#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
CALML6	163688	hgsc.bcm.edu	37	1	1847882	1847882	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:1847882A>G	ENST00000307786.3	+	3	535	c.81A>G	c.(79-81)acA>acG	p.T27T	CALML6_ENST00000462293.1_Intron	NM_138705.2	NP_619650.2	Q8TD86	CALL6_HUMAN	calmodulin-like 6	27						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(1)|prostate(2)	7	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.94e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.83e-23)|GBM - Glioblastoma multiforme(42;3.23e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		CCCTGCAGACAGAGCGCCTGT	0.632																																					p.T27T		Atlas-SNP	.											.	CALML6	18	.	0			c.A81G						.						46.0	46.0	46.0					1																	1847882		2149	4247	6396	SO:0001819	synonymous_variant	163688	exon3			GCAGACAGAGCGC	AF490905	CCDS30566.1	1p36.33	2013-01-10			ENSG00000169885	ENSG00000169885		"""EF-hand domain containing"""	24193	protein-coding gene	gene with protein product		610171					Standard	NM_138705		Approved	CAGLP	uc001aih.1	Q8TD86	OTTHUMG00000000943	ENST00000307786.3:c.81A>G	chr1.hg19:g.1847882A>G		134.0	0.0		117.0	5.0	NM_138705	A2A2M3|Q6Q2C4	Silent	SNP	ENST00000307786.3	hg19	CCDS30566.1																																																																																			.	.		0.632	CALML6-004	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276929.1	NM_138705	
EPHA2	1969	hgsc.bcm.edu	37	1	16475439	16475439	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:16475439A>G	ENST00000358432.5	-	3	411	c.257T>C	c.(256-258)gTg>gCg	p.V86A	EPHA2_ENST00000461614.1_5'UTR	NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	86	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.|Mediates interaction with CLDN4.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	TCCTCGGTACACCCAGTTGGT	0.537																																					p.V86A		Atlas-SNP	.											.	EPHA2	102	.	0			c.T257C						.						113.0	95.0	101.0					1																	16475439		2203	4300	6503	SO:0001583	missense	1969	exon3			CGGTACACCCAGT	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3386	protein-coding gene	gene with protein product		176946	"""EphA2"""	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.257T>C	chr1.hg19:g.16475439A>G	ENSP00000351209:p.Val86Ala	105.0	0.0		121.0	5.0	NM_004431	B5A968|Q8N3Z2	Missense_Mutation	SNP	ENST00000358432.5	hg19	CCDS169.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.599982	0.87055	.	.	ENSG00000142627	ENST00000358432	T	0.11821	2.74	5.35	5.35	0.76521	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.155316	0.31438	N	0.007646	T	0.27169	0.0666	L	0.49126	1.545	0.50467	D	0.999875	P;B	0.52061	0.95;0.448	P;P	0.58172	0.834;0.511	T	0.00872	-1.1532	10	0.87932	D	0	.	13.2736	0.60175	1.0:0.0:0.0:0.0	.	86;86	B5A968;P29317	.;EPHA2_HUMAN	A	86	ENSP00000351209:V86A	ENSP00000351209:V86A	V	-	2	0	EPHA2	16348026	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.335000	0.96500	2.024000	0.59613	0.459000	0.35465	GTG	.	.		0.537	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
SLC9A1	6548	hgsc.bcm.edu	37	1	27428223	27428223	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:27428223T>C	ENST00000263980.3	-	10	2605	c.2030A>G	c.(2029-2031)gAg>gGg	p.E677G	SLC9A1_ENST00000545949.1_Missense_Mutation_p.E338G|SLC9A1_ENST00000490329.1_5'Flank	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	677					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	TACCTTCTGCTCCAGCTGCCG	0.602																																					p.E677G		Atlas-SNP	.											.	SLC9A1	68	.	0			c.A2030G						.						34.0	32.0	33.0					1																	27428223		2203	4299	6502	SO:0001583	missense	6548	exon10			TTCTGCTCCAGCT	M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"""Solute carriers"""	11071	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 143"""	107310	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 1"""	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.2030A>G	chr1.hg19:g.27428223T>C	ENSP00000263980:p.Glu677Gly	73.0	0.0		120.0	6.0	NM_003047	B1ALD6|D3DPL4|Q96EM2	Missense_Mutation	SNP	ENST00000263980.3	hg19	CCDS295.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.897770	0.91962	.	.	ENSG00000090020	ENST00000263980;ENST00000374089;ENST00000545949;ENST00000447808	T;T	0.52983	0.64;0.64	4.97	4.97	0.65823	.	0.215214	0.47852	D	0.000217	T	0.48696	0.1514	M	0.70275	2.135	0.80722	D	1	B	0.18610	0.029	B	0.13407	0.009	T	0.48980	-0.8986	10	0.46703	T	0.11	.	14.4627	0.67462	0.0:0.0:0.0:1.0	.	677	P19634	SL9A1_HUMAN	G	677;181;338;98	ENSP00000263980:E677G;ENSP00000445520:E338G	ENSP00000263980:E677G	E	-	2	0	SLC9A1	27300810	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.737000	0.55060	2.082000	0.62665	0.459000	0.35465	GAG	.	.		0.602	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047	
PHACTR4	65979	hgsc.bcm.edu	37	1	28818190	28818190	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:28818190T>C	ENST00000373839.3	+	12	2168	c.1907T>C	c.(1906-1908)cTc>cCc	p.L636P	PHACTR4_ENST00000373836.3_Missense_Mutation_p.L646P|PHACTR4_ENST00000493669.1_3'UTR	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	636					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		GTCGCTGAACTCCTTGCCAGG	0.458																																					p.L646P		Atlas-SNP	.											.	PHACTR4	64	.	0			c.T1937C						.						87.0	92.0	90.0					1																	28818190		1965	4158	6123	SO:0001583	missense	65979	exon11			CTGAACTCCTTGC	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"""Phosphatase and actin regulators"""	25793	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 124"""	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.1907T>C	chr1.hg19:g.28818190T>C	ENSP00000362945:p.Leu636Pro	109.0	0.0		118.0	5.0	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	hg19	CCDS41293.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.644786	0.87859	.	.	ENSG00000204138	ENST00000373839;ENST00000373836	T;T	0.57273	0.41;0.44	5.67	5.67	0.87782	.	0.066491	0.64402	D	0.000007	T	0.73289	0.3568	M	0.80183	2.485	0.80722	D	1	D;D	0.58268	0.982;0.979	D;D	0.69479	0.964;0.925	T	0.77523	-0.2556	10	0.87932	D	0	-4.5027	15.1316	0.72530	0.0:0.0:0.0:1.0	.	646;636	Q8IZ21-2;Q8IZ21	.;PHAR4_HUMAN	P	636;646	ENSP00000362945:L636P;ENSP00000362942:L646P	ENSP00000362942:L646P	L	+	2	0	PHACTR4	28690777	1.000000	0.71417	0.884000	0.34674	0.990000	0.78478	8.000000	0.88501	2.172000	0.68678	0.456000	0.33151	CTC	.	.		0.458	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923	
BAI2	576	hgsc.bcm.edu	37	1	32207725	32207725	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:32207725G>A	ENST00000373658.3	-	8	1687	c.1346C>T	c.(1345-1347)gCg>gTg	p.A449V	BAI2_ENST00000398547.1_Missense_Mutation_p.A382V|BAI2_ENST00000398556.3_Missense_Mutation_p.A397V|BAI2_ENST00000373655.2_Missense_Mutation_p.A449V|BAI2_ENST00000527361.1_Missense_Mutation_p.A449V|BAI2_ENST00000257070.4_Missense_Mutation_p.A449V|BAI2_ENST00000398538.1_Missense_Mutation_p.A437V|BAI2_ENST00000440175.2_Missense_Mutation_p.A91V|BAI2_ENST00000398542.1_Missense_Mutation_p.A382V	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	449	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A449V(1)		breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GGCTGGGCCCGCCACGCTGCA	0.657																																					p.A449V		Atlas-SNP	.											BAI2,NS,carcinoma,0,1	BAI2	128	.	1	Substitution - Missense(1)	lung(1)	c.C1346T						.						30.0	35.0	33.0					1																	32207725		2201	4296	6497	SO:0001583	missense	576	exon8			GGGCCCGCCACGC	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.1346C>T	chr1.hg19:g.32207725G>A	ENSP00000362762:p.Ala449Val	88.0	0.0		139.0	61.0	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	hg19	CCDS346.2	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271041	0.59540	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538;ENST00000420125;ENST00000533175	T;T;T;T;T;T;T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62	4.1	3.17	0.36434	.	0.200067	0.24996	N	0.033949	T	0.38214	0.1032	N	0.17345	0.48	0.29032	N	0.885631	P;P;P;P;P;D;P	0.54964	0.89;0.936;0.936;0.709;0.89;0.969;0.89	P;B;B;B;B;P;P	0.48270	0.523;0.388;0.388;0.426;0.322;0.572;0.523	T	0.33369	-0.9871	10	0.54805	T	0.06	.	12.9627	0.58468	0.0:0.1647:0.8352:0.0	.	382;449;437;91;382;449;449	A2A3C3;O60241-4;O60241-3;B4DKC3;A2A3C1;O60241-2;O60241	.;.;.;.;.;.;BAI2_HUMAN	V	397;382;449;449;382;449;449;91;437;387;428	ENSP00000381564:A397V;ENSP00000381555:A382V;ENSP00000362762:A449V;ENSP00000362759:A449V;ENSP00000381550:A382V;ENSP00000257070:A449V;ENSP00000435397:A449V;ENSP00000391071:A91V;ENSP00000381548:A437V;ENSP00000410921:A387V;ENSP00000437219:A428V	ENSP00000257070:A449V	A	-	2	0	BAI2	31980312	1.000000	0.71417	0.918000	0.36340	0.806000	0.45545	9.594000	0.98254	1.049000	0.40321	0.561000	0.74099	GCG	.	.		0.657	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
CSMD2	114784	hgsc.bcm.edu	37	1	34011768	34011768	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:34011768C>T	ENST00000373381.4	-	57	9145	c.8969G>A	c.(8968-8970)cGt>cAt	p.R2990H		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2963	Sushi 22. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R2846H(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GTCCCCCAAACGGATGCCATG	0.567																																					p.R2846H		Atlas-SNP	.											CSMD2,NS,carcinoma,0,2	CSMD2	946	.	1	Substitution - Missense(1)	prostate(1)	c.G8537A						.						59.0	53.0	55.0					1																	34011768		2203	4300	6503	SO:0001583	missense	114784	exon56			CCCAAACGGATGC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.8969G>A	chr1.hg19:g.34011768C>T	ENSP00000362479:p.Arg2990His	106.0	0.0		114.0	45.0	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	C	20.8	4.056281	0.76074	.	.	ENSG00000121904	ENST00000373381	T	0.64803	-0.12	4.97	4.97	0.65823	Complement control module (2);Sushi/SCR/CCP (3);	0.061352	0.64402	D	0.000003	T	0.67664	0.2917	M	0.69523	2.12	0.80722	D	1	P;B	0.46457	0.878;0.139	P;B	0.46339	0.513;0.072	T	0.68685	-0.5343	10	0.36615	T	0.2	.	17.4042	0.87469	0.0:1.0:0.0:0.0	.	2846;2990	Q7Z408;E7EUA6	CSMD2_HUMAN;.	H	2990	ENSP00000362479:R2990H	ENSP00000241312:R2846H	R	-	2	0	CSMD2	33784355	1.000000	0.71417	0.951000	0.38953	0.596000	0.36781	7.629000	0.83207	2.591000	0.87537	0.650000	0.86243	CGT	.	.		0.567	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
AGO4	192670	hgsc.bcm.edu	37	1	36291638	36291638	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:36291638T>C	ENST00000373210.3	+	6	982	c.737T>C	c.(736-738)gTc>gCc	p.V246A		NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	246	PAZ. {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)										TCCCAGCGTGTCAAATTTACC	0.453																																					p.V246A		Atlas-SNP	.											.	.	.	.	0			c.T737C						.						121.0	115.0	117.0					1																	36291638		2203	4300	6503	SO:0001583	missense	192670	exon6			AGCGTGTCAAATT	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.737T>C	chr1.hg19:g.36291638T>C	ENSP00000362306:p.Val246Ala	93.0	0.0		118.0	5.0	NM_017629	A7MD27	Missense_Mutation	SNP	ENST00000373210.3	hg19	CCDS397.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.167221	0.78339	.	.	ENSG00000134698	ENST00000373210	T	0.12774	2.65	5.53	5.53	0.82687	Argonaute/Dicer protein, PAZ (4);	0.000000	0.85682	D	0.000000	T	0.27866	0.0686	M	0.76328	2.33	0.80722	D	1	B	0.18461	0.028	B	0.40329	0.326	T	0.07693	-1.0759	10	0.23302	T	0.38	-13.8332	15.6642	0.77213	0.0:0.0:0.0:1.0	.	246	Q9HCK5	AGO4_HUMAN	A	246	ENSP00000362306:V246A	ENSP00000362306:V246A	V	+	2	0	EIF2C4	36064225	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.098000	0.63641	0.455000	0.32223	GTC	.	.		0.453	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629	
HEYL	26508	hgsc.bcm.edu	37	1	40105230	40105230	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:40105230T>C	ENST00000372852.3	-	1	387	c.68A>G	c.(67-69)gAg>gGg	p.E23G		NM_014571.3	NP_055386	Q9NQ87	HEYL_HUMAN	hes-related family bHLH transcription factor with YRPW motif-like	23					atrioventricular valve morphogenesis (GO:0003181)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to BMP stimulus (GO:0071773)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|glomerulus development (GO:0032835)|mesenchymal cell development (GO:0014031)|negative regulation of androgen receptor activity (GO:2000824)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|pulmonary valve morphogenesis (GO:0003184)|skeletal muscle cell differentiation (GO:0035914)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-1 domain binding (GO:0050683)|microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|protein heterodimerization activity (GO:0046982)|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 core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	7	Lung NSC(20;3.81e-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;1.1e-18)|Epithelial(16;2.77e-17)|all cancers(16;5.64e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			CAGCTGGCCCTCTTGGCCCAC	0.751																																					p.E23G		Atlas-SNP	.											.	HEYL	27	.	0			c.A68G						.						11.0	11.0	11.0					1																	40105230		2186	4285	6471	SO:0001583	missense	26508	exon1			TGGCCCTCTTGGC	BC006087	CCDS439.1	1p34.3	2013-10-17	2013-10-17		ENSG00000163909	ENSG00000163909		"""Basic helix-loop-helix proteins"""	4882	protein-coding gene	gene with protein product	"""hairy/enhancer-of-split related with YRPW motif 3"""	609034	"""hairy/enhancer-of-split related with YRPW motif-like"""			10415358, 10860664	Standard	NM_014571		Approved	bHLHb33, HEY3, HESR3	uc001cdp.3	Q9NQ87	OTTHUMG00000000458	ENST00000372852.3:c.68A>G	chr1.hg19:g.40105230T>C	ENSP00000361943:p.Glu23Gly	87.0	0.0		80.0	5.0	NM_014571	Q5TG99	Missense_Mutation	SNP	ENST00000372852.3	hg19	CCDS439.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.388348	0.42308	.	.	ENSG00000163909	ENST00000372852	T	0.63580	-0.05	3.68	3.68	0.42216	.	0.553967	0.19177	N	0.120783	T	0.57242	0.2040	L	0.57536	1.79	0.80722	D	1	B	0.20368	0.044	B	0.24848	0.056	T	0.61481	-0.7054	10	0.87932	D	0	-15.647	8.9953	0.36048	0.0:0.0:0.0:1.0	.	23	Q9NQ87	HEYL_HUMAN	G	23	ENSP00000361943:E23G	ENSP00000361943:E23G	E	-	2	0	HEYL	39877817	0.994000	0.37717	0.951000	0.38953	0.108000	0.19459	2.862000	0.48388	1.884000	0.54569	0.533000	0.62120	GAG	.	.		0.751	HEYL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001179.2	NM_014571	
INADL	10207	hgsc.bcm.edu	37	1	62550289	62550289	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:62550289T>C	ENST00000371158.2	+	33	4460	c.4346T>C	c.(4345-4347)cTc>cCc	p.L1449P	INADL_ENST00000543708.1_Missense_Mutation_p.L233P|INADL_ENST00000545929.1_Missense_Mutation_p.L122P|INADL_ENST00000316485.6_Missense_Mutation_p.L1449P	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1449	PDZ 8. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GGGCTTGGTCTCAGCATTGTG	0.468																																					p.L1449P		Atlas-SNP	.											.	INADL	179	.	0			c.T4346C						.						102.0	101.0	101.0					1																	62550289		2203	4300	6503	SO:0001583	missense	10207	exon33			TTGGTCTCAGCAT	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4346T>C	chr1.hg19:g.62550289T>C	ENSP00000360200:p.Leu1449Pro	108.0	0.0		110.0	5.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	T	19.94	3.919454	0.73098	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000543708;ENST00000545929	T;T;T;T	0.31510	1.96;1.49;1.49;1.96	5.02	5.02	0.67125	PDZ/DHR/GLGF (4);	0.000000	0.56097	D	0.000022	T	0.65739	0.2720	M	0.93507	3.425	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.984	D;D;D;D;D;D	0.97110	0.999;1.0;1.0;0.999;1.0;0.952	T	0.76451	-0.2954	10	0.87932	D	0	.	15.0292	0.71694	0.0:0.0:0.0:1.0	.	122;233;908;1449;1449;1449	F5GY89;B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;.;INADL_HUMAN;.	P	1449;1449;1449;1449;233;122	ENSP00000360200:L1449P;ENSP00000326199:L1449P;ENSP00000445790:L233P;ENSP00000440094:L122P	ENSP00000326199:L1449P	L	+	2	0	INADL	62322877	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.588000	0.74076	2.005000	0.58758	0.533000	0.62120	CTC	.	.		0.468	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
LEPR	3953	hgsc.bcm.edu	37	1	66067119	66067119	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:66067119A>C	ENST00000349533.6	+	9	1224	c.1039A>C	c.(1039-1041)Aat>Cat	p.N347H	LEPR_ENST00000371060.3_Missense_Mutation_p.N347H|LEPR_ENST00000406510.3_Intron|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000371059.3_Missense_Mutation_p.N347H|LEPR_ENST00000344610.8_Missense_Mutation_p.N347H|LEPR_ENST00000371058.1_Missense_Mutation_p.N347H	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					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)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		TGTTGGGTCTAATGTTTCTTT	0.343																																					p.N347H		Atlas-SNP	.											.	LEPR	284	.	0			c.A1039C						.						123.0	118.0	120.0					1																	66067119		2203	4300	6503	SO:0001583	missense	3953	exon9			GGGTCTAATGTTT	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.1039A>C	chr1.hg19:g.66067119A>C	ENSP00000330393:p.Asn347His	66.0	0.0		79.0	28.0	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	hg19	CCDS631.1	.	.	.	.	.	.	.	.	.	.	A	16.20	3.056426	0.55325	.	.	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37;-1.37	4.98	4.98	0.66077	Immunoglobulin-like (1);Immunoglobulin C2-set-like, ligand-binding (1);Immunoglobulin-like fold (1);	0.277175	0.45606	D	0.000356	D	0.86916	0.6048	M	0.73598	2.24	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.991	D	0.88639	0.3174	10	0.66056	D	0.02	-24.6842	14.8343	0.70172	1.0:0.0:0.0:0.0	.	347;347;347	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	H	347	ENSP00000340884:N347H;ENSP00000330393:N347H;ENSP00000360099:N347H;ENSP00000360098:N347H;ENSP00000360097:N347H	ENSP00000340884:N347H	N	+	1	0	LEPR	65839707	1.000000	0.71417	0.436000	0.26797	0.618000	0.37518	6.549000	0.73900	2.087000	0.62958	0.533000	0.62120	AAT	.	.		0.343	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
RPE65	6121	hgsc.bcm.edu	37	1	68896995	68896995	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:68896995T>C	ENST00000262340.5	-	12	1361	c.1308A>G	c.(1306-1308)ggA>ggG	p.G436G		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	436			G -> V (in RP20). {ECO:0000269|PubMed:11095629}.		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						TCAAGCCAAGTCCATACGCAT	0.353																																					p.G436G		Atlas-SNP	.											.	RPE65	87	.	0			c.A1308G						.						99.0	91.0	94.0					1																	68896995		2203	4300	6503	SO:0001819	synonymous_variant	6121	exon12			GCCAAGTCCATAC	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.1308A>G	chr1.hg19:g.68896995T>C		113.0	0.0		93.0	4.0	NM_000329	A8K1L0|Q5T9U3	Silent	SNP	ENST00000262340.5	hg19	CCDS643.1																																																																																			.	.		0.353	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329	
IFI44	10561	hgsc.bcm.edu	37	1	79115893	79115893	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:79115893A>G	ENST00000370747.4	+	2	98	c.13A>G	c.(13-15)Act>Gct	p.T5A	IFI44_ENST00000495254.1_Intron|IFI44_ENST00000545124.1_Intron	NM_006417.4	NP_006408.3	Q8TCB0	IFI44_HUMAN	interferon-induced protein 44	5					response to virus (GO:0009615)	cytoplasm (GO:0005737)				central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21						GGCAGTGACAACTCGTTTGAC	0.358																																					p.T5A		Atlas-SNP	.											.	IFI44	55	.	0			c.A13G						.						91.0	85.0	87.0					1																	79115893		2203	4300	6503	SO:0001583	missense	10561	exon2			GTGACAACTCGTT	D28915	CCDS688.1	1p31.1	2013-03-14			ENSG00000137965	ENSG00000137965			16938	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 5"""	610468				7925411	Standard	NM_006417		Approved	MTAP44, p44, TLDC5	uc001dip.4	Q8TCB0	OTTHUMG00000009723	ENST00000370747.4:c.13A>G	chr1.hg19:g.79115893A>G	ENSP00000359783:p.Thr5Ala	117.0	0.0		141.0	6.0	NM_006417	B7ZAG3|D3DQ80|Q14496	Missense_Mutation	SNP	ENST00000370747.4	hg19	CCDS688.1	.	.	.	.	.	.	.	.	.	.	A	8.520	0.868638	0.17322	.	.	ENSG00000137965	ENST00000370747	T	0.08896	3.04	3.3	2.17	0.27698	.	0.075957	0.53938	D	0.000047	T	0.09555	0.0235	M	0.64404	1.975	0.21105	N	0.999787	D;D	0.76494	0.999;0.999	D;D	0.75484	0.986;0.981	T	0.08351	-1.0726	10	0.46703	T	0.11	-10.591	5.2677	0.15607	0.8668:0.0:0.1332:0.0	.	5;5	B7ZB11;Q8TCB0	.;IFI44_HUMAN	A	5	ENSP00000359783:T5A	ENSP00000359783:T5A	T	+	1	0	IFI44	78888481	0.601000	0.26907	0.207000	0.23584	0.023000	0.10783	0.704000	0.25661	0.656000	0.30886	-0.467000	0.05162	ACT	.	.		0.358	IFI44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026825.1	NM_006417	
GBP5	115362	hgsc.bcm.edu	37	1	89729600	89729600	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:89729600C>A	ENST00000370459.3	-	8	1308	c.1181G>T	c.(1180-1182)tGt>tTt	p.C394F	RP4-620F22.2_ENST00000437128.1_RNA|GBP5_ENST00000471171.1_5'Flank|GBP5_ENST00000343435.5_Missense_Mutation_p.C394F			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	394						cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		GTTCCGTTTACAAATGTCATT	0.368																																					p.C394F		Atlas-SNP	.											.	GBP5	65	.	0			c.G1181T						.						136.0	141.0	139.0					1																	89729600		2203	4300	6503	SO:0001583	missense	115362	exon9			CGTTTACAAATGT	AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.1181G>T	chr1.hg19:g.89729600C>A	ENSP00000359488:p.Cys394Phe	68.0	0.0		92.0	10.0	NM_052942	B2RCE1|Q86TM5	Missense_Mutation	SNP	ENST00000370459.3	hg19	CCDS722.1	.	.	.	.	.	.	.	.	.	.	C	8.934	0.964062	0.18583	.	.	ENSG00000154451	ENST00000343435;ENST00000370459;ENST00000443807	T;T;T	0.54675	0.56;0.56;0.56	5.12	-1.2	0.09554	Guanylate-binding protein, C-terminal (3);	0.566743	0.20220	N	0.096703	T	0.18509	0.0444	L	0.46741	1.465	0.09310	N	1	B	0.18310	0.027	B	0.28385	0.089	T	0.24440	-1.0160	10	0.39692	T	0.17	0.5771	1.786	0.03041	0.1275:0.3928:0.1245:0.3552	.	394	Q96PP8	GBP5_HUMAN	F	394	ENSP00000340396:C394F;ENSP00000359488:C394F;ENSP00000403010:C394F	ENSP00000340396:C394F	C	-	2	0	GBP5	89502188	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.404000	0.07205	-0.262000	0.09392	-0.335000	0.08231	TGT	.	.		0.368	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942	
GBP6	163351	hgsc.bcm.edu	37	1	89847413	89847413	+	Silent	SNP	C	C	T	rs373830740		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:89847413C>T	ENST00000370456.4	+	7	1125	c.1032C>T	c.(1030-1032)ctC>ctT	p.L344L	GBP6_ENST00000535065.1_Silent_p.L214L	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	344			L -> F (in dbSNP:rs4658360). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		GAGTGAAGCTCCCCACAGACA	0.572																																					p.L344L		Atlas-SNP	.											.	GBP6	87	.	0			c.C1032T						.						81.0	74.0	76.0					1																	89847413		2203	4300	6503	SO:0001819	synonymous_variant	163351	exon7			GAAGCTCCCCACA	BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.1032C>T	chr1.hg19:g.89847413C>T		173.0	0.0		221.0	9.0	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Silent	SNP	ENST00000370456.4	hg19	CCDS723.1																																																																																			.	.		0.572	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460	
HIPK1	204851	hgsc.bcm.edu	37	1	114500897	114500897	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:114500897T>C	ENST00000369558.1	+	8	2197	c.1965T>C	c.(1963-1965)tgT>tgC	p.C655C	HIPK1_ENST00000369559.4_Silent_p.C655C|HIPK1_ENST00000369554.2_Silent_p.C655C|HIPK1_ENST00000369553.1_Silent_p.C261C|HIPK1_ENST00000369561.4_Silent_p.C621C|HIPK1_ENST00000340480.4_Silent_p.C281C|HIPK1_ENST00000426820.2_Silent_p.C655C|HIPK1_ENST00000369555.2_Silent_p.C655C|HIPK1_ENST00000406344.1_Silent_p.C261C			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	655					anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTATAGTATGTCCACCTGCGT	0.458																																					p.C655C		Atlas-SNP	.											.	HIPK1	195	.	0			c.T1965C						.						77.0	73.0	75.0					1																	114500897		2203	4300	6503	SO:0001819	synonymous_variant	204851	exon8			AGTATGTCCACCT	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.1965T>C	chr1.hg19:g.114500897T>C		99.0	0.0		122.0	5.0	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Silent	SNP	ENST00000369558.1	hg19	CCDS867.1																																																																																			.	.		0.458	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268	
SPRR1A	6698	hgsc.bcm.edu	37	1	152957833	152957833	+	Missense_Mutation	SNP	C	C	A	rs17882377	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:152957833C>A	ENST00000368762.1	+	1	127	c.127C>A	c.(127-129)Ccc>Acc	p.P43T	SPRR1A_ENST00000307122.2_Missense_Mutation_p.P43T			P35321	SPR1A_HUMAN	small proline-rich protein 1A	43	6 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.P43A(1)		breast(2)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)	7	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCCCTGCCACCCCAAGGTGCC	0.647																																					p.P43T		Atlas-SNP	.											SPRR1A,NS,carcinoma,0,1	SPRR1A	17	.	1	Substitution - Missense(1)	endometrium(1)	c.C127A						.						122.0	126.0	124.0					1																	152957833		2203	4300	6503	SO:0001583	missense	6698	exon2			TGCCACCCCAAGG	L05187	CCDS1032.1	1q21-q22	2008-02-05			ENSG00000169474	ENSG00000169474			11259	protein-coding gene	gene with protein product		182265				8325635	Standard	NM_005987		Approved		uc001faw.3	P35321	OTTHUMG00000014404	ENST00000368762.1:c.127C>A	chr1.hg19:g.152957833C>A	ENSP00000357751:p.Pro43Thr	182.0	0.0		363.0	0.0	NM_001199828	B1AN47|D3DV31|Q2M303|Q9UDG4	Missense_Mutation	SNP	ENST00000368762.1	hg19	CCDS1032.1	.	.	.	.	.	.	.	.	.	.	C	9.534	1.111525	0.20714	.	.	ENSG00000169474	ENST00000307122;ENST00000368762	T;T	0.10288	2.89;2.89	4.77	-1.11	0.09840	.	0.217028	0.23470	N	0.047830	T	0.01976	0.0062	.	.	.	0.25456	N	0.987967	B	0.34329	0.449	B	0.34873	0.191	T	0.43458	-0.9390	9	0.14252	T	0.57	5.8114	13.074	0.59077	0.6996:0.3004:0.0:0.0	.	43	P35321	SPR1A_HUMAN	T	43	ENSP00000307340:P43T;ENSP00000357751:P43T	ENSP00000307340:P43T	P	+	1	0	SPRR1A	151224457	0.574000	0.26684	0.960000	0.40013	0.738000	0.42128	-0.504000	0.06375	-0.541000	0.06257	-0.330000	0.08379	CCC	.	.		0.647	SPRR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040062.1	NM_005987	
OR10J5	127385	hgsc.bcm.edu	37	1	159505581	159505581	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:159505581A>T	ENST00000334857.2	-	1	261	c.217T>A	c.(217-219)Tac>Aac	p.Y73N		NM_001004469.1	NP_001004469.1	Q8NHC4	O10J5_HUMAN	olfactory receptor, family 10, subfamily J, member 5	73						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	22	all_hematologic(112;0.0429)					ACCAGTGTGTACACCGTCTCT	0.428																																					p.Y73N		Atlas-SNP	.											.	OR10J5	68	.	0			c.T217A						.						170.0	136.0	148.0					1																	159505581		2203	4300	6503	SO:0001583	missense	127385	exon1			GTGTGTACACCGT		CCDS30910.1	1q23.2	2012-08-09			ENSG00000184155	ENSG00000184155		"""GPCR / Class A : Olfactory receptors"""	14993	protein-coding gene	gene with protein product							Standard	NM_001004469		Approved		uc010piw.2	Q8NHC4	OTTHUMG00000022738	ENST00000334857.2:c.217T>A	chr1.hg19:g.159505581A>T	ENSP00000334441:p.Tyr73Asn	116.0	0.0		202.0	43.0	NM_001004469	B9EH35|Q6IFH2	Missense_Mutation	SNP	ENST00000334857.2	hg19	CCDS30910.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.981560	0.34942	.	.	ENSG00000184155	ENST00000334857	T	0.00397	7.57	4.31	4.31	0.51392	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00784	0.0026	H	0.94345	3.525	0.35231	D	0.77694	D	0.89917	1.0	D	0.91635	0.999	T	0.22068	-1.0227	9	0.87932	D	0	.	11.7208	0.51680	1.0:0.0:0.0:0.0	.	73	Q8NHC4	O10J5_HUMAN	N	73	ENSP00000334441:Y73N	ENSP00000334441:Y73N	Y	-	1	0	OR10J5	157772205	0.030000	0.19436	0.510000	0.27712	0.058000	0.15608	2.989000	0.49393	1.923000	0.55706	0.377000	0.23210	TAC	.	.		0.428	OR10J5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059021.1	NM_001004469	
UHMK1	127933	hgsc.bcm.edu	37	1	162473569	162473569	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:162473569A>G	ENST00000489294.1	+	4	937	c.779A>G	c.(778-780)cAc>cGc	p.H260R	UHMK1_ENST00000538489.1_Missense_Mutation_p.H260R|UHMK1_ENST00000282169.8_3'UTR|UHMK1_ENST00000545294.1_Missense_Mutation_p.H186R	NM_175866.4	NP_787062.1	Q8TAS1	UHMK1_HUMAN	U2AF homology motif (UHM) kinase 1	260	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				cell cycle arrest (GO:0007050)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of translational initiation (GO:0045948)|protein autophosphorylation (GO:0046777)|regulation of protein export from nucleus (GO:0046825)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|neuronal ribonucleoprotein granule (GO:0071598)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)|transferase activity (GO:0016740)			endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	11	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			ATTATTGATCACATATTTGCC	0.363																																					p.H260R		Atlas-SNP	.											.	UHMK1	65	.	0			c.A779G						.						142.0	129.0	134.0					1																	162473569		2203	4300	6503	SO:0001583	missense	127933	exon4			TTGATCACATATT	BC026046	CCDS1239.1, CCDS53423.1, CCDS53424.1	1q23.1	2013-02-12			ENSG00000152332	ENSG00000152332		"""RNA binding motif (RRM) containing"""	19683	protein-coding gene	gene with protein product		608849				12093740, 12782393	Standard	NM_175866		Approved	KIS, Kist	uc001gcc.2	Q8TAS1	OTTHUMG00000031373	ENST00000489294.1:c.779A>G	chr1.hg19:g.162473569A>G	ENSP00000420270:p.His260Arg	66.0	0.0		100.0	4.0	NM_175866	A8K8K4|G3V1M1|Q96C22	Missense_Mutation	SNP	ENST00000489294.1	hg19	CCDS1239.1	.	.	.	.	.	.	.	.	.	.	A	13.99	2.400809	0.42613	.	.	ENSG00000152332	ENST00000545294;ENST00000538489;ENST00000489294	T;T;T	0.63417	-0.04;-0.04;-0.04	6.07	6.07	0.98685	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.110634	0.64402	D	0.000006	T	0.16342	0.0393	N	0.03084	-0.415	.	.	.	B;B;B	0.12013	0.004;0.005;0.001	B;B;B	0.10450	0.003;0.005;0.003	T	0.12837	-1.0532	9	0.10377	T	0.69	-14.0615	9.109	0.36716	0.919:0.0:0.081:0.0	.	260;260;186	Q8TAS1-2;Q8TAS1;G3V1M1	.;UHMK1_HUMAN;.	R	186;260;260	ENSP00000441226:H186R;ENSP00000446416:H260R;ENSP00000420270:H260R	ENSP00000420270:H260R	H	+	2	0	UHMK1	160740193	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.453000	0.60061	2.326000	0.78906	0.533000	0.62120	CAC	.	.		0.363	UHMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076788.1	NM_175866	
SCYL3	57147	hgsc.bcm.edu	37	1	169839479	169839479	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:169839479A>G	ENST00000367770.1	-	5	589	c.542T>C	c.(541-543)cTc>cCc	p.L181P	SCYL3_ENST00000367772.4_Missense_Mutation_p.L181P|SCYL3_ENST00000367771.6_Missense_Mutation_p.L181P|SCYL3_ENST00000470238.1_5'UTR			Q8IZE3	PACE1_HUMAN	SCY1-like 3 (S. cerevisiae)	181	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell migration (GO:0016477)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					ACACTCTGGGAGAGTTGTGAA	0.413																																					p.L181P		Atlas-SNP	.											.	SCYL3	116	.	0			c.T542C						.						82.0	82.0	82.0					1																	169839479		2203	4300	6503	SO:0001583	missense	57147	exon6			TCTGGGAGAGTTG	BC014662	CCDS1286.1, CCDS1287.1	1q24.2	2008-02-05			ENSG00000000457	ENSG00000000457			19285	protein-coding gene	gene with protein product	"""ezrin-binding partner PACE-1"""	608192				12651155	Standard	NM_020423		Approved	PACE-1, PACE1	uc001ggs.3	Q8IZE3	OTTHUMG00000035941	ENST00000367770.1:c.542T>C	chr1.hg19:g.169839479A>G	ENSP00000356744:p.Leu181Pro	64.0	0.0		122.0	5.0	NM_020423	A8K8Z2|Q5THA6|Q5THA8|Q8IZN9|Q96C56|Q9UBK6	Missense_Mutation	SNP	ENST00000367770.1	hg19	CCDS1287.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.099246	0.76983	.	.	ENSG00000000457	ENST00000367772;ENST00000367771;ENST00000367770;ENST00000423670	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.27	5.27	0.74061	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.064489	0.64402	D	0.000005	T	0.69433	0.3110	L	0.53729	1.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	T	0.73269	-0.4036	10	0.62326	D	0.03	-14.7759	15.1525	0.72713	1.0:0.0:0.0:0.0	.	181;181	Q8IZE3-2;Q8IZE3	.;PACE1_HUMAN	P	181	ENSP00000356746:L181P;ENSP00000356745:L181P;ENSP00000356744:L181P;ENSP00000407993:L181P	ENSP00000356744:L181P	L	-	2	0	SCYL3	168106103	1.000000	0.71417	0.657000	0.29651	0.987000	0.75469	8.491000	0.90468	2.113000	0.64589	0.455000	0.32223	CTC	.	.		0.413	SCYL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087550.4	NM_181093	
SERPINC1	462	hgsc.bcm.edu	37	1	173876589	173876589	+	Splice_Site	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:173876589T>C	ENST00000367698.3	-	6	1335	c.1217A>G	c.(1216-1218)gAg>gGg	p.E406G		NM_000488.3	NP_000479.1	P01008	ANT3_HUMAN	serpin peptidase inhibitor, clade C (antithrombin), member 1	406					blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of inflammatory response (GO:0050728)|regulation of blood coagulation, intrinsic pathway (GO:2000266)|regulation of proteolysis (GO:0030162)|response to nutrient (GO:0007584)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(15)|ovary(1)	25					Ardeparin(DB00407)|Dalteparin(DB06779)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Nadroparin(DB08813)|Sulodexide(DB06271)|Tinzaparin(DB06822)	TGTACTCACCTCAAGAAATGC	0.478																																					p.E406G		Atlas-SNP	.											.	SERPINC1	57	.	0			c.A1217G						.						283.0	261.0	269.0					1																	173876589		2203	4300	6503	SO:0001630	splice_region_variant	462	exon6			CTCACCTCAAGAA	X68793	CCDS1313.1	1q25.1	2014-02-18	2005-08-18		ENSG00000117601	ENSG00000117601		"""Serine (or cysteine) peptidase inhibitors"""	775	protein-coding gene	gene with protein product	"""antithrombin III"", ""signal peptide antithrombin part 1"", ""coding sequence signal peptide antithrombin part 1"", ""antithrombin (aa 375-432)"""	107300	"""serine (or cysteine) proteinase inhibitor, clade C (antithrombin), member 1"""	AT3		3979120, 24172014	Standard	NM_000488		Approved	ATIII, MGC22579	uc001gjt.3	P01008	OTTHUMG00000037276	ENST00000367698.3:c.1218+1A>G	chr1.hg19:g.173876589T>C		122.0	0.0		184.0	11.0	NM_000488	B2R6P0|P78439|P78447|Q13815|Q5TC78|Q7KZ43|Q7KZ97|Q9UC78	Missense_Mutation	SNP	ENST00000367698.3	hg19	CCDS1313.1	.	.	.	.	.	.	.	.	.	.	T	32	5.131952	0.94473	.	.	ENSG00000117601	ENST00000367698;ENST00000351522	D	0.86694	-2.16	5.98	5.98	0.97165	Serpin domain (3);	0.046461	0.85682	D	0.000000	D	0.92616	0.7654	M	0.90977	3.165	0.80722	D	1	D	0.60575	0.988	P	0.59825	0.864	D	0.92237	0.5797	10	0.34782	T	0.22	.	16.2018	0.82087	0.0:0.0:0.0:1.0	.	406	P01008	ANT3_HUMAN	G	406;201	ENSP00000356671:E406G	ENSP00000307953:E201G	E	-	2	0	SERPINC1	172143212	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	6.915000	0.75770	2.307000	0.77673	0.529000	0.55759	GAG	.	.		0.478	SERPINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090734.1	NM_000488	Missense_Mutation
PAPPA2	60676	hgsc.bcm.edu	37	1	176708893	176708893	+	Silent	SNP	T	T	C	rs371375924		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:176708893T>C	ENST00000367662.3	+	13	5094	c.3930T>C	c.(3928-3930)tcT>tcC	p.S1310S		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1310					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						GCAACCACTCTCTTGGTGAGT	0.473																																					p.S1310S		Atlas-SNP	.											.	PAPPA2	665	.	0			c.T3930C						.	T		0,3986		0,0,1993	60.0	59.0	60.0		3930	1.9	1.0	1		60	1,8325		0,1,4162	no	coding-synonymous	PAPPA2	NM_020318.2		0,1,6155	CC,CT,TT		0.012,0.0,0.0081		1310/1792	176708893	1,12311	1993	4163	6156	SO:0001819	synonymous_variant	60676	exon13			CCACTCTCTTGGT	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.3930T>C	chr1.hg19:g.176708893T>C		60.0	0.0		124.0	5.0	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	hg19	CCDS41438.1																																																																																			.	.		0.473	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1		
TOR1AIP1	26092	hgsc.bcm.edu	37	1	179887126	179887126	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:179887126G>A	ENST00000606911.2	+	10	1695	c.1504G>A	c.(1504-1506)Gcc>Acc	p.A502T	TOR1AIP1_ENST00000271583.3_Missense_Mutation_p.A518T|TOR1AIP1_ENST00000528443.2_Missense_Mutation_p.A503T|TOR1AIP1_ENST00000435319.4_Missense_Mutation_p.A381T			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1	502	Interaction with TOR1A.				positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)	p.A502S(1)		breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						TGAAAACGCGGCCTTCAAAGA	0.423																																					p.A503T		Atlas-SNP	.											TOR1AIP1,leg,malignant_melanoma,0,1	TOR1AIP1	58	.	1	Substitution - Missense(1)	skin(1)	c.G1507A						.						94.0	96.0	95.0					1																	179887126		2203	4300	6503	SO:0001583	missense	26092	exon10			AACGCGGCCTTCA		CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"""lamina associated polypeptide 1B"""	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.1504G>A	chr1.hg19:g.179887126G>A	ENSP00000476687:p.Ala502Thr	150.0	1.0		237.0	0.0	NM_001267578	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Missense_Mutation	SNP	ENST00000606911.2	hg19	CCDS1335.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.980768	0.92982	.	.	ENSG00000143337	ENST00000325993;ENST00000271583;ENST00000435319	T;T	0.35789	1.29;1.29	5.96	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.62938	0.2469	M	0.80616	2.505	0.58432	D	0.999995	D	0.89917	1.0	D	0.91635	0.999	T	0.67098	-0.5756	9	.	.	.	-8.2699	16.26	0.82535	0.0:0.0:0.8661:0.1339	.	502	Q5JTV8	TOIP1_HUMAN	T	297;518;502	ENSP00000271583:A518T;ENSP00000393292:A502T	.	A	+	1	0	TOR1AIP1	178153749	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	9.338000	0.96553	1.519000	0.48950	0.655000	0.94253	GCC	.	.		0.423	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602	
PTPRC	5788	hgsc.bcm.edu	37	1	198678836	198678836	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:198678836A>G	ENST00000367376.2	+	11	1219	c.1048A>G	c.(1048-1050)Aaa>Gaa	p.K350E	PTPRC_ENST00000352140.3_Missense_Mutation_p.K302E|PTPRC_ENST00000348564.6_Missense_Mutation_p.K191E|PTPRC_ENST00000442510.2_Missense_Mutation_p.K352E|PTPRC_ENST00000594404.1_Missense_Mutation_p.K189E	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	350					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						ATTTGATAATAAAGAAATTAA	0.254																																					p.K352E		Atlas-SNP	.											.	PTPRC	229	.	0			c.A1054G						.						29.0	35.0	33.0					1																	198678836		2139	4247	6386	SO:0001583	missense	5788	exon11			GATAATAAAGAAA	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.1048A>G	chr1.hg19:g.198678836A>G	ENSP00000356346:p.Lys350Glu	86.0	0.0		186.0	129.0	NM_002838	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	hg19		.	.	.	.	.	.	.	.	.	.	A	0.078	-1.189267	0.01607	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000530727;ENST00000442510;ENST00000367367;ENST00000348564	T	0.02579	4.24	4.21	-3.39	0.04868	.	2.390670	0.01835	N	0.034923	T	0.01387	0.0045	N	0.03324	-0.35	0.09310	N	1	B;B;B;B;B	0.06786	0.001;0.001;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.001;0.0;0.0;0.0	T	0.43605	-0.9381	10	0.08381	T	0.77	.	5.4709	0.16670	0.3809:0.2846:0.3344:0.0	.	286;286;191;302;350	F5GXZ3;B4DSZ5;B1ALS3;E9PC28;P08575	.;.;.;.;PTPRC_HUMAN	E	352;286;302;302;236;350;284;189	ENSP00000193532:K302E	ENSP00000306782:K189E	K	+	1	0	PTPRC	196945459	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.531000	0.00220	-1.197000	0.02673	-1.431000	0.01090	AAA	.	.		0.254	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
PPP1R12B	4660	hgsc.bcm.edu	37	1	202394742	202394742	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:202394742A>G	ENST00000608999.1	+	4	743	c.590A>G	c.(589-591)cAg>cGg	p.Q197R	PPP1R12B_ENST00000356764.2_Missense_Mutation_p.Q197R|PPP1R12B_ENST00000336894.4_Missense_Mutation_p.Q197R|PPP1R12B_ENST00000480184.1_Missense_Mutation_p.Q197R	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	197					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			CAGATGTTGCAGGATGCCCGC	0.512																																					p.Q197R		Atlas-SNP	.											.	PPP1R12B	100	.	0			c.A590G						.						180.0	198.0	192.0					1																	202394742		2203	4300	6503	SO:0001583	missense	4660	exon4			TGTTGCAGGATGC	AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	7619	protein-coding gene	gene with protein product	"""myosin phosphatase regulatory subunit"", ""myosin phosphatase, target subunit 2"""	603768	"""protein phosphatase 1, regulatory (inhibitor) subunit 12B"""	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.590A>G	chr1.hg19:g.202394742A>G	ENSP00000476755:p.Gln197Arg	93.0	0.0		164.0	8.0	NM_002481	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Missense_Mutation	SNP	ENST00000608999.1	hg19	CCDS1426.1	.	.	.	.	.	.	.	.	.	.	A	5.524	0.281558	0.10458	.	.	ENSG00000077157	ENST00000406302;ENST00000336894;ENST00000480184;ENST00000356764	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	5.5	5.5	0.81552	Ankyrin repeat-containing domain (3);	0.000000	0.64402	D	0.000015	T	0.33469	0.0864	N	0.01493	-0.835	0.42160	D	0.99159	B;B;P;D	0.65815	0.001;0.112;0.532;0.995	B;B;B;D	0.78314	0.018;0.021;0.259;0.991	T	0.46076	-0.9217	10	0.02654	T	1	.	10.0332	0.42114	0.9246:0.0:0.0754:0.0	.	197;197;197;197	O60237-2;O60237;F8W8M3;Q2TAI8	.;MYPT2_HUMAN;.;.	R	197	ENSP00000384496:Q197R;ENSP00000337897:Q197R;ENSP00000417159:Q197R;ENSP00000349206:Q197R	ENSP00000337897:Q197R	Q	+	2	0	PPP1R12B	200661365	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.698000	0.54771	2.090000	0.63153	0.377000	0.23210	CAG	.	.		0.512	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105	
DTL	51514	hgsc.bcm.edu	37	1	212238257	212238257	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:212238257A>G	ENST00000366991.4	+	7	840		c.e7-1		DTL_ENST00000542077.1_Splice_Site|DTL_ENST00000475419.1_Splice_Site	NM_016448.2	NP_057532.2	Q9NZJ0	DTL_HUMAN	denticleless E3 ubiquitin protein ligase homolog (Drosophila)						cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|chromosome (GO:0005694)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(81;0.00796)|all cancers(67;0.0385)|Epithelial(68;0.102)		AATATCTTTCAGATGGGTTTT	0.343																																					.		Atlas-SNP	.											.	DTL	52	.	0			c.527-2A>G						.						93.0	95.0	95.0					1																	212238257		2203	4300	6503	SO:0001630	splice_region_variant	51514	exon7			TCTTTCAGATGGG	AF195765	CCDS1502.1, CCDS65778.1	1q32	2013-01-10	2012-02-23		ENSG00000143476	ENSG00000143476		"""DDB1 and CUL4 associated factors"", ""WD repeat domain containing"""	30288	protein-coding gene	gene with protein product	"""RA regulated nuclear matrix associated protein"", ""DDB1 and CUL4 associated factor 2"""	610617	"""denticleless homolog (Drosophila)"""			11278750	Standard	NM_001286229		Approved	RAMP, L2DTL, DCAF2	uc009xdc.3	Q9NZJ0	OTTHUMG00000037133	ENST00000366991.4:c.527-1A>G	chr1.hg19:g.212238257A>G		56.0	0.0		81.0	4.0	NM_016448	A8K8H8|D3DT98|Q5VT77|Q96SN0|Q9NW03|Q9NW34|Q9NWM5	Splice_Site	SNP	ENST00000366991.4	hg19	CCDS1502.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.302938	0.81136	.	.	ENSG00000143476	ENST00000366991;ENST00000542077	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8947	0.70636	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DTL	210304880	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.921000	0.87530	2.216000	0.71823	0.533000	0.62120	.	.	.		0.343	DTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090182.1	NM_016448	Intron
USH2A	7399	hgsc.bcm.edu	37	1	216592004	216592004	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:216592004G>C	ENST00000307340.3	-	3	889	c.503C>G	c.(502-504)aCa>aGa	p.T168R	USH2A_ENST00000366943.2_Missense_Mutation_p.T168R|USH2A_ENST00000366942.3_Missense_Mutation_p.T168R	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	168					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.T168I(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CCCATCTACTGTCTTTTCTAT	0.383										HNSCC(13;0.011)																											p.T168R		Atlas-SNP	.											USH2A,NS,carcinoma,0,1	USH2A	1168	.	1	Substitution - Missense(1)	lung(1)	c.C503G						.						117.0	109.0	112.0					1																	216592004		2203	4300	6503	SO:0001583	missense	7399	exon3			TCTACTGTCTTTT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.503C>G	chr1.hg19:g.216592004G>C	ENSP00000305941:p.Thr168Arg	133.0	0.0		214.0	0.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	10.07	1.249778	0.22880	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.72942	-0.7;-0.7;-0.7	5.62	2.77	0.32553	Concanavalin A-like lectin/glucanase (1);LamG-like jellyroll fold (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.177681	0.27043	U	0.021204	T	0.66257	0.2771	L	0.44542	1.39	0.09310	N	0.999999	B;P	0.46142	0.355;0.873	B;P	0.46629	0.205;0.522	T	0.59478	-0.7447	10	0.72032	D	0.01	.	10.4097	0.44285	0.2096:0.0:0.7904:0.0	.	168;168	O75445-2;O75445	.;USH2A_HUMAN	R	168	ENSP00000305941:T168R;ENSP00000355910:T168R;ENSP00000355909:T168R	ENSP00000305941:T168R	T	-	2	0	USH2A	214658627	0.985000	0.35326	0.012000	0.15200	0.439000	0.31926	2.441000	0.44864	0.328000	0.23435	0.655000	0.94253	ACA	.	.		0.383	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
SUSD4	55061	hgsc.bcm.edu	37	1	223402546	223402546	+	Silent	SNP	G	G	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:223402546G>T	ENST00000343846.3	-	5	1542	c.909C>A	c.(907-909)atC>atA	p.I303I	SUSD4_ENST00000484758.2_Silent_p.I234I|SUSD4_ENST00000494793.2_Silent_p.I303I|SUSD4_ENST00000366878.4_Silent_p.I303I|SUSD4_ENST00000454695.2_Silent_p.I143I|SUSD4_ENST00000478605.1_Intron			Q5VX71	SUSD4_HUMAN	sushi domain containing 4	303	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(131;0.0611)		TACCTGATTTGATGCAGTAGA	0.498																																					p.I303I		Atlas-SNP	.											.	SUSD4	82	.	0			c.C909A						.						119.0	125.0	123.0					1																	223402546		2069	4219	6288	SO:0001819	synonymous_variant	55061	exon6			TGATTTGATGCAG	AK096265	CCDS31034.1, CCDS41471.1	1q41	2008-05-14			ENSG00000143502	ENSG00000143502			25470	protein-coding gene	gene with protein product		615827				12477932	Standard	NM_017982		Approved	FLJ10052	uc001hny.4	Q5VX71	OTTHUMG00000037936	ENST00000343846.3:c.909C>A	chr1.hg19:g.223402546G>T		149.0	0.0		234.0	67.0	NM_017982	D3DTB9|Q6UX62|Q9BSR0|Q9NWG0	Silent	SNP	ENST00000343846.3	hg19	CCDS41471.1																																																																																			.	.		0.498	SUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092592.2	NM_017982	
ITPKB	3707	hgsc.bcm.edu	37	1	226923526	226923526	+	Missense_Mutation	SNP	G	G	A	rs149543375		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:226923526G>A	ENST00000272117.3	-	1	1633	c.1634C>T	c.(1633-1635)cCg>cTg	p.P545L	ITPKB_ENST00000366784.1_Missense_Mutation_p.P545L|ITPKB_ENST00000429204.1_Missense_Mutation_p.P545L			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	545					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				TAGCAGCTCCGGACTTGGGAG	0.597																																					p.P545L	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.C1634T						.	G	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	41.0	39.0	40.0		1634	-3.2	0.0	1	dbSNP_134	40	0,8600		0,0,4300	no	missense	ITPKB	NM_002221.3	98	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	545/947	226923526	1,13005	2203	4300	6503	SO:0001583	missense	3707	exon2			AGCTCCGGACTTG	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.1634C>T	chr1.hg19:g.226923526G>A	ENSP00000272117:p.Pro545Leu	72.0	0.0		132.0	46.0	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	hg19	CCDS1555.1	.	.	.	.	.	.	.	.	.	.	G	5.501	0.277439	0.10403	2.27E-4	0.0	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	T;T;T	0.21932	1.98;1.98;1.98	5.43	-3.18	0.05186	.	1.426790	0.04261	N	0.340381	T	0.11836	0.0288	N	0.19112	0.55	0.09310	N	1	B	0.15719	0.014	B	0.08055	0.003	T	0.33904	-0.9850	10	0.52906	T	0.07	1.5012	2.8086	0.05434	0.2829:0.2641:0.3599:0.0931	.	545	P27987	IP3KB_HUMAN	L	545	ENSP00000272117:P545L;ENSP00000411152:P545L;ENSP00000355748:P545L	ENSP00000272117:P545L	P	-	2	0	ITPKB	224990149	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.825000	0.04433	-0.164000	0.10927	-0.339000	0.08088	CCG	.	G|1.000;A|0.000		0.597	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
EDARADD	128178	hgsc.bcm.edu	37	1	236577581	236577581	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:236577581G>A	ENST00000334232.4	+	3	309	c.142G>A	c.(142-144)Gat>Aat	p.D48N	EDARADD_ENST00000359362.5_Missense_Mutation_p.D38N	NM_145861.2	NP_665860.2	Q8WWZ3	EDAD_HUMAN	EDAR-associated death domain	48					cell differentiation (GO:0030154)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	cytoplasm (GO:0005737)				endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|stomach(1)	12	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TCCCATTCAAGATACGGAACT	0.318																																					p.D48N		Atlas-SNP	.											.	EDARADD	31	.	0			c.G142A						.						100.0	103.0	102.0					1																	236577581		2203	4299	6502	SO:0001583	missense	128178	exon3			ATTCAAGATACGG	AY028914	CCDS1610.1, CCDS31065.1	1q42.3	2013-05-22			ENSG00000186197	ENSG00000186197			14341	protein-coding gene	gene with protein product		606603				11780064	Standard	NM_145861		Approved		uc001hxu.1	Q8WWZ3	OTTHUMG00000039954	ENST00000334232.4:c.142G>A	chr1.hg19:g.236577581G>A	ENSP00000335076:p.Asp48Asn	75.0	0.0		164.0	55.0	NM_145861	A2VCK5|A8K7B5|B1AL54|B9ZVW5|Q5VYJ7	Missense_Mutation	SNP	ENST00000334232.4	hg19	CCDS1610.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057813	0.76074	.	.	ENSG00000186197	ENST00000439430;ENST00000334232;ENST00000359362	T;T;D	0.83163	-0.04;-1.13;-1.69	4.72	4.72	0.59763	.	0.148151	0.28952	U	0.013607	D	0.89556	0.6749	M	0.71581	2.175	0.36604	D	0.874813	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	D	0.92304	0.5852	10	0.87932	D	0	.	13.0389	0.58887	0.0:0.0:1.0:0.0	.	38;48	A8K7B5;Q8WWZ3	.;EDAD_HUMAN	N	26;48;38	ENSP00000405815:D26N;ENSP00000335076:D48N;ENSP00000352320:D38N	ENSP00000335076:D48N	D	+	1	0	EDARADD	234644204	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	4.693000	0.61753	2.465000	0.83290	0.563000	0.77884	GAT	.	.		0.318	EDARADD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000096368.1	NM_145861	
HEATR1	55127	hgsc.bcm.edu	37	1	236750749	236750749	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:236750749A>T	ENST00000366582.3	-	14	1782	c.1668T>A	c.(1666-1668)aaT>aaA	p.N556K	HEATR1_ENST00000366581.2_Missense_Mutation_p.N556K	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	556					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			GATTCAGAAGATTTGAAATCG	0.323																																					p.N556K		Atlas-SNP	.											.	HEATR1	197	.	0			c.T1668A						.						46.0	44.0	45.0					1																	236750749		2197	4289	6486	SO:0001583	missense	55127	exon14			CAGAAGATTTGAA	BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"""UTP10, small subunit (SSU) processome component, homolog (yeast)"""					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.1668T>A	chr1.hg19:g.236750749A>T	ENSP00000355541:p.Asn556Lys	185.0	0.0		265.0	141.0	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	hg19	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	A	10.33	1.319392	0.23994	.	.	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.65732	-0.17;0.92	5.58	0.587	0.17439	Armadillo-like helical (1);Armadillo-type fold (1);	0.580156	0.19042	N	0.124248	T	0.47581	0.1453	L	0.47716	1.5	0.09310	N	0.999997	B	0.25169	0.119	B	0.28465	0.09	T	0.28202	-1.0051	10	0.19590	T	0.45	.	5.3855	0.16216	0.5651:0.1416:0.2933:0.0	.	556	Q9H583	HEAT1_HUMAN	K	556	ENSP00000355541:N556K;ENSP00000355540:N556K	ENSP00000355540:N556K	N	-	3	2	HEATR1	234817372	0.754000	0.28360	0.015000	0.15790	0.181000	0.23173	1.292000	0.33342	0.062000	0.16340	-0.313000	0.08912	AAT	.	.		0.323	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853	
TAF1B	9014	hgsc.bcm.edu	37	2	10045015	10045015	+	Nonsense_Mutation	SNP	A	A	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:10045015A>T	ENST00000263663.5	+	9	1023	c.835A>T	c.(835-837)Aaa>Taa	p.K279*	TAF1B_ENST00000396242.3_Nonsense_Mutation_p.K24*	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	279	C-terminal cyclin fold.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GGACATCTACAAAAAAACAGT	0.328																																					p.K279X		Atlas-SNP	.											TAF1B,NS,carcinoma,0,1	TAF1B	62	.	0			c.A835T						.						75.0	65.0	68.0					2																	10045015		2203	4300	6503	SO:0001587	stop_gained	9014	exon9			ATCTACAAAAAAA	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"""			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.835A>T	chr2.hg19:g.10045015A>T	ENSP00000263663:p.Lys279*	43.0	0.0		45.0	0.0	NM_005680	B4DI42|F8WD72|Q15574|Q8WVC3	Nonsense_Mutation	SNP	ENST00000263663.5	hg19	CCDS33143.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.648783	0.87958	.	.	ENSG00000115750	ENST00000263663;ENST00000396242	.	.	.	5.46	0.00658	0.14068	.	0.641420	0.17120	N	0.186264	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.238	2.8251	0.05483	0.6069:0.1237:0.1497:0.1198	.	.	.	.	X	279;24	.	.	K	+	1	0	TAF1B	9962466	0.964000	0.33143	0.630000	0.29268	0.414000	0.31173	0.565000	0.23578	0.355000	0.24131	0.383000	0.25322	AAA	.	.		0.328	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680	
APOB	338	hgsc.bcm.edu	37	2	21263838	21263838	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:21263838A>G	ENST00000233242.1	-	4	482	c.355T>C	c.(355-357)Tct>Cct	p.S119P	APOB_ENST00000399256.4_Missense_Mutation_p.S119P	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	119	Heparin-binding.|Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AACTCCTCAGAGTTCTTGGTT	0.512																																					p.S119P		Atlas-SNP	.											.	APOB	761	.	0			c.T355C						.						112.0	88.0	96.0					2																	21263838		2203	4300	6503	SO:0001583	missense	338	exon4			CCTCAGAGTTCTT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.355T>C	chr2.hg19:g.21263838A>G	ENSP00000233242:p.Ser119Pro	109.0	0.0		139.0	6.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.202606	0.79127	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.40476	1.03;1.03	4.9	4.9	0.64082	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.000000	0.56097	D	0.000028	T	0.64897	0.2640	M	0.78637	2.42	0.42803	D	0.993934	D	0.89917	1.0	D	0.91635	0.999	T	0.70428	-0.4874	10	0.72032	D	0.01	.	13.8314	0.63382	1.0:0.0:0.0:0.0	.	119	P04114	APOB_HUMAN	P	119	ENSP00000233242:S119P;ENSP00000382200:S119P	ENSP00000233242:S119P	S	-	1	0	APOB	21117343	1.000000	0.71417	0.998000	0.56505	0.937000	0.57800	2.630000	0.46494	1.974000	0.57490	0.533000	0.62120	TCT	.	.		0.512	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
HADHA	3030	hgsc.bcm.edu	37	2	26426951	26426951	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:26426951T>C	ENST00000380649.3	-	12	1329	c.1200A>G	c.(1198-1200)ggA>ggG	p.G400G		NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	400					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTGTTGCTGTCCTCGGTCTA	0.498																																					p.G400G		Atlas-SNP	.											.	HADHA	87	.	0			c.A1200G						.						365.0	343.0	350.0					2																	26426951		2203	4300	6503	SO:0001819	synonymous_variant	3030	exon12			TTGCTGTCCTCGG	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"""gastrin-binding protein"", ""long-chain-3-hydroxyacyl-CoA dehydrogenase"", ""long-chain 2-enoyl-CoA hydratase"", ""mitochondrial trifunctional protein, alpha subunit"""	600890	"""hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"""			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.1200A>G	chr2.hg19:g.26426951T>C		112.0	0.0		163.0	7.0	NM_000182	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Silent	SNP	ENST00000380649.3	hg19	CCDS1721.1																																																																																			.	.		0.498	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182	
TRMT61B	55006	hgsc.bcm.edu	37	2	29087914	29087914	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:29087914A>G	ENST00000306108.5	-	2	794	c.771T>C	c.(769-771)tcT>tcC	p.S257S		NM_017910.3	NP_060380.3	Q9BVS5	TR61B_HUMAN	tRNA methyltransferase 61 homolog B (S. cerevisiae)	257					mitochondrial tRNA methylation (GO:0070901)|protein homooligomerization (GO:0051260)	mitochondrion (GO:0005739)|tRNA (m1A) methyltransferase complex (GO:0031515)	tRNA (adenine-N1-)-methyltransferase activity (GO:0016429)			endometrium(2)|kidney(1)|large_intestine(2)|lung(8)	13						TCATTCCACCAGAGCCTGAGC	0.373																																					p.S257S		Atlas-SNP	.											.	TRMT61B	28	.	0			c.T771C						.						70.0	63.0	65.0					2																	29087914		2203	4300	6503	SO:0001819	synonymous_variant	55006	exon2			TCCACCAGAGCCT	BC010365	CCDS1768.1	2p23.2	2009-01-09			ENSG00000171103	ENSG00000171103			26070	protein-coding gene	gene with protein product						11230166	Standard	NM_017910		Approved	FLJ20628	uc002rmm.3	Q9BVS5	OTTHUMG00000128433	ENST00000306108.5:c.771T>C	chr2.hg19:g.29087914A>G		86.0	0.0		88.0	4.0	NM_017910	Q9H0Q9|Q9NWS7	Silent	SNP	ENST00000306108.5	hg19	CCDS1768.1																																																																																			.	.		0.373	TRMT61B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250224.1	NM_017910	
SLC30A6	55676	hgsc.bcm.edu	37	2	32417462	32417462	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:32417462A>G	ENST00000282587.5	+	6	379	c.342A>G	c.(340-342)ggA>ggG	p.G114G	SLC30A6_ENST00000406369.1_Silent_p.G40G|SLC30A6_ENST00000435660.1_Silent_p.G114G|SLC30A6_ENST00000538303.1_Silent_p.G85G|SLC30A6_ENST00000357055.3_5'UTR|SLC30A6_ENST00000379343.2_Silent_p.G154G	NM_017964.3	NP_060434.2	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter), member 6	114					cellular protein metabolic process (GO:0044267)|Golgi to endosome transport (GO:0006895)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(4)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					CACAGTTGGGAGCTCTCTTTA	0.368																																					p.G154G		Atlas-SNP	.											.	SLC30A6	37	.	0			c.A462G						.						108.0	108.0	108.0					2																	32417462		2203	4300	6503	SO:0001819	synonymous_variant	55676	exon7			GTTGGGAGCTCTC	AK055663	CCDS1780.1, CCDS54341.1, CCDS54342.1, CCDS54343.1	2p22.3	2013-05-22			ENSG00000152683	ENSG00000152683		"""Solute carriers"""	19305	protein-coding gene	gene with protein product		611148					Standard	NM_017964		Approved	FLJ31101, ZNT6	uc002rof.2	Q6NXT4	OTTHUMG00000128456	ENST00000282587.5:c.342A>G	chr2.hg19:g.32417462A>G		95.0	0.0		93.0	4.0	NM_001193513	A5YM45|B7Z901|Q8N5C9|Q96NC3	Silent	SNP	ENST00000282587.5	hg19	CCDS1780.1																																																																																			.	.		0.368	SLC30A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250254.2		
EML4	27436	hgsc.bcm.edu	37	2	42544610	42544610	+	Silent	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:42544610C>T	ENST00000318522.5	+	19	2362	c.2100C>T	c.(2098-2100)taC>taT	p.Y700Y	EML4_ENST00000453191.2_Intron|EML4_ENST00000402711.2_Silent_p.Y642Y|EML4_ENST00000401738.3_Silent_p.Y711Y	NM_019063.3	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	700					microtubule-based process (GO:0007017)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|mitotic spindle (GO:0072686)			EML4/ALK(543)	NS(2)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	12						ACTTTATTTACCTCTATGTAG	0.323			T	ALK	NSCLC																																p.Y700Y		Atlas-SNP	.		Dom	yes		2	2p21	27436	echinoderm microtubule associated protein like 4		E	.	EML4	92	.	0			c.C2100T						.						119.0	119.0	119.0					2																	42544610		2203	4298	6501	SO:0001819	synonymous_variant	27436	exon19			TATTTACCTCTAT	AF177377	CCDS1807.1, CCDS46266.1	2p21	2013-01-10		2002-02-15	ENSG00000143924	ENSG00000143924		"""WD repeat domain containing"""	1316	protein-coding gene	gene with protein product		607442		C2orf2			Standard	NM_019063		Approved	ROPP120, ELP120	uc002rsi.3	Q9HC35	OTTHUMG00000128603	ENST00000318522.5:c.2100C>T	chr2.hg19:g.42544610C>T		88.0	0.0		98.0	4.0	NM_019063	A6H8Y6|B2RBK3|B2RTW7|B5MCW9|Q3SWW0|Q53R29|Q53TW8|Q6PJ45|Q9NV40	Silent	SNP	ENST00000318522.5	hg19	CCDS1807.1																																																																																			.	.		0.323	EML4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250463.3	NM_019063	
SRBD1	55133	hgsc.bcm.edu	37	2	45812867	45812867	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:45812867A>G	ENST00000263736.4	-	5	757	c.695T>C	c.(694-696)aTc>aCc	p.I232T		NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	232					nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			GAGACGAATGATGTTGGCACA	0.313																																					p.I232T		Atlas-SNP	.											.	SRBD1	107	.	0			c.T695C						.						104.0	109.0	108.0					2																	45812867		2203	4300	6503	SO:0001583	missense	55133	exon5			CGAATGATGTTGG	AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.695T>C	chr2.hg19:g.45812867A>G	ENSP00000263736:p.Ile232Thr	58.0	0.0		75.0	4.0	NM_018079	Q53T56|Q96TA4|Q9NW11	Missense_Mutation	SNP	ENST00000263736.4	hg19	CCDS1823.1	.	.	.	.	.	.	.	.	.	.	A	9.156	1.017428	0.19355	.	.	ENSG00000068784	ENST00000263736	T	0.41400	1.0	5.04	2.69	0.31865	Tex-like protein, N-terminal (1);Tex-like protein, HTH domain (1);	0.156225	0.36972	N	0.002320	T	0.30479	0.0766	L	0.33792	1.035	0.80722	D	1	B	0.09022	0.002	B	0.15870	0.014	T	0.05616	-1.0874	10	0.24483	T	0.36	.	12.1881	0.54252	0.9233:0.0:0.0767:0.0	.	232	Q8N5C6	SRBD1_HUMAN	T	232	ENSP00000263736:I232T	ENSP00000263736:I232T	I	-	2	0	SRBD1	45666371	1.000000	0.71417	0.993000	0.49108	0.545000	0.35147	4.739000	0.62080	0.398000	0.25338	-1.438000	0.01074	ATC	.	.		0.313	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079	
MSH6	2956	hgsc.bcm.edu	37	2	48027194	48027194	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:48027194T>C	ENST00000234420.5	+	4	2224	c.2072T>C	c.(2071-2073)cTc>cCc	p.L691P	MSH6_ENST00000540021.1_Missense_Mutation_p.L561P|FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_Missense_Mutation_p.L389P	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	691					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GTCTTCTACCTCAAAAAATGC	0.418			"""Mis, N, F, S"""		colorectal	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.L691P		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T2072C						.						167.0	161.0	163.0					2																	48027194		2203	4300	6503	SO:0001583	missense	2956	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	TCTACCTCAAAAA	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"""mutS (E. coli) homolog 6"", ""mutS homolog 6 (E. coli)"""	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.2072T>C	chr2.hg19:g.48027194T>C	ENSP00000234420:p.Leu691Pro	81.0	0.0		95.0	4.0	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Missense_Mutation	SNP	ENST00000234420.5	hg19	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	T	16.63	3.177804	0.57692	.	.	ENSG00000116062	ENST00000234420;ENST00000544857;ENST00000540021;ENST00000538136	D;D;D	0.90900	-2.75;-2.75;-2.75	5.01	5.01	0.66863	DNA mismatch repair protein MutS, connector (1);	0.000000	0.85682	D	0.000000	D	0.96414	0.8830	M	0.93808	3.46	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	D	0.97467	1.0038	10	0.87932	D	0	-10.0182	14.8876	0.70582	0.0:0.0:0.0:1.0	.	561;691;691	B4DF41;P52701;P52701-2	.;MSH6_HUMAN;.	P	691;689;561;389	ENSP00000234420:L691P;ENSP00000446475:L561P;ENSP00000438580:L389P	ENSP00000234420:L691P	L	+	2	0	MSH6	47880698	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.809000	0.86057	2.108000	0.64289	0.377000	0.23210	CTC	.	.		0.418	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179	
PSME4	23198	hgsc.bcm.edu	37	2	54128608	54128608	+	Missense_Mutation	SNP	G	G	C	rs369867748		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:54128608G>C	ENST00000404125.1	-	28	3219	c.3164C>G	c.(3163-3165)gCg>gGg	p.A1055G	PSME4_ENST00000421748.2_Missense_Mutation_p.A199G	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1055					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			AGAAACAATCGCTGGCCACGT	0.443																																					p.A1055G		Atlas-SNP	.											.	PSME4	247	.	0			c.C3164G						.						143.0	136.0	138.0					2																	54128608		2203	4300	6503	SO:0001583	missense	23198	exon28			ACAATCGCTGGCC	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.3164C>G	chr2.hg19:g.54128608G>C	ENSP00000384211:p.Ala1055Gly	93.0	0.0		106.0	43.0	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	hg19	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	G	22.8	4.342604	0.82022	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.28069	1.63;1.69	5.6	5.6	0.85130	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.48352	0.1495	M	0.71581	2.175	0.80722	D	1	D;P;P	0.53151	0.958;0.783;0.93	P;P;P	0.54140	0.743;0.452;0.558	T	0.29212	-1.0019	10	0.21014	T	0.42	.	19.6148	0.95629	0.0:0.0:1.0:0.0	.	430;199;1055	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	G	199;1055	ENSP00000410830:A199G;ENSP00000384211:A1055G	ENSP00000384211:A1055G	A	-	2	0	PSME4	53982112	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.939000	0.87685	2.634000	0.89283	0.557000	0.71058	GCG	.	.		0.443	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
PSME4	23198	hgsc.bcm.edu	37	2	54133824	54133824	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:54133824T>C	ENST00000404125.1	-	26	2909	c.2854A>G	c.(2854-2856)Aca>Gca	p.T952A	PSME4_ENST00000421748.2_Missense_Mutation_p.T96A	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	952					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			ACAGTTAGTGTCCGTAGCTAA	0.308																																					p.T952A		Atlas-SNP	.											.	PSME4	247	.	0			c.A2854G						.						125.0	124.0	124.0					2																	54133824		2203	4300	6503	SO:0001583	missense	23198	exon26			TTAGTGTCCGTAG	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.2854A>G	chr2.hg19:g.54133824T>C	ENSP00000384211:p.Thr952Ala	91.0	0.0		95.0	4.0	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	hg19	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	T	13.84	2.357921	0.41801	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.10860	2.83;2.83	5.57	5.57	0.84162	Armadillo-type fold (1);	0.046373	0.85682	D	0.000000	T	0.08133	0.0203	L	0.29908	0.895	0.51482	D	0.999925	B;B;B	0.30824	0.296;0.205;0.196	B;B;B	0.26416	0.069;0.023;0.021	T	0.11372	-1.0590	10	0.07030	T	0.85	.	16.0388	0.80650	0.0:0.0:0.0:1.0	.	327;96;952	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	A	96;952	ENSP00000410830:T96A;ENSP00000384211:T952A	ENSP00000384211:T952A	T	-	1	0	PSME4	53987328	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.655000	0.83696	2.242000	0.73789	0.528000	0.53228	ACA	.	.		0.308	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
C2orf42	54980	hgsc.bcm.edu	37	2	70402864	70402864	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:70402864C>T	ENST00000264434.2	-	5	1359	c.980G>A	c.(979-981)aGt>aAt	p.S327N	C2orf42_ENST00000420306.1_Missense_Mutation_p.S327N	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	327										endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						CCTTAGATTACTGCTCACTGC	0.408																																					p.S327N		Atlas-SNP	.											.	C2orf42	30	.	0			c.G980A						.						215.0	212.0	213.0					2																	70402864		2203	4300	6503	SO:0001583	missense	54980	exon5			AGATTACTGCTCA	AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.980G>A	chr2.hg19:g.70402864C>T	ENSP00000264434:p.Ser327Asn	120.0	0.0		117.0	43.0	NM_017880	D6W5G3|Q9H629	Missense_Mutation	SNP	ENST00000264434.2	hg19	CCDS1899.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.444671	0.43429	.	.	ENSG00000115998	ENST00000264434;ENST00000420306	D;D	0.93247	-3.19;-3.19	4.86	4.86	0.63082	.	0.448742	0.25596	N	0.029598	D	0.86793	0.6018	N	0.22421	0.69	0.26026	N	0.981805	B	0.33238	0.403	B	0.30029	0.11	T	0.78585	-0.2147	10	0.29301	T	0.29	-18.4621	13.335	0.60512	0.0:1.0:0.0:0.0	.	327	Q9NWW7	CB042_HUMAN	N	327	ENSP00000264434:S327N;ENSP00000404515:S327N	ENSP00000264434:S327N	S	-	2	0	C2orf42	70256368	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.937000	0.40193	2.516000	0.84829	0.491000	0.48974	AGT	.	.		0.408	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880	
ALMS1	7840	hgsc.bcm.edu	37	2	73653590	73653590	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:73653590A>G	ENST00000264448.6	+	6	1358	c.1247A>G	c.(1246-1248)cAg>cGg	p.Q416R	ALMS1_ENST00000377715.1_Missense_Mutation_p.Q416R|ALMS1_ENST00000409009.1_Missense_Mutation_p.Q374R	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	416					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GAGGGCCTGCAGGGGAAGGTT	0.433																																					p.Q416R		Atlas-SNP	.											.	ALMS1	384	.	0			c.A1247G						.						236.0	225.0	229.0					2																	73653590		1938	4139	6077	SO:0001583	missense	7840	exon6			GCCTGCAGGGGAA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.1247A>G	chr2.hg19:g.73653590A>G	ENSP00000264448:p.Gln416Arg	131.0	0.0		158.0	7.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.031238	0.35797	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.21191	2.9;2.9;2.02	5.2	4.02	0.46733	.	0.158118	0.30356	N	0.009813	T	0.30696	0.0773	L	0.36672	1.1	0.22701	N	0.998836	D;D	0.71674	0.998;0.998	D;D	0.66351	0.943;0.943	T	0.04413	-1.0953	10	0.87932	D	0	.	8.2798	0.31894	0.8238:0.0:0.0:0.1762	.	374;416	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	R	374;416;416	ENSP00000386627:Q374R;ENSP00000264448:Q416R;ENSP00000366944:Q416R	ENSP00000264448:Q416R	Q	+	2	0	ALMS1	73507098	0.956000	0.32656	1.000000	0.80357	0.547000	0.35210	1.156000	0.31712	1.074000	0.40909	0.533000	0.62120	CAG	.	.		0.433	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
POLR1A	25885	hgsc.bcm.edu	37	2	86297358	86297358	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:86297358A>G	ENST00000263857.6	-	13	2027	c.1649T>C	c.(1648-1650)cTg>cCg	p.L550P	POLR1A_ENST00000409681.1_Missense_Mutation_p.L550P			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	550					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						CTGTCGGTTCAGTAGCAGAAT	0.577																																					p.L550P		Atlas-SNP	.											.	POLR1A	137	.	0			c.T1649C						.						76.0	83.0	80.0					2																	86297358		2132	4228	6360	SO:0001583	missense	25885	exon13			CGGTTCAGTAGCA	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.1649T>C	chr2.hg19:g.86297358A>G	ENSP00000263857:p.Leu550Pro	139.0	0.0		186.0	9.0	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	hg19	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	A	18.32	3.597932	0.66332	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.76316	-1.01;-1.01	5.3	5.3	0.74995	RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.91676	0.7369	H	0.96111	3.77	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94197	0.7446	10	0.87932	D	0	-13.9506	14.9235	0.70859	1.0:0.0:0.0:0.0	.	550	O95602	RPA1_HUMAN	P	550	ENSP00000263857:L550P;ENSP00000386300:L550P	ENSP00000263857:L550P	L	-	2	0	POLR1A	86150869	1.000000	0.71417	0.980000	0.43619	0.986000	0.74619	8.935000	0.92923	2.007000	0.58848	0.533000	0.62120	CTG	.	.		0.577	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
ZAP70	7535	hgsc.bcm.edu	37	2	98351044	98351044	+	Silent	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:98351044C>T	ENST00000264972.5	+	9	1166	c.951C>T	c.(949-951)agC>agT	p.S317S	ZAP70_ENST00000442208.1_Silent_p.S191S|ZAP70_ENST00000451498.2_Silent_p.S10S|ZAP70_ENST00000463643.1_3'UTR	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	317	Interdomain B.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|beta selection (GO:0043366)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative thymic T cell selection (GO:0045060)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell activation (GO:0042110)|T cell aggregation (GO:0070489)|T cell differentiation (GO:0030217)|T cell migration (GO:0072678)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	29						TGTATGAGAGCCCCTACAGCG	0.587																																					p.S317S		Atlas-SNP	.											.	ZAP70	77	.	0			c.C951T						.						116.0	101.0	106.0					2																	98351044		2203	4300	6503	SO:0001819	synonymous_variant	7535	exon9			TGAGAGCCCCTAC	L05148	CCDS33254.1, CCDS33255.1	2q11-q13	2014-09-17	2002-08-29		ENSG00000115085	ENSG00000115085		"""SH2 domain containing"""	12858	protein-coding gene	gene with protein product		176947	"""zeta-chain (TCR) associated protein kinase (70 kD)"""	SRK		1423621	Standard	NM_001079		Approved	ZAP-70, STD	uc002syd.1	P43403	OTTHUMG00000153060	ENST00000264972.5:c.951C>T	chr2.hg19:g.98351044C>T		80.0	0.0		99.0	4.0	NM_001079	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Silent	SNP	ENST00000264972.5	hg19	CCDS33254.1																																																																																			.	.		0.587	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1		
RANBP2	5903	hgsc.bcm.edu	37	2	109392277	109392277	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:109392277A>G	ENST00000283195.6	+	24	8508	c.8382A>G	c.(8380-8382)gaA>gaG	p.E2794E		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2794					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						GTAAATCTGAAGAACCTGATT	0.378																																					p.E2794E		Atlas-SNP	.											.	RANBP2	488	.	0			c.A8382G						.						161.0	160.0	160.0					2																	109392277		2203	4300	6503	SO:0001819	synonymous_variant	5903	exon24			ATCTGAAGAACCT	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.8382A>G	chr2.hg19:g.109392277A>G		83.0	0.0		96.0	4.0	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	hg19	CCDS2079.1																																																																																			.	.		0.378	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
TMEM87B	84910	hgsc.bcm.edu	37	2	112839016	112839016	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:112839016A>G	ENST00000283206.4	+	8	1128	c.759A>G	c.(757-759)gcA>gcG	p.A253A		NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	253						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						TCTGGATTGCAGCTGTTATTT	0.358																																					p.A253A		Atlas-SNP	.											.	TMEM87B	52	.	0			c.A759G						.						137.0	148.0	144.0					2																	112839016		2203	4300	6503	SO:0001819	synonymous_variant	84910	exon8			GATTGCAGCTGTT	AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214			25913	protein-coding gene	gene with protein product							Standard	NM_032824		Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.759A>G	chr2.hg19:g.112839016A>G		95.0	0.0		117.0	5.0	NM_032824	A8K2M9|Q1RLN2|Q53R54	Silent	SNP	ENST00000283206.4	hg19	CCDS33275.1																																																																																			.	.		0.358	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330500.1	NM_032824	
LCT	3938	hgsc.bcm.edu	37	2	136594658	136594658	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:136594658A>G	ENST00000264162.2	-	1	92	c.82T>C	c.(82-84)Ttc>Ctc	p.F28L		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	28					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GTGGAAATGAAATTTCTATCA	0.468																																					p.F28L		Atlas-SNP	.											.	LCT	309	.	0			c.T82C						.						51.0	52.0	52.0					2																	136594658		2203	4300	6503	SO:0001583	missense	3938	exon1			AAATGAAATTTCT	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.82T>C	chr2.hg19:g.136594658A>G	ENSP00000264162:p.Phe28Leu	68.0	0.0		94.0	42.0	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	hg19	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	a	13.41	2.230199	0.39399	.	.	ENSG00000115850	ENST00000264162	T	0.31769	1.48	5.16	3.98	0.46160	Glycoside hydrolase, superfamily (1);	0.130956	0.51477	D	0.000090	T	0.20455	0.0492	L	0.36672	1.1	0.38355	D	0.944447	P	0.49090	0.919	B	0.37550	0.253	T	0.07214	-1.0784	10	0.18710	T	0.47	-21.1719	12.0775	0.53652	0.8559:0.1441:0.0:0.0	.	28	P09848	LPH_HUMAN	L	28	ENSP00000264162:F28L	ENSP00000264162:F28L	F	-	1	0	LCT	136311128	0.995000	0.38212	0.875000	0.34327	0.149000	0.21700	3.430000	0.52807	0.944000	0.37579	0.529000	0.55759	TTC	.	.		0.468	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
LRP1B	53353	hgsc.bcm.edu	37	2	141739764	141739764	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:141739764T>C	ENST00000389484.3	-	18	3823	c.2852A>G	c.(2851-2853)gAc>gGc	p.D951G		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	951	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GTCACCACAGTCGTCTTCCCT	0.448										TSP Lung(27;0.18)																											p.D951G	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A2852G						.						150.0	130.0	137.0					2																	141739764		2203	4300	6503	SO:0001583	missense	53353	exon18			CCACAGTCGTCTT	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.2852A>G	chr2.hg19:g.141739764T>C	ENSP00000374135:p.Asp951Gly	89.0	0.0		120.0	5.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.456410	0.84317	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.98947	-5.26;-5.26	5.43	5.43	0.79202	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	U	0.000000	D	0.99536	0.9834	H	0.98802	4.335	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.997	D	0.97791	1.0238	10	0.72032	D	0.01	.	15.4805	0.75521	0.0:0.0:0.0:1.0	.	134;951	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	G	951;889;96	ENSP00000374135:D951G;ENSP00000413239:D96G	ENSP00000374135:D951G	D	-	2	0	LRP1B	141456234	1.000000	0.71417	1.000000	0.80357	0.700000	0.40528	7.292000	0.78731	2.053000	0.61076	0.533000	0.62120	GAC	.	.		0.448	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
ARL5A	26225	hgsc.bcm.edu	37	2	152668893	152668893	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:152668893A>G	ENST00000295087.8	-	4	628	c.317T>C	c.(316-318)cTc>cCc	p.L106P	ARL5A_ENST00000428992.2_Missense_Mutation_p.L69P	NM_001037174.1|NM_012097.3	NP_001032251.1|NP_036229.1	Q9Y689	ARL5A_HUMAN	ADP-ribosylation factor-like 5A	106					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			breast(1)|large_intestine(2)|liver(1)|lung(2)	6				BRCA - Breast invasive adenocarcinoma(221;0.153)		CATTTTATAGAGTTCTTCTCT	0.318																																					p.L106P		Atlas-SNP	.											.	ARL5A	12	.	0			c.T317C						.						78.0	75.0	76.0					2																	152668893		2202	4296	6498	SO:0001583	missense	26225	exon4			TTATAGAGTTCTT	AF100740	CCDS2195.1, CCDS46425.1	2q23.3	2014-05-09	2005-11-03	2005-11-03	ENSG00000162980	ENSG00000162980		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	696	protein-coding gene	gene with protein product		608960	"""ADP-ribosylation factor-like 5"""	ARL5			Standard	NM_012097		Approved		uc002txx.1	Q9Y689	OTTHUMG00000131887	ENST00000295087.8:c.317T>C	chr2.hg19:g.152668893A>G	ENSP00000295087:p.Leu106Pro	84.0	0.0		143.0	6.0	NM_012097	Q580I5	Missense_Mutation	SNP	ENST00000295087.8	hg19	CCDS2195.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.376076	0.82682	.	.	ENSG00000162980	ENST00000295087;ENST00000452215;ENST00000428992	T;T	0.77098	-1.07;-1.07	5.01	5.01	0.66863	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.93575	0.7949	H	0.99770	4.765	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96305	0.9224	10	0.87932	D	0	-8.2811	14.7257	0.69343	1.0:0.0:0.0:0.0	.	106	Q9Y689	ARL5A_HUMAN	P	106;69;69	ENSP00000295087:L106P;ENSP00000415950:L69P	ENSP00000295087:L106P	L	-	2	0	ARL5A	152377139	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.339000	0.96797	1.886000	0.54624	0.377000	0.23210	CTC	.	.		0.318	ARL5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254837.1		
