift_variant	80856	exon10			.	AB051502	CCDS33332.1	2q31	2014-06-27			ENSG00000144320	ENSG00000144320			21610	protein-coding gene	gene with protein product	"""lunapark"", ""limb and neural patterns"""	610236				11214970, 22729086	Standard	NM_030650		Approved	ulnaless, Ul, LNP1, LNP	uc002ukc.1	Q9C0E8	OTTHUMG00000154112	ENST00000272748.4:c.751delC	chr2.hg19:g.176804341delG	ENSP00000272748:p.Arg251fs	184.0	0.0		200.0	12.0	NM_030650	B7ZLA8|Q2M2V8|Q2YD99|Q658W8|Q8N5V9|Q96MS5	Frame_Shift_Del	DEL	ENST00000272748.4	hg19	CCDS33332.1																																																																																			.	.		0.323	KIAA1715-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333949.3	XM_042834	
DSCAML1	57453	hgsc.bcm.edu	37	11	117306420	117306420	+	Frame_Shift_Del	DEL	C	C	-	rs138082991		TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr11:117306420delC	ENST00000321322.6	-	27	4997	c.4996delG	c.(4996-4998)gtgfs	p.V1666fs	DSCAML1_ENST00000527706.1_Frame_Shift_Del_p.V1396fs	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1606					axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		AGCAGTGCCACCCCCAGTGTG	0.577																																					p.V1666fs		Atlas-INDEL	.											.	DSCAML1	286	.	0			c.4997delT						.						129.0	100.0	110.0					11																	117306420		2201	4296	6497	SO:0001589	frameshift_variant	57453	exon27			.		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.4996delG	chr11.hg19:g.117306420delC	ENSP00000315465:p.Val1666fs	86.0	0.0		144.0	10.0	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Frame_Shift_Del	DEL	ENST00000321322.6	hg19	CCDS8384.1																																																																																			.	.		0.577	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
CD163L1	283316	hgsc.bcm.edu	37	12	7527201	7527201	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:7527201delG	ENST00000313599.3	-	13	3303	c.3246delC	c.(3244-3246)gccfs	p.A1082fs	CD163L1_ENST00000544331.1_5'Flank|CD163L1_ENST00000396630.1_Frame_Shift_Del_p.A1082fs|CD163L1_ENST00000416109.2_Frame_Shift_Del_p.A1092fs			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1082	SRCR 10. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						TGGCATTGAAGGCCACTCCAC	0.592											OREG0021653	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F1083fs		Atlas-INDEL	.											.	CD163L1	238	.	0			c.3247delT						.						93.0	83.0	86.0					12																	7527201		2203	4300	6503	SO:0001589	frameshift_variant	283316	exon13			.	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.3246delC	chr12.hg19:g.7527201delG	ENSP00000315945:p.Ala1082fs	218.0	0.0	642	163.0	10.0	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Frame_Shift_Del	DEL	ENST00000313599.3	hg19	CCDS8577.1																																																																																			.	.		0.592	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
MMP17	4326	hgsc.bcm.edu	37	12	132335715	132335715	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:132335715delC	ENST00000360564.1	+	10	1810	c.1708delC	c.(1708-1710)cccfs	p.P571fs	MMP17_ENST00000535004.1_Frame_Shift_Del_p.P111fs|MMP17_ENST00000535291.1_Frame_Shift_Del_p.P487fs	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	571					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	GGCATCCTCTCCCCCGGGGGC	0.716																																					p.S569fs		Atlas-INDEL	.											.	MMP17	77	.	0			c.1707delT						.						12.0	13.0	12.0					12																	132335715		2154	4241	6395	SO:0001589	frameshift_variant	4326	exon10			.	X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"""matrix metalloproteinase 17 (membrane-inserted)"""			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.1708delC	chr12.hg19:g.132335715delC	ENSP00000353767:p.Pro571fs	81.0	0.0		152.0	10.0	NM_016155	Q14850	Frame_Shift_Del	DEL	ENST00000360564.1	hg19	CCDS31927.1																																																																																			.	.		0.716	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155	