LY75	4065	hgsc.bcm.edu	37	2	160661583	160661583	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:160661583T>C	ENST00000263636.4	-	35	5168	c.5141A>G	c.(5140-5142)gAg>gGg	p.E1714G	LY75_ENST00000554112.1_Intron|LY75_ENST00000553424.1_Intron|LY75-CD302_ENST00000504764.1_Intron|LY75-CD302_ENST00000505052.1_Intron	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1714					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)		AAGCATAATCTCATCTTCATT	0.403																																					p.E1714G		Atlas-SNP	.											.	LY75	151	.	0			c.A5141G						.						80.0	76.0	77.0					2																	160661583		2203	4300	6503	SO:0001583	missense	4065	exon35			ATAATCTCATCTT	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.5141A>G	chr2.hg19:g.160661583T>C	ENSP00000263636:p.Glu1714Gly	86.0	0.0		97.0	4.0	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.365558	0.82463	.	.	ENSG00000054219	ENST00000263636	T	0.11930	2.73	5.57	5.57	0.84162	.	1.577580	0.04385	N	0.361427	T	0.29716	0.0742	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.63488	0.915	T	0.00062	-1.2157	10	0.42905	T	0.14	.	13.2425	0.60006	0.0:0.0:0.0:1.0	.	1714	O60449	LY75_HUMAN	G	1714	ENSP00000263636:E1714G	ENSP00000263636:E1714G	E	-	2	0	LY75	160369829	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.502000	0.60400	2.128000	0.65567	0.533000	0.62120	GAG	.	.		0.403	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
SCN1A	6323	hgsc.bcm.edu	37	2	166866301	166866301	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:166866301T>C	ENST00000303395.4	-	20	3929	c.3930A>G	c.(3928-3930)ggA>ggG	p.G1310G	AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Silent_p.G1299G|SCN1A_ENST00000409050.1_Silent_p.G1282G|SCN1A_ENST00000423058.2_Silent_p.G1310G			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1310					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)	ATTTGATGGCTCCAAGTTCTG	0.378																																					p.G1310G		Atlas-SNP	.											.	SCN1A	641	.	0			c.A3930G						.						91.0	90.0	90.0					2																	166866301		2203	4300	6503	SO:0001819	synonymous_variant	6323	exon20			GATGGCTCCAAGT	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.3930A>G	chr2.hg19:g.166866301T>C		61.0	0.0		96.0	4.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.378	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
ABCB11	8647	hgsc.bcm.edu	37	2	169874628	169874628	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:169874628T>C	ENST00000263817.6	-	2	132	c.8A>G	c.(7-9)gAc>gGc	p.D3G		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	3					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	AATTACTGAGTCAGACATGGT	0.348																																					p.D3G		Atlas-SNP	.											.	ABCB11	136	.	0			c.A8G						.						109.0	103.0	105.0					2																	169874628		1833	4087	5920	SO:0001583	missense	8647	exon2			ACTGAGTCAGACA	AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"""ATP binding cassette transporters / subfamily B"""	42	protein-coding gene	gene with protein product	"""ABC member 16, MDR/TAP subfamily"""	603201	"""progressive familial intrahepatic cholestasis 2"", ""bile salt export pump"""	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.8A>G	chr2.hg19:g.169874628T>C	ENSP00000263817:p.Asp3Gly	50.0	0.0		82.0	4.0	NM_003742	Q53TL2|Q9UNB2	Missense_Mutation	SNP	ENST00000263817.6	hg19	CCDS46444.1	.	.	.	.	.	.	.	.	.	.	T	9.611	1.131152	0.21041	.	.	ENSG00000073734	ENST00000263817	D	0.86865	-2.18	5.86	5.86	0.93980	.	0.598116	0.18524	N	0.138690	T	0.75700	0.3885	N	0.08118	0	0.36440	D	0.865428	B	0.15141	0.012	B	0.09377	0.004	T	0.74019	-0.3799	10	0.33141	T	0.24	-8.9785	14.0078	0.64475	0.0:0.0:0.0:1.0	.	3	O95342	ABCBB_HUMAN	G	3	ENSP00000263817:D3G	ENSP00000263817:D3G	D	-	2	0	ABCB11	169582874	0.999000	0.42202	0.945000	0.38365	0.098000	0.18820	3.519000	0.53458	2.240000	0.73641	0.533000	0.62120	GAC	.	.		0.348	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
TTN	7273	hgsc.bcm.edu	37	2	179560924	179560924	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:179560924A>G	ENST00000591111.1	-	112	30148	c.29924T>C	c.(29923-29925)gTt>gCt	p.V9975A	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V9048A|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.V10292A|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-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)			TTCTTTCTGAACCTCTTTCTT	0.348																																					p.V10292A		Atlas-SNP	.											.	TTN	18412	.	0			c.T30875C						.						68.0	55.0	59.0					2																	179560924		1802	4045	5847	SO:0001583	missense	7273	exon114			TTCTGAACCTCTT	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.29924T>C	chr2.hg19:g.179560924A>G	ENSP00000465570:p.Val9975Ala	67.0	0.0		99.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.96	2.093867	0.36952	.	.	ENSG00000155657	ENST00000342992;ENST00000414766	T	0.65549	-0.16	5.28	5.28	0.74379	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.56016	0.1957	L	0.51422	1.61	0.80722	D	1	B;B	0.32507	0.021;0.373	B;B	0.31495	0.014;0.131	T	0.60840	-0.7183	9	0.87932	D	0	.	11.6393	0.51222	1.0:0.0:0.0:0.0	.	9975;9975	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	A	9048;170	ENSP00000343764:V9048A	ENSP00000343764:V9048A	V	-	2	0	TTN	179269169	1.000000	0.71417	1.000000	0.80357	0.368000	0.29767	4.525000	0.60559	2.004000	0.58718	0.528000	0.53228	GTT	.	.		0.348	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179579232	179579232	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:179579232T>C	ENST00000591111.1	-	89	25542	c.25318A>G	c.(25318-25320)Act>Gct	p.T8440A	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T7513A|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.T8757A|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12611	Ig-like 67.				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)			TCAATGGTAGTCTGCAGCTGA	0.408																																					p.T8757A		Atlas-SNP	.											.	TTN	18412	.	0			c.A26269G						.						64.0	59.0	60.0					2																	179579232		1862	4102	5964	SO:0001583	missense	7273	exon91			TGGTAGTCTGCAG	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.25318A>G	chr2.hg19:g.179579232T>C	ENSP00000465570:p.Thr8440Ala	98.0	0.0		93.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	7.880	0.729943	0.15507	.	.	ENSG00000155657	ENST00000342992	T	0.38401	1.14	5.96	-5.91	0.02269	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.10252	0.0251	N	0.00124	-2.055	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39035	-0.9633	9	0.87932	D	0	.	21.5632	0.99956	0.0:0.8617:0.0:0.1383	.	8440	Q8WZ42	TITIN_HUMAN	A	7513	ENSP00000343764:T7513A	ENSP00000343764:T7513A	T	-	1	0	TTN	179287477	0.017000	0.18338	0.076000	0.20297	0.005000	0.04900	-0.151000	0.10175	-1.020000	0.03354	-0.408000	0.06270	ACT	.	.		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
INPP1	3628	hgsc.bcm.edu	37	2	191233941	191233941	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:191233941A>G	ENST00000322522.4	+	5	1035	c.579A>G	c.(577-579)acA>acG	p.T193T	INPP1_ENST00000541441.1_Silent_p.T193T|INPP1_ENST00000392329.2_Silent_p.T193T	NM_002194.3	NP_002185.1	P49441	INPP_HUMAN	inositol polyphosphate-1-phosphatase	193					dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	inositol-1,3,4-trisphosphate 1-phosphatase activity (GO:0052829)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|metal ion binding (GO:0046872)			cervix(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.000286)|Epithelial(96;0.0186)|all cancers(119;0.057)			ACATACAGACAGGGGTTCCCC	0.408																																					p.T193T	Melanoma(130;184 1743 2185 19805 38428)	Atlas-SNP	.											.	INPP1	29	.	0			c.A579G						.						129.0	127.0	127.0					2																	191233941		2203	4300	6503	SO:0001819	synonymous_variant	3628	exon5			ACAGACAGGGGTT		CCDS2305.1	2q32	2008-02-07			ENSG00000151689	ENSG00000151689	3.1.3.57		6071	protein-coding gene	gene with protein product		147263				8390685	Standard	NM_002194		Approved		uc010fsb.3	P49441	OTTHUMG00000132672	ENST00000322522.4:c.579A>G	chr2.hg19:g.191233941A>G		107.0	0.0		145.0	6.0	NM_002194		Silent	SNP	ENST00000322522.4	hg19	CCDS2305.1																																																																																			.	.		0.408	INPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255932.2		
PLCL1	5334	hgsc.bcm.edu	37	2	198950766	198950766	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:198950766T>A	ENST00000428675.1	+	2	2923	c.2525T>A	c.(2524-2526)tTt>tAt	p.F842Y	PLCL1_ENST00000437704.2_Missense_Mutation_p.F744Y	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	842					gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	GTAACCCTTTTTGTCCACATA	0.458																																					p.F842Y		Atlas-SNP	.											.	PLCL1	358	.	0			c.T2525A						.						150.0	125.0	133.0					2																	198950766		2203	4300	6503	SO:0001583	missense	5334	exon2			CCCTTTTTGTCCA	D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"""phospholipase C related, but catalytically inactive protein"", ""protein phosphatase 1, regulatory subunit 127"""	600597	"""phospholipase C, epsilon"""	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.2525T>A	chr2.hg19:g.198950766T>A	ENSP00000402861:p.Phe842Tyr	164.0	0.0		205.0	78.0	NM_006226	Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	hg19	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	T	19.34	3.808520	0.70797	.	.	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.14640	2.49;2.49	5.41	5.41	0.78517	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000004	T	0.42630	0.1211	M	0.85945	2.785	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	T	0.43228	-0.9404	9	.	.	.	.	15.6048	0.76658	0.0:0.0:0.0:1.0	.	842;768	Q15111;B4DYZ4	PLCL1_HUMAN;.	Y	842;744	ENSP00000402861:F842Y;ENSP00000414138:F744Y	.	F	+	2	0	PLCL1	198659011	1.000000	0.71417	0.995000	0.50966	0.955000	0.61496	7.857000	0.86963	2.270000	0.75569	0.482000	0.46254	TTT	.	.		0.458	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226	
C2orf47	79568	hgsc.bcm.edu	37	2	200824539	200824539	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:200824539T>C	ENST00000392290.1	+	3	781	c.585T>C	c.(583-585)gcT>gcC	p.A195A	C2orf47_ENST00000469156.1_3'UTR|C2orf47_ENST00000295079.2_Silent_p.A195A			Q8WWC4	CB047_HUMAN	chromosome 2 open reading frame 47	195						mitochondrion (GO:0005739)				cervix(1)|endometrium(2)|large_intestine(1)|lung(5)	9						ATGCCCTTGCTGCTAACATAG	0.358																																					p.A195A		Atlas-SNP	.											.	C2orf47	20	.	0			c.T585C						.						115.0	105.0	108.0					2																	200824539		2203	4298	6501	SO:0001819	synonymous_variant	79568	exon4			CCTTGCTGCTAAC	BC017959	CCDS2329.1	2q33.1	2011-03-08			ENSG00000162972	ENSG00000162972			26198	protein-coding gene	gene with protein product						12477932	Standard	NM_024520		Approved	DKFZp666A212, FLJ22555	uc002uvm.3	Q8WWC4	OTTHUMG00000132771	ENST00000392290.1:c.585T>C	chr2.hg19:g.200824539T>C		71.0	0.0		95.0	4.0	NM_024520	Q658V9|Q9H671	Silent	SNP	ENST00000392290.1	hg19	CCDS2329.1	.	.	.	.	.	.	.	.	.	.	T	10.35	1.327125	0.24080	.	.	ENSG00000162972	ENST00000435773	.	.	.	5.97	4.83	0.62350	.	.	.	.	.	T	0.54515	0.1863	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53781	-0.8390	4	.	.	.	-12.2038	5.6195	0.17450	0.2446:0.0741:0.0:0.6813	.	.	.	.	P	188	.	.	L	+	2	0	C2orf47	200532784	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	1.608000	0.36847	2.277000	0.76020	0.482000	0.46254	CTG	.	.		0.358	C2orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256146.1	NM_024520	
ZDBF2	57683	hgsc.bcm.edu	37	2	207162017	207162017	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:207162017T>C	ENST00000374423.3	+	4	494	c.108T>C	c.(106-108)cgT>cgC	p.R36R		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	36							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AGAGTAGACGTCAAATATGTA	0.378																																					p.R36R		Atlas-SNP	.											.	ZDBF2	531	.	0			c.T108C						.						128.0	118.0	121.0					2																	207162017		1875	4120	5995	SO:0001819	synonymous_variant	57683	exon4			TAGACGTCAAATA	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.108T>C	chr2.hg19:g.207162017T>C		116.0	0.0		134.0	6.0	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	hg19	CCDS46501.1																																																																																			.	.		0.378	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
ERBB4	2066	hgsc.bcm.edu	37	2	212537944	212537944	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:212537944T>C	ENST00000342788.4	-	14	1971	c.1661A>G	c.(1660-1662)gAg>gGg	p.E554G	ERBB4_ENST00000436443.1_Missense_Mutation_p.E554G|ERBB4_ENST00000402597.1_Missense_Mutation_p.E554G	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	554	Cys-rich.				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)	GGGGTCACACTCCACACAGAT	0.468										TSP Lung(8;0.080)																											p.E554G		Atlas-SNP	.											.	ERBB4	480	.	0			c.A1661G						.						132.0	106.0	115.0					2																	212537944		2203	4300	6503	SO:0001583	missense	2066	exon14			TCACACTCCACAC	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.1661A>G	chr2.hg19:g.212537944T>C	ENSP00000342235:p.Glu554Gly	80.0	0.0		108.0	6.0	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.94|14.94	2.685276|2.685276	0.47991|0.47991	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597|ENST00000260943	T;T;T|.	0.46063|.	0.88;0.88;0.88|.	5.33|5.33	5.33|5.33	0.75918|0.75918	Growth factor, receptor (1);|.	0.092238|.	0.85682|.	D|.	0.000000|.	T|T	0.73544|0.73544	0.3600|0.3600	M|M	0.79926|0.79926	2.475|2.475	0.53005|0.53005	D|D	0.999965|0.999965	P;B;B;P;B|.	0.35872|.	0.525;0.377;0.11;0.525;0.391|.	B;B;B;B;B|.	0.34722|.	0.188;0.11;0.042;0.188;0.091|.	T|T	0.75368|0.75368	-0.3342|-0.3342	9|5	.|.	.|.	.|.	.|.	10.5161|10.5161	0.44889|0.44889	0.1446:0.0:0.0:0.8554|0.1446:0.0:0.0:0.8554	.|.	554;554;413;554;554|.	Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303|.	.;.;.;.;ERBB4_HUMAN|.	G|G	554|554	ENSP00000342235:E554G;ENSP00000403204:E554G;ENSP00000385565:E554G|.	.|.	E|S	-|-	2|1	0|0	ERBB4|ERBB4	212246189|212246189	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	5.766000|5.766000	0.68843|0.68843	2.005000|2.005000	0.58758|0.58758	0.455000|0.455000	0.32223|0.32223	GAG|AGT	.	.		0.468	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	
SMARCAL1	50485	hgsc.bcm.edu	37	2	217329366	217329366	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:217329366C>T	ENST00000357276.4	+	13	2447	c.2117C>T	c.(2116-2118)gCt>gTt	p.A706V	SMARCAL1_ENST00000358207.5_Missense_Mutation_p.A706V	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	706					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		AACAGAACAGCTGAAGCTAAA	0.383									Schimke Immuno-Osseous Dysplasia																												p.A706V		Atlas-SNP	.											.	SMARCAL1	93	.	0			c.C2117T						.						159.0	157.0	158.0					2																	217329366		2203	4300	6503	SO:0001583	missense	50485	exon13	Familial Cancer Database	SIOD	GAACAGCTGAAGC	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"""HepA-related protein"", ""ATP-driven annealing helicase"""	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.2117C>T	chr2.hg19:g.217329366C>T	ENSP00000349823:p.Ala706Val	70.0	0.0		91.0	4.0	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Missense_Mutation	SNP	ENST00000357276.4	hg19	CCDS2403.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.724593	0.89298	.	.	ENSG00000138375	ENST00000357276;ENST00000358207;ENST00000392128	T;T;T	0.80123	-1.34;-1.34;-1.34	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.90143	0.6920	M	0.86343	2.81	0.58432	D	0.999996	P	0.51791	0.948	P	0.61132	0.884	D	0.91337	0.5094	10	0.72032	D	0.01	-14.0005	17.6906	0.88268	0.0:1.0:0.0:0.0	.	706	Q9NZC9	SMAL1_HUMAN	V	706;706;548	ENSP00000349823:A706V;ENSP00000350940:A706V;ENSP00000375974:A548V	ENSP00000349823:A706V	A	+	2	0	SMARCAL1	217037611	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	5.933000	0.70130	2.765000	0.95021	0.650000	0.86243	GCT	.	.		0.383	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2		
USP37	57695	hgsc.bcm.edu	37	2	219353045	219353045	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:219353045A>G	ENST00000258399.3	-	15	1984	c.1572T>C	c.(1570-1572)tcT>tcC	p.S524S	USP37_ENST00000418019.1_Silent_p.S524S|USP37_ENST00000475553.1_5'Flank|USP37_ENST00000454775.1_Silent_p.S524S|USP37_ENST00000415516.1_Silent_p.S452S	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	524	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)		AAAGATCAAGAGAATCTTGAA	0.318																																					p.S524S		Atlas-SNP	.											.	USP37	76	.	0			c.T1572C						.						87.0	88.0	88.0					2																	219353045		2203	4300	6503	SO:0001819	synonymous_variant	57695	exon15			ATCAAGAGAATCT	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.1572T>C	chr2.hg19:g.219353045A>G		119.0	0.0		158.0	9.0	NM_020935	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Silent	SNP	ENST00000258399.3	hg19	CCDS2418.1																																																																																			.	.		0.318	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935	
PTPRN	5798	hgsc.bcm.edu	37	2	220159739	220159739	+	Missense_Mutation	SNP	T	T	C	rs376114976		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:220159739T>C	ENST00000295718.2	-	19	2873	c.2633A>G	c.(2632-2634)gAg>gGg	p.E878G	PTPRN_ENST00000409251.3_Missense_Mutation_p.E849G|MIR153-1_ENST00000384914.1_RNA|PTPRN_ENST00000497977.1_5'UTR|PTPRN_ENST00000423636.2_Missense_Mutation_p.E788G	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	878	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		CGGTGTGCCCTCTGCCGGCCA	0.711																																					p.E878G		Atlas-SNP	.											.	PTPRN	138	.	0			c.A2633G						.	T	GLY/GLU,GLY/GLU,GLY/GLU	0,4398		0,0,2199	32.0	37.0	35.0		2633,2363,2546	5.2	1.0	2		35	1,8597		0,1,4298	no	missense,missense,missense	PTPRN	NM_002846.3,NM_001199764.1,NM_001199763.1	98,98,98	0,1,6497	CC,CT,TT		0.0116,0.0,0.0077	benign,benign,benign	878/980,788/890,849/951	220159739	1,12995	2199	4299	6498	SO:0001583	missense	5798	exon19			GTGCCCTCTGCCG		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.2633A>G	chr2.hg19:g.220159739T>C	ENSP00000295718:p.Glu878Gly	117.0	0.0		105.0	5.0	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	hg19	CCDS2440.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.63|18.63	3.664962|3.664962	0.67700|0.67700	0.0|0.0	1.16E-4|1.16E-4	ENSG00000054356|ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666|ENST00000443981	T;T;T|.	0.12672|.	2.66;2.66;2.66|.	5.18|5.18	5.18|5.18	0.71444|0.71444	Protein-tyrosine phosphatase, receptor/non-receptor type (4);|.	0.377447|.	0.28140|.	N|.	0.016448|.	T|T	0.41534|0.41534	0.1163|0.1163	N|N	0.11756|0.11756	0.17|0.17	0.54753|0.54753	D|D	0.99998|0.99998	D;B|.	0.76494|.	0.999;0.134|.	D;B|.	0.66979|.	0.948;0.039|.	T|T	0.32771|0.32771	-0.9894|-0.9894	10|5	0.51188|.	T|.	0.08|.	.|.	14.8751|14.8751	0.70488|0.70488	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	849;878|.	Q6NSL1;Q16849|.	.;PTPRN_HUMAN|.	G|G	849;878;849;788|81	ENSP00000386638:E849G;ENSP00000295718:E878G;ENSP00000444244:E788G|.	ENSP00000295718:E878G|.	E|R	-|-	2|1	0|2	PTPRN|PTPRN	219867983|219867983	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.031000|4.031000	0.57267|0.57267	2.172000|2.172000	0.68678|0.68678	0.519000|0.519000	0.50382|0.50382	GAG|AGG	.	.		0.711	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2		
COL4A3	1285	hgsc.bcm.edu	37	2	228174007	228174007	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:228174007T>C	ENST00000396578.3	+	50	4890	c.4728T>C	c.(4726-4728)tcT>tcC	p.S1576S	AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000433324.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	1576	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		GCTGGATTTCTCTCTGGAAAG	0.448																																					p.S1576S		Atlas-SNP	.											.	COL4A3	293	.	0			c.T4728C						.						67.0	67.0	67.0					2																	228174007		1956	4153	6109	SO:0001819	synonymous_variant	1285	exon50			GATTTCTCTCTGG		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"""Collagens"""	2204	protein-coding gene	gene with protein product	"""tumstatin"""	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.4728T>C	chr2.hg19:g.228174007T>C		134.0	0.0		112.0	5.0	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Silent	SNP	ENST00000396578.3	hg19	CCDS42829.1																																																																																			.	.		0.448	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
FBXO36	130888	hgsc.bcm.edu	37	2	230861591	230861591	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:230861591T>C	ENST00000283946.3	+	3	348	c.330T>C	c.(328-330)gaT>gaC	p.D110D	FBXO36_ENST00000373652.3_Silent_p.D79D|FBXO36_ENST00000409992.1_Silent_p.D90D	NM_174899.4	NP_777559.3	Q8NEA4	FBX36_HUMAN	F-box protein 36	110	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.									endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	7		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		CTTATCTGGATCTTGAAGATA	0.348																																					p.D110D		Atlas-SNP	.											.	FBXO36	22	.	0			c.T330C						.						166.0	164.0	165.0					2																	230861591		2203	4300	6503	SO:0001819	synonymous_variant	130888	exon3			TCTGGATCTTGAA	BC033935	CCDS2472.1	2q37.1	2008-02-05	2004-06-15		ENSG00000153832	ENSG00000153832		"""F-boxes /  ""other"""""	27020	protein-coding gene	gene with protein product		609105	"""F-box only protein 36"""			12477932	Standard	NM_174899		Approved	Fbx36, FLJ37592	uc002vqa.3	Q8NEA4	OTTHUMG00000133206	ENST00000283946.3:c.330T>C	chr2.hg19:g.230861591T>C		165.0	0.0		223.0	10.0	NM_174899	B3KVQ6|Q53TE6|Q8WWD4	Silent	SNP	ENST00000283946.3	hg19	CCDS2472.1																																																																																			.	.		0.348	FBXO36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256919.2	NM_174899	
DIS3L2	129563	hgsc.bcm.edu	37	2	233113947	233113947	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:233113947A>G	ENST00000409307.1	+	11	1317		c.e11-1		DIS3L2_ENST00000273009.6_Splice_Site|DIS3L2_ENST00000325385.7_Splice_Site					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		CTCTATTTACAGGTGGTCCCC	0.552																																					.		Atlas-SNP	.											.	DIS3L2	77	.	0			c.1318-2A>G						.						80.0	87.0	85.0					2																	233113947		2157	4260	6417	SO:0001630	splice_region_variant	129563	exon12			ATTTACAGGTGGT	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"""family with sequence similarity 6, member A"", ""DIS3 mitotic control homolog (S. cerevisiae)-like 2"""	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.1318-1A>G	chr2.hg19:g.233113947A>G		114.0	0.0		125.0	5.0	NM_152383		Splice_Site	SNP	ENST00000409307.1	hg19	CCDS42834.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.216563	0.79352	.	.	ENSG00000144535	ENST00000273009;ENST00000542873;ENST00000325385;ENST00000431466;ENST00000409307;ENST00000424049	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1596	0.81693	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DIS3L2	232822191	1.000000	0.71417	0.997000	0.53966	0.940000	0.58332	8.670000	0.91168	2.216000	0.71823	0.533000	0.62120	.	.	.		0.552	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383	Intron
UGT1A5	54579	hgsc.bcm.edu	37	2	234622002	234622002	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:234622002T>C	ENST00000373414.3	+	1	365	c.365T>C	c.(364-366)tTg>tCg	p.L122S	UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000608381.1_Missense_Mutation_p.L122S|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A10_ENST00000373445.1_Intron			P35504	UD15_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A5	122						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		AATATGTCTTTGATCATACAT	0.413																																					p.L122S		Atlas-SNP	.											.	UGT1A5	66	.	0			c.T365C						.						173.0	168.0	170.0					2																	234622002		2203	4300	6503	SO:0001583	missense	54579	exon1			TGTCTTTGATCAT	M84129	CCDS33404.1	2q37	2010-03-05	2005-07-20		ENSG00000240224	ENSG00000240224		"""UDP glucuronosyltransferases"""	12537	other	complex locus constituent		606430	"""UDP glycosyltransferase 1 family, polypeptide A5"""			9295054, 1339448	Standard	NM_019078		Approved	UGT1E		P35504	OTTHUMG00000059120	ENST00000373414.3:c.365T>C	chr2.hg19:g.234622002T>C	ENSP00000362513:p.Leu122Ser	179.0	0.0		232.0	89.0	NM_019078	B8K294	Missense_Mutation	SNP	ENST00000373414.3	hg19	CCDS33404.1	.	.	.	.	.	.	.	.	.	.	T	5.192	0.221009	0.09863	.	.	ENSG00000240224	ENST00000373414	T	0.58797	0.31	4.69	-9.37	0.00626	.	3.783170	0.01269	N	0.009403	T	0.30103	0.0754	N	0.11284	0.12	0.09310	N	1	B;B	0.19583	0.037;0.037	B;B	0.19666	0.026;0.026	T	0.10382	-1.0632	10	0.26408	T	0.33	.	4.0361	0.09730	0.2323:0.4383:0.0787:0.2506	.	122;122	Q5DSZ9;P35504	.;UD15_HUMAN	S	122	ENSP00000362513:L122S	ENSP00000362513:L122S	L	+	2	0	UGT1A5	234286741	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.690000	0.05138	-1.286000	0.02384	-0.531000	0.04308	TTG	.	.		0.413	UGT1A5-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130985.1	NM_019078	
HDAC4	9759	hgsc.bcm.edu	37	2	240274391	240274391	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:240274391T>C	ENST00000345617.3	-	2	795	c.4A>G	c.(4-6)Agc>Ggc	p.S2G	MIR2467_ENST00000584559.1_RNA	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	2					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)		CTTTGGGAGCTCATTGCTAGC	0.493																																					p.S2G		Atlas-SNP	.											.	HDAC4	127	.	0			c.A4G						.						68.0	68.0	68.0					2																	240274391		2195	4274	6469	SO:0001583	missense	9759	exon2			GGGAGCTCATTGC	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.4A>G	chr2.hg19:g.240274391T>C	ENSP00000264606:p.Ser2Gly	88.0	0.0		110.0	5.0	NM_006037	Q9UND6	Missense_Mutation	SNP	ENST00000345617.3	hg19	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	T	9.445	1.088958	0.20390	.	.	ENSG00000068024	ENST00000345617;ENST00000544989	T	0.59364	0.27	3.73	3.73	0.42828	.	1.437920	0.05036	U	0.475568	T	0.31979	0.0814	N	0.02011	-0.69	0.80722	D	1	B	0.16603	0.018	B	0.15870	0.014	T	0.13229	-1.0517	9	.	.	.	.	9.4103	0.38487	0.0:0.0:0.0:1.0	.	2	P56524	HDAC4_HUMAN	G	2	ENSP00000264606:S2G	.	S	-	1	0	HDAC4	239939328	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	3.549000	0.53681	1.659000	0.50751	0.528000	0.53228	AGC	.	.		0.493	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
PPP1R7	5510	hgsc.bcm.edu	37	2	242089946	242089946	+	Silent	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:242089946G>A	ENST00000234038.6	+	1	510	c.36G>A	c.(34-36)tcG>tcA	p.S12S	PPP1R7_ENST00000401987.1_Silent_p.S12S|PASK_ENST00000234040.4_5'Flank|PPP1R7_ENST00000402734.1_Intron|PPP1R7_ENST00000406106.3_Silent_p.S12S|PASK_ENST00000358649.4_5'Flank|PASK_ENST00000405260.1_5'Flank|PASK_ENST00000403638.3_5'Flank|PPP1R7_ENST00000272983.8_Silent_p.S12S|PPP1R7_ENST00000407025.1_Silent_p.S12S|PPP1R7_ENST00000404405.3_Silent_p.S12S|PASK_ENST00000539818.1_5'Flank	NM_001282412.1|NM_001282413.1|NM_002712.1	NP_001269341.1|NP_001269342.1|NP_002703.1	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	12					positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	enzyme regulator activity (GO:0030234)|protein phosphatase type 1 regulator activity (GO:0008599)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)	23		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		AGCAACAGTCGCAGGAGATGA	0.701																																					p.S12S	NSCLC(62;446 1299 5417 11238 27640)	Atlas-SNP	.											.	PPP1R7	35	.	0			c.G36A						.						15.0	19.0	18.0					2																	242089946		2187	4284	6471	SO:0001819	synonymous_variant	5510	exon1			ACAGTCGCAGGAG	AF067136	CCDS2546.1, CCDS63190.1, CCDS63192.1, CCDS63193.1, CCDS63194.1	2q37.3	2012-04-17	2011-10-04		ENSG00000115685	ENSG00000115685		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9295	protein-coding gene	gene with protein product		602877	"""protein phosphatase 1, regulatory (inhibitor) subunit 7"""			7498485, 7670491, 10231361	Standard	NM_001282413		Approved	sds22	uc002wat.1	Q15435	OTTHUMG00000133390	ENST00000234038.6:c.36G>A	chr2.hg19:g.242089946G>A		93.0	0.0		78.0	4.0	NM_002712	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Silent	SNP	ENST00000234038.6	hg19	CCDS2546.1																																																																																			.	.		0.701	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712	
XYLB	9942	hgsc.bcm.edu	37	3	38417621	38417621	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:38417621T>C	ENST00000207870.3	+	13	1108	c.1018T>C	c.(1018-1020)Tcc>Ccc	p.S340P	XYLB_ENST00000542835.1_Missense_Mutation_p.S203P	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)	340					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		TAAAAATGGCTCCCTCATGAG	0.532																																					p.S340P		Atlas-SNP	.											.	XYLB	50	.	0			c.T1018C						.						146.0	148.0	147.0					3																	38417621		2203	4300	6503	SO:0001583	missense	9942	exon13			AATGGCTCCCTCA	AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"""xylulokinase (H. influenzae) homolog"""			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.1018T>C	chr3.hg19:g.38417621T>C	ENSP00000207870:p.Ser340Pro	129.0	0.0		128.0	8.0	NM_005108	B2RAW4|B4DDT2|B9EH64	Missense_Mutation	SNP	ENST00000207870.3	hg19	CCDS2678.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.191084	0.78902	.	.	ENSG00000093217	ENST00000207870;ENST00000542835	T;T	0.44482	0.92;0.92	4.91	4.91	0.64330	Carbohydrate kinase, FGGY, C-terminal (1);	0.060785	0.64402	D	0.000002	T	0.69993	0.3173	M	0.92169	3.28	0.47659	D	0.999488	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.992	T	0.76258	-0.3025	10	0.56958	D	0.05	.	11.2238	0.48871	0.0:0.0:0.0:1.0	.	203;340	B4DDT2;O75191	.;XYLB_HUMAN	P	340;203	ENSP00000207870:S340P;ENSP00000443659:S203P	ENSP00000207870:S340P	S	+	1	0	XYLB	38392625	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.606000	0.74159	1.966000	0.57179	0.379000	0.24179	TCC	.	.		0.532	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254062.2	NM_005108	
CCR5	1234	hgsc.bcm.edu	37	3	46415316	46415316	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:46415316T>C	ENST00000292303.4	+	2	1069	c.923T>C	c.(922-924)cTc>cCc	p.L308P	RP11-24F11.2_ENST00000451485.1_RNA|CCR5_ENST00000445772.1_Missense_Mutation_p.L308P|CCR5_ENST00000343801.4_Missense_Mutation_p.L308P	NM_001100168.1	NP_001093638.1	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5 (gene/pseudogene)	308					calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|signaling (GO:0023052)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)|phosphatidylinositol phospholipase C activity (GO:0004435)			central_nervous_system(1)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	AGAAACTACCTCTTAGTCTTC	0.493																																					p.L308P		Atlas-SNP	.											.	CCR5	128	.	0			c.T923C						.						184.0	178.0	180.0					3																	46415316		2203	4296	6499	SO:0001583	missense	1234	exon3			ACTACCTCTTAGT		CCDS2739.1	3p21	2012-08-08	2012-01-23		ENSG00000160791	ENSG00000160791		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1606	protein-coding gene	gene with protein product		601373	"""chemokine (C-C motif) receptor 5"""	CMKBR5		8639485	Standard	NM_001100168		Approved	CKR-5, CC-CKR-5, CKR5, CD195, IDDM22	uc003cpo.4	P51681	OTTHUMG00000133481	ENST00000292303.4:c.923T>C	chr3.hg19:g.46415316T>C	ENSP00000292303:p.Leu308Pro	76.0	0.0		96.0	5.0	NM_000579	O14692|O14693|O14695|O14696|O14697|O14698|O14699|O14700|O14701|O14702|O14703|O14704|O14705|O14706|O14707|O14708|O15538|Q9UPA4	Missense_Mutation	SNP	ENST00000292303.4	hg19	CCDS2739.1	.	.	.	.	.	.	.	.	.	.	T	16.33	3.092527	0.56075	.	.	ENSG00000160791	ENST00000343801;ENST00000400886;ENST00000292303;ENST00000445772	T;T;T	0.48522	0.81;0.81;0.81	5.69	5.69	0.88448	.	0.165190	0.25631	U	0.029349	T	0.72334	0.3447	M	0.93420	3.415	0.46774	D	0.999191	D	0.67145	0.996	P	0.61275	0.886	T	0.79581	-0.1744	10	0.87932	D	0	.	11.0514	0.47893	0.0:0.072:0.0:0.928	.	308	P51681	CCR5_HUMAN	P	308;288;308;308	ENSP00000343985:L308P;ENSP00000292303:L308P;ENSP00000404881:L308P	ENSP00000292303:L308P	L	+	2	0	CCR5	46390320	0.538000	0.26394	0.430000	0.26722	0.899000	0.52679	4.125000	0.57931	2.162000	0.67917	0.459000	0.35465	CTC	.	.		0.493	CCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257377.2	NM_000579	
SETD2	29072	hgsc.bcm.edu	37	3	47168143	47168143	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:47168143T>C	ENST00000409792.3	-	2	124	c.82A>G	c.(82-84)Aat>Gat	p.N28D		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	28					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CTTACCTCATTTTCTTCTTCT	0.264			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.N28D		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.A82G						.						122.0	103.0	108.0					3																	47168143		1475	3412	4887	SO:0001583	missense	29072	exon2			CCTCATTTTCTTC	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.82A>G	chr3.hg19:g.47168143T>C	ENSP00000386759:p.Asn28Asp	33.0	0.0		35.0	4.0	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	16.73	3.205346	0.58234	.	.	ENSG00000181555	ENST00000409792	D	0.88818	-2.43	4.46	4.46	0.54185	.	.	.	.	.	D	0.88584	0.6476	N	0.14661	0.345	0.24154	N	0.995682	D	0.63880	0.993	D	0.70935	0.971	T	0.80603	-0.1309	9	0.87932	D	0	.	11.5254	0.50576	0.0:0.0:0.0:1.0	.	28	Q9BYW2	SETD2_HUMAN	D	28	ENSP00000386759:N28D	ENSP00000386759:N28D	N	-	1	0	SETD2	47143147	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	4.399000	0.59703	1.996000	0.58369	0.402000	0.26972	AAT	.	.		0.264	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
APEH	327	hgsc.bcm.edu	37	3	49722912	49722912	+	IGR	SNP	T	T	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:49722912T>G	ENST00000296456.5	+	0	3220				MST1_ENST00000449682.2_Missense_Mutation_p.D472A|MST1_ENST00000383728.3_3'UTR|MST1_ENST00000494828.2_5'Flank|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)		ACCTGGGGGGTCCAGGATTGA	0.587																																					p.D472A		Atlas-SNP	.											.	MST1	84	.	0			c.A1415C						.						29.0	32.0	31.0					3																	49722912		2202	4299	6501	SO:0001628	intergenic_variant	4485	exon12			GGGGGGTCCAGGA	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.49722912T>G		304.0	0.0		488.0	30.0	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	T	11.73	1.724622	0.30593	.	.	ENSG00000173531	ENST00000449682	T	0.79454	-1.27	4.78	4.78	0.61160	.	0.707688	0.11995	N	0.509451	T	0.58278	0.2111	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.51293	-0.8724	10	0.16420	T	0.52	.	11.2685	0.49124	0.0:0.0:0.0:1.0	rs11393273	472	G3XAK1	.	A	472	ENSP00000414287:D472A	ENSP00000414287:D472A	D	-	2	0	MST1	49697916	1.000000	0.71417	0.990000	0.47175	0.783000	0.44284	4.165000	0.58196	2.087000	0.62958	0.533000	0.62120	GAC	.	.		0.587	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
NEK4	6787	hgsc.bcm.edu	37	3	52775439	52775439	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:52775439T>C	ENST00000233027.5	-	13	2283	c.2081A>G	c.(2080-2082)gAt>gGt	p.D694G	NEK4_ENST00000535191.1_Missense_Mutation_p.D605G|NEK4_ENST00000383721.4_Missense_Mutation_p.D648G	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	694					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		TTCCCCGTAATCCCCATCTGA	0.323																																					p.D694G		Atlas-SNP	.											.	NEK4	51	.	0			c.A2081G						.						126.0	119.0	122.0					3																	52775439		2203	4300	6503	SO:0001583	missense	6787	exon13			CCGTAATCCCCAT	L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"""serine/threonine protein kinase-2"""	601959	"""serine/threonine kinase 2"", ""NIMA (never in mitosis gene a)-related kinase 4"""	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.2081A>G	chr3.hg19:g.52775439T>C	ENSP00000233027:p.Asp694Gly	71.0	0.0		91.0	4.0	NM_003157	A5YM70|B2R633|B7Z200|Q6P576	Missense_Mutation	SNP	ENST00000233027.5	hg19	CCDS2863.1	.	.	.	.	.	.	.	.	.	.	T	14.06	2.421719	0.43020	.	.	ENSG00000114904	ENST00000233027;ENST00000535191;ENST00000383721;ENST00000461689	T;T;T;T	0.78924	2.32;2.32;-1.22;2.32	5.66	4.51	0.55191	.	0.143577	0.47093	N	0.000241	T	0.68063	0.2960	L	0.43152	1.355	0.49483	D	0.999793	B;B;B	0.33288	0.182;0.406;0.284	B;B;B	0.31191	0.085;0.125;0.085	T	0.66850	-0.5819	10	0.52906	T	0.07	.	9.417	0.38528	0.0:0.0819:0.0:0.9181	.	605;648;694	B7Z200;P51957-2;P51957	.;.;NEK4_HUMAN	G	694;605;648;605	ENSP00000233027:D694G;ENSP00000437703:D605G;ENSP00000373227:D648G;ENSP00000419666:D605G	ENSP00000233027:D694G	D	-	2	0	NEK4	52750479	1.000000	0.71417	0.994000	0.49952	0.626000	0.37791	4.851000	0.62896	1.089000	0.41292	0.533000	0.62120	GAT	.	.		0.323	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157	
RFT1	91869	hgsc.bcm.edu	37	3	53125923	53125923	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:53125923G>C	ENST00000296292.3	-	13	1683	c.1622C>G	c.(1621-1623)aCa>aGa	p.T541R	RP11-894J14.5_ENST00000607203.1_Intron|RFT1_ENST00000394738.3_Missense_Mutation_p.T502R	NM_052859.3	NP_443091.1	Q96AA3	RFT1_HUMAN	RFT1 homolog (S. cerevisiae)	541					carbohydrate transport (GO:0008643)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)	lipid transporter activity (GO:0005319)			NS(1)|breast(1)|kidney(1)|lung(5)|skin(2)|urinary_tract(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)		CTGAAGTCATGTCATTTTGTC	0.547																																					p.T541R		Atlas-SNP	.											RFT1,colon,carcinoma,0,1	RFT1	34	.	0			c.C1622G						.						119.0	99.0	106.0					3																	53125923		2203	4300	6503	SO:0001583	missense	91869	exon13			AGTCATGTCATTT	AJ318099	CCDS2869.1	3p21.1	2014-02-06	2005-01-26		ENSG00000163933	ENSG00000163933			30220	protein-coding gene	gene with protein product	"""congenital disorder of glycosylation 1N"""	611908	"""RFT1, requiring fifty three 1 homolog (S. cerevisiae)"""			12477932	Standard	NM_052859		Approved	CDG1N	uc003dgj.3	Q96AA3	OTTHUMG00000074035	ENST00000296292.3:c.1622C>G	chr3.hg19:g.53125923G>C	ENSP00000296292:p.Thr541Arg	235.0	0.0		228.0	0.0	NM_052859	Q96J03	Missense_Mutation	SNP	ENST00000296292.3	hg19	CCDS2869.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.981026	0.34942	.	.	ENSG00000163933	ENST00000296292;ENST00000394738	D;D	0.86164	-2.08;-1.89	5.55	1.74	0.24563	.	0.311043	0.39407	N	0.001378	T	0.81088	0.4750	L	0.53249	1.67	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.71715	-0.4509	10	0.72032	D	0.01	.	5.8914	0.18915	0.2386:0.1411:0.6203:0.0	.	502;541	B5MDE0;Q96AA3	.;RFT1_HUMAN	R	541;502	ENSP00000296292:T541R;ENSP00000378223:T502R	ENSP00000296292:T541R	T	-	2	0	RFT1	53100963	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.595000	0.24029	0.304000	0.22809	0.561000	0.74099	ACA	.	.		0.547	RFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157136.2	NM_052859	
CCDC66	285331	hgsc.bcm.edu	37	3	56651451	56651451	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:56651451T>C	ENST00000394672.3	+	14	2225	c.2155T>C	c.(2155-2157)Tac>Cac	p.Y719H	CCDC66_ENST00000436465.2_Missense_Mutation_p.Y719H|CCDC66_ENST00000326595.7_Missense_Mutation_p.Y685H	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	719					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		ATCAGAAAAGTACCCTAAACA	0.353																																					p.Y719H		Atlas-SNP	.											.	CCDC66	145	.	0			c.T2155C						.						48.0	51.0	50.0					3																	56651451		2203	4299	6502	SO:0001583	missense	285331	exon14			GAAAAGTACCCTA	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.2155T>C	chr3.hg19:g.56651451T>C	ENSP00000378167:p.Tyr719His	96.0	0.0		100.0	4.0	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	hg19	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.334206	0.81801	.	.	ENSG00000180376	ENST00000394672;ENST00000326595;ENST00000436465	T;T;T	0.36340	1.26;1.26;1.26	5.68	5.68	0.88126	.	0.000000	0.64402	D	0.000001	T	0.61590	0.2359	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65928	-0.6049	10	0.87932	D	0	-7.9358	15.9259	0.79615	0.0:0.0:0.0:1.0	.	719	A2RUB6	CCD66_HUMAN	H	719;685;719	ENSP00000378167:Y719H;ENSP00000326050:Y685H;ENSP00000404320:Y719H	ENSP00000326050:Y685H	Y	+	1	0	CCDC66	56626491	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.089000	0.71384	2.161000	0.67846	0.460000	0.39030	TAC	.	.		0.353	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786761	75786761	+	Silent	SNP	C	C	T	rs145576551		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:75786761C>T	ENST00000478296.1	-	4	2139	c.1863G>A	c.(1861-1863)ggG>ggA	p.G621G	ZNF717_ENST00000422325.1_Silent_p.G671G|ZNF717_ENST00000400845.3_Silent_p.G664G|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	661					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)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TACGGTTTTTCCCCGTGTGAG	0.408																																					p.G671G		Atlas-SNP	.											.,4	ZNF717	160	.	0			c.G2013A						.						12.0	11.0	11.0					3																	75786761		587	1452	2039	SO:0001819	synonymous_variant	100131827	exon5			GTTTTTCCCCGTG	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1863G>A	chr3.hg19:g.75786761C>T		14.0	0.0		16.0	3.0	NM_001128223		Silent	SNP	ENST00000478296.1	hg19																																																																																				.	.		0.408	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
EPHA3	2042	hgsc.bcm.edu	37	3	89521694	89521694	+	Missense_Mutation	SNP	G	G	C	rs150555764		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:89521694G>C	ENST00000336596.2	+	16	2996	c.2771G>C	c.(2770-2772)tGg>tCg	p.W924S	EPHA3_ENST00000494014.1_Intron	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	924	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.		W -> R (in dbSNP:rs35124509). {ECO:0000269|PubMed:1311845, ECO:0000269|PubMed:17344846}.		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)		AATGGTGTCTGGACAGCACAC	0.423										TSP Lung(6;0.00050)																											p.W924S		Atlas-SNP	.											EPHA3,NS,carcinoma,-1,1	EPHA3	501	.	0			c.G2771C						.						148.0	138.0	141.0					3																	89521694		2203	4300	6503	SO:0001583	missense	2042	exon16			GTGTCTGGACAGC	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.2771G>C	chr3.hg19:g.89521694G>C	ENSP00000337451:p.Trp924Ser	144.0	0.0		206.0	0.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.902669	0.52227	.	.	ENSG00000044524	ENST00000336596	D	0.83992	-1.79	5.73	5.73	0.89815	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.000000	0.85682	D	0.000000	T	0.61615	0.2361	N	0.02539	-0.55	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.60352	-0.7280	9	.	.	.	.	13.1385	0.59423	0.0728:0.0:0.9271:0.0	.	924	P29320	EPHA3_HUMAN	S	924	ENSP00000337451:W924S	.	W	+	2	0	EPHA3	89604384	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.370000	0.66144	2.700000	0.92200	0.655000	0.94253	TGG	.	G|1.000;A|0.000		0.423	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
PHLDB2	90102	hgsc.bcm.edu	37	3	111639163	111639163	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:111639163A>G	ENST00000431670.2	+	5	2309	c.1898A>G	c.(1897-1899)cAg>cGg	p.Q633R	PHLDB2_ENST00000412622.1_Missense_Mutation_p.Q633R|PHLDB2_ENST00000481953.1_Missense_Mutation_p.Q633R|PHLDB2_ENST00000393923.3_Missense_Mutation_p.Q660R|PHLDB2_ENST00000495180.1_Missense_Mutation_p.Q219R|PHLDB2_ENST00000393925.3_Missense_Mutation_p.Q633R	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	633						cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						GATGGAGAACAGAAATCTGAA	0.403																																					p.Q660R		Atlas-SNP	.											.	PHLDB2	449	.	0			c.A1979G						.						131.0	136.0	135.0					3																	111639163		2203	4300	6503	SO:0001583	missense	90102	exon6			GAGAACAGAAATC		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"""Pleckstrin homology (PH) domain containing"""	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.1898A>G	chr3.hg19:g.111639163A>G	ENSP00000405405:p.Gln633Arg	81.0	0.0		108.0	5.0	NM_001134437	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Missense_Mutation	SNP	ENST00000431670.2	hg19	CCDS46886.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.192457	0.38707	.	.	ENSG00000144824	ENST00000359729;ENST00000393923;ENST00000431670;ENST00000412622;ENST00000498699;ENST00000393925;ENST00000481953;ENST00000495180	T;T;T;T;T;T;T	0.31510	1.49;1.53;1.49;1.51;1.53;1.49;1.63	5.13	5.13	0.70059	.	0.141393	0.47455	D	0.000223	T	0.34919	0.0914	N	0.20328	0.56	0.44995	D	0.998014	B;B;D;D	0.89917	0.041;0.112;1.0;1.0	B;B;D;D	0.70716	0.019;0.082;0.97;0.97	T	0.08249	-1.0731	10	0.12430	T	0.62	.	12.492	0.55905	1.0:0.0:0.0:0.0	.	219;633;633;660	E9PGF6;Q86SQ0;Q86SQ0-2;Q86SQ0-3	.;PHLB2_HUMAN;.;.	R	660;660;633;633;633;633;633;219	ENSP00000377500:Q660R;ENSP00000405405:Q633R;ENSP00000405292:Q633R;ENSP00000418296:Q633R;ENSP00000377502:Q633R;ENSP00000418319:Q633R;ENSP00000420303:Q219R	ENSP00000352764:Q660R	Q	+	2	0	PHLDB2	113121853	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.831000	0.86748	1.938000	0.56188	0.455000	0.32223	CAG	.	.		0.403	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753	
GCSAM	257144	hgsc.bcm.edu	37	3	111842506	111842506	+	Silent	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:111842506G>A	ENST00000308910.4	-	6	517	c.333C>T	c.(331-333)ccC>ccT	p.P111P	GCSAM_ENST00000484193.1_Silent_p.P113P|C3orf52_ENST00000467942.2_Intron	NM_001190259.1|NM_001190260.1|NM_152785.4	NP_001177188.1|NP_001177189.1|NP_689998.1	Q8N6F7	GCSAM_HUMAN	germinal center-associated, signaling and motility	111					negative regulation of lymphocyte migration (GO:2000402)|regulation of B cell receptor signaling pathway (GO:0050855)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|myosin II binding (GO:0045159)|protein kinase binding (GO:0019901)										CAGCTTTGCAGGGAACATTCT	0.507																																					p.P113P		Atlas-SNP	.											.	.	.	.	0			c.C339T						.						117.0	110.0	112.0					3																	111842506		2203	4300	6503	SO:0001819	synonymous_variant	257144	exon6			TTTGCAGGGAACA	BC030506	CCDS2964.1, CCDS54621.1, CCDS54622.1	3q13.13	2012-09-03	2012-08-23	2012-08-23	ENSG00000174500	ENSG00000174500			20253	protein-coding gene	gene with protein product	"""human germinal center-associated lymphoma"""	607792	"""germinal center expressed transcript 2"""	GCET2			Standard	NM_152785		Approved	MGC40441, HGAL	uc021xcl.1	Q8N6F7	OTTHUMG00000159231	ENST00000308910.4:c.333C>T	chr3.hg19:g.111842506G>A		217.0	0.0		271.0	90.0	NM_001190259	C9JD17|C9JUG6	Silent	SNP	ENST00000308910.4	hg19	CCDS2964.1																																																																																			.	.		0.507	GCSAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353967.2	NM_152785	
SPICE1	152185	hgsc.bcm.edu	37	3	113188037	113188037	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:113188037C>A	ENST00000295872.4	-	8	919	c.660G>T	c.(658-660)ttG>ttT	p.L220F		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	220					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						TGTCAGTCCACAACTTACTAA	0.353																																					p.L220F		Atlas-SNP	.											.	SPICE1	130	.	0			c.G660T						.						104.0	99.0	101.0					3																	113188037		2203	4300	6503	SO:0001583	missense	152185	exon8			AGTCCACAACTTA	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.660G>T	chr3.hg19:g.113188037C>A	ENSP00000295872:p.Leu220Phe	142.0	0.0		158.0	55.0	NM_144718	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	hg19	CCDS2973.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.22|15.22	2.769395|2.769395	0.49680|0.49680	.|.	.|.	ENSG00000163611|ENSG00000163611	ENST00000467618|ENST00000295872	.|T	.|0.34472	.|1.36	4.91|4.91	0.802|0.802	0.18686|0.18686	.|.	.|0.000000	.|0.49305	.|D	.|0.000155	T|T	0.50956|0.50956	0.1646|0.1646	M|M	0.70595|0.70595	2.14|2.14	0.33229|0.33229	D|D	0.555739|0.555739	.|D;D	.|0.89917	.|0.979;1.0	.|P;D	.|0.87578	.|0.858;0.998	T|T	0.58239|0.58239	-0.7671|-0.7671	5|10	.|0.54805	.|T	.|0.06	-8.0979|-8.0979	5.8902|5.8902	0.18909|0.18909	0.0:0.6236:0.1403:0.236|0.0:0.6236:0.1403:0.236	.|.	.|116;220	.|B3KX77;Q8N0Z3	.|.;SPICE_HUMAN	F|F	32|220	.|ENSP00000295872:L220F	.|ENSP00000295872:L220F	C|L	-|-	2|3	0|2	SPICE1|SPICE1	114670727|114670727	0.993000|0.993000	0.37304|0.37304	0.996000|0.996000	0.52242|0.52242	0.796000|0.796000	0.44982|0.44982	0.097000|0.097000	0.15168|0.15168	0.161000|0.161000	0.19458|0.19458	0.591000|0.591000	0.81541|0.81541	TGT|TTG	.	.		0.353	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	
ATP6V1A	523	hgsc.bcm.edu	37	3	113514007	113514007	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:113514007T>C	ENST00000273398.3	+	10	1290	c.1182T>C	c.(1180-1182)tgT>tgC	p.C394C	ATP6V1A_ENST00000538620.1_Silent_p.C361C	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	394					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	GGGTGAAATGTCTTGGAAATC	0.408																																					p.C394C		Atlas-SNP	.											.	ATP6V1A	71	.	0			c.T1182C						.						55.0	57.0	57.0					3																	113514007		2203	4300	6503	SO:0001819	synonymous_variant	523	exon10			GAAATGTCTTGGA	L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"""ATPases / V-type"""	851	protein-coding gene	gene with protein product		607027	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"""	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.1182T>C	chr3.hg19:g.113514007T>C		75.0	0.0		90.0	4.0	NM_001690	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Silent	SNP	ENST00000273398.3	hg19	CCDS2976.1																																																																																			.	.		0.408	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690	
GOLGB1	2804	hgsc.bcm.edu	37	3	121416461	121416461	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:121416461T>C	ENST00000340645.5	-	13	3019	c.2894A>G	c.(2893-2895)gAg>gGg	p.E965G	GOLGB1_ENST00000393667.3_Missense_Mutation_p.E970G	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	965					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		TGGGCTCATCTCATCATAATT	0.383																																					p.E970G		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A2909G						.						85.0	89.0	87.0					3																	121416461		2203	4300	6503	SO:0001583	missense	2804	exon13			CTCATCTCATCAT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.2894A>G	chr3.hg19:g.121416461T>C	ENSP00000341848:p.Glu965Gly	58.0	0.0		57.0	4.0	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.709|4.709	0.131878|0.131878	0.08981|0.08981	.|.	.|.	ENSG00000173230|ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235|ENST00000489400	T;T;T|.	0.26957|.	2.3;2.3;1.7|.	5.13|5.13	5.13|5.13	0.70059|0.70059	.|.	0.507164|.	0.19854|.	N|.	0.104568|.	T|T	0.54127|0.54127	0.1839|0.1839	L|L	0.56769|0.56769	1.78|1.78	0.22745|0.22745	N|N	0.998788|0.998788	P;B;D;D;P|.	0.89917|.	0.952;0.433;0.972;1.0;0.952|.	P;B;P;D;P|.	0.80764|.	0.461;0.084;0.691;0.994;0.599|.	T|T	0.49031|0.49031	-0.8981|-0.8981	10|5	0.38643|.	T|.	0.18|.	.|.	12.9343|12.9343	0.58305|0.58305	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	890;929;970;970;965|.	F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789|.	.;.;.;.;GOGB1_HUMAN|.	G|G	965;970;929;777|836	ENSP00000341848:E965G;ENSP00000377275:E970G;ENSP00000418231:E929G|.	ENSP00000341848:E965G|.	E|R	-|-	2|1	0|2	GOLGB1|GOLGB1	122899151|122899151	0.958000|0.958000	0.32768|0.32768	0.778000|0.778000	0.31720|0.31720	0.182000|0.182000	0.23217|0.23217	3.169000|3.169000	0.50809|0.50809	2.152000|2.152000	0.67230|0.67230	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.	.		0.383	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
ITGB5	3693	hgsc.bcm.edu	37	3	124578237	124578237	+	Silent	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:124578237G>A	ENST00000296181.4	-	3	509	c.213C>T	c.(211-213)gtC>gtT	p.V71V		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	71	PSI.				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)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		AGCCATTTTTGACAAGGTTTG	0.592																																					p.V71V		Atlas-SNP	.											.	ITGB5	66	.	0			c.C213T						.						81.0	75.0	77.0					3																	124578237		2203	4300	6503	SO:0001819	synonymous_variant	3693	exon3			ATTTTTGACAAGG	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"""Integrins"""	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.213C>T	chr3.hg19:g.124578237G>A		165.0	0.0		226.0	87.0	NM_002213	B0LPF8|B2RD70	Silent	SNP	ENST00000296181.4	hg19	CCDS3030.1																																																																																			.	.		0.592	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213	
RHO	6010	hgsc.bcm.edu	37	3	129251109	129251109	+	Silent	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:129251109C>T	ENST00000296271.3	+	3	640	c.546C>T	c.(544-546)ggC>ggT	p.G182G		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	182			G -> S (in RP4). {ECO:0000269|PubMed:1897520}.		G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)			breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	TCCCCGAGGGCCTGCAGTGCT	0.592																																					p.G182G	Esophageal Squamous(118;214 1623 30842 43234 46940)	Atlas-SNP	.											.	RHO	57	.	0			c.C546T						.						199.0	159.0	173.0					3																	129251109		2203	4300	6503	SO:0001819	synonymous_variant	6010	exon3			CGAGGGCCTGCAG	AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"""GPCR / Class A : Opsin receptors"""	10012	protein-coding gene	gene with protein product	"""opsin 2, rod pigment"""	180380	"""retinitis pigmentosa 4, autosomal dominant"""	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.546C>T	chr3.hg19:g.129251109C>T		172.0	0.0		203.0	92.0	NM_000539	Q16414|Q2M249	Silent	SNP	ENST00000296271.3	hg19	CCDS3063.1																																																																																			.	.		0.592	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135721003	135721003	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:135721003T>C	ENST00000264977.3	+	2	1280	c.663T>C	c.(661-663)gaT>gaC	p.D221D	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	221					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ATAAAATAGATAATTTTTCTT	0.333																																					p.D221D		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.T663C						.						43.0	48.0	46.0					3																	135721003		2184	4288	6472	SO:0001819	synonymous_variant	5523	exon2			AATAGATAATTTT	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.663T>C	chr3.hg19:g.135721003T>C		34.0	0.0		34.0	14.0	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	hg19	CCDS3087.1																																																																																			.	.		0.333	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
DZIP1L	199221	hgsc.bcm.edu	37	3	137790628	137790628	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:137790628A>G	ENST00000327532.2	-	12	1834	c.1472T>C	c.(1471-1473)cTg>cCg	p.L491P	DZIP1L_ENST00000488595.1_Intron|DZIP1L_ENST00000469243.1_Missense_Mutation_p.L491P	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	491					cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						CTGGACTCTCAGCAGGGATTC	0.522																																					p.L491P		Atlas-SNP	.											.	DZIP1L	88	.	0			c.T1472C						.						48.0	51.0	50.0					3																	137790628		2203	4300	6503	SO:0001583	missense	199221	exon13			ACTCTCAGCAGGG	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"""DAZ interacting protein 1-like"""			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1472T>C	chr3.hg19:g.137790628A>G	ENSP00000332148:p.Leu491Pro	83.0	0.0		89.0	4.0	NM_001170538	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	hg19	CCDS3096.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.134802	0.37728	.	.	ENSG00000158163	ENST00000327532;ENST00000469243;ENST00000536706	T;T	0.40756	1.14;1.02	4.86	4.86	0.63082	.	0.126271	0.34268	N	0.004102	T	0.61726	0.2370	M	0.71581	2.175	0.44816	D	0.997826	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.972	T	0.65664	-0.6113	10	0.72032	D	0.01	-14.5635	11.9778	0.53103	1.0:0.0:0.0:0.0	.	491;491	Q8IYY4-2;Q8IYY4	.;DZI1L_HUMAN	P	491	ENSP00000332148:L491P;ENSP00000419486:L491P	ENSP00000332148:L491P	L	-	2	0	DZIP1L	139273318	0.262000	0.24073	0.242000	0.24170	0.122000	0.20287	5.856000	0.69518	1.815000	0.52974	0.533000	0.62120	CTG	.	.		0.522	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543	
CEP70	80321	hgsc.bcm.edu	37	3	138227297	138227297	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:138227297T>C	ENST00000264982.3	-	12	1300	c.1034A>G	c.(1033-1035)gAc>gGc	p.D345G	CEP70_ENST00000481834.1_Missense_Mutation_p.D345G|CEP70_ENST00000542237.1_Missense_Mutation_p.D325G|CEP70_ENST00000484888.1_Missense_Mutation_p.D345G|CEP70_ENST00000489254.1_Missense_Mutation_p.D193G	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	345					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						GTATCTCTGGTCAATTAGGGC	0.363																																					p.D345G		Atlas-SNP	.											.	CEP70	51	.	0			c.A1034G						.						210.0	221.0	217.0					3																	138227297		2203	4300	6503	SO:0001583	missense	80321	exon12			CTCTGGTCAATTA	AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.1034A>G	chr3.hg19:g.138227297T>C	ENSP00000264982:p.Asp345Gly	191.0	0.0		256.0	11.0	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Missense_Mutation	SNP	ENST00000264982.3	hg19	CCDS3102.1	.	.	.	.	.	.	.	.	.	.	T	10.95	1.494594	0.26774	.	.	ENSG00000114107	ENST00000264982;ENST00000542237;ENST00000489254;ENST00000484888;ENST00000474781;ENST00000481834	T;T;T;T;T;T	0.45668	1.46;1.47;0.89;1.46;1.47;1.45	5.24	2.83	0.33086	.	0.530335	0.20801	N	0.085429	T	0.41073	0.1143	L	0.56769	1.78	0.22918	N	0.998561	B;P;P;P	0.49961	0.004;0.93;0.763;0.93	B;P;B;P	0.49829	0.006;0.623;0.382;0.623	T	0.18808	-1.0325	10	0.22109	T	0.4	-4.7183	5.1626	0.15070	0.0:0.0922:0.1824:0.7254	.	193;325;345;345	B7Z2D2;F5GZX8;Q8NHQ1-2;Q8NHQ1	.;.;.;CEP70_HUMAN	G	345;325;193;345;327;345	ENSP00000264982:D345G;ENSP00000444128:D325G;ENSP00000417821:D193G;ENSP00000419231:D345G;ENSP00000419833:D327G;ENSP00000417465:D345G	ENSP00000264982:D345G	D	-	2	0	CEP70	139709987	1.000000	0.71417	0.910000	0.35882	0.940000	0.58332	2.058000	0.41374	0.436000	0.26393	0.533000	0.62120	GAC	.	.		0.363	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491	
CPA3	1359	hgsc.bcm.edu	37	3	148599385	148599385	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:148599385T>C	ENST00000296046.3	+	7	705	c.653T>C	c.(652-654)tTc>tCc	p.F218S	RP11-680B3.2_ENST00000488190.1_RNA	NM_001870.2	NP_001861.2	P15088	CBPA3_HUMAN	carboxypeptidase A3 (mast cell)	218					angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			CTTCCTGTGTTCAATGTTGAT	0.343																																					p.F218S		Atlas-SNP	.											.	CPA3	75	.	0			c.T653C						.						129.0	121.0	124.0					3																	148599385		2203	4300	6503	SO:0001583	missense	1359	exon7			CTGTGTTCAATGT		CCDS3138.1	3q24	2012-02-10			ENSG00000163751	ENSG00000163751	3.4.17.1		2298	protein-coding gene	gene with protein product	"""mast cell carboxypeptidase A"", ""tissue carboxypeptidase A"""	114851					Standard	NM_001870		Approved		uc003ewm.3	P15088	OTTHUMG00000159526	ENST00000296046.3:c.653T>C	chr3.hg19:g.148599385T>C	ENSP00000296046:p.Phe218Ser	72.0	0.0		96.0	4.0	NM_001870	Q96E94	Missense_Mutation	SNP	ENST00000296046.3	hg19	CCDS3138.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.601936	0.87055	.	.	ENSG00000163751	ENST00000296046	T	0.11277	2.79	5.06	5.06	0.68205	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.25121	0.0610	L	0.60957	1.885	0.54753	D	0.999987	P	0.50272	0.933	P	0.58077	0.832	T	0.00477	-1.1716	10	0.66056	D	0.02	.	13.9293	0.63983	0.0:0.0:0.0:1.0	.	218	P15088	CBPA3_HUMAN	S	218	ENSP00000296046:F218S	ENSP00000296046:F218S	F	+	2	0	CPA3	150082075	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.856000	0.62932	2.111000	0.64477	0.533000	0.62120	TTC	.	.		0.343	CPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355974.1	NM_001870	
IGSF10	285313	hgsc.bcm.edu	37	3	151176327	151176327	+	Silent	SNP	G	G	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:151176327G>T	ENST00000282466.3	-	1	170	c.171C>A	c.(169-171)ccC>ccA	p.P57P		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	57					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GTTCCACATTGGGCGGGATGC	0.532																																					p.P57P		Atlas-SNP	.											.	IGSF10	279	.	0			c.C171A						.						120.0	98.0	106.0					3																	151176327		2203	4300	6503	SO:0001819	synonymous_variant	285313	exon1			CACATTGGGCGGG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.171C>A	chr3.hg19:g.151176327G>T		192.0	0.0		244.0	17.0	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	hg19	CCDS3160.1																																																																																			.	.		0.532	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
MME	4311	hgsc.bcm.edu	37	3	154802867	154802867	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:154802867A>G	ENST00000460393.1	+	3	300	c.180A>G	c.(178-180)tcA>tcG	p.S60S	MME_ENST00000493237.1_Silent_p.S60S|MME_ENST00000382989.3_Silent_p.S60S|MME_ENST00000360490.2_Silent_p.S60S|MME_ENST00000492661.1_Silent_p.S60S|MME_ENST00000462745.1_Silent_p.S60S	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	60					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	gcaagtcatcagactgcataa	0.239																																					p.S60S		Atlas-SNP	.											.	MME	133	.	0			c.A180G						.						36.0	38.0	38.0					3																	154802867		2182	4255	6437	SO:0001819	synonymous_variant	4311	exon3			GTCATCAGACTGC		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"""CD molecules"""	7154	protein-coding gene	gene with protein product	"""neutral endopeptidase"", ""enkephalinase"", ""neprilysin"""	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.180A>G	chr3.hg19:g.154802867A>G		177.0	0.0		196.0	8.0	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Silent	SNP	ENST00000460393.1	hg19	CCDS3172.1																																																																																			.	.		0.239	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902	
KCNAB1	7881	hgsc.bcm.edu	37	3	155861084	155861084	+	Intron	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:155861084T>C	ENST00000490337.1	+	1	339				KCNAB1_ENST00000389636.5_Intron|KCNAB1_ENST00000471742.1_Silent_p.P39P	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1						learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			AGACTCAGCCTCAGGCGGCCT	0.527																																					p.P39P		Atlas-SNP	.											.	KCNAB1	176	.	0			c.T117C						.						58.0	57.0	57.0					3																	155861084		2203	4300	6503	SO:0001627	intron_variant	7881	exon1			TCAGCCTCAGGCG	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"""Potassium channels"", ""Aldo-keto reductases"""	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.275+22409T>C	chr3.hg19:g.155861084T>C		110.0	0.0		169.0	7.0	NM_003471	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Silent	SNP	ENST00000490337.1	hg19	CCDS3174.1																																																																																			.	.		0.527	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471	
LXN	56925	hgsc.bcm.edu	37	3	158387376	158387376	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:158387376A>G	ENST00000264265.3	-	3	430	c.216T>C	c.(214-216)gcT>gcC	p.A72A	GFM1_ENST00000486715.1_Intron|GFM1_ENST00000478576.1_Intron|GFM1_ENST00000264263.5_Intron	NM_020169.3	NP_064554.3	Q9BS40	LXN_HUMAN	latexin	72	Cystatin-like fold 1. {ECO:0000250}.				detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|metalloendopeptidase inhibitor activity (GO:0008191)			breast(2)|endometrium(1)|kidney(2)	5			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			AAAGTACTTCAGCTGTGCAGT	0.348																																					p.A72A		Atlas-SNP	.											.	LXN	14	.	0			c.T216C						.						91.0	88.0	89.0					3																	158387376		2203	4300	6503	SO:0001819	synonymous_variant	56925	exon3			TACTTCAGCTGTG	AF087851	CCDS3183.1	3q25.32	2004-05-10			ENSG00000079257	ENSG00000079257			13347	protein-coding gene	gene with protein product		609305					Standard	NM_020169		Approved		uc003fch.3	Q9BS40	OTTHUMG00000158807	ENST00000264265.3:c.216T>C	chr3.hg19:g.158387376A>G		122.0	0.0		145.0	6.0	NM_020169	Q96PN2|Q9NQS6	Silent	SNP	ENST00000264265.3	hg19	CCDS3183.1	.	.	.	.	.	.	.	.	.	.	A	11.27	1.590659	0.28357	.	.	ENSG00000079257	ENST00000482640	.	.	.	5.14	-1.95	0.07548	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.0337	4.7898	0.13243	0.4195:0.0:0.1338:0.4467	.	.	.	.	R	3	.	.	X	-	1	0	LXN	159870070	0.360000	0.24964	0.999000	0.59377	0.989000	0.77384	-0.535000	0.06142	-0.001000	0.14495	0.477000	0.44152	TGA	.	.		0.348	LXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352284.1	NM_020169	
OTOL1	131149	hgsc.bcm.edu	37	3	161221375	161221375	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:161221375T>C	ENST00000327928.4	+	4	1079	c.1079T>C	c.(1078-1080)aTc>aCc	p.I360T		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	360	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						AACATCCCCATCAAATTTGAA	0.463																																					p.I360T		Atlas-SNP	.											.	OTOL1	63	.	0			c.T1079C						.						55.0	50.0	51.0					3																	161221375		1869	4098	5967	SO:0001583	missense	131149	exon4			TCCCCATCAAATT		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"""C1q and tumor necrosis factor related protein 15"""		"""otolin 1 homolog (zebrafish)"""			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.1079T>C	chr3.hg19:g.161221375T>C	ENSP00000330808:p.Ile360Thr	64.0	0.0		121.0	5.0	NM_001080440		Missense_Mutation	SNP	ENST00000327928.4	hg19	CCDS46948.1	.	.	.	.	.	.	.	.	.	.	T	11.19	1.564280	0.27915	.	.	ENSG00000182447	ENST00000327928	T	0.78595	-1.19	5.23	5.23	0.72850	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.049996	0.85682	D	0.000000	D	0.90031	0.6887	M	0.92970	3.365	0.40943	D	0.984485	D	0.65815	0.995	D	0.77557	0.99	D	0.91594	0.5289	10	0.44086	T	0.13	.	13.9732	0.64255	0.0:0.0:0.0:1.0	.	360	A6NHN0	OTOL1_HUMAN	T	360	ENSP00000330808:I360T	ENSP00000330808:I360T	I	+	2	0	OTOL1	162704069	1.000000	0.71417	0.120000	0.21714	0.048000	0.14542	7.748000	0.85085	1.966000	0.57179	0.455000	0.32223	ATC	.	.		0.463	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440	
SI	6476	hgsc.bcm.edu	37	3	164735840	164735840	+	Silent	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:164735840G>A	ENST00000264382.3	-	29	3500	c.3438C>T	c.(3436-3438)tcC>tcT	p.S1146S		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1146	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	GAAATCCATAGGAATTAAGTT	0.299										HNSCC(35;0.089)																											p.S1146S		Atlas-SNP	.											.	SI	500	.	0			c.C3438T						.						86.0	86.0	86.0					3																	164735840		2203	4300	6503	SO:0001819	synonymous_variant	6476	exon29			TCCATAGGAATTA	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.3438C>T	chr3.hg19:g.164735840G>A		76.0	0.0		99.0	4.0	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	hg19	CCDS3196.1																																																																																			.	.		0.299	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
LRRC31	79782	hgsc.bcm.edu	37	3	169566057	169566057	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:169566057A>G	ENST00000316428.5	-	8	1235	c.1178T>C	c.(1177-1179)cTc>cCc	p.L393P	LRRC31_ENST00000523069.1_Missense_Mutation_p.L393P|LRRC31_ENST00000264676.5_Missense_Mutation_p.L337P	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	393										cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			CAGAGCAGAGAGGTGAACAGA	0.413																																					p.L393P		Atlas-SNP	.											.	LRRC31	66	.	0			c.T1178C						.						65.0	62.0	63.0					3																	169566057		1936	4139	6075	SO:0001583	missense	79782	exon8			GCAGAGAGGTGAA	AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248			26261	protein-coding gene	gene with protein product						12975309	Standard	NM_001277127		Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.1178T>C	chr3.hg19:g.169566057A>G	ENSP00000325978:p.Leu393Pro	72.0	0.0		100.0	5.0	NM_024727	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	Missense_Mutation	SNP	ENST00000316428.5	hg19	CCDS43167.1	.	.	.	.	.	.	.	.	.	.	A	10.35	1.326882	0.24080	.	.	ENSG00000114248	ENST00000316428;ENST00000264676;ENST00000523069	T;T;T	0.57907	0.37;0.37;0.37	4.61	4.61	0.57282	.	0.000000	0.64402	D	0.000002	T	0.72342	0.3448	M	0.80982	2.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.991	T	0.74420	-0.3671	10	0.41790	T	0.15	-1.7842	14.0296	0.64606	1.0:0.0:0.0:0.0	.	337;393	Q6UY01-2;Q6UY01	.;LRC31_HUMAN	P	393;337;393	ENSP00000325978:L393P;ENSP00000264676:L337P;ENSP00000429145:L393P	ENSP00000264676:L337P	L	-	2	0	LRRC31	171048751	1.000000	0.71417	0.052000	0.19188	0.010000	0.07245	5.814000	0.69208	1.707000	0.51288	0.533000	0.62120	CTC	.	.		0.413	LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378699.1	NM_024727	
NAALADL2	254827	hgsc.bcm.edu	37	3	175181236	175181236	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:175181236A>G	ENST00000454872.1	+	7	1410	c.1282A>G	c.(1282-1284)Aca>Gca	p.T428A	NAALADL2_ENST00000473253.1_3'UTR	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	428						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		AAAATTGAAAACAGTTACTAA	0.284																																					p.T428A		Atlas-SNP	.											.	NAALADL2	86	.	0			c.A1282G						.						75.0	75.0	75.0					3																	175181236		1827	4079	5906	SO:0001583	missense	254827	exon7			TTGAAAACAGTTA		CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase II-type non-peptidase homologue"""	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.1282A>G	chr3.hg19:g.175181236A>G	ENSP00000404705:p.Thr428Ala	46.0	0.0		61.0	4.0	NM_207015	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Missense_Mutation	SNP	ENST00000454872.1	hg19	CCDS46960.1	.	.	.	.	.	.	.	.	.	.	A	2.054	-0.417083	0.04766	.	.	ENSG00000177694	ENST00000454872	T	0.44083	0.93	5.23	2.84	0.33178	.	0.222920	0.40064	N	0.001200	T	0.28267	0.0698	L	0.32530	0.975	0.20196	N	0.999926	B	0.13145	0.007	B	0.09377	0.004	T	0.15780	-1.0425	10	0.34782	T	0.22	-6.3495	7.6056	0.28100	0.7624:0.0:0.2375:0.0	.	428	Q58DX5	NADL2_HUMAN	A	428	ENSP00000404705:T428A	ENSP00000404705:T428A	T	+	1	0	NAALADL2	176663930	1.000000	0.71417	0.085000	0.20634	0.056000	0.15407	2.002000	0.40835	0.397000	0.25310	-0.371000	0.07208	ACA	.	.		0.284	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015	
HRG	3273	hgsc.bcm.edu	37	3	186390578	186390578	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:186390578A>G	ENST00000232003.4	+	5	641	c.561A>G	c.(559-561)agA>agG	p.R187R		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	187	Cystatin 2.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		TGTTCTAGAGAGGAGGGGAAG	0.413																																					p.R187R		Atlas-SNP	.											.	HRG	81	.	0			c.A561G						.						92.0	89.0	90.0					3																	186390578		2203	4300	6503	SO:0001819	synonymous_variant	3273	exon5			CTAGAGAGGAGGG		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"""histidine-proline rich glycoprotein"", ""thrombophilia due to elevated HRG"""	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.561A>G	chr3.hg19:g.186390578A>G		84.0	0.0		94.0	5.0	NM_000412	B9EK35|D3DNU7	Silent	SNP	ENST00000232003.4	hg19	CCDS3280.1																																																																																			.	.		0.413	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412	
RFC4	5984	hgsc.bcm.edu	37	3	186507957	186507957	+	Nonsense_Mutation	SNP	T	T	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:186507957T>A	ENST00000392481.2	-	10	1251	c.970A>T	c.(970-972)Aag>Tag	p.K324*	RFC4_ENST00000296273.2_Nonsense_Mutation_p.K324*|SNORA63_ENST00000363450.1_RNA|SNORA4_ENST00000584302.1_RNA|RFC4_ENST00000433496.1_Nonsense_Mutation_p.K297*	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	324					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)			breast(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		ATAATAGACTTCTGTTTATCA	0.338																																					p.K324X		Atlas-SNP	.											.	RFC4	54	.	0			c.A970T						.						106.0	103.0	104.0					3																	186507957		2203	4300	6503	SO:0001587	stop_gained	5984	exon10			TAGACTTCTGTTT		CCDS3283.1	3q27	2010-04-21	2002-08-29		ENSG00000163918	ENSG00000163918		"""ATPases / AAA-type"""	9972	protein-coding gene	gene with protein product	"""A1 37 kDa subunit"", ""activator 1 37 kDa subunit"", ""RFC 37 kDa subunit"""	102577	"""replication factor C (activator 1) 4 (37kD)"""			7774928	Standard	NM_181573		Approved	A1, RFC37	uc003fqz.3	P35249	OTTHUMG00000156515	ENST00000392481.2:c.970A>T	chr3.hg19:g.186507957T>A	ENSP00000376272:p.Lys324*	148.0	0.0		160.0	61.0	NM_181573	B4DM41|D3DNV2|Q6FHX7	Nonsense_Mutation	SNP	ENST00000392481.2	hg19	CCDS3283.1	.	.	.	.	.	.	.	.	.	.	T	38	6.877691	0.97904	.	.	ENSG00000163918	ENST00000433496;ENST00000392481;ENST00000296273;ENST00000417876	.	.	.	5.75	4.55	0.56014	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.566	0.45173	0.1436:0.0:0.0:0.8564	.	.	.	.	X	297;324;324;99	.	ENSP00000296273:K324X	K	-	1	0	RFC4	187990651	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.705000	0.68355	2.191000	0.70037	0.533000	0.62120	AAG	.	.		0.338	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916	
ATP13A5	344905	hgsc.bcm.edu	37	3	193029641	193029641	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:193029641T>C	ENST00000342358.4	-	20	2526	c.2409A>G	c.(2407-2409)caA>caG	p.Q803Q	ATP13A5_ENST00000495496.1_5'UTR|ATP13A5-AS1_ENST00000414634.1_RNA	NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	803						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		GAAATATCACTTGGTATGATT	0.413																																					p.Q803Q		Atlas-SNP	.											.	ATP13A5	171	.	0			c.A2409G						.						128.0	116.0	120.0					3																	193029641		2203	4300	6503	SO:0001819	synonymous_variant	344905	exon20			TATCACTTGGTAT	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"""ATPases / P-type"""	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.2409A>G	chr3.hg19:g.193029641T>C		80.0	0.0		98.0	4.0	NM_198505	Q6UWS4|Q6ZWL0	Silent	SNP	ENST00000342358.4	hg19	CCDS33914.1																																																																																			.	.		0.413	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
MUC4	4585	hgsc.bcm.edu	37	3	195498669	195498669	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:195498669T>C	ENST00000346145.4	-	4	427	c.388A>G	c.(388-390)Atc>Gtc	p.I130V	MUC4_ENST00000349607.4_Missense_Mutation_p.I79V|MUC4_ENST00000475231.1_Missense_Mutation_p.I4366V|MUC4_ENST00000463781.3_Missense_Mutation_p.I4366V	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1123					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)		GGGAAGATGATCTGGCCATTG	0.567																																					p.I4366V		Atlas-SNP	.											.	MUC4	1505	.	0			c.A13096G						.						162.0	144.0	150.0					3																	195498669		2203	4300	6503	SO:0001583	missense	4585	exon5			AGATGATCTGGCC	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	ENST00000346145.4:c.388A>G	chr3.hg19:g.195498669T>C	ENSP00000304207:p.Ile130Val	77.0	0.0		87.0	5.0	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	ENST00000346145.4	hg19	CCDS3310.1	.	.	.	.	.	.	.	.	.	.	.	11.15	1.552544	0.27739	.	.	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.57752	0.38;0.73;0.54;0.43	5.5	5.5	0.81552	.	0.000000	0.53938	D	0.000050	T	0.67487	0.2898	M	0.70595	2.14	0.26241	N	0.978876	D;P;P;P	0.53885	0.963;0.816;0.745;0.745	P;B;B;B	0.62089	0.898;0.288;0.27;0.27	T	0.62072	-0.6931	10	0.33141	T	0.24	-30.229	13.4362	0.61086	0.0:0.0:0.0:1.0	.	4238;1123;79;130	E7ESK3;Q99102;Q99102-12;Q99102-13	.;MUC4_HUMAN;.;.	V	79;130;4366;4366;1092	ENSP00000338109:I79V;ENSP00000304207:I130V;ENSP00000417498:I4366V;ENSP00000420243:I4366V	ENSP00000304207:I130V	I	-	1	0	MUC4	196984303	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	2.739000	0.47409	2.122000	0.65172	0.458000	0.33432	ATC	.	.		0.567	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
TNIP2	79155	hgsc.bcm.edu	37	4	2749657	2749657	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:2749657T>C	ENST00000315423.7	-	2	378	c.292A>G	c.(292-294)Act>Gct	p.T98A	TNIP2_ENST00000510267.1_5'UTR|TNIP2_ENST00000505186.1_5'Flank|TNIP2_ENST00000503235.1_Missense_Mutation_p.T98A	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2											breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		AGTCGCTCAGTCAGCCTCTCA	0.473																																					p.T98A		Atlas-SNP	.											.	TNIP2	28	.	0			c.A292G						.						31.0	33.0	32.0					4																	2749657		2203	4300	6503	SO:0001583	missense	79155	exon2			GCTCAGTCAGCCT	BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.292A>G	chr4.hg19:g.2749657T>C	ENSP00000321203:p.Thr98Ala	69.0	0.0		95.0	4.0	NM_024309		Missense_Mutation	SNP	ENST00000315423.7	hg19	CCDS3362.1	.	.	.	.	.	.	.	.	.	.	t	10.11	1.260152	0.23051	.	.	ENSG00000168884	ENST00000315423;ENST00000503235	T;T	0.23348	1.91;1.91	3.62	0.807	0.18714	.	0.834029	0.10437	N	0.674834	T	0.17746	0.0426	L	0.43152	1.355	0.09310	N	0.999998	B;B	0.22003	0.048;0.063	B;B	0.22386	0.036;0.039	T	0.36866	-0.9730	10	0.15952	T	0.53	-6.1241	4.5043	0.11879	0.3937:0.0:0.1454:0.4608	.	98;98	D6RGJ2;Q8NFZ5	.;TNIP2_HUMAN	A	98	ENSP00000321203:T98A;ENSP00000426314:T98A	ENSP00000321203:T98A	T	-	1	0	TNIP2	2719455	0.938000	0.31826	0.000000	0.03702	0.956000	0.61745	2.576000	0.46033	0.053000	0.16036	0.449000	0.29647	ACT	.	.		0.473	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309	
EVC2	132884	hgsc.bcm.edu	37	4	5664909	5664909	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:5664909T>C	ENST00000344408.5	-	9	1123	c.1070A>G	c.(1069-1071)gAc>gGc	p.D357G	EVC2_ENST00000310917.2_Missense_Mutation_p.D277G|EVC2_ENST00000344938.1_Missense_Mutation_p.D357G	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	357					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						AAGGGAAAGGTCCTCATTCAC	0.458																																					p.D357G		Atlas-SNP	.											.	EVC2	202	.	0			c.A1070G						.						142.0	136.0	138.0					4																	5664909		2203	4300	6503	SO:0001583	missense	132884	exon9			GAAAGGTCCTCAT	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1070A>G	chr4.hg19:g.5664909T>C	ENSP00000342144:p.Asp357Gly	84.0	0.0		87.0	4.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	T	17.76	3.468891	0.63625	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.79247	-1.25;-1.25;-1.25	5.27	4.09	0.47781	.	0.406333	0.24818	N	0.035349	D	0.83298	0.5224	M	0.62723	1.935	0.32763	N	0.504886	D	0.76494	0.999	D	0.72982	0.979	D	0.85700	0.1312	10	0.72032	D	0.01	-21.1828	7.2396	0.26090	0.0:0.0986:0.0:0.9014	.	357	Q86UK5	LBN_HUMAN	G	357;277;357	ENSP00000339954:D357G;ENSP00000311683:D277G;ENSP00000342144:D357G	ENSP00000311683:D277G	D	-	2	0	EVC2	5715810	0.997000	0.39634	0.753000	0.31225	0.787000	0.44495	2.373000	0.44266	2.103000	0.63969	0.533000	0.62120	GAC	.	.		0.458	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