SGCE	8910	hgsc.bcm.edu	37	7	94232644	94232644	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:94232644delT	ENST00000265735.7	-	6	893	c.783delA	c.(781-783)aaafs	p.K261fs	SGCE_ENST00000415788.2_Frame_Shift_Del_p.K297fs|SGCE_ENST00000447873.1_Frame_Shift_Del_p.K261fs|SGCE_ENST00000445866.2_Frame_Shift_Del_p.K261fs|SGCE_ENST00000428696.2_Frame_Shift_Del_p.K261fs|SGCE_ENST00000437425.2_Frame_Shift_Del_p.K220fs	NM_003919.2	NP_003910.1	O43556	SGCE_HUMAN	sarcoglycan, epsilon	261	Cys-rich.				cell-matrix adhesion (GO:0007160)|muscle organ development (GO:0007517)	cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|dystrophin-associated glycoprotein complex (GO:0016010)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	14	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GAGTACGAAATTTTTTATCAC	0.318																																					p.F262fs		Atlas-INDEL	.											.	SGCE	68	.	0			c.784delT						.						83.0	80.0	81.0					7																	94232644		2203	4300	6503	SO:0001589	frameshift_variant	8910	exon6			.	AF036364	CCDS5637.1, CCDS47642.1, CCDS47643.1, CCDS75634.1	7q21.3	2014-09-17			ENSG00000127990	ENSG00000127990			10808	protein-coding gene	gene with protein product		604149		DYT11		9475163, 9405466	Standard	NM_001099401		Approved		uc003unn.2	O43556	OTTHUMG00000022828	ENST00000265735.7:c.783delA	chr7.hg19:g.94232644delT	ENSP00000265735:p.Lys261fs	142.0	0.0		166.0	12.0	NM_001099401	B2R8N2|D6W5Q8|E9PF60|G5E9K6|Q6L8P0|Q75MH8|Q8NFG8|Q8WW28	Frame_Shift_Del	DEL	ENST00000265735.7	hg19	CCDS5637.1																																																																																			.	.		0.318	SGCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255251.2		
PAPD5	64282	hgsc.bcm.edu	37	16	50257145	50257145	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr16:50257145delT	ENST00000561678.1	+	6	927	c.853delT	c.(853-855)tttfs	p.F286fs	PAPD5_ENST00000357464.3_Frame_Shift_Del_p.F317fs|PAPD5_ENST00000436909.3_Frame_Shift_Del_p.F396fs|PAPD5_ENST00000573002.1_3'UTR			Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5	317					histone mRNA catabolic process (GO:0071044)|mitotic nuclear division (GO:0007067)|mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|polynucleotide adenylyltransferase activity (GO:0004652)			endometrium(1)|kidney(1)|lung(2)	4		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)		CTTAATAGAATTTTTTGAATT	0.338																																					p.E394fs		Atlas-INDEL	.											.	PAPD5	57	.	0			c.1182delA						.						79.0	78.0	78.0					16																	50257145		1803	4071	5874	SO:0001589	frameshift_variant	64282	exon8			.	AF089897	CCDS54006.1	16q12.1	2010-11-18				ENSG00000121274			30758	protein-coding gene	gene with protein product	"""TUTase3"""	605540				10066793	Standard	NM_001040284		Approved	TRF4-2	uc010vgo.2	Q8NDF8		ENST00000561678.1:c.853delT	chr16.hg19:g.50257145delT	ENSP00000455837:p.Phe286fs	147.0	0.0		163.0	11.0	NM_001040284	B4DV38|Q9NW67|Q9Y6C0	Frame_Shift_Del	DEL	ENST00000561678.1	hg19																																																																																				.	.		0.338	PAPD5-002	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000423150.1	NM_022447	