SH3TC1	54436	hgsc.bcm.edu	37	4	8230126	8230126	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:8230126A>G	ENST00000245105.3	+	12	2772	c.2705A>G	c.(2704-2706)cAg>cGg	p.Q902R	SH3TC1_ENST00000539824.1_Missense_Mutation_p.Q826R	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	902										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						CAAAGGAACCAGGCAGTGGGG	0.701																																					p.Q902R	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.A2705G						.						36.0	43.0	41.0					4																	8230126		2202	4297	6499	SO:0001583	missense	54436	exon12			GGAACCAGGCAGT	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"""Tetratricopeptide (TTC) repeat domain containing"""	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.2705A>G	chr4.hg19:g.8230126A>G	ENSP00000245105:p.Gln902Arg	86.0	0.0		75.0	5.0	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	hg19	CCDS3399.1	.	.	.	.	.	.	.	.	.	.	A	13.10	2.136918	0.37728	.	.	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265	T;T	0.62788	-0.0;-0.0	4.63	4.63	0.57726	Tetratricopeptide-like helical (1);	0.212960	0.42682	D	0.000673	T	0.68485	0.3006	M	0.78049	2.395	0.31092	N	0.710711	P	0.43287	0.802	P	0.45343	0.477	T	0.76239	-0.3032	10	0.66056	D	0.02	-29.9447	14.0349	0.64638	1.0:0.0:0.0:0.0	.	902	Q8TE82	S3TC1_HUMAN	R	640;902;826;731	ENSP00000245105:Q902R;ENSP00000441045:Q826R	ENSP00000245105:Q902R	Q	+	2	0	SH3TC1	8281026	1.000000	0.71417	0.996000	0.52242	0.235000	0.25334	3.114000	0.50383	1.716000	0.51395	0.459000	0.35465	CAG	.	.		0.701	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
SH3TC1	54436	hgsc.bcm.edu	37	4	8230236	8230236	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:8230236G>C	ENST00000245105.3	+	12	2882	c.2815G>C	c.(2815-2817)Ggg>Cgg	p.G939R	SH3TC1_ENST00000539824.1_Missense_Mutation_p.G863R	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	939										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GCTGCCCCTTGGGGAGTGTGG	0.706																																					p.G939R	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.G2815C						.						20.0	23.0	22.0					4																	8230236		2197	4294	6491	SO:0001583	missense	54436	exon12			CCCCTTGGGGAGT	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"""Tetratricopeptide (TTC) repeat domain containing"""	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.2815G>C	chr4.hg19:g.8230236G>C	ENSP00000245105:p.Gly939Arg	164.0	0.0		141.0	6.0	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	hg19	CCDS3399.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.658883	0.00772	.	.	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265	T;T	0.67865	-0.29;-0.29	4.06	-3.09	0.05331	Tetratricopeptide-like helical (1);	1.841800	0.02336	N	0.074412	T	0.41050	0.1142	N	0.12746	0.255	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.14868	-1.0457	10	0.11794	T	0.64	-9.1413	1.8813	0.03228	0.4062:0.2187:0.2643:0.1108	.	939	Q8TE82	S3TC1_HUMAN	R	677;939;863;768	ENSP00000245105:G939R;ENSP00000441045:G863R	ENSP00000245105:G939R	G	+	1	0	SH3TC1	8281136	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.576000	0.05854	-0.557000	0.06126	-1.459000	0.01027	GGG	.	.		0.706	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
BOD1L1	259282	hgsc.bcm.edu	37	4	13582665	13582665	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:13582665T>C	ENST00000040738.5	-	21	8817	c.8682A>G	c.(8680-8682)aaA>aaG	p.K2894K		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2894						nucleus (GO:0005634)	DNA binding (GO:0003677)										CAGTATCTGTTTTGGAGTCGT	0.308																																					p.K2894K		Atlas-SNP	.											.	.	.	.	0			c.A8682G						.						80.0	78.0	78.0					4																	13582665		2201	4295	6496	SO:0001819	synonymous_variant	259282	exon21			ATCTGTTTTGGAG	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.8682A>G	chr4.hg19:g.13582665T>C		78.0	0.0		83.0	4.0	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Silent	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	1.524	-0.546022	0.04024	.	.	ENSG00000038219	ENST00000507943	T	0.52526	0.66	5.52	3.03	0.35002	.	0.000000	0.64402	D	0.000014	T	0.50803	0.1637	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45644	-0.9247	7	0.54805	T	0.06	-9.1104	5.7277	0.18022	0.1489:0.0797:0.0:0.7714	.	.	.	.	R	3	ENSP00000425492:K3R	ENSP00000425492:K3R	K	-	2	0	BOD1L	13191763	0.980000	0.34600	0.993000	0.49108	0.150000	0.21749	1.134000	0.31442	0.368000	0.24481	-0.336000	0.08194	AAA	.	.		0.308	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
PI4K2B	55300	hgsc.bcm.edu	37	4	25254053	25254053	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:25254053T>C	ENST00000264864.6	+	2	568	c.379T>C	c.(379-381)Tct>Cct	p.S127P	PI4K2B_ENST00000512921.1_Missense_Mutation_p.S31P	NM_018323.3	NP_060793.2	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta	127					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|skin(3)	15		Breast(46;0.173)				AGAAAGAATCTCTCAAGGTTC	0.363																																					p.S127P		Atlas-SNP	.											.	PI4K2B	42	.	0			c.T379C						.						110.0	117.0	115.0					4																	25254053		2203	4300	6503	SO:0001583	missense	55300	exon2			AGAATCTCTCAAG	AK001967	CCDS3433.1	4p15.31	2009-05-07			ENSG00000038210	ENSG00000038210			18215	protein-coding gene	gene with protein product		612101				11923287	Standard	NM_018323		Approved	PI4KIIB, FLJ11105, PIK42B	uc003grk.2	Q8TCG2	OTTHUMG00000128564	ENST00000264864.6:c.379T>C	chr4.hg19:g.25254053T>C	ENSP00000264864:p.Ser127Pro	86.0	0.0		113.0	6.0	NM_018323	Q9NUW2	Missense_Mutation	SNP	ENST00000264864.6	hg19	CCDS3433.1	.	.	.	.	.	.	.	.	.	.	T	14.37	2.516251	0.44763	.	.	ENSG00000038210	ENST00000512921;ENST00000264864;ENST00000537420	T	0.48201	0.82	5.43	2.93	0.34026	.	0.102171	0.64402	D	0.000001	T	0.37652	0.1011	L	0.50333	1.59	0.51767	D	0.999938	B	0.10296	0.003	B	0.13407	0.009	T	0.11767	-1.0574	10	0.31617	T	0.26	-4.7481	7.2615	0.26205	0.1296:0.0708:0.0:0.7997	.	127	Q8TCG2	P4K2B_HUMAN	P	31;127;96	ENSP00000264864:S127P	ENSP00000264864:S127P	S	+	1	0	PI4K2B	24863151	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	4.184000	0.58323	0.345000	0.23873	0.383000	0.25322	TCT	.	.		0.363	PI4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250415.1	NM_018323	
N4BP2	55728	hgsc.bcm.edu	37	4	40121838	40121838	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:40121838A>G	ENST00000261435.6	+	9	2523	c.2107A>G	c.(2107-2109)Ata>Gta	p.I703V		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	703					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						AAACGAGCAAATAGAAATGGT	0.368																																					p.I703V		Atlas-SNP	.											.	N4BP2	166	.	0			c.A2107G						.						91.0	98.0	96.0					4																	40121838		2203	4300	6503	SO:0001583	missense	55728	exon9			GAGCAAATAGAAA	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.2107A>G	chr4.hg19:g.40121838A>G	ENSP00000261435:p.Ile703Val	48.0	0.0		50.0	4.0	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	hg19	CCDS3457.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0|0	-2.687186|-2.687186	0.00100|0.00100	.|.	.|.	ENSG00000078177|ENSG00000078177	ENST00000261435;ENST00000381804|ENST00000513269	T|.	0.15603|.	2.41|.	5.19|5.19	2.35|2.35	0.29111|0.29111	.|.	1.190420|.	0.06024|.	N|.	0.651874|.	T|T	0.06962|0.06962	0.0177|0.0177	N|N	0.00436|0.00436	-1.5|-1.5	0.09310|0.09310	N|N	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.36040|0.36040	-0.9764|-0.9764	10|5	0.02654|.	T|.	1|.	-1.4195|-1.4195	3.628|3.628	0.08120|0.08120	0.0837:0.1441:0.4759:0.2963|0.0837:0.1441:0.4759:0.2963	.|.	703;703|.	Q86UW6-2;Q86UW6|.	.;N4BP2_HUMAN|.	V|S	703;623|349	ENSP00000261435:I703V|.	ENSP00000261435:I703V|.	I|N	+|+	1|2	0|0	N4BP2|N4BP2	39798233|39798233	0.000000|0.000000	0.05858|0.05858	0.126000|0.126000	0.21872|0.21872	0.037000|0.037000	0.13140|0.13140	0.156000|0.156000	0.16382|0.16382	0.151000|0.151000	0.19162|0.19162	-0.375000|-0.375000	0.07067|0.07067	ATA|AAT	.	.		0.368	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
CWH43	80157	hgsc.bcm.edu	37	4	49063874	49063874	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:49063874T>A	ENST00000226432.4	+	16	2250	c.2067T>A	c.(2065-2067)caT>caA	p.H689Q	CWH43_ENST00000513409.1_Missense_Mutation_p.H662Q	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	689			H -> N (in dbSNP:rs1051447). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						ACAACCATCATTTTCATATGA	0.249																																					p.H689Q		Atlas-SNP	.											.	CWH43	101	.	0			c.T2067A						.						28.0	26.0	27.0					4																	49063874		2183	4238	6421	SO:0001583	missense	80157	exon16			CCATCATTTTCAT		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.2067T>A	chr4.hg19:g.49063874T>A	ENSP00000226432:p.His689Gln	92.0	0.0		157.0	7.0	NM_025087	B2RPD7	Missense_Mutation	SNP	ENST00000226432.4	hg19	CCDS3486.1	.	.	.	.	.	.	.	.	.	.	T	13.02	2.112985	0.37242	.	.	ENSG00000109182	ENST00000226432;ENST00000513409	T;T	0.41758	1.58;0.99	4.59	2.18	0.27775	.	0.209202	0.34025	N	0.004323	T	0.40909	0.1136	L	0.43152	1.355	0.36487	D	0.868185	D	0.56746	0.977	P	0.53593	0.73	T	0.41610	-0.9499	9	.	.	.	.	6.0925	0.20003	0.0:0.2:0.0:0.8	.	689	Q9H720	PG2IP_HUMAN	Q	689;662	ENSP00000226432:H689Q;ENSP00000422802:H662Q	.	H	+	3	2	CWH43	48758631	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	1.024000	0.30077	0.520000	0.28426	-0.379000	0.06801	CAT	.	.		0.249	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087	
TMPRSS11B	132724	hgsc.bcm.edu	37	4	69100333	69100333	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:69100333G>A	ENST00000332644.5	-	5	478	c.317C>T	c.(316-318)gCc>gTc	p.A106V		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	106	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.					extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						TGAACCATTGGCATTAGGCCT	0.338																																					p.A106V		Atlas-SNP	.											.	TMPRSS11B	66	.	0			c.C317T						.						82.0	76.0	78.0					4																	69100333		2203	4300	6503	SO:0001583	missense	132724	exon5			CCATTGGCATTAG	BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"""Serine peptidases / Transmembrane"""	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.317C>T	chr4.hg19:g.69100333G>A	ENSP00000330475:p.Ala106Val	112.0	0.0		134.0	6.0	NM_182502	A8K4D9	Missense_Mutation	SNP	ENST00000332644.5	hg19	CCDS3521.1	.	.	.	.	.	.	.	.	.	.	G	9.583	1.124050	0.20959	.	.	ENSG00000185873	ENST00000332644	T	0.33654	1.4	5.02	-0.132	0.13489	SEA (2);	1.431730	0.04911	N	0.453172	T	0.17789	0.0427	N	0.08118	0	0.09310	N	1	B	0.24483	0.104	B	0.25614	0.062	T	0.16867	-1.0388	10	0.33141	T	0.24	.	2.0873	0.03649	0.1695:0.2848:0.3995:0.1462	.	106	Q86T26	TM11B_HUMAN	V	106	ENSP00000330475:A106V	ENSP00000330475:A106V	A	-	2	0	TMPRSS11B	68782928	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.709000	0.05030	-0.303000	0.08856	0.655000	0.94253	GCC	.	.		0.338	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502	
ART3	419	hgsc.bcm.edu	37	4	77003227	77003227	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:77003227A>G	ENST00000355810.4	+	3	439	c.320A>G	c.(319-321)gAg>gGg	p.E107G	ART3_ENST00000513494.1_3'UTR|ART3_ENST00000349321.3_Missense_Mutation_p.E107G|ART3_ENST00000341029.5_Missense_Mutation_p.E107G	NM_001130016.2	NP_001123488.1	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3	107					protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|stomach(1)	16			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GAAGCTCAAGAGCAAACTCCC	0.423																																					p.E107G		Atlas-SNP	.											.	ART3	34	.	0			c.A320G						.						75.0	75.0	75.0					4																	77003227		2203	4300	6503	SO:0001583	missense	419	exon3			CTCAAGAGCAAAC	X95827	CCDS3575.1, CCDS47079.1, CCDS47080.1	4q21.1	2008-05-15			ENSG00000156219	ENSG00000156219			725	protein-coding gene	gene with protein product		603086				9119374	Standard	NM_001130017		Approved		uc003hjo.3	Q13508	OTTHUMG00000130110	ENST00000355810.4:c.320A>G	chr4.hg19:g.77003227A>G	ENSP00000348064:p.Glu107Gly	52.0	0.0		78.0	4.0	NM_001130017	Q53XW3|Q6FHT7|Q8WVJ7|Q93069|Q96HL1	Missense_Mutation	SNP	ENST00000355810.4	hg19	CCDS47079.1	.	.	.	.	.	.	.	.	.	.	A	11.88	1.769559	0.31320	.	.	ENSG00000156219	ENST00000513353;ENST00000341029;ENST00000513122;ENST00000504914;ENST00000355810;ENST00000349321;ENST00000510423	T;T;T;T;T;T;T	0.49720	0.77;3.18;2.69;1.45;3.18;3.18;2.46	6.04	3.32	0.38043	.	0.762936	0.12436	N	0.469141	T	0.43787	0.1263	M	0.63428	1.95	0.09310	N	0.999997	B;B;B;B;B;B;B	0.30914	0.016;0.039;0.3;0.004;0.131;0.052;0.002	B;B;B;B;B;B;B	0.27262	0.03;0.065;0.065;0.01;0.078;0.033;0.009	T	0.38824	-0.9643	10	0.56958	D	0.05	-20.0283	9.4093	0.38482	0.8323:0.0:0.1677:0.0	.	77;107;107;107;107;107;107	D6RBN3;E7ESB3;B4DHX3;E7ER42;Q13508;Q13508-3;Q13508-2	.;.;.;.;NAR3_HUMAN;.;.	G	107	ENSP00000421345:E107G;ENSP00000343843:E107G;ENSP00000422287:E107G;ENSP00000421431:E107G;ENSP00000348064:E107G;ENSP00000304313:E107G;ENSP00000425327:E107G	ENSP00000343843:E107G	E	+	2	0	ART3	77222251	0.656000	0.27385	0.696000	0.30242	0.576000	0.36127	0.833000	0.27504	1.103000	0.41568	0.460000	0.39030	GAG	.	.		0.423	ART3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252416.2	NM_001179	
FRAS1	80144	hgsc.bcm.edu	37	4	79239975	79239975	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:79239975T>C	ENST00000325942.6	+	18	2412	c.1972T>C	c.(1972-1974)Tcc>Ccc	p.S658P	FRAS1_ENST00000264899.6_Missense_Mutation_p.S658P|FRAS1_ENST00000264895.6_Missense_Mutation_p.S658P	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	658					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CTGTCACTCCTCCTGCCTGGC	0.458																																					p.S658P		Atlas-SNP	.											.	FRAS1	779	.	0			c.T1972C						.						92.0	87.0	89.0					4																	79239975		1942	4140	6082	SO:0001583	missense	80144	exon18			CACTCCTCCTGCC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.1972T>C	chr4.hg19:g.79239975T>C	ENSP00000326330:p.Ser658Pro	97.0	0.0		126.0	6.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.73|13.73	2.325055|2.325055	0.41197|0.41197	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000508900|ENST00000325942;ENST00000264895;ENST00000264899	.|T;T;T	.|0.76578	.|-1.03;-1.03;-1.03	5.93|5.93	4.73|4.73	0.59995|0.59995	.|Growth factor, receptor (1);	.|0.121046	.|0.56097	.|D	.|0.000023	D|D	0.87172|0.87172	0.6111|0.6111	M|M	0.82716|0.82716	2.605|2.605	0.53005|0.53005	D|D	0.999969|0.999969	.|D;D;D;D	.|0.67145	.|0.996;0.996;0.992;0.977	.|D;D;D;P	.|0.68039	.|0.955;0.955;0.921;0.905	D|D	0.88003|0.88003	0.2757|0.2757	5|10	.|0.87932	.|D	.|0	.|.	11.4759|11.4759	0.50297|0.50297	0.135:0.0:0.0:0.8649|0.135:0.0:0.0:0.8649	.|.	.|658;658;658;658	.|E9PHH6;Q86XX4;E7EWM9;A2RRR8	.|.;FRAS1_HUMAN;.;.	P|P	500|658	.|ENSP00000326330:S658P;ENSP00000264895:S658P;ENSP00000264899:S658P	.|ENSP00000264895:S658P	L|S	+|+	2|1	0|0	FRAS1|FRAS1	79458999|79458999	0.993000|0.993000	0.37304|0.37304	0.706000|0.706000	0.30403|0.30403	0.023000|0.023000	0.10783|0.10783	3.321000|3.321000	0.51999|0.51999	1.027000|1.027000	0.39758|0.39758	0.533000|0.533000	0.62120|0.62120	CTC|TCC	.	.		0.458	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
HNRNPDL	9987	hgsc.bcm.edu	37	4	83352029	83352029	+	5'Flank	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:83352029A>G	ENST00000295470.5	-	0	0				HNRNPDL_ENST00000349655.4_5'Flank|HNRNPDL_ENST00000514511.1_5'Flank|ENOPH1_ENST00000509635.1_5'UTR|HNRNPDL_ENST00000502762.1_5'Flank|ENOPH1_ENST00000273920.3_Missense_Mutation_p.D16G|HNRNPDL_ENST00000602300.1_5'Flank	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like						regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										ATCCTGTTAGATATCGAAGGT	0.542																																					p.D16G		Atlas-SNP	.											.	ENOPH1	26	.	0			c.A47G						.						90.0	77.0	82.0					4																	83352029		2203	4300	6503	SO:0001631	upstream_gene_variant	58478	exon1			TGTTAGATATCGA	D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"""RNA binding motif (RRM) containing"""	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299		chr4.hg19:g.83352029A>G	Exception_encountered	73.0	0.0		85.0	4.0	NM_021204	Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Missense_Mutation	SNP	ENST00000295470.5	hg19	CCDS3593.1	.	.	.	.	.	.	.	.	.	.	a	28.3	4.906413	0.92107	.	.	ENSG00000145293	ENST00000273920;ENST00000456931	T	0.54866	0.55	5.57	5.57	0.84162	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);2,3-diketo-5-methylthio-1-phosphopentane phosphatase (1);	0.000000	0.85682	D	0.000000	T	0.80586	0.4651	H	0.96208	3.785	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	D	0.86855	0.2026	10	0.87932	D	0	-19.5014	14.5624	0.68151	1.0:0.0:0.0:0.0	.	16	Q9UHY7	ENOPH_HUMAN	G	16	ENSP00000273920:D16G	ENSP00000273920:D16G	D	+	2	0	ENOPH1	83571053	1.000000	0.71417	1.000000	0.80357	0.620000	0.37586	4.754000	0.62191	2.110000	0.64415	0.459000	0.35465	GAT	.	.		0.542	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463	
PTPN13	5783	hgsc.bcm.edu	37	4	87556466	87556466	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:87556466A>G	ENST00000411767.2	+	2	120	c.57A>G	c.(55-57)gaA>gaG	p.E19E	PTPN13_ENST00000511467.1_Silent_p.E19E|PTPN13_ENST00000316707.6_Silent_p.E19E|PTPN13_ENST00000436978.1_Silent_p.E19E|PTPN13_ENST00000427191.2_Silent_p.E19E|PTPN13_ENST00000502971.1_Silent_p.E19E			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	19	KIND. {ECO:0000255|PROSITE- ProRule:PRU00709}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TTCAGGAGGAAGAAATATGGG	0.453																																					p.E19E		Atlas-SNP	.											.	PTPN13	203	.	0			c.A57G						.						62.0	63.0	63.0					4																	87556466		1923	4129	6052	SO:0001819	synonymous_variant	5783	exon2			GGAGGAAGAAATA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.57A>G	chr4.hg19:g.87556466A>G		97.0	0.0		85.0	38.0	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	hg19	CCDS47094.1																																																																																			.	.		0.453	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
SLC9B1	150159	hgsc.bcm.edu	37	4	103911043	103911043	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:103911043T>C	ENST00000296422.7	-	3	266	c.125A>G	c.(124-126)gAt>gGt	p.D42G	SLC9B1_ENST00000394789.3_Missense_Mutation_p.D42G	NM_139173.3	NP_631912	Q4ZJI4	SL9B1_HUMAN	solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1	42					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										TTCTTCTGTATCTGATAAGAC	0.308																																					p.D42G		Atlas-SNP	.											.	.	.	.	0			c.A125G						.						170.0	151.0	157.0					4																	103911043		2201	4293	6494	SO:0001583	missense	150159	exon3			TCTGTATCTGATA	AF447585	CCDS34041.1, CCDS47119.1	4q24	2013-05-22	2012-03-22	2011-07-26	ENSG00000164037	ENSG00000164037		"""Solute carriers"""	24244	protein-coding gene	gene with protein product		611527	"""Na+/H+ exchanger domain containing 1"", ""solute carrier family 9, subfamily B (cation proton antiporter 2), member 1"""	NHEDC1		16850186	Standard	NM_139173		Approved	NHA1	uc003hww.3	Q4ZJI4	OTTHUMG00000161114	ENST00000296422.7:c.125A>G	chr4.hg19:g.103911043T>C	ENSP00000296422:p.Asp42Gly	91.0	0.0		92.0	4.0	NM_001100874	A1KXV1|B9EH04|C9JBP7|Q49A30|Q8NCV2|Q8WVZ0	Missense_Mutation	SNP	ENST00000296422.7	hg19	CCDS34041.1	.	.	.	.	.	.	.	.	.	.	T	7.782	0.709690	0.15239	.	.	ENSG00000164037	ENST00000394789;ENST00000296422;ENST00000514340;ENST00000452285;ENST00000510559	T;T;T;T	0.55234	2.21;2.23;1.87;0.53	3.74	2.55	0.30701	.	22.639300	0.00166	N	0.000001	T	0.37625	0.1010	N	0.19112	0.55	0.09310	N	1	B;B	0.19073	0.033;0.001	B;B	0.12156	0.007;0.003	T	0.18777	-1.0326	10	0.17832	T	0.49	-3.1	5.7884	0.18347	0.0:0.1197:0.0:0.8803	.	42;42	Q4ZJI4;Q4ZJI4-3	SL9B1_HUMAN;.	G	42	ENSP00000378269:D42G;ENSP00000296422:D42G;ENSP00000426056:D42G;ENSP00000426325:D42G	ENSP00000296422:D42G	D	-	2	0	SLC9B1	104130492	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.673000	0.25203	0.805000	0.34159	0.377000	0.23210	GAT	.	.		0.308	SLC9B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363841.1	NM_139173	
ENPEP	2028	hgsc.bcm.edu	37	4	111409837	111409837	+	Splice_Site	SNP	C	C	T	rs373049379		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:111409837C>T	ENST00000265162.5	+	2	1127	c.785C>T	c.(784-786)gCg>gTg	p.A262V		NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	262					angiogenesis (GO:0001525)|angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|glomerulus development (GO:0032835)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloaminopeptidase activity (GO:0070006)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(1)	54		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)		ATGCCAGTGGCGGTAAGTATT	0.358																																					p.A262V		Atlas-SNP	.											ENPEP,NS,carcinoma,0,2	ENPEP	149	.	0			c.C785T						.	C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	93.0	92.0	92.0		785	-1.1	1.0	4		92	0,8600		0,0,4300	no	missense-near-splice	ENPEP	NM_001977.3	64	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	262/958	111409837	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	2028	exon2			CAGTGGCGGTAAG	L12468	CCDS3691.1	4q25	2008-02-05			ENSG00000138792	ENSG00000138792	3.4.11.7	"""CD molecules"""	3355	protein-coding gene	gene with protein product		138297				9268642	Standard	NM_001977		Approved	gp160, CD249	uc003iab.4	Q07075	OTTHUMG00000132546	ENST00000265162.5:c.786+1C>T	chr4.hg19:g.111409837C>T		57.0	0.0		32.0	19.0	NM_001977	Q504U2	Missense_Mutation	SNP	ENST00000265162.5	hg19	CCDS3691.1	.	.	.	.	.	.	.	.	.	.	C	14.62	2.588973	0.46110	2.27E-4	0.0	ENSG00000138792	ENST00000265162	T	0.02579	4.24	4.61	-1.13	0.09775	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.425182	0.24999	N	0.033928	T	0.01454	0.0047	N	0.05574	-0.02	0.31035	N	0.716968	P	0.47350	0.894	B	0.40165	0.321	T	0.52102	-0.8620	10	0.28530	T	0.3	.	8.6135	0.33817	0.463:0.4203:0.0:0.1166	.	262	Q07075	AMPE_HUMAN	V	262	ENSP00000265162:A262V	ENSP00000265162:A262V	A	+	2	0	ENPEP	111629286	0.616000	0.27035	0.991000	0.47740	0.798000	0.45092	1.105000	0.31086	-0.498000	0.06632	-0.251000	0.11542	GCG	.	.		0.358	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2		Missense_Mutation
CCNA2	890	hgsc.bcm.edu	37	4	122742218	122742218	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	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	157.0	0.0		120.0	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	
INTU	27152	hgsc.bcm.edu	37	4	128635178	128635178	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:128635178T>C	ENST00000335251.6	+	15	2750	c.2647T>C	c.(2647-2649)Ttt>Ctt	p.F883L		NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	883					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						TGGTGTGTTGTTTGAATGTTC	0.363																																					p.F883L		Atlas-SNP	.											.	INTU	92	.	0			c.T2647C						.						142.0	142.0	142.0					4																	128635178		2203	4300	6503	SO:0001583	missense	27152	exon15			GTGTTGTTTGAAT	BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"""PDZ domain containing 6"", ""inturned planar cell polarity effector homolog (Drosophila)"""	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.2647T>C	chr4.hg19:g.128635178T>C	ENSP00000334003:p.Phe883Leu	82.0	0.0		65.0	4.0	NM_015693	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Missense_Mutation	SNP	ENST00000335251.6	hg19	CCDS34061.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.832049	0.91036	.	.	ENSG00000164066	ENST00000335251	.	.	.	4.2	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.76912	0.4054	M	0.71206	2.165	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.80241	-0.1464	9	0.87932	D	0	-19.9757	13.455	0.61193	0.0:0.0:0.0:1.0	.	883	Q9ULD6	PDZD6_HUMAN	L	883	.	ENSP00000334003:F883L	F	+	1	0	INTU	128854628	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.142000	0.77339	1.751000	0.51876	0.528000	0.53228	TTT	.	.		0.363	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707	
CLGN	1047	hgsc.bcm.edu	37	4	141320135	141320135	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:141320135T>C	ENST00000325617.5	-	8	1194	c.754A>G	c.(754-756)Agc>Ggc	p.S252G	CLGN_ENST00000537281.1_Missense_Mutation_p.S252G|CLGN_ENST00000414773.1_Missense_Mutation_p.S252G	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	252					binding of sperm to zona pellucida (GO:0007339)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(5)|ovary(2)|prostate(3)|skin(4)|urinary_tract(1)	25	all_hematologic(180;0.162)					TCTAGGAGGCTTCCTTTGTTT	0.358																																					p.S252G		Atlas-SNP	.											.	CLGN	76	.	0			c.A754G						.						128.0	122.0	124.0					4																	141320135		2203	4300	6503	SO:0001583	missense	1047	exon9			GGAGGCTTCCTTT	D86322	CCDS3751.1	4q28.3-q31.1	2008-02-05			ENSG00000153132	ENSG00000153132			2060	protein-coding gene	gene with protein product		601858					Standard	NM_004362		Approved		uc003iii.3	O14967	OTTHUMG00000133414	ENST00000325617.5:c.754A>G	chr4.hg19:g.141320135T>C	ENSP00000326699:p.Ser252Gly	143.0	0.0		80.0	4.0	NM_001130675	B3KS90|B4DXV8|D3DNY8	Missense_Mutation	SNP	ENST00000325617.5	hg19	CCDS3751.1	.	.	.	.	.	.	.	.	.	.	T	18.43	3.622996	0.66901	.	.	ENSG00000153132	ENST00000325617;ENST00000414773;ENST00000537281;ENST00000545667	T;T;T	0.53206	0.63;0.63;0.63	5.74	5.74	0.90152	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.110160	0.85682	D	0.000000	T	0.56790	0.2009	M	0.83852	2.665	0.52099	D	0.999942	B	0.17667	0.023	B	0.26310	0.068	T	0.59005	-0.7535	10	0.87932	D	0	-3.9327	16.0359	0.80628	0.0:0.0:0.0:1.0	.	252	O14967	CLGN_HUMAN	G	252;252;252;169	ENSP00000326699:S252G;ENSP00000392782:S252G;ENSP00000439381:S252G	ENSP00000326699:S252G	S	-	1	0	CLGN	141539585	1.000000	0.71417	0.977000	0.42913	0.783000	0.44284	7.997000	0.88414	2.187000	0.69744	0.519000	0.50382	AGC	.	.		0.358	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362	
USP38	84640	hgsc.bcm.edu	37	4	144109051	144109051	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:144109051T>C	ENST00000307017.4	+	2	1261	c.755T>C	c.(754-756)cTc>cCc	p.L252P	USP38_ENST00000510377.1_Missense_Mutation_p.L252P	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	252					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)					ATTACAGTTCTCATCAGGAGC	0.383																																					p.L252P		Atlas-SNP	.											.	USP38	92	.	0			c.T755C						.						103.0	98.0	100.0					4																	144109051		2203	4300	6503	SO:0001583	missense	84640	exon2			CAGTTCTCATCAG	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.755T>C	chr4.hg19:g.144109051T>C	ENSP00000303434:p.Leu252Pro	100.0	0.0		87.0	4.0	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Missense_Mutation	SNP	ENST00000307017.4	hg19	CCDS3758.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.597610	0.87055	.	.	ENSG00000170185	ENST00000510377;ENST00000307017	T;T	0.76186	-0.96;-1.0	5.2	5.2	0.72013	.	0.000000	0.64402	D	0.000001	T	0.81269	0.4787	L	0.44542	1.39	0.80722	D	1	D;D	0.76494	0.995;0.999	D;D	0.71184	0.931;0.972	T	0.83119	-0.0119	10	0.66056	D	0.02	-11.0503	15.0837	0.72133	0.0:0.0:0.0:1.0	.	252;252	Q8NB14;Q3ZCV1	UBP38_HUMAN;.	P	252	ENSP00000427647:L252P;ENSP00000303434:L252P	ENSP00000303434:L252P	L	+	2	0	USP38	144328501	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	1.972000	0.57404	0.383000	0.25322	CTC	.	.		0.383	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557	
GAB1	2549	hgsc.bcm.edu	37	4	144361320	144361320	+	Missense_Mutation	SNP	G	G	A	rs369383480		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:144361320G>A	ENST00000262994.4	+	6	1672	c.1370G>A	c.(1369-1371)cGa>cAa	p.R457Q	GAB1_ENST00000262995.4_Missense_Mutation_p.R457Q|GAB1_ENST00000505913.1_Missense_Mutation_p.R354Q	NM_002039.3	NP_002030.2	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1	457	Pro-rich.				activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					TCACCACCACGACAACATTCC	0.383																																					p.R457Q		Atlas-SNP	.											.	GAB1	80	.	0			c.G1370A						.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	138.0	131.0	134.0		1370,1370	5.9	0.9	4		134	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GAB1	NM_002039.3,NM_207123.2	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	457/695,457/725	144361320	1,13005	2203	4300	6503	SO:0001583	missense	2549	exon6			CACCACGACAACA	U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458		"""Pleckstrin homology (PH) domain containing"""	4066	protein-coding gene	gene with protein product		604439				8596638	Standard	NM_207123		Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262994.4:c.1370G>A	chr4.hg19:g.144361320G>A	ENSP00000262994:p.Arg457Gln	195.0	0.0		159.0	7.0	NM_207123	A8K152|Q4W5G2|Q6P1W2	Missense_Mutation	SNP	ENST00000262994.4	hg19	CCDS3759.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.742467	0.69418	0.0	1.16E-4	ENSG00000109458	ENST00000262995;ENST00000262994;ENST00000505913	T;T;T	0.18338	2.69;2.71;2.22	5.91	5.91	0.95273	.	0.063133	0.64402	D	0.000003	T	0.28101	0.0693	L	0.43152	1.355	0.44048	D	0.996782	P;D	0.63880	0.913;0.993	B;P	0.55303	0.357;0.773	T	0.01010	-1.1482	10	0.12766	T	0.61	-2.8214	20.3011	0.98612	0.0:0.0:1.0:0.0	.	457;457	Q13480;Q13480-2	GAB1_HUMAN;.	Q	457;457;354	ENSP00000262995:R457Q;ENSP00000262994:R457Q;ENSP00000424554:R354Q	ENSP00000262994:R457Q	R	+	2	0	GAB1	144580770	1.000000	0.71417	0.906000	0.35671	0.989000	0.77384	7.353000	0.79414	2.804000	0.96469	0.650000	0.86243	CGA	.	.		0.383	GAB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364998.1	NM_002039	
PRMT9	90826	hgsc.bcm.edu	37	4	148559833	148559833	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:148559833T>C	ENST00000322396.6	-	12	2630	c.2388A>G	c.(2386-2388)gaA>gaG	p.E796E	PRMT10_ENST00000541232.1_Silent_p.E683E|TMEM184C_ENST00000508208.1_Intron	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		796	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						ACCTAATCTCTTCATCAAGGT	0.373																																					p.E796E		Atlas-SNP	.											.	PRMT10	68	.	0			c.A2388G						.						89.0	81.0	84.0					4																	148559833		2203	4300	6503	SO:0001819	synonymous_variant	90826	exon12			AATCTCTTCATCA																												ENST00000322396.6:c.2388A>G	chr4.hg19:g.148559833T>C		115.0	0.0		86.0	4.0	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Silent	SNP	ENST00000322396.6	hg19	CCDS3771.1																																																																																			.	.		0.373	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1		
LRBA	987	hgsc.bcm.edu	37	4	151773390	151773390	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:151773390C>T	ENST00000357115.3	-	23	3715	c.3472G>A	c.(3472-3474)Gaa>Aaa	p.E1158K	LRBA_ENST00000535741.1_Missense_Mutation_p.E1158K|LRBA_ENST00000510413.1_Missense_Mutation_p.E1158K|LRBA_ENST00000507224.1_Missense_Mutation_p.E1158K	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	1158						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)					GGTTTTCCTTCTTGAAATATT	0.393																																					p.E1158K		Atlas-SNP	.											.	LRBA	253	.	0			c.G3472A						.						72.0	73.0	73.0					4																	151773390		2203	4300	6503	SO:0001583	missense	987	exon23			TTCCTTCTTGAAA	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.3472G>A	chr4.hg19:g.151773390C>T	ENSP00000349629:p.Glu1158Lys	112.0	0.0		93.0	4.0	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	hg19	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	C	8.123	0.781444	0.16120	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.55760	0.92;1.07;0.92;0.5	5.45	4.6	0.57074	.	0.846744	0.10452	N	0.673006	T	0.39200	0.1069	N	0.24115	0.695	0.18873	N	0.999988	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.06110	-1.0845	10	0.13470	T	0.59	.	14.4517	0.67389	0.0:0.9282:0.0:0.0718	.	1158;1158	P50851;P50851-2	LRBA_HUMAN;.	K	1158	ENSP00000446299:E1158K;ENSP00000421552:E1158K;ENSP00000349629:E1158K;ENSP00000422180:E1158K	ENSP00000349629:E1158K	E	-	1	0	LRBA	151992840	0.918000	0.31147	0.523000	0.27875	0.018000	0.09664	1.324000	0.33712	2.941000	0.99782	0.655000	0.94253	GAA	.	.		0.393	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1		
GRIA2	2891	hgsc.bcm.edu	37	4	158238831	158238831	+	Missense_Mutation	SNP	G	G	C	rs199950609		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:158238831G>C	ENST00000264426.9	+	5	967	c.688G>C	c.(688-690)Gtt>Ctt	p.V230L	GRIA2_ENST00000507898.1_Missense_Mutation_p.V183L|GRIA2_ENST00000449365.1_Missense_Mutation_p.V183L|GRIA2_ENST00000393815.2_Missense_Mutation_p.V183L|GRIA2_ENST00000296526.7_Missense_Mutation_p.V230L	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	230					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|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)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TGGAAAACATGTTAAAGGGTA	0.229																																					p.V230L		Atlas-SNP	.											GRIA2_ENST00000264426,NS,carcinoma,0,2	GRIA2	358	.	0			c.G688C						.						37.0	39.0	38.0					4																	158238831		2195	4288	6483	SO:0001583	missense	2891	exon5			AAACATGTTAAAG		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.688G>C	chr4.hg19:g.158238831G>C	ENSP00000264426:p.Val230Leu	121.0	0.0		111.0	0.0	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	hg19	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.038022	0.75617	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365;ENST00000503437	T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98	5.17	5.17	0.71159	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	T	0.27419	0.0673	N	0.24115	0.695	0.80722	D	1	P;B;B	0.37955	0.612;0.001;0.351	P;B;B	0.48425	0.577;0.005;0.373	T	0.05971	-1.0853	10	0.59425	D	0.04	.	19.041	0.92999	0.0:0.0:1.0:0.0	.	230;230;183	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	L	183;183;230;230;183;103	ENSP00000426845:V183L;ENSP00000377403:V183L;ENSP00000296526:V230L;ENSP00000264426:V230L;ENSP00000389837:V183L	ENSP00000264426:V230L	V	+	1	0	GRIA2	158458281	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.466000	0.80914	2.547000	0.85894	0.563000	0.77884	GTT	.	G|0.999;A|0.001		0.229	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2		
NAF1	92345	hgsc.bcm.edu	37	4	164085383	164085383	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:164085383C>G	ENST00000274054.2	-	2	719	c.526G>C	c.(526-528)Gaa>Caa	p.E176Q	NAF1_ENST00000422287.2_Missense_Mutation_p.E176Q	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	176					pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				AGAAGTAATTCATCTTTTGTT	0.308																																					p.E176Q		Atlas-SNP	.											.	NAF1	69	.	0			c.G526C						.						29.0	31.0	30.0					4																	164085383		2200	4299	6499	SO:0001583	missense	92345	exon2			GTAATTCATCTTT		CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"""nuclear assembly factor 1 homolog (S. cerevisiae)"""			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.526G>C	chr4.hg19:g.164085383C>G	ENSP00000274054:p.Glu176Gln	128.0	0.0		117.0	11.0	NM_138386	D3DP28|E9PAZ2	Missense_Mutation	SNP	ENST00000274054.2	hg19	CCDS3803.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.943608	0.73672	.	.	ENSG00000145414	ENST00000422287;ENST00000274054	T;T	0.54279	0.78;0.58	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.71576	0.3356	M	0.74881	2.28	0.51012	D	0.999908	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	T	0.74682	-0.3583	10	0.87932	D	0	-27.7111	14.4072	0.67090	0.0:1.0:0.0:0.0	.	176;176	E9PAZ2;Q96HR8	.;NAF1_HUMAN	Q	176	ENSP00000408963:E176Q;ENSP00000274054:E176Q	ENSP00000274054:E176Q	E	-	1	0	NAF1	164304833	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.939000	0.56591	2.678000	0.91216	0.591000	0.81541	GAA	.	.		0.308	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386	
NSUN2	54888	hgsc.bcm.edu	37	5	6607400	6607400	+	Missense_Mutation	SNP	G	G	T	rs374268482		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:6607400G>T	ENST00000264670.6	-	13	1732	c.1421C>A	c.(1420-1422)cCg>cAg	p.P474Q	NSUN2_ENST00000539938.1_Missense_Mutation_p.P238Q|NSUN2_ENST00000506139.1_Missense_Mutation_p.P439Q	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	474					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)	p.P474Q(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						TGTGAATGACGGACTTTCCAG	0.478																																					p.P474Q		Atlas-SNP	.											NSUN2,colon,carcinoma,0,1	NSUN2	82	.	1	Substitution - Missense(1)	lung(1)	c.C1421A						.						252.0	238.0	242.0					5																	6607400		2203	4300	6503	SO:0001583	missense	54888	exon13			AATGACGGACTTT	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"""NOP2/Sun domain containing"""	25994	protein-coding gene	gene with protein product	"""tRNA methyltransferase 4 homolog (S. cerevisiae)"", ""Myc-induced SUN-domain-containing protein"""	610916	"""NOL1/NOP2/Sun domain family, member 2"", ""NOP2/Sun domain family, member 2"", ""mental retardation, non-syndromic, autosomal recessive, 5"""	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.1421C>A	chr5.hg19:g.6607400G>T	ENSP00000264670:p.Pro474Gln	386.0	0.0		466.0	0.0	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	hg19	CCDS3869.1	.	.	.	.	.	.	.	.	.	.	G	8.838	0.941559	0.18281	.	.	ENSG00000037474	ENST00000264670;ENST00000539938;ENST00000506139	T;T;T	0.54479	1.31;0.57;1.31	5.61	1.85	0.25348	.	0.693519	0.14807	N	0.297283	T	0.27967	0.0689	N	0.10874	0.06	0.09310	N	1	B;B	0.14438	0.01;0.002	B;B	0.10450	0.005;0.002	T	0.20075	-1.0286	10	0.13853	T	0.58	-21.3728	7.9826	0.30192	0.0:0.0786:0.465:0.4564	.	439;474	B4DQW2;Q08J23	.;NSUN2_HUMAN	Q	474;238;439	ENSP00000264670:P474Q;ENSP00000444338:P238Q;ENSP00000420957:P439Q	ENSP00000264670:P474Q	P	-	2	0	NSUN2	6660400	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.243000	0.18106	0.459000	0.27016	-0.274000	0.10170	CCG	.	.		0.478	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755	
CDH10	1008	hgsc.bcm.edu	37	5	24488013	24488013	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:24488013T>C	ENST00000264463.4	-	12	2633	c.2126A>G	c.(2125-2127)gAc>gGc	p.D709G	CDH10_ENST00000502921.1_5'UTR	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	709					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)		ATCCCGGACGTCCGTGTTATC	0.468										HNSCC(23;0.051)																											p.D709G		Atlas-SNP	.											.	CDH10	391	.	0			c.A2126G						.						83.0	89.0	87.0					5																	24488013		2203	4300	6503	SO:0001583	missense	1008	exon12			CGGACGTCCGTGT	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.2126A>G	chr5.hg19:g.24488013T>C	ENSP00000264463:p.Asp709Gly	115.0	0.0		119.0	7.0	NM_006727	Q9ULB3	Missense_Mutation	SNP	ENST00000264463.4	hg19	CCDS3892.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.988638	0.74589	.	.	ENSG00000040731	ENST00000264463	T	0.79247	-1.25	5.41	5.41	0.78517	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	T	0.81283	0.4790	M	0.81682	2.555	0.54753	D	0.999983	P	0.38617	0.64	B	0.41764	0.366	T	0.83225	-0.0066	10	0.54805	T	0.06	.	14.6395	0.68714	0.0:0.0:0.0:1.0	.	709	Q9Y6N8	CAD10_HUMAN	G	709	ENSP00000264463:D709G	ENSP00000264463:D709G	D	-	2	0	CDH10	24523770	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	6.177000	0.71961	2.058000	0.61347	0.533000	0.62120	GAC	.	.		0.468	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727	
NADK2	133686	hgsc.bcm.edu	37	5	36226660	36226660	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:36226660T>C	ENST00000381937.4	-	3	394	c.395A>G	c.(394-396)gAg>gGg	p.E132G	NADK2_ENST00000282512.3_5'UTR|NADK2_ENST00000506945.1_5'UTR|NADK2_ENST00000514504.1_Missense_Mutation_p.E132G|NADK2_ENST00000397338.1_5'UTR	NM_001085411.1	NP_001078880.1	Q4G0N4	NAKD2_HUMAN	NAD kinase 2, mitochondrial	132					NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|NAD+ kinase activity (GO:0003951)|protein homodimerization activity (GO:0042803)										CTCAATTCCCTCATTCCTAGG	0.368																																					p.E132G		Atlas-SNP	.											.	NADKD1	47	.	0			c.A395G						.						132.0	120.0	124.0					5																	36226660		1853	4088	5941	SO:0001583	missense	133686	exon3			ATTCCCTCATTCC	BC062567	CCDS3917.1, CCDS47197.1, CCDS75235.1	5p13.2	2013-04-30	2013-04-30	2013-04-30	ENSG00000152620	ENSG00000152620			26404	protein-coding gene	gene with protein product	"""mitochondrial NAD kinase"""	615787	"""chromosome 5 open reading frame 33"", ""NAD kinase domain containing 1"""	C5orf33, NADKD1		23616928	Standard	NM_001085411		Approved	FLJ30596, MNADK	uc003jkf.4	Q4G0N4	OTTHUMG00000131105	ENST00000381937.4:c.395A>G	chr5.hg19:g.36226660T>C	ENSP00000371362:p.Glu132Gly	50.0	0.0		69.0	4.0	NM_001085411	B5MC93|Q6UTX5|Q96NM0	Missense_Mutation	SNP	ENST00000381937.4	hg19	CCDS47197.1	.	.	.	.	.	.	.	.	.	.	T	14.12	2.440998	0.43326	.	.	ENSG00000152620	ENST00000381937;ENST00000514504	T;T	0.42513	0.97;0.97	5.96	5.96	0.96718	ATP-NAD kinase, PpnK-type, alpha/beta (1);ATP-NAD kinase, PpnK-type (1);	.	.	.	.	T	0.29355	0.0731	N	0.05124	-0.11	0.48901	D	0.999721	P	0.43826	0.818	P	0.45449	0.481	T	0.15723	-1.0427	9	0.26408	T	0.33	.	15.4164	0.74974	0.0:0.0:0.0:1.0	.	132	Q4G0N4	NAKD1_HUMAN	G	132	ENSP00000371362:E132G;ENSP00000421029:E132G	ENSP00000371362:E132G	E	-	2	0	NADKD1	36262417	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	4.223000	0.58587	2.270000	0.75569	0.533000	0.62120	GAG	.	.		0.368	NADK2-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367541.1	NM_153013	
NIPBL	25836	hgsc.bcm.edu	37	5	36975946	36975946	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:36975946G>A	ENST00000282516.8	+	9	1436	c.937G>A	c.(937-939)Gat>Aat	p.D313N	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Missense_Mutation_p.D313N	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	313					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			TGTTCCACCAGATATCTTGCT	0.383																																					p.D313N		Atlas-SNP	.											.	NIPBL	513	.	0			c.G937A						.						104.0	108.0	107.0					5																	36975946		2203	4300	6503	SO:0001583	missense	25836	exon9			CCACCAGATATCT	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.937G>A	chr5.hg19:g.36975946G>A	ENSP00000282516:p.Asp313Asn	82.0	0.0		93.0	4.0	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	hg19	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.047233	0.75846	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.96265	-3.94;-3.96	5.14	5.14	0.70334	.	0.141527	0.46758	D	0.000269	D	0.95730	0.8611	L	0.29908	0.895	0.38104	D	0.937345	D;D	0.64830	0.99;0.994	P;P	0.54759	0.58;0.76	D	0.97291	0.9924	10	0.66056	D	0.02	.	18.5966	0.91231	0.0:0.0:1.0:0.0	.	313;313	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	N	313	ENSP00000282516:D313N;ENSP00000406266:D313N	ENSP00000282516:D313N	D	+	1	0	NIPBL	37011703	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.703000	0.91344	2.390000	0.81377	0.467000	0.42956	GAT	.	.		0.383	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
DAB2	1601	hgsc.bcm.edu	37	5	39377005	39377005	+	Silent	SNP	A	A	G	rs538907566		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:39377005A>G	ENST00000320816.6	-	12	2351	c.1884T>C	c.(1882-1884)ccT>ccC	p.P628P	DAB2_ENST00000339788.6_Silent_p.P410P|DAB2_ENST00000545653.1_Silent_p.P607P|DAB2_ENST00000509337.1_Silent_p.P607P	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	628	Sufficient for interaction with GRB2. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			TGTCCTTGGGAGGGCCAGCTC	0.527											OREG0016586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	1	0.000199681	0.0008	0.0	5008	,	,		19965	0.0		0.0	False		,,,				2504	0.0				p.P628P		Atlas-SNP	.											DAB2,lower_third,carcinoma,0,1	DAB2	124	.	0			c.T1884C						.						76.0	90.0	85.0					5																	39377005		2203	4300	6503	SO:0001819	synonymous_variant	1601	exon12			CTTGGGAGGGCCA	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"""disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)"", ""disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"""			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.1884T>C	chr5.hg19:g.39377005A>G		98.0	0.0	885	143.0	6.0	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Silent	SNP	ENST00000320816.6	hg19	CCDS34149.1																																																																																			.	.		0.527	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343	
SLC38A9	153129	hgsc.bcm.edu	37	5	54952575	54952575	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:54952575T>C	ENST00000396865.2	-	9	1316	c.725A>G	c.(724-726)gAc>gGc	p.D242G	SLC38A9_ENST00000515629.1_Missense_Mutation_p.D179G|SLC38A9_ENST00000539768.1_Missense_Mutation_p.D242G|SLC38A9_ENST00000512595.1_Missense_Mutation_p.D215G|SLC38A9_ENST00000416547.2_Missense_Mutation_p.D118G|SLC38A9_ENST00000318672.3_Missense_Mutation_p.D242G	NM_173514.3	NP_775785.2	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9	242					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				CAGTATAGTGTCTGTGTCATT	0.313																																					p.D242G		Atlas-SNP	.											.	SLC38A9	50	.	0			c.A725G						.						105.0	102.0	103.0					5																	54952575		2201	4298	6499	SO:0001583	missense	153129	exon9			ATAGTGTCTGTGT		CCDS3968.1, CCDS58947.1, CCDS58948.1, CCDS75243.1	5q11.2	2013-05-22			ENSG00000177058	ENSG00000177058		"""Solute carriers"""	26907	protein-coding gene	gene with protein product							Standard	NM_173514		Approved	FLJ90709	uc003jqf.3	Q8NBW4	OTTHUMG00000131189	ENST00000396865.2:c.725A>G	chr5.hg19:g.54952575T>C	ENSP00000380074:p.Asp242Gly	87.0	0.0		88.0	4.0	NM_173514	B3KXV1|B7Z7D0|Q0P5S0|Q6MZJ8	Missense_Mutation	SNP	ENST00000396865.2	hg19	CCDS3968.1	.	.	.	.	.	.	.	.	.	.	T	14.39	2.520895	0.44866	.	.	ENSG00000177058	ENST00000396865;ENST00000318672;ENST00000539768;ENST00000515629;ENST00000416547;ENST00000512595;ENST00000512208	T;T;T;T;T;T;T	0.48836	1.87;1.87;0.84;1.9;1.91;1.4;0.8	6.01	6.01	0.97437	.	0.000000	0.85682	D	0.000000	T	0.47040	0.1424	M	0.65975	2.015	0.80722	D	1	B;B	0.29162	0.003;0.235	B;B	0.29524	0.016;0.103	T	0.39272	-0.9622	10	0.19590	T	0.45	-17.3328	14.7662	0.69640	0.0:0.0:0.0:1.0	.	215;242	B3KXV1;Q8NBW4	.;S38A9_HUMAN	G	242;242;242;179;118;215;179	ENSP00000380074:D242G;ENSP00000316596:D242G;ENSP00000437771:D242G;ENSP00000420934:D179G;ENSP00000397429:D118G;ENSP00000427335:D215G;ENSP00000426413:D179G	ENSP00000316596:D242G	D	-	2	0	SLC38A9	54988332	1.000000	0.71417	0.939000	0.37840	0.912000	0.54170	5.082000	0.64450	2.301000	0.77427	0.523000	0.50628	GAC	.	.		0.313	SLC38A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253912.2	NM_173514	
PLK2	10769	hgsc.bcm.edu	37	5	57753128	57753128	+	Silent	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:57753128C>T	ENST00000274289.3	-	7	1188	c.888G>A	c.(886-888)agG>agA	p.R296R	PLK2_ENST00000502671.1_5'UTR	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	296	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		GCATTGTATACCTTGCTTCCC	0.433																																					p.R296R		Atlas-SNP	.											.	PLK2	71	.	0			c.G888A						.						82.0	79.0	80.0					5																	57753128		2203	4300	6503	SO:0001819	synonymous_variant	10769	exon7			TGTATACCTTGCT		CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"""serum-inducible kinase"""	607023	"""polo-like kinase 2 (Drosophila)"""				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.888G>A	chr5.hg19:g.57753128C>T		32.0	0.0		56.0	4.0	NM_006622	O60679|Q96CV7|Q9UE61	Silent	SNP	ENST00000274289.3	hg19	CCDS3974.1																																																																																			.	.		0.433	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622	
MAP1B	4131	hgsc.bcm.edu	37	5	71494401	71494401	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:71494401A>G	ENST00000296755.7	+	5	5517	c.5219A>G	c.(5218-5220)cAg>cGg	p.Q1740R		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1740					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		ACCCCTTCTCAGATCGCTTCT	0.493																																					p.Q1740R	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.A5219G						.						153.0	160.0	158.0					5																	71494401		2203	4300	6503	SO:0001583	missense	4131	exon5			CTTCTCAGATCGC	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.5219A>G	chr5.hg19:g.71494401A>G	ENSP00000296755:p.Gln1740Arg	75.0	0.0		126.0	6.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	A	13.76	2.334459	0.41297	.	.	ENSG00000131711	ENST00000296755	T	0.03801	3.8	5.0	5.0	0.66597	.	0.000000	0.64402	D	0.000012	T	0.06005	0.0156	L	0.29908	0.895	0.54753	D	0.999989	P;P	0.47106	0.89;0.791	P;B	0.45232	0.474;0.272	T	0.35001	-0.9806	10	0.59425	D	0.04	-18.8371	11.6428	0.51244	0.8516:0.1484:0.0:0.0	.	1614;1740	A2BDK6;P46821	.;MAP1B_HUMAN	R	1740	ENSP00000296755:Q1740R	ENSP00000296755:Q1740R	Q	+	2	0	MAP1B	71530157	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.877000	0.75562	2.015000	0.59207	0.368000	0.22195	CAG	.	.		0.493	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
DMGDH	29958	hgsc.bcm.edu	37	5	78324266	78324266	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:78324266T>C	ENST00000255189.3	-	12	2050	c.2022A>G	c.(2020-2022)atA>atG	p.I674M	DMGDH_ENST00000380311.4_Missense_Mutation_p.I473M|DMGDH_ENST00000540686.1_Missense_Mutation_p.I294M	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	674					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		CAGTATAAGATATCCTAATAG	0.313																																					p.I674M		Atlas-SNP	.											DMGDH,NS,carcinoma,0,1	DMGDH	88	.	0			c.A2022G						.						51.0	53.0	52.0					5																	78324266		2203	4300	6503	SO:0001583	missense	29958	exon12			ATAAGATATCCTA	AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.2022A>G	chr5.hg19:g.78324266T>C	ENSP00000255189:p.Ile674Met	57.0	0.0		66.0	3.0	NM_013391	B2RBN0|B4E1J9	Missense_Mutation	SNP	ENST00000255189.3	hg19	CCDS4044.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.057417	0.36277	.	.	ENSG00000132837	ENST00000255189;ENST00000523732;ENST00000380311;ENST00000540686;ENST00000539598	T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87	5.81	1.95	0.26073	Glycine cleavage T-protein, N-terminal (1);	0.042826	0.85682	D	0.000000	T	0.68714	0.3031	L	0.48877	1.53	0.41589	D	0.988787	P;P;B;B	0.42735	0.788;0.753;0.164;0.198	P;B;B;B	0.45167	0.472;0.281;0.138;0.217	T	0.64918	-0.6294	10	0.52906	T	0.07	.	8.8284	0.35069	0.1183:0.0:0.4305:0.4511	.	294;473;524;674	B4E1J9;F8W6P8;F5H1C7;Q9UI17	.;.;.;M2GD_HUMAN	M	674;513;473;294;524	ENSP00000255189:I674M;ENSP00000430972:I513M;ENSP00000369667:I473M;ENSP00000439478:I294M	ENSP00000255189:I674M	I	-	3	3	DMGDH	78360022	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.772000	0.38552	0.092000	0.17331	0.533000	0.62120	ATA	.	.		0.313	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391	
RASGRF2	5924	hgsc.bcm.edu	37	5	80475996	80475996	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:80475996T>C	ENST00000265080.4	+	18	2756	c.2689T>C	c.(2689-2691)Ttt>Ctt	p.F897L		NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	897					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		CTCCTAAGGCTTTAACAACAC	0.438																																					p.F897L		Atlas-SNP	.											.	RASGRF2	165	.	0			c.T2689C						.						174.0	169.0	171.0					5																	80475996		2203	4300	6503	SO:0001583	missense	5924	exon18			TAAGGCTTTAACA	AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.2689T>C	chr5.hg19:g.80475996T>C	ENSP00000265080:p.Phe897Leu	89.0	0.0		89.0	4.0	NM_006909	B9EG89|Q9UK56	Missense_Mutation	SNP	ENST00000265080.4	hg19	CCDS4052.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.006545	0.74932	.	.	ENSG00000113319	ENST00000265080	T	0.27890	1.64	5.93	5.93	0.95920	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (1);	0.099192	0.64402	D	0.000001	T	0.48447	0.1500	M	0.62016	1.91	0.58432	D	0.999998	D	0.69078	0.997	D	0.70716	0.97	T	0.41466	-0.9507	10	0.08179	T	0.78	.	15.3582	0.74443	0.0:0.0:0.0:1.0	.	897	O14827	RGRF2_HUMAN	L	897	ENSP00000265080:F897L	ENSP00000265080:F897L	F	+	1	0	RASGRF2	80511752	1.000000	0.71417	0.961000	0.40146	0.282000	0.26991	7.338000	0.79269	2.270000	0.75569	0.460000	0.39030	TTT	.	.		0.438	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909	
ANKRD32	84250	hgsc.bcm.edu	37	5	94030556	94030556	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:94030556A>G	ENST00000265140.5	+	21	3135	c.2716A>G	c.(2716-2718)Agg>Ggg	p.R906G	ANKRD32_ENST00000493934.1_Intron	NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	906						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		TTTACAACAGAGGAATGCTAA	0.368																																					p.R906G		Atlas-SNP	.											.	ANKRD32	117	.	0			c.A2716G						.						88.0	88.0	88.0					5																	94030556		2203	4298	6501	SO:0001583	missense	84250	exon21			CAACAGAGGAATG	AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"""Ankyrin repeat domain containing"""	25408	protein-coding gene	gene with protein product			"""BRCT domain containing 1"""	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.2716A>G	chr5.hg19:g.94030556A>G	ENSP00000265140:p.Arg906Gly	114.0	0.0		97.0	5.0	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Missense_Mutation	SNP	ENST00000265140.5	hg19	CCDS4071.2	.	.	.	.	.	.	.	.	.	.	A	20.7	4.032548	0.75504	.	.	ENSG00000133302	ENST00000265140	T	0.71934	-0.61	5.62	5.62	0.85841	Ankyrin repeat-containing domain (3);	0.225578	0.46758	D	0.000278	T	0.81384	0.4811	M	0.74647	2.275	0.37407	D	0.913074	D	0.57257	0.979	P	0.57846	0.828	D	0.86007	0.1498	10	0.66056	D	0.02	.	15.823	0.78673	1.0:0.0:0.0:0.0	.	906	Q9BQI6	ANR32_HUMAN	G	906	ENSP00000265140:R906G	ENSP00000265140:R906G	R	+	1	2	ANKRD32	94056312	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	6.352000	0.73027	2.149000	0.67028	0.477000	0.44152	AGG	.	.		0.368	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290	
ELL2	22936	hgsc.bcm.edu	37	5	95226880	95226880	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:95226880T>C	ENST00000237853.4	-	10	2037	c.1688A>G	c.(1687-1689)gAg>gGg	p.E563G	ELL2_ENST00000431061.2_Missense_Mutation_p.E313G	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	563					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		AGCTACAGTCTCCATCCTGGC	0.408																																					p.E563G		Atlas-SNP	.											.	ELL2	63	.	0			c.A1688G						.						189.0	181.0	183.0					5																	95226880		2203	4298	6501	SO:0001583	missense	22936	exon10			ACAGTCTCCATCC	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.1688A>G	chr5.hg19:g.95226880T>C	ENSP00000237853:p.Glu563Gly	143.0	0.0		149.0	7.0	NM_012081	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	hg19	CCDS4080.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.7|28.7	4.939091|4.939091	0.92526|0.92526	.|.	.|.	ENSG00000118985|ENSG00000118985	ENST00000237853;ENST00000431061|ENST00000508757	T;T|.	0.22743|.	1.94;1.94|.	6.16|6.16	6.16|6.16	0.99307|0.99307	Occludin/RNA polymerase II elongation factor, ELL domain (1);|.	0.087556|.	0.85682|.	D|.	0.000000|.	T|T	0.56848|0.56848	0.2013|0.2013	L|L	0.28458|0.28458	0.855|0.855	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.81914|.	0.995|.	T|T	0.52548|0.52548	-0.8561|-0.8561	10|5	0.48119|.	T|.	0.1|.	0.4799|0.4799	16.4675|16.4675	0.84087|0.84087	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	563|.	O00472|.	ELL2_HUMAN|.	G|G	563;313|81	ENSP00000237853:E563G;ENSP00000399704:E313G|.	ENSP00000237853:E563G|.	E|R	-|-	2|1	0|2	ELL2|ELL2	95252636|95252636	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.977000|7.977000	0.88081|0.88081	2.367000|2.367000	0.80283|0.80283	0.528000|0.528000	0.53228|0.53228	GAG|AGA	.	.		0.408	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
ERAP1	51752	hgsc.bcm.edu	37	5	96130756	96130756	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:96130756A>G	ENST00000443439.2	-	5	974	c.908T>C	c.(907-909)cTa>cCa	p.L303P	ERAP1_ENST00000296754.3_Missense_Mutation_p.L303P	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	303					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TTGTTTGGGTAGGGGATACGG	0.393																																					p.L303P		Atlas-SNP	.											.	ERAP1	59	.	0			c.T908C						.						76.0	72.0	73.0					5																	96130756		2203	4300	6503	SO:0001583	missense	51752	exon5			TTGGGTAGGGGAT	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"""aminopeptidase regulator of TNFR1 shedding"", ""adipocyte-derived leucine aminopeptidase"", ""puromycin-insensitive leucyl-specific aminopeptidase"""	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.908T>C	chr5.hg19:g.96130756A>G	ENSP00000406304:p.Leu303Pro	77.0	0.0		116.0	5.0	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	hg19	CCDS47250.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.294803	0.81025	.	.	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.04406	3.63;3.63	5.91	5.91	0.95273	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.64402	D	0.000001	T	0.38639	0.1048	H	0.98682	4.3	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.62234	-0.6897	10	0.87932	D	0	.	15.9979	0.80265	1.0:0.0:0.0:0.0	.	303;303;303	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	P	303	ENSP00000296754:L303P;ENSP00000406304:L303P	ENSP00000296754:L303P	L	-	2	0	ERAP1	96156512	1.000000	0.71417	0.999000	0.59377	0.891000	0.51852	8.760000	0.91671	2.252000	0.74401	0.528000	0.53228	CTA	.	.		0.393	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
SEMA6A	57556	hgsc.bcm.edu	37	5	115824677	115824677	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:115824677T>C	ENST00000343348.6	-	8	1349	c.562A>G	c.(562-564)Act>Gct	p.T188A	SEMA6A_ENST00000257414.8_Missense_Mutation_p.T188A|SEMA6A_ENST00000503962.1_5'UTR|CTB-118N6.3_ENST00000514214.1_RNA|CTB-118N6.3_ENST00000508640.1_RNA|SEMA6A_ENST00000510263.1_Missense_Mutation_p.T188A|CTB-118N6.3_ENST00000510682.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	188	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		AGGAAGTCAGTCACTGTGGCT	0.473																																					p.T188A		Atlas-SNP	.											.	SEMA6A	93	.	0			c.A562G						.						43.0	40.0	41.0					5																	115824677		1955	4163	6118	SO:0001583	missense	57556	exon8			AGTCAGTCACTGT	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"""Semaphorins"""	10738	protein-coding gene	gene with protein product	"""sema VIa"""	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.562A>G	chr5.hg19:g.115824677T>C	ENSP00000345512:p.Thr188Ala	89.0	0.0		111.0	5.0	NM_020796	Q9P2H9	Missense_Mutation	SNP	ENST00000343348.6	hg19	CCDS47256.1	.	.	.	.	.	.	.	.	.	.	T	12.36	1.914488	0.33815	.	.	ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000510263	T;T;T	0.09630	2.96;2.96;2.96	5.58	5.58	0.84498	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.17577	0.0422	N	0.25957	0.775	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.998	T	0.02639	-1.1130	10	0.02654	T	1	.	15.4142	0.74952	0.0:0.0:0.0:1.0	.	188;188	Q9H2E6;Q9H2E6-2	SEM6A_HUMAN;.	A	188	ENSP00000345512:T188A;ENSP00000257414:T188A;ENSP00000424388:T188A	ENSP00000257414:T188A	T	-	1	0	SEMA6A	115852576	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	6.276000	0.72601	2.130000	0.65690	0.528000	0.53228	ACT	.	.		0.473	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796	
DMXL1	1657	hgsc.bcm.edu	37	5	118569090	118569090	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:118569090A>G	ENST00000311085.8	+	38	8411	c.8331A>G	c.(8329-8331)caA>caG	p.Q2777Q	DMXL1_ENST00000539542.1_Silent_p.Q2798Q|DMXL1_ENST00000505312.1_3'UTR	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2777										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GCCATTCTCAACAAATAACCT	0.343																																					p.Q2777Q		Atlas-SNP	.											.	DMXL1	268	.	0			c.A8331G						.						116.0	110.0	112.0					5																	118569090		2202	4300	6502	SO:0001819	synonymous_variant	1657	exon38			TTCTCAACAAATA	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.8331A>G	chr5.hg19:g.118569090A>G		115.0	0.0		122.0	6.0	NM_005509		Silent	SNP	ENST00000311085.8	hg19	CCDS4125.1																																																																																			.	.		0.343	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
RAPGEF6	51735	hgsc.bcm.edu	37	5	130769319	130769319	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:130769319T>C	ENST00000509018.1	-	25	3983	c.3778A>G	c.(3778-3780)Aac>Gac	p.N1260D	RAPGEF6_ENST00000296859.6_Missense_Mutation_p.N1268D|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.N1268D|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.N1310D|RAPGEF6_ENST00000307984.5_Missense_Mutation_p.N1273D	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1260	Ser-rich.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TCAGACAAGTTGTCAGATTTA	0.443																																					p.N1273D	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.A3817G						.						98.0	91.0	93.0					5																	130769319		2203	4300	6503	SO:0001583	missense	51735	exon27			ACAAGTTGTCAGA	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 2"""	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.3778A>G	chr5.hg19:g.130769319T>C	ENSP00000421684:p.Asn1260Asp	79.0	0.0		92.0	4.0	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	hg19	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	T	31	5.083514	0.94050	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000514667	T;T;T;T;T	0.31247	1.62;1.5;1.5;1.62;1.72	5.83	5.83	0.93111	.	0.094015	0.85682	D	0.000000	T	0.50633	0.1627	M	0.69823	2.125	0.80722	D	1	P;P;P;D;P	0.54772	0.945;0.945;0.945;0.968;0.945	P;P;P;P;P	0.56960	0.65;0.549;0.549;0.81;0.549	T	0.51787	-0.8661	10	0.54805	T	0.06	.	16.2141	0.82191	0.0:0.0:0.0:1.0	.	1268;1268;1310;1273;1260	A3KN82;B7ZML2;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;RPGF6_HUMAN	D	1260;1273;1268;1268;1273;1310	ENSP00000421684:N1260D;ENSP00000309298:N1273D;ENSP00000426081:N1268D;ENSP00000296859:N1268D;ENSP00000426948:N1310D	ENSP00000426948:N1310D	N	-	1	0	RAPGEF6;FNIP1	130797218	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.364000	0.66110	2.224000	0.72417	0.528000	0.53228	AAC	.	.		0.443	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340	
SEPT8	23176	hgsc.bcm.edu	37	5	132096620	132096620	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:132096620T>C	ENST00000378719.2	-	9	1397	c.1160A>G	c.(1159-1161)aAg>aGg	p.K387R	SEPT8_ENST00000378706.1_Missense_Mutation_p.K387R|SEPT8_ENST00000378701.1_Missense_Mutation_p.K385R|SEPT8_ENST00000378721.4_Missense_Mutation_p.K385R|SEPT8_ENST00000296873.7_Missense_Mutation_p.K387R|SEPT8_ENST00000458488.2_Missense_Mutation_p.K387R|SEPT8_ENST00000378699.2_Missense_Mutation_p.K327R|SEPT8_ENST00000481030.1_5'Flank|SEPT8_ENST00000448933.1_Missense_Mutation_p.K327R	NM_001098811.1	NP_001092281.1	Q92599	SEPT8_HUMAN	septin 8	387					cell cycle (GO:0007049)	septin complex (GO:0031105)	GTP binding (GO:0005525)		SEPT8/AFF4(2)	kidney(2)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTCCCGGCGCTTTTCCTCCAC	0.637																																					p.K387R		Atlas-SNP	.											.	SEPT8	28	.	0			c.A1160G						.						102.0	109.0	107.0					5																	132096620		2044	4171	6215	SO:0001583	missense	23176	exon9			CGGCGCTTTTCCT	AF179995	CCDS43358.1, CCDS43359.1, CCDS43360.1, CCDS47262.1, CCDS75298.1	5q31	2013-01-21			ENSG00000164402	ENSG00000164402		"""Septins"""	16511	protein-coding gene	gene with protein product		608418				9039502, 9149945	Standard	NM_001098812		Approved	KIAA0202, SEP2	uc003kxr.2	Q92599	OTTHUMG00000059735	ENST00000378719.2:c.1160A>G	chr5.hg19:g.132096620T>C	ENSP00000367991:p.Lys387Arg	73.0	0.0		78.0	4.0	NM_015146	A6NC65|A6NKP6|F6W7K9|Q8IX36|Q8IX37|Q9BVB3	Missense_Mutation	SNP	ENST00000378719.2	hg19	CCDS43358.1	.	.	.	.	.	.	.	.	.	.	T	18.45	3.627307	0.66901	.	.	ENSG00000164402	ENST00000378719;ENST00000378721;ENST00000296873;ENST00000448933;ENST00000378706;ENST00000378699;ENST00000378701;ENST00000458488	D;D;D;D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86;-1.86;-1.86;-1.86	5.7	5.7	0.88788	.	0.170387	0.49916	D	0.000121	D	0.85323	0.5670	L	0.46157	1.445	0.54753	D	0.999986	P;P;B;P	0.51791	0.908;0.948;0.037;0.948	B;P;B;P	0.48952	0.419;0.516;0.104;0.596	D	0.85481	0.1179	10	0.44086	T	0.13	.	15.9745	0.80049	0.0:0.0:0.0:1.0	.	385;385;387;387	B7ZVZ1;A6NFQ9;F6W7K9;Q92599	.;.;.;SEPT8_HUMAN	R	387;385;387;327;387;327;385;387	ENSP00000367991:K387R;ENSP00000367993:K385R;ENSP00000296873:K387R;ENSP00000399840:K327R;ENSP00000367978:K387R;ENSP00000367971:K327R;ENSP00000367973:K385R;ENSP00000394766:K387R	ENSP00000296873:K387R	K	-	2	0	SEPT8	132124519	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	6.289000	0.72696	2.168000	0.68352	0.533000	0.62120	AAG	.	.		0.637	SEPT8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132827.2	XM_034872	
SPINK6	404203	hgsc.bcm.edu	37	5	147593498	147593498	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:147593498C>A	ENST00000325630.2	+	3	363	c.107C>A	c.(106-108)cCc>cAc	p.P36H		NM_001195290.1|NM_205841.3	NP_001182219.1|NP_995313.2	Q6UWN8	ISK6_HUMAN	serine peptidase inhibitor, Kazal type 6	36	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.		P -> T (in dbSNP:rs12186491). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20667819}.			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCAGGACCCCAAGGTCTAC	0.458																																					p.P36H		Atlas-SNP	.											.	SPINK6	8	.	0			c.C107A						.						134.0	110.0	118.0					5																	147593498		2203	4300	6503	SO:0001583	missense	404203	exon3			AGGACCCCAAGGT	AY358716	CCDS34268.1	5q32	2011-08-31	2005-08-17		ENSG00000178172	ENSG00000178172		"""Serine peptidase inhibitors, Kazal type"""	29486	protein-coding gene	gene with protein product	"""protease inhibitor H"""	615868	"""serine protease inhibitor, Kazal type 6"""			15060002	Standard	NM_205841		Approved	MGC21394, UNQ844, BUSI2	uc021yff.1	Q6UWN8	OTTHUMG00000163425	ENST00000325630.2:c.107C>A	chr5.hg19:g.147593498C>A	ENSP00000324870:p.Pro36His	145.0	0.0		153.0	7.0	NM_205841	E0X656|Q8N5P0	Missense_Mutation	SNP	ENST00000325630.2	hg19	CCDS34268.1	.	.	.	.	.	.	.	.	.	.	C	13.19	2.164563	0.38217	.	.	ENSG00000178172	ENST00000514389;ENST00000325630	T;T	0.79554	-1.28;-0.88	5.75	5.75	0.90469	Proteinase inhibitor I1, Kazal (2);	0.000000	0.64402	D	0.000004	D	0.89581	0.6756	.	.	.	0.39180	D	0.962751	D	0.89917	1.0	D	0.91635	0.999	D	0.90728	0.4640	9	0.72032	D	0.01	-9.9478	15.8177	0.78615	0.0:1.0:0.0:0.0	.	36	Q6UWN8	ISK6_HUMAN	H	36	ENSP00000421119:P36H;ENSP00000324870:P36H	ENSP00000324870:P36H	P	+	2	0	SPINK6	147573691	0.065000	0.20965	1.000000	0.80357	0.407000	0.30961	1.151000	0.31651	2.885000	0.99019	0.655000	0.94253	CCC	.	.		0.458	SPINK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373332.1	NM_205841	
SLC6A7	6534	hgsc.bcm.edu	37	5	149583547	149583547	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:149583547C>A	ENST00000230671.2	+	10	1649	c.1278C>A	c.(1276-1278)ttC>ttA	p.F426L	SLC6A7_ENST00000524041.1_Missense_Mutation_p.F426L	NM_014228.3	NP_055043.2	Q99884	SC6A7_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 7	426					proline transport (GO:0015824)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(1)|stomach(1)	16		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)	AGGCGGTGTTCTCAGGGCTCA	0.587																																					p.F426L		Atlas-SNP	.											.	SLC6A7	52	.	0			c.C1278A						.						98.0	68.0	78.0					5																	149583547		2203	4300	6503	SO:0001583	missense	6534	exon10			GGTGTTCTCAGGG	S80071	CCDS4305.1	5q32	2013-07-19	2013-07-19		ENSG00000011083	ENSG00000011083		"""Solute carriers"""	11054	protein-coding gene	gene with protein product	"""brain-specific L-proline transporter"", ""sodium-dependent proline transporter"""	606205	"""solute carrier family 6 (neurotransmitter transporter, L-proline), member 7"""			7651355	Standard	NM_014228		Approved	PROT	uc003lrr.3	Q99884	OTTHUMG00000130046	ENST00000230671.2:c.1278C>A	chr5.hg19:g.149583547C>A	ENSP00000230671:p.Phe426Leu	205.0	0.0		236.0	73.0	NM_014228	Q0VG81|Q52LU6	Missense_Mutation	SNP	ENST00000230671.2	hg19	CCDS4305.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.814341	0.32053	.	.	ENSG00000011083	ENST00000230671;ENST00000524041	T;T	0.73575	-0.76;-0.76	5.04	4.17	0.49024	.	0.000000	0.85682	D	0.000000	T	0.59362	0.2188	N	0.13327	0.33	0.58432	D	0.999999	B	0.24317	0.101	B	0.32533	0.147	T	0.55101	-0.8193	10	0.21540	T	0.41	.	12.8423	0.57811	0.0:0.9212:0.0:0.0788	.	426	Q99884	SC6A7_HUMAN	L	426	ENSP00000230671:F426L;ENSP00000428200:F426L	ENSP00000230671:F426L	F	+	3	2	SLC6A7	149563740	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	2.656000	0.46716	2.323000	0.78572	0.561000	0.74099	TTC	.	.		0.587	SLC6A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252325.1	NM_014228	
CD74	972	hgsc.bcm.edu	37	5	149792276	149792276	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:149792276G>A	ENST00000009530.7	-	1	38	c.37C>T	c.(37-39)Cag>Tag	p.Q13*	CD74_ENST00000353334.6_Nonsense_Mutation_p.Q13*|CD74_ENST00000377795.3_Nonsense_Mutation_p.Q13*|CD74_ENST00000524315.1_Nonsense_Mutation_p.Q13*			P04233	HG2A_HUMAN	CD74 molecule, major histocompatibility complex, class II invariant chain	13					activation of MAPK activity (GO:0000187)|antigen processing and presentation of endogenous antigen (GO:0019883)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell proliferation (GO:0008283)|chaperone mediated protein folding requiring cofactor (GO:0051085)|defense response (GO:0006952)|immunoglobulin mediated immune response (GO:0016064)|intracellular protein transport (GO:0006886)|macrophage migration inhibitory factor signaling pathway (GO:0035691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of peptide secretion (GO:0002792)|negative regulation of T cell differentiation (GO:0045581)|negative thymic T cell selection (GO:0045060)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type 2 immune response (GO:0002830)|positive thymic T cell selection (GO:0045059)|prostaglandin biosynthetic process (GO:0001516)|protein complex assembly (GO:0006461)|regulation of macrophage activation (GO:0043030)|signal transduction (GO:0007165)|T cell selection (GO:0045058)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|macrophage migration inhibitory factor receptor complex (GO:0035692)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|NOS2-CD74 complex (GO:0035693)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)|vacuole (GO:0005773)	beta-amyloid binding (GO:0001540)|cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|macrophage migration inhibitory factor binding (GO:0035718)|MHC class II protein binding (GO:0042289)|MHC class II protein binding, via antigen binding groove (GO:0042658)|MHC class II protein complex binding (GO:0023026)|protein binding involved in protein folding (GO:0044183)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)	5		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACTGGCTTCTGATCTTCCCGA	0.607			T	ROS1	NSCLC																																p.Q13X		Atlas-SNP	.		Dom	yes		5	5q32	972	"""CD74 molecule, major histocompatibility complex, class II invariant chain"""		E	.	CD74	35	.	0			c.C37T						.						150.0	152.0	152.0					5																	149792276		2203	4300	6503	SO:0001587	stop_gained	972	exon1			GCTTCTGATCTTC		CCDS34276.1, CCDS47308.1, CCDS47309.1	5q32	2012-09-20	2006-03-28		ENSG00000019582	ENSG00000019582		"""CD molecules"""	1697	protein-coding gene	gene with protein product	"""HLA-DR-gamma"", ""Ia-associated invariant chain"", ""gamma chain of class II antigens"", ""MHC HLA-DR gamma chain"""	142790	"""CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)"""	DHLAG		6324166, 3001652	Standard	NM_004355		Approved		uc003lsc.3	P04233	OTTHUMG00000163559	ENST00000009530.7:c.37C>T	chr5.hg19:g.149792276G>A	ENSP00000009530:p.Gln13*	105.0	0.0		122.0	5.0	NM_001025159	A8K7R1|B4DNE8|D3DQG3|D3DQG4|Q14597|Q29832|Q5U0J8|Q8SNA0|Q8WLP6	Nonsense_Mutation	SNP	ENST00000009530.7	hg19	CCDS47309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.42|17.42	3.385145|3.385145	0.61956|0.61956	.|.	.|.	ENSG00000019582|ENSG00000019582	ENST00000377795;ENST00000353334;ENST00000524315;ENST00000009530|ENST00000518797	.|.	.|.	.|.	5.13|5.13	3.33|3.33	0.38152|0.38152	.|.	1.222100|.	0.05855|.	N|.	0.621922|.	.|T	.|0.43322	.|0.1242	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.51348	.|-0.8717	.|3	0.49607|.	T|.	0.09|.	-3.3246|-3.3246	7.3893|7.3893	0.26901|0.26901	0.2051:0.0:0.7949:0.0|0.2051:0.0:0.7949:0.0	.|.	.|.	.|.	.|.	X|L	13|7	.|.	ENSP00000009530:Q13X|.	Q|S	-|-	1|2	0|0	CD74|CD74	149772469|149772469	0.992000|0.992000	0.36948|0.36948	0.652000|0.652000	0.29579|0.29579	0.099000|0.099000	0.18886|0.18886	2.272000|2.272000	0.43373|0.43373	0.538000|0.538000	0.28769|0.28769	0.591000|0.591000	0.81541|0.81541	CAG|TCA	.	.		0.607	CD74-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374178.1	NM_004355	
HMMR	3161	hgsc.bcm.edu	37	5	162891750	162891750	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:162891750T>C	ENST00000358715.3	+	3	203	c.167T>C	c.(166-168)gTt>gCt	p.V56A	HMMR_ENST00000353866.3_Missense_Mutation_p.V56A|HMMR_ENST00000393915.4_Missense_Mutation_p.V56A|HMMR_ENST00000432118.2_Intron			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	56					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	AATCTTAATGTTGACAAAGAT	0.343																																					p.V56A		Atlas-SNP	.											.	HMMR	64	.	0			c.T167C						.						122.0	121.0	121.0					5																	162891750		2203	4300	6503	SO:0001583	missense	3161	exon3			TTAATGTTGACAA	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"""CD molecules"""	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.167T>C	chr5.hg19:g.162891750T>C	ENSP00000351554:p.Val56Ala	65.0	0.0		73.0	4.0	NM_012485	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	hg19	CCDS4362.1	.	.	.	.	.	.	.	.	.	.	T	1.522	-0.546775	0.04024	.	.	ENSG00000072571	ENST00000353866;ENST00000434157;ENST00000393915;ENST00000426586;ENST00000358715	T;T;T	0.08282	3.11;3.19;3.19	4.85	0.829	0.18847	.	1.167870	0.05896	N	0.629184	T	0.03695	0.0105	N	0.08118	0	0.09310	N	1	B;B;B	0.23249	0.018;0.082;0.082	B;B;B	0.25140	0.031;0.058;0.058	T	0.38134	-0.9675	10	0.02654	T	1	-1.1384	5.0531	0.14518	0.177:0.0:0.3658:0.4572	.	56;56;56	O75330-3;O75330-2;O75330	.;.;HMMR_HUMAN	A	56	ENSP00000185942:V56A;ENSP00000377492:V56A;ENSP00000351554:V56A	ENSP00000185942:V56A	V	+	2	0	HMMR	162824328	0.367000	0.25023	0.427000	0.26684	0.038000	0.13279	0.419000	0.21247	0.771000	0.33359	0.460000	0.39030	GTT	.	.		0.343	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484	
STC2	8614	hgsc.bcm.edu	37	5	172744893	172744893	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:172744893T>C	ENST00000265087.4	-	4	2175	c.866A>G	c.(865-867)gAg>gGg	p.E289G	STC2_ENST00000520593.1_5'Flank	NM_003714.2	NP_003705.1	O76061	STC2_HUMAN	stanniocalcin 2	289					cellular calcium ion homeostasis (GO:0006874)|cellular response to hypoxia (GO:0071456)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|regulation of hormone biosynthetic process (GO:0046885)|regulation of store-operated calcium entry (GO:2001256)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(3)	25	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GTCTTCCCACTCGCTGCTTCC	0.577																																					p.E289G		Atlas-SNP	.											.	STC2	59	.	0			c.A866G						.						83.0	87.0	86.0					5																	172744893		2203	4300	6503	SO:0001583	missense	8614	exon4			TCCCACTCGCTGC	AB012664	CCDS4388.1	5q35.2	2004-05-17			ENSG00000113739	ENSG00000113739			11374	protein-coding gene	gene with protein product		603665				9723890, 9753616	Standard	NM_003714		Approved	STC-2	uc003mco.1	O76061	OTTHUMG00000130542	ENST00000265087.4:c.866A>G	chr5.hg19:g.172744893T>C	ENSP00000265087:p.Glu289Gly	80.0	0.0		81.0	4.0	NM_003714		Missense_Mutation	SNP	ENST00000265087.4	hg19	CCDS4388.1	.	.	.	.	.	.	.	.	.	.	T	15.94	2.982278	0.53827	.	.	ENSG00000113739	ENST00000265087	.	.	.	4.78	4.78	0.61160	.	0.167000	0.52532	D	0.000068	T	0.36991	0.0987	N	0.24115	0.695	0.43263	D	0.995204	P	0.35433	0.501	B	0.27608	0.081	T	0.39542	-0.9609	9	0.56958	D	0.05	-29.9991	14.5043	0.67743	0.0:0.0:0.0:1.0	.	289	O76061	STC2_HUMAN	G	289	.	ENSP00000265087:E289G	E	-	2	0	STC2	172677499	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	3.650000	0.54424	2.008000	0.58898	0.528000	0.53228	GAG	.	.		0.577	STC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252965.1	NM_003714	
PDLIM7	9260	hgsc.bcm.edu	37	5	176910650	176910650	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:176910650C>G	ENST00000355841.2	-	13	1435	c.1369G>C	c.(1369-1371)Gtg>Ctg	p.V457L	PDLIM7_ENST00000359895.2_Missense_Mutation_p.V423L|PDLIM7_ENST00000505746.1_5'Flank|PDLIM7_ENST00000356618.4_3'UTR	NM_005451.3	NP_005442.2	Q9NR12	PDLI7_HUMAN	PDZ and LIM domain 7 (enigma)	457	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of osteoblast differentiation (GO:0045669)|receptor-mediated endocytosis (GO:0006898)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ruffle (GO:0001726)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGGGCTCACACATGAGAGAAG	0.582																																					p.V457L		Atlas-SNP	.											.	PDLIM7	32	.	0			c.G1369C						.						71.0	68.0	69.0					5																	176910650		2203	4300	6503	SO:0001583	missense	9260	exon13			CTCACACATGAGA	BC001093	CCDS4422.1, CCDS4423.1, CCDS4424.1	5q35.3	2008-02-05			ENSG00000196923	ENSG00000196923			22958	protein-coding gene	gene with protein product		605903				11874232	Standard	NM_005451		Approved	ENIGMA	uc003mhc.1	Q9NR12	OTTHUMG00000130853	ENST00000355841.2:c.1369G>C	chr5.hg19:g.176910650C>G	ENSP00000348099:p.Val457Leu	206.0	0.0		277.0	106.0	NM_005451	Q14250|Q5XG82|Q6NVZ5|Q96C91|Q9BXB8|Q9BXB9	Missense_Mutation	SNP	ENST00000355841.2	hg19	CCDS4422.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.007169	0.93287	.	.	ENSG00000196923	ENST00000359895;ENST00000355841	T;T	0.49720	0.88;0.77	5.53	5.53	0.82687	Zinc finger, LIM-type (1);	0.000000	0.47455	D	0.000239	T	0.52108	0.1714	N	0.08118	0	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	T	0.63225	-0.6685	10	0.66056	D	0.02	.	19.128	0.93393	0.0:1.0:0.0:0.0	.	457;423	Q9NR12;Q9NR12-2	PDLI7_HUMAN;.	L	423;457	ENSP00000352964:V423L;ENSP00000348099:V457L	ENSP00000348099:V457L	V	-	1	0	PDLIM7	176843256	0.999000	0.42202	0.977000	0.42913	0.833000	0.47200	5.471000	0.66762	2.625000	0.88918	0.650000	0.86243	GTG	.	.		0.582	PDLIM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253423.1	NM_005451	
GFPT2	9945	hgsc.bcm.edu	37	5	179762947	179762947	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:179762947T>C	ENST00000253778.8	-	4	390	c.221A>G	c.(220-222)gAc>gGc	p.D74G		NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	74	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	GTCCATGCTGTCTTGTTCTAA	0.537																																					p.D74G		Atlas-SNP	.											.	GFPT2	74	.	0			c.A221G						.						147.0	167.0	161.0					5																	179762947		2027	4189	6216	SO:0001583	missense	9945	exon4			ATGCTGTCTTGTT	AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"""glutamine: fructose-6-phosphate aminotransferase 2"""	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.221A>G	chr5.hg19:g.179762947T>C	ENSP00000253778:p.Asp74Gly	131.0	0.0		174.0	7.0	NM_005110	Q53XM2|Q9BWS4	Missense_Mutation	SNP	ENST00000253778.8	hg19	CCDS43411.1	.	.	.	.	.	.	.	.	.	.	T	12.56	1.975261	0.34848	.	.	ENSG00000131459	ENST00000253778	T	0.76578	-1.03	5.21	5.21	0.72293	Glutamine amidotransferase, type II (1);	0.096682	0.64402	D	0.000001	T	0.68044	0.2958	N	0.25647	0.755	0.80722	D	1	B	0.19935	0.04	B	0.29440	0.102	T	0.62627	-0.6814	9	.	.	.	-31.9146	14.7751	0.69726	0.0:0.0:0.0:1.0	.	74	O94808	GFPT2_HUMAN	G	74	ENSP00000253778:D74G	.	D	-	2	0	GFPT2	179695553	1.000000	0.71417	1.000000	0.80357	0.314000	0.28054	6.032000	0.70918	1.965000	0.57142	0.533000	0.62120	GAC	.	.		0.537	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110	
EXOC2	55770	hgsc.bcm.edu	37	6	556010	556010	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:556010A>G	ENST00000230449.4	-	19	2071	c.1936T>C	c.(1936-1938)Ttc>Ctc	p.F646L	EXOC2_ENST00000448181.3_Missense_Mutation_p.F241L	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	646					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		GGTTGTTGGAAGACCTGTAAG	0.348																																					p.F646L		Atlas-SNP	.											.	EXOC2	81	.	0			c.T1936C						.						130.0	123.0	125.0					6																	556010		2203	4300	6503	SO:0001583	missense	55770	exon19			GTTGGAAGACCTG	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.1936T>C	chr6.hg19:g.556010A>G	ENSP00000230449:p.Phe646Leu	94.0	0.0		115.0	5.0	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Missense_Mutation	SNP	ENST00000230449.4	hg19	CCDS34327.1	.	.	.	.	.	.	.	.	.	.	A	13.20	2.165846	0.38217	.	.	ENSG00000112685	ENST00000230449;ENST00000448181	T;T	0.21191	2.02;2.02	5.6	5.6	0.85130	.	0.194343	0.51477	D	0.000084	T	0.09291	0.0229	L	0.47190	1.495	0.58432	D	0.999995	B	0.15141	0.012	B	0.12156	0.007	T	0.09574	-1.0668	10	0.14656	T	0.56	-0.0157	14.6565	0.68835	1.0:0.0:0.0:0.0	.	646	Q96KP1	EXOC2_HUMAN	L	646;241	ENSP00000230449:F646L;ENSP00000398113:F241L	ENSP00000230449:F646L	F	-	1	0	EXOC2	501010	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	5.571000	0.67404	2.248000	0.74166	0.460000	0.39030	TTC	.	.		0.348	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303	