FERMT2	10979	hgsc.bcm.edu	37	14	53326414	53326414	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr14:53326414delT	ENST00000395631.2	-	14	1962	c.1746delA	c.(1744-1746)aaafs	p.K582fs	FERMT2_ENST00000553373.1_Frame_Shift_Del_p.K589fs|FERMT2_ENST00000341590.3_Frame_Shift_Del_p.K582fs|FERMT2_ENST00000343279.4_Frame_Shift_Del_p.K589fs|FERMT2_ENST00000557255.1_5'UTR|FERMT2_ENST00000399304.3_Frame_Shift_Del_p.K589fs			Q96AC1	FERM2_HUMAN	fermitin family member 2	582	FERM.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|focal adhesion assembly (GO:0048041)|integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|protein localization to membrane (GO:0072657)|regulation of cell shape (GO:0008360)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)		ERO1L/FERMT2(2)	NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Breast(41;0.0342)					TAAGTTCTTCTTTTTTGCCCC	0.398																																					p.E590fs		Atlas-INDEL	.											.	FERMT2	59	.	0			c.1768delG						.						118.0	103.0	108.0					14																	53326414		2203	4298	6501	SO:0001589	frameshift_variant	10979	exon15			.	Z24725	CCDS9713.1, CCDS45107.1, CCDS45108.1	14q22.1	2013-01-10	2010-06-24	2007-12-14	ENSG00000073712	ENSG00000073712		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15767	protein-coding gene	gene with protein product	"""kindlin-2"""	607746	"""pleckstrin homology domain containing, family C (with FERM domain) member 1"", ""fermitin family homolog 2 (Drosophila)"""	PLEKHC1		8175911, 12697302	Standard	NM_006832		Approved	mig-2, KIND2, UNC112B	uc001xac.3	Q96AC1	OTTHUMG00000140309	ENST00000395631.2:c.1746delA	chr14.hg19:g.53326414delT	ENSP00000378993:p.Lys582fs	229.0	0.0		269.0	18.0	NM_001135000	B5TJY2|Q14840|Q86TY7	Frame_Shift_Del	DEL	ENST00000395631.2	hg19	CCDS9713.1																																																																																			.	.		0.398	FERMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276907.2	NM_006832	
SLFN13	146857	hgsc.bcm.edu	37	17	33772591	33772591	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr17:33772591delT	ENST00000285013.6	-	3	384	c.109delA	c.(109-111)actfs	p.T37fs	SLFN13_ENST00000542635.1_Frame_Shift_Del_p.T37fs|SLFN13_ENST00000360502.2_Intron|SLFN13_ENST00000526861.1_Frame_Shift_Del_p.T37fs|SLFN13_ENST00000534689.1_Intron|SLFN13_ENST00000533791.1_Frame_Shift_Del_p.T37fs	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	37						intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		TCTCTCTGAGTTTTCTGTAGC	0.483																																					p.T37fs		Atlas-INDEL	.											.	SLFN13	79	.	0			c.110delC						.						98.0	97.0	97.0					17																	33772591		2203	4300	6503	SO:0001589	frameshift_variant	146857	exon3			.	AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.109delA	chr17.hg19:g.33772591delT	ENSP00000285013:p.Thr37fs	188.0	0.0		174.0	11.0	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Frame_Shift_Del	DEL	ENST00000285013.6	hg19	CCDS32620.1																																																																																			.	.		0.483	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
TENM3	55714	hgsc.bcm.edu	37	4	183713573	183713573	+	Frame_Shift_Del	DEL	C	C	-	rs80197208	byFrequency	TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr4:183713573delC	ENST00000511685.1	+	26	5871	c.5748delC	c.(5746-5748)aacfs	p.N1916fs	TENM3_ENST00000406950.2_Frame_Shift_Del_p.N1916fs			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1916					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.E1919fs*37(1)									ACATATACAACCCCCCGGAAA	0.532																																					p.N1916fs		Atlas-INDEL	.											.,1	.	.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.5747delA						.						70.0	73.0	72.0					4																	183713573		2022	4170	6192	SO:0001589	frameshift_variant	55714	exon25			.	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.5748delC	chr4.hg19:g.183713573delC	ENSP00000424226:p.Asn1916fs	139.0	0.0		175.0	11.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Frame_Shift_Del	DEL	ENST00000511685.1	hg19	CCDS47165.1																																																																																			.	.		0.532	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