PHACTR1	221692	hgsc.bcm.edu	37	6	13206215	13206215	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:13206215T>C	ENST00000379350.1	+	7	962	c.833T>C	c.(832-834)gTc>gCc	p.V278A	PHACTR1_ENST00000332995.7_Missense_Mutation_p.V278A|PHACTR1_ENST00000457702.2_Missense_Mutation_p.V133A|PHACTR1_ENST00000379345.2_Intron			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	278					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			CACCACACTGTCCTGCCCTCC	0.667																																					p.V278A		Atlas-SNP	.											.	PHACTR1	94	.	0			c.T833C						.						44.0	54.0	51.0					6																	13206215		2136	4229	6365	SO:0001583	missense	221692	exon8			ACACTGTCCTGCC	AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"""Phosphatase and actin regulators"""	20990	protein-coding gene	gene with protein product		608723	"""RPEL repeat containing 1"""	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379350.1:c.833T>C	chr6.hg19:g.13206215T>C	ENSP00000368655:p.Val278Ala	99.0	0.0		126.0	6.0	NM_030948	A8K1V2|Q3MJ93|Q5JSJ2	Missense_Mutation	SNP	ENST00000379350.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.0|22.0	4.229746|4.229746	0.79688|0.79688	.|.	.|.	ENSG00000112137|ENSG00000112137	ENST00000415087|ENST00000379350;ENST00000332995;ENST00000432934;ENST00000457702	.|T;T;T	.|0.32272	.|1.46;1.48;1.52	5.12|5.12	5.12|5.12	0.69794|0.69794	.|.	.|0.279063	.|0.35378	.|N	.|0.003248	T|T	0.21631|0.21631	0.0521|0.0521	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	.|D;P;P	.|0.56287	.|0.975;0.779;0.859	.|D;B;B	.|0.67103	.|0.949;0.204;0.351	T|T	0.04191|0.04191	-1.0970|-1.0970	5|10	.|0.08381	.|T	.|0.77	-16.2317|-16.2317	14.251|14.251	0.66019|0.66019	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|347;278;278	.|E7ESR5;Q9C0D0;Q9C0D0-2	.|.;PHAR1_HUMAN;.	P|A	113|278;278;347;133	.|ENSP00000368655:V278A;ENSP00000329880:V278A;ENSP00000397669:V133A	.|ENSP00000329880:V278A	S|V	+|+	1|2	0|0	PHACTR1|PHACTR1	13314194|13314194	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.962000|0.962000	0.63368|0.63368	4.110000|4.110000	0.57831|0.57831	2.143000|2.143000	0.66587|0.66587	0.459000|0.459000	0.35465|0.35465	TCC|GTC	.	.		0.667	PHACTR1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039876.1	XM_166420	
DDR1	780	hgsc.bcm.edu	37	6	30865154	30865154	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:30865154A>G	ENST00000324771.8	+	17	2545		c.e17-1		DDR1_ENST00000446312.1_Splice_Site|DDR1_ENST00000361741.4_Splice_Site|DDR1_ENST00000418800.2_Splice_Site|DDR1_ENST00000452441.1_Splice_Site|DDR1_ENST00000513240.1_Missense_Mutation_p.R672G|DDR1_ENST00000376575.3_Missense_Mutation_p.R672G|DDR1_ENST00000454612.2_Splice_Site|DDR1_ENST00000508312.1_Splice_Site|DDR1_ENST00000376569.3_Splice_Site|DDR1_ENST00000376570.4_Splice_Site|DDR1_ENST00000376568.3_Splice_Site|DDR1_ENST00000376567.2_Splice_Site			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1						branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	CTTGTTCTCCAGGAATGATTT	0.617																																					p.R672G		Atlas-SNP	.											.	DDR1	213	.	0			c.A2014G						.						56.0	55.0	55.0					6																	30865154		2203	4300	6503	SO:0001630	splice_region_variant	780	exon14			TTCTCCAGGAATG	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1998-1A>G	chr6.hg19:g.30865154A>G		57.0	0.0		79.0	4.0	NM_013994	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	hg19	CCDS34385.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	19.18|19.18|19.18	3.778524|3.778524|3.778524	0.70107|0.70107|0.70107	.|.|.	.|.|.	ENSG00000204580|ENSG00000204580|ENSG00000204580	ENST00000324771;ENST00000418800;ENST00000454612;ENST00000376569;ENST00000376570;ENST00000376568;ENST00000452441;ENST00000508312;ENST00000376567;ENST00000417521;ENST00000361741;ENST00000484556|ENST00000514434|ENST00000376575;ENST00000513240	.|.|D;D	.|.|0.83250	.|.|-1.7;-1.7	5.39|5.39|5.39	5.39|5.39|5.39	0.77823|0.77823|0.77823	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|D|D	.|0.88310|0.88310	.|0.6402|0.6402	M|M|M	0.75884|0.75884|0.75884	2.315|2.315|2.315	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D	.|.|0.89917	.|.|1.0	.|.|D	.|.|0.80764	.|.|0.994	.|D|D	.|0.90136|0.90136	.|0.4210|0.4210	.|5|9	.|.|0.87932	.|.|D	.|.|0	.|.|.	13.3551|13.3551|13.3551	0.60623|0.60623|0.60623	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	.|.|672	.|.|Q08345-5	.|.|.	.|R|G	-1|163|672	.|.|ENSP00000365759:R672G;ENSP00000427552:R672G	.|.|ENSP00000365759:R672G	.|Q|R	+|+|+	.|2|1	.|0|2	DDR1|DDR1|DDR1	30973133|30973133|30973133	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.898000|0.898000|0.898000	0.52572|0.52572|0.52572	9.178000|9.178000|9.178000	0.94855|0.94855|0.94855	2.043000|2.043000|2.043000	0.60533|0.60533|0.60533	0.379000|0.379000|0.379000	0.24179|0.24179|0.24179	.|CAG|AGG	.	.		0.617	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	Intron
SKIV2L	6499	hgsc.bcm.edu	37	6	31929439	31929439	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:31929439A>T	ENST00000375394.2	+	9	1018	c.905A>T	c.(904-906)cAg>cTg	p.Q302L	NELFE_ENST00000375425.5_5'Flank|SKIV2L_ENST00000544581.1_Missense_Mutation_p.Q109L|NELFE_ENST00000375429.3_5'Flank|NELFE_ENST00000444811.2_5'Flank	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	302					ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						CTCATTCCCCAGCCAGCCTTC	0.602																																					p.Q302L		Atlas-SNP	.											.	SKIV2L	97	.	0			c.A905T						.						115.0	102.0	107.0					6																	31929439		1511	2709	4220	SO:0001583	missense	6499	exon9			TTCCCCAGCCAGC		CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"""superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"""	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.905A>T	chr6.hg19:g.31929439A>T	ENSP00000364543:p.Gln302Leu	58.0	0.0		117.0	36.0	NM_006929	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	hg19	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	A	19.74	3.884208	0.72410	.	.	ENSG00000204351	ENST00000375394;ENST00000433155;ENST00000544581	T;T	0.49432	0.92;0.78	5.58	5.58	0.84498	.	0.203542	0.45126	D	0.000396	T	0.25606	0.0623	L	0.37561	1.115	0.43430	D	0.995596	B	0.17667	0.023	B	0.12837	0.008	T	0.08126	-1.0737	10	0.44086	T	0.13	-14.2619	14.7342	0.69404	1.0:0.0:0.0:0.0	.	302	Q15477	SKIV2_HUMAN	L	302;144;109	ENSP00000364543:Q302L;ENSP00000442645:Q109L	ENSP00000364543:Q302L	Q	+	2	0	SKIV2L	32037418	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.509000	0.81698	2.131000	0.65755	0.533000	0.62120	CAG	.	.		0.602	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3		
BTNL2	56244	hgsc.bcm.edu	37	6	32370747	32370747	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:32370747A>G	ENST00000374993.1	-	3	673	c.674T>C	c.(673-675)cTc>cCc	p.L225P	BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000374995.3_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000454136.3_Missense_Mutation_p.L225P|BTNL2_ENST00000544175.1_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	225	Ig-like V-type 2.					integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						CTCCTCAGTGAGGACGGGGTT	0.592																																					p.L225P		Atlas-SNP	.											.	BTNL2	50	.	0			c.T674C						.						70.0	59.0	63.0					6																	32370747		1511	2708	4219	SO:0001583	missense	56244	exon3			TCAGTGAGGACGG	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.674T>C	chr6.hg19:g.32370747A>G	ENSP00000364132:p.Leu225Pro	173.0	0.0		193.0	8.0	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.89	2.671742	0.47781	.	.	ENSG00000204290	ENST00000468270;ENST00000374993	T	0.17854	2.25	4.49	3.34	0.38264	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.160951	0.29916	N	0.010867	T	0.33440	0.0863	M	0.93462	3.42	0.19775	N	0.99996	D	0.89917	1.0	D	0.97110	1.0	T	0.28554	-1.0040	10	0.87932	D	0	.	6.5935	0.22659	0.8925:0.0:0.1075:0.0	.	225	Q9UIR0	BTNL2_HUMAN	P	225	ENSP00000364132:L225P	ENSP00000364132:L225P	L	-	2	0	BTNL2	32478725	0.083000	0.21467	0.008000	0.14137	0.084000	0.17831	3.018000	0.49625	0.911000	0.36747	0.509000	0.49947	CTC	.	.		0.592	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
RNF8	9025	hgsc.bcm.edu	37	6	37344709	37344709	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:37344709A>G	ENST00000373479.4	+	6	1329	c.1136A>G	c.(1135-1137)aAg>aGg	p.K379R	RNF8_ENST00000469731.1_Missense_Mutation_p.K379R	NM_003958.3|NM_183078.2	NP_003949.1|NP_898901.1	O76064	RNF8_HUMAN	ring finger protein 8, E3 ubiquitin protein ligase	379					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|histone exchange (GO:0043486)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A ubiquitination (GO:0033522)|histone H2B ubiquitination (GO:0033523)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|mitotic nuclear division (GO:0007067)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|response to ionizing radiation (GO:0010212)|spermatid development (GO:0007286)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome, telomeric region (GO:0000781)|nucleolus (GO:0005730)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	13						CAGGAAGAGAAGGAGAAGATG	0.403																																					p.K379R		Atlas-SNP	.											.	RNF8	78	.	0			c.A1136G						.						136.0	124.0	128.0					6																	37344709		2203	4300	6503	SO:0001583	missense	9025	exon6			AAGAGAAGGAGAA	AB012770	CCDS4833.1, CCDS4834.1	6p21.3	2013-01-09	2012-02-23		ENSG00000112130	ENSG00000112130		"""RING-type (C3HC4) zinc fingers"""	10071	protein-coding gene	gene with protein product		611685	"""ring finger protein (C3HC4 type) 8"", ""ring finger protein 8"""			9734811, 9852682	Standard	NM_003958		Approved	KIAA0646	uc003onq.4	O76064	OTTHUMG00000014620	ENST00000373479.4:c.1136A>G	chr6.hg19:g.37344709A>G	ENSP00000362578:p.Lys379Arg	63.0	0.0		90.0	5.0	NM_003958	A6NN24|A8MYC0|B4DPG0|Q53H16|Q5NKW5	Missense_Mutation	SNP	ENST00000373479.4	hg19	CCDS4834.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.689319	0.88735	.	.	ENSG00000112130	ENST00000373479;ENST00000469731	D;T	0.84660	-1.88;-0.4	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.89223	0.6654	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.90435	0.4427	10	0.62326	D	0.03	.	14.8201	0.70065	1.0:0.0:0.0:0.0	.	379	O76064	RNF8_HUMAN	R	379	ENSP00000362578:K379R;ENSP00000418879:K379R	ENSP00000362578:K379R	K	+	2	0	RNF8	37452687	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	8.962000	0.93254	2.093000	0.63338	0.533000	0.62120	AAG	.	.		0.403	RNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040403.2		
MDGA1	266727	hgsc.bcm.edu	37	6	37631783	37631783	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:37631783A>G	ENST00000434837.3	-	2	1345	c.167T>C	c.(166-168)cTc>cCc	p.L56P	MDGA1_ENST00000505425.1_Missense_Mutation_p.L56P|MDGA1_ENST00000297153.7_Missense_Mutation_p.L56P	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	56	Ig-like 1.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						CTGCAGCATGAGGGTGTCCCC	0.637																																					p.L56P		Atlas-SNP	.											.	MDGA1	104	.	0			c.T167C						.						77.0	79.0	79.0					6																	37631783		2119	4230	6349	SO:0001583	missense	266727	exon2			AGCATGAGGGTGT	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.167T>C	chr6.hg19:g.37631783A>G	ENSP00000402584:p.Leu56Pro	148.0	0.0		175.0	7.0	NM_153487	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	hg19	CCDS47417.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.722819	0.89298	.	.	ENSG00000112139	ENST00000434837;ENST00000297153;ENST00000505425	T;T;T	0.52983	0.64;0.64;0.64	5.25	5.25	0.73442	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.40818	N	0.001019	T	0.65354	0.2683	M	0.85945	2.785	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.72846	-0.4169	10	0.72032	D	0.01	.	14.3559	0.66738	1.0:0.0:0.0:0.0	.	56	Q8NFP4	MDGA1_HUMAN	P	56	ENSP00000402584:L56P;ENSP00000297153:L56P;ENSP00000422042:L56P	ENSP00000297153:L56P	L	-	2	0	MDGA1	37739761	1.000000	0.71417	0.968000	0.41197	0.985000	0.73830	9.339000	0.96797	1.994000	0.58287	0.533000	0.62120	CTC	.	.		0.637	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		
TRERF1	55809	hgsc.bcm.edu	37	6	42232472	42232472	+	Silent	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:42232472C>T	ENST00000372922.4	-	7	2167	c.1605G>A	c.(1603-1605)ggG>ggA	p.G535G	TRERF1_ENST00000372917.4_Silent_p.G535G|TRERF1_ENST00000340840.2_Silent_p.G535G|TRERF1_ENST00000354325.2_Silent_p.G535G|TRERF1_ENST00000541110.1_Silent_p.G535G	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	535	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CCCTCATTCCCCCGTGGGACC	0.567																																					p.G535G		Atlas-SNP	.											.	TRERF1	124	.	0			c.G1605A						.						96.0	85.0	89.0					6																	42232472		2203	4300	6503	SO:0001819	synonymous_variant	55809	exon7			CATTCCCCCGTGG	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.1605G>A	chr6.hg19:g.42232472C>T		98.0	0.0		121.0	5.0	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	hg19	CCDS4867.1																																																																																			.	.		0.567	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
ABCC10	89845	hgsc.bcm.edu	37	6	43413441	43413441	+	Silent	SNP	C	C	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:43413441C>A	ENST00000372530.4	+	15	3350	c.3135C>A	c.(3133-3135)atC>atA	p.I1045I	ABCC10_ENST00000244533.3_Silent_p.I1017I	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	1045	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	TCCTCAACATCCTCCTGGCCA	0.627																																					p.I1045I		Atlas-SNP	.											.	ABCC10	118	.	0			c.C3135A						.						64.0	56.0	58.0					6																	43413441		2203	4300	6503	SO:0001819	synonymous_variant	89845	exon15			CAACATCCTCCTG	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"""ATP binding cassette transporters / subfamily C"""	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.3135C>A	chr6.hg19:g.43413441C>A		258.0	0.0		251.0	102.0	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Silent	SNP	ENST00000372530.4	hg19	CCDS56430.1																																																																																			.	.		0.627	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
TJAP1	93643	hgsc.bcm.edu	37	6	43473140	43473140	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:43473140A>G	ENST00000372445.5	+	11	1597	c.1221A>G	c.(1219-1221)gaA>gaG	p.E407E	TJAP1_ENST00000438588.2_Silent_p.E407E|TJAP1_ENST00000259751.1_Silent_p.E397E|TJAP1_ENST00000372444.2_Silent_p.E397E|TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000436109.2_Silent_p.E397E|TJAP1_ENST00000372452.1_Silent_p.E397E|TJAP1_ENST00000372449.1_Silent_p.E407E	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	407					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			CCAGCTCTGAAGAGGACCTGC	0.667																																					p.E407E		Atlas-SNP	.											.	TJAP1	35	.	0			c.A1221G						.						38.0	39.0	39.0					6																	43473140		2203	4300	6503	SO:0001819	synonymous_variant	93643	exon11			CTCTGAAGAGGAC	AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"""tight junction protein 4 (peripheral)"""	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.1221A>G	chr6.hg19:g.43473140A>G		55.0	0.0		79.0	4.0	NM_001146016	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Silent	SNP	ENST00000372445.5	hg19	CCDS55004.1																																																																																			.	.		0.667	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604	
ANKRD66	100287718	hgsc.bcm.edu	37	6	46726514	46726514	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:46726514T>C	ENST00000565422.1	+	5	617	c.612T>C	c.(610-612)ccT>ccC	p.P204P	RP11-268F1.3_ENST00000438738.1_lincRNA|ANKRD66_ENST00000536046.1_Silent_p.P175P	NM_001162435.2	NP_001155907.2	B4E2M5	ANR66_HUMAN	ankyrin repeat domain 66	204																	AGGGGCTGCCTCTGGATGAGC	0.517																																					p.P204P		Atlas-SNP	.											.	.	.	.	0			c.T612C						.						42.0	42.0	42.0					6																	46726514		692	1591	2283	SO:0001819	synonymous_variant	100287718	exon5			GCTGCCTCTGGAT	AK304342	CCDS59024.1	6p12.3	2013-01-11			ENSG00000230062	ENSG00000230062		"""Ankyrin repeat domain containing"""	44669	protein-coding gene	gene with protein product							Standard	NM_001162435		Approved		uc011dwf.2	B4E2M5	OTTHUMG00000014791	ENST00000565422.1:c.612T>C	chr6.hg19:g.46726514T>C		41.0	0.0		101.0	6.0	NM_001162435		Silent	SNP	ENST00000565422.1	hg19	CCDS59024.1																																																																																			.	.		0.517	ANKRD66-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432045.1	NM_001162435	
EYS	346007	hgsc.bcm.edu	37	6	66204564	66204564	+	Missense_Mutation	SNP	G	G	A	rs367977860	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:66204564G>A	ENST00000370621.3	-	4	1266	c.740C>T	c.(739-741)cCa>cTa	p.P247L	EYS_ENST00000370618.3_Missense_Mutation_p.P247L|EYS_ENST00000393380.2_Missense_Mutation_p.P247L|EYS_ENST00000342421.5_Missense_Mutation_p.P247L|EYS_ENST00000503581.1_Missense_Mutation_p.P247L|EYS_ENST00000370616.2_Missense_Mutation_p.P247L			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	247	EGF-like 2. {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						ACCTGTAAATGGTGGGTGACA	0.284													G|||	3	0.000599042	0.0023	0.0	5008	,	,		16336	0.0		0.0	False		,,,				2504	0.0				p.P247L		Atlas-SNP	.											.	EYS	527	.	0			c.C740T						.	G	LEU/PRO,LEU/PRO,LEU/PRO	4,4388		0,4,2192	14.0	14.0	14.0		740,740,740	-4.2	0.0	6		14	0,8560		0,0,4280	no	missense,missense,missense	EYS	NM_001142800.1,NM_001142801.1,NM_198283.1	98,98,98	0,4,6472	AA,AG,GG		0.0,0.0911,0.0309	possibly-damaging,possibly-damaging,possibly-damaging	247/3145,247/620,247/595	66204564	4,12948	2196	4280	6476	SO:0001583	missense	346007	exon4			GTAAATGGTGGGT		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.740C>T	chr6.hg19:g.66204564G>A	ENSP00000359655:p.Pro247Leu	62.0	0.0		73.0	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		.	.	.	.	.	.	.	.	.	.	G	14.46	2.540902	0.45280	9.11E-4	0.0	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	D;D;D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08;-3.08;-3.08	4.72	-4.15	0.03881	.	.	.	.	.	T	0.75810	0.3900	N	0.08118	0	0.09310	N	1	P;P;P	0.44139	0.557;0.793;0.827	B;B;P	0.47827	0.085;0.422;0.558	T	0.70839	-0.4763	9	0.87932	D	0	.	9.0906	0.36607	0.089:0.0:0.1952:0.7158	.	247;247;247	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	L	247	ENSP00000424243:P247L;ENSP00000359655:P247L;ENSP00000359650:P247L;ENSP00000377042:P247L;ENSP00000341818:P247L;ENSP00000359652:P247L	ENSP00000341818:P247L	P	-	2	0	EYS	66261285	0.289000	0.24334	0.004000	0.12327	0.896000	0.52359	0.673000	0.25203	-0.453000	0.07076	0.591000	0.81541	CCA	.	.		0.284	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
DDX43	55510	hgsc.bcm.edu	37	6	74125911	74125911	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:74125911A>G	ENST00000370336.4	+	16	2067	c.1909A>G	c.(1909-1911)Atg>Gtg	p.M637V	MB21D1_ENST00000370318.1_Intron	NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	637					ATP catabolic process (GO:0006200)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						GGAAAGAAAAATGGAAAGACC	0.378																																					p.M637V		Atlas-SNP	.											.	DDX43	69	.	0			c.A1909G						.						112.0	111.0	112.0					6																	74125911		2203	4300	6503	SO:0001583	missense	55510	exon16			AGAAAAATGGAAA		CCDS4977.1	6q13	2014-01-21			ENSG00000080007	ENSG00000080007		"""DEAD-boxes"""	18677	protein-coding gene	gene with protein product	"""cancer/testis antigen 13"""	606286				10919659	Standard	NM_018665		Approved	HAGE, DKFZp434H2114, CT13	uc003pgw.3	Q9NXZ2	OTTHUMG00000015033	ENST00000370336.4:c.1909A>G	chr6.hg19:g.74125911A>G	ENSP00000359361:p.Met637Val	57.0	0.0		71.0	4.0	NM_018665	B4E0C8|Q6NXR1	Missense_Mutation	SNP	ENST00000370336.4	hg19	CCDS4977.1	.	.	.	.	.	.	.	.	.	.	A	6.548	0.469322	0.12461	.	.	ENSG00000080007	ENST00000370336	T	0.14266	2.52	5.26	-0.547	0.11836	.	0.548016	0.18229	N	0.147631	T	0.02119	0.0066	L	0.36672	1.1	0.23581	N	0.997368	B	0.15719	0.014	B	0.12837	0.008	T	0.45175	-0.9279	10	0.16896	T	0.51	-8.7957	2.6132	0.04897	0.3832:0.0897:0.0848:0.4424	.	637	Q9NXZ2	DDX43_HUMAN	V	637	ENSP00000359361:M637V	ENSP00000359361:M637V	M	+	1	0	DDX43	74182632	0.000000	0.05858	0.995000	0.50966	0.973000	0.67179	-0.607000	0.05648	0.085000	0.17107	0.482000	0.46254	ATG	.	.		0.378	DDX43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041219.3	NM_018665	
TTK	7272	hgsc.bcm.edu	37	6	80721476	80721476	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:80721476A>G	ENST00000369798.2	+	7	870	c.759A>G	c.(757-759)atA>atG	p.I253M	TTK_ENST00000230510.3_Missense_Mutation_p.I253M|TTK_ENST00000509894.1_Missense_Mutation_p.I253M	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	253					chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		ATGCAGAAATAGGTTACCGGA	0.333																																					p.I253M		Atlas-SNP	.											.	TTK	199	.	0			c.A759G						.						59.0	54.0	56.0					6																	80721476		2201	4298	6499	SO:0001583	missense	7272	exon7			AGAAATAGGTTAC		CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"""cancer/testis antigen 96"", ""monopolar spindle 1 kinase"""	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.759A>G	chr6.hg19:g.80721476A>G	ENSP00000358813:p.Ile253Met	104.0	0.0		125.0	5.0	NM_003318	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	hg19	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	A	11.38	1.622276	0.28889	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798	D;D;D	0.88509	-2.39;-2.39;-2.39	5.36	1.1	0.20463	.	0.389746	0.30820	N	0.008803	T	0.63367	0.2505	L	0.34521	1.04	0.20975	N	0.999816	B;B	0.15141	0.01;0.012	B;B	0.08055	0.002;0.003	T	0.55121	-0.8190	10	0.33940	T	0.23	.	3.5593	0.07875	0.5676:0.1947:0.2377:0.0	.	253;253	P33981;A8K8U5	TTK_HUMAN;.	M	253	ENSP00000422936:I253M;ENSP00000230510:I253M;ENSP00000358813:I253M	ENSP00000230510:I253M	I	+	3	3	TTK	80778195	0.005000	0.15991	0.693000	0.30195	0.812000	0.45895	-0.045000	0.12003	0.374000	0.24650	0.533000	0.62120	ATA	.	.		0.333	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2		
NDUFAF4	29078	hgsc.bcm.edu	37	6	97338980	97338980	+	Nonstop_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:97338980T>C	ENST00000316149.7	-	3	607	c.528A>G	c.(526-528)tgA>tgG	p.*176W	NDUFAF4_ENST00000489477.1_5'Flank	NM_014165.3	NP_054884.1	Q9P032	NDUF4_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 4	0					mitochondrial respiratory chain complex I assembly (GO:0032981)	mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)				large_intestine(5)|lung(3)|ovary(1)|skin(1)	10						GTGATTTTCTTCATTTTGATC	0.299																																					p.X176W		Atlas-SNP	.											.	NDUFAF4	16	.	0			c.A528G						.						64.0	61.0	62.0					6																	97338980		2202	4297	6499	SO:0001578	stop_lost	29078	exon3			TTTTCTTCATTTT	AF161474	CCDS5037.1	6q16.3	2012-10-12	2012-05-08	2009-03-18	ENSG00000123545	ENSG00000123545		"""Mitochondrial respiratory chain complex assembly factors"""	21034	protein-coding gene	gene with protein product		611776	"""chromosome 6 open reading frame 66"", ""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 4"""	C6orf66		11042152, 18179882	Standard	NM_014165		Approved	HSPC125, bA22L21.1, My013, HRPAP20	uc003pow.3	Q9P032	OTTHUMG00000015246	ENST00000316149.7:c.528A>G	chr6.hg19:g.97338980T>C	ENSP00000358272:p.*176Cysext*28	47.0	0.0		87.0	4.0	NM_014165	B2R4J5	Missense_Mutation	SNP	ENST00000316149.7	hg19	CCDS5037.1	.	.	.	.	.	.	.	.	.	.	T	13.12	2.141894	0.37825	.	.	ENSG00000123545	ENST00000316149	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0252	0.42068	0.1504:0.0:0.0:0.8496	.	.	.	.	W	176	.	.	X	-	3	0	NDUFAF4	97445701	1.000000	0.71417	1.000000	0.80357	0.516000	0.34256	5.084000	0.64462	1.870000	0.54199	0.533000	0.62120	TGA	.	.		0.299	NDUFAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041567.1	NM_014165	
PRDM1	639	hgsc.bcm.edu	37	6	106536122	106536122	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:106536122C>T	ENST00000369096.4	+	2	323	c.89C>T	c.(88-90)gCa>gTa	p.A30V	PRDM1_ENST00000369091.2_5'UTR	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	30					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		CAGGGATTGGCAGAGGGGACC	0.517			"""D, N, Mis, F, S"""		DLBCL																																p.A30V		Atlas-SNP	.		Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	.	PRDM1	195	.	0			c.C89T						.						93.0	82.0	86.0					6																	106536122		2203	4300	6503	SO:0001583	missense	639	exon2			GATTGGCAGAGGG		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"""Zinc fingers, C2H2-type"""	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.89C>T	chr6.hg19:g.106536122C>T	ENSP00000358092:p.Ala30Val	130.0	0.0		172.0	59.0	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	hg19	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	C	6.475	0.455764	0.12283	.	.	ENSG00000057657	ENST00000369096	T	0.07021	3.23	5.68	3.66	0.41972	.	.	.	.	.	T	0.00998	0.0033	N	0.02011	-0.69	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.42292	-0.9460	9	0.31617	T	0.26	-1.9257	4.8248	0.13410	0.0:0.5646:0.1843:0.251	.	30	O75626	PRDM1_HUMAN	V	30	ENSP00000358092:A30V	ENSP00000358092:A30V	A	+	2	0	PRDM1	106642815	0.749000	0.28305	0.999000	0.59377	0.644000	0.38419	0.020000	0.13466	1.402000	0.46780	0.655000	0.94253	GCA	.	.		0.517	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3		
PRDM1	639	hgsc.bcm.edu	37	6	106553019	106553019	+	Silent	SNP	C	C	T	rs542551556		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:106553019C>T	ENST00000369096.4	+	5	1218	c.984C>T	c.(982-984)ccC>ccT	p.P328P	PRDM1_ENST00000369089.3_Silent_p.P194P|PRDM1_ENST00000369091.2_Silent_p.P292P	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	328					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		CTCGCTCCCCCATTCCATCCT	0.607			"""D, N, Mis, F, S"""		DLBCL																																p.P328P		Atlas-SNP	.		Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	.	PRDM1	195	.	0			c.C984T						.						76.0	70.0	72.0					6																	106553019		2203	4300	6503	SO:0001819	synonymous_variant	639	exon5			CTCCCCCATTCCA		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"""Zinc fingers, C2H2-type"""	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.984C>T	chr6.hg19:g.106553019C>T		26.0	0.0		44.0	18.0	NM_001198	B2REA6|E1P5E0|Q86WM7	Silent	SNP	ENST00000369096.4	hg19	CCDS5054.2																																																																																			.	.		0.607	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3		
C6orf203	51250	hgsc.bcm.edu	37	6	107372314	107372314	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:107372314A>G	ENST00000405204.2	+	4	1204	c.597A>G	c.(595-597)ggA>ggG	p.G199G	C6orf203_ENST00000311381.5_Silent_p.G199G|C6orf203_ENST00000443043.1_Silent_p.G204G	NM_001142468.1	NP_001135940.1	Q9P0P8	CF203_HUMAN	chromosome 6 open reading frame 203	199						mitochondrion (GO:0005739)				large_intestine(4)|lung(2)|prostate(1)|urinary_tract(1)	8	Breast(9;0.00124)|all_epithelial(6;0.0729)	all_cancers(87;0.00461)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|Colorectal(196;0.171)|all_epithelial(87;0.23)	BRCA - Breast invasive adenocarcinoma(8;0.000395)|all cancers(7;0.00065)|Epithelial(6;0.000834)|OV - Ovarian serous cystadenocarcinoma(5;0.244)	BRCA - Breast invasive adenocarcinoma(108;0.117)		AAGAAGCAGGAACAGAGACAG	0.393																																					p.G204G		Atlas-SNP	.											.	C6orf203	26	.	0			c.A612G						.						109.0	114.0	112.0					6																	107372314		2203	4300	6503	SO:0001819	synonymous_variant	51250	exon5			AGCAGGAACAGAG	AF151064	CCDS5058.1	6q21	2012-02-22			ENSG00000130349	ENSG00000130349			17971	protein-coding gene	gene with protein product						11042152, 11707072	Standard	XM_005267008		Approved	HSPC230, PRED31	uc003prq.3	Q9P0P8	OTTHUMG00000015307	ENST00000405204.2:c.597A>G	chr6.hg19:g.107372314A>G		64.0	0.0		93.0	4.0	NM_001142470	B3KRG9	Silent	SNP	ENST00000405204.2	hg19	CCDS5058.1																																																																																			.	.		0.393	C6orf203-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041684.1	NM_016487	
OSTM1	28962	hgsc.bcm.edu	37	6	108370618	108370618	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:108370618T>C	ENST00000193322.3	-	5	873	c.788A>G	c.(787-789)aAc>aGc	p.N263S		NM_014028.3	NP_054747.2	Q86WC4	OSTM1_HUMAN	osteopetrosis associated transmembrane protein 1	263					ion transmembrane transport (GO:0034220)|osteoclast differentiation (GO:0030316)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0131)|Epithelial(106;0.0438)|OV - Ovarian serous cystadenocarcinoma(136;0.0571)|all cancers(137;0.0581)		TCGAGTGATGTTCATCTGGAA	0.333																																					p.N263S	Melanoma(162;1427 1909 3096 17430 21396)	Atlas-SNP	.											.	OSTM1	22	.	0			c.A788G						.						120.0	114.0	116.0					6																	108370618		2203	4300	6503	SO:0001583	missense	28962	exon5			GTGATGTTCATCT	AF533891	CCDS5062.1	6q21	2014-06-17			ENSG00000081087	ENSG00000081087			21652	protein-coding gene	gene with protein product	"""CLCN7 accessory beta subunit"""	607649				12627228, 21527911	Standard	NM_014028		Approved	HSPC019, GL	uc003psd.3	Q86WC4	OTTHUMG00000015317	ENST00000193322.3:c.788A>G	chr6.hg19:g.108370618T>C	ENSP00000193322:p.Asn263Ser	82.0	0.0		100.0	4.0	NM_014028	E1P5E3|Q5R391|Q6PCA7|Q7RTW6|Q8NC29|Q8TC82|Q9Y2S9	Missense_Mutation	SNP	ENST00000193322.3	hg19	CCDS5062.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.211517	0.79240	.	.	ENSG00000081087	ENST00000193322;ENST00000440575	T	0.79141	-1.24	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.87285	0.6139	M	0.85945	2.785	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89687	0.3895	10	0.87932	D	0	-8.0917	15.6053	0.76664	0.0:0.0:0.0:1.0	.	263	Q86WC4	OSTM1_HUMAN	S	263;116	ENSP00000193322:N263S	ENSP00000193322:N263S	N	-	2	0	OSTM1	108477311	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	7.694000	0.84235	2.095000	0.63458	0.482000	0.46254	AAC	.	.		0.333	OSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041709.3	NM_014028	
MICAL1	64780	hgsc.bcm.edu	37	6	109773524	109773524	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:109773524T>C	ENST00000358807.3	-	6	1068	c.757A>G	c.(757-759)Aca>Gca	p.T253A	MICAL1_ENST00000368952.4_Missense_Mutation_p.T272A|MICAL1_ENST00000483856.1_5'UTR|MICAL1_ENST00000358577.3_Missense_Mutation_p.T253A	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	253	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein phosphorylation (GO:0001933)|oxidation-reduction process (GO:0055114)|signal transduction (GO:0007165)|sulfur oxidation (GO:0019417)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		GGCACCTGTGTCTCCTCCACG	0.537																																					p.T253A		Atlas-SNP	.											.	MICAL1	79	.	0			c.A757G						.						124.0	121.0	122.0					6																	109773524		2203	4300	6503	SO:0001583	missense	64780	exon6			CCTGTGTCTCCTC	AB048948	CCDS5076.1, CCDS55047.1	6q21	2013-03-26	2013-03-26	2005-02-16	ENSG00000135596	ENSG00000135596			20619	protein-coding gene	gene with protein product		607129	"""NEDD9 interacting protein with calponin homology and LIM domains"""	NICAL		11827972	Standard	NM_022765		Approved	MICAL, FLJ11937, DKFZp434B1517, FLJ21739	uc003ptk.3	Q8TDZ2	OTTHUMG00000015350	ENST00000358807.3:c.757A>G	chr6.hg19:g.109773524T>C	ENSP00000351664:p.Thr253Ala	80.0	0.0		128.0	6.0	NM_001159291	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Missense_Mutation	SNP	ENST00000358807.3	hg19	CCDS5076.1	.	.	.	.	.	.	.	.	.	.	T	7.749	0.703019	0.15172	.	.	ENSG00000135596	ENST00000358807;ENST00000368952;ENST00000358577	T;T;T	0.05382	3.45;3.45;3.45	5.63	5.63	0.86233	.	0.122445	0.56097	D	0.000034	T	0.00784	0.0026	N	0.04805	-0.155	0.27264	N	0.958543	B;B;B	0.21688	0.006;0.059;0.035	B;B;B	0.20955	0.006;0.032;0.014	T	0.46925	-0.9156	10	0.02654	T	1	.	8.3661	0.32387	0.0:0.0873:0.0:0.9127	.	272;253;253	B7Z3R5;Q8TDZ2-2;Q8TDZ2	.;.;MICA1_HUMAN	A	253;272;253	ENSP00000351664:T253A;ENSP00000357948:T272A;ENSP00000351385:T253A	ENSP00000351385:T253A	T	-	1	0	MICAL1	109880217	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	4.959000	0.63666	2.140000	0.66376	0.448000	0.29417	ACA	.	.		0.537	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765	
MED23	9439	hgsc.bcm.edu	37	6	131931307	131931307	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:131931307T>C	ENST00000368068.3	-	11	1135	c.956A>G	c.(955-957)gAg>gGg	p.E319G	MED23_ENST00000368053.4_Missense_Mutation_p.E325G|MED23_ENST00000539158.1_Missense_Mutation_p.E319G|MED23_ENST00000368060.3_Missense_Mutation_p.E319G|MED23_ENST00000368058.1_Missense_Mutation_p.E325G|MED23_ENST00000354577.4_Missense_Mutation_p.E325G|MED23_ENST00000403834.3_Missense_Mutation_p.E325G|MED23_ENST00000540546.1_Missense_Mutation_p.E325G|MED23_ENST00000545957.1_Missense_Mutation_p.E8G	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	319					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		GTCAAACTTCTCCTCGGTCTC	0.493																																					p.E325G		Atlas-SNP	.											.	MED23	112	.	0			c.A974G						.						115.0	108.0	110.0					6																	131931307		2203	4300	6503	SO:0001583	missense	9439	exon12			AACTTCTCCTCGG	AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"""cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"""	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.956A>G	chr6.hg19:g.131931307T>C	ENSP00000357047:p.Glu319Gly	44.0	0.0		78.0	4.0	NM_015979	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Missense_Mutation	SNP	ENST00000368068.3	hg19	CCDS5147.1	.	.	.	.	.	.	.	.	.	.	T	18.09	3.545336	0.65198	.	.	ENSG00000112282	ENST00000354577;ENST00000368068;ENST00000403834;ENST00000368060;ENST00000368058;ENST00000545957;ENST00000368053;ENST00000540546;ENST00000539158	T;T;T;T;T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14	5.76	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.74084	0.3670	L	0.39898	1.24	0.80722	D	1	P;B;D;D	0.63046	0.625;0.435;0.992;0.99	B;B;D;P	0.63113	0.265;0.179;0.911;0.856	T	0.72487	-0.4278	10	0.29301	T	0.29	-0.0437	12.3052	0.54898	0.1264:0.0:0.0:0.8736	.	8;325;319;325	B4E3G4;Q9ULK4-2;Q9ULK4;Q9ULK4-3	.;.;MED23_HUMAN;.	G	325;319;325;319;325;8;325;325;319	ENSP00000346588:E325G;ENSP00000357047:E319G;ENSP00000384536:E325G;ENSP00000357039:E319G;ENSP00000357037:E325G;ENSP00000439977:E8G;ENSP00000357032:E325G;ENSP00000437818:E325G;ENSP00000445072:E319G	ENSP00000346588:E325G	E	-	2	0	MED23	131973000	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	6.281000	0.72632	2.204000	0.70986	0.482000	0.46254	GAG	.	.		0.493	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1		
HBS1L	10767	hgsc.bcm.edu	37	6	135358603	135358603	+	Intron	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:135358603T>C	ENST00000367837.5	-	4	637				HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367822.5_Missense_Mutation_p.E331G|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000415177.2_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		AGTCATATTTTCCAACGAGCT	0.289																																					p.E331G		Atlas-SNP	.											.	HBS1L	75	.	0			c.A992G						.						32.0	26.0	28.0					6																	135358603		692	1590	2282	SO:0001627	intron_variant	10767	exon5			ATATTTTCCAACG	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+2107A>G	chr6.hg19:g.135358603T>C		106.0	0.0		137.0	6.0	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	hg19	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	T	13.07	2.128182	0.37533	.	.	ENSG00000112339	ENST00000367822	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	T	0.31104	0.0786	.	.	.	0.80722	D	1	B	0.27559	0.181	B	0.30646	0.118	T	0.42599	-0.9442	7	0.54805	T	0.06	.	4.8834	0.13690	0.0:0.1141:0.1863:0.6996	.	331	Q9Y450-2	.	G	331	.	ENSP00000356796:E331G	E	-	2	0	HBS1L	135400296	1.000000	0.71417	0.998000	0.56505	0.510000	0.34073	2.111000	0.41883	2.194000	0.70268	0.533000	0.62120	GAA	.	.		0.289	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
MYB	4602	hgsc.bcm.edu	37	6	135507076	135507076	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:135507076A>G	ENST00000367814.4	+	2	245	c.59A>G	c.(58-60)gAg>gGg	p.E20G	MYB_ENST00000525369.1_Missense_Mutation_p.E20G|MYB_ENST00000527615.1_Missense_Mutation_p.E20G|MYB_ENST00000533624.1_Missense_Mutation_p.E20G|MYB_ENST00000531845.1_3'UTR|MYB_ENST00000442647.2_Missense_Mutation_p.E20G|MYB_ENST00000534044.1_Missense_Mutation_p.E20G|MYB_ENST00000534121.1_Missense_Mutation_p.E20G|MYB_ENST00000341911.5_Missense_Mutation_p.E20G|MYB_ENST00000420123.2_Missense_Mutation_p.E20G|MYB_ENST00000316528.8_Missense_Mutation_p.E20G|MYB_ENST00000528774.1_Missense_Mutation_p.E20G	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog	20					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		GAGGACTTTGAGATGTGTGAC	0.448			T	NFIB	adenoid cystic carcinoma																																p.E20G		Atlas-SNP	.		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	.	MYB	137	.	0			c.A59G						.						179.0	163.0	168.0					6																	135507076		2203	4300	6503	SO:0001583	missense	4602	exon2			ACTTTGAGATGTG		CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.59A>G	chr6.hg19:g.135507076A>G	ENSP00000356788:p.Glu20Gly	80.0	0.0		90.0	4.0	NM_001161660	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	hg19	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	A	19.25	3.792115	0.70452	.	.	ENSG00000118513	ENST00000341911;ENST00000442647;ENST00000316528;ENST00000237302;ENST00000367814;ENST00000527615;ENST00000420123;ENST00000525369;ENST00000528774;ENST00000534121;ENST00000534044;ENST00000533624	T;T;T;T;T;T;T;T;T;T	0.34859	2.57;2.09;2.09;2.1;1.34;1.84;2.56;2.55;1.76;2.17	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.37679	0.1012	M	0.63428	1.95	0.80722	D	1	P;B;P;P;P;D;P;P;P	0.55172	0.682;0.181;0.493;0.653;0.754;0.97;0.73;0.474;0.605	B;B;B;B;B;P;B;B;B	0.51193	0.172;0.054;0.116;0.219;0.306;0.662;0.318;0.097;0.108	T	0.39210	-0.9625	10	0.87932	D	0	-15.4352	15.2562	0.73588	1.0:0.0:0.0:0.0	.	20;20;20;20;20;20;20;20;20	E9PI07;E9PLZ5;P10242-2;E9PNL6;E9PRS2;E9PNA4;P10242-4;P10242;Q708E1	.;.;.;.;.;.;.;MYB_HUMAN;.	G	20	ENSP00000339992:E20G;ENSP00000410825:E20G;ENSP00000326328:E20G;ENSP00000356788:E20G;ENSP00000433227:E20G;ENSP00000435938:E20G;ENSP00000434723:E20G;ENSP00000432851:E20G;ENSP00000435055:E20G;ENSP00000436605:E20G	ENSP00000237302:E20G	E	+	2	0	MYB	135548769	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.071000	0.62044	0.460000	0.39030	GAG	.	.		0.448	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4		
MAP3K5	4217	hgsc.bcm.edu	37	6	136935403	136935403	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:136935403T>C	ENST00000359015.4	-	16	2532	c.2172A>G	c.(2170-2172)gaA>gaG	p.E724E	MAP3K5_ENST00000355845.4_5'UTR	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	724	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		ATGCTATTTCTTCATGCAGGG	0.353																																					p.E724E		Atlas-SNP	.											.	MAP3K5	136	.	0			c.A2172G						.						171.0	166.0	168.0					6																	136935403		2203	4300	6503	SO:0001819	synonymous_variant	4217	exon16			TATTTCTTCATGC	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6857	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 1"""	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.2172A>G	chr6.hg19:g.136935403T>C		57.0	0.0		76.0	4.0	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	ENST00000359015.4	hg19	CCDS5179.1																																																																																			.	.		0.353	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1		
ECT2L	345930	hgsc.bcm.edu	37	6	139197610	139197610	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:139197610A>G	ENST00000423192.1	+	13	1741	c.1580A>G	c.(1579-1581)gAa>gGa	p.E527G	RP3-509I19.6_ENST00000572284.1_RNA|ECT2L_ENST00000541398.1_Splice_Site_p.E458G|ECT2L_ENST00000367682.2_Splice_Site_p.E527G			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	527			E -> K (in dbSNP:rs1529151).				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						AATCTTCAGGAAAGAAATGTT	0.413			"""N, Splice, Mis"""		ETP ALL																																p.E527G		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.A1580G						.						64.0	61.0	62.0					6																	139197610		1859	4099	5958	SO:0001630	splice_region_variant	345930	exon13			TTCAGGAAAGAAA		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"""Rho guanine nucleotide exchange factors"", ""F-boxes /  ""other"""""	21118	protein-coding gene	gene with protein product	"""lung specific F-box and DH domain containing protein"", ""F-box protein 49"""		"""chromosome 6 open reading frame 91"", ""epithelial cell transforming sequence 2 oncogene-like"""	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.1579-1A>G	chr6.hg19:g.139197610A>G		64.0	0.0		72.0	4.0	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	hg19	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	A	11.84	1.758092	0.31137	.	.	ENSG00000203734	ENST00000423192;ENST00000367682;ENST00000541398	T;T;T	0.77098	0.06;0.06;-1.07	5.25	-0.205	0.13196	Dbl homology (DH) domain (1);	0.000000	0.41712	U	0.000821	T	0.48857	0.1523	L	0.60455	1.87	0.25093	N	0.990847	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.46048	-0.9219	10	0.44086	T	0.13	22.768	4.6103	0.12399	0.5108:0.3155:0.1737:0.0	.	458;527	F5H7S9;Q008S8	.;ECT2L_HUMAN	G	527;527;458	ENSP00000387388:E527G;ENSP00000356655:E527G;ENSP00000442307:E458G	ENSP00000356655:E527G	E	+	2	0	ECT2L	139239303	0.997000	0.39634	0.063000	0.19743	0.092000	0.18411	1.273000	0.33121	0.022000	0.15160	0.528000	0.53228	GAA	.	.		0.413	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706	Missense_Mutation
ADGB	79747	hgsc.bcm.edu	37	6	147049711	147049711	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:147049711A>G	ENST00000397944.3	+	20	2430	c.2354A>G	c.(2353-2355)gAg>gGg	p.E785G	ADGB_ENST00000367493.3_Splice_Site_p.E204G	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	785					oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			breast(1)|endometrium(2)|kidney(2)	5						TCTTCACAGGAGAGCTGCCGA	0.368																																					p.E785G		Atlas-SNP	.											.	ADGB	93	.	0			c.A2354G						.						194.0	174.0	180.0					6																	147049711		692	1591	2283	SO:0001630	splice_region_variant	79747	exon20			CACAGGAGAGCTG	AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.2353-1A>G	chr6.hg19:g.147049711A>G		88.0	0.0		94.0	5.0	NM_024694	Q5T402|Q5T904|Q5T905	Missense_Mutation	SNP	ENST00000397944.3	hg19		.	.	.	.	.	.	.	.	.	.	A	16.87	3.243186	0.58995	.	.	ENSG00000118492	ENST00000397944;ENST00000367493	T	0.70399	-0.48	5.59	5.59	0.84812	Globin, structural domain (1);	.	.	.	.	T	0.78059	0.4224	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.81378	-0.0960	9	0.72032	D	0.01	.	13.2875	0.60251	1.0:0.0:0.0:0.0	.	785	Q8N7X0	CAN7L_HUMAN	G	785;204	ENSP00000381036:E785G	ENSP00000356463:E204G	E	+	2	0	C6orf103	147091404	1.000000	0.71417	1.000000	0.80357	0.195000	0.23768	5.841000	0.69409	2.145000	0.66743	0.482000	0.46254	GAG	.	.		0.368	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	Missense_Mutation
STXBP5	134957	hgsc.bcm.edu	37	6	147631274	147631274	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:147631274A>G	ENST00000321680.6	+	10	972	c.972A>G	c.(970-972)agA>agG	p.R324R	STXBP5_ENST00000179882.6_5'UTR|STXBP5_ENST00000367481.3_Silent_p.R324R|STXBP5_ENST00000367480.3_Silent_p.R324R	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	324					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		TAGGAAGAAGACCTTGCTTAA	0.348																																					p.R324R		Atlas-SNP	.											.	STXBP5	163	.	0			c.A972G						.						132.0	137.0	136.0					6																	147631274		2203	4300	6503	SO:0001819	synonymous_variant	134957	exon10			AAGAAGACCTTGC	AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"""WD repeat domain containing"""	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.972A>G	chr6.hg19:g.147631274A>G		81.0	0.0		70.0	4.0	NM_139244	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Silent	SNP	ENST00000321680.6	hg19	CCDS47499.1																																																																																			.	.		0.348	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1		
LATS1	9113	hgsc.bcm.edu	37	6	149997708	149997708	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:149997708T>C	ENST00000543571.1	-	6	3306	c.2759A>G	c.(2758-2760)gAa>gGa	p.E920G	LATS1_ENST00000253339.5_Missense_Mutation_p.E920G|LATS1_ENST00000542747.1_5'UTR	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		TAGCAACACTTCAGGTGCAAT	0.448																																					p.E920G		Atlas-SNP	.											.	LATS1	241	.	0			c.A2759G						.						65.0	65.0	65.0					6																	149997708		2203	4300	6503	SO:0001583	missense	9113	exon6			AACACTTCAGGTG	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"""LATS (large tumor suppressor, Drosophila) homolog 1"", ""LATS, large tumor suppressor, homolog 1 (Drosophila)"""			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2759A>G	chr6.hg19:g.149997708T>C	ENSP00000437550:p.Glu920Gly	63.0	0.0		81.0	4.0	NM_004690		Missense_Mutation	SNP	ENST00000543571.1	hg19	CCDS34551.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.799498	0.90538	.	.	ENSG00000131023	ENST00000543571;ENST00000253339	T;T	0.38887	1.11;1.11	5.81	5.81	0.92471	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	0.000011	T	0.70011	0.3175	H	0.94886	3.595	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80058	-0.1541	9	.	.	.	.	16.1708	0.81812	0.0:0.0:0.0:1.0	.	920	O95835	LATS1_HUMAN	G	920	ENSP00000437550:E920G;ENSP00000253339:E920G	.	E	-	2	0	LATS1	150039401	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.698000	0.84413	2.225000	0.72522	0.533000	0.62120	GAA	.	.		0.448	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690	
GPR31	2853	hgsc.bcm.edu	37	6	167571153	167571153	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:167571153A>G	ENST00000366834.1	-	1	664	c.167T>C	c.(166-168)cTg>cCg	p.L56P		NM_005299.2	NP_005290.2	O00270	GPR31_HUMAN	G protein-coupled receptor 31	56					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(4)|large_intestine(4)|lung(7)|prostate(1)	17		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;4.81e-20)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;0.00492)		AGCCAGGGCCAGGTTGAGCAG	0.667																																					p.L56P		Atlas-SNP	.											.	GPR31	44	.	0			c.T167C						.						55.0	42.0	47.0					6																	167571153		2201	4300	6501	SO:0001583	missense	2853	exon1			AGGGCCAGGTTGA	U65402	CCDS5299.1	6q27	2012-08-21				ENSG00000120436		"""GPCR / Class A : Orphans"""	4486	protein-coding gene	gene with protein product	"""hydroxyeicosatetraenoic (HETE) acid receptor 1"", ""12-(S)-HETE acid receptor"""	602043				9205127, 21712392	Standard	NM_005299		Approved	HETER1, 12-HETER	uc011egq.2	O00270		ENST00000366834.1:c.167T>C	chr6.hg19:g.167571153A>G	ENSP00000355799:p.Leu56Pro	196.0	0.0		151.0	7.0	NM_005299	B0M0K2|Q4VBL3|Q9NQ20	Missense_Mutation	SNP	ENST00000366834.1	hg19	CCDS5299.1	.	.	.	.	.	.	.	.	.	.	A	14.37	2.516398	0.44763	.	.	ENSG00000120436	ENST00000366834	D	0.91521	-2.86	3.54	3.54	0.40534	GPCR, rhodopsin-like superfamily (1);	0.000000	0.30109	N	0.010393	D	0.95335	0.8486	M	0.93594	3.435	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95783	0.8818	10	0.87932	D	0	-15.3335	11.0872	0.48093	1.0:0.0:0.0:0.0	.	56	O00270	GPR31_HUMAN	P	56	ENSP00000355799:L56P	ENSP00000355799:L56P	L	-	2	0	GPR31	167491143	1.000000	0.71417	0.934000	0.37439	0.082000	0.17680	7.874000	0.87199	1.473000	0.48159	0.260000	0.18958	CTG	.	.		0.667	GPR31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043111.1	NM_005299	
FOXK1	221937	hgsc.bcm.edu	37	7	4798978	4798978	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:4798978T>C	ENST00000328914.4	+	7	1448	c.1448T>C	c.(1447-1449)gTg>gCg	p.V483A	FOXK1_ENST00000446823.1_Missense_Mutation_p.V320A	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)		ATCATGGCCGTGCCTCCCCGA	0.736																																					p.V483A		Atlas-SNP	.											.	FOXK1	64	.	0			c.T1448C						.						19.0	20.0	20.0					7																	4798978		2194	4295	6489	SO:0001583	missense	221937	exon7			TGGCCGTGCCTCC	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.1448T>C	chr7.hg19:g.4798978T>C	ENSP00000328720:p.Val483Ala	68.0	0.0		30.0	4.0	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	hg19	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.461008	0.43736	.	.	ENSG00000164916	ENST00000446823;ENST00000450194;ENST00000328914;ENST00000545598	D;D	0.96011	-3.45;-3.88	5.34	5.34	0.76211	.	0.126422	0.53938	D	0.000044	D	0.92397	0.7587	L	0.42245	1.32	0.47659	D	0.999486	B;B	0.27625	0.057;0.183	B;B	0.26416	0.01;0.069	D	0.90058	0.4154	10	0.25751	T	0.34	.	14.7896	0.69830	0.0:0.0:0.0:1.0	.	483;320	P85037;P85037-2	FOXK1_HUMAN;.	A	320;239;483;366	ENSP00000394442:V320A;ENSP00000328720:V483A	ENSP00000328720:V483A	V	+	2	0	FOXK1	4765504	1.000000	0.71417	0.948000	0.38648	0.442000	0.32017	5.699000	0.68310	2.153000	0.67306	0.482000	0.46254	GTG	.	.		0.736	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2		
RBAK	57786	hgsc.bcm.edu	37	7	5104405	5104405	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:5104405C>T	ENST00000353796.3	+	6	1642	c.1318C>T	c.(1318-1320)Cgg>Tgg	p.R440W	RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK-RBAKDN_ENST00000407184.1_Intron|RBAK_ENST00000396912.1_Missense_Mutation_p.R440W	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	440	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|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)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		ATTCTTTTCTCGGGTGTCATA	0.398																																					p.R440W		Atlas-SNP	.											RBAK_ENST00000396912,NS,malignant_melanoma,0,2	RBAK	82	.	0			c.C1318T						.						52.0	51.0	51.0					7																	5104405		2202	4299	6501	SO:0001583	missense	57786	exon6			TTTTCTCGGGTGT	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"""Zinc fingers, C2H2-type"", ""-"""	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.1318C>T	chr7.hg19:g.5104405C>T	ENSP00000275423:p.Arg440Trp	61.0	0.0		72.0	3.0	NM_001204456	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Missense_Mutation	SNP	ENST00000353796.3	hg19	CCDS5337.1	.	.	.	.	.	.	.	.	.	.	C	16.06	3.015536	0.54468	.	.	ENSG00000146587	ENST00000353796;ENST00000396912	T;T	0.16073	2.37;2.37	3.76	1.82	0.25136	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44902	D	0.000410	T	0.36166	0.0957	M	0.72353	2.195	0.32329	N	0.561318	D	0.89917	1.0	D	0.87578	0.998	T	0.48175	-0.9058	8	.	.	.	.	10.1859	0.42998	0.3584:0.6416:0.0:0.0	.	440	Q9NYW8	RBAK_HUMAN	W	440	ENSP00000275423:R440W;ENSP00000380120:R440W	.	R	+	1	2	RBAK	5070931	0.000000	0.05858	0.817000	0.32601	0.984000	0.73092	0.185000	0.16958	0.490000	0.27771	0.555000	0.69702	CGG	.	.		0.398	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163	
COL28A1	340267	hgsc.bcm.edu	37	7	7555463	7555463	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:7555463A>G	ENST00000399429.3	-	8	1004	c.864T>C	c.(862-864)ccT>ccC	p.P288P		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	288					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CCTTGTACCCAGGAATTCCCT	0.284																																					p.P288P		Atlas-SNP	.											.	COL28A1	113	.	0			c.T864C						.						77.0	73.0	74.0					7																	7555463		1791	4051	5842	SO:0001819	synonymous_variant	340267	exon8			GTACCCAGGAATT	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.864T>C	chr7.hg19:g.7555463A>G		84.0	0.0		94.0	4.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	ENST00000399429.3	hg19	CCDS43553.1																																																																																			.	.		0.284	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
OSBPL3	26031	hgsc.bcm.edu	37	7	24911688	24911688	+	Splice_Site	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:24911688C>T	ENST00000313367.2	-	3	548	c.97G>A	c.(97-99)Gac>Aac	p.D33N	OSBPL3_ENST00000396431.1_Splice_Site_p.D33N|OSBPL3_ENST00000353930.1_Splice_Site_p.D33N|OSBPL3_ENST00000352860.1_Splice_Site_p.D33N|OSBPL3_ENST00000431825.2_Splice_Site_p.D33N|OSBPL3_ENST00000409069.1_Splice_Site_p.D33N|OSBPL3_ENST00000396429.1_Splice_Site_p.D33N	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	33					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						TCCCAGCTGTCCTGTTCCAAC	0.413																																					p.D33N		Atlas-SNP	.											.	OSBPL3	100	.	0			c.G97A						.						86.0	80.0	82.0					7																	24911688		2203	4300	6503	SO:0001630	splice_region_variant	26031	exon3			AGCTGTCCTGTTC	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.97-1G>A	chr7.hg19:g.24911688C>T		90.0	0.0		114.0	46.0	NM_145321	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Missense_Mutation	SNP	ENST00000313367.2	hg19	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	C	34	5.328783	0.95733	.	.	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069;ENST00000415162;ENST00000441059;ENST00000415952	T;T;T;T;T;T;T;T;T;T	0.30714	2.76;2.76;2.76;2.76;2.76;2.76;2.76;2.76;2.76;1.52	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.57213	0.2038	M	0.68952	2.095	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.48779	-0.9005	10	0.42905	T	0.14	-2.2432	20.5407	0.99260	0.0:1.0:0.0:0.0	.	33;33;33;33	Q9H4L5-4;Q9H4L5-2;Q9H4L5-3;Q9H4L5	.;.;.;OSBL3_HUMAN	N	33	ENSP00000315410:D33N;ENSP00000315331:D33N;ENSP00000315277:D33N;ENSP00000389779:D33N;ENSP00000379708:D33N;ENSP00000379706:D33N;ENSP00000386953:D33N;ENSP00000407829:D33N;ENSP00000403374:D33N;ENSP00000411249:D33N	ENSP00000315410:D33N	D	-	1	0	OSBPL3	24878213	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.380000	0.79704	2.865000	0.98341	0.655000	0.94253	GAC	.	.		0.413	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		Missense_Mutation
SKAP2	8935	hgsc.bcm.edu	37	7	26765146	26765146	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:26765146T>C	ENST00000345317.2	-	9	1010	c.697A>G	c.(697-699)Aga>Gga	p.R233G	SKAP2_ENST00000539623.1_Missense_Mutation_p.R61G|SKAP2_ENST00000489977.1_5'UTR	NM_003930.3	NP_003921.2	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2	233					B cell activation (GO:0042113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(3)	17						AATTCTCCTCTCTCATCATAA	0.299																																					p.R233G		Atlas-SNP	.											.	SKAP2	40	.	0			c.A697G						.						119.0	118.0	118.0					7																	26765146		2203	4300	6503	SO:0001583	missense	8935	exon9			CTCCTCTCTCATC		CCDS5400.1	7p15.2	2013-01-10	2006-09-28	2006-09-28	ENSG00000005020	ENSG00000005020		"""Pleckstrin homology (PH) domain containing"""	15687	protein-coding gene	gene with protein product		605215	"""src family associated phosphoprotein 2"""	SCAP2		9837776, 9755858	Standard	NM_003930		Approved	RA70, SKAP-HOM, SKAP55R, SAPS	uc003syc.3	O75563	OTTHUMG00000023495	ENST00000345317.2:c.697A>G	chr7.hg19:g.26765146T>C	ENSP00000005587:p.Arg233Gly	68.0	0.0		91.0	4.0	NM_003930	A4D173|Q53GP6|Q75MK6|Q75MZ4|Q9UBZ3|Q9UED8	Missense_Mutation	SNP	ENST00000345317.2	hg19	CCDS5400.1	.	.	.	.	.	.	.	.	.	.	T	8.498	0.863483	0.17250	.	.	ENSG00000005020	ENST00000345317;ENST00000539623;ENST00000535331	T;T	0.31247	2.04;1.5	5.86	4.71	0.59529	.	0.533626	0.23314	N	0.049527	T	0.17450	0.0419	N	0.19112	0.55	0.30063	N	0.810719	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.16305	-1.0407	10	0.20519	T	0.43	-8.7302	7.4719	0.27353	0.0:0.1655:0.0:0.8345	.	218;233	B7Z5N4;O75563	.;SKAP2_HUMAN	G	233;61;218	ENSP00000005587:R233G;ENSP00000443593:R61G	ENSP00000005587:R233G	R	-	1	2	SKAP2	26731671	0.978000	0.34361	1.000000	0.80357	0.990000	0.78478	0.179000	0.16840	1.047000	0.40274	0.533000	0.62120	AGA	.	.		0.299	SKAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214128.1		
ANLN	54443	hgsc.bcm.edu	37	7	36445866	36445866	+	Silent	SNP	T	T	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:36445866T>G	ENST00000265748.2	+	4	785	c.564T>G	c.(562-564)ctT>ctG	p.L188L	ANLN_ENST00000396068.2_Silent_p.L188L	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	188	Nuclear localization.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						GACCTCTGCTTTCAAATGCCT	0.473																																					p.L188L		Atlas-SNP	.											.	ANLN	101	.	0			c.T564G						.						75.0	76.0	76.0					7																	36445866		2203	4300	6503	SO:0001819	synonymous_variant	54443	exon4			TCTGCTTTCAAAT	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"""Pleckstrin homology (PH) domain containing"""	14082	protein-coding gene	gene with protein product			"""anillin (Drosophila Scraps homolog), actin binding protein"", ""anillin, actin binding protein (scraps homolog, Drosophila)"""			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.564T>G	chr7.hg19:g.36445866T>G		117.0	0.0		133.0	44.0	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Silent	SNP	ENST00000265748.2	hg19	CCDS5447.1																																																																																			.	.		0.473	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685	
GLI3	2737	hgsc.bcm.edu	37	7	42012094	42012094	+	Silent	SNP	G	G	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:42012094G>T	ENST00000395925.3	-	13	2029	c.1945C>A	c.(1945-1947)Cgg>Agg	p.R649R	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	649					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|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)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GGTGGCGGCCGAGGATGGATG	0.612									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.R649R		Atlas-SNP	.											.	GLI3	312	.	0			c.C1945A						.						86.0	88.0	88.0					7																	42012094		2203	4300	6503	SO:0001819	synonymous_variant	2737	exon13	Familial Cancer Database	;	GCGGCCGAGGATG		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.1945C>A	chr7.hg19:g.42012094G>T		129.0	0.0		190.0	79.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	hg19	CCDS5465.1																																																																																			.	.		0.612	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
YKT6	10652	hgsc.bcm.edu	37	7	44247796	44247796	+	Splice_Site	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:44247796T>C	ENST00000223369.2	+	5	545	c.458T>C	c.(457-459)cTg>cCg	p.L153P	YKT6_ENST00000496112.1_Splice_Site_p.L153P|YKT6_ENST00000447123.1_3'UTR	NM_006555.3	NP_006546.1	O15498	YKT6_HUMAN	YKT6 v-SNARE homolog (S. cerevisiae)	153	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				ER to Golgi vesicle-mediated transport (GO:0006888)|metabolic process (GO:0008152)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle docking involved in exocytosis (GO:0006904)|vesicle targeting (GO:0006903)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|SNARE complex (GO:0031201)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	7						AAAATCATTCTGGTAAGCAGG	0.468																																					p.L153P		Atlas-SNP	.											.	YKT6	12	.	0			c.T458C						.						72.0	62.0	65.0					7																	44247796		2203	4300	6503	SO:0001630	splice_region_variant	10652	exon5			TCATTCTGGTAAG	BC007319	CCDS5482.1	7p13	2006-07-07			ENSG00000106636	ENSG00000106636			16959	protein-coding gene	gene with protein product	"""R-SNARE"""	606209				15479160, 15544955	Standard	NM_006555		Approved		uc003tkm.3	O15498	OTTHUMG00000129089	ENST00000223369.2:c.459+1T>C	chr7.hg19:g.44247796T>C		61.0	0.0		92.0	4.0	NM_006555	B4DR94|Q53F01|Q6FGU9|Q6IB15	Missense_Mutation	SNP	ENST00000223369.2	hg19	CCDS5482.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.679652	0.88542	.	.	ENSG00000106636	ENST00000496112;ENST00000223369	T	0.48201	0.82	5.88	5.88	0.94601	Synaptobrevin (2);	0.000000	0.85682	D	0.000000	T	0.77232	0.4100	H	0.95365	3.66	0.80722	D	1	D;D	0.63880	0.993;0.99	P;D	0.67382	0.878;0.951	D	0.84440	0.0582	10	0.87932	D	0	-6.8608	15.2725	0.73717	0.0:0.0:0.0:1.0	.	153;153	B4DR94;O15498	.;YKT6_HUMAN	P	153	ENSP00000223369:L153P	ENSP00000223369:L153P	L	+	2	0	YKT6	44214321	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.190000	0.77755	2.241000	0.73720	0.528000	0.53228	CTG	.	.		0.468	YKT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251125.2	NM_006555	Missense_Mutation
SUMF2	25870	hgsc.bcm.edu	37	7	56136261	56136261	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:56136261G>A	ENST00000413756.1	+	2	177	c.154G>A	c.(154-156)Ggg>Agg	p.G52R	SUMF2_ENST00000275607.9_Intron|SUMF2_ENST00000342190.6_Missense_Mutation_p.G71R|SUMF2_ENST00000437307.2_Missense_Mutation_p.G52R|SUMF2_ENST00000395435.2_Missense_Mutation_p.G71R|SUMF2_ENST00000434526.2_Missense_Mutation_p.G71R|SUMF2_ENST00000395436.2_Missense_Mutation_p.G71R			Q8NBJ7	SUMF2_HUMAN	sulfatase modifying factor 2	52					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	14	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			AGATGGTGACGGGCCTGTGCG	0.493																																					p.G71R		Atlas-SNP	.											SUMF2_ENST00000342190,NS,carcinoma,0,4	SUMF2	56	.	0			c.G211A						.						69.0	62.0	64.0					7																	56136261		2203	4300	6503	SO:0001583	missense	25870	exon2			GGTGACGGGCCTG	AK075477	CCDS5524.2, CCDS43588.2, CCDS43589.2, CCDS47589.1, CCDS55111.1	7q11.1	2004-04-30			ENSG00000129103	ENSG00000129103			20415	protein-coding gene	gene with protein product		607940				12757706	Standard	NM_015411		Approved	DKFZp566I1024	uc003trv.3	Q8NBJ7	OTTHUMG00000129373	ENST00000413756.1:c.154G>A	chr7.hg19:g.56136261G>A	ENSP00000406445:p.Gly52Arg	96.0	0.0		128.0	0.0	NM_015411	B4DU41|B4DWQ0|Q14DW5|Q53ZE3|Q96BH2|Q9BRN3|Q9BWI1|Q9Y405	Missense_Mutation	SNP	ENST00000413756.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.99	2.102779	0.37145	.	.	ENSG00000129103	ENST00000395436;ENST00000434526;ENST00000395435;ENST00000413952;ENST00000342190;ENST00000437307;ENST00000413756;ENST00000451338	D;D;D;D;D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38;-3.38;-3.38;-3.38;-3.38	5.01	4.13	0.48395	C-type lectin fold (1);Formylglycine-generating sulphatase enzyme domain (2);	0.276505	0.41712	D	0.000834	D	0.93331	0.7874	L	0.31845	0.965	0.80722	D	1	P;D;D;D;D;D	0.89917	0.868;0.999;0.966;0.999;1.0;1.0	P;P;B;P;D;D	0.72075	0.483;0.887;0.308;0.87;0.96;0.976	D	0.92822	0.6273	10	0.66056	D	0.02	-15.0969	8.9043	0.35515	0.1732:0.0:0.8268:0.0	.	52;71;71;52;71;71	Q8NBJ7-5;A8MXB9;E7EMF9;Q8NBJ7;F8WA42;C9JL30	.;.;.;SUMF2_HUMAN;.;.	R	71;71;71;71;71;52;52;49	ENSP00000378824:G71R;ENSP00000400922:G71R;ENSP00000378823:G71R;ENSP00000414434:G71R;ENSP00000341938:G71R;ENSP00000415989:G52R;ENSP00000406445:G52R;ENSP00000410796:G49R	ENSP00000341938:G71R	G	+	1	0	SUMF2	56103755	1.000000	0.71417	1.000000	0.80357	0.238000	0.25445	2.971000	0.49248	1.248000	0.43934	0.484000	0.47621	GGG	.	.		0.493	SUMF2-013	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000341457.2	NM_015411	
ZNF92	168374	hgsc.bcm.edu	37	7	64863524	64863524	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:64863524G>A	ENST00000328747.7	+	4	696	c.497G>A	c.(496-498)aGa>aAa	p.R166K	ZNF92_ENST00000431504.1_Missense_Mutation_p.R90K|ZNF92_ENST00000357512.2_Missense_Mutation_p.R134K|ZNF92_ENST00000450302.2_Missense_Mutation_p.R97K	NM_152626.2	NP_689839.1	Q03936	ZNF92_HUMAN	zinc finger protein 92	166					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1)	13		Lung NSC(55;0.159)				AATAAGATAAGACATACTGGA	0.299																																					p.R166K		Atlas-SNP	.											.	ZNF92	68	.	0			c.G497A						.						34.0	37.0	36.0					7																	64863524		2203	4293	6496	SO:0001583	missense	168374	exon4			AGATAAGACATAC	M61872	CCDS34646.1, CCDS47596.1, CCDS75608.1, CCDS75609.1	7q11.21	2013-01-08	2006-05-12		ENSG00000146757	ENSG00000146757		"""Zinc fingers, C2H2-type"", ""-"""	13168	protein-coding gene	gene with protein product		603974	"""zinc finger protein 92 (HTF12)"""			8467795	Standard	NM_001287533		Approved	HPF12, TF12	uc003ttz.3	Q03936	OTTHUMG00000156557	ENST00000328747.7:c.497G>A	chr7.hg19:g.64863524G>A	ENSP00000332595:p.Arg166Lys	37.0	0.0		91.0	4.0	NM_152626	A6NNF9|Q8N492|Q8NB35	Missense_Mutation	SNP	ENST00000328747.7	hg19	CCDS34646.1	.	.	.	.	.	.	.	.	.	.	G	0.028	-1.352673	0.01256	.	.	ENSG00000146757	ENST00000328747;ENST00000431504;ENST00000357512;ENST00000450302	T;T;T;T	0.27890	2.47;1.64;1.64;1.64	0.427	-0.854	0.10705	.	.	.	.	.	T	0.20820	0.0501	L	0.59967	1.855	0.19575	N	0.999961	P;B	0.35411	0.5;0.075	B;B	0.35312	0.2;0.081	T	0.29640	-1.0005	9	0.05620	T	0.96	.	4.3647	0.11218	0.0:0.0:0.3617:0.6382	.	134;166	Q03936-3;Q03936	.;ZNF92_HUMAN	K	166;90;134;97	ENSP00000332595:R166K;ENSP00000400495:R90K;ENSP00000350113:R134K;ENSP00000396126:R97K	ENSP00000332595:R166K	R	+	2	0	ZNF92	64500959	0.000000	0.05858	0.024000	0.17045	0.023000	0.10783	-0.162000	0.10012	-0.514000	0.06488	-0.518000	0.04402	AGA	.	.		0.299	ZNF92-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344589.2	NM_152626	
CACNA2D1	781	hgsc.bcm.edu	37	7	81662161	81662161	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:81662161T>C	ENST00000356253.5	-	12	1350	c.1095A>G	c.(1093-1095)ggA>ggG	p.G365G	CACNA2D1_ENST00000356860.3_Silent_p.G365G|MIR1255B1_ENST00000439234.1_RNA|CACNA2D1_ENST00000464354.1_5'UTR			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	365	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	CTCTCTCTTCTCCTCCATCCG	0.279																																					p.G365G		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.A1095G						.						76.0	77.0	76.0					7																	81662161		2203	4297	6500	SO:0001819	synonymous_variant	781	exon12			CTCTTCTCCTCCA	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.1095A>G	chr7.hg19:g.81662161T>C		37.0	0.0		91.0	5.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Silent	SNP	ENST00000356253.5	hg19																																																																																				.	.		0.279	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			
CROT	54677	hgsc.bcm.edu	37	7	86988625	86988625	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:86988625A>G	ENST00000331536.3	+	4	404	c.219A>G	c.(217-219)agA>agG	p.R73R	CROT_ENST00000419147.2_Silent_p.R101R|CROT_ENST00000412227.2_Silent_p.R73R|CROT_ENST00000442291.1_Silent_p.R73R	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase	73					carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	TGCTTGAAAGAGCAAAAGGAA	0.249																																					p.R101R		Atlas-SNP	.											.	CROT	81	.	0			c.A303G						.						61.0	71.0	68.0					7																	86988625		2203	4289	6492	SO:0001819	synonymous_variant	54677	exon5			TGAAAGAGCAAAA		CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.219A>G	chr7.hg19:g.86988625A>G		68.0	0.0		141.0	6.0	NM_001143935	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Silent	SNP	ENST00000331536.3	hg19	CCDS5604.1																																																																																			.	.		0.249	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151	
CASD1	64921	hgsc.bcm.edu	37	7	94166946	94166946	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:94166946A>G	ENST00000297273.4	+	9	1293	c.1006A>G	c.(1006-1008)Aat>Gat	p.N336D		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	336						integral component of membrane (GO:0016021)				NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	31	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			AATTCATCGTAATGCTCATCG	0.343																																					p.N336D		Atlas-SNP	.											.	CASD1	70	.	0			c.A1006G						.						99.0	106.0	104.0					7																	94166946		2203	4300	6503	SO:0001583	missense	64921	exon9			CATCGTAATGCTC	AF355594	CCDS5636.1	7q22	2006-03-09			ENSG00000127995	ENSG00000127995			16014	protein-coding gene	gene with protein product	"""chromosome 7 open reading frame 12"""	611686				11703667, 11528394	Standard	NM_022900		Approved	FLJ21213, FLJ21879, C7orf12	uc003uni.4	Q96PB1	OTTHUMG00000023356	ENST00000297273.4:c.1006A>G	chr7.hg19:g.94166946A>G	ENSP00000297273:p.Asn336Asp	104.0	0.0		228.0	47.0	NM_022900	B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Missense_Mutation	SNP	ENST00000297273.4	hg19	CCDS5636.1	.	.	.	.	.	.	.	.	.	.	A	11.12	1.544602	0.27563	.	.	ENSG00000127995	ENST00000297273	T	0.41400	1.0	5.27	4.08	0.47627	.	0.135452	0.64402	D	0.000003	T	0.25901	0.0631	N	0.08118	0	0.38203	D	0.940245	P;P	0.38711	0.643;0.643	B;B	0.40506	0.331;0.331	T	0.21965	-1.0230	10	0.35671	T	0.21	.	12.8372	0.57780	0.8208:0.1792:0.0:0.0	.	336;336	Q8WZ77;Q96PB1	.;CASD1_HUMAN	D	336	ENSP00000297273:N336D	ENSP00000297273:N336D	N	+	1	0	CASD1	94004882	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.296000	0.65698	2.124000	0.65301	0.482000	0.46254	AAT	.	.		0.343	CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900	
PEG10	23089	hgsc.bcm.edu	37	7	94293774	94293774	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:94293774T>C	ENST00000482108.1	+	2	1385	c.906T>C	c.(904-906)ggT>ggC	p.G302G	PEG10_ENST00000488574.1_Silent_p.G302G	NM_001040152.1|NM_001172438.1|NM_001184962.1	NP_001035242.1|NP_001165909.1|NP_001171891.1	Q86TG7	PEG10_HUMAN	paternally expressed 10	302					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|placenta development (GO:0001890)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(9)|prostate(3)|skin(1)	21	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)			GAACAGGAGGTCACTACGCTG	0.597																																					p.G378G		Atlas-SNP	.											.	PEG10	36	.	0			c.T1134C						.						22.0	28.0	26.0					7																	94293774		1976	4156	6132	SO:0001819	synonymous_variant	23089	exon2			AGGAGGTCACTAC	AB049834	CCDS55126.1, CCDS75636.1, CCDS75637.1	7q21	2007-12-07			ENSG00000242265	ENSG00000242265			14005	protein-coding gene	gene with protein product		609810				11318613, 15716091, 16093683	Standard	NM_001172437		Approved	KIAA1051, HB-1, MEF3L, RGAG3, Mar2, Mart2	uc011kie.2	Q86TG7	OTTHUMG00000155578	ENST00000482108.1:c.906T>C	chr7.hg19:g.94293774T>C		96.0	0.0		180.0	9.0	NM_001172438	Q96A68|Q9UPV1	Silent	SNP	ENST00000482108.1	hg19	CCDS55126.1																																																																																			.	.		0.597	PEG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340751.1	NM_015068	
TMEM130	222865	hgsc.bcm.edu	37	7	98452869	98452869	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:98452869A>G	ENST00000416379.2	-	5	801	c.797T>C	c.(796-798)cTg>cCg	p.L266P	TMEM130_ENST00000546258.1_Missense_Mutation_p.L247P|TMEM130_ENST00000339375.4_Missense_Mutation_p.L266P|TMEM130_ENST00000450876.1_Missense_Mutation_p.L182P|TMEM130_ENST00000345589.4_Missense_Mutation_p.L164P			Q8N3G9	TM130_HUMAN	transmembrane protein 130	266						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	25	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TTACCTCCCCAGGAAGTTCAA	0.582																																					p.L266P		Atlas-SNP	.											.	TMEM130	54	.	0			c.T797C						.						114.0	101.0	105.0					7																	98452869		2203	4300	6503	SO:0001583	missense	222865	exon5			CTCCCCAGGAAGT		CCDS5658.1, CCDS47649.1, CCDS47650.1	7q22.1	2006-03-09			ENSG00000166448	ENSG00000166448			25429	protein-coding gene	gene with protein product						12975309	Standard	NM_152913		Approved	DKFZp761L1417, FLJ42643	uc003upo.3	Q8N3G9	OTTHUMG00000154419	ENST00000416379.2:c.797T>C	chr7.hg19:g.98452869A>G	ENSP00000413163:p.Leu266Pro	89.0	0.0		167.0	7.0	NM_152913	A4D266|B7Z364|Q8IY46|Q8N0W9|Q8N3R2	Missense_Mutation	SNP	ENST00000416379.2	hg19	CCDS47650.1	.	.	.	.	.	.	.	.	.	.	A	11.74	1.729952	0.30684	.	.	ENSG00000166448	ENST00000416379;ENST00000339375;ENST00000450876;ENST00000345589;ENST00000546258	T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93	4.01	2.87	0.33458	.	0.934094	0.08847	N	0.884975	T	0.38188	0.1031	L	0.51422	1.61	0.42957	D	0.99439	D;D;D;D	0.69078	0.99;0.99;0.997;0.994	D;D;D;P	0.66979	0.912;0.912;0.948;0.827	T	0.31861	-0.9928	10	0.27785	T	0.31	-12.6495	5.5051	0.16850	0.8757:0.0:0.1243:0.0	.	266;247;266;164	Q8N3G9-2;B7Z2F1;Q8N3G9;Q8N3G9-3	.;.;TM130_HUMAN;.	P	266;266;182;164;247	ENSP00000413163:L266P;ENSP00000341256:L266P;ENSP00000390200:L182P;ENSP00000330262:L164P;ENSP00000445869:L247P	ENSP00000341256:L266P	L	-	2	0	TMEM130	98290805	1.000000	0.71417	0.999000	0.59377	0.203000	0.24098	2.441000	0.44864	1.797000	0.52628	0.455000	0.32223	CTG	.	.		0.582	TMEM130-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380713.1	NM_152913	
TRRAP	8295	hgsc.bcm.edu	37	7	98574152	98574152	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:98574152A>G	ENST00000359863.4	+	54	8194	c.7985A>G	c.(7984-7986)cAg>cGg	p.Q2662R	TRRAP_ENST00000355540.3_Missense_Mutation_p.Q2644R|TRRAP_ENST00000446306.3_Missense_Mutation_p.Q2644R	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2662					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GGCAGTCACCAGGTGCAGCGG	0.567																																					p.Q2662R		Atlas-SNP	.											.	TRRAP	863	.	0			c.A7985G						.						63.0	60.0	61.0					7																	98574152		2203	4300	6503	SO:0001583	missense	8295	exon54			GTCACCAGGTGCA	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.7985A>G	chr7.hg19:g.98574152A>G	ENSP00000352925:p.Gln2662Arg	19.0	0.0		84.0	4.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	hg19	CCDS59066.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.0|22.0	4.225129|4.225129	0.79576|0.79576	.|.	.|.	ENSG00000196367|ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306|ENST00000456197	T;T|.	0.64438|.	-0.1;-0.1|.	6.06|6.06	6.06|6.06	0.98353|0.98353	Armadillo-like helical (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.58337|0.58337	0.2115|0.2115	L|L	0.31926|0.31926	0.97|0.97	0.80722|0.80722	D|D	1|1	B;B;B|.	0.31910|.	0.295;0.207;0.346|.	B;B;B|.	0.31495|.	0.131;0.093;0.093|.	T|T	0.53913|0.53913	-0.8371|-0.8371	10|5	0.15952|.	T|.	0.53|.	.|.	16.6093|16.6093	0.84858|0.84858	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	2644;2383;2662|.	Q9Y4A5-2;Q59FH1;Q9Y4A5|.	.;.;TRRAP_HUMAN|.	R|G	2662;2644;2643|2384	ENSP00000352925:Q2662R;ENSP00000347733:Q2644R|.	ENSP00000347733:Q2644R|.	Q|R	+|+	2|1	0|2	TRRAP|TRRAP	98412088|98412088	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.917000|0.917000	0.54804|0.54804	9.040000|9.040000	0.93783|0.93783	2.324000|2.324000	0.78689|0.78689	0.533000|0.533000	0.62120|0.62120	CAG|AGG	.	.		0.567	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
NRCAM	4897	hgsc.bcm.edu	37	7	107866100	107866100	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:107866100T>C	ENST00000425651.2	-	7	766	c.767A>G	c.(766-768)gAg>gGg	p.E256G	NRCAM_ENST00000379022.4_Missense_Mutation_p.E256G|NRCAM_ENST00000351718.4_Missense_Mutation_p.E250G|NRCAM_ENST00000379028.3_Missense_Mutation_p.E256G|NRCAM_ENST00000379024.4_Intron|NRCAM_ENST00000413765.2_Intron	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	256					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						ACCATAAAACTCAGTGTCACT	0.353																																					p.E256G		Atlas-SNP	.											.	NRCAM	267	.	0			c.A767G						.						208.0	205.0	206.0					7																	107866100		2203	4300	6503	SO:0001583	missense	4897	exon7			TAAAACTCAGTGT		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.767A>G	chr7.hg19:g.107866100T>C	ENSP00000401244:p.Glu256Gly	60.0	0.0		84.0	4.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	hg19	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.531062	0.64972	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000537765;ENST00000351718;ENST00000425651;ENST00000379022;ENST00000445979;ENST00000417701	T;T;T;T;T	0.69435	0.3;0.27;0.3;0.31;-0.4	5.86	5.86	0.93980	.	0.049690	0.85682	D	0.000000	T	0.49949	0.1587	N	0.08118	0	0.43403	D	0.995536	B;B;B	0.13145	0.007;0.002;0.001	B;B;B	0.14578	0.011;0.002;0.003	T	0.47749	-0.9093	10	0.56958	D	0.05	.	16.5602	0.84551	0.0:0.0:0.0:1.0	.	256;250;256	Q92823-5;Q92823-4;Q92823	.;.;NRCAM_HUMAN	G	256;256;256;250;256;256;250;250	ENSP00000368314:E256G;ENSP00000325269:E250G;ENSP00000401244:E256G;ENSP00000368308:E256G;ENSP00000390421:E250G	ENSP00000325269:E250G	E	-	2	0	NRCAM	107653336	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.636000	0.83301	2.367000	0.80283	0.528000	0.53228	GAG	.	.		0.353	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
C7orf66	154907	hgsc.bcm.edu	37	7	108524086	108524086	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:108524086A>G	ENST00000379007.2	-	2	380	c.326T>C	c.(325-327)tTt>tCt	p.F109S		NM_001024607.1	NP_001019778.1	A4D0T2	CG066_HUMAN	chromosome 7 open reading frame 66	109						integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	15						TTCCTTTGGAAAAGATTTTGC	0.323																																					p.F109S		Atlas-SNP	.											.	C7orf66	29	.	0			c.T326C						.						115.0	108.0	110.0					7																	108524086		2203	4300	6503	SO:0001583	missense	154907	exon2			TTTGGAAAAGATT	AF103078	CCDS34735.1	7q31.1	2009-03-06			ENSG00000205174	ENSG00000205174			33712	protein-coding gene	gene with protein product							Standard	NM_001024607		Approved		uc003vfo.3	A4D0T2	OTTHUMG00000154867	ENST00000379007.2:c.326T>C	chr7.hg19:g.108524086A>G	ENSP00000368292:p.Phe109Ser	88.0	0.0		89.0	4.0	NM_001024607		Missense_Mutation	SNP	ENST00000379007.2	hg19	CCDS34735.1	.	.	.	.	.	.	.	.	.	.	a	8.917	0.960139	0.18507	.	.	ENSG00000205174	ENST00000379007	.	.	.	3.62	-0.0197	0.13958	.	.	.	.	.	T	0.14442	0.0349	N	0.08118	0	0.09310	N	1	B	0.24963	0.115	B	0.21546	0.035	T	0.26467	-1.0102	7	.	.	.	.	3.2723	0.06886	0.5156:0.2404:0.244:0.0	.	109	A4D0T2	CG066_HUMAN	S	109	.	.	F	-	2	0	C7orf66	108311322	0.099000	0.21834	0.000000	0.03702	0.030000	0.12068	0.899000	0.28417	-0.009000	0.14296	0.451000	0.29950	TTT	.	.		0.323	C7orf66-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337420.1	NM_001024607	
LRRN3	54674	hgsc.bcm.edu	37	7	110764583	110764583	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:110764583A>G	ENST00000422987.3	+	2	2586	c.1755A>G	c.(1753-1755)ccA>ccG	p.P585P	IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000489381.1_Intron|LRRN3_ENST00000451085.1_Silent_p.P585P|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|LRRN3_ENST00000308478.5_Silent_p.P585P|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000331762.3_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	585	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		ATCTGAATCCATCAACTGAGT	0.358																																					p.P585P		Atlas-SNP	.											.	LRRN3	132	.	0			c.A1755G						.						50.0	47.0	48.0					7																	110764583		2203	4300	6503	SO:0001819	synonymous_variant	54674	exon2			GAATCCATCAACT	AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17200	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 5"""					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.1755A>G	chr7.hg19:g.110764583A>G		73.0	0.0		65.0	4.0	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	hg19	CCDS5754.1																																																																																			.	.		0.358	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334	
ST7	7982	hgsc.bcm.edu	37	7	116771958	116771958	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:116771958A>G	ENST00000393446.2	+	6	888	c.585A>G	c.(583-585)agA>agG	p.R195R	ST7-AS2_ENST00000442719.1_RNA|ST7-AS2_ENST00000434993.1_RNA|ST7_ENST00000422922.1_Silent_p.R149R|ST7_ENST00000393444.3_Silent_p.R152R|ST7_ENST00000323984.3_Silent_p.R195R|ST7_ENST00000393449.1_Silent_p.R195R|ST7_ENST00000393451.3_Silent_p.R195R|ST7_ENST00000265437.5_Silent_p.R195R|ST7-AS2_ENST00000432541.1_RNA|ST7_ENST00000432298.1_Silent_p.R149R|ST7_ENST00000487459.1_3'UTR|ST7_ENST00000393443.1_Silent_p.R145R|ST7_ENST00000393447.4_Silent_p.R152R|ST7_ENST00000465133.1_Silent_p.R152R			Q9Y561	LRP12_HUMAN	suppression of tumorigenicity 7	0	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				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(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(1)	21	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		AAGCCTGGAGAGAGAGAAACC	0.388																																					p.R195R		Atlas-SNP	.											.	ST7	64	.	0			c.A585G						.						73.0	80.0	77.0					7																	116771958		2203	4300	6503	SO:0001819	synonymous_variant	7982	exon6			CTGGAGAGAGAGA	AJ277291	CCDS5769.1, CCDS5770.1	7q31.2	2008-06-06			ENSG00000004866	ENSG00000004866			11351	protein-coding gene	gene with protein product		600833		FAM4A1		8105370, 8938430	Standard	NM_021908		Approved	TSG7, SEN4, ETS7q, HELG, RAY1, FAM4A	uc003vin.3	Q9NRC1	OTTHUMG00000023888	ENST00000393446.2:c.585A>G	chr7.hg19:g.116771958A>G		45.0	0.0		61.0	5.0	NM_018412	A8K137|B4DRQ2	Silent	SNP	ENST00000393446.2	hg19																																																																																				.	.		0.388	ST7-013	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000319687.1	NM_021908	
ZNF800	168850	hgsc.bcm.edu	37	7	127026148	127026148	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:127026148A>G	ENST00000393313.1	-	3	714	c.123T>C	c.(121-123)tcT>tcC	p.S41S	ZNF800_ENST00000265827.3_Silent_p.S41S|ZNF800_ENST00000393312.1_Silent_p.S41S			Q2TB10	ZN800_HUMAN	zinc finger protein 800	41					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						GTTGAATACCAGATTTGGATG	0.373																																					p.S41S		Atlas-SNP	.											.	ZNF800	78	.	0			c.T123C						.						113.0	107.0	109.0					7																	127026148		2203	4300	6503	SO:0001819	synonymous_variant	168850	exon3			AATACCAGATTTG	AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"""Zinc fingers, C2H2-type"""	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.123T>C	chr7.hg19:g.127026148A>G		83.0	0.0		91.0	4.0	NM_176814	Q9HBN0	Silent	SNP	ENST00000393313.1	hg19	CCDS5795.1																																																																																			.	.		0.373	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814	
SVOPL	136306	hgsc.bcm.edu	37	7	138312173	138312173	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:138312173A>G	ENST00000419765.3	-	11	1136	c.1103T>C	c.(1102-1104)cTg>cCg	p.L368P	SVOPL_ENST00000421622.1_Missense_Mutation_p.L248P|SVOPL_ENST00000288513.5_Missense_Mutation_p.L216P|SVOPL_ENST00000463557.1_5'UTR|SVOPL_ENST00000436657.1_Missense_Mutation_p.L216P|SNORA40_ENST00000516379.1_RNA	NM_001139456.1	NP_001132928.1	Q8N434	SVOPL_HUMAN	SVOP-like	368						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						CCGTCTTCCCAGGAAATTGAT	0.408																																					p.L368P		Atlas-SNP	.											.	SVOPL	111	.	0			c.T1103C						.						97.0	90.0	92.0					7																	138312173		2203	4300	6503	SO:0001583	missense	136306	exon11			CTTCCCAGGAAAT	BC036796	CCDS5848.1, CCDS47721.1	7q34	2011-07-12	2007-04-04		ENSG00000157703	ENSG00000157703			27034	protein-coding gene	gene with protein product		611700	"""SV2 related protein homolog (rat)-like"""				Standard	NM_001139456		Approved	MGC46715	uc011kqh.2	Q8N434	OTTHUMG00000155870	ENST00000419765.3:c.1103T>C	chr7.hg19:g.138312173A>G	ENSP00000405482:p.Leu368Pro	59.0	0.0		90.0	4.0	NM_001139456		Missense_Mutation	SNP	ENST00000419765.3	hg19	CCDS47721.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.978296	0.74360	.	.	ENSG00000157703	ENST00000288513;ENST00000421622;ENST00000436657;ENST00000419765	T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98	5.81	5.81	0.92471	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.187326	0.48286	D	0.000192	D	0.85792	0.5779	M	0.76170	2.325	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.73380	0.979;0.98	D	0.87434	0.2390	10	0.87932	D	0	-16.9639	16.1708	0.81812	1.0:0.0:0.0:0.0	.	368;216	Q8N434;Q8N434-2	SVOPL_HUMAN;.	P	216;248;216;368	ENSP00000288513:L216P;ENSP00000412830:L248P;ENSP00000417018:L216P;ENSP00000405482:L368P	ENSP00000288513:L216P	L	-	2	0	SVOPL	137962713	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	6.414000	0.73318	2.225000	0.72522	0.533000	0.62120	CTG	.	.		0.408	SVOPL-005	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342092.4	NM_174959	
EPHA1	2041	hgsc.bcm.edu	37	7	143088824	143088824	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:143088824G>C	ENST00000275815.3	-	17	2827	c.2741C>G	c.(2740-2742)cCa>cGa	p.P914R	EPHA1_ENST00000458129.1_5'Flank	NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	914	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				GGTTCGATATGGGATCCCATC	0.582																																					p.P914R		Atlas-SNP	.											EPHA1_ENST00000275815,NS,carcinoma,0,2	EPHA1	193	.	0			c.C2741G						.						81.0	63.0	69.0					7																	143088824		2203	4300	6503	SO:0001583	missense	2041	exon17			CGATATGGGATCC	M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3385	protein-coding gene	gene with protein product		179610	"""EphA1"""	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.2741C>G	chr7.hg19:g.143088824G>C	ENSP00000275815:p.Pro914Arg	64.0	0.0		131.0	0.0	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	hg19	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.941320	0.34283	.	.	ENSG00000146904	ENST00000275815	T	0.47528	0.84	4.67	3.77	0.43336	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.109437	0.41194	N	0.000925	T	0.44030	0.1274	L	0.43757	1.38	0.44643	D	0.99762	B	0.18610	0.029	B	0.26202	0.067	T	0.46679	-0.9174	10	0.72032	D	0.01	.	15.2057	0.73177	0.0:0.1413:0.8587:0.0	.	914	P21709	EPHA1_HUMAN	R	914	ENSP00000275815:P914R	ENSP00000275815:P914R	P	-	2	0	EPHA1	142798946	1.000000	0.71417	0.953000	0.39169	0.006000	0.05464	3.709000	0.54853	1.304000	0.44892	-0.305000	0.09177	CCA	.	.		0.582	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1		
TDRP	157695	hgsc.bcm.edu	37	8	442414	442414	+	Silent	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:442414C>T	ENST00000324079.6	-	3	783	c.543G>A	c.(541-543)ccG>ccA	p.P181P	TDRP_ENST00000427263.2_Intron|TDRP_ENST00000523656.1_Intron|TDRP_ENST00000524229.1_5'Flank			Q86YL5	TDRP_HUMAN	testis development related protein	181					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCGCCTCCTCCGGGCTATCTG	0.607																																					p.P181P		Atlas-SNP	.											C8orf42,caecum,carcinoma,0,1	C8orf42	23	.	0			c.G543A						.						10.0	11.0	11.0					8																	442414		2056	4204	6260	SO:0001819	synonymous_variant	157695	exon4			CTCCTCCGGGCTA	AY194292	CCDS47759.1, CCDS59090.1	8p23.3	2013-06-03	2013-06-03	2013-06-03	ENSG00000180190	ENSG00000180190			26951	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 42"""	C8orf42		20170638	Standard	NM_175075		Approved	INM01, TDRP1, TDRP2		Q86YL5	OTTHUMG00000163593	ENST00000324079.6:c.543G>A	chr8.hg19:g.442414C>T		60.0	0.0		49.0	2.0	NM_175075	B6VF03|B9EG53	Silent	SNP	ENST00000324079.6	hg19	CCDS47759.1																																																																																			.	.		0.607	TDRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374442.1	NM_175075	
CSMD1	64478	hgsc.bcm.edu	37	8	2820095	2820095	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:2820095T>A	ENST00000520002.1	-	62	10079	c.9524A>T	c.(9523-9525)aAg>aTg	p.K3175M	CSMD1_ENST00000537824.1_Missense_Mutation_p.K3174M|CSMD1_ENST00000602723.1_Missense_Mutation_p.K2998M|CSMD1_ENST00000400186.3_Missense_Mutation_p.K2998M|CSMD1_ENST00000542608.1_Missense_Mutation_p.K2997M|CSMD1_ENST00000602557.1_Missense_Mutation_p.K3175M			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3175	Sushi 26. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GACTTCGGACTTATAGGTGAA	0.522																																					p.K3174M		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A9521T						.						57.0	56.0	56.0					8																	2820095		1897	4120	6017	SO:0001583	missense	64478	exon61			TCGGACTTATAGG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9524A>T	chr8.hg19:g.2820095T>A	ENSP00000430733:p.Lys3175Met	91.0	0.0		71.0	42.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.95|11.95	1.791085|1.791085	0.31685|0.31685	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608|ENST00000335551	T;T;T;T|.	0.66280|.	-0.2;-0.2;-0.2;-0.2|.	5.6|5.6	0.158|0.158	0.14942|0.14942	Complement control module (2);Sushi/SCR/CCP (3);|.	0.208600|.	0.38436|.	N|.	0.001684|.	T|.	0.52581|.	0.1743|.	M|M	0.73217|0.73217	2.22|2.22	0.09310|0.09310	N|N	1|1	P;P;P|.	0.50617|.	0.912;0.779;0.937|.	P;P;P|.	0.57371|.	0.65;0.608;0.819|.	T|.	0.48210|.	-0.9055|.	10|.	0.54805|.	T|.	0.06|.	.|.	9.5169|9.5169	0.39111|0.39111	0.0:0.4619:0.0:0.5381|0.0:0.4619:0.0:0.5381	.|.	3175;3175;2997|.	E5RIG2;Q96PZ7;F5H2I8|.	.;CSMD1_HUMAN;.|.	M|Y	2998;3175;3036;3174;2997|2591	ENSP00000383047:K2998M;ENSP00000430733:K3175M;ENSP00000441462:K3174M;ENSP00000446243:K2997M|.	ENSP00000320445:K3036M|.	K|X	-|-	2|3	0|2	CSMD1|CSMD1	2807502|2807502	0.005000|0.005000	0.15991|0.15991	0.006000|0.006000	0.13384|0.13384	0.123000|0.123000	0.20343|0.20343	0.317000|0.317000	0.19487|0.19487	0.101000|0.101000	0.17610|0.17610	0.533000|0.533000	0.62120|0.62120	AAG|TAA	.	.		0.522	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
CSMD1	64478	hgsc.bcm.edu	37	8	3216715	3216715	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:3216715C>T	ENST00000520002.1	-	22	3821	c.3266G>A	c.(3265-3267)gGg>gAg	p.G1089E	CSMD1_ENST00000539096.1_Missense_Mutation_p.G1088E|CSMD1_ENST00000537824.1_Missense_Mutation_p.G1088E|CSMD1_ENST00000602723.1_Missense_Mutation_p.G1089E|CSMD1_ENST00000400186.3_Missense_Mutation_p.G1089E|CSMD1_ENST00000542608.1_Missense_Mutation_p.G1088E|CSMD1_ENST00000602557.1_Missense_Mutation_p.G1089E			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1089	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.G817E(1)		breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ACGGCGGCCCCCACCCAGGCA	0.552																																					p.G1088E		Atlas-SNP	.											CSMD1_ENST00000537824,right_lower_lobe,carcinoma,-1,1	CSMD1	1469	.	1	Substitution - Missense(1)	ovary(1)	c.G3263A						.						68.0	73.0	72.0					8																	3216715		2203	4300	6503	SO:0001583	missense	64478	exon21			CGGCCCCCACCCA			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3266G>A	chr8.hg19:g.3216715C>T	ENSP00000430733:p.Gly1089Glu	90.0	1.0		74.0	3.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	32|32	5.145942|5.145942	0.94603|0.94603	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096|ENST00000335551	T;T;T;T;T|.	0.23950|.	1.88;1.88;1.88;1.88;1.88|.	5.34|5.34	5.34|5.34	0.76211|0.76211	Complement control module (2);Sushi/SCR/CCP (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.77003|.	0.4067|.	M|M	0.75085|0.75085	2.285|2.285	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|.	T|.	0.76599|.	-0.2900|.	10|.	0.52906|.	T|.	0.07|.	.|.	19.067|19.067	0.93116|0.93116	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1089;1089;1089|.	E5RIG2;Q96PZ7;Q96PZ7-4|.	.;CSMD1_HUMAN;.|.	E|X	1089;1089;951;1088;1088;1088|568	ENSP00000383047:G1089E;ENSP00000430733:G1089E;ENSP00000441462:G1088E;ENSP00000446243:G1088E;ENSP00000441675:G1088E|.	ENSP00000320445:G951E|.	G|W	-|-	2|3	0|0	CSMD1|CSMD1	3204122|3204122	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	7.612000|7.612000	0.82975|0.82975	2.489000|2.489000	0.83994|0.83994	0.550000|0.550000	0.68814|0.68814	GGG|TGG	.	.		0.552	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
ANGPT2	285	hgsc.bcm.edu	37	8	6389963	6389963	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:6389963T>C	ENST00000325203.5	-	2	808	c.334A>G	c.(334-336)Ata>Gta	p.I112V	ANGPT2_ENST00000338312.6_Intron|ANGPT2_ENST00000415216.1_Missense_Mutation_p.I112V|ANGPT2_ENST00000523120.1_Missense_Mutation_p.I112V|MCPH1_ENST00000344683.5_Intron			O15123	ANGP2_HUMAN	angiopoietin 2	112					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to growth factor stimulus (GO:0071363)|germ cell development (GO:0007281)|glomerulus vasculature development (GO:0072012)|leukocyte migration (GO:0050900)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of positive chemotaxis (GO:0050928)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|Tie signaling pathway (GO:0048014)	cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		TTCTGCTGTATCTCTACCATT	0.418																																					p.I112V		Atlas-SNP	.											.	ANGPT2	126	.	0			c.A334G						.						234.0	207.0	216.0					8																	6389963		2203	4300	6503	SO:0001583	missense	285	exon2			GCTGTATCTCTAC	AF004327	CCDS5958.1, CCDS47761.1	8p23	2013-02-06			ENSG00000091879	ENSG00000091879		"""Fibrinogen C domain containing"""	485	protein-coding gene	gene with protein product		601922				9545648	Standard	NM_001147		Approved	Ang2	uc003wqj.4	O15123	OTTHUMG00000090365	ENST00000325203.5:c.334A>G	chr8.hg19:g.6389963T>C	ENSP00000314897:p.Ile112Val	203.0	0.0		121.0	5.0	NM_001118887	A0AV38|A8K205|B7ZLM7|Q9NRR7|Q9P2Y7	Missense_Mutation	SNP	ENST00000325203.5	hg19	CCDS5958.1	.	.	.	.	.	.	.	.	.	.	T	2.619	-0.289104	0.05605	.	.	ENSG00000091879	ENST00000325203;ENST00000415216;ENST00000523120	D;D;D	0.82984	-1.67;-1.67;-1.67	5.27	1.39	0.22231	.	0.575243	0.20952	N	0.082728	T	0.72953	0.3525	L	0.45228	1.405	0.37254	D	0.906672	B;B;B	0.24823	0.003;0.112;0.001	B;B;B	0.28232	0.01;0.087;0.004	T	0.61123	-0.7126	10	0.23302	T	0.38	.	6.5889	0.22636	0.0:0.0796:0.2949:0.6255	.	112;112;112	E7EVQ3;O15123-3;O15123	.;.;ANGP2_HUMAN	V	112	ENSP00000314897:I112V;ENSP00000400782:I112V;ENSP00000428023:I112V	ENSP00000314897:I112V	I	-	1	0	ANGPT2	6377371	1.000000	0.71417	0.145000	0.22337	0.044000	0.14063	2.000000	0.40816	0.057000	0.16193	0.533000	0.62120	ATA	.	.		0.418	ANGPT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206737.1	NM_001147	
ERI1	90459	hgsc.bcm.edu	37	8	8875834	8875834	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:8875834C>T	ENST00000523898.1	+	6	1289	c.610C>T	c.(610-612)Cct>Tct	p.P204S	ERI1_ENST00000250263.7_Missense_Mutation_p.P204S|ERI1_ENST00000520332.1_3'UTR|ERI1_ENST00000519292.1_Missense_Mutation_p.P204S			Q8IV48	ERI1_HUMAN	exoribonuclease 1	204	Exonuclease.				gene silencing by RNA (GO:0031047)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|rRNA 3'-end processing (GO:0031125)	cytoplasm (GO:0005737)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|histone pre-mRNA stem-loop binding (GO:0071207)|metal ion binding (GO:0046872)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11						TGATACCTTCCCTCAGGTACT	0.358																																					p.P204S		Atlas-SNP	.											.	ERI1	20	.	0			c.C610T						.						58.0	59.0	59.0					8																	8875834		2203	4300	6503	SO:0001583	missense	90459	exon5			ACCTTCCCTCAGG	BC035279	CCDS5972.1	8p23.1	2008-12-16	2008-12-16	2008-12-16	ENSG00000104626	ENSG00000104626		"""Enhanced RNAi three prime mRNA exonucleases"""	23994	protein-coding gene	gene with protein product	"""exoribonuclease 1"", ""enhanced RNAi three prime mRNA exonuclease homolog 1 (C.elegans)"""	608739	"""three prime histone mRNA exonuclease 1"""	THEX1		14536070	Standard	NM_153332		Approved	3'HEXO	uc003wsk.2	Q8IV48	OTTHUMG00000129328	ENST00000523898.1:c.610C>T	chr8.hg19:g.8875834C>T	ENSP00000429615:p.Pro204Ser	114.0	0.0		66.0	4.0	NM_153332	A8K4U7|Q9NSX3	Missense_Mutation	SNP	ENST00000523898.1	hg19	CCDS5972.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.907533	0.92107	.	.	ENSG00000104626	ENST00000523898;ENST00000250263;ENST00000519292	T;T;T	0.21543	2.0;2.0;2.0	5.97	5.97	0.96955	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.046969	0.85682	D	0.000000	T	0.33381	0.0861	M	0.63428	1.95	0.80722	D	1	P	0.39883	0.693	P	0.44623	0.455	T	0.00783	-1.1568	10	0.38643	T	0.18	-15.1539	19.4222	0.94726	0.0:1.0:0.0:0.0	.	204	Q8IV48	ERI1_HUMAN	S	204	ENSP00000429615:P204S;ENSP00000250263:P204S;ENSP00000430190:P204S	ENSP00000250263:P204S	P	+	1	0	ERI1	8913244	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.361000	0.66092	2.838000	0.97847	0.561000	0.74099	CCT	.	.		0.358	ERI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251471.2	NM_153332	
MTMR7	9108	hgsc.bcm.edu	37	8	17159699	17159699	+	Silent	SNP	A	A	G	rs373353287		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:17159699A>G	ENST00000180173.5	-	13	1618	c.1584T>C	c.(1582-1584)acT>acC	p.T528T	MTMR7_ENST00000398099.3_Silent_p.T119T|MTMR7_ENST00000521857.1_Silent_p.T528T	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	528					inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		CTAGCTGCTGAGTTTCTTCCT	0.433																																					p.T528T		Atlas-SNP	.											.	MTMR7	75	.	0			c.T1584C						.	A		2,4404	4.2+/-10.8	0,2,2201	176.0	161.0	166.0		1584	-7.5	0.1	8		166	0,8600		0,0,4300	no	coding-synonymous	MTMR7	NM_004686.4		0,2,6501	GG,GA,AA		0.0,0.0454,0.0154		528/661	17159699	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9108	exon13			CTGCTGAGTTTCT	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.1584T>C	chr8.hg19:g.17159699A>G		130.0	0.0		86.0	4.0	NM_004686	A1L4K9|B4DG87|Q68DX4	Silent	SNP	ENST00000180173.5	hg19	CCDS34851.1																																																																																			.	.		0.433	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686	
INTS10	55174	hgsc.bcm.edu	37	8	19694579	19694579	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:19694579T>C	ENST00000397977.3	+	13	1945	c.1547T>C	c.(1546-1548)gTc>gCc	p.V516A		NM_018142.2	NP_060612.2	Q9NVR2	INT10_HUMAN	integrator complex subunit 10	516					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)		TGTGAAAAAGTCCTTGATTTG	0.383																																					p.V516A		Atlas-SNP	.											.	INTS10	46	.	0			c.T1547C						.						105.0	100.0	102.0					8																	19694579		1857	4102	5959	SO:0001583	missense	55174	exon13			AAAAAGTCCTTGA	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.1547T>C	chr8.hg19:g.19694579T>C	ENSP00000381064:p.Val516Ala	153.0	0.0		96.0	4.0	NM_018142	Q6IA93|Q7L538|Q7L8C8|Q9H3W8	Missense_Mutation	SNP	ENST00000397977.3	hg19	CCDS6011.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.71|14.71	2.616541|2.616541	0.46736|0.46736	.|.	.|.	ENSG00000104613|ENSG00000104613	ENST00000520670|ENST00000397977	.|.	.|.	.|.	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	.|0.186912	.|0.46758	.|D	.|0.000268	T|T	0.40932|0.40932	0.1137|0.1137	N|N	0.14661|0.14661	0.345|0.345	0.42019|0.42019	D|D	0.990975|0.990975	.|B	.|0.16396	.|0.017	.|B	.|0.21360	.|0.034	T|T	0.28713|0.28713	-1.0035|-1.0035	5|9	.|0.20519	.|T	.|0.43	-11.9322|-11.9322	14.5209|14.5209	0.67849|0.67849	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|516	.|Q9NVR2	.|INT10_HUMAN	P|A	6|516	.|.	.|ENSP00000381064:V516A	S|V	+|+	1|2	0|0	INTS10|INTS10	19738859|19738859	1.000000|1.000000	0.71417|0.71417	0.967000|0.967000	0.41034|0.41034	0.945000|0.945000	0.59286|0.59286	7.070000|7.070000	0.76763|0.76763	2.108000|2.108000	0.64289|0.64289	0.533000|0.533000	0.62120|0.62120	TCC|GTC	.	.		0.383	INTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253724.2	NM_018142	
SLC39A14	23516	hgsc.bcm.edu	37	8	22273673	22273673	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:22273673A>G	ENST00000381237.1	+	7	1146	c.1027A>G	c.(1027-1029)Agc>Ggc	p.S343G	SLC39A14_ENST00000289952.5_Missense_Mutation_p.S343G|SLC39A14_ENST00000359741.5_Missense_Mutation_p.S343G|SLC39A14_ENST00000240095.6_Missense_Mutation_p.S343G	NM_001128431.2	NP_001121903.1	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	343					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		GATCACTCTGAGCGACGGCCT	0.552																																					p.S343G		Atlas-SNP	.											.	SLC39A14	59	.	0			c.A1027G						.						101.0	92.0	95.0					8																	22273673		2203	4300	6503	SO:0001583	missense	23516	exon7			ACTCTGAGCGACG	D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635		"""Solute carriers"""	20858	protein-coding gene	gene with protein product		608736	"""solute carrier family 39 (metal ion transporter), member 14"""			12659941	Standard	NM_015359		Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000381237.1:c.1027A>G	chr8.hg19:g.22273673A>G	ENSP00000370635:p.Ser343Gly	174.0	0.0		143.0	6.0	NM_001135153	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	Missense_Mutation	SNP	ENST00000381237.1	hg19	CCDS47823.1	.	.	.	.	.	.	.	.	.	.	A	15.11	2.737514	0.49045	.	.	ENSG00000104635	ENST00000359741;ENST00000240095;ENST00000381237;ENST00000289952;ENST00000517370	T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38	5.99	5.99	0.97316	.	0.073878	0.85682	D	0.000000	T	0.15998	0.0385	N	0.02315	-0.6	0.80722	D	1	B;B;B	0.24576	0.106;0.034;0.034	B;B;B	0.28139	0.086;0.085;0.085	T	0.16158	-1.0412	10	0.02654	T	1	-36.6727	15.4768	0.75489	1.0:0.0:0.0:0.0	.	343;343;343	Q15043-2;Q15043;B6EU88	.;S39AE_HUMAN;.	G	343;343;343;343;166	ENSP00000352779:S343G;ENSP00000240095:S343G;ENSP00000370635:S343G;ENSP00000289952:S343G;ENSP00000427981:S166G	ENSP00000240095:S343G	S	+	1	0	SLC39A14	22329618	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	9.182000	0.94881	2.291000	0.77112	0.533000	0.62120	AGC	.	.		0.552	SLC39A14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215039.2	XM_046677	
ESCO2	157570	hgsc.bcm.edu	37	8	27634369	27634369	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:27634369T>C	ENST00000305188.8	+	3	782	c.544T>C	c.(544-546)Tgt>Cgt	p.C182R	ESCO2_ENST00000523910.1_3'UTR|ESCO2_ENST00000397418.2_5'UTR	NM_001017420.2	NP_001017420.1	Q56NI9	ESCO2_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 2	182					chromosome segregation (GO:0007059)|double-strand break repair (GO:0006302)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|protein localization to chromatin (GO:0071168)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromocenter (GO:0010369)|Golgi apparatus (GO:0005794)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		GGAAAATAATTGTCATTCAGC	0.373									SC Phocomelia syndrome																												p.C182R		Atlas-SNP	.											.	ESCO2	50	.	0			c.T544C						.						55.0	58.0	57.0					8																	27634369		2203	4300	6503	SO:0001583	missense	157570	exon3	Familial Cancer Database	SC-Pseudothalidomide s., incl.: Roberts s.	AATAATTGTCATT	AF306679	CCDS34872.1	8p21.1	2013-05-02	2013-05-02		ENSG00000171320	ENSG00000171320			27230	protein-coding gene	gene with protein product		609353	"""Roberts syndrome"", ""establishment of cohesion 1 homolog 2 (S. cerevisiae)"""	RBS		15958495, 16775838, 15821733, 16380922	Standard	XR_247122		Approved	EFO2	uc003xgg.3	Q56NI9	OTTHUMG00000163901	ENST00000305188.8:c.544T>C	chr8.hg19:g.27634369T>C	ENSP00000306999:p.Cys182Arg	50.0	0.0		54.0	4.0	NM_001017420	B3KW59|Q49AP4	Missense_Mutation	SNP	ENST00000305188.8	hg19	CCDS34872.1	.	.	.	.	.	.	.	.	.	.	T	1.802	-0.476850	0.04414	.	.	ENSG00000171320	ENST00000523566;ENST00000305188	T;T	0.64085	0.83;-0.08	5.93	1.81	0.25067	.	1.026470	0.07659	N	0.933369	T	0.63402	0.2508	L	0.56769	1.78	0.09310	N	0.999996	D;P	0.53151	0.958;0.744	P;B	0.51866	0.682;0.154	T	0.48917	-0.8992	10	0.25751	T	0.34	-0.2848	5.0166	0.14339	0.3938:0.0:0.1481:0.4581	.	182;182	E5RFE4;Q56NI9	.;ESCO2_HUMAN	R	182	ENSP00000428435:C182R;ENSP00000306999:C182R	ENSP00000306999:C182R	C	+	1	0	ESCO2	27690288	0.000000	0.05858	0.084000	0.20598	0.068000	0.16541	0.417000	0.21214	0.435000	0.26365	0.482000	0.46254	TGT	.	.		0.373	ESCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376276.1	NM_001017420	
PROSC	11212	hgsc.bcm.edu	37	8	37633463	37633463	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:37633463T>C	ENST00000328195.3	+	7	692	c.625T>C	c.(625-627)Tgt>Cgt	p.C209R		NM_007198.3	NP_009129.1	O94903	PROSC_HUMAN	proline synthetase co-transcribed homolog (bacterial)	209					alpha-amino acid metabolic process (GO:1901605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrion (GO:0005739)	pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)	7		Lung NSC(58;0.174)	BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)		L-Proline(DB00172)	GGAGGAGCTGTGTAAAAAGCT	0.522																																					p.C209R		Atlas-SNP	.											.	PROSC	20	.	0			c.T625C						.						208.0	202.0	204.0					8																	37633463		2203	4300	6503	SO:0001583	missense	11212	exon7			GAGCTGTGTAAAA	AB018566	CCDS6096.1	8p11.2	2008-01-07	2001-12-04		ENSG00000147471	ENSG00000147471			9457	protein-coding gene	gene with protein product		604436	"""proline synthetase co-transcribed (bacterial homolog)"""				Standard	NM_007198		Approved		uc003xkh.3	O94903	OTTHUMG00000164024	ENST00000328195.3:c.625T>C	chr8.hg19:g.37633463T>C	ENSP00000333551:p.Cys209Arg	51.0	0.0		84.0	4.0	NM_007198	Q6FI94	Missense_Mutation	SNP	ENST00000328195.3	hg19	CCDS6096.1	.	.	.	.	.	.	.	.	.	.	T	14.76	2.630660	0.46944	.	.	ENSG00000147471	ENST00000328195	T	0.39787	1.06	6.07	6.07	0.98685	Alanine racemase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.37598	0.1009	L	0.31065	0.9	0.80722	D	1	B	0.23058	0.079	B	0.29077	0.098	T	0.17018	-1.0383	10	0.59425	D	0.04	.	16.2903	0.82747	0.0:0.0:0.0:1.0	.	209	O94903	PROSC_HUMAN	R	209	ENSP00000333551:C209R	ENSP00000333551:C209R	C	+	1	0	PROSC	37752621	1.000000	0.71417	0.998000	0.56505	0.222000	0.24845	7.761000	0.85260	2.326000	0.78906	0.533000	0.62120	TGT	.	.		0.522	PROSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376796.1	NM_007198	
WHSC1L1	54904	hgsc.bcm.edu	37	8	38205330	38205330	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:38205330T>C	ENST00000317025.8	-	2	877	c.360A>G	c.(358-360)agA>agG	p.R120R	WHSC1L1_ENST00000527502.1_Silent_p.R120R|WHSC1L1_ENST00000433384.2_Silent_p.R120R|WHSC1L1_ENST00000316985.3_Silent_p.R120R	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	120					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)			TTTCATGTGGTCTTGTGTTTG	0.433			T	NUP98	AML																																p.R120R		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.A360G						.						115.0	116.0	116.0					8																	38205330		2203	4300	6503	SO:0001819	synonymous_variant	54904	exon2			ATGTGGTCTTGTG	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.360A>G	chr8.hg19:g.38205330T>C		76.0	0.0		75.0	4.0	NM_017778	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Silent	SNP	ENST00000317025.8	hg19	CCDS43729.1																																																																																			.	.		0.433	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034	
IKBKB	3551	hgsc.bcm.edu	37	8	42176819	42176819	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:42176819T>C	ENST00000520810.1	+	14	1582	c.1396T>C	c.(1396-1398)Tcc>Ccc	p.S466P	IKBKB_ENST00000416505.2_Missense_Mutation_p.S407P|IKBKB_ENST00000379708.3_Missense_Mutation_p.S243P|IKBKB_ENST00000522785.1_3'UTR|IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000520835.1_Missense_Mutation_p.S464P	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	466	Leucine-zipper.				B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|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 phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CAGCTGCCTCTCCAAAATGAA	0.468											OREG0018747	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S466P		Atlas-SNP	.											.	IKBKB	88	.	0			c.T1396C						.						90.0	88.0	88.0					8																	42176819		2203	4300	6503	SO:0001583	missense	3551	exon14			TGCCTCTCCAAAA	AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.1396T>C	chr8.hg19:g.42176819T>C	ENSP00000430684:p.Ser466Pro	72.0	0.0	906	87.0	4.0	NM_001556	B4DZ30|B4E0U4|O75327	Missense_Mutation	SNP	ENST00000520810.1	hg19	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.396695	0.83120	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000520835;ENST00000379708	T;T;T;T	0.75821	-0.89;-0.97;-0.78;2.84	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.80308	0.4599	L	0.34521	1.04	0.58432	D	0.999991	D;D;D;D;D	0.76494	0.999;0.997;0.999;0.979;0.994	D;D;D;P;P	0.83275	0.996;0.921;0.994;0.756;0.885	T	0.79964	-0.1581	10	0.41790	T	0.15	-25.3868	16.0684	0.80907	0.0:0.0:0.0:1.0	.	407;464;243;417;466	B4E0U4;O14920-2;B3KRB7;Q59GL9;O14920	.;.;.;.;IKKB_HUMAN	P	466;407;464;243	ENSP00000430684:S466P;ENSP00000404920:S407P;ENSP00000430868:S464P;ENSP00000369030:S243P	ENSP00000369030:S243P	S	+	1	0	IKBKB	42295976	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	3.218000	0.51192	2.272000	0.75746	0.460000	0.39030	TCC	.	.		0.468	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1		
NSMAF	8439	hgsc.bcm.edu	37	8	59522272	59522272	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:59522272T>C	ENST00000038176.3	-	10	790	c.578A>G	c.(577-579)aAg>aGg	p.K193R	NSMAF_ENST00000519858.1_5'UTR|NSMAF_ENST00000427130.2_Missense_Mutation_p.K224R	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	193	GRAM.				ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				CATGTGCAGCTTTTCAGAAAT	0.413																																					p.K224R		Atlas-SNP	.											.	NSMAF	156	.	0			c.A671G						.						85.0	80.0	81.0					8																	59522272		2203	4300	6503	SO:0001583	missense	8439	exon10			TGCAGCTTTTCAG	X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"""WD repeat domain containing"""	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.578A>G	chr8.hg19:g.59522272T>C	ENSP00000038176:p.Lys193Arg	62.0	0.0		85.0	4.0	NM_001144772	B4DFB0|E9PCH0|Q8IW26	Missense_Mutation	SNP	ENST00000038176.3	hg19	CCDS6173.1	.	.	.	.	.	.	.	.	.	.	T	5.841	0.339458	0.11069	.	.	ENSG00000035681	ENST00000038176;ENST00000427130	D;D	0.87179	-2.22;-2.22	5.31	1.51	0.23008	GRAM (2);PH-BEACH domain (1);	0.412070	0.28877	N	0.013843	T	0.67183	0.2866	N	0.10809	0.05	0.23391	N	0.997774	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.09377	0.004;0.002;0.003	T	0.49021	-0.8982	9	.	.	.	.	2.267	0.04081	0.2007:0.079:0.1876:0.5326	.	224;193;193	Q92636-2;A8K9G4;Q92636	.;.;FAN_HUMAN	R	193;224	ENSP00000038176:K193R;ENSP00000411012:K224R	.	K	-	2	0	NSMAF	59684826	0.331000	0.24713	1.000000	0.80357	0.152000	0.21847	0.164000	0.16542	0.951000	0.37770	-0.280000	0.10049	AAG	.	.		0.413	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580	
KCNB2	9312	hgsc.bcm.edu	37	8	73480531	73480531	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:73480531T>C	ENST00000523207.1	+	2	1150	c.562T>C	c.(562-564)Tca>Cca	p.S188P		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	188					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GAAACCTAACTCATCAGTGGC	0.438																																					p.S188P		Atlas-SNP	.											.	KCNB2	228	.	0			c.T562C						.						69.0	73.0	72.0					8																	73480531		2200	4298	6498	SO:0001583	missense	9312	exon2			CCTAACTCATCAG	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.562T>C	chr8.hg19:g.73480531T>C	ENSP00000430846:p.Ser188Pro	48.0	0.0		74.0	5.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.149108	0.78001	.	.	ENSG00000182674	ENST00000523207	D	0.98135	-4.74	5.77	5.77	0.91146	.	0.485631	0.15369	U	0.265950	D	0.98985	0.9654	H	0.95260	3.645	0.58432	D	0.999998	D	0.53462	0.96	P	0.58266	0.836	D	0.99869	1.1093	10	0.72032	D	0.01	.	16.068	0.80903	0.0:0.0:0.0:1.0	.	188	Q92953	KCNB2_HUMAN	P	188	ENSP00000430846:S188P	ENSP00000430846:S188P	S	+	1	0	KCNB2	73643085	1.000000	0.71417	0.991000	0.47740	0.926000	0.56050	7.997000	0.88414	2.326000	0.78906	0.533000	0.62120	TCA	.	.		0.438	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
CRISPLD1	83690	hgsc.bcm.edu	37	8	75932282	75932282	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:75932282T>C	ENST00000262207.4	+	12	1680	c.1212T>C	c.(1210-1212)tgT>tgC	p.C404C	CRISPLD1_ENST00000523524.1_Silent_p.C216C|CRISPLD1_ENST00000517786.1_Silent_p.C218C	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	404	LCCL 2. {ECO:0000255|PROSITE- ProRule:PRU00123}.				face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			AACAGCTCTGTCCATTTCATA	0.413																																					p.C404C		Atlas-SNP	.											.	CRISPLD1	94	.	0			c.T1212C						.						134.0	121.0	126.0					8																	75932282		2203	4300	6503	SO:0001819	synonymous_variant	83690	exon12			GCTCTGTCCATTT	AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"""LCCL domain containing cysteine-rich secretory protein 1"""	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.1212T>C	chr8.hg19:g.75932282T>C		157.0	0.0		248.0	11.0	NM_031461	B2RA60|B7Z929	Silent	SNP	ENST00000262207.4	hg19	CCDS6219.1																																																																																			.	.		0.413	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461	
RALYL	138046	hgsc.bcm.edu	37	8	85097244	85097244	+	Intron	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:85097244G>C	ENST00000521268.1	+	1	1082				RALYL_ENST00000522455.1_Intron|RALYL_ENST00000521695.1_Intron|RALYL_ENST00000517638.1_Missense_Mutation_p.R4P|RALYL_ENST00000518566.1_Intron	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like								nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)	24						ATGAGTAAACGACGCAGTAGG	0.532																																					p.R4P		Atlas-SNP	.											.	RALYL	123	.	0			c.G11C						.						101.0	108.0	106.0					8																	85097244		2104	4233	6337	SO:0001627	intron_variant	138046	exon1			GTAAACGACGCAG		CCDS55252.1, CCDS55253.1, CCDS75760.1, CCDS75761.1	8q21.2	2013-07-16			ENSG00000184672	ENSG00000184672		"""RNA binding motif (RRM) containing"""	27036	protein-coding gene	gene with protein product		614648				12688537	Standard	NM_001100391		Approved	HNRPCL3	uc003yct.4	Q86SE5	OTTHUMG00000164628	ENST00000521268.1:c.-24+585G>C	chr8.hg19:g.85097244G>C		160.0	0.0		174.0	7.0	NM_001100391	B3KTH2|G3V129|Q6ZW87|Q8N1C2	Missense_Mutation	SNP	ENST00000521268.1	hg19	CCDS55253.1	.	.	.	.	.	.	.	.	.	.	G	10.61	1.397600	0.25205	.	.	ENSG00000184672	ENST00000517638	T	0.10960	2.82	5.2	1.45	0.22620	.	.	.	.	.	T	0.06188	0.0160	N	0.14661	0.345	0.80722	D	1	B	0.23490	0.086	B	0.24269	0.052	T	0.30001	-0.9993	9	0.87932	D	0	.	6.0671	0.19870	0.6026:0.3142:0.0832:0.0	.	4	G3V129	.	P	4	ENSP00000430128:R4P	ENSP00000430128:R4P	R	+	2	0	RALYL	85259799	0.358000	0.24947	0.013000	0.15412	0.927000	0.56198	0.153000	0.16323	0.087000	0.17167	-0.471000	0.05019	CGA	.	.		0.532	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379448.1		
WWP1	11059	hgsc.bcm.edu	37	8	87410810	87410810	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:87410810A>G	ENST00000517970.1	+	7	789	c.482A>G	c.(481-483)cAg>cGg	p.Q161R	WWP1_ENST00000341922.2_Intron|WWP1_ENST00000349423.2_Intron|WWP1_ENST00000265428.4_Missense_Mutation_p.Q161R	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	161					central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						GTAGAAATACAGGAAAATGGT	0.328																																					p.Q161R		Atlas-SNP	.											.	WWP1	97	.	0			c.A482G						.						99.0	100.0	100.0					8																	87410810		2203	4300	6503	SO:0001583	missense	11059	exon7			AAATACAGGAAAA	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.482A>G	chr8.hg19:g.87410810A>G	ENSP00000427793:p.Gln161Arg	132.0	0.0		146.0	6.0	NM_007013	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	hg19	CCDS6242.1	.	.	.	.	.	.	.	.	.	.	A	13.08	2.129496	0.37630	.	.	ENSG00000123124	ENST00000517970;ENST00000265428	T;T	0.45276	0.9;0.9	5.41	4.24	0.50183	.	0.493228	0.21765	N	0.069451	T	0.35038	0.0918	L	0.53249	1.67	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.10268	-1.0637	10	0.15952	T	0.53	.	10.2698	0.43477	0.9172:0.0:0.0828:0.0	.	161	Q9H0M0	WWP1_HUMAN	R	161	ENSP00000427793:Q161R;ENSP00000265428:Q161R	ENSP00000265428:Q161R	Q	+	2	0	WWP1	87479926	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.030000	0.64128	0.987000	0.38709	0.477000	0.44152	CAG	.	.		0.328	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013	
STK3	6788	hgsc.bcm.edu	37	8	99608284	99608284	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:99608284T>C	ENST00000419617.2	-	7	938	c.798A>G	c.(796-798)agA>agG	p.R266R	STK3_ENST00000521768.1_5'UTR|STK3_ENST00000523601.1_Silent_p.R294R	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	266	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		TTGCAGTAGCTCTCTGCTCAG	0.428																																					p.R294R		Atlas-SNP	.											.	STK3	47	.	0			c.A882G						.						71.0	69.0	70.0					8																	99608284		1895	4105	6000	SO:0001819	synonymous_variant	6788	exon9			AGTAGCTCTCTGC	BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"""serine/threonine kinase 3 (Ste20, yeast homolog)"""			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.798A>G	chr8.hg19:g.99608284T>C		182.0	0.0		247.0	10.0	NM_001256312	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Silent	SNP	ENST00000419617.2	hg19	CCDS47900.1																																																																																			.	.		0.428	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379635.1	NM_006281	
STK3	6788	hgsc.bcm.edu	37	8	99718796	99718796	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:99718796C>T	ENST00000419617.2	-	6	723	c.583G>A	c.(583-585)Gaa>Aaa	p.E195K	STK3_ENST00000523601.1_Missense_Mutation_p.E223K	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	195	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		TAGCCTATTTCTTGAATCACC	0.403																																					p.E223K		Atlas-SNP	.											STK3,NS,carcinoma,0,2	STK3	47	.	0			c.G667A						.						142.0	142.0	142.0					8																	99718796		2035	4217	6252	SO:0001583	missense	6788	exon8			CTATTTCTTGAAT	BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"""serine/threonine kinase 3 (Ste20, yeast homolog)"""			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.583G>A	chr8.hg19:g.99718796C>T	ENSP00000390500:p.Glu195Lys	80.0	0.0		110.0	5.0	NM_001256312	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Missense_Mutation	SNP	ENST00000419617.2	hg19	CCDS47900.1	.	.	.	.	.	.	.	.	.	.	C	35	5.439199	0.96168	.	.	ENSG00000104375	ENST00000419617;ENST00000523601	T;T	0.13420	2.59;2.59	4.78	4.78	0.61160	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	0.85682	D	0.000000	T	0.20495	0.0493	N	0.11201	0.11	0.80722	D	1	P;D	0.76494	0.69;0.999	P;D	0.69479	0.479;0.964	T	0.29610	-1.0006	10	0.87932	D	0	.	17.3864	0.87417	0.0:1.0:0.0:0.0	.	195;223	Q13188;B3KYA7	STK3_HUMAN;.	K	195;223	ENSP00000390500:E195K;ENSP00000429744:E223K	ENSP00000390500:E195K	E	-	1	0	STK3	99787972	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.794000	0.85869	2.196000	0.70406	0.467000	0.42956	GAA	.	.		0.403	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379635.1	NM_006281	
TNFRSF11B	4982	hgsc.bcm.edu	37	8	119945174	119945174	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:119945174T>C	ENST00000297350.4	-	2	774	c.396A>G	c.(394-396)caA>caG	p.Q132Q		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	132					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			ACGTACCAGCTTGCACCACTC	0.463																																					p.Q132Q		Atlas-SNP	.											.	TNFRSF11B	87	.	0			c.A396G						.						47.0	48.0	48.0					8																	119945174		2203	4300	6503	SO:0001819	synonymous_variant	4982	exon2			ACCAGCTTGCACC	U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"""Tumor necrosis factor receptor superfamily"""	11909	protein-coding gene	gene with protein product		602643	"""osteoprotegerin"""	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.396A>G	chr8.hg19:g.119945174T>C		78.0	0.0		90.0	4.0	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Silent	SNP	ENST00000297350.4	hg19	CCDS6326.1																																																																																			.	.		0.463	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1		
MTSS1	9788	hgsc.bcm.edu	37	8	125569986	125569986	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:125569986T>C	ENST00000518547.1	-	11	1639	c.1166A>G	c.(1165-1167)gAc>gGc	p.D389G	MTSS1_ENST00000354184.4_Intron|MTSS1_ENST00000524090.1_Missense_Mutation_p.D279G|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000325064.5_Missense_Mutation_p.D393G|MTSS1_ENST00000431961.2_Intron|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000378017.3_Intron|MTSS1_ENST00000395508.2_Missense_Mutation_p.D163G	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	389					actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			ATGAGCGTAGTCTGGAAGGTG	0.602																																					p.D389G	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-SNP	.											.	MTSS1	79	.	0			c.A1166G						.						115.0	84.0	94.0					8																	125569986		2203	4300	6503	SO:0001583	missense	9788	exon11			GCGTAGTCTGGAA	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.1166A>G	chr8.hg19:g.125569986T>C	ENSP00000429064:p.Asp389Gly	120.0	0.0		142.0	7.0	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Missense_Mutation	SNP	ENST00000518547.1	hg19	CCDS6353.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.670812	0.47781	.	.	ENSG00000170873	ENST00000518547;ENST00000395508;ENST00000325064;ENST00000524090;ENST00000522118	T;T;T;T;T	0.54071	1.4;1.34;1.4;1.38;0.59	5.14	5.14	0.70334	.	0.175996	0.52532	D	0.000074	T	0.33673	0.0871	N	0.22421	0.69	0.54753	D	0.999987	P;B;B	0.43094	0.799;0.028;0.295	B;B;B	0.30179	0.112;0.015;0.055	T	0.19128	-1.0315	10	0.30854	T	0.27	-22.2155	14.9595	0.71144	0.0:0.0:0.0:1.0	.	279;163;389	E7EWW5;B7Z3B6;O43312	.;.;MTSS1_HUMAN	G	389;163;393;279;189	ENSP00000429064:D389G;ENSP00000378884:D163G;ENSP00000322804:D393G;ENSP00000428319:D279G;ENSP00000428145:D189G	ENSP00000322804:D393G	D	-	2	0	MTSS1	125639167	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.771000	0.68881	1.931000	0.55961	0.459000	0.35465	GAC	.	.		0.602	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751	
KIAA0196	9897	hgsc.bcm.edu	37	8	126052109	126052109	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:126052109A>G	ENST00000318410.7	-	24	3231	c.2882T>C	c.(2881-2883)aTt>aCt	p.I961T	KIAA0196_ENST00000517845.1_Missense_Mutation_p.I813T|KIAA0196-AS1_ENST00000519140.1_RNA	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	961					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			TTCATTGGCAATCTGTTGTCT	0.428																																					p.I961T		Atlas-SNP	.											.	KIAA0196	90	.	0			c.T2882C						.						76.0	70.0	72.0					8																	126052109		2203	4300	6503	SO:0001583	missense	9897	exon24			TTGGCAATCTGTT		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"""strumpellin"""	610657	"""spastic paraplegia 8 (autosomal dominant)"""	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.2882T>C	chr8.hg19:g.126052109A>G	ENSP00000318016:p.Ile961Thr	63.0	0.0		81.0	4.0	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Missense_Mutation	SNP	ENST00000318410.7	hg19	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.497961	0.85069	.	.	ENSG00000164961	ENST00000318410;ENST00000517845	D;D	0.91351	-2.83;-2.83	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.95834	0.8644	M	0.86651	2.83	0.80722	D	1	D;P	0.89917	1.0;0.901	D;P	0.83275	0.996;0.559	D	0.96516	0.9382	10	0.87932	D	0	-21.0437	15.7714	0.78173	1.0:0.0:0.0:0.0	.	813;961	E7EQI7;Q12768	.;STRUM_HUMAN	T	961;813	ENSP00000318016:I961T;ENSP00000429676:I813T	ENSP00000318016:I961T	I	-	2	0	KIAA0196	126121291	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.299000	0.96137	2.127000	0.65507	0.459000	0.35465	ATT	.	.		0.428	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846	
PTK2	5747	hgsc.bcm.edu	37	8	141675017	141675017	+	Splice_Site	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:141675017T>C	ENST00000522684.1	-	31	3174	c.2945A>G	c.(2944-2946)gAg>gGg	p.E982G	PTK2_ENST00000517712.1_Splice_Site_p.E45G|PTK2_ENST00000430260.2_Splice_Site_p.E292G|PTK2_ENST00000340930.3_Splice_Site_p.E995G|PTK2_ENST00000517887.1_Splice_Site_p.E1026G|PTK2_ENST00000522950.1_5'Flank|PTK2_ENST00000521059.1_Splice_Site_p.E982G|PTK2_ENST00000538769.1_Splice_Site_p.E650G|PTK2_ENST00000535192.1_Splice_Site_p.E936G|PTK2_ENST00000519419.1_Splice_Site_p.E1026G|PTK2_ENST00000519465.1_Splice_Site_p.E610G|PTK2_ENST00000395218.2_Splice_Site_p.E995G	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	982	Interaction with ARHGEF28. {ECO:0000250}.|Interaction with TGFB1I1.				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)			GTGCCCTACCTCTCGGTGGGT	0.577																																					p.E1004G		Atlas-SNP	.											.	PTK2	311	.	0			c.A3011G						.						132.0	86.0	101.0					8																	141675017		2203	4300	6503	SO:0001630	splice_region_variant	5747	exon31			CCTACCTCTCGGT	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.2946+1A>G	chr8.hg19:g.141675017T>C		89.0	0.0		123.0	6.0	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	hg19	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.111148	0.77210	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000517712;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000430260;ENST00000521986	T;T;T;T;T;T;T;T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19	5.77	5.77	0.91146	Focal adhesion kinase, targeting (FAT) domain (3);	0.000000	0.85682	D	0.000000	T	0.48978	0.1530	M	0.67397	2.05	0.80722	D	1	B;B;P;B;B;B;B;P;B;B	0.41008	0.154;0.017;0.735;0.129;0.302;0.104;0.307;0.529;0.325;0.07	B;B;P;B;B;B;B;B;B;B	0.47402	0.229;0.107;0.546;0.161;0.333;0.121;0.398;0.331;0.269;0.133	T	0.51148	-0.8742	10	0.66056	D	0.02	.	15.7592	0.78063	0.0:0.0:0.0:1.0	.	995;680;905;982;1004;936;937;809;650;610	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.;.;.;FAK1_HUMAN;.;.;.;.;.;.	G	982;936;610;1026;982;937;995;906;680;45;654;995;650;1026;292;683	ENSP00000429911:E982G;ENSP00000438009:E936G;ENSP00000429170:E610G;ENSP00000429082:E1026G;ENSP00000429474:E982G;ENSP00000378644:E995G;ENSP00000430916:E45G;ENSP00000428492:E654G;ENSP00000341189:E995G;ENSP00000445742:E650G;ENSP00000429129:E1026G;ENSP00000403416:E292G;ENSP00000430603:E683G	ENSP00000341189:E995G	E	-	2	0	PTK2	141744199	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.687000	0.84139	2.216000	0.71823	0.528000	0.53228	GAG	.	.		0.577	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	Missense_Mutation
MROH6	642475	hgsc.bcm.edu	37	8	144654667	144654667	+	Missense_Mutation	SNP	G	G	A	rs368816807		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:144654667G>A	ENST00000398882.3	-	1	474	c.218C>T	c.(217-219)gCc>gTc	p.A73V	NAPRT1_ENST00000460623.1_5'Flank|RP11-661A12.9_ENST00000531730.1_RNA|MROH6_ENST00000533679.1_5'Flank	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	73																	AGGGACGGTGGCCCCACGTCC	0.682																																					p.A73V		Atlas-SNP	.											.	.	.	.	0			c.C218T						.		VAL/ALA	0,3968		0,0,1984	15.0	20.0	19.0		218	1.4	0.0	8		19	1,8303		0,1,4151	no	missense	C8orf73	NM_001100878.1	64	0,1,6135	AA,AG,GG		0.012,0.0,0.0081	benign	73/720	144654667	1,12271	1984	4152	6136	SO:0001583	missense	642475	exon1			ACGGTGGCCCCAC	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"""maestro heat-like repeat containing"""	27814	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 73"""	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164	ENST00000398882.3:c.218C>T	chr8.hg19:g.144654667G>A	ENSP00000381857:p.Ala73Val	62.0	0.0		93.0	16.0	NM_001100878	A8MWB1	Missense_Mutation	SNP	ENST00000398882.3	hg19	CCDS47928.1	.	.	.	.	.	.	.	.	.	.	g	12.09	1.835002	0.32421	0.0	1.2E-4	ENSG00000204839	ENST00000398882;ENST00000529971	T;T	0.24151	4.3;1.87	3.8	1.37	0.22104	.	.	.	.	.	T	0.12050	0.0293	N	0.14661	0.345	0.19775	N	0.999953	B;B	0.19331	0.035;0.002	B;B	0.14023	0.01;0.003	T	0.32587	-0.9901	9	0.23302	T	0.38	-2.2287	4.1419	0.10198	0.1943:0.2146:0.5911:0.0	.	73;73	E9PPP7;A6NGR9	.;CH073_HUMAN	V	73	ENSP00000381857:A73V;ENSP00000436959:A73V	ENSP00000381857:A73V	A	-	2	0	C8orf73	144725810	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.207000	0.09384	0.133000	0.18654	0.558000	0.71614	GCC	.	.		0.682	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878	
ERMP1	79956	hgsc.bcm.edu	37	9	5805053	5805053	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:5805053A>G	ENST00000339450.5	-	10	1977	c.1888T>C	c.(1888-1890)Tgt>Cgt	p.C630R	ERMP1_ENST00000214893.5_5'UTR|ERMP1_ENST00000381506.3_Intron|ERMP1_ENST00000543230.1_Missense_Mutation_p.C208R	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	630						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		ATCATTGTACAGCCAGCCAAA	0.378																																					p.C630R		Atlas-SNP	.											.	ERMP1	63	.	0			c.T1888C						.						83.0	76.0	78.0					9																	5805053		2203	4300	6503	SO:0001583	missense	79956	exon10			TTGTACAGCCAGC	AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"""Felix-ina"""	611156	"""KIAA1815"""	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.1888T>C	chr9.hg19:g.5805053A>G	ENSP00000340427:p.Cys630Arg	105.0	0.0		77.0	4.0	NM_024896	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Missense_Mutation	SNP	ENST00000339450.5	hg19	CCDS34983.1	.	.	.	.	.	.	.	.	.	.	A	11.93	1.785491	0.31593	.	.	ENSG00000099219	ENST00000339450;ENST00000543230	T;T	0.23147	1.92;1.92	5.7	5.7	0.88788	.	0.145914	0.64402	D	0.000007	T	0.18964	0.0455	L	0.43152	1.355	0.80722	D	1	P	0.46952	0.887	B	0.35931	0.214	T	0.04165	-1.0972	10	0.25106	T	0.35	-21.0705	11.7192	0.51672	0.8603:0.0:0.0:0.1397	.	630	Q7Z2K6	ERMP1_HUMAN	R	630;208	ENSP00000340427:C630R;ENSP00000439368:C208R	ENSP00000340427:C630R	C	-	1	0	ERMP1	5795053	0.975000	0.34042	0.180000	0.23079	0.807000	0.45602	4.165000	0.58196	2.170000	0.68504	0.482000	0.46254	TGT	.	.		0.378	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896	
MPDZ	8777	hgsc.bcm.edu	37	9	13168371	13168371	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:13168371T>C	ENST00000319217.7	-	22	3495	c.3248A>G	c.(3247-3249)gAc>gGc	p.D1083G	MPDZ_ENST00000381022.2_Missense_Mutation_p.D1083G|MPDZ_ENST00000546205.1_Missense_Mutation_p.D1083G|MPDZ_ENST00000538841.1_5'Flank|MPDZ_ENST00000381015.4_Missense_Mutation_p.D1083G|MPDZ_ENST00000541718.1_Missense_Mutation_p.D1083G|MPDZ_ENST00000536827.1_Missense_Mutation_p.D1083G|MPDZ_ENST00000447879.1_Missense_Mutation_p.D1083G	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1083	PDZ 6. {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)		TTACTTTATGTCAGGGCCAAT	0.388																																					p.D1083G		Atlas-SNP	.											.	MPDZ	324	.	0			c.A3248G						.						173.0	165.0	168.0					9																	13168371		1880	4122	6002	SO:0001583	missense	8777	exon22			TTTATGTCAGGGC	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.3248A>G	chr9.hg19:g.13168371T>C	ENSP00000320006:p.Asp1083Gly	95.0	0.0		84.0	5.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	hg19		.	.	.	.	.	.	.	.	.	.	T	21.1	4.101891	0.76983	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000545857;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13;1.13;1.13;1.13	5.23	4.1	0.47936	.	0.000000	0.45867	D	0.000322	T	0.55386	0.1917	L	0.61218	1.895	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.999	P;D;D	0.70227	0.848;0.968;0.928	T	0.51348	-0.8717	10	0.17832	T	0.49	.	10.9259	0.47191	0.0:0.0737:0.0:0.9263	.	1083;1083;1083	B7ZMI4;O75970-3;O75970-2	.;.;.	G	1083;1083;1083;89;1083;1083;1083;1033;1083	ENSP00000320006:D1083G;ENSP00000439807:D1083G;ENSP00000370410:D1083G;ENSP00000444230:D89G;ENSP00000444151:D1083G;ENSP00000415208:D1083G;ENSP00000370403:D1083G;ENSP00000446358:D1083G	ENSP00000320006:D1083G	D	-	2	0	MPDZ	13158371	1.000000	0.71417	0.998000	0.56505	0.931000	0.56810	7.655000	0.83696	0.936000	0.37367	0.460000	0.39030	GAC	.	.		0.388	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
FREM1	158326	hgsc.bcm.edu	37	9	14737508	14737508	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:14737508A>G	ENST00000380880.3	-	37	7209	c.6426T>C	c.(6424-6426)tcT>tcC	p.S2142S	FREM1_ENST00000422223.2_Silent_p.S2142S|FREM1_ENST00000380881.4_Silent_p.S2143S|FREM1_ENST00000380894.1_Silent_p.S678S			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	2142	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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)		TGGAGCGTTGAGAGGGCCCTC	0.478																																					p.S2142S		Atlas-SNP	.											.	FREM1	261	.	0			c.T6426C						.						66.0	65.0	65.0					9																	14737508		1907	4127	6034	SO:0001819	synonymous_variant	158326	exon38			GCGTTGAGAGGGC	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.6426T>C	chr9.hg19:g.14737508A>G		133.0	0.0		93.0	4.0	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	hg19	CCDS47952.1																																																																																			.	.		0.478	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
PLIN2	123	hgsc.bcm.edu	37	9	19123604	19123604	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:19123604T>C	ENST00000276914.2	-	4	447	c.268A>G	c.(268-270)Att>Gtt	p.I90V	PLIN2_ENST00000411567.1_Missense_Mutation_p.I90V|PLIN2_ENST00000380464.3_Missense_Mutation_p.I90V|PLIN2_ENST00000380465.3_Missense_Mutation_p.I90V	NM_001122.3	NP_001113.2	Q99541	PLIN2_HUMAN	perilipin 2	90					cellular lipid metabolic process (GO:0044255)|lipid storage (GO:0019915)|long-chain fatty acid transport (GO:0015909)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	19						CTCTCCTCAATCCTGTCTAGC	0.413																																					p.I90V		Atlas-SNP	.											.	PLIN2	41	.	0			c.A268G						.						123.0	96.0	105.0					9																	19123604		2203	4300	6503	SO:0001583	missense	123	exon4			CCTCAATCCTGTC	X97324	CCDS6490.1	9p22.1	2009-08-12	2009-08-12	2009-08-12	ENSG00000147872	ENSG00000147872		"""Perilipins"""	248	protein-coding gene	gene with protein product	"""adipophilin"""	103195	"""adipose differentiation-related protein"""	ADFP		9003395, 19638644	Standard	NM_001122		Approved	ADRP	uc003zno.3	Q99541	OTTHUMG00000019624	ENST00000276914.2:c.268A>G	chr9.hg19:g.19123604T>C	ENSP00000276914:p.Ile90Val	130.0	0.0		96.0	4.0	NM_001122	Q9BSC3	Missense_Mutation	SNP	ENST00000276914.2	hg19	CCDS6490.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.222425	0.39300	.	.	ENSG00000147872	ENST00000411567;ENST00000276914;ENST00000434144;ENST00000380465;ENST00000380464	T;T;T;T;T	0.05717	3.4;3.4;3.4;3.4;3.4	5.94	4.8	0.61643	.	0.092733	0.64402	N	0.000001	T	0.06872	0.0175	L	0.47016	1.485	0.37812	D	0.928078	B;B	0.12630	0.006;0.005	B;B	0.21708	0.01;0.036	T	0.24440	-1.0160	10	0.15066	T	0.55	.	10.0527	0.42225	0.0:0.1355:0.0:0.8645	.	90;90	E9PG83;Q99541	.;PLIN2_HUMAN	V	90	ENSP00000415270:I90V;ENSP00000276914:I90V;ENSP00000403421:I90V;ENSP00000369832:I90V;ENSP00000369831:I90V	ENSP00000276914:I90V	I	-	1	0	PLIN2	19113604	1.000000	0.71417	0.999000	0.59377	0.837000	0.47467	3.724000	0.54962	1.054000	0.40438	0.482000	0.46254	ATT	.	.		0.413	PLIN2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051835.1	NM_001122	
IFNA2	3440	hgsc.bcm.edu	37	9	21385289	21385289	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:21385289G>A	ENST00000380206.2	-	1	107	c.40C>T	c.(40-42)Ctc>Ttc	p.L14F		NM_000605.3	NP_000596.2	P01563	IFNA2_HUMAN	interferon, alpha 2	14					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of gene expression (GO:0010629)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	type I interferon receptor binding (GO:0005132)			breast(2)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)	13				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		TTGCAGCTGAGCACCAGGAGG	0.537																																					p.L14F		Atlas-SNP	.											.	IFNA2	32	.	0			c.C40T						.						109.0	96.0	100.0					9																	21385289		2203	4300	6503	SO:0001583	missense	3440	exon1			AGCTGAGCACCAG		CCDS6506.1	9p22	2010-08-24			ENSG00000188379	ENSG00000188379		"""Interferons"""	5423	protein-coding gene	gene with protein product	"""alpha-2a interferon"", ""interferon alpha 2b"", ""interferon alpha A"""	147562				1385305	Standard	NM_000605		Approved	IFNA, IFN-alphaA	uc003zpb.3	P01563	OTTHUMG00000019674	ENST00000380206.2:c.40C>T	chr9.hg19:g.21385289G>A	ENSP00000369554:p.Leu14Phe	133.0	0.0		118.0	67.0	NM_000605	H2DF54|H2DF55|P01564|Q14606|Q6DJX8|Q96KI6	Missense_Mutation	SNP	ENST00000380206.2	hg19	CCDS6506.1	.	.	.	.	.	.	.	.	.	.	G	7.915	0.737272	0.15574	.	.	ENSG00000188379	ENST00000380206	T	0.03689	3.84	3.24	1.17	0.20885	.	0.094776	0.44688	D	0.000430	T	0.09423	0.0232	M	0.86097	2.795	0.09310	N	1	D	0.54047	0.964	P	0.50314	0.637	T	0.11036	-1.0604	10	0.52906	T	0.07	.	5.3592	0.16077	0.0:0.1916:0.3847:0.4236	.	14	Q6DJX8	.	F	14	ENSP00000369554:L14F	ENSP00000369554:L14F	L	-	1	0	IFNA2	21375289	0.004000	0.15560	0.002000	0.10522	0.013000	0.08279	0.405000	0.21015	0.052000	0.16007	0.484000	0.47621	CTC	.	.		0.537	IFNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051903.1	NM_000605	
TEK	7010	hgsc.bcm.edu	37	9	27169566	27169566	+	Silent	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:27169566C>T	ENST00000380036.4	+	4	1009	c.567C>T	c.(565-567)taC>taT	p.Y189Y	TEK_ENST00000519097.1_Silent_p.Y85Y|TEK_ENST00000406359.4_Silent_p.Y189Y	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	189					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	CTGGAGTGTACTCGGCCAGGT	0.512																																					p.Y189Y		Atlas-SNP	.											.	TEK	250	.	0			c.C567T						.						147.0	138.0	141.0					9																	27169566		2203	4300	6503	SO:0001819	synonymous_variant	7010	exon4			AGTGTACTCGGCC	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.567C>T	chr9.hg19:g.27169566C>T		94.0	0.0		77.0	4.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	hg19	CCDS6519.1																																																																																			.	.		0.512	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
DNAJA1	3301	hgsc.bcm.edu	37	9	33037024	33037024	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:33037024A>G	ENST00000330899.4	+	8	1069	c.886A>G	c.(886-888)Aag>Gag	p.K296E	DNAJA1_ENST00000495015.1_3'UTR|DNAJA1_ENST00000544625.1_Missense_Mutation_p.K139E	NM_001539.2	NP_001530.1	P31689	DNJA1_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 1	296					androgen receptor signaling pathway (GO:0030521)|DNA damage response, detection of DNA damage (GO:0042769)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of apoptotic process (GO:0043065)|protein folding (GO:0006457)|protein localization to mitochondrion (GO:0070585)|regulation of protein transport (GO:0051223)|response to heat (GO:0009408)|response to unfolded protein (GO:0006986)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasmic side of endoplasmic reticulum membrane (GO:0098554)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|G-protein coupled receptor binding (GO:0001664)|Hsp70 protein binding (GO:0030544)|low-density lipoprotein particle receptor binding (GO:0050750)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			large_intestine(2)|ovary(1)|skin(3)	6			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.102)		TCAGATTGTCAAGCATGGAGA	0.383																																					p.K296E		Atlas-SNP	.											.	DNAJA1	26	.	0			c.A886G						.						136.0	122.0	127.0					9																	33037024		2203	4300	6503	SO:0001583	missense	3301	exon8			ATTGTCAAGCATG	L08069	CCDS6533.1	9p13.3	2011-09-02			ENSG00000086061	ENSG00000086061		"""Heat shock proteins / DNAJ (HSP40)"""	5229	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 7"""	602837		HSJ2		8334160, 11147971	Standard	NM_001539		Approved	HSPF4, hdj-2, dj-2, NEDD7	uc003zsd.1	P31689	OTTHUMG00000019760	ENST00000330899.4:c.886A>G	chr9.hg19:g.33037024A>G	ENSP00000369127:p.Lys296Glu	51.0	0.0		82.0	4.0	NM_001539	Q5T7Q0|Q86TL9	Missense_Mutation	SNP	ENST00000330899.4	hg19	CCDS6533.1	.	.	.	.	.	.	.	.	.	.	A	17.15	3.316808	0.60524	.	.	ENSG00000086061	ENST00000330899;ENST00000539152;ENST00000544625	T;T	0.48522	0.81;0.81	5.33	5.33	0.75918	Chaperone DnaJ, C-terminal (1);HSP40/DnaJ peptide-binding (1);	0.000000	0.85682	D	0.000000	T	0.53818	0.1820	M	0.74389	2.26	0.80722	D	1	B;B	0.29481	0.118;0.245	B;B	0.37346	0.108;0.247	T	0.54774	-0.8243	10	0.40728	T	0.16	-19.7625	13.5499	0.61726	1.0:0.0:0.0:0.0	.	296;296	Q86TL9;P31689	.;DNJA1_HUMAN	E	296;139;139	ENSP00000369127:K296E;ENSP00000439010:K139E	ENSP00000369127:K296E	K	+	1	0	DNAJA1	33027024	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.465000	0.80898	2.157000	0.67596	0.482000	0.46254	AAG	.	.		0.383	DNAJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052031.1		
OMD	4958	hgsc.bcm.edu	37	9	95179318	95179318	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:95179318A>G	ENST00000375550.4	-	2	798	c.523T>C	c.(523-525)Tcc>Ccc	p.S175P	CENPP_ENST00000375587.3_Intron	NM_005014.2	NP_005005.1	Q99983	OMD_HUMAN	osteomodulin	175					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|skin(2)	16						TGCAGTTTGGAGATTTCATTG	0.338			T	USP6	aneurysmal bone cysts																																p.S175P		Atlas-SNP	.		Dom	yes		9	9q22.31	4958	osteomodulin		M	.	OMD	42	.	0			c.T523C						.						107.0	106.0	106.0					9																	95179318		2203	4300	6503	SO:0001583	missense	4958	exon2			GTTTGGAGATTTC	AB000114	CCDS6696.1	9q22.31	2008-02-05			ENSG00000127083	ENSG00000127083		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	8134	protein-coding gene	gene with protein product	"""osteoadherin proteoglycan"""						Standard	NM_005014		Approved	osteoadherin, SLRR2C	uc004asd.4	Q99983	OTTHUMG00000020225	ENST00000375550.4:c.523T>C	chr9.hg19:g.95179318A>G	ENSP00000364700:p.Ser175Pro	109.0	0.0		142.0	6.0	NM_005014	Q5TBF4	Missense_Mutation	SNP	ENST00000375550.4	hg19	CCDS6696.1	.	.	.	.	.	.	.	.	.	.	a	18.99	3.739644	0.69304	.	.	ENSG00000127083	ENST00000375550	T	0.05447	3.44	5.41	5.41	0.78517	.	0.080378	0.50627	D	0.000107	T	0.20780	0.0500	M	0.73753	2.245	0.46678	D	0.99915	D	0.76494	0.999	P	0.61477	0.889	T	0.00259	-1.1870	10	0.72032	D	0.01	-6.1556	11.7062	0.51599	0.8524:0.1476:0.0:0.0	.	175	Q99983	OMD_HUMAN	P	175	ENSP00000364700:S175P	ENSP00000364700:S175P	S	-	1	0	OMD	94219139	1.000000	0.71417	0.984000	0.44739	0.960000	0.62799	4.708000	0.61859	2.178000	0.69098	0.477000	0.44152	TCC	.	.		0.338	OMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053090.1	NM_005014	
NCBP1	4686	hgsc.bcm.edu	37	9	100429054	100429054	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:100429054T>C	ENST00000375147.3	+	20	2167	c.1911T>C	c.(1909-1911)gtT>gtC	p.V637V		NM_002486.4	NP_002477.1	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	637					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)				GATTGTTTGTTTGGGAAATTT	0.338																																					p.V637V	Ovarian(36;879 898 2893 44212 50307)	Atlas-SNP	.											.	NCBP1	64	.	0			c.T1911C						.						87.0	86.0	87.0					9																	100429054		2203	4300	6503	SO:0001819	synonymous_variant	4686	exon20			GTTTGTTTGGGAA	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.1911T>C	chr9.hg19:g.100429054T>C		70.0	0.0		83.0	4.0	NM_002486	B2R718|Q59G76|Q5T1V0|Q5T7X2	Silent	SNP	ENST00000375147.3	hg19	CCDS6728.1																																																																																			.	.		0.338	NCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053337.1	NM_002486	
COL15A1	1306	hgsc.bcm.edu	37	9	101829178	101829178	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:101829178T>C	ENST00000375001.3	+	40	4089	c.3666T>C	c.(3664-3666)gcT>gcC	p.A1222A		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	1222	Nonhelical region 10 (NC10).				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)			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)				ATTTGGCTGCTCTGAACATGC	0.478																																					p.A1222A		Atlas-SNP	.											.	COL15A1	211	.	0			c.T3666C						.						116.0	107.0	110.0					9																	101829178		2203	4300	6503	SO:0001819	synonymous_variant	1306	exon40			GGCTGCTCTGAAC	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.3666T>C	chr9.hg19:g.101829178T>C		80.0	0.0		102.0	5.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	hg19	CCDS35081.1																																																																																			.	.		0.478	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
ABCA1	19	hgsc.bcm.edu	37	9	107581925	107581925	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:107581925A>G	ENST00000374736.3	-	22	3577	c.3183T>C	c.(3181-3183)gcT>gcC	p.A1061A		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1061	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	GGTCCACACCAGCTGTGGGTT	0.488																																					p.A1061A		Atlas-SNP	.											.	ABCA1	244	.	0			c.T3183C						.						111.0	114.0	113.0					9																	107581925		2203	4300	6503	SO:0001819	synonymous_variant	19	exon22			CACACCAGCTGTG	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.3183T>C	chr9.hg19:g.107581925A>G		147.0	0.0		132.0	6.0	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	hg19	CCDS6762.1																																																																																			.	.		0.488	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
RGS3	5998	hgsc.bcm.edu	37	9	116359110	116359110	+	Silent	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:116359110C>T	ENST00000374140.2	+	26	3683	c.3474C>T	c.(3472-3474)ggC>ggT	p.G1158G	RGS3_ENST00000462403.1_Silent_p.G271G|RGS3_ENST00000350696.5_Silent_p.G1158G|RGS3_ENST00000343817.5_Silent_p.G877G|RGS3_ENST00000374134.3_Silent_p.G479G|RGS3_ENST00000342620.5_Silent_p.G128G|RGS3_ENST00000394646.3_Silent_p.G551G|RGS3_ENST00000462143.1_Silent_p.G479G	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	1158	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						TCACGCGGGGCTGCTTCGACC	0.602																																					p.G1158G		Atlas-SNP	.											.	RGS3	251	.	0			c.C3474T						.						142.0	111.0	121.0					9																	116359110		2203	4300	6503	SO:0001819	synonymous_variant	5998	exon26			GCGGGGCTGCTTC	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.3474C>T	chr9.hg19:g.116359110C>T		111.0	0.0		144.0	6.0	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Silent	SNP	ENST00000374140.2	hg19	CCDS43869.1																																																																																			.	.		0.602	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
COL27A1	85301	hgsc.bcm.edu	37	9	117052561	117052561	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:117052561A>T	ENST00000356083.3	+	47	4709	c.4318A>T	c.(4318-4320)Atc>Ttc	p.I1440F		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1440	Collagen-like 13.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						CCTCGAGGGCATCGCTGGACC	0.647																																					p.I1440F		Atlas-SNP	.											.	COL27A1	200	.	0			c.A4318T						.						29.0	23.0	25.0					9																	117052561		2191	4287	6478	SO:0001583	missense	85301	exon47			GAGGGCATCGCTG	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.4318A>T	chr9.hg19:g.117052561A>T	ENSP00000348385:p.Ile1440Phe	186.0	0.0		211.0	27.0	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	hg19	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	A	8.277	0.814710	0.16607	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.96136	-3.92	5.32	-5.66	0.02451	.	.	.	.	.	D	0.88581	0.6475	L	0.35414	1.06	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.76252	-0.3027	9	0.54805	T	0.06	.	2.8828	0.05653	0.5308:0.1868:0.1822:0.1003	.	1440	Q8IZC6	CORA1_HUMAN	F	1440	ENSP00000348385:I1440F	ENSP00000348385:I1440F	I	+	1	0	COL27A1	116092382	0.000000	0.05858	0.000000	0.03702	0.978000	0.69477	0.013000	0.13310	-0.840000	0.04206	0.402000	0.26972	ATC	.	.		0.647	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
CNTRL	11064	hgsc.bcm.edu	37	9	123857214	123857214	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:123857214A>G	ENST00000373855.1	+	5	657	c.397A>G	c.(397-399)Agc>Ggc	p.S133G	CNTRL_ENST00000238341.5_Missense_Mutation_p.S133G|CNTRL_ENST00000373865.2_Missense_Mutation_p.S133G			Q7Z7A1	CNTRL_HUMAN	centriolin	133					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						ACTGAATCTCAGCTATAATCT	0.284																																					p.S133G		Atlas-SNP	.											.	CNTRL	161	.	0			c.A397G						.						75.0	78.0	77.0					9																	123857214		2202	4298	6500	SO:0001583	missense	11064	exon3			AATCTCAGCTATA	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"""centrosomal protein 1"", ""centrosomal protein 110kDa"""	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.397A>G	chr9.hg19:g.123857214A>G	ENSP00000362962:p.Ser133Gly	80.0	0.0		86.0	4.0	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	hg19	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	A	18.99	3.740140	0.69304	.	.	ENSG00000119397	ENST00000373865;ENST00000373855;ENST00000238341;ENST00000454238	T;T	0.54675	0.56;0.56	5.57	5.57	0.84162	.	.	.	.	.	T	0.66781	0.2824	L	0.56280	1.765	0.41027	D	0.985122	D	0.69078	0.997	D	0.70716	0.97	T	0.66284	-0.5962	9	0.39692	T	0.17	.	14.9182	0.70815	1.0:0.0:0.0:0.0	.	133	Q7Z7A1	CNTRL_HUMAN	G	133	ENSP00000362962:S133G;ENSP00000238341:S133G	ENSP00000238341:S133G	S	+	1	0	CNTRL	122897035	1.000000	0.71417	1.000000	0.80357	0.720000	0.41350	7.343000	0.79319	2.123000	0.65237	0.533000	0.62120	AGC	.	.		0.284	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	
LHX2	9355	hgsc.bcm.edu	37	9	126774713	126774713	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:126774713T>C	ENST00000373615.4	+	1	825	c.86T>C	c.(85-87)aTc>aCc	p.I29T	RP11-85O21.4_ENST00000421041.1_RNA	NM_004789.3	NP_004780.3	P50458	LHX2_HUMAN	LIM homeobox 2	29					axon extension (GO:0048675)|axon guidance (GO:0007411)|cerebral cortex development (GO:0021987)|dorsal/ventral pattern formation (GO:0009953)|mesoderm development (GO:0007498)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|neural tube closure (GO:0001843)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|retina development in camera-type eye (GO:0060041)|telencephalon regionalization (GO:0021978)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)	10						GCTCCCGCCATCAGCTCCGCC	0.726																																					p.I29T		Atlas-SNP	.											.	LHX2	30	.	0			c.T86C						.						6.0	8.0	7.0					9																	126774713		2081	4114	6195	SO:0001583	missense	9355	exon1			CCGCCATCAGCTC	U11701	CCDS6853.1	9q33.3	2011-06-20			ENSG00000106689	ENSG00000106689		"""Homeoboxes / LIM class"""	6594	protein-coding gene	gene with protein product		603759				8649822, 10051612	Standard	NM_004789		Approved	LH-2, hLhx2	uc004boe.1	P50458	OTTHUMG00000020647	ENST00000373615.4:c.86T>C	chr9.hg19:g.126774713T>C	ENSP00000362717:p.Ile29Thr	41.0	0.0		45.0	4.0	NM_004789	O95860|Q52M57|Q8N1Z3	Missense_Mutation	SNP	ENST00000373615.4	hg19	CCDS6853.1	.	.	.	.	.	.	.	.	.	.	t	14.81	2.645110	0.47258	.	.	ENSG00000106689	ENST00000373615	D	0.83335	-1.71	5.07	3.93	0.45458	.	0.000000	0.85682	D	0.000000	T	0.69682	0.3138	L	0.27053	0.805	0.41898	D	0.990408	P;B	0.36789	0.57;0.421	B;B	0.32465	0.146;0.027	T	0.65417	-0.6173	10	0.33141	T	0.24	.	9.9851	0.41837	0.0:0.0806:0.0:0.9194	.	29;29	B3KNJ5;P50458	.;LHX2_HUMAN	T	29	ENSP00000362717:I29T	ENSP00000362717:I29T	I	+	2	0	LHX2	125814534	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.874000	0.69652	0.778000	0.33520	0.414000	0.27820	ATC	.	.		0.726	LHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054010.2		
GARNL3	84253	hgsc.bcm.edu	37	9	130087373	130087373	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:130087373A>G	ENST00000373387.4	+	7	945	c.593A>G	c.(592-594)gAg>gGg	p.E198G	GARNL3_ENST00000435213.2_Splice_Site_p.E176G|GARNL3_ENST00000314904.5_Splice_Site_p.E198G	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	198	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						GAAGAACAAGAGGTGAGTAAT	0.373																																					p.E198G		Atlas-SNP	.											.	GARNL3	83	.	0			c.A593G						.						119.0	105.0	110.0					9																	130087373		2203	4300	6503	SO:0001630	splice_region_variant	84253	exon7			AACAAGAGGTGAG	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 3"""			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.594+1A>G	chr9.hg19:g.130087373A>G		74.0	0.0		96.0	4.0	NM_032293	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Missense_Mutation	SNP	ENST00000373387.4	hg19	CCDS6869.2	.	.	.	.	.	.	.	.	.	.	A	20.2	3.955707	0.73902	.	.	ENSG00000136895	ENST00000439286;ENST00000373399;ENST00000435213;ENST00000314904;ENST00000373387	D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28	5.91	5.91	0.95273	Rap/ran-GAP (1);	0.192085	0.53938	D	0.000052	D	0.94689	0.8287	L	0.44542	1.39	0.58432	D	0.999992	D;D	0.76494	0.998;0.999	D;D	0.69654	0.965;0.931	D	0.94073	0.7337	9	.	.	.	.	15.1723	0.72884	1.0:0.0:0.0:0.0	.	198;176	Q5VVW2;B7Z3Q6	GARL3_HUMAN;.	G	221;221;176;198;198	ENSP00000400579:E221G;ENSP00000396205:E176G;ENSP00000313970:E198G;ENSP00000362485:E198G	.	E	+	2	0	GARNL3	129127194	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.078000	0.76821	2.254000	0.74563	0.533000	0.62120	GAG	.	.		0.373	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293	Missense_Mutation
SPTAN1	6709	hgsc.bcm.edu	37	9	131374459	131374459	+	Silent	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:131374459G>C	ENST00000372731.4	+	38	5072	c.4962G>C	c.(4960-4962)ctG>ctC	p.L1654L	SPTAN1_ENST00000372739.3_Silent_p.L1659L|SPTAN1_ENST00000358161.5_Silent_p.L1659L	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1654					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GCCAGAAACTGAAAGAAGCCA	0.522																																					p.L1659L	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.G4977C						.						125.0	124.0	125.0					9																	131374459		2203	4300	6503	SO:0001819	synonymous_variant	6709	exon39			GAAACTGAAAGAA	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.4962G>C	chr9.hg19:g.131374459G>C		123.0	0.0		196.0	85.0	NM_001130438	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	hg19	CCDS6905.1																																																																																			.	.		0.522	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
NUP214	8021	hgsc.bcm.edu	37	9	134073130	134073130	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:134073130A>G	ENST00000359428.5	+	29	4393	c.4249A>G	c.(4249-4251)Acc>Gcc	p.T1417A	NUP214_ENST00000483497.2_Missense_Mutation_p.T243A|NUP214_ENST00000451030.1_Missense_Mutation_p.T1418A|NUP214_ENST00000465486.2_3'UTR|NUP214_ENST00000411637.2_Missense_Mutation_p.T1407A			P35658	NU214_HUMAN	nucleoporin 214kDa	1417	11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				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)		TCTGCCAGTCACCAGTGCAGG	0.537			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																p.T1417A	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.A4249G						.						84.0	82.0	83.0					9																	134073130		2203	4300	6503	SO:0001583	missense	8021	exon29			CCAGTCACCAGTG	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.4249A>G	chr9.hg19:g.134073130A>G	ENSP00000352400:p.Thr1417Ala	87.0	0.0		89.0	4.0	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	A	14.12	2.441630	0.43326	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605;ENST00000483497;ENST00000531600;ENST00000541688	T;T;T;T;T	0.56103	1.32;1.33;1.41;0.82;0.48	5.58	-6.7	0.01766	.	0.329934	0.21905	N	0.067390	T	0.18467	0.0443	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.23377	0.084;0.021;0.084;0.001;0.0	B;B;B;B;B	0.18561	0.022;0.022;0.022;0.004;0.003	T	0.06552	-1.0820	10	0.31617	T	0.26	-1.6062	0.5819	0.00713	0.2944:0.2331:0.267:0.2056	.	243;846;1011;1407;1417	B7ZAV2;F5H131;Q5JUP9;P35658-4;P35658	.;.;.;.;NU214_HUMAN	A	1417;1407;1418;1396;1011;846;243;194;194	ENSP00000352400:T1417A;ENSP00000396576:T1407A;ENSP00000405014:T1418A;ENSP00000436793:T243A;ENSP00000435364:T194A	ENSP00000352400:T1417A	T	+	1	0	NUP214	133062951	0.000000	0.05858	0.000000	0.03702	0.550000	0.35303	-0.408000	0.07169	-1.319000	0.02286	0.402000	0.26972	ACC	.	.		0.537	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
RAPGEF1	2889	hgsc.bcm.edu	37	9	134514137	134514137	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:134514137A>G	ENST00000372189.3	-	5	608	c.485T>C	c.(484-486)cTc>cCc	p.L162P	RAPGEF1_ENST00000372190.3_Missense_Mutation_p.L180P|RAPGEF1_ENST00000372195.1_Missense_Mutation_p.L179P|RAPGEF1_ENST00000481260.1_5'UTR	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	162					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		GAGGTTGGCGAGGCTTTGGTA	0.498																																					p.L180P		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.T539C						.						75.0	75.0	75.0					9																	134514137		2047	4202	6249	SO:0001583	missense	2889	exon5			TTGGCGAGGCTTT	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"""guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"""	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.485T>C	chr9.hg19:g.134514137A>G	ENSP00000361263:p.Leu162Pro	142.0	0.0		199.0	8.0	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	hg19	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.662359	0.88251	.	.	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000357686;ENST00000438647;ENST00000427994	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.64483	0.2602	M	0.72894	2.215	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	0.68055	-0.5510	10	0.87932	D	0	.	15.263	0.73640	1.0:0.0:0.0:0.0	.	179;162;180	Q68DL3;Q13905;Q13905-3	.;RPGF1_HUMAN;.	P	162;179;56;162;180;142;88;179;141;180	ENSP00000361269:L179P;ENSP00000361263:L162P;ENSP00000361264:L180P;ENSP00000410640:L141P;ENSP00000402174:L180P	ENSP00000266110:L162P	L	-	2	0	RAPGEF1	133503958	1.000000	0.71417	0.977000	0.42913	0.986000	0.74619	8.661000	0.91125	2.206000	0.71126	0.455000	0.32223	CTC	.	.		0.498	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312	
COL5A1	1289	hgsc.bcm.edu	37	9	137726974	137726974	+	Missense_Mutation	SNP	G	G	A	rs150608071		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:137726974G>A	ENST00000371817.3	+	65	5708	c.5294G>A	c.(5293-5295)cGc>cAc	p.R1765H		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1765	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				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)		AAGGCCCTCCGCTTCCTGGGC	0.657													G|||	1	0.000199681	0.0	0.0	5008	,	,		16790	0.0		0.001	False		,,,				2504	0.0				p.R1765H		Atlas-SNP	.											.	COL5A1	323	.	0			c.G5294A						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	89.0	70.0	76.0		5294	5.0	1.0	9	dbSNP_134	76	0,8600		0,0,4300	no	missense	COL5A1	NM_000093.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1765/1839	137726974	1,13005	2203	4300	6503	SO:0001583	missense	1289	exon65			CCCTCCGCTTCCT	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.5294G>A	chr9.hg19:g.137726974G>A	ENSP00000360882:p.Arg1765His	122.0	0.0		129.0	53.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.612809	0.87258	2.27E-4	0.0	ENSG00000130635	ENST00000371817;ENST00000355306	T	0.74632	-0.86	5.03	5.03	0.67393	Fibrillar collagen, C-terminal (4);	0.000000	0.64402	U	0.000002	T	0.82263	0.4999	L	0.41961	1.31	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82165	-0.0592	10	0.44086	T	0.13	.	18.3643	0.90385	0.0:0.0:1.0:0.0	.	1765	P20908	CO5A1_HUMAN	H	1765;302	ENSP00000360882:R1765H	ENSP00000347458:R302H	R	+	2	0	COL5A1	136866795	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.659000	0.98597	2.340000	0.79590	0.561000	0.74099	CGC	.	G|1.000;A|0.000		0.657	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
SOHLH1	402381	hgsc.bcm.edu	37	9	138586277	138586277	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:138586277T>C	ENST00000298466.5	-	7	962	c.902A>G	c.(901-903)gAt>gGt	p.D301G	SOHLH1_ENST00000425225.1_Missense_Mutation_p.D301G	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1	301					oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(5)|prostate(1)	12		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)		GGACGTCCCATCGTCCACATC	0.627																																					p.D301G		Atlas-SNP	.											.	SOHLH1	70	.	0			c.A902G						.						80.0	67.0	71.0					9																	138586277		2202	4300	6502	SO:0001583	missense	402381	exon7			GTCCCATCGTCCA	BC031861	CCDS35174.1, CCDS48054.1	9q34.3	2013-05-21	2006-03-16	2006-03-16	ENSG00000165643	ENSG00000165643		"""Basic helix-loop-helix proteins"""	27845	protein-coding gene	gene with protein product	"""spermatogenesis associated 27"""	610224	"""chromosome 9 open reading frame 157"""	C9orf157		12477932	Standard	NM_001012415		Approved	NOHLH, TEB2, bA100C15.3, bHLHe80, SPATA27	uc010nbe.3	Q5JUK2	OTTHUMG00000020915	ENST00000298466.5:c.902A>G	chr9.hg19:g.138586277T>C	ENSP00000298466:p.Asp301Gly	40.0	0.0		68.0	4.0	NM_001012415	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Missense_Mutation	SNP	ENST00000298466.5	hg19	CCDS35174.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.007886	0.54361	.	.	ENSG00000165643	ENST00000298466;ENST00000425225	T;T	0.39229	1.25;1.09	4.08	2.93	0.34026	.	0.244290	0.21097	N	0.080233	T	0.33585	0.0868	L	0.52573	1.65	0.19775	N	0.999957	B;B	0.27013	0.166;0.104	B;B	0.24974	0.057;0.026	T	0.32981	-0.9886	10	0.87932	D	0	-12.8959	6.1542	0.20328	0.0:0.1175:0.0:0.8825	.	301;301	Q5JUK2-2;Q5JUK2	.;SOLH1_HUMAN	G	301	ENSP00000298466:D301G;ENSP00000404438:D301G	ENSP00000298466:D301G	D	-	2	0	SOHLH1	137726098	0.005000	0.15991	0.021000	0.16686	0.011000	0.07611	0.507000	0.22675	0.739000	0.32628	0.444000	0.29173	GAT	.	.		0.627	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415	