HLA-G	3135	hgsc.bcm.edu	37	6	29797196	29797196	+	Splice_Site	DEL	C	C	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr6:29797196delC	ENST00000360323.6	+	4	645	c.621delC	c.(619-621)gac>ga	p.D207fs	HLA-G_ENST00000376818.3_Splice_Site_p.N115fs|HLA-G_ENST00000376828.2_Splice_Site_p.D212fs|HLA-G_ENST00000428701.1_Splice_Site_p.D207fs|HLA-G_ENST00000376815.3_Intron			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	207	Alpha-3.				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)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						TCCTTTCAGACCCCCCCAAGA	0.537																																					p.D207fs		Pindel	.											.,1	HLA-G	90	.	0			c.620delA						.						91.0	98.0	95.0					6																	29797196		2203	4300	6503	SO:0001630	splice_region_variant	3135	exon5			.		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.620-1C>-	chr6.hg19:g.29797196delC		150.0	0.0		227.0	10.0	NM_002127		Frame_Shift_Del	DEL	ENST00000360323.6	hg19	CCDS4668.1																																																																																			.	.		0.537	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	Frame_Shift_Del
PIPSL	266971	hgsc.bcm.edu	37	10	95720426	95720426	+	RNA	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr10:95720426delA	ENST00000480546.1	-	0	871					NR_002319.2		A2A3N6	PIPSL_HUMAN	PIP5K1A and PSMD4-like, pseudogene							cytoplasm (GO:0005737)	phosphatidylinositol phosphate kinase activity (GO:0016307)										GTCAGCATCCAAAAAAAGACC	0.483																																					.		Pindel	.											.	.	.	.	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.95720426delA		195.0	0.0		224.0	10.0	.	Q6NUK8	RNA	DEL	ENST00000480546.1	hg19																																																																																				.	.		0.483	PIPSL-002	PUTATIVE	basic	processed_transcript	pseudogene	OTTHUMT00000351483.1	NR_002319	
C7orf61	402573	hgsc.bcm.edu	37	7	100061288	100061288	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr7:100061288delT	ENST00000332375.3	-	2	330	c.85delA	c.(85-87)attfs	p.I29fs	TSC22D4_ENST00000496728.1_5'UTR|RN7SL161P_ENST00000582642.1_RNA	NM_001004323.1	NP_001004323.1	Q8IZ16	CG061_HUMAN	chromosome 7 open reading frame 61	29						nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|prostate(1)|skin(1)	4						GTTGGTTTAATTTTTTGCCTC	0.488																																					p.I29fs		Pindel	.											.	C7orf61	12	.	0			c.86delT						.						57.0	63.0	61.0					7																	100061288		2027	4210	6237	SO:0001589	frameshift_variant	402573	exon2			.		CCDS47661.1	7q22.1	2013-10-11			ENSG00000185955	ENSG00000185955			22135	protein-coding gene	gene with protein product						12690205	Standard	NM_001004323		Approved	IMAGE:4839025	uc003uuz.1	Q8IZ16	OTTHUMG00000150234	ENST00000332375.3:c.85delA	chr7.hg19:g.100061288delT	ENSP00000327732:p.Ile29fs	167.0	0.0		243.0	11.0	NM_001004323		Frame_Shift_Del	DEL	ENST00000332375.3	hg19	CCDS47661.1																																																																																			.	.		0.488	C7orf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316976.2	NM_001004323	
ESYT1	23344	hgsc.bcm.edu	37	12	56531342	56531342	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr12:56531342delG	ENST00000394048.5	+	18	2262	c.1998delG	c.(1996-1998)ttgfs	p.L666fs	ESYT1_ENST00000541590.1_Frame_Shift_Del_p.L676fs|ESYT1_ENST00000267113.4_Frame_Shift_Del_p.L676fs	NM_001184796.1|NM_015292.2	NP_001171725.1|NP_056107.1	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	666	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid transport (GO:0006869)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(4)|lung(10)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	28						ACCGTTTCTTGGGGGGACTGG	0.552																																					p.L676fs		Pindel	.											.	ESYT1	84	.	0			c.2027delT						.						154.0	158.0	157.0					12																	56531342		2203	4300	6503	SO:0001589	frameshift_variant	23344	exon18			.	AK074368	CCDS8904.1, CCDS53801.1	12q13.2	2014-07-02	2009-06-23	2009-06-23		ENSG00000139641		"""Synaptotagmins"""	29534	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member A"""	FAM62A		9872452, 10350628, 17672888	Standard	NM_015292		Approved	MBC2, KIAA0747	uc001sjr.3	Q9BSJ8		ENST00000394048.5:c.1998delG	chr12.hg19:g.56531342delG	ENSP00000377612:p.Leu666fs	100.0	0.0		141.0	10.0	NM_001184796	A0FGR7|A8K2S2|O94848|Q6PJN4|Q9H6J1|Q9H6W2|Q9Y416	Frame_Shift_Del	DEL	ENST00000394048.5	hg19	CCDS8904.1																																																																																			.	.		0.552	ESYT1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407906.1	NM_015292	