ITIH2	3698	hgsc.bcm.edu	37	10	7751097	7751097	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:7751097A>G	ENST00000358415.4	+	4	471	c.305A>G	c.(304-306)cAg>cGg	p.Q102R	ITIH2_ENST00000480387.1_Intron|ITIH2_ENST00000379587.4_Missense_Mutation_p.Q91R	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	102	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)|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)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						CCGCAGCCTCAGAATGTCGTG	0.443																																					p.Q102R		Atlas-SNP	.											.	ITIH2	144	.	0			c.A305G						.						137.0	129.0	131.0					10																	7751097		2203	4300	6503	SO:0001583	missense	3698	exon4			AGCCTCAGAATGT	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.305A>G	chr10.hg19:g.7751097A>G	ENSP00000351190:p.Gln102Arg	117.0	0.0		153.0	7.0	NM_002216	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	hg19	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	A	15.21	2.766878	0.49574	.	.	ENSG00000151655	ENST00000358415;ENST00000429820;ENST00000379587	T;T;T	0.23754	1.89;1.89;1.89	5.79	4.65	0.58169	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.054507	0.85682	N	0.000000	T	0.26304	0.0642	L	0.50993	1.605	0.58432	D	0.999998	B	0.20988	0.05	B	0.31686	0.134	T	0.03761	-1.1006	10	0.22706	T	0.39	-13.5033	11.7175	0.51661	0.931:0.0:0.069:0.0	.	102	P19823	ITIH2_HUMAN	R	102;77;91	ENSP00000351190:Q102R;ENSP00000388826:Q77R;ENSP00000368906:Q91R	ENSP00000351190:Q102R	Q	+	2	0	ITIH2	7791103	1.000000	0.71417	0.852000	0.33557	0.799000	0.45148	7.163000	0.77524	1.021000	0.39600	0.477000	0.44152	CAG	.	.		0.443	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
USP6NL	9712	hgsc.bcm.edu	37	10	11505825	11505825	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:11505825T>C	ENST00000609104.1	-	15	1496	c.1102A>G	c.(1102-1104)Aag>Gag	p.K368E	USP6NL_ENST00000277575.5_Missense_Mutation_p.K385E|USP6NL_ENST00000379237.2_Missense_Mutation_p.K391E	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	368					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						CCCAAGGGCTTCTTTGGATAT	0.507																																					p.K385E		Atlas-SNP	.											.	USP6NL	57	.	0			c.A1153G						.						20.0	24.0	23.0					10																	11505825		1883	4089	5972	SO:0001583	missense	9712	exon14			AGGGCTTCTTTGG	BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"""related to the N terminus of tre"""	605405	"""USP6NL intronic transcript 1 (non-protein coding)"""	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.1102A>G	chr10.hg19:g.11505825T>C	ENSP00000476462:p.Lys368Glu	64.0	0.0		82.0	4.0	NM_001080491	A8KA79|Q15400|Q5VV10|Q7L0K9	Missense_Mutation	SNP	ENST00000609104.1	hg19	CCDS53492.1	.	.	.	.	.	.	.	.	.	.	T	18.13	3.554638	0.65425	.	.	ENSG00000148429	ENST00000535316;ENST00000277575;ENST00000379237	T;T	0.05081	3.5;3.51	5.53	5.53	0.82687	.	0.146826	0.64402	D	0.000012	T	0.23806	0.0576	M	0.75447	2.3	0.58432	D	0.999999	D;D	0.61697	0.983;0.99	P;D	0.66084	0.874;0.941	T	0.00478	-1.1715	10	0.45353	T	0.12	.	15.6709	0.77274	0.0:0.0:0.0:1.0	.	368;385	Q92738;Q92738-2	US6NL_HUMAN;.	E	368;385;368	ENSP00000277575:K385E;ENSP00000368539:K368E	ENSP00000277575:K385E	K	-	1	0	USP6NL	11545831	1.000000	0.71417	1.000000	0.80357	0.042000	0.13812	5.754000	0.68743	2.099000	0.63709	0.482000	0.46254	AAG	.	.		0.507	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688	
CUBN	8029	hgsc.bcm.edu	37	10	17113457	17113457	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:17113457T>C	ENST00000377833.4	-	19	2658	c.2593A>G	c.(2593-2595)Agt>Ggt	p.S865G		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	865	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGGGCAGAACTTCCAATTTCA	0.383																																					p.S865G		Atlas-SNP	.											.	CUBN	515	.	0			c.A2593G						.						85.0	83.0	84.0					10																	17113457		2203	4300	6503	SO:0001583	missense	8029	exon19			CAGAACTTCCAAT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.2593A>G	chr10.hg19:g.17113457T>C	ENSP00000367064:p.Ser865Gly	77.0	0.0		122.0	5.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	8.706	0.910891	0.17833	.	.	ENSG00000107611	ENST00000377833	T	0.18338	2.22	5.47	-1.12	0.09808	CUB (5);	0.458452	0.18463	N	0.140464	T	0.04724	0.0128	N	0.04245	-0.25	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.40308	-0.9570	10	0.02654	T	1	.	5.2611	0.15573	0.0:0.2753:0.262:0.4627	.	865	O60494	CUBN_HUMAN	G	865	ENSP00000367064:S865G	ENSP00000367064:S865G	S	-	1	0	CUBN	17153463	0.000000	0.05858	0.211000	0.23655	0.894000	0.52154	0.479000	0.22228	-0.189000	0.10482	0.411000	0.27672	AGT	.	.		0.383	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
NEBL	10529	hgsc.bcm.edu	37	10	21134239	21134239	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:21134239T>C	ENST00000377122.4	-	12	1571	c.1175A>G	c.(1174-1176)gAc>gGc	p.D392G	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	392					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TGGAGTCTTGTCTAAATCCAG	0.308																																					p.D392G		Atlas-SNP	.											.	NEBL	199	.	0			c.A1175G						.						132.0	131.0	131.0					10																	21134239		2203	4300	6503	SO:0001583	missense	10529	exon12			GTCTTGTCTAAAT	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.1175A>G	chr10.hg19:g.21134239T>C	ENSP00000366326:p.Asp392Gly	47.0	0.0		80.0	5.0	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000377122.4	hg19	CCDS7134.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.651277	0.88056	.	.	ENSG00000078114	ENST00000377122	T	0.06218	3.33	5.99	5.99	0.97316	.	0.050585	0.85682	D	0.000000	T	0.18800	0.0451	L	0.57536	1.79	0.80722	D	1	D	0.62365	0.991	D	0.63703	0.917	T	0.00785	-1.1567	10	0.32370	T	0.25	.	14.0175	0.64533	0.0:0.0:0.0:1.0	.	392	O76041	NEBL_HUMAN	G	392	ENSP00000366326:D392G	ENSP00000366326:D392G	D	-	2	0	NEBL	21174245	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.303000	0.65738	2.291000	0.77112	0.533000	0.62120	GAC	.	.		0.308	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393	
BMI1	648	hgsc.bcm.edu	37	10	22618212	22618212	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:22618212A>G	ENST00000376663.3	+	10	1227	c.722A>G	c.(721-723)gAt>gGt	p.D241G	COMMD3-BMI1_ENST00000602390.1_Missense_Mutation_p.D384G	NM_005180.8	NP_005171.4	P35226	BMI1_HUMAN	BMI1 proto-oncogene, polycomb ring finger	241					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|regulation of gene expression (GO:0010468)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|ubiquitin ligase complex (GO:0000151)	RING-like zinc finger domain binding (GO:0071535)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|urinary_tract(1)	12						CACCAGAGAGATGGACTGACA	0.438																																					p.D384G		Atlas-SNP	.											.	.	.	.	0			c.A1151G						.						64.0	61.0	62.0					10																	22618212		2203	4300	6503	SO:0001583	missense	0	exon14			AGAGAGATGGACT	BC011652	CCDS7138.1	10p13	2014-06-26	2014-06-26	2006-04-26	ENSG00000168283	ENSG00000168283		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	1066	protein-coding gene	gene with protein product		164831	"""polycomb group ring finger 4"", ""B lymphoma Mo-MLV insertion region 1 homolog (mouse)"""	PCGF4		8268912	Standard	NM_005180		Approved	RNF51		P35226	OTTHUMG00000017807	ENST00000376663.3:c.722A>G	chr10.hg19:g.22618212A>G	ENSP00000365851:p.Asp241Gly	61.0	0.0		66.0	4.0	NM_001204062	Q16030|Q5T8Z3|Q96F37	Missense_Mutation	SNP	ENST00000376663.3	hg19	CCDS7138.1	.	.	.	.	.	.	.	.	.	.	A	13.30	2.195977	0.38806	.	.	ENSG00000168283	ENST00000376691;ENST00000376663;ENST00000443519	T;T	0.47869	1.44;0.83	5.68	5.68	0.88126	.	0.211158	0.52532	D	0.000079	T	0.24160	0.0585	N	0.02011	-0.69	0.52099	D	0.999949	B;B	0.22080	0.003;0.064	B;B	0.20767	0.004;0.031	T	0.12372	-1.0550	10	0.30854	T	0.27	-16.8412	14.7675	0.69651	1.0:0.0:0.0:0.0	.	241;241	Q5U0M5;P35226	.;BMI1_HUMAN	G	153;241;146	ENSP00000365851:D241G;ENSP00000390768:D146G	ENSP00000365851:D241G	D	+	2	0	BMI1	22658218	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.908000	0.75730	2.169000	0.68431	0.528000	0.53228	GAT	.	.		0.438	BMI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047176.1	NM_005180	
YME1L1	10730	hgsc.bcm.edu	37	10	27408356	27408356	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:27408356A>G	ENST00000326799.3	-	15	1753	c.1605T>C	c.(1603-1605)gcT>gcC	p.A535A	YME1L1_ENST00000376016.3_Silent_p.A478A|YME1L1_ENST00000375972.3_Silent_p.A445A	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	535					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						CAGTACCTCGAGCTATAATTT	0.403																																					p.A535A		Atlas-SNP	.											.	YME1L1	71	.	0			c.T1605C						.						73.0	72.0	72.0					10																	27408356		2203	4300	6503	SO:0001819	synonymous_variant	10730	exon15			ACCTCGAGCTATA	AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"""ATPases / AAA-type"""	12843	protein-coding gene	gene with protein product		607472	"""YME1 (S.cerevisiae)-like 1"", ""YME1-like 1 (S. cerevisiae)"""			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.1605T>C	chr10.hg19:g.27408356A>G		43.0	0.0		65.0	4.0	NM_139312	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Silent	SNP	ENST00000326799.3	hg19	CCDS7152.1																																																																																			.	.		0.403	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1	NM_139312	
TSPAN15	23555	hgsc.bcm.edu	37	10	71211441	71211441	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:71211441T>C	ENST00000373290.2	+	1	213	c.91T>C	c.(91-93)Ttc>Ctc	p.F31L		NM_012339.3	NP_036471.1	O95858	TSN15_HUMAN	tetraspanin 15	31					establishment of protein localization to plasma membrane (GO:0090002)|protein maturation (GO:0051604)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)	9						TTCCACCGTGTTCTGGGTGAG	0.657																																					p.F31L		Atlas-SNP	.											.	TSPAN15	22	.	0			c.T91C						.						32.0	30.0	31.0					10																	71211441		2193	4280	6473	SO:0001583	missense	23555	exon1			ACCGTGTTCTGGG	AY358934	CCDS7294.1	10q22.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000099282	ENSG00000099282		"""Tetraspanins"""	23298	protein-coding gene	gene with protein product		613140	"""transmembrane 4 superfamily member 15"""	TM4SF15		11739647, 10719184	Standard	NM_012339		Approved	NET-7	uc001jpo.1	O95858	OTTHUMG00000018381	ENST00000373290.2:c.91T>C	chr10.hg19:g.71211441T>C	ENSP00000362387:p.Phe31Leu	64.0	0.0		90.0	4.0	NM_012339	Q6UW79	Missense_Mutation	SNP	ENST00000373290.2	hg19	CCDS7294.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.187200	0.78789	.	.	ENSG00000099282	ENST00000373290	T	0.80909	-1.43	5.65	5.65	0.86999	.	0.235800	0.44688	D	0.000436	D	0.83672	0.5305	M	0.68728	2.09	0.80722	D	1	P	0.44659	0.84	P	0.48952	0.596	D	0.85404	0.1133	10	0.66056	D	0.02	-46.3035	13.6952	0.62575	0.0:0.0:0.0:1.0	.	31	O95858	TSN15_HUMAN	L	31	ENSP00000362387:F31L	ENSP00000362387:F31L	F	+	1	0	TSPAN15	70881447	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	4.201000	0.58439	2.284000	0.76573	0.533000	0.62120	TTC	.	.		0.657	TSPAN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048444.1	NM_012339	
PTEN	5728	hgsc.bcm.edu	37	10	89717725	89717725	+	Nonsense_Mutation	SNP	T	T	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:89717725T>A	ENST00000371953.3	+	7	2107	c.750T>A	c.(748-750)tgT>tgA	p.C250*	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	250	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.C250fs*2(5)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)|p.C250*(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TACCTGTGTGTGGTGATATCA	0.403		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.C250X		Atlas-SNP	.	yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	PTEN,NS,carcinoma,0,5	PTEN	3652	.	54	Whole gene deletion(37)|Deletion - Frameshift(14)|Substitution - Nonsense(1)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|endometrium(3)|breast(3)|ovary(3)|vulva(2)|urinary_tract(2)|large_intestine(1)|soft_tissue(1)	c.T750A						.						126.0	110.0	116.0					10																	89717725		2203	4300	6503	SO:0001587	stop_gained	5728	exon7	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	TGTGTGTGGTGAT	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.750T>A	chr10.hg19:g.89717725T>A	ENSP00000361021:p.Cys250*	124.0	0.0		74.0	50.0	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Nonsense_Mutation	SNP	ENST00000371953.3	hg19	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	48	14.739521	0.99808	.	.	ENSG00000171862	ENST00000371953	.	.	.	5.15	4.02	0.46733	.	0.127565	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.1324	7.3482	0.26676	0.0:0.2568:0.0:0.7432	.	.	.	.	X	250	.	.	C	+	3	2	PTEN	89707705	0.990000	0.36364	1.000000	0.80357	0.991000	0.79684	0.211000	0.17474	0.801000	0.34066	0.477000	0.44152	TGT	.	.		0.403	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
CPEB3	22849	hgsc.bcm.edu	37	10	93904731	93904731	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:93904731A>G	ENST00000265997.4	-	5	1506	c.1334T>C	c.(1333-1335)gTt>gCt	p.V445A	CPEB3_ENST00000412050.4_Missense_Mutation_p.V431A	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	445	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|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)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				AAGTCCTCCAACAAACACCTT	0.438																																					p.V445A		Atlas-SNP	.											.	CPEB3	43	.	0			c.T1334C						.						147.0	131.0	136.0					10																	93904731		2203	4300	6503	SO:0001583	missense	22849	exon5			CCTCCAACAAACA	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"""RNA binding motif (RRM) containing"""	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.1334T>C	chr10.hg19:g.93904731A>G	ENSP00000265997:p.Val445Ala	70.0	0.0		72.0	4.0	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Missense_Mutation	SNP	ENST00000265997.4	hg19	CCDS31246.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.956130	0.92726	.	.	ENSG00000107864	ENST00000394210;ENST00000412050;ENST00000265997	T;T	0.36157	1.27;1.27	5.8	5.8	0.92144	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.056550	0.64402	D	0.000001	T	0.70245	0.3202	M	0.93763	3.455	0.80722	D	1	P;D;D	0.61697	0.524;0.979;0.99	P;D;D	0.81914	0.799;0.995;0.994	T	0.79097	-0.1943	10	0.87932	D	0	-8.262	16.1639	0.81739	1.0:0.0:0.0:0.0	.	445;431;431	Q8NE35;Q5QP71;Q8NE35-2	CPEB3_HUMAN;.;.	A	431;431;445	ENSP00000398310:V431A;ENSP00000265997:V445A	ENSP00000265997:V445A	V	-	2	0	CPEB3	93894711	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.211000	0.95120	2.219000	0.72066	0.533000	0.62120	GTT	.	.		0.438	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912	
EXOC6	54536	hgsc.bcm.edu	37	10	94688164	94688164	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:94688164A>G	ENST00000260762.6	+	9	971	c.957A>G	c.(955-957)caA>caG	p.Q319Q	EXOC6_ENST00000443748.2_Silent_p.Q296Q|EXOC6_ENST00000371552.4_Silent_p.Q314Q|EXOC6_ENST00000371547.4_Silent_p.Q335Q	NM_019053.4	NP_061926.3	Q8TAG9	EXOC6_HUMAN	exocyst complex component 6	319					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	26		Colorectal(252;0.123)				TGGTATTGCAACCCCAGTCGA	0.333																																					p.Q319Q		Atlas-SNP	.											.	EXOC6	147	.	0			c.A957G						.						106.0	110.0	109.0					10																	94688164		2203	4300	6503	SO:0001819	synonymous_variant	54536	exon9			ATTGCAACCCCAG	BC028395	CCDS7424.2, CCDS31247.1	10q23.33	2013-01-22	2006-11-07	2006-11-07	ENSG00000138190	ENSG00000138190			23196	protein-coding gene	gene with protein product		609672	"""SEC15-like 1 (S. cerevisiae)"""	SEC15L1		8889548	Standard	NM_001013848		Approved	SEC15L, FLJ1125, DKFZp761I2124, MGC33397, Sec15p, EXOC6A	uc001kig.3	Q8TAG9	OTTHUMG00000018767	ENST00000260762.6:c.957A>G	chr10.hg19:g.94688164A>G		81.0	0.0		60.0	4.0	NM_019053	E9PHI3|Q5VXH8|Q9NZ24	Silent	SNP	ENST00000260762.6	hg19	CCDS7424.2																																																																																			.	.		0.333	EXOC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049410.2	NM_019053	
TLL2	7093	hgsc.bcm.edu	37	10	98170214	98170214	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:98170214G>T	ENST00000357947.3	-	9	1291	c.1066C>A	c.(1066-1068)Cag>Aag	p.Q356K	TLL2_ENST00000469598.1_5'UTR	NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	356	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		GTTGTGTCCTGCAGGGTCTCC	0.577																																					p.Q356K		Atlas-SNP	.											.	TLL2	122	.	0			c.C1066A						.						86.0	74.0	78.0					10																	98170214		2203	4300	6503	SO:0001583	missense	7093	exon9			TGTCCTGCAGGGT	AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.1066C>A	chr10.hg19:g.98170214G>T	ENSP00000350630:p.Gln356Lys	102.0	0.0		59.0	40.0	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	hg19	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	G	32	5.133537	0.94517	.	.	ENSG00000095587	ENST00000357947	T	0.34472	1.36	5.64	5.64	0.86602	CUB (5);	0.000000	0.43416	D	0.000567	T	0.55641	0.1933	L	0.53729	1.69	0.80722	D	1	D	0.60160	0.987	D	0.70016	0.967	T	0.38845	-0.9642	10	0.27785	T	0.31	.	19.0544	0.93058	0.0:0.0:1.0:0.0	.	356	Q9Y6L7	TLL2_HUMAN	K	356	ENSP00000350630:Q356K	ENSP00000350630:Q356K	Q	-	1	0	TLL2	98160204	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.736000	0.98828	2.826000	0.97356	0.561000	0.74099	CAG	.	.		0.577	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1		
MORN4	118812	hgsc.bcm.edu	37	10	99376156	99376156	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:99376156A>G	ENST00000307450.6	-	5	468	c.305T>C	c.(304-306)tTc>tCc	p.F102S	PI4K2A_ENST00000370649.3_Intron|MORN4_ENST00000335628.3_Missense_Mutation_p.F160S|PI4K2A_ENST00000555577.1_Intron|MORN4_ENST00000478953.1_Silent_p.F65F	NM_001098831.1|NM_178832.3	NP_001092301.1|NP_849154.1	Q8NDC4	MORN4_HUMAN	MORN repeat containing 4	102										large_intestine(1)|lung(1)|stomach(2)	4						ACCATCAGGGAAAGTCAGCAG	0.493																																					p.F102S		Atlas-SNP	.											.	MORN4	24	.	0			c.T305C						.						44.0	43.0	44.0					10																	99376156		2203	4300	6503	SO:0001583	missense	118812	exon5			TCAGGGAAAGTCA	AJ431726	CCDS7468.1	10q24.2	2008-06-23	2008-06-23	2008-06-23	ENSG00000171160	ENSG00000171160			24001	protein-coding gene	gene with protein product	"""44050 protein"""		"""chromosome 10 open reading frame 83"""	C10orf83		12477932	Standard	NM_178832		Approved	bA548K23.4, FLJ25925	uc001koe.3	Q8NDC4	OTTHUMG00000018861	ENST00000307450.6:c.305T>C	chr10.hg19:g.99376156A>G	ENSP00000307636:p.Phe102Ser	79.0	0.0		53.0	4.0	NM_001098831	Q86Y54	Missense_Mutation	SNP	ENST00000307450.6	hg19	CCDS7468.1	.	.	.	.	.	.	.	.	.	.	A	19.99	3.928027	0.73327	.	.	ENSG00000171160	ENST00000307450;ENST00000515674;ENST00000335628	T;T	0.58652	0.32;0.32	5.03	5.03	0.67393	.	0.099330	0.64402	D	0.000001	T	0.70343	0.3213	M	0.65320	2	0.80722	D	1	D;D	0.89917	1.0;0.96	D;P	0.74674	0.984;0.657	T	0.73036	-0.4109	10	0.72032	D	0.01	-6.224	10.2083	0.43126	0.8519:0.0:0.0:0.1481	.	160;102	Q8NDC4-2;Q8NDC4	.;MORN4_HUMAN	S	102;102;160	ENSP00000307636:F102S;ENSP00000335498:F160S	ENSP00000307636:F102S	F	-	2	0	MORN4	99366146	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.106000	0.77039	2.119000	0.64992	0.459000	0.35465	TTC	.	.		0.493	MORN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049730.1	NM_178832	
GOLGA7B	401647	hgsc.bcm.edu	37	10	99619216	99619216	+	Splice_Site	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:99619216T>C	ENST00000370602.1	+	2	79	c.14T>C	c.(13-15)gTc>gCc	p.V5A		NM_001010917.2	NP_001010917.1	Q2TAP0	GOG7B_HUMAN	golgin A7 family, member B	5						Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(1)|large_intestine(3)|prostate(1)	5						TCTCCTCAGGTCCACAATCTG	0.557																																					p.V5A		Atlas-SNP	.											.	GOLGA7B	11	.	0			c.T14C						.						59.0	51.0	54.0					10																	99619216		2203	4300	6503	SO:0001630	splice_region_variant	401647	exon2			CTCAGGTCCACAA	BC008047	CCDS31265.1	10q24.2	2011-10-25	2010-02-12	2008-10-03	ENSG00000155265	ENSG00000155265			31668	protein-coding gene	gene with protein product		614189	"""chromosome 10 open reading frame 133"", ""chromosome 10 open reading frame 132"", ""golgi autoantigen, golgin subfamily a, 7B"""	C10orf133, C10orf132			Standard	NM_001010917		Approved	bA459F3.4, bA451M19.3	uc001kos.3	Q2TAP0	OTTHUMG00000018869	ENST00000370602.1:c.13-1T>C	chr10.hg19:g.99619216T>C		77.0	0.0		69.0	4.0	NM_001010917	Q5T4F5	Missense_Mutation	SNP	ENST00000370602.1	hg19	CCDS31265.1	.	.	.	.	.	.	.	.	.	.	T	12.37	1.918922	0.33908	.	.	ENSG00000155265	ENST00000370602	.	.	.	4.71	3.56	0.40772	.	0.068494	0.64402	D	0.000014	T	0.30386	0.0763	N	0.08118	0	0.37472	D	0.91565	B	0.18461	0.028	B	0.09377	0.004	T	0.20773	-1.0265	9	0.30854	T	0.27	-47.6928	12.2438	0.54558	0.0:0.0:0.1511:0.8489	.	5	Q2TAP0	GOG7B_HUMAN	A	5	.	ENSP00000359634:V5A	V	+	2	0	GOLGA7B	99609206	0.998000	0.40836	1.000000	0.80357	0.910000	0.53928	2.951000	0.49089	1.994000	0.58287	0.454000	0.30748	GTC	.	.		0.557	GOLGA7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049752.1	NM_001010917	Missense_Mutation
GBF1	8729	hgsc.bcm.edu	37	10	104128552	104128552	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:104128552T>C	ENST00000369983.3	+	23	3193	c.2933T>C	c.(2932-2934)aTc>aCc	p.I978T		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	978					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		GACAATCTCATCATCTCTCTA	0.512																																					p.I979T		Atlas-SNP	.											.	GBF1	142	.	0			c.T2936C						.						162.0	144.0	150.0					10																	104128552		2203	4300	6503	SO:0001583	missense	8729	exon23			ATCTCATCATCTC	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"""golgi-specific brefeldin A resistance factor 1"""			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.2933T>C	chr10.hg19:g.104128552T>C	ENSP00000359000:p.Ile978Thr	153.0	0.0		80.0	4.0	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.429649	0.83776	.	.	ENSG00000107862	ENST00000369983	T	0.70045	-0.45	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	D	0.83686	0.5308	M	0.84433	2.695	0.80722	D	1	P;D;D	0.69078	0.911;0.997;0.993	P;P;D	0.72338	0.505;0.88;0.977	D	0.86256	0.1652	10	0.87932	D	0	-17.7878	16.5763	0.84648	0.0:0.0:0.0:1.0	.	978;978;978	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	T	978	ENSP00000359000:I978T	ENSP00000359000:I978T	I	+	2	0	GBF1	104118542	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.317000	0.78254	0.459000	0.35465	ATC	.	.		0.512	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1		
NT5C2	22978	hgsc.bcm.edu	37	10	104849568	104849568	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:104849568T>C	ENST00000404739.3	-	17	1570	c.1547A>G	c.(1546-1548)gAc>gGc	p.D516G	NT5C2_ENST00000369857.4_5'UTR|CNNM2_ENST00000369878.4_3'UTR|NT5C2_ENST00000343289.5_Missense_Mutation_p.D516G|NT5C2_ENST00000423468.2_Missense_Mutation_p.D487G			P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II	516					cell death (GO:0008219)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|nucleobase-containing small molecule metabolic process (GO:0055086)|phosphorylation (GO:0016310)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleoside phosphotransferase activity (GO:0050146)|nucleotide binding (GO:0000166)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|urinary_tract(1)	16		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)	GTAGTCAGTGTCTTTGAAATC	0.507																																					p.D516G		Atlas-SNP	.											.	NT5C2	41	.	0			c.A1547G						.						149.0	124.0	132.0					10																	104849568		2203	4300	6503	SO:0001583	missense	22978	exon19			TCAGTGTCTTTGA	D38524	CCDS7544.1	10q24.32	2014-03-03	2002-04-18	2002-04-19	ENSG00000076685	ENSG00000076685			8022	protein-coding gene	gene with protein product	"""purine 5' nucleotidase"""	600417	"""5'-nucleotidase (purine), cytosolic type B"""	NT5B		7999131, 24482476	Standard	NM_012229		Approved	PNT5, GMP, cN-II, SPG65	uc001kwq.3	P49902	OTTHUMG00000018981	ENST00000404739.3:c.1547A>G	chr10.hg19:g.104849568T>C	ENSP00000383960:p.Asp516Gly	185.0	0.0		134.0	6.0	NM_012229	B7Z382|D3DR91|Q5JUV5	Missense_Mutation	SNP	ENST00000404739.3	hg19	CCDS7544.1	.	.	.	.	.	.	.	.	.	.	T	14.49	2.551289	0.45383	.	.	ENSG00000076685	ENST00000343289;ENST00000404739;ENST00000423468	T;T;T	0.25085	2.14;2.14;1.82	5.96	5.96	0.96718	.	0.092833	0.64402	D	0.000001	T	0.16428	0.0395	N	0.14661	0.345	0.58432	D	0.999999	B;B;B	0.30482	0.099;0.281;0.18	B;B;B	0.27170	0.016;0.077;0.047	T	0.11299	-1.0593	10	0.19147	T	0.46	-20.79	16.4484	0.83959	0.0:0.0:0.0:1.0	.	487;363;516	B7Z382;B3KXN5;P49902	.;.;5NTC_HUMAN	G	516;516;487	ENSP00000339479:D516G;ENSP00000383960:D516G;ENSP00000392236:D487G	ENSP00000339479:D516G	D	-	2	0	NT5C2	104839558	1.000000	0.71417	0.982000	0.44146	0.501000	0.33797	4.972000	0.63756	2.285000	0.76669	0.533000	0.62120	GAC	.	.		0.507	NT5C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050121.1	NM_012229	
CFAP43	80217	hgsc.bcm.edu	37	10	105921776	105921776	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:105921776A>G	ENST00000357060.3	-	26	3472	c.3357T>C	c.(3355-3357)gcT>gcC	p.A1119A	WDR96_ENST00000428666.1_Silent_p.A1120A	NM_025145.5	NP_079421.5														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						TGTCCATCAGAGCTCGGAGTC	0.483																																					p.A1119A		Atlas-SNP	.											.	WDR96	183	.	0			c.T3357C						.						240.0	245.0	243.0					10																	105921776		2203	4300	6503	SO:0001819	synonymous_variant	80217	exon26			CATCAGAGCTCGG																												ENST00000357060.3:c.3357T>C	chr10.hg19:g.105921776A>G		114.0	0.0		95.0	4.0	NM_025145		Silent	SNP	ENST00000357060.3	hg19	CCDS31281.1	.	.	.	.	.	.	.	.	.	.	A	3.651	-0.071434	0.07228	.	.	ENSG00000197748	ENST00000434629	.	.	.	5.73	1.34	0.21922	.	.	.	.	.	T	0.52256	0.1723	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43766	-0.9371	4	.	.	.	.	5.9649	0.19320	0.2974:0.0:0.5652:0.1374	.	.	.	.	P	480	.	.	L	-	2	0	WDR96	105911766	0.991000	0.36638	1.000000	0.80357	0.248000	0.25809	0.054000	0.14205	0.756000	0.33013	-0.261000	0.10672	CTC	.	.		0.483	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ADD3	120	hgsc.bcm.edu	37	10	111883900	111883900	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:111883900T>C	ENST00000356080.4	+	10	1636	c.1269T>C	c.(1267-1269)tcT>tcC	p.S423S	ADD3_ENST00000277900.8_Silent_p.S423S|ADD3_ENST00000360162.3_Silent_p.S423S	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	423						cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		TGCCACTCTCTCCTCTCAAAT	0.468																																					p.S423S		Atlas-SNP	.											.	ADD3	89	.	0			c.T1269C						.						132.0	109.0	117.0					10																	111883900		2203	4300	6503	SO:0001819	synonymous_variant	120	exon10			ACTCTCTCCTCTC	U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.1269T>C	chr10.hg19:g.111883900T>C		125.0	0.0		100.0	4.0	NM_001121	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Silent	SNP	ENST00000356080.4	hg19	CCDS7561.1																																																																																			.	.		0.468	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903	
SHOC2	8036	hgsc.bcm.edu	37	10	112769581	112769581	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:112769581A>G	ENST00000369452.4	+	8	1878	c.1533A>G	c.(1531-1533)gaA>gaG	p.E511E	SHOC2_ENST00000265277.5_Silent_p.E465E|SHOC2_ENST00000489390.1_3'UTR	NM_007373.3	NP_031399.2	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog (C. elegans)	511					fibroblast growth factor receptor signaling pathway (GO:0008543)|positive regulation of Ras protein signal transduction (GO:0046579)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase binding (GO:0019903)|protein phosphatase regulator activity (GO:0019888)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(2)	17				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)		ACCTTCCTGAAGAAATTGGTA	0.393																																					p.E511E		Atlas-SNP	.											.	SHOC2	49	.	0			c.A1533G						.						98.0	86.0	90.0					10																	112769581		2203	4300	6503	SO:0001819	synonymous_variant	8036	exon8			TCCTGAAGAAATT	AB020669	CCDS7568.1, CCDS58095.1	10q25	2014-09-17	2001-11-28		ENSG00000108061	ENSG00000108061			15454	protein-coding gene	gene with protein product		602775	"""soc-2 (suppressor of clear, C.elegans) homolog"""			9618511, 9674433, 10783161	Standard	NM_007373		Approved	KIAA0862, SOC2, SUR-8, SOC-2, SUR8	uc001kzl.4	Q9UQ13	OTTHUMG00000019047	ENST00000369452.4:c.1533A>G	chr10.hg19:g.112769581A>G		127.0	0.0		96.0	4.0	NM_007373	A8K9W8|B3KR23|O76063|Q5VZS8|Q5VZS9	Silent	SNP	ENST00000369452.4	hg19	CCDS7568.1																																																																																			.	.		0.393	SHOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050355.1	NM_007373	
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118196248	118196248	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:118196248A>G	ENST00000369230.3	+	2	221	c.75A>G	c.(73-75)ttA>ttG	p.L25L		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	25					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)		ATGAAAGGTTAGGGTGTTTCA	0.443																																					p.L25L		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.A75G						.						148.0	140.0	143.0					10																	118196248		2203	4300	6503	SO:0001819	synonymous_variant	119548	exon2			AAGGTTAGGGTGT	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.75A>G	chr10.hg19:g.118196248A>G		88.0	0.0		94.0	4.0	NM_001011709		Silent	SNP	ENST00000369230.3	hg19	CCDS31292.1																																																																																			.	.		0.443	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
SLC18A2	6571	hgsc.bcm.edu	37	10	119026263	119026263	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:119026263T>C	ENST00000298472.5	+	11	1154	c.1011T>C	c.(1009-1011)gcT>gcC	p.A337A	SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	337					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	TCTTGCCAGCTAGTATCTCTT	0.353																																					p.A337A		Atlas-SNP	.											.	SLC18A2	58	.	0			c.T1011C						.						167.0	165.0	166.0					10																	119026263		2203	4300	6503	SO:0001819	synonymous_variant	6571	exon11			GCCAGCTAGTATC	L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"""Solute carriers"""	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.1011T>C	chr10.hg19:g.119026263T>C		139.0	0.0		85.0	4.0	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Silent	SNP	ENST00000298472.5	hg19	CCDS7599.1																																																																																			.	.		0.353	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054	
EIF3A	8661	hgsc.bcm.edu	37	10	120828985	120828985	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:120828985T>C	ENST00000369144.3	-	6	1050	c.923A>G	c.(922-924)aAg>aGg	p.K308R	EIF3A_ENST00000541549.1_Missense_Mutation_p.K274R	NM_003750.2	NP_003741.1	P56537	IF6_HUMAN	eukaryotic translation initiation factor 3, subunit A	0					mature ribosome assembly (GO:0042256)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal subunit export from nucleus (GO:0000054)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lamin filament (GO:0005638)|nucleus (GO:0005634)	ribosomal large subunit binding (GO:0043023)|ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)			endometrium(8)|kidney(4)|large_intestine(14)|lung(22)|prostate(1)|skin(4)|urinary_tract(3)	56		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		TGTGAGATTCTTTCTCATTTC	0.318																																					p.K308R		Atlas-SNP	.											.	EIF3A	142	.	0			c.A923G						.						98.0	90.0	93.0					10																	120828985		2203	4300	6503	SO:0001583	missense	8661	exon6			AGATTCTTTCTCA	U78311	CCDS7608.1	10q26.11	2007-08-03	2007-07-27	2007-07-27	ENSG00000107581	ENSG00000107581			3271	protein-coding gene	gene with protein product		602039	"""eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa"""	EIF3, EIF3S10		9054404, 8590280	Standard	NM_003750		Approved	eIF3-theta, eIF3-p170, KIAA0139, eIF3a, TIF32	uc001ldu.3	Q14152	OTTHUMG00000019144	ENST00000369144.3:c.923A>G	chr10.hg19:g.120828985T>C	ENSP00000358140:p.Lys308Arg	93.0	0.0		68.0	4.0	NM_003750	B7ZBG9|Q6IBN8|Q96TD5	Missense_Mutation	SNP	ENST00000369144.3	hg19	CCDS7608.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.000719	0.74818	.	.	ENSG00000107581	ENST00000369144;ENST00000541549	T;T	0.46063	0.88;0.88	5.87	5.87	0.94306	.	0.000000	0.41097	D	0.000944	T	0.61274	0.2334	L	0.60904	1.88	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	T	0.60063	-0.7336	10	0.46703	T	0.11	-34.5111	16.5764	0.84681	0.0:0.0:0.0:1.0	.	308	Q14152	EIF3A_HUMAN	R	308;274	ENSP00000358140:K308R;ENSP00000438178:K274R	ENSP00000358140:K308R	K	-	2	0	EIF3A	120818975	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.965000	0.87945	2.371000	0.80710	0.533000	0.62120	AAG	.	.		0.318	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050634.1	NM_003750	
KNDC1	85442	hgsc.bcm.edu	37	10	134980888	134980888	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:134980888A>G	ENST00000304613.3	+	2	127	c.106A>G	c.(106-108)Aac>Gac	p.N36D	KNDC1_ENST00000368571.2_5'UTR|KNDC1_ENST00000368572.2_Missense_Mutation_p.N36D|KNDC1_ENST00000530127.1_3'UTR			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	36					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TTGGCAGGAGAACGTGTCTCT	0.701																																					p.N36D		Atlas-SNP	.											.	KNDC1	155	.	0			c.A106G						.						17.0	16.0	17.0					10																	134980888		2195	4284	6479	SO:0001583	missense	85442	exon2			CAGGAGAACGTGT	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.106A>G	chr10.hg19:g.134980888A>G	ENSP00000304437:p.Asn36Asp	103.0	0.0		125.0	5.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	.	13.91	2.377048	0.42105	.	.	ENSG00000171798	ENST00000304613;ENST00000368572	T;T	0.74106	-0.81;-0.81	3.98	3.98	0.46160	.	0.000000	0.53938	D	0.000049	D	0.83362	0.5238	M	0.70595	2.14	0.45216	D	0.998225	D	0.89917	1.0	D	0.80764	0.994	D	0.84529	0.0632	10	0.62326	D	0.03	-15.0533	11.1105	0.48230	1.0:0.0:0.0:0.0	.	36	Q76NI1	VKIND_HUMAN	D	36	ENSP00000304437:N36D;ENSP00000357561:N36D	ENSP00000304437:N36D	N	+	1	0	KNDC1	134830878	1.000000	0.71417	0.995000	0.50966	0.176000	0.22953	8.734000	0.91543	1.583000	0.49898	0.172000	0.16884	AAC	.	.		0.701	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
KNDC1	85442	hgsc.bcm.edu	37	10	134999520	134999520	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:134999520A>G	ENST00000304613.3	+	6	689	c.668A>G	c.(667-669)aAc>aGc	p.N223S	KNDC1_ENST00000368571.2_Missense_Mutation_p.N158S|KNDC1_ENST00000368572.2_Missense_Mutation_p.N223S			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	223					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		GCCCCAGGAAACGCTGGGCCC	0.716																																					p.N223S		Atlas-SNP	.											.	KNDC1	155	.	0			c.A668G						.						8.0	10.0	9.0					10																	134999520		2123	4205	6328	SO:0001583	missense	85442	exon6			CAGGAAACGCTGG	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.668A>G	chr10.hg19:g.134999520A>G	ENSP00000304437:p.Asn223Ser	117.0	0.0		92.0	5.0	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	A	0.091	-1.167444	0.01660	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.15603	2.91;2.91;2.41	4.05	-1.53	0.08611	.	1.239190	0.05937	N	0.636354	T	0.07143	0.0181	N	0.04880	-0.145	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.37220	-0.9715	10	0.23891	T	0.37	.	3.9334	0.09296	0.3551:0.3607:0.2842:0.0	.	158;223	Q76NI1-2;Q76NI1	.;VKIND_HUMAN	S	223;223;158	ENSP00000304437:N223S;ENSP00000357561:N223S;ENSP00000357560:N158S	ENSP00000304437:N223S	N	+	2	0	KNDC1	134849510	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.328000	0.19681	-0.161000	0.10983	-0.401000	0.06369	AAC	.	.		0.716	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
B4GALNT4	338707	hgsc.bcm.edu	37	11	376081	376081	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:376081T>C	ENST00000329962.6	+	12	1103	c.1103T>C	c.(1102-1104)cTg>cCg	p.L368P		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	368					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CAGGTGTACCTGTCCTTCGTT	0.672																																					p.L368P		Atlas-SNP	.											.	B4GALNT4	83	.	0			c.T1103C						.						27.0	28.0	27.0					11																	376081		2197	4290	6487	SO:0001583	missense	338707	exon12			TGTACCTGTCCTT	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.1103T>C	chr11.hg19:g.376081T>C	ENSP00000328277:p.Leu368Pro	55.0	0.0		62.0	4.0	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	hg19	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	t	17.34	3.363741	0.61513	.	.	ENSG00000182272	ENST00000329962	T	0.73152	-0.72	2.83	2.83	0.33086	.	0.286546	0.27636	N	0.018484	T	0.80166	0.4573	M	0.62723	1.935	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.82078	-0.0635	10	0.87932	D	0	-10.2847	11.839	0.52342	0.0:0.0:0.0:1.0	.	368	Q76KP1	B4GN4_HUMAN	P	368	ENSP00000328277:L368P	ENSP00000328277:L368P	L	+	2	0	B4GALNT4	366081	1.000000	0.71417	1.000000	0.80357	0.566000	0.35808	5.765000	0.68834	1.533000	0.49186	0.358000	0.22013	CTG	.	.		0.672	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
ZNF195	7748	hgsc.bcm.edu	37	11	3380971	3380971	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:3380971A>G	ENST00000399602.4	-	6	1393	c.1267T>C	c.(1267-1269)Tca>Cca	p.S423P	ZNF195_ENST00000005082.9_Missense_Mutation_p.S400P|ZNF195_ENST00000526601.1_Missense_Mutation_p.S404P|ZNF195_ENST00000528796.1_Intron|ZNF195_ENST00000429541.2_Missense_Mutation_p.S355P|ZNF195_ENST00000343338.7_Missense_Mutation_p.S355P|ZNF195_ENST00000354599.6_Missense_Mutation_p.S351P	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	423					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)	17		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		GTAAGGTCTGAGAACCACTTG	0.423																																					p.S423P		Atlas-SNP	.											.	ZNF195	77	.	0			c.T1267C						.						112.0	117.0	115.0					11																	3380971		2140	4270	6410	SO:0001583	missense	7748	exon6			GGTCTGAGAACCA		CCDS41604.1, CCDS44521.1, CCDS44522.1, CCDS55736.1, CCDS55737.1, CCDS58111.1	11p15.5	2013-01-08			ENSG00000005801	ENSG00000005801		"""Zinc fingers, C2H2-type"", ""-"""	12986	protein-coding gene	gene with protein product		602187				9344677	Standard	NM_001130520		Approved		uc001lxt.3	O14628	OTTHUMG00000011694	ENST00000399602.4:c.1267T>C	chr11.hg19:g.3380971A>G	ENSP00000382511:p.Ser423Pro	59.0	0.0		68.0	4.0	NM_001130520	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Missense_Mutation	SNP	ENST00000399602.4	hg19	CCDS44522.1	.	.	.	.	.	.	.	.	.	.	a	12.51	1.960294	0.34565	.	.	ENSG00000005801	ENST00000354599;ENST00000399602;ENST00000343338;ENST00000429541;ENST00000005082;ENST00000526601	T;T;T;T;T;T	0.07908	3.15;3.15;3.15;3.15;3.15;3.15	1.27	1.27	0.21489	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.24275	0.0588	M	0.82323	2.585	0.09310	N	1	P;D;D;D;D;D	0.65815	0.782;0.992;0.981;0.995;0.967;0.995	P;P;D;P;D;P	0.68621	0.838;0.588;0.959;0.766;0.91;0.766	T	0.06427	-1.0827	9	0.87932	D	0	.	4.0656	0.09859	0.6251:0.3749:0.0:0.0	.	404;282;400;355;423;351	O14628-6;Q59EZ7;O14628-5;O14628-7;O14628;O14628-4	.;.;.;.;ZN195_HUMAN;.	P	351;423;355;355;400;404	ENSP00000346613:S351P;ENSP00000382511:S423P;ENSP00000344483:S355P;ENSP00000387998:S355P;ENSP00000005082:S400P;ENSP00000435828:S404P	ENSP00000005082:S400P	S	-	1	0	ZNF195	3337547	0.000000	0.05858	0.002000	0.10522	0.199000	0.23934	-0.161000	0.10026	0.535000	0.28714	0.254000	0.18369	TCA	.	.		0.423	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2		
RRM1	6240	hgsc.bcm.edu	37	11	4127278	4127278	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:4127278T>C	ENST00000300738.5	+	3	315	c.111T>C	c.(109-111)gcT>gcC	p.A37A	RRM1_ENST00000423050.2_Intron	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	37	ATP-cone. {ECO:0000255|PROSITE- ProRule:PRU00492}.				cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	TTTTGTAGGCTCAGATCACCA	0.413																																					p.A37A	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.T111C						.						75.0	68.0	71.0					11																	4127278		2201	4298	6499	SO:0001819	synonymous_variant	6240	exon3			GTAGGCTCAGATC	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"""ribonucleotide reductase M1 polypeptide"""			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.111T>C	chr11.hg19:g.4127278T>C		68.0	0.0		82.0	5.0	NM_001033	Q9UNN2	Silent	SNP	ENST00000300738.5	hg19	CCDS7750.1																																																																																			.	.		0.413	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033	
SMPD1	6609	hgsc.bcm.edu	37	11	6411941	6411941	+	Missense_Mutation	SNP	C	C	T	rs550365194|rs550067660|rs71467507|rs78250081|rs558809956|rs3838786	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:6411941C>T	ENST00000342245.4	+	1	281	c.113C>T	c.(112-114)gCg>gTg	p.A38V	SMPD1_ENST00000533196.1_3'UTR|SMPD1_ENST00000356761.2_Missense_Mutation_p.A38V|SMPD1_ENST00000299397.3_Missense_Mutation_p.A38V|SMPD1_ENST00000527275.1_Missense_Mutation_p.A38V	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	38					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	ctggtgctggcgctggcgctg	0.711																																					p.A38V		Atlas-SNP	.											.	SMPD1	108	.	0			c.C113T						.						11.0	14.0	13.0					11																	6411941		2185	4258	6443	SO:0001583	missense	6609	exon1			TGCTGGCGCTGGC	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"""acid sphingomyelinase"""	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.113C>T	chr11.hg19:g.6411941C>T	ENSP00000340409:p.Ala38Val	13.0	0.0		20.0	5.0	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation	SNP	ENST00000342245.4	hg19	CCDS44531.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.234305	0.39498	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	T;T;T;T	0.09723	2.95;2.95;2.95;2.95	4.54	-1.08	0.09936	.	.	.	.	.	T	0.04363	0.0120	N	0.08118	0	0.09310	N	1	B;B	0.15473	0.002;0.013	B;B	0.10450	0.002;0.005	T	0.47275	-0.9130	9	0.12103	T	0.63	.	6.8659	0.24093	0.0:0.5614:0.262:0.1766	.	38;38	E9PKS3;G3XAB5	.;.	V	38	ENSP00000299397:A38V;ENSP00000349203:A38V;ENSP00000340409:A38V;ENSP00000435350:A38V	ENSP00000299397:A38V	A	+	2	0	SMPD1	6368517	0.000000	0.05858	0.130000	0.21974	0.033000	0.12548	-2.110000	0.01334	-0.479000	0.06813	-1.305000	0.01319	GCG	.	.		0.711	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543	
OR6A2	8590	hgsc.bcm.edu	37	11	6816516	6816516	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:6816516T>C	ENST00000332601.3	-	1	612	c.424A>G	c.(424-426)Agt>Ggt	p.S142G		NM_003696.2	NP_003687.2	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A, member 2	142					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(4)|pancreas(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	29		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AGCCGGCCACTGACAATGACT	0.517																																					p.S142G		Atlas-SNP	.											.	OR6A2	68	.	0			c.A424G						.						62.0	62.0	62.0					11																	6816516		2201	4296	6497	SO:0001583	missense	8590	exon1			GGCCACTGACAAT	AB065822	CCDS7772.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184933	ENSG00000184933		"""GPCR / Class A : Olfactory receptors"""	15301	protein-coding gene	gene with protein product		608495		OR6A2P, OR6A1			Standard	NM_003696		Approved	OR11-55	uc001mes.1	O95222	OTTHUMG00000165736	ENST00000332601.3:c.424A>G	chr11.hg19:g.6816516T>C	ENSP00000330384:p.Ser142Gly	66.0	0.0		78.0	4.0	NM_003696	Q3MJC7|Q6IF35|Q9H206	Missense_Mutation	SNP	ENST00000332601.3	hg19	CCDS7772.1	.	.	.	.	.	.	.	.	.	.	T	11.30	1.597517	0.28445	.	.	ENSG00000184933	ENST00000332601	T	0.01998	4.51	5.07	5.07	0.68467	GPCR, rhodopsin-like superfamily (1);	0.278035	0.31145	N	0.008167	T	0.03871	0.0109	L	0.59912	1.85	0.36081	D	0.842809	B	0.10296	0.003	B	0.09377	0.004	T	0.19451	-1.0305	10	0.52906	T	0.07	.	13.1051	0.59244	0.0:0.0:0.0:1.0	.	142	O95222	OR6A2_HUMAN	G	142	ENSP00000330384:S142G	ENSP00000330384:S142G	S	-	1	0	OR6A2	6773092	0.762000	0.28451	0.345000	0.25642	0.081000	0.17604	0.895000	0.28363	2.264000	0.75181	0.533000	0.62120	AGT	.	.		0.517	OR6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385981.1	NM_003696	
NLRP14	338323	hgsc.bcm.edu	37	11	7092523	7092523	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:7092523G>T	ENST00000299481.4	+	12	3612	c.3266G>T	c.(3265-3267)tGg>tTg	p.W1089L		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	1089					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GATGTGTCTTGGTGGTGGTGT	0.368																																					p.W1089L		Atlas-SNP	.											.	NLRP14	187	.	0			c.G3266T						.						121.0	115.0	117.0					11																	7092523		2201	4296	6497	SO:0001583	missense	338323	exon12			TGTCTTGGTGGTG	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.3266G>T	chr11.hg19:g.7092523G>T	ENSP00000299481:p.Trp1089Leu	52.0	0.0		74.0	22.0	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	hg19	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.974465	0.53720	.	.	ENSG00000158077	ENST00000299481	T	0.70045	-0.45	4.17	3.26	0.37387	.	0.000000	0.41712	D	0.000823	T	0.72374	0.3452	L	0.46157	1.445	0.32892	D	0.511986	D	0.89917	1.0	D	0.80764	0.994	T	0.77175	-0.2684	10	0.66056	D	0.02	.	7.8046	0.29195	0.1123:0.0:0.8877:0.0	.	1089	Q86W24	NAL14_HUMAN	L	1089	ENSP00000299481:W1089L	ENSP00000299481:W1089L	W	+	2	0	NLRP14	7049099	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	1.000000	0.29770	1.354000	0.45846	0.655000	0.94253	TGG	.	.		0.368	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
ZBED5	58486	hgsc.bcm.edu	37	11	10875063	10875063	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:10875063A>G	ENST00000432999.2	-	3	1928	c.1430T>C	c.(1429-1431)cTt>cCt	p.L477P	ZBED5_ENST00000413761.2_Missense_Mutation_p.L477P|ZBED5_ENST00000525350.1_Intron	NM_001143667.1|NM_021211.3	NP_001137139.1|NP_067034.2	Q49AG3	ZBED5_HUMAN	zinc finger, BED-type containing 5	477							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)	4						aatatctgcaagatatgcaag	0.308																																					p.L477P		Atlas-SNP	.											.	ZBED5	50	.	0			c.T1430C						.						26.0	23.0	24.0					11																	10875063		692	1590	2282	SO:0001583	missense	58486	exon3			TCTGCAAGATATG	AF205601		11p15.3	2013-05-03			ENSG00000236287	ENSG00000236287		"""Zinc fingers, BED-type"""	30803	protein-coding gene	gene with protein product		615251				10607616, 23533661	Standard	NM_021211		Approved	Buster1	uc009ygh.3	Q49AG3	OTTHUMG00000150341	ENST00000432999.2:c.1430T>C	chr11.hg19:g.10875063A>G	ENSP00000398106:p.Leu477Pro	95.0	0.0		94.0	4.0	NM_021211	B2RCC1|Q05D82|Q86WW3|Q9NT24|Q9UBJ4	Missense_Mutation	SNP	ENST00000432999.2	hg19		.	.	.	.	.	.	.	.	.	.	A	13.26	2.183131	0.38511	.	.	ENSG00000236287	ENST00000432999;ENST00000413761	T;T	0.27402	1.67;1.67	4.18	4.18	0.49190	Ribonuclease H-like (1);	.	.	.	.	T	0.54013	0.1832	M	0.80847	2.515	0.53688	D	0.999973	D	0.89917	1.0	D	0.78314	0.991	T	0.58918	-0.7551	9	0.87932	D	0	.	9.917	0.41442	1.0:0.0:0.0:0.0	.	477	Q49AG3	ZBED5_HUMAN	P	477	ENSP00000398106:L477P;ENSP00000415939:L477P	ENSP00000415939:L477P	L	-	2	0	ZBED5	10831639	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.190000	0.50973	2.117000	0.64856	0.528000	0.53228	CTT	.	.		0.308	ZBED5-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000317691.1	NM_021211	
CCDC73	493860	hgsc.bcm.edu	37	11	32722338	32722338	+	Splice_Site	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:32722338T>C	ENST00000335185.5	-	5	357	c.314A>G	c.(313-315)aAg>aGg	p.K105R	CCDC73_ENST00000534415.1_5'UTR|CCDC73_ENST00000531481.1_Splice_Site_p.K105R	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	105										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					tataaataCCTTTTCTTCTTC	0.259																																					p.C105C		Atlas-SNP	.											.	CCDC73	136	.	0			c.G314G						.						15.0	13.0	14.0					11																	32722338		900	2018	2918	SO:0001630	splice_region_variant	493860	exon5			AATACCTTTTCTT	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.315+1A>G	chr11.hg19:g.32722338T>C		62.0	0.0		82.0	4.0	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	Silent	SNP	ENST00000335185.5	hg19	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.129783	0.77549	.	.	ENSG00000186714	ENST00000335185;ENST00000531481	.	.	.	4.72	4.72	0.59763	.	.	.	.	.	T	0.67776	0.2929	L	0.56769	1.78	0.33360	D	0.572167	D;D;D	0.89917	0.974;0.998;1.0	D;D;D	0.87578	0.969;0.994;0.998	T	0.75806	-0.3188	8	0.48119	T	0.1	.	13.4851	0.61359	0.0:0.0:0.0:1.0	.	105;105;105	A6H8Y7;Q6ZRK6-2;Q6ZRK6	.;.;CCD73_HUMAN	R	105	.	ENSP00000335325:K105R	K	-	2	0	CCDC73	32678914	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.185000	0.50934	1.899000	0.54978	0.459000	0.35465	AAG	.	.		0.259	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391	Missense_Mutation
NAT10	55226	hgsc.bcm.edu	37	11	34158558	34158558	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:34158558T>C	ENST00000257829.3	+	21	2402	c.2196T>C	c.(2194-2196)taT>taC	p.Y732Y	NAT10_ENST00000531159.2_Silent_p.Y660Y|NAT10_ENST00000527971.1_Intron	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	732	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.|Required for localization to the nucleolus and midbody.					membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				TTCCTGTTTATCTGAGACAGA	0.512																																					p.Y732Y		Atlas-SNP	.											.	NAT10	78	.	0			c.T2196C						.						128.0	116.0	120.0					11																	34158558		2202	4298	6500	SO:0001819	synonymous_variant	55226	exon21			TGTTTATCTGAGA	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"""N-acetyltransferase 10"""			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.2196T>C	chr11.hg19:g.34158558T>C		95.0	0.0		122.0	6.0	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Silent	SNP	ENST00000257829.3	hg19	CCDS7889.1																																																																																			.	.		0.512	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662	
PDHX	8050	hgsc.bcm.edu	37	11	35016619	35016619	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:35016619T>C	ENST00000227868.4	+	11	1490	c.1406T>C	c.(1405-1407)gTc>gCc	p.V469A	PDHX_ENST00000430469.2_Missense_Mutation_p.V242A|PDHX_ENST00000477173.3_Intron|PDHX_ENST00000448838.3_Missense_Mutation_p.V454A			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	469					cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			CTCATAACAGTCACAATGTCA	0.493																																					p.V469A		Atlas-SNP	.											.	PDHX	40	.	0			c.T1406C						.						126.0	117.0	120.0					11																	35016619		2202	4298	6500	SO:0001583	missense	8050	exon11			TAACAGTCACAAT	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491	ENST00000227868.4:c.1406T>C	chr11.hg19:g.35016619T>C	ENSP00000227868:p.Val469Ala	84.0	0.0		98.0	4.0	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000227868.4	hg19	CCDS7896.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.51|16.51	3.144021|3.144021	0.57044|0.57044	.|.	.|.	ENSG00000110435|ENSG00000110435	ENST00000526309|ENST00000448838;ENST00000227868;ENST00000430469	.|T;T;T	.|0.50001	.|0.76;0.76;0.76	6.04|6.04	6.04|6.04	0.98038|0.98038	.|2-oxoacid dehydrogenase acyltransferase, catalytic domain (1);Chloramphenicol acetyltransferase-like domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.66848|0.66848	0.2831|0.2831	M|M	0.69248|0.69248	2.105|2.105	0.80722|0.80722	D|D	1|1	.|D;D;P	.|0.76494	.|0.999;0.977;0.756	.|D;D;P	.|0.80764	.|0.994;0.934;0.456	T|T	0.65915|0.65915	-0.6052|-0.6052	5|10	.|0.41790	.|T	.|0.15	-22.7959|-22.7959	15.7697|15.7697	0.78157|0.78157	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|242;454;469	.|E9PBP7;E9PB14;O00330	.|.;.;ODPX_HUMAN	P|A	157|454;469;242	.|ENSP00000389404:V454A;ENSP00000227868:V469A;ENSP00000415695:V242A	.|ENSP00000227868:V469A	S|V	+|+	1|2	0|0	PDHX|PDHX	34973195|34973195	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.698000|0.698000	0.40448|0.40448	7.647000|7.647000	0.83462|0.83462	2.317000|2.317000	0.78254|0.78254	0.460000|0.460000	0.39030|0.39030	TCA|GTC	.	.		0.493	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
C11orf84	144097	hgsc.bcm.edu	37	11	63586119	63586119	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:63586119A>G	ENST00000294244.4	+	4	1027	c.728A>G	c.(727-729)gAc>gGc	p.D243G		NM_138471.1	NP_612480.1	Q9BUA3	CK084_HUMAN	chromosome 11 open reading frame 84	243	Pro-rich.									endometrium(3)|kidney(1)|lung(3)|skin(1)	8						CTGGACCCTGACCCAGGTGAA	0.617																																					p.D243G		Atlas-SNP	.											.	C11orf84	33	.	0			c.A728G						.						41.0	48.0	45.0					11																	63586119		2201	4298	6499	SO:0001583	missense	144097	exon4			ACCCTGACCCAGG	BC007540	CCDS31594.1	11q13.1	2014-02-10			ENSG00000168005	ENSG00000168005			25115	protein-coding gene	gene with protein product						12477932	Standard	NM_138471		Approved		uc001nxt.3	Q9BUA3	OTTHUMG00000167746	ENST00000294244.4:c.728A>G	chr11.hg19:g.63586119A>G	ENSP00000294244:p.Asp243Gly	34.0	0.0		73.0	5.0	NM_138471	Q68CV7|Q6PHS2|Q96IH0	Missense_Mutation	SNP	ENST00000294244.4	hg19	CCDS31594.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.583846	0.28268	.	.	ENSG00000168005	ENST00000294244;ENST00000540893	T	0.50001	0.76	5.59	1.8	0.24995	.	0.534807	0.17920	N	0.157523	T	0.35364	0.0929	L	0.51422	1.61	0.25275	N	0.98948	B	0.06786	0.001	B	0.09377	0.004	T	0.35176	-0.9799	10	0.87932	D	0	-11.1871	2.6359	0.04957	0.5927:0.0:0.2125:0.1948	.	243	Q9BUA3	CK084_HUMAN	G	243;18	ENSP00000294244:D243G	ENSP00000294244:D243G	D	+	2	0	C11orf84	63342695	0.986000	0.35501	0.935000	0.37517	0.832000	0.47134	1.276000	0.33156	0.963000	0.38082	0.533000	0.62120	GAC	.	.		0.617	C11orf84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396084.1	NM_138471	
RCOR2	283248	hgsc.bcm.edu	37	11	63681765	63681765	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:63681765C>T	ENST00000301459.4	-	7	1030	c.643G>A	c.(643-645)Gga>Aga	p.G215R	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	215					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						TCGGGCTCTCCCTCACTCACG	0.632																																					p.G215R		Atlas-SNP	.											RCOR2,colon,carcinoma,0,1	RCOR2	43	.	0			c.G643A						.						65.0	54.0	58.0					11																	63681765		2201	4297	6498	SO:0001583	missense	283248	exon7			GCTCTCCCTCACT	BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.643G>A	chr11.hg19:g.63681765C>T	ENSP00000301459:p.Gly215Arg	121.0	0.0		221.0	64.0	NM_173587	Q96FP3	Missense_Mutation	SNP	ENST00000301459.4	hg19	CCDS8052.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.260926	0.39995	.	.	ENSG00000167771	ENST00000301459	T	0.28895	1.59	4.73	4.73	0.59995	.	0.465811	0.21906	N	0.067380	T	0.16769	0.0403	N	0.14661	0.345	0.30039	N	0.812813	B	0.02656	0.0	B	0.04013	0.001	T	0.10291	-1.0636	10	0.16896	T	0.51	.	10.5414	0.45035	0.0:0.9086:0.0:0.0914	.	215	Q8IZ40	RCOR2_HUMAN	R	215	ENSP00000301459:G215R	ENSP00000301459:G215R	G	-	1	0	RCOR2	63438341	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	4.124000	0.57924	2.333000	0.79357	0.561000	0.74099	GGA	.	.		0.632	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587	
CDC42BPG	55561	hgsc.bcm.edu	37	11	64598997	64598997	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:64598997G>A	ENST00000342711.5	-	28	3283	c.3284C>T	c.(3283-3285)aCg>aTg	p.T1095M	CDC42BPG_ENST00000491280.1_5'UTR	NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						AGCGCAGAGCGTGTGAGGCAG	0.657											OREG0004016	type=REGULATORY REGION|Gene=CDC42BPG|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T1095M		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.C3284T						.						50.0	48.0	49.0					11																	64598997		2195	4290	6485	SO:0001583	missense	55561	exon28			CAGAGCGTGTGAG	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"""Pleckstrin homology (PH) domain containing"""	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.3284C>T	chr11.hg19:g.64598997G>A	ENSP00000345133:p.Thr1095Met	180.0	0.0	1077	240.0	30.0	NM_017525		Missense_Mutation	SNP	ENST00000342711.5	hg19	CCDS31601.1	.	.	.	.	.	.	.	.	.	.	G	12.62	1.991419	0.35131	.	.	ENSG00000171219	ENST00000342711	T	0.68765	-0.35	4.33	4.33	0.51752	Citron-like (1);	0.500739	0.16910	N	0.194528	T	0.60907	0.2305	L	0.39147	1.195	0.28328	N	0.921926	D	0.59767	0.986	B	0.43809	0.432	T	0.62201	-0.6904	10	0.66056	D	0.02	.	14.7225	0.69317	0.0:0.0:1.0:0.0	.	1095	Q6DT37	MRCKG_HUMAN	M	1095	ENSP00000345133:T1095M	ENSP00000345133:T1095M	T	-	2	0	CDC42BPG	64355573	0.898000	0.30612	0.439000	0.26833	0.277000	0.26821	5.264000	0.65513	2.416000	0.81992	0.467000	0.42956	ACG	.	.		0.657	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	
CST6	1474	hgsc.bcm.edu	37	11	65779730	65779730	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:65779730C>T	ENST00000312134.2	+	1	419	c.215C>T	c.(214-216)aCg>aTg	p.T72M		NM_001323.3	NP_001314.1	Q15828	CYTM_HUMAN	cystatin E/M	72					anatomical structure morphogenesis (GO:0009653)|epidermis development (GO:0008544)|negative regulation of endopeptidase activity (GO:0010951)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			large_intestine(1)|lung(1)|ovary(1)	3						TTCCGAGACACGCACATCATC	0.697																																					p.T72M		Atlas-SNP	.											.	CST6	14	.	0			c.C215T						.						14.0	13.0	14.0					11																	65779730		2072	4116	6188	SO:0001583	missense	1474	exon1			GAGACACGCACAT	U62800	CCDS8126.1	11q13	2005-09-29			ENSG00000175315	ENSG00000175315			2478	protein-coding gene	gene with protein product		601891				9154125, 9099741	Standard	NM_001323		Approved		uc001ogr.3	Q15828	OTTHUMG00000166750	ENST00000312134.2:c.215C>T	chr11.hg19:g.65779730C>T	ENSP00000311313:p.Thr72Met	60.0	0.0		94.0	4.0	NM_001323	Q540N7	Missense_Mutation	SNP	ENST00000312134.2	hg19	CCDS8126.1	.	.	.	.	.	.	.	.	.	.	C	10.46	1.357715	0.24598	.	.	ENSG00000175315	ENST00000312134	T	0.26373	1.74	5.11	-0.399	0.12415	Proteinase inhibitor I25, cystatin (2);	0.448476	0.23450	N	0.048046	T	0.16642	0.0400	L	0.46157	1.445	0.09310	N	1	B	0.34226	0.443	B	0.31946	0.138	T	0.10314	-1.0635	10	0.42905	T	0.14	-18.5484	4.3212	0.11018	0.0:0.4217:0.1806:0.3977	.	72	Q15828	CYTM_HUMAN	M	72	ENSP00000311313:T72M	ENSP00000311313:T72M	T	+	2	0	CST6	65536306	0.296000	0.24398	0.102000	0.21198	0.005000	0.04900	0.598000	0.24074	0.197000	0.20387	-0.768000	0.03414	ACG	.	.		0.697	CST6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391348.1	NM_001323	
RIN1	9610	hgsc.bcm.edu	37	11	66101126	66101126	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:66101126T>C	ENST00000311320.4	-	8	1721	c.1595A>G	c.(1594-1596)gAg>gGg	p.E532G	RIN1_ENST00000530056.1_Missense_Mutation_p.E366G|RIN1_ENST00000424433.2_Missense_Mutation_p.E427G|RIN1_ENST00000524804.1_5'Flank|RP11-867G23.12_ENST00000526655.1_RNA	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	532	Ras and 14-3-3 protein binding region.|VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						ACCCGCGCCCTCCCCTGTGGG	0.612																																					p.E532G		Atlas-SNP	.											.	RIN1	64	.	0			c.A1595G						.						36.0	39.0	38.0					11																	66101126		2200	4295	6495	SO:0001583	missense	9610	exon8			GCGCCCTCCCCTG	L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.1595A>G	chr11.hg19:g.66101126T>C	ENSP00000310406:p.Glu532Gly	172.0	0.0		221.0	9.0	NM_004292	O15010|Q00427|Q96CC8	Missense_Mutation	SNP	ENST00000311320.4	hg19	CCDS31614.1	.	.	.	.	.	.	.	.	.	.	T	12.20	1.865936	0.32977	.	.	ENSG00000174791	ENST00000311320;ENST00000424433;ENST00000530056	T;T;T	0.32023	1.47;1.47;1.47	4.49	4.49	0.54785	Vacuolar sorting protein 9, subgroup (1);Vacuolar sorting protein 9 (2);	0.255042	0.37437	N	0.002095	T	0.40862	0.1134	L	0.41573	1.285	0.37105	D	0.900093	B;D;B	0.64830	0.025;0.994;0.071	B;P;B	0.62298	0.089;0.9;0.18	T	0.45366	-0.9266	10	0.52906	T	0.07	-20.8263	10.7295	0.46087	0.0:0.0:0.0:1.0	.	366;163;532	E9PNR2;B4DW96;Q13671	.;.;RIN1_HUMAN	G	532;427;366	ENSP00000310406:E532G;ENSP00000400560:E427G;ENSP00000432798:E366G	ENSP00000310406:E532G	E	-	2	0	RIN1	65857702	0.752000	0.28338	0.935000	0.37517	0.194000	0.23727	3.079000	0.50104	1.967000	0.57214	0.379000	0.24179	GAG	.	.		0.612	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292	
PELI3	246330	hgsc.bcm.edu	37	11	66243164	66243164	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:66243164T>C	ENST00000320740.7	+	8	1096	c.936T>C	c.(934-936)gcT>gcC	p.A312A	PELI3_ENST00000531856.1_Intron|CTD-3074O7.5_ENST00000533502.1_RNA|PELI3_ENST00000349459.6_Silent_p.A288A|CTD-3074O7.5_ENST00000527274.2_RNA|CTD-3074O7.5_ENST00000525142.1_RNA|CTD-3074O7.5_ENST00000527092.1_RNA|CTD-3074O7.5_ENST00000602951.1_RNA	NM_001243136.1|NM_145065.2	NP_001230065.1|NP_659502.2	Q8N2H9	PELI3_HUMAN	pellino E3 ubiquitin protein ligase family member 3	312					defense response to Gram-negative bacterium (GO:0050829)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Toll signaling pathway (GO:0045751)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon production (GO:0032480)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|protein K63-linked ubiquitination (GO:0070534)|regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070428)|Toll signaling pathway (GO:0008063)	cytosol (GO:0005829)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	15						TGCTGCGGGCTCCCACACTGA	0.692																																					p.A312A		Atlas-SNP	.											.	PELI3	36	.	0			c.T936C						.						22.0	24.0	23.0					11																	66243164		2164	4233	6397	SO:0001819	synonymous_variant	246330	exon8			GCGGGCTCCCACA	AL834395	CCDS31615.1, CCDS41675.1, CCDS73328.1	11q13.2	2012-02-23	2012-02-23		ENSG00000174516	ENSG00000174516		"""Pellino homologs"""	30010	protein-coding gene	gene with protein product		609827	"""pellino homolog 3 (Drosophila)"""			12874243, 15917247	Standard	NM_145065		Approved	MGC35521	uc001oic.4	Q8N2H9	OTTHUMG00000167109	ENST00000320740.7:c.936T>C	chr11.hg19:g.66243164T>C		127.0	0.0		216.0	10.0	NM_145065	Q8N3E1|Q8N9Q6|Q8TAW7|Q8TED5	Silent	SNP	ENST00000320740.7	hg19	CCDS31615.1																																																																																			.	.		0.692	PELI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393226.1	NM_145065	
RPS6KB2	6199	hgsc.bcm.edu	37	11	67200629	67200629	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:67200629A>G	ENST00000312629.5	+	9	785	c.740A>G	c.(739-741)aAc>aGc	p.N247S	AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	247	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			AGTGGCCACAACCGGGCTGTG	0.692																																					p.N247S		Atlas-SNP	.											.	RPS6KB2	92	.	0			c.A740G						.						13.0	16.0	15.0					11																	67200629		1966	4125	6091	SO:0001583	missense	6199	exon9			GCCACAACCGGGC	AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"""ribosomal protein S6 kinase, 70kD, polypeptide 2"""			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.740A>G	chr11.hg19:g.67200629A>G	ENSP00000308413:p.Asn247Ser	60.0	0.0		87.0	24.0	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Missense_Mutation	SNP	ENST00000312629.5	hg19	CCDS41677.1	.	.	.	.	.	.	.	.	.	.	A	16.18	3.049764	0.55218	.	.	ENSG00000175634	ENST00000312629	T	0.21932	1.98	4.88	3.73	0.42828	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.058351	0.64402	D	0.000004	T	0.15825	0.0381	N	0.02315	-0.6	0.80722	D	1	P;D	0.56035	0.637;0.974	B;P	0.60012	0.414;0.867	T	0.17531	-1.0366	10	0.17369	T	0.5	.	11.5682	0.50818	0.8502:0.1498:0.0:0.0	.	247;247	Q9BRS0;Q9UBS0	.;KS6B2_HUMAN	S	247	ENSP00000308413:N247S	ENSP00000308413:N247S	N	+	2	0	RPS6KB2	66957205	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.465000	0.90383	0.861000	0.35504	0.459000	0.35465	AAC	.	.		0.692	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952	
PITPNM1	9600	hgsc.bcm.edu	37	11	67261213	67261213	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:67261213A>G	ENST00000534749.1	-	20	3292	c.3104T>C	c.(3103-3105)gTc>gCc	p.V1035A	PITPNM1_ENST00000526450.1_5'UTR|PITPNM1_ENST00000436757.2_Missense_Mutation_p.V1034A|PITPNM1_ENST00000356404.3_Missense_Mutation_p.V1035A			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	1035					brain development (GO:0007420)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|phototransduction (GO:0007602)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol transporter activity (GO:0008526)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(3)	18						CATGATGGAGACGCTGGCGGT	0.667																																					p.V1035A	GBM(28;144 709 4607 5525)	Atlas-SNP	.											.	PITPNM1	84	.	0			c.T3104C						.						26.0	23.0	24.0					11																	67261213		2092	4115	6207	SO:0001583	missense	9600	exon21			ATGGAGACGCTGG	X98654	CCDS31620.1, CCDS44659.1	11q13	2008-07-21		2003-05-16	ENSG00000110697	ENSG00000110697			9003	protein-coding gene	gene with protein product	"""PYK2 N-terminal domain-interacting receptor 2"", ""retinal degeneration B alpha 1"""	608794		PITPNM		9680295	Standard	NM_004910		Approved	DRES9, NIR2, RDGB1, RDGBA1, Rd9, RDGB	uc001oly.3	O00562	OTTHUMG00000167675	ENST00000534749.1:c.3104T>C	chr11.hg19:g.67261213A>G	ENSP00000437286:p.Val1035Ala	114.0	0.0		193.0	10.0	NM_004910	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Missense_Mutation	SNP	ENST00000534749.1	hg19	CCDS31620.1	.	.	.	.	.	.	.	.	.	.	A	29.6	5.022898	0.93462	.	.	ENSG00000110697	ENST00000534749;ENST00000436757;ENST00000356404	T;T;T	0.78246	-1.16;-1.16;-1.16	4.2	4.2	0.49525	HAD-like domain (2);LNS2, Lipin/Ned1/Smp2 (2);	0.000000	0.44097	D	0.000486	D	0.88351	0.6413	M	0.87180	2.865	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.993;0.994	D	0.90043	0.4143	10	0.72032	D	0.01	-42.8079	12.4022	0.55420	1.0:0.0:0.0:0.0	.	1034;1035	O00562-2;O00562	.;PITM1_HUMAN	A	1035;1034;1035	ENSP00000437286:V1035A;ENSP00000398787:V1034A;ENSP00000348772:V1035A	ENSP00000348772:V1035A	V	-	2	0	PITPNM1	67017789	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.283000	0.95860	1.673000	0.50895	0.402000	0.26972	GTC	.	.		0.667	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910	
ALG8	79053	hgsc.bcm.edu	37	11	77812229	77812229	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:77812229A>G	ENST00000299626.5	-	13	1433	c.1362T>C	c.(1360-1362)ccT>ccC	p.P454P	ALG8_ENST00000532552.2_5'UTR|ALG8_ENST00000376156.3_3'UTR	NM_024079.4	NP_076984.2	Q9BVK2	ALG8_HUMAN	ALG8, alpha-1,3-glucosyltransferase	454					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)			NS(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	30	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			AATTAAAAAGAGGTTTTTCTT	0.423																																					p.P454P		Atlas-SNP	.											.	ALG8	54	.	0			c.T1362C						.						40.0	43.0	42.0					11																	77812229		2200	4292	6492	SO:0001819	synonymous_variant	79053	exon13			AAAAAGAGGTTTT	AJ224875	CCDS8258.1, CCDS41692.1	11q14.1	2013-03-01	2013-03-01		ENSG00000159063	ENSG00000159063	2.4.1.265		23161	protein-coding gene	gene with protein product	"""dolichyl-P-Glc:Glc(1)Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"""	608103	"""asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase)"", ""asparagine-linked glycosylation 8, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"""				Standard	XM_005274247		Approved	MGC2840	uc001oza.1	Q9BVK2	OTTHUMG00000166594	ENST00000299626.5:c.1362T>C	chr11.hg19:g.77812229A>G		58.0	0.0		94.0	5.0	NM_024079	A6NDW6|O60860	Silent	SNP	ENST00000299626.5	hg19	CCDS8258.1	.	.	.	.	.	.	.	.	.	.	A	10.64	1.406086	0.25378	.	.	ENSG00000159063	ENST00000530608;ENST00000532306	.	.	.	4.81	4.81	0.61882	.	.	.	.	.	T	0.61540	0.2355	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60172	-0.7315	4	.	.	.	-2.0507	10.9174	0.47144	0.843:0.157:0.0:0.0	.	.	.	.	P	156;241	.	.	L	-	2	0	ALG8	77489877	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.577000	0.36515	2.131000	0.65755	0.460000	0.39030	CTC	.	.		0.423	ALG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390637.1	NM_024079	
USP35	57558	hgsc.bcm.edu	37	11	77920940	77920940	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:77920940A>G	ENST00000529308.1	+	10	2300	c.2039A>G	c.(2038-2040)gAg>gGg	p.E680G	USP35_ENST00000530267.1_Missense_Mutation_p.E248G|USP35_ENST00000530535.1_3'UTR|USP35_ENST00000526425.1_Missense_Mutation_p.E411G|USP35_ENST00000441408.2_Missense_Mutation_p.E266G	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	680	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			ATAgagagggaggaagaaggg	0.582																																					p.E680G		Atlas-SNP	.											.	USP35	179	.	0			c.A2039G						.						61.0	79.0	73.0					11																	77920940		2017	4176	6193	SO:0001583	missense	57558	exon10			AGAGGGAGGAAGA	AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"""Ubiquitin-specific peptidases"""	20061	protein-coding gene	gene with protein product			"""ubiquitin specific protease 35"""			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.2039A>G	chr11.hg19:g.77920940A>G	ENSP00000431876:p.Glu680Gly	109.0	0.0		188.0	9.0	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	hg19	CCDS41693.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.133231	0.37630	.	.	ENSG00000118369	ENST00000530267;ENST00000529308;ENST00000441408;ENST00000526425	T;T;T;T	0.10382	3.15;3.2;3.2;2.88	5.11	3.99	0.46301	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	1.601320	0.04148	N	0.320886	T	0.08802	0.0218	N	0.22421	0.69	0.09310	N	1	B;P	0.37914	0.322;0.611	B;B	0.34824	0.142;0.19	T	0.31998	-0.9923	10	0.30854	T	0.27	-0.8059	7.2851	0.26333	0.9025:0.0:0.0975:0.0	.	680;266	Q9P2H5;E7EWV7	UBP35_HUMAN;.	G	248;680;266;411	ENSP00000435468:E248G;ENSP00000431876:E680G;ENSP00000400825:E266G;ENSP00000434942:E411G	ENSP00000400825:E266G	E	+	2	0	USP35	77598588	0.690000	0.27699	0.005000	0.12908	0.002000	0.02628	1.423000	0.34837	0.978000	0.38470	0.496000	0.49642	GAG	.	.		0.582	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
TMEM135	65084	hgsc.bcm.edu	37	11	87020678	87020678	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:87020678T>C	ENST00000305494.5	+	10	939	c.900T>C	c.(898-900)ctT>ctC	p.L300L	TMEM135_ENST00000532959.1_Silent_p.L171L|TMEM135_ENST00000340353.7_Silent_p.L278L|TMEM135_ENST00000535167.1_Silent_p.L161L	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	300					peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				ACTTCCAGCTTGGAGCTTTTC	0.383																																					p.L300L		Atlas-SNP	.											.	TMEM135	40	.	0			c.T900C						.						78.0	86.0	83.0					11																	87020678		2201	4299	6500	SO:0001819	synonymous_variant	65084	exon10			CCAGCTTGGAGCT	BX648678	CCDS8280.1, CCDS53692.1	11q14.2	2006-03-09			ENSG00000166575	ENSG00000166575			26167	protein-coding gene	gene with protein product						12477932	Standard	NM_022918		Approved	FLJ22104	uc001pch.3	Q86UB9	OTTHUMG00000167248	ENST00000305494.5:c.900T>C	chr11.hg19:g.87020678T>C		55.0	0.0		105.0	5.0	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Silent	SNP	ENST00000305494.5	hg19	CCDS8280.1																																																																																			.	.		0.383	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918	
TYR	7299	hgsc.bcm.edu	37	11	89028385	89028385	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:89028385G>C	ENST00000263321.5	+	5	1943	c.1441G>C	c.(1441-1443)Gcg>Ccg	p.A481P		NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	481					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	GCTCCTTGGGGCGGCGATGGT	0.512																																					p.A481P		Atlas-SNP	.											.	TYR	130	.	0			c.G1441C						.						63.0	64.0	64.0					11																	89028385		2201	4299	6500	SO:0001583	missense	7299	exon5			CTTGGGGCGGCGA	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.1441G>C	chr11.hg19:g.89028385G>C	ENSP00000263321:p.Ala481Pro	238.0	0.0		384.0	25.0	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	hg19	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.278972	0.59758	.	.	ENSG00000077498	ENST00000263321	D	0.99304	-5.72	5.02	5.02	0.67125	.	0.111169	0.64402	D	0.000011	D	0.99345	0.9770	M	0.79258	2.445	0.58432	D	0.999999	D	0.76494	0.999	D	0.83275	0.996	D	0.99184	1.0868	9	.	.	.	.	17.4703	0.87645	0.0:0.0:1.0:0.0	.	481	P14679	TYRO_HUMAN	P	481	ENSP00000263321:A481P	.	A	+	1	0	TYR	88668033	1.000000	0.71417	0.929000	0.37066	0.176000	0.22953	6.287000	0.72671	2.488000	0.83962	0.455000	0.32223	GCG	.	.		0.512	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372	
CNTN5	53942	hgsc.bcm.edu	37	11	99715962	99715962	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:99715962T>C	ENST00000524871.1	+	6	835	c.545T>C	c.(544-546)aTt>aCt	p.I182T	CNTN5_ENST00000528682.1_Missense_Mutation_p.I182T|CNTN5_ENST00000418526.2_Missense_Mutation_p.I108T|CNTN5_ENST00000279463.3_Missense_Mutation_p.I182T|CNTN5_ENST00000527185.1_Missense_Mutation_p.I182T	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	182	Ig-like C2-type 1.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		GTGGGGAGTATTCTTAGTAGA	0.343																																					p.I182T		Atlas-SNP	.											.	CNTN5	324	.	0			c.T545C						.						141.0	132.0	135.0					11																	99715962		1828	4097	5925	SO:0001583	missense	53942	exon5			GGAGTATTCTTAG	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.545T>C	chr11.hg19:g.99715962T>C	ENSP00000435637:p.Ile182Thr	51.0	0.0		86.0	4.0	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	T	16.99	3.273069	0.59649	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19	5.8	5.8	0.92144	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.232270	0.43260	D	0.000584	T	0.68063	0.2960	L	0.46819	1.47	0.58432	D	0.999993	P;P;P	0.49447	0.924;0.697;0.924	P;B;P	0.53185	0.72;0.42;0.635	T	0.70791	-0.4776	10	0.66056	D	0.02	.	15.3151	0.74069	0.0:0.0:0.0:1.0	.	182;108;182	E9PKE8;O94779-2;O94779	.;.;CNTN5_HUMAN	T	182;182;182;108;182	ENSP00000433575:I182T;ENSP00000436185:I182T;ENSP00000435637:I182T;ENSP00000393229:I108T;ENSP00000279463:I182T	ENSP00000279463:I182T	I	+	2	0	CNTN5	99221172	1.000000	0.71417	1.000000	0.80357	0.447000	0.32167	5.896000	0.69822	2.216000	0.71823	0.528000	0.53228	ATT	.	.		0.343	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
TRPC6	7225	hgsc.bcm.edu	37	11	101454149	101454149	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:101454149T>C	ENST00000344327.3	-	1	510	c.86A>G	c.(85-87)cAg>cGg	p.Q29R	TRPC6_ENST00000348423.4_Missense_Mutation_p.Q29R|TRPC6_ENST00000360497.4_Missense_Mutation_p.Q29R|RP11-748H22.1_ENST00000527374.1_RNA|TRPC6_ENST00000532133.1_Missense_Mutation_p.Q29R|TRPC6_ENST00000526713.1_Intron	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	29					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		CAGATAGTCCTGGCTCTCGTT	0.711																																					p.Q29R	Colon(166;1315 1927 11094 12848 34731)	Atlas-SNP	.											.	TRPC6	132	.	0			c.A86G						.						14.0	15.0	15.0					11																	101454149		2193	4279	6472	SO:0001583	missense	7225	exon1			TAGTCCTGGCTCT	AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12338	protein-coding gene	gene with protein product		603652	"""focal segmental glomerulosclerosis 2"""	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.86A>G	chr11.hg19:g.101454149T>C	ENSP00000340913:p.Gln29Arg	42.0	0.0		67.0	4.0	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	hg19	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	T	9.153	1.016658	0.19355	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;T;T;T	0.78481	-1.0;-1.08;-0.92;-1.18	5.02	2.7	0.31948	.	0.705449	0.12815	N	0.436907	T	0.59514	0.2199	N	0.14661	0.345	0.25956	N	0.982688	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.002	T	0.49437	-0.8940	10	0.46703	T	0.11	-2.4914	6.4429	0.21859	0.0:0.1975:0.0:0.8025	.	29;29;29	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	R	29	ENSP00000340913:Q29R;ENSP00000435574:Q29R;ENSP00000343672:Q29R;ENSP00000353687:Q29R	ENSP00000340913:Q29R	Q	-	2	0	TRPC6	100959359	0.997000	0.39634	0.999000	0.59377	0.993000	0.82548	0.380000	0.20602	0.272000	0.22027	0.459000	0.35465	CAG	.	.		0.711	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621	
ABCG4	64137	hgsc.bcm.edu	37	11	119028987	119028987	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:119028987T>C	ENST00000449422.2	+	10	1300	c.1112T>C	c.(1111-1113)cTc>cCc	p.L371P	AP002956.1_ENST00000599663.1_5'Flank|ABCG4_ENST00000531739.1_Missense_Mutation_p.L371P|ABCG4_ENST00000307417.3_Missense_Mutation_p.L371P	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	371					cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		ACCAGCACCCTCACACAGTTC	0.577																																					p.L371P		Atlas-SNP	.											.	ABCG4	77	.	0			c.T1112C						.						294.0	275.0	281.0					11																	119028987		2200	4295	6495	SO:0001583	missense	64137	exon10			GCACCCTCACACA	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"""ATP binding cassette transporters / subfamily G"""	13884	protein-coding gene	gene with protein product	"""putative ABC transporter"", ""ATP-binding cassette, subfamily G, member 4"""	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.1112T>C	chr11.hg19:g.119028987T>C	ENSP00000406874:p.Leu371Pro	117.0	0.0		174.0	7.0	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	hg19	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.073509	0.76415	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739;ENST00000534402	D;D;D;T	0.88046	-2.33;-2.33;-2.33;0.24	5.46	5.46	0.80206	.	0.178675	0.49916	D	0.000136	D	0.85660	0.5748	L	0.59436	1.845	0.80722	D	1	B	0.29085	0.232	B	0.36608	0.229	T	0.83001	-0.0177	10	0.37606	T	0.19	-20.679	10.7027	0.45937	0.0:0.0767:0.0:0.9233	.	371	Q9H172	ABCG4_HUMAN	P	371;371;371;49	ENSP00000304111:L371P;ENSP00000406874:L371P;ENSP00000434318:L371P;ENSP00000434571:L49P	ENSP00000304111:L371P	L	+	2	0	ABCG4	118534197	0.917000	0.31117	0.998000	0.56505	0.912000	0.54170	4.894000	0.63206	2.055000	0.61198	0.455000	0.32223	CTC	.	.		0.577	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169	
EI24	9538	hgsc.bcm.edu	37	11	125452299	125452299	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:125452299G>A	ENST00000343678.4	+	9	973	c.731G>A	c.(730-732)aGa>aAa	p.R244K	STT3A-AS1_ENST00000532714.1_RNA|STT3A-AS1_ENST00000530526.1_RNA|EI24_ENST00000530985.1_3'UTR|EI24_ENST00000278903.6_Splice_Site_p.K281K	NM_001007277.1	NP_001007278.1	O14681	EI24_HUMAN	etoposide induced 2.4	0					apoptotic process (GO:0006915)|autophagy (GO:0006914)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of cell growth (GO:0030308)|neuromuscular process controlling balance (GO:0050885)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|response to drug (GO:0042493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				large_intestine(1)|lung(9)|ovary(1)	11	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.64e-07)|OV - Ovarian serous cystadenocarcinoma(99;0.0975)		ATGAAGCAAAGACCCTGGCAA	0.358																																					p.R244K		Atlas-SNP	.											EI24_ENST00000278903,caecum,carcinoma,0,2	EI24	33	.	0			c.G731A						.						32.0	32.0	32.0					11																	125452299		1819	4073	5892	SO:0001583	missense	9538	exon9			AGCAAAGACCCTG	AF010313	CCDS73410.1	11q24.2	2012-11-19	2012-11-16		ENSG00000149547	ENSG00000149547			13276	protein-coding gene	gene with protein product	"""ectopic P-granules autophagy protein 4 homolog (C. elegans)"""	605170	"""etoposide induced 2.4 mRNA"""			10594026, 9305847	Standard	NM_001290135		Approved	PIG8, TP53I8, EPG4	uc001qcb.3	O14681	OTTHUMG00000165851	ENST00000343678.4:c.731G>A	chr11.hg19:g.125452299G>A	ENSP00000364081:p.Arg244Lys	36.0	1.0		35.0	4.0	NM_001007277	A8K7D6|B4DKL6|Q9BUQ1	Missense_Mutation	SNP	ENST00000343678.4	hg19		.	.	.	.	.	.	.	.	.	.	G	19.25	3.791980	0.70452	.	.	ENSG00000149547	ENST00000343678	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	T	0.28167	0.0695	.	.	.	0.22226	N	0.999272	B	0.06786	0.001	B	0.04013	0.001	T	0.09596	-1.0667	6	.	.	.	.	11.4257	0.50009	0.0837:0.0:0.9163:0.0	.	244	A6NES3	.	K	244	.	.	R	+	2	0	EI24	124957509	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.959000	0.70339	2.534000	0.85438	0.557000	0.71058	AGA	.	.		0.358	EI24-202	KNOWN	basic	protein_coding	protein_coding		NM_004879	
WNT5B	81029	hgsc.bcm.edu	37	12	1741875	1741875	+	Silent	SNP	C	C	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:1741875C>G	ENST00000397196.2	+	3	364	c.132C>G	c.(130-132)gcC>gcG	p.A44A	WNT5B_ENST00000537031.1_Silent_p.A44A|WNT5B_ENST00000310594.3_Silent_p.A44A|WNT5B_ENST00000542408.1_Silent_p.A44A	NM_032642.2	NP_116031.1	Q9H1J7	WNT5B_HUMAN	wingless-type MMTV integration site family, member 5B	44					cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|fat cell differentiation (GO:0045444)|lens fiber cell development (GO:0070307)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuron differentiation (GO:0030182)|positive regulation of cell migration (GO:0030335)|positive regulation of fat cell differentiation (GO:0045600)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor binding (GO:0005102)			skin(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00109)			TCATCGGTGCCCAGCCCGTGT	0.562																																					p.A44A		Atlas-SNP	.											.	WNT5B	27	.	0			c.C132G						.						107.0	111.0	110.0					12																	1741875		2203	4300	6503	SO:0001819	synonymous_variant	81029	exon3			CGGTGCCCAGCCC	AB060966	CCDS8510.1	12p13.3	2008-07-07			ENSG00000111186	ENSG00000111186		"""Wingless-type MMTV integration sites"""	16265	protein-coding gene	gene with protein product		606361				11445850	Standard	NM_030775		Approved		uc001qjk.3	Q9H1J7	OTTHUMG00000090375	ENST00000397196.2:c.132C>G	chr12.hg19:g.1741875C>G		129.0	0.0		147.0	61.0	NM_032642	A8K315|D3DUP9|Q96S49|Q9BV04	Silent	SNP	ENST00000397196.2	hg19	CCDS8510.1																																																																																			.	.		0.562	WNT5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206747.2		
DYRK4	8798	hgsc.bcm.edu	37	12	4700393	4700393	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:4700393G>C	ENST00000540757.2	+	3	207	c.47G>C	c.(46-48)aGc>aCc	p.S16T	DYRK4_ENST00000543431.1_Missense_Mutation_p.S16T|DYRK4_ENST00000010132.5_Missense_Mutation_p.S16T	NM_001282285.1|NM_001282286.1|NM_003845.1	NP_001269214.1|NP_001269215.1|NP_003836.1	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	16						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27			Colorectal(7;0.103)			TTCCACCCTAGCATTAAAACC	0.498																																					p.S16T		Atlas-SNP	.											.	DYRK4	75	.	0			c.G47C						.						89.0	80.0	83.0					12																	4700393		2203	4300	6503	SO:0001583	missense	8798	exon3			ACCCTAGCATTAA	Y09305	CCDS8530.1	12p13.32	2014-09-11			ENSG00000010219	ENSG00000010219			3095	protein-coding gene	gene with protein product		609181				9748265	Standard	NM_003845		Approved		uc001qmx.3	Q9NR20	OTTHUMG00000168204	ENST00000540757.2:c.47G>C	chr12.hg19:g.4700393G>C	ENSP00000441755:p.Ser16Thr	170.0	0.0		197.0	66.0	NM_003845	A8K8F7|Q8NEF2|Q92631	Missense_Mutation	SNP	ENST00000540757.2	hg19	CCDS8530.1	.	.	.	.	.	.	.	.	.	.	G	10.21	1.288611	0.23478	.	.	ENSG00000010219	ENST00000542744;ENST00000540757;ENST00000010132;ENST00000543431	T;T;T;T	0.64438	-0.1;-0.03;-0.03;-0.03	4.34	0.201	0.15186	.	1.896970	0.02033	N	0.048652	T	0.52629	0.1746	L	0.44542	1.39	0.09310	N	1	B;B;B	0.28636	0.218;0.11;0.139	B;B;B	0.25291	0.059;0.059;0.027	T	0.24584	-1.0156	10	0.35671	T	0.21	.	5.3065	0.15807	0.2707:0.16:0.5693:0.0	.	131;16;16	F5H6L9;Q9NR20-2;Q9NR20	.;.;DYRK4_HUMAN	T	131;16;16;16	ENSP00000437534:S131T;ENSP00000441755:S16T;ENSP00000010132:S16T;ENSP00000439697:S16T	ENSP00000010132:S16T	S	+	2	0	DYRK4	4570654	0.003000	0.15002	0.000000	0.03702	0.293000	0.27360	0.383000	0.20651	-0.074000	0.12820	-0.430000	0.05897	AGC	.	.		0.498	DYRK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398780.2		
NOP2	4839	hgsc.bcm.edu	37	12	6672806	6672806	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:6672806A>G	ENST00000322166.5	-	7	783	c.662T>C	c.(661-663)cTg>cCg	p.L221P	NOP2_ENST00000541778.1_Missense_Mutation_p.L217P|NOP2_ENST00000545200.1_Missense_Mutation_p.L217P|NOP2_ENST00000399466.2_Missense_Mutation_p.L217P|NOP2_ENST00000537442.1_Missense_Mutation_p.L221P|NOP2_ENST00000382421.3_Missense_Mutation_p.L254P|NOP2_ENST00000542015.1_Intron	NM_001258308.1|NM_006170.3	NP_001245237.1|NP_006161.2	P46087	NOP2_HUMAN	NOP2 nucleolar protein	221					positive regulation of cell proliferation (GO:0008284)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	19						AGCAGGGGGCAGCACAAATGG	0.562											OREG0021630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L254P		Atlas-SNP	.											.	NOP2	44	.	0			c.T761C						.						47.0	49.0	49.0					12																	6672806		1974	4146	6120	SO:0001583	missense	4839	exon8			GGGGGCAGCACAA		CCDS44811.1, CCDS58202.1, CCDS58203.1, CCDS58204.1	12p13	2012-12-10	2012-12-10	2008-10-13	ENSG00000111641	ENSG00000111641		"""NOP2/Sun domain containing"""	7867	protein-coding gene	gene with protein product	"""NOP2/Sun domain family, member 1"""	164031	"""nucleolar protein 1 (120kD)"", ""nucleolar protein 1, 120kDa"", ""nucleolar protein 2 homolog (yeast)"", ""NOP2 nucleolar protein homolog (yeast)"""	NOL1		8088812	Standard	NM_006170		Approved	NOP120, NSUN1, p120	uc021qtz.2	P46087	OTTHUMG00000169163	ENST00000322166.5:c.662T>C	chr12.hg19:g.6672806A>G	ENSP00000313272:p.Leu221Pro	96.0	0.0	635	95.0	4.0	NM_001258309	A1A4Z3|B3KPD6|Q05BA7|Q0P5S5|Q3KQS4|Q58F30	Missense_Mutation	SNP	ENST00000322166.5	hg19	CCDS58203.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.951896	0.73787	.	.	ENSG00000111641	ENST00000537442;ENST00000382421;ENST00000545200;ENST00000399466;ENST00000322166;ENST00000541778;ENST00000542944;ENST00000542867	T;T;T;T;T;T;T;T	0.71103	1.92;1.7;2.08;1.9;1.92;1.9;0.39;-0.54	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000004	D	0.83050	0.5170	M	0.93197	3.39	0.80722	D	1	P;P	0.39576	0.63;0.679	B;P	0.46825	0.328;0.528	D	0.86931	0.2073	10	0.87932	D	0	-15.4916	14.2848	0.66240	1.0:0.0:0.0:0.0	.	254;217	Q3KQS4;P46087-2	.;.	P	221;254;217;217;221;217;97;217	ENSP00000444437:L221P;ENSP00000371858:L254P;ENSP00000439422:L217P;ENSP00000382392:L217P;ENSP00000313272:L221P;ENSP00000443150:L217P;ENSP00000440754:L97P;ENSP00000443035:L217P	ENSP00000313272:L221P	L	-	2	0	NOP2	6543067	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	6.076000	0.71267	2.063000	0.61619	0.460000	0.39030	CTG	.	.		0.562	NOP2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402614.1	NM_006170	
LPAR5	57121	hgsc.bcm.edu	37	12	6729711	6729711	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:6729711A>G	ENST00000329858.4	-	2	1460	c.704T>C	c.(703-705)cTc>cCc	p.L235P	LPAR5_ENST00000431922.1_Missense_Mutation_p.L235P|LPAR5_ENST00000540335.1_5'UTR	NM_020400.5	NP_065133.1	Q9H1C0	LPAR5_HUMAN	lysophosphatidic acid receptor 5	235						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|skin(2)	7						AGCCAGCAGGAGGCGCACGGT	0.701																																					p.L235P	NSCLC(74;891 2312 37538)	Atlas-SNP	.											.	LPAR5	30	.	0			c.T704C						.						10.0	6.0	8.0					12																	6729711		2113	4105	6218	SO:0001583	missense	57121	exon2			AGCAGGAGGCGCA	AJ272207	CCDS8553.1	12p13.31	2012-08-08	2008-04-11	2008-04-11		ENSG00000184574		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	13307	protein-coding gene	gene with protein product		606926	"""G protein-coupled receptor 92"""	GPR93, GPR92		11062477, 11574155, 16774927, 16651401	Standard	NM_020400		Approved	KPG_010, LPA5	uc009zer.2	Q9H1C0		ENST00000329858.4:c.704T>C	chr12.hg19:g.6729711A>G	ENSP00000327875:p.Leu235Pro	42.0	0.0		30.0	4.0	NM_001142961		Missense_Mutation	SNP	ENST00000329858.4	hg19	CCDS8553.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.152688	0.78001	.	.	ENSG00000184574	ENST00000329858;ENST00000431922;ENST00000435659	T;T	0.40225	1.04;1.04	4.93	4.93	0.64822	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000039	T	0.70124	0.3188	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.77869	-0.2427	10	0.87932	D	0	.	14.7338	0.69402	1.0:0.0:0.0:0.0	.	235	Q9H1C0	LPAR5_HUMAN	P	235	ENSP00000327875:L235P;ENSP00000393098:L235P	ENSP00000327875:L235P	L	-	2	0	LPAR5	6599972	0.998000	0.40836	1.000000	0.80357	0.988000	0.76386	4.770000	0.62309	2.077000	0.62373	0.459000	0.35465	CTC	.	.		0.701	LPAR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400699.1	NM_020400	
ATN1	1822	hgsc.bcm.edu	37	12	7050600	7050600	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:7050600A>G	ENST00000356654.4	+	9	3659	c.3422A>G	c.(3421-3423)cAg>cGg	p.Q1141R	RNU7-1_ENST00000458811.1_RNA|C12orf57_ENST00000229281.5_5'Flank|C12orf57_ENST00000544681.1_5'Flank|C12orf57_ENST00000540506.2_5'Flank|U47924.31_ENST00000607421.1_RNA|C12orf57_ENST00000537087.1_5'Flank|ATN1_ENST00000396684.2_Missense_Mutation_p.Q1141R	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	1141					cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						CATCAGCTGCAGGCCATGCAC	0.652																																					p.Q1141R		Atlas-SNP	.											.	ATN1	95	.	0			c.A3422G						.						62.0	63.0	62.0					12																	7050600		2202	4298	6500	SO:0001583	missense	1822	exon9			AGCTGCAGGCCAT	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"""dentatorubral-pallidoluysian atrophy (atrophin-1)"""	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.3422A>G	chr12.hg19:g.7050600A>G	ENSP00000349076:p.Gln1141Arg	78.0	0.0		81.0	4.0	NM_001007026	Q99495|Q99621|Q9UEK7	Missense_Mutation	SNP	ENST00000356654.4	hg19	CCDS31734.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.631954	0.87660	.	.	ENSG00000111676	ENST00000356654;ENST00000396684;ENST00000544325;ENST00000229279	T;T;T	0.70399	-0.48;-0.48;-0.48	4.32	4.32	0.51571	.	0.000000	0.32401	U	0.006153	T	0.81182	0.4769	M	0.62723	1.935	0.80722	D	1	D	0.57571	0.98	D	0.75020	0.985	D	0.83576	0.0115	10	0.87932	D	0	.	13.987	0.64341	1.0:0.0:0.0:0.0	.	1141	P54259	ATN1_HUMAN	R	1141;1141;1141;726	ENSP00000349076:Q1141R;ENSP00000379915:Q1141R;ENSP00000441744:Q1141R	ENSP00000229279:Q726R	Q	+	2	0	ATN1	6920861	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.139000	0.94554	1.961000	0.56991	0.533000	0.62120	CAG	.	.		0.652	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940	
CLSTN3	9746	hgsc.bcm.edu	37	12	7295529	7295529	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:7295529T>C	ENST00000266546.6	+	11	2055	c.1605T>C	c.(1603-1605)ggT>ggC	p.G535G	CLSTN3_ENST00000537408.1_Silent_p.G547G	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	535					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						TGCGCTCAGGTCGCCTGGAGA	0.587																																					p.G535G		Atlas-SNP	.											.	CLSTN3	84	.	0			c.T1605C						.						116.0	89.0	98.0					12																	7295529		2203	4300	6503	SO:0001819	synonymous_variant	9746	exon11			CTCAGGTCGCCTG	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"""Cadherins / Cadherin-related"""	18371	protein-coding gene	gene with protein product	"""cadherin-related family member 14"""	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.1605T>C	chr12.hg19:g.7295529T>C		183.0	0.0		233.0	11.0	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Silent	SNP	ENST00000266546.6	hg19	CCDS8575.1																																																																																			.	.		0.587	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718	
LRP6	4040	hgsc.bcm.edu	37	12	12300340	12300340	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:12300340A>G	ENST00000261349.4	-	15	3433	c.3357T>C	c.(3355-3357)gcT>gcC	p.A1119A	LRP6_ENST00000543091.1_Silent_p.A1119A	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1119	Beta-propeller 4.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|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)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				GATCTGAATCAGCCCAAAAGA	0.418																																					p.A1119A		Atlas-SNP	.											.	LRP6	170	.	0			c.T3357C						.						100.0	101.0	101.0					12																	12300340		2203	4300	6503	SO:0001819	synonymous_variant	4040	exon15			TGAATCAGCCCAA	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.3357T>C	chr12.hg19:g.12300340A>G		92.0	0.0		117.0	5.0	NM_002336	Q17RZ2	Silent	SNP	ENST00000261349.4	hg19	CCDS8647.1																																																																																			.	.		0.418	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
CDKN1B	1027	hgsc.bcm.edu	37	12	12871837	12871837	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:12871837A>G	ENST00000228872.4	+	2	1270	c.554A>G	c.(553-555)gAg>gGg	p.E185G	CDKN1B_ENST00000477087.1_3'UTR|CDKN1B_ENST00000396340.1_Intron	NM_004064.3	NP_004055.1	P46527	CDN1B_HUMAN	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	185					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|autophagic cell death (GO:0048102)|cell cycle arrest (GO:0007050)|cellular response to antibiotic (GO:0071236)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular component movement (GO:0051271)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of kinase activity (GO:0033673)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|potassium ion transport (GO:0006813)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein phosphatase binding (GO:0019903)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)			breast(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(5)	13		Prostate(47;0.0322)|all_epithelial(100;0.159)		BRCA - Breast invasive adenocarcinoma(232;0.0336)		GGTTCTGTGGAGCAGACGCCC	0.498																																					p.E185G		Atlas-SNP	.											.	CDKN1B	48	.	0			c.A554G						.						78.0	86.0	83.0					12																	12871837		2203	4300	6503	SO:0001583	missense	1027	exon2			CTGTGGAGCAGAC	AF480891	CCDS8653.1	12p13.1-p12	2008-08-04			ENSG00000111276	ENSG00000111276			1785	protein-coding gene	gene with protein product		600778				8033212	Standard	NM_004064		Approved	KIP1, P27KIP1	uc001rat.2	P46527	OTTHUMG00000149914	ENST00000228872.4:c.554A>G	chr12.hg19:g.12871837A>G	ENSP00000228872:p.Glu185Gly	62.0	0.0		71.0	4.0	NM_004064	Q16307|Q5U0H2|Q9BUS6	Missense_Mutation	SNP	ENST00000228872.4	hg19	CCDS8653.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.826681	0.90955	.	.	ENSG00000111276	ENST00000228872;ENST00000535674;ENST00000442489	T;T	0.59772	0.24;0.24	5.37	5.37	0.77165	.	.	.	.	.	T	0.73651	0.3614	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.76675	-0.2872	9	0.72032	D	0.01	.	13.9531	0.64131	1.0:0.0:0.0:0.0	.	185	P46527	CDN1B_HUMAN	G	185;134;91	ENSP00000228872:E185G;ENSP00000407597:E91G	ENSP00000228872:E185G	E	+	2	0	CDKN1B	12763104	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.539000	0.73856	2.024000	0.59613	0.533000	0.62120	GAG	.	.		0.498	CDKN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313878.2	NM_004064	
PLEKHA5	54477	hgsc.bcm.edu	37	12	19475253	19475253	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:19475253A>G	ENST00000299275.6	+	14	1924	c.1918A>G	c.(1918-1920)Agc>Ggc	p.S640G	PLEKHA5_ENST00000538714.1_Missense_Mutation_p.S698G|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.S559G|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.S398G|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.S571G|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.S743G|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.S698G|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.S640G|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.S640G	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	640					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					GGCCAAGTTAAGCCGATTATG	0.343																																					p.S743G	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A2227G						.						93.0	92.0	92.0					12																	19475253		2203	4300	6503	SO:0001583	missense	54477	exon19			AAGTTAAGCCGAT	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"""Pleckstrin homology (PH) domain containing"""	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.1918A>G	chr12.hg19:g.19475253A>G	ENSP00000299275:p.Ser640Gly	18.0	0.0		53.0	4.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	12.17	1.858438	0.32791	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974	T;T;T;T;T;T;T;T;T;T	0.39787	1.07;1.06;1.07;1.06;1.07;1.07;1.06;1.06;1.06;1.06	4.76	4.76	0.60689	.	0.042036	0.85682	D	0.000000	T	0.50377	0.1612	L	0.42245	1.32	0.39951	D	0.974546	D;P;B;D;B;P;B	0.76494	0.999;0.49;0.357;0.997;0.038;0.497;0.127	D;B;B;D;B;B;B	0.87578	0.998;0.217;0.108;0.91;0.028;0.108;0.147	T	0.45687	-0.9244	10	0.06757	T	0.87	-14.9551	12.9989	0.58664	1.0:0.0:0.0:0.0	.	640;559;571;743;743;640;698	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;PKHA5_HUMAN;.	G	640;698;640;744;743;640;398;698;571;559;532	ENSP00000325155:S640G;ENSP00000347560:S698G;ENSP00000352104:S640G;ENSP00000404296:S743G;ENSP00000299275:S640G;ENSP00000440611:S398G;ENSP00000439673:S698G;ENSP00000400411:S571G;ENSP00000439837:S559G;ENSP00000440371:S532G	ENSP00000299275:S640G	S	+	1	0	PLEKHA5	19366520	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	8.091000	0.89528	1.992000	0.58205	0.455000	0.32223	AGC	.	.		0.343	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012	
GYS2	2998	hgsc.bcm.edu	37	12	21692268	21692268	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:21692268T>C	ENST00000261195.2	-	15	2068	c.1814A>G	c.(1813-1815)tAc>tGc	p.Y605C		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	605					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GGCATGCTGGTAATACTATTG	0.333																																					p.Y605C	Colon(149;9 1820 3690 10544 50424)	Atlas-SNP	.											.	GYS2	110	.	0			c.A1814G						.						146.0	153.0	151.0					12																	21692268		2203	4300	6503	SO:0001583	missense	2998	exon15			TGCTGGTAATACT		CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.1814A>G	chr12.hg19:g.21692268T>C	ENSP00000261195:p.Tyr605Cys	101.0	0.0		89.0	4.0	NM_021957	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	hg19	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.990812	0.74589	.	.	ENSG00000111713	ENST00000261195	T	0.73575	-0.76	5.3	5.3	0.74995	.	0.064498	0.64402	D	0.000004	D	0.86318	0.5904	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88259	0.2922	10	0.87932	D	0	-16.451	14.569	0.68200	0.0:0.0:0.0:1.0	.	605	P54840	GYS2_HUMAN	C	605	ENSP00000261195:Y605C	ENSP00000261195:Y605C	Y	-	2	0	GYS2	21583535	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.002000	0.76304	2.218000	0.71995	0.528000	0.53228	TAC	.	.		0.333	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957	
ABCC9	10060	hgsc.bcm.edu	37	12	21960279	21960279	+	Splice_Site	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:21960279C>T	ENST00000261201.4	-	36	4449		c.e36+1		ABCC9_ENST00000345162.2_Splice_Site|ABCC9_ENST00000261200.4_Splice_Site	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9						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)	AATGCACTCACTGTGGCCATG	0.403																																					.		Atlas-SNP	.											.	ABCC9	411	.	0			c.4449+1G>A						.						163.0	154.0	157.0					12																	21960279		2203	4300	6503	SO:0001630	splice_region_variant	10060	exon37			CACTCACTGTGGC	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.4449+1G>A	chr12.hg19:g.21960279C>T		96.0	0.0		97.0	5.0	NM_020297	O60707	Splice_Site	SNP	ENST00000261201.4	hg19	CCDS8694.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.826729	0.90955	.	.	ENSG00000069431	ENST00000261200;ENST00000544039;ENST00000261201;ENST00000345162	.	.	.	5.15	5.15	0.70609	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8248	0.92114	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABCC9	21851546	1.000000	0.71417	0.997000	0.53966	0.981000	0.71138	7.534000	0.82004	2.654000	0.90174	0.655000	0.94253	.	.	.		0.403	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691	Intron
OVCH1	341350	hgsc.bcm.edu	37	12	29630051	29630051	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:29630051T>C	ENST00000318184.5	-	12	1360	c.1361A>G	c.(1360-1362)gAg>gGg	p.E454G	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	454	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					AATGTGCTTCTCTGGAGCACA	0.393																																					p.E454G		Atlas-SNP	.											.	OVCH1	195	.	0			c.A1361G						.						80.0	79.0	79.0					12																	29630051		1888	4110	5998	SO:0001583	missense	341350	exon12			TGCTTCTCTGGAG	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.1361A>G	chr12.hg19:g.29630051T>C	ENSP00000326708:p.Glu454Gly	86.0	0.0		89.0	4.0	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	hg19		.	.	.	.	.	.	.	.	.	.	T	6.608	0.480572	0.12581	.	.	ENSG00000187950	ENST00000318184	T	0.58210	0.35	2.73	-2.36	0.06663	CUB (5);	.	.	.	.	T	0.37625	0.1010	L	0.39467	1.215	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	T	0.25641	-1.0126	9	0.42905	T	0.14	.	5.716	0.17960	0.0:0.4222:0.1557:0.4222	.	454	Q7RTY7	OVCH1_HUMAN	G	454	ENSP00000326708:E454G	ENSP00000326708:E454G	E	-	2	0	OVCH1	29521318	0.022000	0.18835	0.000000	0.03702	0.001000	0.01503	-0.258000	0.08733	-0.581000	0.05937	-0.304000	0.09214	GAG	.	.		0.393	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
TMTC1	83857	hgsc.bcm.edu	37	12	29904627	29904627	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:29904627A>G	ENST00000539277.1	-	5	968	c.910T>C	c.(910-912)Tcc>Ccc	p.S304P	TMTC1_ENST00000381224.2_Missense_Mutation_p.S196P|TMTC1_ENST00000256062.5_Missense_Mutation_p.S196P|TMTC1_ENST00000552618.1_Missense_Mutation_p.S304P|TMTC1_ENST00000551659.1_Missense_Mutation_p.S304P	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	304						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					gctcgtggggACACTGGGAAT	0.582																																					p.S304P		Atlas-SNP	.											.	TMTC1	147	.	0			c.T910C						.						112.0	100.0	104.0					12																	29904627		2203	4300	6503	SO:0001583	missense	83857	exon5			GTGGGGACACTGG		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"""Tetratricopeptide (TTC) repeat domain containing"""	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.910T>C	chr12.hg19:g.29904627A>G	ENSP00000442046:p.Ser304Pro	91.0	0.0		103.0	5.0	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	hg19	CCDS53772.1	.	.	.	.	.	.	.	.	.	.	A	3.009	-0.204394	0.06180	.	.	ENSG00000133687	ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277;ENST00000381224	T;T;T;T;T	0.69175	-0.36;-0.14;-0.38;-0.22;1.43	4.51	1.99	0.26369	.	0.628295	0.16615	N	0.206723	T	0.30510	0.0767	N	0.02120	-0.675	0.09310	N	1	B;B	0.14438	0.01;0.002	B;B	0.11329	0.006;0.002	T	0.13980	-1.0489	9	.	.	.	-4.486	1.8015	0.03072	0.5629:0.175:0.0938:0.1683	.	196;304	Q8IUR5-3;Q8IUR5	.;TMTC1_HUMAN	P	196;304;304;304;196	ENSP00000256062:S196P;ENSP00000448112:S304P;ENSP00000449043:S304P;ENSP00000442046:S304P;ENSP00000370622:S196P	.	S	-	1	0	TMTC1	29795894	0.961000	0.32948	0.032000	0.17829	0.406000	0.30931	1.745000	0.38278	0.278000	0.22164	-0.341000	0.08007	TCC	.	.		0.582	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920	
DENND5B	160518	hgsc.bcm.edu	37	12	31632582	31632582	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:31632582T>C	ENST00000389082.5	-	3	1109	c.845A>G	c.(844-846)aAc>aGc	p.N282S	DENND5B_ENST00000354285.4_Missense_Mutation_p.N304S|DENND5B_ENST00000536562.1_Missense_Mutation_p.N317S|DENND5B_ENST00000306833.6_Missense_Mutation_p.N317S|DENND5B_ENST00000545147.1_Intron	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	282	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						CTGCACCAGGTTCTCTAATCC	0.473																																					p.N282S		Atlas-SNP	.											.	DENND5B	114	.	0			c.A845G						.						21.0	20.0	20.0					12																	31632582		1824	4078	5902	SO:0001583	missense	160518	exon3			ACCAGGTTCTCTA	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"""DENN/MADD domain containing"""	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.845A>G	chr12.hg19:g.31632582T>C	ENSP00000373734:p.Asn282Ser	76.0	0.0		95.0	4.0	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	hg19	CCDS44857.1	.	.	.	.	.	.	.	.	.	.	T	15.66	2.898681	0.52227	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285;ENST00000546299	T;T;T;T;T	0.13538	2.58;2.58;2.58;2.58;2.58	4.56	4.56	0.56223	DENN (3);	0.000000	0.85682	D	0.000000	T	0.30978	0.0782	M	0.64676	1.99	0.80722	D	1	P;P;D;P;P	0.54397	0.843;0.929;0.966;0.763;0.925	P;P;D;P;P	0.63033	0.53;0.674;0.91;0.657;0.792	T	0.01791	-1.1273	10	0.39692	T	0.17	-29.5519	14.1051	0.65083	0.0:0.0:0.0:1.0	.	317;204;304;282;317	Q6ZUT9-2;Q6ZUT9-3;Q6ZUT9-4;Q6ZUT9;G3V1S3	.;.;.;DEN5B_HUMAN;.	S	282;317;317;304;234	ENSP00000373734:N282S;ENSP00000306482:N317S;ENSP00000444889:N317S;ENSP00000346238:N304S;ENSP00000442938:N234S	ENSP00000306482:N317S	N	-	2	0	DENND5B	31523849	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.663000	0.83820	1.924000	0.55735	0.533000	0.62120	AAC	.	.		0.473	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43822261	43822261	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:43822261T>C	ENST00000389420.3	-	26	3727	c.3728A>G	c.(3727-3729)gAg>gGg	p.E1243G	ADAMTS20_ENST00000395541.2_Missense_Mutation_p.E361G|ADAMTS20_ENST00000553158.1_Missense_Mutation_p.E1243G	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1243	TSP type-1 8. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		ACAGTAATTCTCATCAATTGG	0.463																																					p.E1243G		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A3728G						.						60.0	62.0	61.0					12																	43822261		2203	4300	6503	SO:0001583	missense	80070	exon26			TAATTCTCATCAA	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.3728A>G	chr12.hg19:g.43822261T>C	ENSP00000374071:p.Glu1243Gly	153.0	0.0		162.0	7.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	T	16.44	3.123471	0.56613	.	.	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	5.35	5.35	0.76521	.	0.000000	0.51477	D	0.000094	T	0.58264	0.2110	L	0.31664	0.95	0.44110	D	0.99688	B;D	0.63046	0.107;0.992	B;D	0.63192	0.199;0.912	T	0.53927	-0.8369	10	0.27082	T	0.32	.	16.0388	0.80650	0.0:0.0:0.0:1.0	.	1243;361	P59510;E9PBD5	ATS20_HUMAN;.	G	1243;373;361;1243;1243	ENSP00000374071:E1243G;ENSP00000447427:E373G;ENSP00000378911:E361G;ENSP00000448341:E1243G	ENSP00000374068:E1243G	E	-	2	0	ADAMTS20	42108528	1.000000	0.71417	0.999000	0.59377	0.934000	0.57294	3.106000	0.50322	2.330000	0.79161	0.477000	0.44152	GAG	.	.		0.463	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
ANO6	196527	hgsc.bcm.edu	37	12	45771870	45771870	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:45771870T>C	ENST00000320560.8	+	10	1341	c.1139T>C	c.(1138-1140)gTc>gCc	p.V380A	ANO6_ENST00000435642.1_Missense_Mutation_p.V380A|ANO6_ENST00000441606.2_Missense_Mutation_p.V362A|ANO6_ENST00000423947.3_Missense_Mutation_p.V401A|ANO6_ENST00000426898.2_3'UTR|ANO6_ENST00000425752.2_Missense_Mutation_p.V380A	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	380					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						GGAACCCTGGTCTTTGCAGTA	0.313																																					p.V401A		Atlas-SNP	.											.	ANO6	163	.	0			c.T1202C						.						176.0	178.0	177.0					12																	45771870		2203	4300	6503	SO:0001583	missense	196527	exon11			CCCTGGTCTTTGC	AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	25240	protein-coding gene	gene with protein product		608663	"""transmembrane protein 16F"""	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.1139T>C	chr12.hg19:g.45771870T>C	ENSP00000320087:p.Val380Ala	80.0	0.0		94.0	5.0	NM_001204803	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	hg19	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.122971	0.56613	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.23	5.23	0.72850	.	0.339267	0.30989	N	0.008469	T	0.58906	0.2155	L	0.48174	1.505	0.38052	D	0.935795	B;B;B;B	0.23591	0.01;0.002;0.088;0.013	B;B;B;B	0.30495	0.038;0.012;0.116;0.05	T	0.61729	-0.7003	10	0.49607	T	0.09	.	14.3961	0.67013	0.0:0.0:0.0:1.0	.	362;401;380;380	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	A	380;401;380;380;362	ENSP00000391417:V380A;ENSP00000409126:V401A;ENSP00000413840:V380A;ENSP00000320087:V380A;ENSP00000413137:V362A	ENSP00000320087:V380A	V	+	2	0	ANO6	44058137	1.000000	0.71417	0.757000	0.31301	0.925000	0.55904	5.103000	0.64578	2.279000	0.76181	0.533000	0.62120	GTC	.	.		0.313	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743	
RAPGEF3	10411	hgsc.bcm.edu	37	12	48134787	48134787	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:48134787A>G	ENST00000449771.2	-	20	2048	c.1960T>C	c.(1960-1962)Tct>Cct	p.S654P	RAPGEF3_ENST00000548919.1_Missense_Mutation_p.S563P|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.S654P|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.S612P|RP1-197B17.3_ENST00000547799.1_lincRNA|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.S612P|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.S612P			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	654					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		CCCTCAGCAGAGCCCACAGTG	0.652																																					p.S654P		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.T1960C						.						22.0	21.0	21.0					12																	48134787		2203	4300	6503	SO:0001583	missense	10411	exon20			CAGCAGAGCCCAC	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"""exchange protein directly activated by cAMP 1"""	606057	"""RAP guanine-nucleotide-exchange factor (GEF) 3"""			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.1960T>C	chr12.hg19:g.48134787A>G	ENSP00000395708:p.Ser654Pro	192.0	0.0		198.0	9.0	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	hg19	CCDS41775.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.730539	0.48939	.	.	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919	T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58	3.87	3.87	0.44632	Ras guanine nucleotide exchange factor, domain (1);	0.165039	0.39544	N	0.001338	T	0.34542	0.0901	N	0.24115	0.695	0.41254	D	0.986732	D	0.76494	0.999	D	0.66351	0.943	T	0.13926	-1.0491	10	0.54805	T	0.06	.	7.6408	0.28292	0.8108:0.0:0.0:0.1892	.	654	O95398	RPGF3_HUMAN	P	612;654;301;612;612;612;654;617;563	ENSP00000384521:S612P;ENSP00000395708:S654P;ENSP00000448619:S612P;ENSP00000171000:S612P;ENSP00000373864:S654P;ENSP00000448480:S563P	ENSP00000171000:S612P	S	-	1	0	RAPGEF3	46421054	0.127000	0.22367	0.999000	0.59377	0.991000	0.79684	0.373000	0.20484	1.552000	0.49463	0.379000	0.24179	TCT	.	.		0.652	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105	
DIP2B	57609	hgsc.bcm.edu	37	12	51077012	51077012	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:51077012A>G	ENST00000301180.5	+	10	1332	c.1298A>G	c.(1297-1299)gAg>gGg	p.E433G		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	433						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						GTGCCTATAGAGGTACCTCTT	0.438																																					p.E433G		Atlas-SNP	.											.	DIP2B	167	.	0			c.A1298G						.						150.0	140.0	144.0					12																	51077012		2203	4300	6503	SO:0001583	missense	57609	exon10			CTATAGAGGTACC	AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.1298A>G	chr12.hg19:g.51077012A>G	ENSP00000301180:p.Glu433Gly	53.0	0.0		82.0	4.0	NM_173602	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	hg19	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.559283	0.86335	.	.	ENSG00000066084	ENST00000301180	T	0.10477	2.87	4.98	4.98	0.66077	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.34048	0.0884	M	0.83953	2.67	0.80722	D	1	D	0.63046	0.992	D	0.66979	0.948	T	0.10382	-1.0632	10	0.38643	T	0.18	-20.033	14.8272	0.70122	1.0:0.0:0.0:0.0	.	433	Q9P265	DIP2B_HUMAN	G	433	ENSP00000301180:E433G	ENSP00000301180:E433G	E	+	2	0	DIP2B	49363279	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.107000	0.94261	2.091000	0.63221	0.533000	0.62120	GAG	.	.		0.438	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602	
TFCP2	7024	hgsc.bcm.edu	37	12	51510142	51510142	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:51510142T>C	ENST00000257915.5	-	4	871	c.413A>G	c.(412-414)gAg>gGg	p.E138G	TFCP2_ENST00000307660.4_Missense_Mutation_p.E138G|TFCP2_ENST00000549867.1_Missense_Mutation_p.E138G|TFCP2_ENST00000548115.1_Missense_Mutation_p.E138G	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	138	DNA-binding.				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)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						CCTCCAGCCCTCTAGCTGCTG	0.448																																					p.E138G		Atlas-SNP	.											.	TFCP2	49	.	0			c.A413G						.						116.0	103.0	108.0					12																	51510142		2203	4300	6503	SO:0001583	missense	7024	exon4			CAGCCCTCTAGCT	U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.413A>G	chr12.hg19:g.51510142T>C	ENSP00000257915:p.Glu138Gly	166.0	0.0		200.0	10.0	NM_001173452	A8K5E9|Q12801|Q9UD75|Q9UD77	Missense_Mutation	SNP	ENST00000257915.5	hg19	CCDS8808.1	.	.	.	.	.	.	.	.	.	.	T	14.51	2.557249	0.45590	.	.	ENSG00000135457	ENST00000257915;ENST00000307660;ENST00000549867;ENST00000548115;ENST00000548108	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	4.86	3.69	0.42338	CP2 transcription factor (1);	0.108853	0.64402	D	0.000010	T	0.33702	0.0872	M	0.75264	2.295	0.58432	D	0.99999	P;B;P;B	0.45768	0.557;0.094;0.866;0.039	B;B;P;B	0.49421	0.234;0.126;0.61;0.067	T	0.15263	-1.0443	10	0.72032	D	0.01	-19.9447	11.1675	0.48552	0.0:0.0:0.1546:0.8454	.	138;138;138;138	Q12800-2;F8VX55;Q12800;Q12800-4	.;.;TFCP2_HUMAN;.	G	138;138;138;138;40	ENSP00000257915:E138G;ENSP00000304411:E138G;ENSP00000449742:E138G;ENSP00000447991:E138G;ENSP00000449280:E40G	ENSP00000257915:E138G	E	-	2	0	TFCP2	49796409	1.000000	0.71417	1.000000	0.80357	0.061000	0.15899	7.772000	0.85439	0.982000	0.38575	-0.316000	0.08728	GAG	.	.		0.448	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653	
ACVR1B	91	hgsc.bcm.edu	37	12	52385707	52385707	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:52385707A>G	ENST00000257963.4	+	8	1399	c.1322A>G	c.(1321-1323)gAg>gGg	p.E441G	ACVR1B_ENST00000426655.2_Missense_Mutation_p.E441G|ACVR1B_ENST00000541224.1_Missense_Mutation_p.E482G|ACVR1B_ENST00000542485.1_Missense_Mutation_p.E389G|ACVR1B_ENST00000563121.1_3'UTR	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	441	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|central nervous system development (GO:0007417)|development of primary female sexual characteristics (GO:0046545)|extrinsic apoptotic signaling pathway (GO:0097191)|G1/S transition of mitotic cell cycle (GO:0000082)|hair follicle development (GO:0001942)|in utero embryonic development (GO:0001701)|negative regulation of cell growth (GO:0030308)|nodal signaling pathway (GO:0038092)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of trophoblast cell migration (GO:1901165)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|inhibin binding (GO:0034711)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|endometrium(4)|kidney(5)|large_intestine(12)|lung(10)|ovary(1)|pancreas(6)|prostate(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	CCTTCCATTGAGGAAATGCGA	0.483																																					p.E482G		Atlas-SNP	.											.	ACVR1B	167	.	0			c.A1445G						.						181.0	161.0	168.0					12																	52385707		2203	4300	6503	SO:0001583	missense	91	exon9			CCATTGAGGAAAT		CCDS8816.1, CCDS44893.1, CCDS44894.1, CCDS44893.2, CCDS44894.2	12q13	2006-11-09			ENSG00000135503	ENSG00000135503			172	protein-coding gene	gene with protein product		601300		ACVRLK4		8397373	Standard	NM_020327		Approved	ALK4, SKR2, ActRIB	uc010snn.2	P36896	OTTHUMG00000167920	ENST00000257963.4:c.1322A>G	chr12.hg19:g.52385707A>G	ENSP00000257963:p.Glu441Gly	140.0	0.0		150.0	6.0	NM_020328	B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Missense_Mutation	SNP	ENST00000257963.4	hg19	CCDS8816.1	.	.	.	.	.	.	.	.	.	.	A	19.27	3.794416	0.70452	.	.	ENSG00000135503	ENST00000257963;ENST00000541224;ENST00000426655;ENST00000542485	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	4.05	4.05	0.47172	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.051797	0.85682	D	0.000000	T	0.66117	0.2757	L	0.52126	1.63	0.80722	D	1	B;B;B	0.32071	0.242;0.215;0.355	B;B;B	0.39904	0.222;0.313;0.218	T	0.71374	-0.4612	10	0.87932	D	0	.	14.0635	0.64815	1.0:0.0:0.0:0.0	.	482;441;441	P36896-4;P36896;P36896-2	.;ACV1B_HUMAN;.	G	441;482;441;389	ENSP00000257963:E441G;ENSP00000442656:E482G;ENSP00000390477:E441G;ENSP00000442885:E389G	ENSP00000257963:E441G	E	+	2	0	ACVR1B	50671974	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.044000	0.93805	2.059000	0.61396	0.379000	0.24179	GAG	.	.		0.483	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397000.1	NM_020328	
KRT1	3848	hgsc.bcm.edu	37	12	53069297	53069297	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:53069297A>G	ENST00000252244.3	-	9	1673	c.1615T>C	c.(1615-1617)Tat>Cat	p.Y539H		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	539	Gly/Ser-rich.|Tail.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)	p.Y539N(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						ccagaaccatagctaccacct	0.677																																					p.Y539H		Atlas-SNP	.											KRT1,NS,carcinoma,0,1	KRT1	110	.	1	Substitution - Missense(1)	lung(1)	c.T1615C						.						16.0	17.0	17.0					12																	53069297		2201	4299	6500	SO:0001583	missense	3848	exon9			AACCATAGCTACC	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1615T>C	chr12.hg19:g.53069297A>G	ENSP00000252244:p.Tyr539His	43.0	0.0		56.0	3.0	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	hg19	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	A	9.015	0.983400	0.18889	.	.	ENSG00000167768	ENST00000252244	T	0.77877	-1.13	3.52	0.923	0.19413	.	.	.	.	.	T	0.51958	0.1705	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.33394	-0.9870	9	0.15952	T	0.53	.	4.9696	0.14108	0.5319:0.359:0.1091:0.0	.	539	P04264	K2C1_HUMAN	H	539	ENSP00000252244:Y539H	ENSP00000252244:Y539H	Y	-	1	0	KRT1	51355564	0.013000	0.17824	0.007000	0.13788	0.191000	0.23601	0.921000	0.28718	0.316000	0.23135	0.374000	0.22700	TAT	.	.		0.677	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
ITGA5	3678	hgsc.bcm.edu	37	12	54797420	54797420	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:54797420T>C	ENST00000293379.4	-	17	2026	c.1765A>G	c.(1765-1767)Atc>Gtc	p.I589V	RP11-753H16.3_ENST00000550474.1_RNA|RP11-753H16.5_ENST00000552785.1_RNA	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	589					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						CTGAGGTAGATCTTCATCTCT	0.622																																					p.I589V		Atlas-SNP	.											.	ITGA5	99	.	0			c.A1765G						.						71.0	71.0	71.0					12																	54797420		2203	4300	6503	SO:0001583	missense	3678	exon17			GGTAGATCTTCAT		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.1765A>G	chr12.hg19:g.54797420T>C	ENSP00000293379:p.Ile589Val	71.0	0.0		111.0	5.0	NM_002205	Q96HA5	Missense_Mutation	SNP	ENST00000293379.4	hg19	CCDS8880.1	.	.	.	.	.	.	.	.	.	.	T	2.663	-0.279223	0.05642	.	.	ENSG00000161638	ENST00000293379	T	0.39592	1.07	5.05	0.0378	0.14198	Integrin alpha-2 (1);	0.149585	0.64402	N	0.000017	T	0.16642	0.0400	N	0.05414	-0.055	0.44030	D	0.996753	B	0.16166	0.016	B	0.21708	0.036	T	0.27088	-1.0084	10	0.05525	T	0.97	.	8.28	0.31896	0.0:0.3406:0.0:0.6594	.	589	P08648	ITA5_HUMAN	V	589	ENSP00000293379:I589V	ENSP00000293379:I589V	I	-	1	0	ITGA5	53083687	1.000000	0.71417	0.999000	0.59377	0.966000	0.64601	1.424000	0.34848	0.053000	0.16036	-0.379000	0.06801	ATC	.	.		0.622	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1		
PDE1B	5153	hgsc.bcm.edu	37	12	54968906	54968906	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:54968906T>C	ENST00000243052.3	+	11	1525	c.1089T>C	c.(1087-1089)tcT>tcC	p.S363S	PDE1B_ENST00000538346.1_Silent_p.S322S|PDE1B_ENST00000550620.1_Silent_p.S343S|PDE1B_ENST00000394277.3_3'UTR	NM_000924.3	NP_000915.1	Q01064	PDE1B_HUMAN	phosphodiesterase 1B, calmodulin-dependent	363	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|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)|locomotory behavior (GO:0007626)|monocyte differentiation (GO:0030224)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of dopamine metabolic process (GO:0042053)|regulation of neurotransmitter levels (GO:0001505)|response to amphetamine (GO:0001975)|serotonin metabolic process (GO:0042428)|signal transduction (GO:0007165)|visual learning (GO:0008542)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)	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)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(4)	31					Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	AGGCCCTGTCTCTACTGCTCC	0.542																																					p.S363S		Atlas-SNP	.											.	PDE1B	76	.	0			c.T1089C						.						130.0	117.0	121.0					12																	54968906		2203	4300	6503	SO:0001819	synonymous_variant	5153	exon11			CCTGTCTCTACTG	U56976	CCDS8882.1, CCDS53800.1, CCDS73477.1	12q13	2008-03-18				ENSG00000123360	3.1.4.17	"""Phosphodiesterases"""	8775	protein-coding gene	gene with protein product		171891		PDES1B		8855339, 9419816	Standard	NM_000924		Approved		uc001sgd.2	Q01064	OTTHUMG00000169844	ENST00000243052.3:c.1089T>C	chr12.hg19:g.54968906T>C		89.0	0.0		95.0	4.0	NM_000924	Q92825|Q96KP3	Silent	SNP	ENST00000243052.3	hg19	CCDS8882.1																																																																																			.	.		0.542	PDE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406203.1		
OR6C70	390327	hgsc.bcm.edu	37	12	55863303	55863303	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:55863303A>G	ENST00000327335.4	-	1	619	c.620T>C	c.(619-621)gTc>gCc	p.V207A	RP11-110A12.2_ENST00000555146.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA	NM_001005499.1	NP_001005499.1	A6NIJ9	O6C70_HUMAN	olfactory receptor, family 6, subfamily C, member 70	207						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	18						AAACAATGTGACAATAAGTGT	0.358																																					p.V207A		Atlas-SNP	.											.	OR6C70	35	.	0			c.T620C						.						118.0	123.0	121.0					12																	55863303		2203	4300	6503	SO:0001583	missense	390327	exon1			AATGTGACAATAA		CCDS31825.1	12q13.2	2013-09-23			ENSG00000184954	ENSG00000184954		"""GPCR / Class A : Olfactory receptors"""	31299	protein-coding gene	gene with protein product							Standard	NM_001005499		Approved		uc010spn.2	A6NIJ9	OTTHUMG00000171127	ENST00000327335.4:c.620T>C	chr12.hg19:g.55863303A>G	ENSP00000329153:p.Val207Ala	66.0	0.0		100.0	6.0	NM_001005499		Missense_Mutation	SNP	ENST00000327335.4	hg19	CCDS31825.1	.	.	.	.	.	.	.	.	.	.	A	8.759	0.923233	0.18056	.	.	ENSG00000184954	ENST00000327335	T	0.39229	1.09	4.13	1.73	0.24493	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46145	D	0.000303	T	0.44307	0.1287	L	0.45581	1.43	0.09310	N	1	D	0.55385	0.971	P	0.60068	0.868	T	0.32161	-0.9917	10	0.72032	D	0.01	.	1.6624	0.02795	0.5567:0.1394:0.1685:0.1354	.	207	A6NIJ9	O6C70_HUMAN	A	207	ENSP00000329153:V207A	ENSP00000329153:V207A	V	-	2	0	OR6C70	54149570	0.000000	0.05858	0.026000	0.17262	0.003000	0.03518	0.258000	0.18387	0.255000	0.21593	-0.253000	0.11424	GTC	.	.		0.358	OR6C70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411820.1		
GLI1	2735	hgsc.bcm.edu	37	12	57857530	57857530	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:57857530T>C	ENST00000228682.2	+	2	147	c.56T>C	c.(55-57)cTc>cCc	p.L19P	GLI1_ENST00000543426.1_Intron|GLI1_ENST00000546141.1_Missense_Mutation_p.L19P	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	19	SNAG domain. {ECO:0000250}.				cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			CCCTGCTGTCTCCGGCCCCTC	0.592																																					p.L19P	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											.	GLI1	141	.	0			c.T56C						.						78.0	70.0	73.0					12																	57857530		2203	4300	6503	SO:0001583	missense	2735	exon2			GCTGTCTCCGGCC		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"""Zinc fingers, C2H2-type"""	4317	protein-coding gene	gene with protein product		165220	"""glioma-associated oncogene homolog 1 (zinc finger protein)"", ""glioma-associated oncogene family zinc finger 1"""	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.56T>C	chr12.hg19:g.57857530T>C	ENSP00000228682:p.Leu19Pro	48.0	0.0		53.0	4.0	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	hg19	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	T	18.76	3.693279	0.68386	.	.	ENSG00000111087	ENST00000228682;ENST00000546141;ENST00000528432;ENST00000528467	T;T;T	0.18016	2.24;2.33;2.33	4.42	4.42	0.53409	.	0.470469	0.17701	N	0.164920	T	0.21347	0.0514	N	0.17082	0.46	0.80722	D	1	D	0.63880	0.993	P	0.59595	0.86	T	0.02844	-1.1103	10	0.56958	D	0.05	.	11.572	0.50839	0.0:0.0:0.0:1.0	.	19	P08151	GLI1_HUMAN	P	19	ENSP00000228682:L19P;ENSP00000441006:L19P;ENSP00000434408:L19P	ENSP00000228682:L19P	L	+	2	0	GLI1	56143797	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.974000	0.56852	1.983000	0.57843	0.528000	0.53228	CTC	.	.		0.592	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269	
SLC16A7	9194	hgsc.bcm.edu	37	12	60098572	60098572	+	Splice_Site	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:60098572G>A	ENST00000552432.1	+	3	269		c.e3-1		SLC16A7_ENST00000547379.1_5'UTR|SLC16A7_ENST00000552024.1_5'UTR|SLC16A7_ENST00000549588.1_3'UTR|SLC16A7_ENST00000549465.1_5'UTR|SLC16A7_ENST00000543448.1_5'UTR|SLC16A7_ENST00000261187.4_5'UTR	NM_001270622.1|NM_001270623.1	NP_001257551.1|NP_001257552.1	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7						lactate transmembrane transport (GO:0035873)|pyruvate transmembrane transport (GO:1901475)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|pyruvate secondary active transmembrane transporter activity (GO:0005477)|pyruvate transmembrane transporter activity (GO:0050833)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			endometrium(1)|large_intestine(14)|liver(2)|lung(11)|ovary(1)|skin(1)	30				GBM - Glioblastoma multiforme(3;0.0303)	Gamma Hydroxybutyric Acid(DB01440)|Niflumic Acid(DB04552)|Probenecid(DB01032)|Pyruvic acid(DB00119)	ATTTCCACTAGAGGAGCAGAA	0.393																																					.		Atlas-SNP	.											.	SLC16A7	82	.	0			.						.						49.0	44.0	46.0					12																	60098572		2203	4300	6503	SO:0001630	splice_region_variant	9194	.			CCACTAGAGGAGC	AF049608	CCDS8961.1	12q14.1	2013-07-18	2013-07-18		ENSG00000118596	ENSG00000118596		"""Solute carriers"""	10928	protein-coding gene	gene with protein product		603654	"""solute carrier family 16 (monocarboxylic acid transporters), member 7"""			9786900	Standard	NM_004731		Approved	MCT2	uc001sqt.4	O60669	OTTHUMG00000169923	ENST00000552432.1:c.-10-1G>A	chr12.hg19:g.60098572G>A		100.0	0.0		92.0	38.0	.	Q8NEM3|Q9UPB3	Splice_Site	SNP	ENST00000552432.1	hg19	CCDS8961.1																																																																																			.	.		0.393	SLC16A7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406582.1	NM_004731	Intron
CEP290	80184	hgsc.bcm.edu	37	12	88454605	88454606	+	Splice_Site	DNP	AC	AC	TA			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:88454605_88454606AC>TA	ENST00000552810.1	-	47	6866		c.e47+1		CEP290_ENST00000397838.3_Splice_Site|CEP290_ENST00000309041.7_Splice_Site|CEP290_ENST00000547691.2_Splice_Site	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa						cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						AAAAAAAATTACCTTCAATTTT	0.262																																					.		Atlas-SNP	.											.	CEP290	195	.	0			c.6522+2T>A|c.6522+1G>T						.																																			SO:0001630	splice_region_variant	80184	exon48			AAAATTACCTTCA|AAATTACCTTCAA	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.6523_6523delinsTA	chr12.hg19:g.88454605_88454606delinsTA		84.0|86.0	0.0		80.0|82.0	7.0|5.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Splice_Site	SNP	ENST00000552810.1	hg19	CCDS55858.1																																																																																			.	.		0.262	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	Intron
CEP83	51134	hgsc.bcm.edu	37	12	94769731	94769731	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:94769731A>G	ENST00000397809.5	-	8	1413	c.864T>C	c.(862-864)agT>agC	p.S288S	CCDC41_ENST00000397807.2_Silent_p.S255S|CCDC41_ENST00000549352.1_5'UTR|CCDC41_ENST00000547575.1_Silent_p.S288S|CCDC41_ENST00000339839.5_Silent_p.S288S	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		280					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						TATTTTGTTCACTGCTTGATT	0.284																																					p.S288S		Atlas-SNP	.											.	CCDC41	59	.	0			c.T864C						.						79.0	77.0	77.0					12																	94769731		1807	4068	5875	SO:0001819	synonymous_variant	51134	exon8			TTGTTCACTGCTT																												ENST00000397809.5:c.864T>C	chr12.hg19:g.94769731A>G		71.0	0.0		69.0	4.0	NM_016122	A4FVB1|Q08AP1	Silent	SNP	ENST00000397809.5	hg19	CCDS41820.1																																																																																			.	.		0.284	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3		
NEDD1	121441	hgsc.bcm.edu	37	12	97328852	97328852	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:97328852T>C	ENST00000266742.4	+	7	927	c.588T>C	c.(586-588)agT>agC	p.S196S	NEDD1_ENST00000411739.2_Silent_p.S107S|NEDD1_ENST00000557644.1_Silent_p.S203S|NEDD1_ENST00000555114.1_3'UTR|NEDD1_ENST00000429527.2_Silent_p.S196S|NEDD1_ENST00000457368.2_Silent_p.S107S	NM_152905.3	NP_690869.1	Q8NHV4	NEDD1_HUMAN	neural precursor cell expressed, developmentally down-regulated 1	196					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	apical part of cell (GO:0045177)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|pericentriolar material (GO:0000242)|spindle pole (GO:0000922)				breast(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)	22						ATAGTCAGAGTCCATACCATA	0.408																																					p.S203S		Atlas-SNP	.											.	NEDD1	47	.	0			c.T609C						.						223.0	210.0	215.0					12																	97328852		2203	4300	6503	SO:0001819	synonymous_variant	121441	exon6			TCAGAGTCCATAC		CCDS9063.1, CCDS44955.1, CCDS44956.1	12q23.1	2013-01-10			ENSG00000139350	ENSG00000139350		"""WD repeat domain containing"""	7723	protein-coding gene	gene with protein product		600372					Standard	NM_001135175		Approved	GCP-WD, TUBGCP7	uc001tev.4	Q8NHV4	OTTHUMG00000170604	ENST00000266742.4:c.588T>C	chr12.hg19:g.97328852T>C		192.0	0.0		203.0	9.0	NM_001135175	B0AZN0|B4E145|G3V3F1|Q8NA30	Silent	SNP	ENST00000266742.4	hg19	CCDS9063.1																																																																																			.	.		0.408	NEDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409792.1		
APAF1	317	hgsc.bcm.edu	37	12	99060128	99060128	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:99060128A>G	ENST00000551964.1	+	9	2091	c.1355A>G	c.(1354-1356)cAg>cGg	p.Q452R	APAF1_ENST00000359972.2_Missense_Mutation_p.Q441R|APAF1_ENST00000547045.1_Missense_Mutation_p.Q452R|APAF1_ENST00000550527.1_Missense_Mutation_p.Q441R|APAF1_ENST00000333991.1_Intron|APAF1_ENST00000549007.1_Missense_Mutation_p.Q452R|APAF1_ENST00000357310.1_Missense_Mutation_p.Q452R|APAF1_ENST00000339433.3_Missense_Mutation_p.Q452R|APAF1_ENST00000552268.1_Intron	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	452					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	AATTGCAGCCAGCTTCAGGTA	0.289																																					p.Q452R		Atlas-SNP	.											.	APAF1	111	.	0			c.A1355G						.						89.0	95.0	93.0					12																	99060128		2203	4300	6503	SO:0001583	missense	317	exon9			GCAGCCAGCTTCA	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"""WD repeat domain containing"""	576	protein-coding gene	gene with protein product		602233	"""apoptotic protease activating factor"", ""apoptotic peptidase activating factor"""			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.1355A>G	chr12.hg19:g.99060128A>G	ENSP00000448165:p.Gln452Arg	75.0	0.0		99.0	4.0	NM_181868	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	18.44	3.624000	0.66901	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T	0.59906	0.24;0.35;0.32;0.43;0.23;0.32;0.43	5.77	4.62	0.57501	.	0.052584	0.85682	D	0.000000	T	0.65760	0.2722	L	0.50333	1.59	0.80722	D	1	B;B;B;P	0.51653	0.078;0.01;0.023;0.947	B;B;B;D	0.65323	0.142;0.04;0.027;0.934	T	0.63422	-0.6641	10	0.40728	T	0.16	-21.8531	8.8201	0.35020	0.8556:0.0:0.1444:0.0	.	452;441;452;441	O14727-4;O14727-3;O14727;O14727-2	.;.;APAF_HUMAN;.	R	452;441;452;452;441;452;452	ENSP00000448165:Q452R;ENSP00000353059:Q441R;ENSP00000349862:Q452R;ENSP00000341830:Q452R;ENSP00000448449:Q441R;ENSP00000449791:Q452R;ENSP00000448161:Q452R	ENSP00000341830:Q452R	Q	+	2	0	APAF1	97584259	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	4.832000	0.62759	1.012000	0.39366	0.477000	0.44152	CAG	.	.		0.289	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1	
ANKS1B	56899	hgsc.bcm.edu	37	12	99129364	99129364	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:99129364T>C	ENST00000547776.2	-	26	3720	c.3721A>G	c.(3721-3723)Act>Gct	p.T1241A	ANKS1B_ENST00000547010.1_Missense_Mutation_p.T757A|ANKS1B_ENST00000549558.2_Missense_Mutation_p.T407A|ANKS1B_ENST00000341752.7_Missense_Mutation_p.T247A|ANKS1B_ENST00000329257.7_Missense_Mutation_p.T1241A	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	1241						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		GCCTCCTCAGTGTGTCTCTCT	0.353																																					p.T1241A		Atlas-SNP	.											.	ANKS1B	180	.	0			c.A3721G						.						117.0	112.0	113.0					12																	99129364		1841	4094	5935	SO:0001583	missense	56899	exon26			CCTCAGTGTGTCT	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.3721A>G	chr12.hg19:g.99129364T>C	ENSP00000449629:p.Thr1241Ala	64.0	0.0		67.0	4.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	T	12.63	1.994346	0.35226	.	.	ENSG00000185046	ENST00000341752;ENST00000549558;ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702	T;T;T;T;T	0.64260	-0.09;-0.08;1.1;0.28;1.1	2.95	2.95	0.34219	.	1.415530	0.05657	U	0.586107	T	0.60560	0.2278	N	0.08118	0	0.22213	N	0.999284	P;P;P	0.52842	0.874;0.956;0.917	P;D;P	0.65010	0.641;0.931;0.878	T	0.56878	-0.7906	10	0.66056	D	0.02	0.4115	7.7143	0.28696	0.0:0.0:0.0:1.0	.	757;1241;407	Q7Z6G8-6;Q7Z6G8;Q7Z6G8-7	.;ANS1B_HUMAN;.	A	247;407;1241;757;1241;756	ENSP00000345510:T247A;ENSP00000448993:T407A;ENSP00000449629:T1241A;ENSP00000448512:T757A;ENSP00000331381:T1241A	ENSP00000331381:T1241A	T	-	1	0	ANKS1B	97653495	0.001000	0.12720	0.004000	0.12327	0.908000	0.53690	0.330000	0.19715	1.587000	0.49959	0.379000	0.24179	ACT	.	.		0.353	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
ANKS1B	56899	hgsc.bcm.edu	37	12	100173672	100173672	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:100173672A>G	ENST00000547776.2	-	6	823	c.824T>C	c.(823-825)cTc>cCc	p.L275P	ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000329257.7_Missense_Mutation_p.L275P	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	275						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		TGCAATCTGGAGAGATTTCTG	0.343																																					p.L275P		Atlas-SNP	.											.	ANKS1B	180	.	0			c.T824C						.						156.0	153.0	154.0					12																	100173672		1829	4091	5920	SO:0001583	missense	56899	exon6			ATCTGGAGAGATT	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.824T>C	chr12.hg19:g.100173672A>G	ENSP00000449629:p.Leu275Pro	133.0	0.0		167.0	7.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	A	17.20	3.328604	0.60743	.	.	ENSG00000185046	ENST00000547776;ENST00000329257	T;T	0.46819	0.86;0.86	5.95	5.95	0.96441	Ankyrin repeat-containing domain (2);	0.084158	0.52532	D	0.000068	T	0.54481	0.1861	L	0.47716	1.5	0.80722	D	1	D	0.53745	0.962	P	0.54590	0.756	T	0.51601	-0.8685	9	.	.	.	-7.7214	13.9333	0.64010	1.0:0.0:0.0:0.0	.	275	Q7Z6G8	ANS1B_HUMAN	P	275	ENSP00000449629:L275P;ENSP00000331381:L275P	.	L	-	2	0	ANKS1B	98697803	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.946000	0.56644	2.280000	0.76307	0.460000	0.39030	CTC	.	.		0.343	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
GNPTAB	79158	hgsc.bcm.edu	37	12	102155033	102155033	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:102155033T>C	ENST00000299314.7	-	15	3269	c.3007A>G	c.(3007-3009)Agt>Ggt	p.S1003G		NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	1003					carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						TGCACTGCACTCATGAGATAA	0.413																																					p.S1003G		Atlas-SNP	.											.	GNPTAB	120	.	0			c.A3007G						.						96.0	94.0	95.0					12																	102155033		2203	4300	6503	SO:0001583	missense	79158	exon15			CTGCACTCATGAG	AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"""EF-hand domain containing"""	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.3007A>G	chr12.hg19:g.102155033T>C	ENSP00000299314:p.Ser1003Gly	67.0	0.0		94.0	4.0	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Missense_Mutation	SNP	ENST00000299314.7	hg19	CCDS9088.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.240692	0.58995	.	.	ENSG00000111670	ENST00000299314	D	0.92099	-2.97	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.94341	0.8181	L	0.55017	1.72	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	D	0.92377	0.5910	10	0.18276	T	0.48	-26.3129	16.255	0.82510	0.0:0.0:0.0:1.0	.	1003	Q3T906	GNPTA_HUMAN	G	1003	ENSP00000299314:S1003G	ENSP00000299314:S1003G	S	-	1	0	GNPTAB	100679164	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.240000	0.73641	0.533000	0.62120	AGT	.	.		0.413	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1		
NAA25	80018	hgsc.bcm.edu	37	12	112479858	112479858	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:112479858G>C	ENST00000261745.4	-	20	2673	c.2425C>G	c.(2425-2427)Cta>Gta	p.L809V		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	809						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						AACTGGTCTAGTAAAGACTTA	0.318																																					p.L809V		Atlas-SNP	.											.	NAA25	105	.	0			c.C2425G						.						86.0	80.0	82.0					12																	112479858		2188	4297	6485	SO:0001583	missense	80018	exon20			GGTCTAGTAAAGA	AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"""N(alpha)-acetyltransferase subunits"""	25783	protein-coding gene	gene with protein product		612755	"""chromosome 12 open reading frame 30"""	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.2425C>G	chr12.hg19:g.112479858G>C	ENSP00000261745:p.Leu809Val	17.0	0.0		25.0	6.0	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	hg19	CCDS9159.1	.	.	.	.	.	.	.	.	.	.	G	9.682	1.149581	0.21288	.	.	ENSG00000111300	ENST00000261745;ENST00000550701	T	0.26223	1.75	5.9	2.78	0.32641	.	0.157403	0.44902	D	0.000416	T	0.11707	0.0285	N	0.17082	0.46	0.29966	N	0.818958	B	0.06786	0.001	B	0.08055	0.003	T	0.15378	-1.0439	10	0.25106	T	0.35	-6.2634	2.4052	0.04411	0.2487:0.1231:0.5018:0.1265	.	809	Q14CX7	NAA25_HUMAN	V	809;15	ENSP00000261745:L809V	ENSP00000261745:L809V	L	-	1	2	NAA25	110964241	0.996000	0.38824	1.000000	0.80357	0.844000	0.47949	0.198000	0.17217	0.265000	0.21872	0.655000	0.94253	CTA	.	.		0.318	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953	
HECTD4	283450	hgsc.bcm.edu	37	12	112703054	112703054	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:112703054T>C	ENST00000430131.2	-	15	2393	c.1248A>G	c.(1246-1248)cgA>cgG	p.R416R	HECTD4_ENST00000377560.5_Silent_p.R666R|HECTD4_ENST00000550722.1_Silent_p.R704R|RN7SKP71_ENST00000364558.1_RNA			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	416					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)										TACAGGATTCTCGTACAACAA	0.299																																					p.R704R		Atlas-SNP	.											.	.	.	.	0			c.A2112G						.						100.0	106.0	104.0					12																	112703054		2203	4299	6502	SO:0001819	synonymous_variant	283450	exon16			GGATTCTCGTACA	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.1248A>G	chr12.hg19:g.112703054T>C		74.0	0.0		92.0	4.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	hg19																																																																																				.	.		0.299	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
TBX3	6926	hgsc.bcm.edu	37	12	115112498	115112498	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:115112498A>G	ENST00000257566.3	-	7	1631	c.1242T>C	c.(1240-1242)gcT>gcC	p.A414A	TBX3_ENST00000349155.2_Silent_p.A394A	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	414					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		CGAAAAGGTGAGCCTTGACCG	0.697																																					p.A414A		Atlas-SNP	.											.	TBX3	106	.	0			c.T1242C						.						16.0	18.0	17.0					12																	115112498		2197	4292	6489	SO:0001819	synonymous_variant	6926	exon7			AAGGTGAGCCTTG	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.1242T>C	chr12.hg19:g.115112498A>G		89.0	0.0		67.0	4.0	NM_016569	Q8TB20|Q9UKF8	Silent	SNP	ENST00000257566.3	hg19	CCDS9176.1																																																																																			.	.		0.697	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996	
ORAI1	84876	hgsc.bcm.edu	37	12	122064777	122064777	+	Missense_Mutation	SNP	C	C	G	rs141919534|rs531278468		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:122064777C>G	ENST00000330079.7	+	1	323	c.130C>G	c.(130-132)Cca>Gca	p.P44A		NM_032790.3	NP_116179	Q96D31	CRCM1_HUMAN	ORAI calcium release-activated calcium modulator 1	0	Pro-rich.				blood coagulation (GO:0007596)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|regulation of calcium ion transport (GO:0051924)|store-operated calcium entry (GO:0002115)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|store-operated calcium channel activity (GO:0015279)	p.P43_P44delPP(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)		gggggccccgccaccgccacc	0.751																																					p.P44A		Atlas-SNP	.											.	ORAI1	66	.	1	Deletion - In frame(1)	breast(1)	c.C130G						.						2.0	2.0	2.0					12																	122064777		1171	2472	3643	SO:0001583	missense	84876	exon1			GCCCCGCCACCGC	AK027372		12q24.31	2014-09-17	2007-08-14	2007-08-14	ENSG00000182500	ENSG00000276045		"""ORAI calcium release-activated calcium modulators"""	25896	protein-coding gene	gene with protein product	"""calcium release-activated calcium modulator 1"""	610277	"""transmembrane protein 142A"""	TMEM142A		16582901	Standard	NM_032790		Approved	FLJ14466, CRACM1	uc021rff.1	Q96D31		ENST00000330079.7:c.130C>G	chr12.hg19:g.122064777C>G	ENSP00000328216:p.Pro44Ala	6.0	0.0		13.0	5.0	NM_032790	Q3MHV3|Q6DHX2|Q96BP7|Q96K71	Missense_Mutation	SNP	ENST00000330079.7	hg19	CCDS41851.1	.	.	.	.	.	.	.	.	.	.	C	0.076	-1.193262	0.01607	.	.	ENSG00000182500	ENST00000330079	D	0.87334	-2.24	3.79	0.849	0.18972	.	1.175890	0.06482	N	0.732998	T	0.79246	0.4413	.	.	.	0.36521	D	0.870159	.	.	.	.	.	.	T	0.63932	-0.6525	7	0.11794	T	0.64	-18.2923	7.7875	0.29101	0.0:0.7001:0.0:0.2999	.	.	.	.	A	44	ENSP00000328216:P44A	ENSP00000328216:P44A	P	+	1	0	ORAI1	120549160	.	.	0.663000	0.29738	0.096000	0.18686	.	.	0.049000	0.15920	0.195000	0.17529	CCA	.	.		0.751	ORAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402151.1	NM_032790	
DNAH10	196385	hgsc.bcm.edu	37	12	124323027	124323027	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:124323027C>A	ENST00000409039.3	+	28	4598	c.4573C>A	c.(4573-4575)Ccc>Acc	p.P1525T		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1525	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CTTAAAAGACCCCGTGATCAA	0.552																																					p.P1525T		Atlas-SNP	.											.	DNAH10	888	.	0			c.C4573A						.						41.0	43.0	42.0					12																	124323027		2010	4167	6177	SO:0001583	missense	196385	exon28			AAAGACCCCGTGA	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.4573C>A	chr12.hg19:g.124323027C>A	ENSP00000386770:p.Pro1525Thr	72.0	0.0		50.0	19.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	14.86	2.662236	0.47572	.	.	ENSG00000197653	ENST00000409039	T	0.62498	0.02	5.57	5.57	0.84162	Dynein heavy chain, domain-2 (1);	0.248516	0.33272	U	0.005089	T	0.66674	0.2813	L	0.60067	1.865	0.80722	D	1	P	0.42456	0.78	P	0.45232	0.474	T	0.65117	-0.6246	10	0.37606	T	0.19	.	19.554	0.95333	0.0:1.0:0.0:0.0	.	1525	Q8IVF4	DYH10_HUMAN	T	1525	ENSP00000386770:P1525T	ENSP00000386770:P1525T	P	+	1	0	DNAH10	122888980	1.000000	0.71417	0.997000	0.53966	0.240000	0.25518	7.584000	0.82572	2.632000	0.89209	0.650000	0.86243	CCC	.	.		0.552	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
DNAH10	196385	hgsc.bcm.edu	37	12	124354958	124354958	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:124354958A>G	ENST00000409039.3	+	43	7236	c.7211A>G	c.(7210-7212)aAt>aGt	p.N2404S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2404					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AACAAACGGAATCAATGGGTC	0.398																																					p.N2404S		Atlas-SNP	.											.	DNAH10	888	.	0			c.A7211G						.						98.0	93.0	95.0					12																	124354958		1875	4113	5988	SO:0001583	missense	196385	exon43			AACGGAATCAATG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.7211A>G	chr12.hg19:g.124354958A>G	ENSP00000386770:p.Asn2404Ser	78.0	0.0		65.0	4.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	A	7.640	0.680644	0.14907	.	.	ENSG00000197653	ENST00000409039	T	0.21031	2.03	5.21	1.52	0.23074	.	0.665037	0.13286	N	0.399382	T	0.16981	0.0408	L	0.47716	1.5	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.31308	-0.9948	10	0.20519	T	0.43	.	9.1845	0.37163	0.7913:0.0:0.2087:0.0	.	2404	Q8IVF4	DYH10_HUMAN	S	2404	ENSP00000386770:N2404S	ENSP00000386770:N2404S	N	+	2	0	DNAH10	122920911	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	5.213000	0.65230	0.018000	0.15052	-0.290000	0.09829	AAT	.	.		0.398	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
FBRSL1	57666	hgsc.bcm.edu	37	12	133102379	133102379	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:133102379A>G	ENST00000434748.2	+	3	1569	c.549A>G	c.(547-549)gaA>gaG	p.E183E	FBRSL1_ENST00000261673.6_Silent_p.E110E	NM_001142641.1	NP_001136113.1	Q9HCM7	FBSL_HUMAN	fibrosin-like 1	183							poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(1)|stomach(1)	4						GCGTCCTCGAAGCCACCAGCT	0.682																																					p.E183E		Atlas-SNP	.											.	FBRSL1	47	.	0			c.A549G						.						54.0	61.0	58.0					12																	133102379		692	1591	2283	SO:0001819	synonymous_variant	57666	exon3			CCTCGAAGCCACC		CCDS45010.1	12q24.33	2008-12-09			ENSG00000112787	ENSG00000112787			29308	protein-coding gene	gene with protein product						10997877	Standard	NM_001142641		Approved	KIAA1545	uc001ukf.3	Q9HCM7	OTTHUMG00000167991	ENST00000434748.2:c.549A>G	chr12.hg19:g.133102379A>G		101.0	0.0		74.0	4.0	NM_001142641	Q86XQ1	Silent	SNP	ENST00000434748.2	hg19	CCDS45010.1																																																																																			.	.		0.682	FBRSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397404.2		
SACS	26278	hgsc.bcm.edu	37	13	23907453	23907453	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:23907453A>G	ENST00000382292.3	-	9	10835	c.10562T>C	c.(10561-10563)cTg>cCg	p.L3521P	SACS_ENST00000382298.3_Missense_Mutation_p.L3521P|SACS_ENST00000402364.1_Missense_Mutation_p.L2771P			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3521					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TAAACTTTCCAGTTTTTCAAA	0.328																																					p.L3521P		Atlas-SNP	.											.	SACS	871	.	0			c.T10562C						.						38.0	39.0	38.0					13																	23907453		2202	4293	6495	SO:0001583	missense	26278	exon10			CTTTCCAGTTTTT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.10562T>C	chr13.hg19:g.23907453A>G	ENSP00000371729:p.Leu3521Pro	125.0	0.0		87.0	4.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	A	18.73	3.685799	0.68157	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.93659	-3.07;-3.26;-3.07	6.04	6.04	0.98038	.	0.000000	0.64402	D	0.000002	D	0.94538	0.8241	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95406	0.8494	10	0.87932	D	0	.	16.5763	0.84648	1.0:0.0:0.0:0.0	.	3521	Q9NZJ4	SACS_HUMAN	P	3521;2771;3521	ENSP00000371729:L3521P;ENSP00000385844:L2771P;ENSP00000371735:L3521P	ENSP00000371729:L3521P	L	-	2	0	SACS	22805453	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	9.339000	0.96797	2.317000	0.78254	0.459000	0.35465	CTG	.	.		0.328	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
USP12	219333	hgsc.bcm.edu	37	13	27664255	27664255	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:27664255T>C	ENST00000282344.6	-	5	870	c.614A>G	c.(613-615)gAc>gGc	p.D205G		NM_182488.3	NP_872294.2	O75317	UBP12_HUMAN	ubiquitin specific peptidase 12	205	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)		TTGTTCCACGTCAACAGAAAG	0.269																																					p.D205G	Ovarian(37;808 911 7590 44442 44991)	Atlas-SNP	.											.	USP12	35	.	0			c.A614G						.						83.0	77.0	79.0					13																	27664255		2203	4295	6498	SO:0001583	missense	219333	exon5			TCCACGTCAACAG	AL049221	CCDS31952.1	13q12.13	2010-05-12	2005-08-08	2003-10-08	ENSG00000152484	ENSG00000152484		"""Ubiquitin-specific peptidases"""	20485	protein-coding gene	gene with protein product			"""ubiquitin specific protease 12 like 1"", ""ubiquitin specific protease 12"""	USP12L1		12838346	Standard	NM_182488		Approved		uc001uqy.3	O75317	OTTHUMG00000016626	ENST00000282344.6:c.614A>G	chr13.hg19:g.27664255T>C	ENSP00000282344:p.Asp205Gly	130.0	0.0		118.0	5.0	NM_182488	A8K0X0|Q5VZV3|Q8TC49	Missense_Mutation	SNP	ENST00000282344.6	hg19	CCDS31952.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.451886	0.84209	.	.	ENSG00000152484	ENST00000282344	T	0.06608	3.28	5.17	5.17	0.71159	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.40469	U	0.001091	T	0.29556	0.0737	M	0.89030	3	0.80722	D	1	D	0.59767	0.986	D	0.65573	0.936	T	0.16748	-1.0392	10	0.87932	D	0	-18.9994	15.3074	0.74004	0.0:0.0:0.0:1.0	.	205	O75317	UBP12_HUMAN	G	205	ENSP00000282344:D205G	ENSP00000282344:D205G	D	-	2	0	USP12	26562255	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.076000	0.71267	2.087000	0.62958	0.533000	0.62120	GAC	.	.		0.269	USP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044264.1	NM_182488	
USP12	219333	hgsc.bcm.edu	37	13	27679961	27679961	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:27679961A>G	ENST00000282344.6	-	3	506	c.250T>C	c.(250-252)Tta>Cta	p.L84L		NM_182488.3	NP_872294.2	O75317	UBP12_HUMAN	ubiquitin specific peptidase 12	84	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)		AGATCTGCTAAGCATGTAAGA	0.388																																					p.L84L	Ovarian(37;808 911 7590 44442 44991)	Atlas-SNP	.											.	USP12	35	.	0			c.T250C						.						100.0	100.0	100.0					13																	27679961		2203	4298	6501	SO:0001819	synonymous_variant	219333	exon3			CTGCTAAGCATGT	AL049221	CCDS31952.1	13q12.13	2010-05-12	2005-08-08	2003-10-08	ENSG00000152484	ENSG00000152484		"""Ubiquitin-specific peptidases"""	20485	protein-coding gene	gene with protein product			"""ubiquitin specific protease 12 like 1"", ""ubiquitin specific protease 12"""	USP12L1		12838346	Standard	NM_182488		Approved		uc001uqy.3	O75317	OTTHUMG00000016626	ENST00000282344.6:c.250T>C	chr13.hg19:g.27679961A>G		60.0	0.0		54.0	4.0	NM_182488	A8K0X0|Q5VZV3|Q8TC49	Silent	SNP	ENST00000282344.6	hg19	CCDS31952.1																																																																																			.	.		0.388	USP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044264.1	NM_182488	
PAN3	255967	hgsc.bcm.edu	37	13	28854573	28854573	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:28854573G>C	ENST00000380958.3	+	16	2366	c.2214G>C	c.(2212-2214)agG>agC	p.R738S	PAN3_ENST00000282391.5_Missense_Mutation_p.R426S|PAN3_ENST00000399613.1_Missense_Mutation_p.R538S	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit											endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		ACCAAAACAGGATGCGAAGTG	0.378																																					p.R738S		Atlas-SNP	.											.	PAN3	123	.	0			c.G2214C						.						142.0	125.0	131.0					13																	28854573		2203	4300	6503	SO:0001583	missense	255967	exon16			AAACAGGATGCGA	AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520			29991	protein-coding gene	gene with protein product			"""PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"""			14583602	Standard	NM_175854		Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.2214G>C	chr13.hg19:g.28854573G>C	ENSP00000370345:p.Arg738Ser	75.0	0.0		73.0	48.0	NM_175854		Missense_Mutation	SNP	ENST00000380958.3	hg19	CCDS9329.2	.	.	.	.	.	.	.	.	.	.	G	19.44	3.827725	0.71143	.	.	ENSG00000152520	ENST00000380958;ENST00000399613;ENST00000282391	T;T;T	0.41758	0.99;0.99;0.99	5.74	2.98	0.34508	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.57315	0.2045	M	0.71206	2.165	0.80722	D	1	D;D;D	0.71674	0.998;0.982;0.998	D;P;D	0.70487	0.969;0.873;0.937	T	0.51980	-0.8636	10	0.27785	T	0.31	-12.9652	10.1084	0.42548	0.2872:0.0:0.7128:0.0	.	738;426;684	Q58A45;Q58A45-2;Q58A45-3	PAN3_HUMAN;.;.	S	738;538;426	ENSP00000370345:R738S;ENSP00000382522:R538S;ENSP00000282391:R426S	ENSP00000282391:R426S	R	+	3	2	PAN3	27752573	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.656000	0.24948	0.402000	0.25451	0.561000	0.74099	AGG	.	.		0.378	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854	
TRPC4	7223	hgsc.bcm.edu	37	13	38211176	38211176	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:38211176T>C	ENST00000379705.3	-	11	3655	c.2798A>G	c.(2797-2799)gAg>gGg	p.E933G	TRPC4_ENST00000426868.2_3'UTR|TRPC4_ENST00000338947.5_Missense_Mutation_p.E760G|TRPC4_ENST00000379679.1_Missense_Mutation_p.E760G|TRPC4_ENST00000358477.2_Missense_Mutation_p.E849G|TRPC4_ENST00000379673.2_Missense_Mutation_p.E784G|TRPC4_ENST00000355779.2_Missense_Mutation_p.E792G|TRPC4_ENST00000447043.1_Missense_Mutation_p.E792G|TRPC4_ENST00000379681.3_Missense_Mutation_p.E938G			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	933	Binds to ITPR1, ITPR2 and ITPR3.				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)		CACCACCTTCTCTGACTTGAA	0.453																																					p.E938G		Atlas-SNP	.											.	TRPC4	389	.	0			c.A2813G						.						166.0	138.0	147.0					13																	38211176		2203	4300	6503	SO:0001583	missense	7223	exon11			ACCTTCTCTGACT	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.2798A>G	chr13.hg19:g.38211176T>C	ENSP00000369027:p.Glu933Gly	183.0	0.0		125.0	5.0	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	hg19	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	T	14.92	2.679250	0.47886	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000355779;ENST00000358477;ENST00000379673;ENST00000447043	T;T;T;T;T;T;T;T	0.75050	-0.39;-0.4;-0.21;-0.21;-0.64;-0.56;-0.9;-0.64	5.72	5.72	0.89469	.	0.279855	0.31335	N	0.007826	T	0.74642	0.3743	N	0.19112	0.55	0.80722	D	1	B;B;P;B;B;B	0.51933	0.058;0.042;0.949;0.039;0.223;0.079	B;B;P;B;B;B	0.58721	0.037;0.036;0.844;0.034;0.142;0.025	T	0.78486	-0.2185	10	0.72032	D	0.01	-18.7257	14.8693	0.70444	0.0:0.0:0.0:1.0	.	792;784;938;760;849;933	Q9UBN4-3;Q9UBN4-4;Q9UBN4-5;Q9UBN4-6;Q9UBN4-2;Q9UBN4	.;.;.;.;.;TRPC4_HUMAN	G	933;938;760;760;792;849;784;792	ENSP00000369027:E933G;ENSP00000369003:E938G;ENSP00000342580:E760G;ENSP00000369001:E760G;ENSP00000348025:E792G;ENSP00000351264:E849G;ENSP00000368995:E784G;ENSP00000414316:E792G	ENSP00000342580:E760G	E	-	2	0	TRPC4	37109176	1.000000	0.71417	0.998000	0.56505	0.763000	0.43281	2.632000	0.46511	2.311000	0.77944	0.533000	0.62120	GAG	.	.		0.453	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
ALG11	440138	hgsc.bcm.edu	37	13	52602568	52602568	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:52602568A>G	ENST00000521508.1	+	4	1326	c.1321A>G	c.(1321-1323)Agt>Ggt	p.S441G	ALG11_ENST00000519151.1_3'UTR|UTP14C_ENST00000521776.2_5'UTR|ALG11_ENST00000523764.1_3'UTR	NM_001004127.2	NP_001004127.2	Q2TAA5	ALG11_HUMAN	ALG11, alpha-1,2-mannosyltransferase	441					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GDP-Man:Man3GlcNAc2-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0004377)			endometrium(1)|large_intestine(6)|lung(4)|ovary(2)	13		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.44e-08)		TCTGGCTGAGAGTGAAGAAGA	0.453																																					p.S441G		Atlas-SNP	.											.	ALG11	39	.	0			c.A1321G						.						124.0	111.0	116.0					13																	52602568		2203	4300	6503	SO:0001583	missense	440138	exon4			GCTGAGAGTGAAG	AK025456	CCDS31977.1	13q14.3	2013-02-22	2013-02-22		ENSG00000253710	ENSG00000253710	2.4.1.131	"""Glycosyltransferase group 1 domain containing"""	32456	protein-coding gene	gene with protein product	"""GDP-Man:Man(3)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"""	613666	"""asparagine-linked glycosylation 11 homolog (S. cerevisiae, alpha-1,2-mannosyltransferase)"", ""asparagine-linked glycosylation 11, alpha-1,2-mannosyltransferase homolog (yeast)"""			20080937	Standard	NM_001004127		Approved	KIAA0266		Q2TAA5	OTTHUMG00000016959	ENST00000521508.1:c.1321A>G	chr13.hg19:g.52602568A>G	ENSP00000430236:p.Ser441Gly	115.0	0.0		99.0	4.0	NM_001004127	A5PLP3|B4DKW9|Q5TAN9|Q6DKI6|Q96FI7	Missense_Mutation	SNP	ENST00000521508.1	hg19	CCDS31977.1	.	.	.	.	.	.	.	.	.	.	A	12.45	1.942875	0.34283	.	.	ENSG00000253710	ENST00000521508	T	0.80653	-1.4	5.82	5.82	0.92795	Glycosyl transferase, family 1 (1);	0.344698	0.33110	U	0.005274	T	0.75613	0.3873	L	0.50333	1.59	0.29812	N	0.831557	B	0.06786	0.001	B	0.12156	0.007	T	0.70938	-0.4736	10	0.45353	T	0.12	.	12.0169	0.53319	0.9312:0.0:0.0688:0.0	.	441	Q2TAA5	ALG11_HUMAN	G	441	ENSP00000430236:S441G	ENSP00000430236:S441G	S	+	1	0	ALG11	51500569	0.005000	0.15991	0.935000	0.37517	0.881000	0.50899	1.821000	0.39041	2.225000	0.72522	0.460000	0.39030	AGT	.	.		0.453	ALG11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045050.1	NM_001004127	
NEK3	4752	hgsc.bcm.edu	37	13	52707932	52707932	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:52707932T>C	ENST00000400357.2	-	13	2571	c.1278A>G	c.(1276-1278)aaA>aaG	p.K426K	NEK3_ENST00000339406.3_Silent_p.K443K|NEK3_ENST00000378101.2_Silent_p.K443K|NEK3_ENST00000452082.2_Silent_p.K447K			P51956	NEK3_HUMAN	NIMA-related kinase 3	443					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		ACAGGGGGCCTTTCAAGAACC	0.413																																					p.K443K		Atlas-SNP	.											.	NEK3	41	.	0			c.A1329G						.						39.0	37.0	38.0					13																	52707932		1868	4110	5978	SO:0001819	synonymous_variant	4752	exon15			GGGGCCTTTCAAG	AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"""serine/threonine-protein kinase NEK3"", ""phosphorylase B kinase kinase"", ""glycogen synthase A kinase"", ""hydroxyalkyl-protein kinase"""	604044	"""NIMA (never in mitosis gene a)-related kinase 3"""			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.1278A>G	chr13.hg19:g.52707932T>C		84.0	0.0		60.0	4.0	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Silent	SNP	ENST00000400357.2	hg19	CCDS53871.1																																																																																			.	.		0.413	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3		