CDC42	998	hgsc.bcm.edu	37	1	22413358	22413358	+	Splice_Site	DEL	A	A	-			TCGA-DD-A39Y-01A-11D-A20W-10	TCGA-DD-A39Y-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f8cf411-5c5e-428b-b586-681ff7341d19	913c971b-4d3d-445d-92b6-feda7a575e32	g.chr1:22413358delA	ENST00000344548.3	+	6	736	c.485delA	c.(484-486)cag>cg	p.Q162fs	CDC42_ENST00000315554.8_Splice_Site_p.Q162fs|CDC42_ENST00000421089.2_Splice_Site_p.Q204fs|CDC42_ENST00000400259.1_Splice_Site_p.Q162fs|CDC42_ENST00000498236.1_3'UTR	NM_001039802.1	NP_001034891.1	P60953	CDC42_HUMAN	cell division cycle 42	162					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cellular protein localization (GO:0034613)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell-cell adhesion (GO:0090136)|epithelial-mesenchymal cell signaling (GO:0060684)|establishment of Golgi localization (GO:0051683)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|keratinization (GO:0031424)|keratinocyte development (GO:0003334)|macrophage differentiation (GO:0030225)|multicellular organism growth (GO:0035264)|muscle cell differentiation (GO:0042692)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of gene expression (GO:0010629)|negative regulation of protein complex assembly (GO:0031333)|neuron fate determination (GO:0048664)|nuclear migration (GO:0007097)|nucleus localization (GO:0051647)|organelle transport along microtubule (GO:0072384)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of JNK cascade (GO:0046330)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of synapse structural plasticity (GO:0051835)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of filopodium assembly (GO:0051489)|regulation of mitosis (GO:0007088)|regulation of protein catabolic process (GO:0042176)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein kinase activity (GO:0045859)|regulation of protein stability (GO:0031647)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|sprouting angiogenesis (GO:0002040)|submandibular salivary gland formation (GO:0060661)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	apical part of cell (GO:0045177)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|spindle midzone (GO:0051233)	apolipoprotein A-I receptor binding (GO:0034191)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)	12		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)		GCACTTACACAGGTAAGAATG	0.443																																					p.Q162fs		Pindel	.											.	CDC42	26	.	0			c.484delC						.						123.0	123.0	123.0					1																	22413358		2203	4300	6503	SO:0001630	splice_region_variant	998	exon6			.	BC018266	CCDS221.1, CCDS222.1	1p36.1	2013-01-17	2013-01-17		ENSG00000070831	ENSG00000070831			1736	protein-coding gene	gene with protein product	"""GTP binding protein, 25kDa"""	116952	"""cell division cycle 42 (GTP-binding protein, 25kD)"", ""cell division cycle 42 (GTP binding protein, 25kDa)"""			2124704, 2122236	Standard	NM_001039802		Approved	G25K, CDC42Hs	uc001bfr.3	P60953	OTTHUMG00000002753	ENST00000344548.3:c.486+1A>-	chr1.hg19:g.22413358delA		47.0	0.0		97.0	22.0	NM_001039802	P21181|P25763|Q7L8R5|Q9UDI2	Frame_Shift_Del	DEL	ENST00000344548.3	hg19	CCDS221.1																																																																																			.	.		0.443	CDC42-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007787.1	NM_001791	Frame_Shift_Del