PCDH8	5100	hgsc.bcm.edu	37	13	53418699	53418699	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:53418699A>G	ENST00000377942.3	-	3	3412	c.3209T>C	c.(3208-3210)gTg>gCg	p.V1070A	PCDH8_ENST00000338862.4_Missense_Mutation_p.V973A	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	1070					cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		ATGGGATTACACATTTTCATT	0.502																																					p.V1070A	GBM(36;25 841 9273 49207)	Atlas-SNP	.											.	PCDH8	95	.	0			c.T3209C						.						52.0	56.0	55.0					13																	53418699		2203	4300	6503	SO:0001583	missense	5100	exon3			GATTACACATTTT	AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"""Cadherins / Protocadherins : Non-clustered"""	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.3209T>C	chr13.hg19:g.53418699A>G	ENSP00000367177:p.Val1070Ala	123.0	0.0		95.0	4.0	NM_002590	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Missense_Mutation	SNP	ENST00000377942.3	hg19	CCDS9438.1	.	.	.	.	.	.	.	.	.	.	A	12.79	2.043593	0.36085	.	.	ENSG00000136099	ENST00000377942;ENST00000338862;ENST00000418407;ENST00000448969	T;T	0.56444	0.55;0.46	6.07	6.07	0.98685	.	0.000000	0.39834	N	0.001257	T	0.23210	0.0561	N	0.02011	-0.69	0.25048	N	0.991151	B;B	0.09022	0.001;0.002	B;B	0.10450	0.005;0.002	T	0.04255	-1.0965	10	0.87932	D	0	.	2.867	0.05604	0.6247:0.1518:0.0785:0.145	.	973;1070	O95206-2;O95206	.;PCDH8_HUMAN	A	1070;973;596;913	ENSP00000367177:V1070A;ENSP00000341350:V973A	ENSP00000341350:V973A	V	-	2	0	PCDH8	52316700	0.653000	0.27358	1.000000	0.80357	0.988000	0.76386	0.862000	0.27899	2.326000	0.78906	0.533000	0.62120	GTG	.	.		0.502	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590	
DIS3	22894	hgsc.bcm.edu	37	13	73342977	73342977	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:73342977A>G	ENST00000377767.4	-	14	1929	c.1829T>C	c.(1828-1830)cTc>cCc	p.L610P	DIS3_ENST00000545453.1_Missense_Mutation_p.L448P|DIS3_ENST00000377780.4_Missense_Mutation_p.L580P	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	610					CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		CAGTCCACGGAGACTAGTGGT	0.299										Multiple Myeloma(4;0.011)																											p.L610P		Atlas-SNP	.											.	DIS3	103	.	0			c.T1829C						.						84.0	86.0	85.0					13																	73342977		2201	4298	6499	SO:0001583	missense	22894	exon14			CCACGGAGACTAG	AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"""exosome component 11"""	607533	"""KIAA1008"", ""DIS3 mitotic control homolog (S. cerevisiae)"""	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.1829T>C	chr13.hg19:g.73342977A>G	ENSP00000366997:p.Leu610Pro	214.0	0.0		170.0	7.0	NM_014953	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Missense_Mutation	SNP	ENST00000377767.4	hg19	CCDS9447.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.641932	0.87859	.	.	ENSG00000083520	ENST00000377767;ENST00000377780;ENST00000545453	T;T;T	0.63580	-0.05;-0.05;-0.05	5.87	5.87	0.94306	Ribonuclease II/R (2);	0.114481	0.64402	D	0.000016	D	0.87981	0.6315	H	0.98786	4.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.92806	0.6260	10	0.87932	D	0	.	16.2806	0.82678	1.0:0.0:0.0:0.0	.	580;610	Q9Y2L1-2;Q9Y2L1	.;RRP44_HUMAN	P	610;580;448	ENSP00000366997:L610P;ENSP00000367011:L580P;ENSP00000440058:L448P	ENSP00000366997:L610P	L	-	2	0	DIS3	72240978	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.169000	0.94788	2.248000	0.74166	0.533000	0.62120	CTC	.	.		0.299	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953	
GPC5	2262	hgsc.bcm.edu	37	13	92345688	92345688	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:92345688A>G	ENST00000377067.3	+	3	945	c.573A>G	c.(571-573)tcA>tcG	p.S191S		NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	191					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				TGGAATACTCAGAATGCATCC	0.483																																					p.S191S		Atlas-SNP	.											.	GPC5	140	.	0			c.A573G						.						99.0	97.0	98.0					13																	92345688		2203	4300	6503	SO:0001819	synonymous_variant	2262	exon3			ATACTCAGAATGC	AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"""Proteoglycans / Cell Surface : Glypicans"""	4453	protein-coding gene	gene with protein product	"""glypican proteoglycan 5"""	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.573A>G	chr13.hg19:g.92345688A>G		85.0	0.0		74.0	5.0	NM_004466	B2R726|O60436|Q9BX27	Silent	SNP	ENST00000377067.3	hg19	CCDS9468.1																																																																																			.	.		0.483	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466	
TPP2	7174	hgsc.bcm.edu	37	13	103268804	103268804	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:103268804G>T	ENST00000376065.4	+	4	485	c.449G>T	c.(448-450)tGt>tTt	p.C150F	TPP2_ENST00000376052.3_Missense_Mutation_p.C150F	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	150	Peptidase S8.				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)					GCAGAAGCCTGTAGAAAACAG	0.408																																					p.C150F		Atlas-SNP	.											.	TPP2	124	.	0			c.G449T						.						94.0	102.0	100.0					13																	103268804		2203	4300	6503	SO:0001583	missense	7174	exon4			AAGCCTGTAGAAA	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.449G>T	chr13.hg19:g.103268804G>T	ENSP00000365233:p.Cys150Phe	58.0	0.0		73.0	38.0	NM_003291	Q5VZU8	Missense_Mutation	SNP	ENST00000376065.4	hg19	CCDS9502.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.841963	0.51057	.	.	ENSG00000134900	ENST00000376065;ENST00000376052	.	.	.	5.64	5.64	0.86602	Peptidase S8/S53, subtilisin/kexin/sedolisin (2);	0.102040	0.64402	D	0.000001	T	0.48223	0.1488	L	0.29908	0.895	0.49389	D	0.999781	P	0.39601	0.68	B	0.36378	0.223	T	0.40961	-0.9535	9	0.30078	T	0.28	.	20.0769	0.97748	0.0:0.0:1.0:0.0	.	150	P29144	TPP2_HUMAN	F	150	.	ENSP00000365220:C150F	C	+	2	0	TPP2	102066805	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.172000	0.71932	2.820000	0.97059	0.650000	0.86243	TGT	.	.		0.408	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2		
ARHGEF7	8874	hgsc.bcm.edu	37	13	111919988	111919988	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:111919988T>C	ENST00000375741.2	+	10	1357	c.1107T>C	c.(1105-1107)ccT>ccC	p.P369P	ARHGEF7_ENST00000375739.2_Silent_p.P319P|ARHGEF7_ENST00000370623.3_Silent_p.P276P|ARHGEF7_ENST00000478679.1_Silent_p.P113P|ARHGEF7_ENST00000375723.1_Silent_p.P191P|ARHGEF7_ENST00000218789.5_Silent_p.P191P|ARHGEF7_ENST00000426073.2_Silent_p.P191P|ARHGEF7_ENST00000483189.1_3'UTR|ARHGEF7_ENST00000544132.1_Missense_Mutation_p.F72L|ARHGEF7_ENST00000375737.5_Silent_p.P266P|ARHGEF7_ENST00000375736.4_Silent_p.P191P|ARHGEF7_ENST00000317133.5_Silent_p.P348P	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	369	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CCAATCACCCTTCTGCAGTGA	0.517																																					p.P369P		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.T1107C						.						181.0	130.0	147.0					13																	111919988		2203	4300	6503	SO:0001819	synonymous_variant	8874	exon10			TCACCCTTCTGCA	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	15607	protein-coding gene	gene with protein product	"""SH3 domain-containing proline-rich protein"", ""PAK-interacting exchange factor beta"", ""rho"", ""guanine nucleotide exchange factor 7"""	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.1107T>C	chr13.hg19:g.111919988T>C		90.0	0.0		96.0	4.0	NM_001113511	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Silent	SNP	ENST00000375741.2	hg19	CCDS45068.1	.	.	.	.	.	.	.	.	.	.	T	14.09	2.432566	0.43224	.	.	ENSG00000102606	ENST00000544132	.	.	.	4.29	-7.74	0.01241	.	.	.	.	.	T	0.09468	0.0233	.	.	.	0.23309	N	0.997931	.	.	.	.	.	.	T	0.32771	-0.9894	5	0.02654	T	1	.	5.4464	0.16537	0.2787:0.0:0.3891:0.3322	.	.	.	.	L	72	.	ENSP00000445384:F72L	F	+	1	0	ARHGEF7	110717989	0.000000	0.05858	0.952000	0.39060	0.885000	0.51271	-2.928000	0.00690	-1.052000	0.03222	-1.304000	0.01323	TTC	.	.		0.517	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511	
TUBGCP3	10426	hgsc.bcm.edu	37	13	113170854	113170854	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:113170854T>C	ENST00000261965.3	-	17	2172	c.1986A>G	c.(1984-1986)agA>agG	p.R662R	TUBGCP3_ENST00000375669.3_Silent_p.R662R	NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	662					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|single fertilization (GO:0007338)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|polar microtubule (GO:0005827)|spindle (GO:0005819)	gamma-tubulin binding (GO:0043015)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|urinary_tract(1)	25	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					AGTTAAATACTCTTAGGTAGT	0.463																																					p.R662R		Atlas-SNP	.											.	TUBGCP3	74	.	0			c.A1986G						.						119.0	100.0	107.0					13																	113170854		2203	4300	6503	SO:0001819	synonymous_variant	10426	exon17			AAATACTCTTAGG	AF042378	CCDS9525.1, CCDS66584.1, CCDS73599.1	13q34	2008-07-18			ENSG00000126216	ENSG00000126216			18598	protein-coding gene	gene with protein product	"""spindle pole body protein"""					9566967, 9566969	Standard	XM_005268293		Approved	GCP3, Spc98p, SPBC98	uc001vse.1	Q96CW5	OTTHUMG00000017367	ENST00000261965.3:c.1986A>G	chr13.hg19:g.113170854T>C		87.0	0.0		95.0	4.0	NM_006322	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Silent	SNP	ENST00000261965.3	hg19	CCDS9525.1																																																																																			.	.		0.463	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322	
RIPK3	11035	hgsc.bcm.edu	37	14	24807655	24807655	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:24807655T>C	ENST00000216274.5	-	4	808	c.590A>G	c.(589-591)aAg>aGg	p.K197R	RP11-934B9.3_ENST00000555591.1_5'Flank|RIPK3_ENST00000554338.1_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	197	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		TGTGGAGGCCTTCCGGTTTAC	0.587																																					p.K197R	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.A590G						.						129.0	136.0	133.0					14																	24807655		2203	4300	6503	SO:0001583	missense	11035	exon4			GAGGCCTTCCGGT	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.590A>G	chr14.hg19:g.24807655T>C	ENSP00000216274:p.Lys197Arg	47.0	0.0		72.0	4.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Missense_Mutation	SNP	ENST00000216274.5	hg19	CCDS9628.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.652481	0.29336	.	.	ENSG00000129465	ENST00000216274	T	0.66280	-0.2	4.51	-0.947	0.10382	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.573247	0.15817	N	0.243178	T	0.51719	0.1691	N	0.11000	0.08	0.09310	N	1	D	0.57899	0.981	D	0.66602	0.945	T	0.50355	-0.8838	10	0.16420	T	0.52	-17.8474	7.8234	0.29300	0.0:0.4955:0.0:0.5045	.	197	Q9Y572	RIPK3_HUMAN	R	197	ENSP00000216274:K197R	ENSP00000216274:K197R	K	-	2	0	RIPK3	23877495	0.000000	0.05858	0.001000	0.08648	0.206000	0.24218	-0.205000	0.09411	-0.036000	0.13669	0.459000	0.35465	AAG	.	.		0.587	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871	
HECTD1	25831	hgsc.bcm.edu	37	14	31576779	31576779	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:31576779A>G	ENST00000399332.1	-	37	7100	c.6612T>C	c.(6610-6612)tcT>tcC	p.S2204S	HECTD1_ENST00000553700.1_Silent_p.S2204S	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2204	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TTACGTGACGAGATTCATCAT	0.398																																					p.S2204S		Atlas-SNP	.											.	HECTD1	159	.	0			c.T6612C						.						77.0	71.0	73.0					14																	31576779		1874	4116	5990	SO:0001819	synonymous_variant	25831	exon37			GTGACGAGATTCA	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.6612T>C	chr14.hg19:g.31576779A>G		55.0	0.0		54.0	4.0	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	A	5.588	0.293241	0.10567	.	.	ENSG00000092148	ENST00000554882	.	.	.	5.55	3.16	0.36331	.	.	.	.	.	T	0.45438	0.1342	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31971	-0.9924	4	.	.	.	-11.5924	2.1063	0.03692	0.5933:0.134:0.1439:0.1288	.	.	.	.	P	570	.	.	L	-	2	0	HECTD1	30646530	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	0.764000	0.26532	0.381000	0.24851	-1.506000	0.00953	CTC	.	.		0.398	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
NUBPL	80224	hgsc.bcm.edu	37	14	32142559	32142559	+	Splice_Site	SNP	A	A	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:32142559A>C	ENST00000281081.7	+	5	427		c.e5-1		NUBPL_ENST00000536705.1_Splice_Site	NM_001201573.1|NM_001201574.1|NM_025152.2	NP_001188502.1|NP_001188503.1|NP_079428.2	Q8TB37	NUBPL_HUMAN	nucleotide binding protein-like						mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrion morphogenesis (GO:0070584)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			endometrium(1)|lung(2)|prostate(1)|skin(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)		TTTTTTTTCCAGGCAACCTAA	0.244																																					.		Atlas-SNP	.											.	NUBPL	21	.	0			c.383-2A>C						.						33.0	32.0	32.0					14																	32142559		1786	4058	5844	SO:0001630	splice_region_variant	80224	exon5			TTTTCCAGGCAAC	AK022722	CCDS41940.1	14q12	2012-10-12	2005-01-07	2005-01-07	ENSG00000151413	ENSG00000151413		"""Mitochondrial respiratory chain complex assembly factors"""	20278	protein-coding gene	gene with protein product	"""iron-sulfur protein required for NADH dehydrogenase"""	613621	"""chromosome 14 open reading frame 127"""	C14orf127			Standard	NM_025152		Approved	FLJ12660, IND1, huInd1	uc001wrk.4	Q8TB37	OTTHUMG00000170521	ENST00000281081.7:c.383-1A>C	chr14.hg19:g.32142559A>C		51.0	0.0		60.0	4.0	NM_025152	B4DHZ1|Q86TZ4|Q9H9M2	Splice_Site	SNP	ENST00000281081.7	hg19	CCDS41940.1	.	.	.	.	.	.	.	.	.	.	A	14.46	2.543163	0.45280	.	.	ENSG00000151413	ENST00000281081;ENST00000551314;ENST00000536705	.	.	.	5.53	5.53	0.82687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3964	0.60856	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NUBPL	31212310	1.000000	0.71417	0.964000	0.40570	0.465000	0.32709	7.779000	0.85648	2.097000	0.63578	0.455000	0.32223	.	.	.		0.244	NUBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409519.1	NM_025152	Intron
PAX9	5083	hgsc.bcm.edu	37	14	37132384	37132384	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:37132384G>A	ENST00000361487.6	+	2	512	c.287G>A	c.(286-288)gGc>gAc	p.G96D	PAX9_ENST00000554201.1_5'UTR|PAX9_ENST00000402703.2_Missense_Mutation_p.G96D			P55771	PAX9_HUMAN	paired box 9	96	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				cellular response to growth factor stimulus (GO:0071363)|endoderm development (GO:0007492)|face morphogenesis (GO:0060325)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|regulation of odontogenesis (GO:0042481)	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)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(3)	12	Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.218)		Lung(8;1.12e-09)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.00357)|all cancers(34;0.00998)|LUSC - Lung squamous cell carcinoma(13;0.0189)	GBM - Glioblastoma multiforme(112;0.0181)		AGAGACCCCGGCATCTTCGCC	0.647																																					p.G96D		Atlas-SNP	.											.	PAX9	34	.	0			c.G287A						.						64.0	67.0	66.0					14																	37132384		2203	4300	6503	SO:0001583	missense	5083	exon3			ACCCCGGCATCTT	AJ238381	CCDS9662.1	14q13.3	2007-07-12	2007-07-12		ENSG00000198807	ENSG00000198807		"""Paired boxes"""	8623	protein-coding gene	gene with protein product		167416	"""paired box gene 9"""			7981748	Standard	NM_006194		Approved		uc001wty.4	P55771	OTTHUMG00000140251	ENST00000361487.6:c.287G>A	chr14.hg19:g.37132384G>A	ENSP00000355245:p.Gly96Asp	112.0	0.0		184.0	11.0	NM_006194	Q99582|Q9UQR4	Missense_Mutation	SNP	ENST00000361487.6	hg19	CCDS9662.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.961383	0.92791	.	.	ENSG00000198807	ENST00000402703;ENST00000361487	D;D	0.99245	-5.62;-5.62	5.21	5.21	0.72293	Paired box protein, N-terminal (3);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99387	0.9784	M	0.79343	2.45	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99177	1.0866	10	0.87932	D	0	.	18.742	0.91777	0.0:0.0:1.0:0.0	.	96	P55771	PAX9_HUMAN	D	96	ENSP00000384817:G96D;ENSP00000355245:G96D	ENSP00000355245:G96D	G	+	2	0	PAX9	36202135	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.440000	0.82611	0.561000	0.74099	GGC	.	.		0.647	PAX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276733.2		
SYNE2	23224	hgsc.bcm.edu	37	14	64494280	64494280	+	Silent	SNP	A	A	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:64494280A>T	ENST00000344113.4	+	43	6695	c.6483A>T	c.(6481-6483)ctA>ctT	p.L2161L	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Silent_p.L2161L|SYNE2_ENST00000358025.3_Silent_p.L2161L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2161					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)		TCATAGAACTAAAGAAGAAAC	0.343																																					p.L2161L		Atlas-SNP	.											.	SYNE2	577	.	0			c.A6483T						.						90.0	84.0	86.0					14																	64494280		1809	4077	5886	SO:0001819	synonymous_variant	23224	exon43			AGAACTAAAGAAG	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.6483A>T	chr14.hg19:g.64494280A>T		125.0	0.0		145.0	6.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.343	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
GSTZ1	2954	hgsc.bcm.edu	37	14	77797449	77797449	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:77797449T>C	ENST00000556627.1	+	8	612	c.481T>C	c.(481-483)Tcc>Ccc	p.S161P	GSTZ1_ENST00000557053.1_Missense_Mutation_p.S91P|GSTZ1_ENST00000393734.1_Missense_Mutation_p.S133P|GSTZ1_ENST00000216465.5_Missense_Mutation_p.S188P|GSTZ1_ENST00000557639.1_Missense_Mutation_p.S133P|GSTZ1_ENST00000361389.4_Missense_Mutation_p.S133P|GSTZ1_ENST00000553586.1_Missense_Mutation_p.S189P|GSTZ1_ENST00000554279.1_Missense_Mutation_p.S174P|GSTZ1_ENST00000349555.3_Missense_Mutation_p.S146P			O43708	MAAI_HUMAN	glutathione S-transferase zeta 1	188	GST C-terminal.				cellular nitrogen compound metabolic process (GO:0034641)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|L-phenylalanine catabolic process (GO:0006559)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|maleylacetoacetate isomerase activity (GO:0016034)|protein homodimerization activity (GO:0042803)			lung(2)|prostate(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	Glutathione(DB00143)	TACCATCAGCTCCATCAACAA	0.562																																					p.S188P		Atlas-SNP	.											.	GSTZ1	35	.	0			c.T562C						.						104.0	91.0	95.0					14																	77797449		2203	4300	6503	SO:0001583	missense	2954	exon9			ATCAGCTCCATCA	U86529	CCDS9858.1, CCDS9859.1, CCDS9860.1	14q24.3	2012-06-22	2012-06-22		ENSG00000100577	ENSG00000100577	5.2.1.2, 2.5.1.18	"""Glutathione S-transferases / Soluble"""	4643	protein-coding gene	gene with protein product	"""maleylacetoacetate isomerase"""	603758	"""glutathione transferase zeta 1"""			9396740, 9417084	Standard	NM_001513		Approved	GSTZ1-1, MAAI, MAI	uc001xtj.3	O43708	OTTHUMG00000171551	ENST00000556627.1:c.481T>C	chr14.hg19:g.77797449T>C	ENSP00000450487:p.Ser161Pro	114.0	0.0		136.0	6.0	NM_145870	A6NED0|A6NNB8|A8MWD7|B2RCK3|O15308|O75430|Q6IB17|Q7Z610|Q9BV63	Missense_Mutation	SNP	ENST00000556627.1	hg19		.	.	.	.	.	.	.	.	.	.	T	8.678	0.904372	0.17760	.	.	ENSG00000100577	ENST00000216465;ENST00000361389;ENST00000554279;ENST00000557639;ENST00000349555;ENST00000556627;ENST00000557053;ENST00000393734;ENST00000553586	T;T;T;T;T;T;T;T;T	0.02158	4.42;4.42;4.42;4.42;4.42;4.42;4.42;4.42;4.42	5.48	4.59	0.56863	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.291066	0.40818	N	0.001010	T	0.03564	0.0102	L	0.42245	1.32	0.09310	N	0.999997	B;B	0.22909	0.072;0.077	B;B	0.32864	0.154;0.087	T	0.30504	-0.9976	10	0.87932	D	0	-2.6754	10.7717	0.46327	0.0:0.908:0.0:0.092	.	146;188	A6NED0;O43708	.;MAAI_HUMAN	P	188;133;174;133;146;161;91;133;189	ENSP00000216465:S188P;ENSP00000354959:S133P;ENSP00000452498:S174P;ENSP00000451927:S133P;ENSP00000314404:S146P;ENSP00000450487:S161P;ENSP00000451150:S91P;ENSP00000377335:S133P;ENSP00000451976:S189P	ENSP00000216465:S188P	S	+	1	0	GSTZ1	76867202	0.682000	0.27624	0.714000	0.30535	0.004000	0.04260	1.159000	0.31749	1.282000	0.44496	-0.468000	0.05107	TCC	.	.		0.562	GSTZ1-012	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414090.1	NM_145870	
EML5	161436	hgsc.bcm.edu	37	14	89206909	89206909	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:89206909C>T	ENST00000380664.5	-	5	532	c.533G>A	c.(532-534)aGt>aAt	p.S178N	EML5_ENST00000352093.5_Missense_Mutation_p.S178N|EML5_ENST00000554922.1_Missense_Mutation_p.S178N			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	178						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						TCCACATAAACTCCAGAACTA	0.363																																					p.S178N		Atlas-SNP	.											.	EML5	141	.	0			c.G533A						.						108.0	102.0	103.0					14																	89206909		1830	4082	5912	SO:0001583	missense	161436	exon5			CATAAACTCCAGA	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.533G>A	chr14.hg19:g.89206909C>T	ENSP00000370039:p.Ser178Asn	116.0	0.0		121.0	6.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.105746	0.37145	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.01258	5.09;5.09;5.09	5.05	4.15	0.48705	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.051418	0.85682	D	0.000000	T	0.01523	0.0049	L	0.41236	1.265	0.45867	D	0.998724	B	0.16396	0.017	B	0.16722	0.016	T	0.55879	-0.8071	10	0.13853	T	0.58	-12.4644	10.3523	0.43943	0.0:0.8476:0.0:0.1524	.	178	Q05BV3	EMAL5_HUMAN	N	178	ENSP00000451998:S178N;ENSP00000298315:S178N;ENSP00000370039:S178N	ENSP00000298315:S178N	S	-	2	0	EML5	88276662	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.172000	0.31908	2.331000	0.79229	0.467000	0.42956	AGT	.	.		0.363	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
TDP1	55775	hgsc.bcm.edu	37	14	90446955	90446955	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:90446955A>G	ENST00000335725.4	+	8	1113	c.863A>G	c.(862-864)gAc>gGc	p.D288G	TDP1_ENST00000357382.3_Missense_Mutation_p.D49G|TDP1_ENST00000555880.1_Missense_Mutation_p.D288G|TDP1_ENST00000393454.2_Missense_Mutation_p.D288G|TDP1_ENST00000393452.3_Missense_Mutation_p.D288G	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	288					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		ATCCATGCTGACTGGCACCAG	0.453								Repair of DNA-protein crosslinks																													p.D288G		Atlas-SNP	.											.	TDP1	47	.	0			c.A863G						.						99.0	90.0	93.0					14																	90446955		2203	4300	6503	SO:0001583	missense	55775	exon8			ATGCTGACTGGCA	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.863A>G	chr14.hg19:g.90446955A>G	ENSP00000337353:p.Asp288Gly	70.0	0.0		88.0	4.0	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	hg19	CCDS9888.1	.	.	.	.	.	.	.	.	.	.	A	17.72	3.458048	0.63401	.	.	ENSG00000042088	ENST00000393452;ENST00000393454;ENST00000553617;ENST00000335725;ENST00000357382;ENST00000555880	T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.85548	0.5722	H	0.95187	3.635	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	0.89724	0.3921	10	0.87932	D	0	-11.2052	16.2903	0.82747	1.0:0.0:0.0:0.0	.	288;288;49;288	G3V2F4;E7EPD8;Q86TV8;Q9NUW8	.;.;.;TYDP1_HUMAN	G	288;288;189;288;49;288	ENSP00000377098:D288G;ENSP00000377099:D288G;ENSP00000450708:D189G;ENSP00000337353:D288G;ENSP00000349952:D49G;ENSP00000450628:D288G	ENSP00000337353:D288G	D	+	2	0	TDP1	89516708	1.000000	0.71417	0.998000	0.56505	0.410000	0.31052	8.727000	0.91480	2.326000	0.78906	0.533000	0.62120	GAC	.	.		0.453	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319	
RIN3	79890	hgsc.bcm.edu	37	14	93022212	93022212	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:93022212A>G	ENST00000216487.7	+	2	320	c.161A>G	c.(160-162)gAg>gGg	p.E54G		NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	54					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				AGCATCCTGGAGAAGCTCATC	0.622																																					p.E54G		Atlas-SNP	.											.	RIN3	81	.	0			c.A161G						.						59.0	57.0	58.0					14																	93022212		2203	4300	6503	SO:0001583	missense	79890	exon2			TCCTGGAGAAGCT	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.161A>G	chr14.hg19:g.93022212A>G	ENSP00000216487:p.Glu54Gly	81.0	0.0		88.0	4.0	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	hg19	CCDS32144.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.295482	0.60086	.	.	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.10288	2.89	5.51	5.51	0.81932	.	0.064919	0.64402	D	0.000019	T	0.33614	0.0869	M	0.78456	2.415	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.08391	-1.0724	10	0.87932	D	0	-29.4605	13.1403	0.59430	1.0:0.0:0.0:0.0	.	54	Q8TB24	RIN3_HUMAN	G	54	ENSP00000216487:E54G	ENSP00000216487:E54G	E	+	2	0	RIN3	92091965	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	6.035000	0.70940	2.079000	0.62486	0.533000	0.62120	GAG	.	.		0.622	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
KLC1	3831	hgsc.bcm.edu	37	14	104143836	104143836	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:104143836A>G	ENST00000348520.6	+	12	1783	c.1464A>G	c.(1462-1464)gaA>gaG	p.E488E	KLC1_ENST00000557575.1_Silent_p.E488E|KLC1_ENST00000347839.6_Silent_p.E488E|KLC1_ENST00000554280.1_Silent_p.E488E|KLC1_ENST00000334553.6_Silent_p.E488E|KLC1_ENST00000389744.4_Silent_p.E488E|KLC1_ENST00000246489.7_Silent_p.E488E|KLC1_ENST00000452929.2_Silent_p.E488E|KLC1_ENST00000445352.4_Silent_p.E486E|KLC1_ENST00000553286.1_Silent_p.E488E|RP11-73M18.2_ENST00000472726.2_Silent_p.E660E|KLC1_ENST00000557450.1_Silent_p.E488E|KLC1_ENST00000555836.1_Silent_p.E488E|KLC1_ENST00000380038.3_Silent_p.E488E	NM_182923.3	NP_891553.2	Q07866	KLC1_HUMAN	kinesin light chain 1	488					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|stress granule disassembly (GO:0035617)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|growth cone (GO:0030426)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)|motor activity (GO:0003774)		KLC1/ALK(2)	NS(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	12		Melanoma(154;0.155)|all_epithelial(191;0.19)				CGTTAGAAGAAGCTGCTATGA	0.403																																					p.E488E		Atlas-SNP	.											.	KLC1	54	.	0			c.A1464G						.						144.0	138.0	140.0					14																	104143836		2203	4300	6503	SO:0001819	synonymous_variant	3831	exon12			AGAAGAAGCTGCT	AF267530	CCDS32165.1, CCDS41996.1, CCDS45168.1	14q32.3	2013-01-10	2007-03-09	2007-03-09	ENSG00000126214	ENSG00000126214		"""Tetratricopeptide (TTC) repeat domain containing"""	6387	protein-coding gene	gene with protein product		600025	"""kinesin 2 60/70kDa"", ""kinesin 2"""	KNS2		8274221, 11106729	Standard	NM_005552		Approved	KNS2A, KLC, hKLC1S, hKLC1N, hKLC1P, hKLC1G, hKLC1R, hKLC1J, hKLC1B	uc010tyf.2	Q07866	OTTHUMG00000169227	ENST00000348520.6:c.1464A>G	chr14.hg19:g.104143836A>G		43.0	0.0		82.0	4.0	NM_182923	A6NF62|F8VTM4|Q7RTM2|Q7RTM3|Q7RTM5|Q7RTP9|Q7RTQ3|Q7RTQ5|Q7RTQ6|Q86SF5|Q86TF5|Q86V74|Q86V75|Q86V76|Q86V77|Q86V78|Q86V79|Q96H62	Silent	SNP	ENST00000348520.6	hg19	CCDS41996.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.267|9.267	1.044712|1.044712	0.19748|0.19748	.|.	.|.	ENSG00000126214|ENSG00000126214	ENST00000553325;ENST00000553436;ENST00000555856|ENST00000537046	.|.	.|.	.|.	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|.	.|.	.|.	.|.	T|T	0.62865|0.62865	0.2463|0.2463	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.62020|0.62020	-0.6942|-0.6942	4|4	.|.	.|.	.|.	-16.5552|-16.5552	10.6404|10.6404	0.45590|0.45590	0.9191:0.0:0.0809:0.0|0.9191:0.0:0.0809:0.0	.|.	.|.	.|.	.|.	R|G	68;64;62|94	.|.	.|.	K|S	+|+	2|1	0|0	KLC1|KLC1	103213589|103213589	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.887000|0.887000	0.51463|0.51463	1.691000|1.691000	0.37721|0.37721	2.234000|2.234000	0.73211|0.73211	0.533000|0.533000	0.62120|0.62120	AAG|AGC	.	.		0.403	KLC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402947.2	NM_005552	
AKT1	207	hgsc.bcm.edu	37	14	105246536	105246536	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:105246536A>G	ENST00000554581.1	-	2	1544	c.64T>C	c.(64-66)Tgg>Cgg	p.W22R	AKT1_ENST00000544168.1_5'Flank|AKT1_ENST00000349310.3_Missense_Mutation_p.W22R|AKT1_ENST00000402615.2_Missense_Mutation_p.W22R|AKT1_ENST00000554848.1_Missense_Mutation_p.W22R|AKT1_ENST00000407796.2_Missense_Mutation_p.W22R|AKT1_ENST00000555528.1_Missense_Mutation_p.W22R			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	22	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation-induced cell death of T cells (GO:0006924)|aging (GO:0007568)|anagen (GO:0042640)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell projection organization (GO:0030030)|cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to mechanical stimulus (GO:0071260)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|execution phase of apoptosis (GO:0097194)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycogen cell differentiation involved in embryonic placenta development (GO:0060709)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|labyrinthine layer blood vessel development (GO:0060716)|mammary gland epithelial cell differentiation (GO:0060644)|maternal placenta development (GO:0001893)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of proteolysis (GO:0045861)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|osteoblast differentiation (GO:0001649)|peptidyl-serine phosphorylation (GO:0018105)|peripheral nervous system myelin maintenance (GO:0032287)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell growth (GO:0030307)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle checkpoint (GO:1901976)|regulation of cell migration (GO:0030334)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of neuron projection development (GO:0010975)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of translation (GO:0006417)|response to fluid shear stress (GO:0034405)|response to food (GO:0032094)|response to heat (GO:0009408)|response to UV-A (GO:0070141)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|striated muscle cell differentiation (GO:0051146)|T cell costimulation (GO:0031295)|translation (GO:0006412)	cell-cell junction (GO:0005911)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|nitric-oxide synthase regulator activity (GO:0030235)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(3)|breast(97)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(7)|lung(10)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|thyroid(10)|urinary_tract(15)	176		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)	CGTGGCCGCCAGGTCTTGATG	0.607		1	Mis		"""breast, colorectal, ovarian, NSCLC"""																																p.W22R		Atlas-SNP	.		Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1	379	.	0			c.T64C						.						138.0	100.0	113.0					14																	105246536		2203	4300	6503	SO:0001583	missense	207	exon3			GCCGCCAGGTCTT	M63167	CCDS9994.1	14q32.33	2014-09-17			ENSG00000142208	ENSG00000142208	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	391	protein-coding gene	gene with protein product		164730					Standard	XM_005267401		Approved	RAC, PKB, PRKBA, AKT	uc001ypn.3	P31749	OTTHUMG00000170795	ENST00000554581.1:c.64T>C	chr14.hg19:g.105246536A>G	ENSP00000451828:p.Trp22Arg	127.0	0.0		153.0	7.0	NM_005163	B2RAM5|B7Z5R1|Q9BWB6	Missense_Mutation	SNP	ENST00000554581.1	hg19	CCDS9994.1	.	.	.	.	.	.	.	.	.	.	A	17.17	3.321365	0.60634	.	.	ENSG00000142208	ENST00000554581;ENST00000407796;ENST00000349310;ENST00000402615;ENST00000555528;ENST00000554848;ENST00000555926	T;T;T;T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26;-1.26;-1.26;-1.26	4.61	4.61	0.57282	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.90300	0.6966	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92522	0.6026	10	0.87932	D	0	.	12.969	0.58501	1.0:0.0:0.0:0.0	.	22	P31749	AKT1_HUMAN	R	22	ENSP00000451828:W22R;ENSP00000384293:W22R;ENSP00000270202:W22R;ENSP00000385326:W22R;ENSP00000450688:W22R;ENSP00000451166:W22R;ENSP00000451824:W22R	ENSP00000270202:W22R	W	-	1	0	AKT1	104317581	0.997000	0.39634	0.989000	0.46669	0.289000	0.27227	4.804000	0.62554	1.939000	0.56221	0.379000	0.24179	TGG	.	.		0.607	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163	
BRF1	2972	hgsc.bcm.edu	37	14	105676904	105676904	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:105676904T>C	ENST00000546474.1	-	18	16977	c.2018A>G	c.(2017-2019)gAg>gGg	p.E673G	BRF1_ENST00000379932.4_Intron|BRF1_ENST00000327359.3_Missense_Mutation_p.E558G|BRF1_ENST00000551787.1_Intron|BRF1_ENST00000379937.2_Missense_Mutation_p.E646G|BRF1_ENST00000392557.4_Missense_Mutation_p.E469G|BRF1_ENST00000440513.3_Missense_Mutation_p.E580G|BRF1_ENST00000446501.2_Missense_Mutation_p.E435G|BRF1_ENST00000547530.1_Missense_Mutation_p.E199G	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	673					gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		GCCGTCGTCCTCATCGCCATC	0.642																																					p.E673G		Atlas-SNP	.											.	BRF1	102	.	0			c.A2018G						.						86.0	68.0	74.0					14																	105676904		2202	4300	6502	SO:0001583	missense	2972	exon18			TCGTCCTCATCGC	U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024		"""General transcription factors"""	11551	protein-coding gene	gene with protein product		604902	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2"", ""BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)"""	TAF3B2, TAF3C, GTF3B		7624363, 8943358	Standard	NM_145685		Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.2018A>G	chr14.hg19:g.105676904T>C	ENSP00000448323:p.Glu673Gly	87.0	0.0		108.0	5.0	NM_001519	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	Missense_Mutation	SNP	ENST00000546474.1	hg19	CCDS10001.1	.	.	.	.	.	.	.	.	.	.	T	9.470	1.095404	0.20471	.	.	ENSG00000185024	ENST00000392557;ENST00000379937;ENST00000546474;ENST00000547530;ENST00000446501;ENST00000327359;ENST00000440513	.	.	.	3.22	3.22	0.36961	.	0.302288	0.29152	N	0.012999	T	0.45256	0.1333	L	0.50333	1.59	0.58432	D	0.999998	B;B;B	0.34290	0.241;0.447;0.319	B;B;B	0.26969	0.075;0.075;0.034	T	0.52503	-0.8567	9	0.72032	D	0.01	.	8.2057	0.31454	0.0:0.0:0.0:1.0	.	580;646;673	F5H5Z7;Q92994-5;Q92994	.;.;TF3B_HUMAN	G	469;646;673;199;435;558;580	.	ENSP00000329029:E558G	E	-	2	0	BRF1	104747949	0.198000	0.23374	0.023000	0.16930	0.005000	0.04900	2.325000	0.43840	1.709000	0.51313	0.460000	0.39030	GAG	.	.		0.642	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074548.4	NM_001519	
RYR3	6263	hgsc.bcm.edu	37	15	34018695	34018695	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:34018695T>C	ENST00000389232.4	+	46	7091	c.7021T>C	c.(7021-7023)Tcc>Ccc	p.S2341P	RYR3_ENST00000415757.3_Missense_Mutation_p.S2341P	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2341	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GAAACTGCCCTCCCTCAACAA	0.622																																					p.S2341P		Atlas-SNP	.											.	RYR3	760	.	0			c.T7021C						.						40.0	42.0	41.0					15																	34018695		2020	4161	6181	SO:0001583	missense	6263	exon46			CTGCCCTCCCTCA		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.7021T>C	chr15.hg19:g.34018695T>C	ENSP00000373884:p.Ser2341Pro	79.0	0.0		108.0	6.0	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.775373	0.31411	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.96554	-4.05;-4.05	4.96	2.42	0.29668	.	0.487971	0.21537	N	0.072951	D	0.90417	0.7000	L	0.27053	0.805	0.09310	N	1	B;B	0.34329	0.256;0.449	B;B	0.33254	0.039;0.16	D	0.83890	0.0284	10	0.45353	T	0.12	.	5.3348	0.15951	0.4277:0.0:0.1303:0.442	.	2341;2341	Q15413-2;Q15413	.;RYR3_HUMAN	P	2341	ENSP00000373884:S2341P;ENSP00000399610:S2341P	ENSP00000354735:S2341P	S	+	1	0	RYR3	31805987	0.861000	0.29849	0.943000	0.38184	0.931000	0.56810	1.927000	0.40094	0.991000	0.38814	0.445000	0.29226	TCC	.	.		0.622	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
KATNBL1	79768	hgsc.bcm.edu	37	15	34455865	34455865	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:34455865T>C	ENST00000256544.3	-	2	155	c.13A>G	c.(13-15)Acc>Gcc	p.T5A		NM_024713.2	NP_078989.1	Q9H079	KTBL1_HUMAN	katanin p80 subunit B-like 1	5						nucleolus (GO:0005730)											ACATTGTGGGTTTCTGATGCC	0.279																																					p.T5A		Atlas-SNP	.											.	.	.	.	0			c.A13G						.						56.0	58.0	57.0					15																	34455865		2201	4289	6490	SO:0001583	missense	79768	exon2			TGTGGGTTTCTGA	AL136908	CCDS10034.1	15q13.2	2012-09-27	2012-09-27	2012-09-27	ENSG00000134152	ENSG00000134152			26199	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 29"""	C15orf29		11230166	Standard	NM_024713		Approved	FLJ22557	uc001zhp.3	Q9H079	OTTHUMG00000129368	ENST00000256544.3:c.13A>G	chr15.hg19:g.34455865T>C	ENSP00000256544:p.Thr5Ala	61.0	0.0		82.0	4.0	NM_024713	A8KAF6|Q2TAC0|Q9H670	Missense_Mutation	SNP	ENST00000256544.3	hg19	CCDS10034.1	.	.	.	.	.	.	.	.	.	.	T	11.16	1.555506	0.27739	.	.	ENSG00000134152	ENST00000256544	.	.	.	4.49	2.17	0.27698	.	0.419216	0.26567	N	0.023648	T	0.13157	0.0319	N	0.08118	0	0.26407	N	0.976323	B	0.02656	0.0	B	0.01281	0.0	T	0.28138	-1.0053	9	0.06625	T	0.88	.	5.0984	0.14747	0.0:0.4575:0.0:0.5425	.	5	Q9H079	CO029_HUMAN	A	5	.	ENSP00000256544:T5A	T	-	1	0	C15orf29	32243157	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.365000	0.44196	0.849000	0.35215	0.455000	0.32223	ACC	.	.		0.279	KATNBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251520.1	NM_024713	
FSIP1	161835	hgsc.bcm.edu	37	15	40031895	40031895	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:40031895T>C	ENST00000350221.3	-	7	960	c.751A>G	c.(751-753)Aac>Gac	p.N251D	FSIP1_ENST00000559692.1_5'UTR	NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	251										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		AAATCCTGGTTGTGTTTACCC	0.338																																					p.N251D		Atlas-SNP	.											.	FSIP1	53	.	0			c.A751G						.						102.0	98.0	99.0					15																	40031895		2202	4296	6498	SO:0001583	missense	161835	exon7			CCTGGTTGTGTTT	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.751A>G	chr15.hg19:g.40031895T>C	ENSP00000280236:p.Asn251Asp	119.0	0.0		118.0	5.0	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	hg19	CCDS10050.1	.	.	.	.	.	.	.	.	.	.	T	16.73	3.204411	0.58234	.	.	ENSG00000150667	ENST00000350221	T	0.23147	1.92	5.77	4.66	0.58398	.	0.308416	0.31020	N	0.008407	T	0.19406	0.0466	L	0.29908	0.895	0.20703	N	0.999862	P	0.46142	0.873	B	0.44044	0.439	T	0.09840	-1.0656	9	.	.	.	-8.0796	7.7222	0.28740	0.0:0.0911:0.0:0.9089	.	251	Q8NA03	FSIP1_HUMAN	D	251	ENSP00000280236:N251D	.	N	-	1	0	FSIP1	37819187	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.499000	0.45372	2.199000	0.70637	0.533000	0.62120	AAC	.	.		0.338	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
CASC5	57082	hgsc.bcm.edu	37	15	40914323	40914323	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:40914323G>A	ENST00000346991.5	+	11	2329	c.1939G>A	c.(1939-1941)Gaa>Aaa	p.E647K	CASC5_ENST00000399668.2_Missense_Mutation_p.E621K|CASC5_ENST00000527044.1_3'UTR			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	647	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		AAGTCGTAATGAACCATTTCA	0.398																																					p.E647K		Atlas-SNP	.											.	CASC5	269	.	0			c.G1939A						.						69.0	66.0	67.0					15																	40914323		1885	4110	5995	SO:0001583	missense	57082	exon11			CGTAATGAACCAT	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.1939G>A	chr15.hg19:g.40914323G>A	ENSP00000335463:p.Glu647Lys	95.0	0.0		97.0	4.0	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	hg19	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	G	3.393	-0.123936	0.06795	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.16597	2.33;2.33	3.92	1.67	0.24075	.	1.360810	0.05590	N	0.574557	T	0.15739	0.0379	L	0.44542	1.39	0.09310	N	1	B;B;B	0.10296	0.002;0.002;0.003	B;B;B	0.12156	0.007;0.007;0.003	T	0.36114	-0.9761	10	0.25751	T	0.34	.	7.0409	0.25019	0.4947:0.0:0.5053:0.0	.	621;647;621	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	K	647;621;621	ENSP00000335463:E647K;ENSP00000382576:E621K	ENSP00000260369:E621K	E	+	1	0	CASC5	38701615	0.003000	0.15002	0.002000	0.10522	0.018000	0.09664	0.856000	0.27818	0.123000	0.18342	0.557000	0.71058	GAA	.	.		0.398	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
RPAP1	26015	hgsc.bcm.edu	37	15	41826958	41826958	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:41826958A>G	ENST00000304330.4	-	6	833	c.717T>C	c.(715-717)gcT>gcC	p.A239A	RPAP1_ENST00000568413.1_5'Flank|RPAP1_ENST00000561603.1_Silent_p.A239A	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	239						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		TCTCCTCAGGAGCCATGGCCT	0.562																																					p.A239A		Atlas-SNP	.											.	RPAP1	111	.	0			c.T717C						.						112.0	89.0	97.0					15																	41826958		2203	4300	6503	SO:0001819	synonymous_variant	26015	exon6			CTCAGGAGCCATG	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.717T>C	chr15.hg19:g.41826958A>G		98.0	0.0		122.0	6.0	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Silent	SNP	ENST00000304330.4	hg19	CCDS10079.1																																																																																			.	.		0.562	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
CCNDBP1	23582	hgsc.bcm.edu	37	15	43483239	43483239	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:43483239A>G	ENST00000300213.4	+	7	820	c.578A>G	c.(577-579)cAg>cGg	p.Q193R	CCNDBP1_ENST00000356633.5_Splice_Site_p.Q32R|EPB42_ENST00000563128.1_Intron	NM_012142.4	NP_036274.3	O95273	CCDB1_HUMAN	cyclin D-type binding-protein 1	193	Interaction with TCF3.|Required for interaction with CCND1.				cell cycle (GO:0007049)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	13		all_cancers(109;3.31e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.42e-07)		GAAATGGAGCAGGTGAGGGGA	0.413																																					p.Q193R		Atlas-SNP	.											.	CCNDBP1	22	.	0			c.A578G						.						108.0	104.0	106.0					15																	43483239		2203	4299	6502	SO:0001630	splice_region_variant	23582	exon7			TGGAGCAGGTGAG	AF082569	CCDS10092.1	15q14-q15	2008-07-18			ENSG00000166946	ENSG00000166946			1587	protein-coding gene	gene with protein product	"""D-type cyclin-interacting protein 1"", ""MAID protein"", ""HHM Protein"", ""grap2 cyclin interacting protein"""	607089				10801854	Standard	NM_012142		Approved	DIP1, GCIP	uc001zqv.3	O95273	OTTHUMG00000130703	ENST00000300213.4:c.579+1A>G	chr15.hg19:g.43483239A>G		104.0	0.0		93.0	7.0	NM_012142	A8K3Q0|A8K3U2|Q6ZQN9|Q7Z519|Q8NBS7|Q8NBY2|Q9NS19|Q9NYH3|Q9UHX9	Missense_Mutation	SNP	ENST00000300213.4	hg19	CCDS10092.1	.	.	.	.	.	.	.	.	.	.	A	7.678	0.688454	0.14973	.	.	ENSG00000166946	ENST00000300213;ENST00000356633;ENST00000444658	T;T	0.47869	0.83;0.83	5.11	-4.54	0.03452	.	0.683858	0.14983	N	0.287154	T	0.30916	0.0780	L	0.31664	0.95	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.003;0.005;0.004	T	0.02789	-1.1110	10	0.36615	T	0.2	-12.4265	12.3289	0.55028	0.7871:0.0:0.2129:0.0	.	193;193;65	O95273-2;O95273;O95273-4	.;CCDB1_HUMAN;.	R	193;32;65	ENSP00000300213:Q193R;ENSP00000349047:Q32R	ENSP00000300213:Q193R	Q	+	2	0	CCNDBP1	41270531	0.978000	0.34361	0.880000	0.34516	0.180000	0.23129	0.129000	0.15830	-0.801000	0.04427	-1.179000	0.01719	CAG	.	.		0.413	CCNDBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253203.1	NM_012142	Missense_Mutation
SPATA5L1	79029	hgsc.bcm.edu	37	15	45707941	45707941	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:45707941A>G	ENST00000305560.6	+	5	1900	c.1801A>G	c.(1801-1803)Aca>Gca	p.T601A	SPATA5L1_ENST00000559860.1_Missense_Mutation_p.T601A	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	601						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		TGGACTTAAGACAATAGAGAG	0.403																																					p.T601A		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.A1801G						.						56.0	54.0	55.0					15																	45707941		2198	4298	6496	SO:0001583	missense	79029	exon5			CTTAAGACAATAG	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"""ATPases / AAA-type"""	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.1801A>G	chr15.hg19:g.45707941A>G	ENSP00000305494:p.Thr601Ala	64.0	0.0		79.0	4.0	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Missense_Mutation	SNP	ENST00000305560.6	hg19	CCDS10123.1	.	.	.	.	.	.	.	.	.	.	A	13.06	2.124180	0.37533	.	.	ENSG00000171763	ENST00000305560	D	0.94046	-3.34	5.54	4.39	0.52855	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.183872	0.47093	D	0.000255	D	0.86822	0.6025	N	0.25485	0.75	0.27516	N	0.951533	B	0.27791	0.189	B	0.27380	0.079	T	0.79259	-0.1877	10	0.51188	T	0.08	-19.2834	7.1502	0.25606	0.7725:0.1496:0.0779:0.0	.	601	Q9BVQ7	SPA5L_HUMAN	A	601	ENSP00000305494:T601A	ENSP00000305494:T601A	T	+	1	0	SPATA5L1	43495233	0.993000	0.37304	0.996000	0.52242	0.997000	0.91878	1.565000	0.36386	0.999000	0.39023	0.533000	0.62120	ACA	.	.		0.403	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063	
HDC	3067	hgsc.bcm.edu	37	15	50534669	50534669	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:50534669T>C	ENST00000267845.3	-	12	2179	c.1777A>G	c.(1777-1779)Agt>Ggt	p.S593G	RN7SL494P_ENST00000461517.2_RNA|HDC_ENST00000543581.1_Missense_Mutation_p.S560G	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		TTCTGAGCACTCACTGGCACA	0.527																																					p.S593G	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											.	HDC	86	.	0			c.A1777G						.						155.0	170.0	165.0					15																	50534669		2196	4295	6491	SO:0001583	missense	3067	exon12			GAGCACTCACTGG		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1777A>G	chr15.hg19:g.50534669T>C	ENSP00000267845:p.Ser593Gly	101.0	0.0		104.0	6.0	NM_002112		Missense_Mutation	SNP	ENST00000267845.3	hg19	CCDS10134.1	.	.	.	.	.	.	.	.	.	.	T	8.433	0.849030	0.17034	.	.	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.09255	3.08;3.0	5.48	-1.75	0.08031	.	0.332817	0.26086	N	0.026433	T	0.04227	0.0117	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27971	-1.0058	10	0.49607	T	0.09	-1.7839	0.9748	0.01423	0.1419:0.2124:0.2895:0.3562	.	560;593	B7ZM01;P19113	.;DCHS_HUMAN	G	593;560	ENSP00000267845:S593G;ENSP00000440252:S560G	ENSP00000267845:S593G	S	-	1	0	HDC	48321961	0.000000	0.05858	0.034000	0.17996	0.592000	0.36648	0.348000	0.20031	0.022000	0.15160	0.460000	0.39030	AGT	.	.		0.527	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1		
AP4E1	23431	hgsc.bcm.edu	37	15	51285814	51285814	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:51285814A>G	ENST00000261842.5	+	17	2444	c.2338A>G	c.(2338-2340)Atc>Gtc	p.I780V	AP4E1_ENST00000560508.1_Missense_Mutation_p.I705V	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	780					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		AGAAAGTACAATCAACCTGGT	0.373																																					p.I780V		Atlas-SNP	.											.	AP4E1	78	.	0			c.A2338G						.						114.0	111.0	112.0					15																	51285814		2196	4294	6490	SO:0001583	missense	23431	exon17			AGTACAATCAACC	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2338A>G	chr15.hg19:g.51285814A>G	ENSP00000261842:p.Ile780Val	75.0	0.0		84.0	4.0	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	hg19	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	A	0.006	-2.102690	0.00356	.	.	ENSG00000081014	ENST00000261842	T	0.14266	2.52	5.37	-8.36	0.00980	.	0.468479	0.23003	N	0.053058	T	0.03695	0.0105	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23048	-1.0199	10	0.02654	T	1	-0.0055	18.3925	0.90487	0.258:0.0:0.742:0.0	.	780	Q9UPM8	AP4E1_HUMAN	V	780	ENSP00000261842:I780V	ENSP00000261842:I780V	I	+	1	0	AP4E1	49073106	0.002000	0.14202	0.011000	0.14972	0.077000	0.17291	-0.267000	0.08619	-1.562000	0.01682	-1.389000	0.01157	ATC	.	.		0.373	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1		
MNS1	55329	hgsc.bcm.edu	37	15	56723587	56723587	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:56723587A>G	ENST00000260453.3	-	9	1543	c.1379T>C	c.(1378-1380)cTa>cCa	p.L460P	MNS1_ENST00000566386.1_5'UTR|TEX9_ENST00000352903.2_Intron|TEX9_ENST00000537232.1_Intron	NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	460					cilium organization (GO:0044782)|left/right axis specification (GO:0070986)|meiotic nuclear division (GO:0007126)	axoneme (GO:0005930)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)|sperm flagellum (GO:0036126)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	20				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		GAGATAGCCTAGTAAGTTTGT	0.363																																					p.L460P		Atlas-SNP	.											.	MNS1	39	.	0			c.T1379C						.						120.0	114.0	116.0					15																	56723587		2192	4292	6484	SO:0001583	missense	55329	exon9			TAGCCTAGTAAGT	AK002084	CCDS10158.1	15q21.3	2013-01-16			ENSG00000138587	ENSG00000138587			29636	protein-coding gene	gene with protein product	"""spermatogenesis associated 40"""	610766				7625268, 8032679	Standard	NM_018365		Approved	FLJ11222, SPATA40	uc002adr.2	Q8NEH6	OTTHUMG00000132034	ENST00000260453.3:c.1379T>C	chr15.hg19:g.56723587A>G	ENSP00000260453:p.Leu460Pro	162.0	0.0		204.0	9.0	NM_018365	Q8IYT6|Q9NUP4	Missense_Mutation	SNP	ENST00000260453.3	hg19	CCDS10158.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.199532	0.79015	.	.	ENSG00000138587	ENST00000260453	T	0.15372	2.43	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.47154	0.1430	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.50320	-0.8842	10	0.72032	D	0.01	-8.5883	15.9872	0.80168	1.0:0.0:0.0:0.0	.	460	Q8NEH6	MNS1_HUMAN	P	460	ENSP00000260453:L460P	ENSP00000260453:L460P	L	-	2	0	MNS1	54510879	1.000000	0.71417	0.923000	0.36655	0.979000	0.70002	7.991000	0.88244	2.367000	0.80283	0.528000	0.53228	CTA	.	.		0.363	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365	
VPS13C	54832	hgsc.bcm.edu	37	15	62283910	62283910	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:62283910T>C	ENST00000261517.5	-	17	1518	c.1445A>G	c.(1444-1446)gAg>gGg	p.E482G	VPS13C_ENST00000249837.3_Missense_Mutation_p.E439G|VPS13C_ENST00000395898.3_Missense_Mutation_p.E439G|VPS13C_ENST00000395896.4_Missense_Mutation_p.E482G	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TTTCTTAGACTCTTTCTTACC	0.368																																					p.E482G		Atlas-SNP	.											.	VPS13C	506	.	0			c.A1445G						.						165.0	173.0	170.0					15																	62283910		2203	4300	6503	SO:0001583	missense	54832	exon17			TTAGACTCTTTCT	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.1445A>G	chr15.hg19:g.62283910T>C	ENSP00000261517:p.Glu482Gly	143.0	0.0		147.0	6.0	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	T	13.99	2.402608	0.42613	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.47177	0.85;0.85;1.02	5.78	5.78	0.91487	.	0.178046	0.48767	D	0.000180	T	0.44286	0.1286	L	0.43923	1.385	0.46564	D	0.999105	B;B;B;B	0.18166	0.011;0.026;0.011;0.015	B;B;B;B	0.22880	0.025;0.042;0.004;0.017	T	0.29150	-1.0021	10	0.46703	T	0.11	.	16.1103	0.81259	0.0:0.0:0.0:1.0	.	439;482;439;482	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	G	439;482;482;482	ENSP00000249837:E439G;ENSP00000261517:E482G;ENSP00000379233:E482G	ENSP00000249837:E439G	E	-	2	0	VPS13C	60071202	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.206000	0.58473	2.207000	0.71202	0.482000	0.46254	GAG	.	.		0.368	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
IGDCC4	57722	hgsc.bcm.edu	37	15	65676554	65676554	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:65676554C>A	ENST00000352385.2	-	20	3755	c.3546G>T	c.(3544-3546)agG>agT	p.R1182S	IGDCC4_ENST00000558048.1_5'UTR	NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	1182						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						CTCCCAACTCCCTGTCCAGCC	0.657																																					p.R1182S		Atlas-SNP	.											.	IGDCC4	95	.	0			c.G3546T						.						23.0	27.0	25.0					15																	65676554		2201	4299	6500	SO:0001583	missense	57722	exon20			CAACTCCCTGTCC		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.3546G>T	chr15.hg19:g.65676554C>A	ENSP00000319623:p.Arg1182Ser	143.0	0.0		178.0	62.0	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	hg19	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	C	7.389	0.630391	0.14322	.	.	ENSG00000103742	ENST00000352385;ENST00000356152	T	0.60672	0.17	5.02	1.62	0.23740	.	0.845108	0.10220	N	0.700982	T	0.42899	0.1223	L	0.29908	0.895	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.31696	-0.9934	10	0.40728	T	0.16	-3.6858	7.4997	0.27511	0.0:0.6794:0.0:0.3206	.	1182	Q8TDY8	IGDC4_HUMAN	S	1182;911	ENSP00000319623:R1182S	ENSP00000319623:R1182S	R	-	3	2	IGDCC4	63463607	0.012000	0.17670	0.637000	0.29366	0.105000	0.19272	0.430000	0.21428	0.545000	0.28902	0.555000	0.69702	AGG	.	.		0.657	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	
LRRC49	54839	hgsc.bcm.edu	37	15	71188254	71188254	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:71188254A>G	ENST00000260382.5	+	3	432	c.172A>G	c.(172-174)Aga>Gga	p.R58G	LRRC49_ENST00000544974.2_Missense_Mutation_p.R48G|LRRC49_ENST00000436542.2_3'UTR|LRRC49_ENST00000443425.2_5'UTR|LRRC49_ENST00000560691.1_5'UTR|LRRC49_ENST00000560369.1_Missense_Mutation_p.R63G	NM_001199017.1|NM_017691.3	NP_001185946.1|NP_060161.2	Q8IUZ0	LRC49_HUMAN	leucine rich repeat containing 49	58						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(3)|skin(3)	34						TGACCTTGAAAGAAACTACTC	0.308																																					p.R63G		Atlas-SNP	.											.	LRRC49	73	.	0			c.A187G						.						78.0	76.0	77.0					15																	71188254		2199	4297	6496	SO:0001583	missense	54839	exon3			CTTGAAAGAAACT		CCDS32282.1, CCDS55971.1, CCDS58376.1, CCDS61694.1	15q23	2005-08-09				ENSG00000137821			25965	protein-coding gene	gene with protein product						12477932	Standard	NM_001199017		Approved	FLJ20156	uc010ukf.2	Q8IUZ0		ENST00000260382.5:c.172A>G	chr15.hg19:g.71188254A>G	ENSP00000260382:p.Arg58Gly	59.0	0.0		90.0	4.0	NM_001199017	B3KVX1|B7Z366|F5H1J4|G5E9T5|H0YLN4|Q9NXM6	Missense_Mutation	SNP	ENST00000260382.5	hg19	CCDS32282.1	.	.	.	.	.	.	.	.	.	.	A	16.48	3.136024	0.56936	.	.	ENSG00000137821	ENST00000544974;ENST00000260382	T;T	0.36157	1.27;1.28	5.37	5.37	0.77165	.	0.077557	0.52532	D	0.000065	T	0.25082	0.0609	N	0.14661	0.345	0.80722	D	1	B;B;B	0.22211	0.039;0.039;0.066	B;B;B	0.24394	0.016;0.016;0.053	T	0.06881	-1.0802	10	0.59425	D	0.04	-19.6097	13.6216	0.62140	1.0:0.0:0.0:0.0	.	63;58;48	B7Z366;Q8IUZ0;F5H1J4	.;LRC49_HUMAN;.	G	48;58	ENSP00000439600:R48G;ENSP00000260382:R58G	ENSP00000260382:R58G	R	+	1	2	LRRC49	68975308	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.831000	0.69330	2.155000	0.67459	0.460000	0.39030	AGA	.	.		0.308	LRRC49-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417209.3	NM_017691	
ANKRD34C	390616	hgsc.bcm.edu	37	15	79586088	79586088	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:79586088A>G	ENST00000558647.2	+	1	462	c.462A>G	c.(460-462)acA>acG	p.T154T	ANKRD34C_ENST00000421388.2_Silent_p.T154T			P0C6C1	AN34C_HUMAN	ankyrin repeat domain 34C	154										endometrium(3)|kidney(1)|skin(1)	5						TTATAACAACAGATAAATCGT	0.443																																					p.T154T		Atlas-SNP	.											.	ANKRD34C	29	.	0			c.A462G						.						57.0	49.0	52.0					15																	79586088		685	1584	2269	SO:0001819	synonymous_variant	390616	exon2			AACAACAGATAAA		CCDS53965.1	15q25.1	2013-01-10			ENSG00000235711	ENSG00000235711		"""Ankyrin repeat domain containing"""	33888	protein-coding gene	gene with protein product							Standard	NM_001146341		Approved		uc002bet.3	P0C6C1		ENST00000558647.2:c.462A>G	chr15.hg19:g.79586088A>G		110.0	0.0		124.0	5.0	NM_001146341	H3BNM1	Silent	SNP	ENST00000558647.2	hg19	CCDS53965.1																																																																																			.	.		0.443	ANKRD34C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416713.2	NM_001146341	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84539614	84539614	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:84539614T>C	ENST00000286744.5	+	9	1087	c.863T>C	c.(862-864)gTc>gCc	p.V288A	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.V288A	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	288						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			AGCCCCGGCGTCTTTCTCGTA	0.378																																					p.V288A		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.T863C						.						61.0	67.0	65.0					15																	84539614		2203	4300	6503	SO:0001583	missense	57188	exon9			CCGGCGTCTTTCT	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.863T>C	chr15.hg19:g.84539614T>C	ENSP00000286744:p.Val288Ala	40.0	0.0		31.0	6.0	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	hg19	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	T	5.437	0.265673	0.10294	.	.	ENSG00000156218	ENST00000286744	T	0.62498	0.02	4.69	2.32	0.28847	.	1.314130	0.05205	N	0.505614	T	0.49115	0.1538	L	0.28458	0.855	0.09310	N	1	B;B	0.24483	0.032;0.104	B;B	0.28991	0.097;0.058	T	0.31223	-0.9951	10	0.09590	T	0.72	.	7.0714	0.25181	0.0:0.2726:0.0:0.7274	.	288;288	P82987-2;P82987	.;ATL3_HUMAN	A	288	ENSP00000286744:V288A	ENSP00000286744:V288A	V	+	2	0	ADAMTSL3	82330618	0.712000	0.27916	0.007000	0.13788	0.039000	0.13416	0.777000	0.26718	0.171000	0.19730	0.379000	0.24179	GTC	.	.		0.378	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
ALPK3	57538	hgsc.bcm.edu	37	15	85400767	85400767	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:85400767A>G	ENST00000258888.5	+	6	3571	c.3404A>G	c.(3403-3405)gAg>gGg	p.E1135G		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1135					heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			ACCAGCAGTGAGGGGGCCTGC	0.627																																					p.E1135G		Atlas-SNP	.											.	ALPK3	289	.	0			c.A3404G						.						36.0	42.0	40.0					15																	85400767		2201	4299	6500	SO:0001583	missense	57538	exon6			GCAGTGAGGGGGC	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.3404A>G	chr15.hg19:g.85400767A>G	ENSP00000258888:p.Glu1135Gly	96.0	0.0		97.0	4.0	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	hg19	CCDS10333.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.418055	0.25552	.	.	ENSG00000136383	ENST00000258888	T	0.61742	0.08	5.17	2.21	0.28008	.	1.559240	0.03447	N	0.210078	T	0.49321	0.1550	L	0.32530	0.975	0.27262	N	0.958594	B	0.27351	0.176	B	0.30251	0.113	T	0.44298	-0.9337	10	0.54805	T	0.06	-27.3278	6.3279	0.21255	0.7036:0.0:0.2964:0.0	.	1135	Q96L96	ALPK3_HUMAN	G	1135	ENSP00000258888:E1135G	ENSP00000258888:E1135G	E	+	2	0	ALPK3	83201771	0.090000	0.21635	0.977000	0.42913	0.199000	0.23934	0.625000	0.24477	0.687000	0.31509	0.460000	0.39030	GAG	.	.		0.627	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
AKAP13	11214	hgsc.bcm.edu	37	15	86207943	86207943	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:86207943A>G	ENST00000394518.2	+	13	5044	c.4949A>G	c.(4948-4950)gAt>gGt	p.D1650G	AKAP13_ENST00000560579.1_3'UTR|AKAP13_ENST00000361243.2_Missense_Mutation_p.D1654G|RP11-815J21.4_ENST00000558980.1_RNA	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1650					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						TCAGAAGAGGATCTGGAGTCA	0.403																																					p.D1654G	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.A4961G						.						101.0	92.0	95.0					15																	86207943		2202	4299	6501	SO:0001583	missense	11214	exon13			AAGAGGATCTGGA	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.4949A>G	chr15.hg19:g.86207943A>G	ENSP00000378026:p.Asp1650Gly	81.0	0.0		94.0	4.0	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.629807	0.46944	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000452008	T;T	0.13420	2.62;2.59	5.64	5.64	0.86602	.	.	.	.	.	T	0.27866	0.0686	L	0.60455	1.87	0.80722	D	1	D;P;D	0.55385	0.971;0.952;0.971	P;P;P	0.55749	0.783;0.612;0.783	T	0.00756	-1.1579	9	0.66056	D	0.02	.	14.1079	0.65104	1.0:0.0:0.0:0.0	.	1632;1650;1654	Q12802-4;Q12802;Q12802-2	.;AKP13_HUMAN;.	G	1654;1650;1653;1631;272	ENSP00000354718:D1654G;ENSP00000378026:D1650G	ENSP00000354718:D1654G	D	+	2	0	AKAP13	84008947	1.000000	0.71417	0.964000	0.40570	0.144000	0.21451	5.933000	0.70130	2.275000	0.75901	0.528000	0.53228	GAT	.	.		0.403	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
CHD2	1106	hgsc.bcm.edu	37	15	93547897	93547897	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:93547897T>C	ENST00000394196.4	+	34	5397	c.4329T>C	c.(4327-4329)ggT>ggC	p.G1443G	CHD2_ENST00000557381.1_Silent_p.G1443G	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1443					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)			GATCTCAGGGTCCTGTCCATA	0.433																																					p.G1443G		Atlas-SNP	.											.	CHD2	280	.	0			c.T4329C						.						173.0	156.0	162.0					15																	93547897		2197	4298	6495	SO:0001819	synonymous_variant	1106	exon34			TCAGGGTCCTGTC	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.4329T>C	chr15.hg19:g.93547897T>C		100.0	0.0		104.0	5.0	NM_001271	C6G482|Q96IP5	Silent	SNP	ENST00000394196.4	hg19	CCDS10374.2																																																																																			.	.		0.433	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
IGF1R	3480	hgsc.bcm.edu	37	15	99434602	99434602	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:99434602G>A	ENST00000268035.6	+	3	1300	c.689G>A	c.(688-690)tGc>tAc	p.C230Y	RP11-654A16.1_ENST00000558736.1_RNA|IGF1R_ENST00000560432.1_3'UTR|IGF1R_ENST00000558762.1_Missense_Mutation_p.C230Y	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	230					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""""""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	AACAATGAGTGCTGCCACCCC	0.652																																					p.C230Y		Atlas-SNP	.											.	IGF1R	147	.	0			c.G689A						.						50.0	41.0	44.0					15																	99434602		2197	4297	6494	SO:0001583	missense	3480	exon3			ATGAGTGCTGCCA	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"""CD molecules"", ""Fibronectin type III domain containing"""	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.689G>A	chr15.hg19:g.99434602G>A	ENSP00000268035:p.Cys230Tyr	50.0	0.0		93.0	4.0	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.544444	0.86022	.	.	ENSG00000140443	ENST00000268035	D	0.89485	-2.52	5.12	5.12	0.69794	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	0.000000	0.64402	D	0.000004	D	0.95981	0.8691	M	0.92833	3.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.96814	0.9599	10	0.87932	D	0	.	18.9213	0.92526	0.0:0.0:1.0:0.0	.	230;230	C9J5X1;P08069	.;IGF1R_HUMAN	Y	230	ENSP00000268035:C230Y	ENSP00000268035:C230Y	C	+	2	0	IGF1R	97252125	1.000000	0.71417	1.000000	0.80357	0.673000	0.39480	9.768000	0.98965	2.549000	0.85964	0.561000	0.74099	TGC	.	.		0.652	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
GNPTG	84572	hgsc.bcm.edu	37	16	1400082	1400082	+	5'Flank	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:1400082T>C	ENST00000204679.4	+	0	0				TSR3_ENST00000007390.2_Missense_Mutation_p.E227G	NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit						carbohydrate phosphorylation (GO:0046835)|N-glycan processing to lysosome (GO:0016256)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7		Hepatocellular(780;0.0893)				CTGGGGGCTCTCCTTGGCATT	0.662																																					p.E227G		Atlas-SNP	.											.	.	.	.	0			c.A680G						.						27.0	30.0	29.0					16																	1400082		2194	4298	6492	SO:0001631	upstream_gene_variant	115939	exon4			GGGCTCTCCTTGG	BC014592	CCDS10436.1	16p13.3	2009-04-17		2004-10-01	ENSG00000090581	ENSG00000090581			23026	protein-coding gene	gene with protein product	"""GlcNAc-phosphotransferase gamma-subunit"""	607838	"""N-acetylglucosamine-1-phosphotransferase, gamma subunit"", ""chromosome 16 open reading frame 27"""	GNPTAG, C16orf27		10712439	Standard	NM_032520		Approved	CAB56184, c316G12.3	uc002clm.3	Q9UJJ9	OTTHUMG00000047835		chr16.hg19:g.1400082T>C	Exception_encountered	70.0	0.0		129.0	6.0	NM_001001410	B2R556|Q6XYD7|Q96L13	Missense_Mutation	SNP	ENST00000204679.4	hg19	CCDS10436.1	.	.	.	.	.	.	.	.	.	.	T	10.86	1.469735	0.26423	.	.	ENSG00000007520	ENST00000007390	.	.	.	5.22	5.22	0.72569	.	0.665917	0.14028	N	0.346356	T	0.41604	0.1166	M	0.72894	2.215	0.09310	N	0.999991	P	0.41313	0.745	B	0.33454	0.164	T	0.46133	-0.9213	9	0.56958	D	0.05	-7.1259	13.0485	0.58942	0.0:0.0:0.0:1.0	.	227	Q9UJK0	TSR3_HUMAN	G	227	.	ENSP00000007390:E227G	E	-	2	0	C16orf42	1340083	0.031000	0.19500	0.089000	0.20774	0.143000	0.21401	2.197000	0.42696	1.969000	0.57287	0.459000	0.35465	GAG	.	.		0.662	GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	NM_032520	
UNKL	64718	hgsc.bcm.edu	37	16	1449385	1449385	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:1449385A>G	ENST00000389221.4	-	5	723	c.724T>C	c.(724-726)Ttc>Ctc	p.F242L	UNKL_ENST00000503648.1_5'Flank|UNKL_ENST00000301712.5_Missense_Mutation_p.F242L|UNKL_ENST00000397462.1_Missense_Mutation_p.F345L|UNKL_ENST00000508903.2_Missense_Mutation_p.F242L	NM_001193388.1	NP_001180317	Q9H9P5	UNKL_HUMAN	unkempt family zinc finger-like	242					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Hepatocellular(780;0.0893)				CTGTACTGGAACCGCCGGGGG	0.697																																					p.F242L		Atlas-SNP	.											.	UNKL	46	.	0			c.T724C						.						24.0	23.0	23.0					16																	1449385		2193	4299	6492	SO:0001583	missense	64718	exon5			ACTGGAACCGCCG	BC011924	CCDS32359.1, CCDS53980.1, CCDS61787.1	16p13.3	2014-03-10	2013-10-17		ENSG00000059145	ENSG00000059145		"""Zinc fingers, CCCH-type domain containing"""	14184	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 28"", ""unkempt homolog (Drosophila)-like"""	C16orf28		20148946	Standard	NM_001193389		Approved	ZC3HDC5L, ZC3H5L, FLJ23360	uc031qup.1	Q9H9P5	OTTHUMG00000128553	ENST00000389221.4:c.724T>C	chr16.hg19:g.1449385A>G	ENSP00000373873:p.Phe242Leu	75.0	0.0		91.0	4.0	NM_001193388	B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8	Missense_Mutation	SNP	ENST00000389221.4	hg19	CCDS53981.1	.	.	.	.	.	.	.	.	.	.	A	19.49	3.838298	0.71373	.	.	ENSG00000059145	ENST00000389221;ENST00000508903;ENST00000397462;ENST00000301712	T	0.64991	-0.13	4.22	4.22	0.49857	.	0.000000	0.85682	D	0.000000	T	0.78091	0.4229	M	0.83953	2.67	0.58432	D	0.999993	D	0.61697	0.99	D	0.72982	0.979	T	0.79553	-0.1756	10	0.46703	T	0.11	.	11.5623	0.50785	1.0:0.0:0.0:0.0	.	242	Q9H9P5-5	.	L	242;242;345;242	ENSP00000373873:F242L	ENSP00000301712:F242L	F	-	1	0	UNKL	1389386	1.000000	0.71417	0.943000	0.38184	0.508000	0.34012	1.849000	0.39318	1.684000	0.51022	0.459000	0.35465	TTC	.	.		0.697	UNKL-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001037125	
CRAMP1L	57585	hgsc.bcm.edu	37	16	1719148	1719148	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:1719148T>C	ENST00000397412.3	+	19	3580	c.3481T>C	c.(3481-3483)Tcg>Ccg	p.S1161P	LA16c-431H6.6_ENST00000454337.1_3'UTR|CRAMP1L_ENST00000293925.5_Missense_Mutation_p.S1161P|CRAMP1L_ENST00000436138.3_Missense_Mutation_p.S1158P|CRAMP1L_ENST00000262317.4_Missense_Mutation_p.S536P			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	1161	Ser-rich.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						CACCGACTCCTCGCTCAGCAG	0.632																																					p.S1161P		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.T3481C						.						37.0	44.0	41.0					16																	1719148		1993	4153	6146	SO:0001583	missense	57585	exon18			GACTCCTCGCTCA	AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"""Crm (Cramped Drosophila)-like"""				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.3481T>C	chr16.hg19:g.1719148T>C	ENSP00000380559:p.Ser1161Pro	90.0	0.0		79.0	4.0	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Missense_Mutation	SNP	ENST00000397412.3	hg19	CCDS10440.2	.	.	.	.	.	.	.	.	.	.	T	14.61	2.585914	0.46110	.	.	ENSG00000007545	ENST00000397412;ENST00000293925;ENST00000436138;ENST00000262317	.	.	.	5.73	5.73	0.89815	.	0.065225	0.64402	D	0.000006	T	0.66752	0.2821	L	0.34521	1.04	0.42796	D	0.993916	D	0.76494	0.999	D	0.69479	0.964	T	0.70766	-0.4783	9	0.87932	D	0	-17.7105	16.0225	0.80509	0.0:0.0:0.0:1.0	.	1161	Q96RY5	CRML_HUMAN	P	1161;1161;1158;536	.	ENSP00000262317:S536P	S	+	1	0	CRAMP1L	1659149	1.000000	0.71417	0.680000	0.29994	0.902000	0.53008	6.060000	0.71141	2.198000	0.70561	0.533000	0.62120	TCG	.	.		0.632	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4		
ZNF598	90850	hgsc.bcm.edu	37	16	2048327	2048327	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:2048327A>G	ENST00000563630.1	-	12	2698	c.2456T>C	c.(2455-2457)cTc>cCc	p.L819P	ZNF598_ENST00000431526.1_Missense_Mutation_p.L874P|AC005606.15_ENST00000567515.1_lincRNA|ZNF598_ENST00000562103.1_Missense_Mutation_p.L819P			Q86UK7	ZN598_HUMAN	zinc finger protein 598	874							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						GCCATGCGCGAGCACCTGCTG	0.667																																					p.L874P		Atlas-SNP	.											.	ZNF598	55	.	0			c.T2621C						.						62.0	73.0	69.0					16																	2048327		2096	4207	6303	SO:0001583	missense	90850	exon14			TGCGCGAGCACCT	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.2456T>C	chr16.hg19:g.2048327A>G	ENSP00000455882:p.Leu819Pro	96.0	0.0		75.0	4.0	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	hg19		.	.	.	.	.	.	.	.	.	.	.	15.30	2.793668	0.50102	.	.	ENSG00000167962	ENST00000431526	T	0.29142	1.58	4.42	4.42	0.53409	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.58538	0.2129	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.66256	-0.5969	10	0.87932	D	0	-22.7937	13.0182	0.58771	1.0:0.0:0.0:0.0	.	874;866	Q86UK7;Q86UK7-2	ZN598_HUMAN;.	P	874	ENSP00000411409:L874P	ENSP00000411409:L874P	L	-	2	0	ZNF598	1988328	1.000000	0.71417	0.865000	0.33974	0.379000	0.30106	8.455000	0.90355	1.858000	0.53909	0.460000	0.39030	CTC	.	.		0.667	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	
CCDC64B	146439	hgsc.bcm.edu	37	16	3085376	3085376	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:3085376C>A	ENST00000572449.1	-	2	184	c.122G>T	c.(121-123)gGc>gTc	p.G41V	CCDC64B_ENST00000573514.1_5'Flank|CCDC64B_ENST00000389347.4_Missense_Mutation_p.G41V|RP11-473M20.5_ENST00000382225.3_RNA			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	41										breast(1)|endometrium(2)|large_intestine(1)	4						AGGCCCTGGGCCCCCTCCCAG	0.677																																					p.G41V		Atlas-SNP	.											.	CCDC64B	19	.	0			c.G122T						.						10.0	13.0	12.0					16																	3085376		1877	4093	5970	SO:0001583	missense	146439	exon1			CCTGGGCCCCCTC	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.122G>T	chr16.hg19:g.3085376C>A	ENSP00000459043:p.Gly41Val	97.0	0.0		134.0	7.0	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	hg19	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	c	14.32	2.500813	0.44455	.	.	ENSG00000162069	ENST00000389347	T	0.28255	1.62	4.35	4.35	0.52113	.	0.401453	0.20157	U	0.098038	T	0.43166	0.1235	L	0.46157	1.445	0.58432	D	0.999996	D	0.89917	1.0	D	0.79784	0.993	T	0.10154	-1.0642	10	0.29301	T	0.29	-32.6859	8.9083	0.35537	0.0:0.8944:0.0:0.1056	.	41	A1A5D9	BICR2_HUMAN	V	41	ENSP00000373998:G41V	ENSP00000373998:G41V	G	-	2	0	CCDC64B	3025377	0.989000	0.36119	1.000000	0.80357	0.946000	0.59487	0.942000	0.29017	2.361000	0.80049	0.457000	0.33378	GGC	.	.		0.677	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1		
GLIS2	84662	hgsc.bcm.edu	37	16	4385330	4385330	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:4385330T>C	ENST00000262366.3	+	7	1532	c.711T>C	c.(709-711)tgT>tgC	p.C237C	GLIS2_ENST00000433375.1_Silent_p.C237C|PAM16_ENST00000577031.1_Intron|RP11-295D4.1_ENST00000574705.1_RNA			Q9BZE0	GLIS2_HUMAN	GLIS family zinc finger 2	237					cell differentiation (GO:0030154)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|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)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(4)|endometrium(1)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	11						CACACCGCTGTCCGACCTGCA	0.642																																					p.C237C		Atlas-SNP	.											.	GLIS2	29	.	0			c.T711C						.						88.0	88.0	88.0					16																	4385330		2196	4300	6496	SO:0001819	synonymous_variant	84662	exon5			CCGCTGTCCGACC	AF325914	CCDS10511.1	16p13.3	2013-01-08			ENSG00000126603	ENSG00000126603		"""Zinc fingers, C2H2-type"""	29450	protein-coding gene	gene with protein product	"""nephrocystin-7"""	608539				11741991, 14500813, 17618285	Standard	NM_032575		Approved	NPHP7	uc002cwc.1	Q9BZE0	OTTHUMG00000129467	ENST00000262366.3:c.711T>C	chr16.hg19:g.4385330T>C		153.0	0.0		162.0	7.0	NM_032575	B3KX84	Silent	SNP	ENST00000262366.3	hg19	CCDS10511.1																																																																																			.	.		0.642	GLIS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251630.1	NM_032575	
VASN	114990	hgsc.bcm.edu	37	16	4432163	4432163	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:4432163G>A	ENST00000304735.3	+	2	1440	c.1285G>A	c.(1285-1287)Gcg>Acg	p.A429T	CORO7_ENST00000539968.1_Intron|CORO7_ENST00000423908.2_Intron|CORO7-PAM16_ENST00000572467.1_Intron|CORO7_ENST00000574025.1_Intron|CORO7_ENST00000251166.4_Intron|CORO7_ENST00000537233.2_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	429	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cellular response to hypoxia (GO:0071456)|cellular response to redox state (GO:0071461)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	transforming growth factor beta binding (GO:0050431)			breast(1)|lung(3)|prostate(1)|skin(1)	6						GCACCACCTGGCGTGCTTGTG	0.692																																					p.A429T		Atlas-SNP	.											.	VASN	21	.	0			c.G1285A						.						17.0	16.0	16.0					16																	4432163		2168	4272	6440	SO:0001583	missense	114990	exon2			CACCTGGCGTGCT	AY358299	CCDS10514.1	16p13.3	2008-02-05	2006-03-30	2006-03-30	ENSG00000168140	ENSG00000168140			18517	protein-coding gene	gene with protein product		608843	"""slit-like 2 (Drosophila)"""	SLITL2		15247411	Standard	NM_138440		Approved		uc002cwj.1	Q6EMK4	OTTHUMG00000129469	ENST00000304735.3:c.1285G>A	chr16.hg19:g.4432163G>A	ENSP00000306864:p.Ala429Thr	124.0	0.0		80.0	4.0	NM_138440	Q6UXL4|Q6UXL5|Q96CX1	Missense_Mutation	SNP	ENST00000304735.3	hg19	CCDS10514.1	.	.	.	.	.	.	.	.	.	.	G	2.558	-0.302473	0.05495	.	.	ENSG00000168140	ENST00000304735	D	0.91521	-2.86	5.63	3.66	0.41972	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.761271	0.12153	N	0.494708	T	0.71443	0.3340	N	0.01277	-0.915	0.20638	N	0.999877	B	0.17038	0.02	B	0.14023	0.01	T	0.60667	-0.7218	10	0.13853	T	0.58	-11.1698	6.1836	0.20486	0.0742:0.1337:0.6538:0.1383	.	429	Q6EMK4	VASN_HUMAN	T	429	ENSP00000306864:A429T	ENSP00000306864:A429T	A	+	1	0	VASN	4372164	0.712000	0.27916	0.771000	0.31576	0.131000	0.20780	1.754000	0.38369	0.734000	0.32515	0.650000	0.86243	GCG	.	.		0.692	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440	
CDR2	1039	hgsc.bcm.edu	37	16	22376296	22376296	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:22376296T>C	ENST00000268383.2	-	2	426	c.119A>G	c.(118-120)gAt>gGt	p.D40G	RP11-21M24.3_ENST00000566764.1_RNA|CDR2_ENST00000569045.1_5'UTR	NM_001802.1	NP_001793.1	Q01850	CDR2_HUMAN	cerebellar degeneration-related protein 2, 62kDa	40						cytoplasm (GO:0005737)				endometrium(3)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	11				GBM - Glioblastoma multiforme(48;0.0188)		TGTGTTCCGATCCAGTAATGT	0.393																																					p.D40G		Atlas-SNP	.											.	CDR2	34	.	0			c.A119G						.						148.0	120.0	129.0					16																	22376296		2197	4300	6497	SO:0001583	missense	1039	exon2			TTCCGATCCAGTA	M63256	CCDS32404.1	16p13.1-p12	2008-02-05	2002-08-29			ENSG00000140743			1799	protein-coding gene	gene with protein product	"""Yo paraneoplastic antigen"""	117340	"""cerebellar degeneration-related protein (62kD)"""			2014264	Standard	NM_001802		Approved	CDR62, Yo	uc002dkn.3	Q01850		ENST00000268383.2:c.119A>G	chr16.hg19:g.22376296T>C	ENSP00000268383:p.Asp40Gly	138.0	0.0		137.0	6.0	NM_001802	A8K8A8|Q13977	Missense_Mutation	SNP	ENST00000268383.2	hg19	CCDS32404.1	.	.	.	.	.	.	.	.	.	.	T	32	5.170362	0.94768	.	.	ENSG00000140743	ENST00000268383	T	0.30448	1.53	5.91	5.91	0.95273	.	0.047350	0.85682	D	0.000000	T	0.52645	0.1747	M	0.64997	1.995	0.80722	D	1	D	0.71674	0.998	D	0.65684	0.937	T	0.54268	-0.8319	10	0.72032	D	0.01	-21.8145	16.3426	0.83092	0.0:0.0:0.0:1.0	.	40	Q01850	CDR2_HUMAN	G	40	ENSP00000268383:D40G	ENSP00000268383:D40G	D	-	2	0	CDR2	22283797	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.390000	0.79816	2.263000	0.75096	0.379000	0.24179	GAT	.	.		0.393	CDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430081.1		
GTF3C1	2975	hgsc.bcm.edu	37	16	27503691	27503691	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:27503691T>C	ENST00000356183.4	-	19	3134	c.3119A>G	c.(3118-3120)gAc>gGc	p.D1040G	GTF3C1_ENST00000561623.1_Missense_Mutation_p.D1040G	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1040					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						GCACTGCAGGTCAAACCAGTA	0.562																																					p.D1040G		Atlas-SNP	.											.	GTF3C1	210	.	0			c.A3119G						.						71.0	73.0	72.0					16																	27503691		2197	4300	6497	SO:0001583	missense	2975	exon19			TGCAGGTCAAACC	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.3119A>G	chr16.hg19:g.27503691T>C	ENSP00000348510:p.Asp1040Gly	115.0	0.0		170.0	8.0	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.039968	0.93630	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.27402	1.67	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.57799	0.2078	M	0.79475	2.455	0.53688	D	0.999974	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.60439	-0.7263	10	0.52906	T	0.07	-26.005	15.8433	0.78868	0.0:0.0:0.0:1.0	.	1040;1040	Q12789;Q12789-3	TF3C1_HUMAN;.	G	1040;1038	ENSP00000348510:D1040G	ENSP00000348510:D1040G	D	-	2	0	GTF3C1	27411192	1.000000	0.71417	0.978000	0.43139	0.974000	0.67602	7.698000	0.84413	2.217000	0.71921	0.533000	0.62120	GAC	.	.		0.562	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
ZNF646	9726	hgsc.bcm.edu	37	16	31089058	31089058	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:31089058T>C	ENST00000394979.2	+	1	1836	c.1413T>C	c.(1411-1413)ggT>ggC	p.G471G	ZNF646_ENST00000300850.5_Silent_p.G471G			O15015	ZN646_HUMAN	zinc finger protein 646	471					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						GTGAGTGTGGTCGTGCTTACC	0.617																																					p.G471G		Atlas-SNP	.											ZNF646,NS,carcinoma,0,1	ZNF646	133	.	0			c.T1413C						.						81.0	84.0	83.0					16																	31089058		2197	4300	6497	SO:0001819	synonymous_variant	9726	exon2			GTGTGGTCGTGCT	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.1413T>C	chr16.hg19:g.31089058T>C		94.0	0.0		109.0	5.0	NM_014699	Q8IVD8	Silent	SNP	ENST00000394979.2	hg19																																																																																				.	.		0.617	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
PRSS36	146547	hgsc.bcm.edu	37	16	31152016	31152016	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:31152016A>G	ENST00000268281.4	-	13	2022	c.1964T>C	c.(1963-1965)cTc>cCc	p.L655P	PRSS36_ENST00000569305.1_Missense_Mutation_p.L650P|PRSS36_ENST00000418068.2_Missense_Mutation_p.L655P	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	655	Peptidase S1 3. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	serine-type endopeptidase activity (GO:0004252)			kidney(2)|large_intestine(4)|lung(8)|ovary(3)	17						GCCCTGTGGGAGGGAGCTGGC	0.642																																					p.L655P		Atlas-SNP	.											.	PRSS36	50	.	0			c.T1964C						.						40.0	43.0	42.0					16																	31152016		2197	4300	6497	SO:0001583	missense	146547	exon13			TGTGGGAGGGAGC	AK075142	CCDS32436.1, CCDS58452.1, CCDS58453.1	16p11.2	2014-09-04			ENSG00000178226			"""Serine peptidases / Serine peptidases"""	26906	protein-coding gene	gene with protein product	"""polyserase 2"""	610560				15536082	Standard	NM_173502		Approved	FLJ90661	uc002ebd.4	Q5K4E3	OTTHUMG00000176751	ENST00000268281.4:c.1964T>C	chr16.hg19:g.31152016A>G	ENSP00000268281:p.Leu655Pro	133.0	0.0		194.0	9.0	NM_001258291	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Missense_Mutation	SNP	ENST00000268281.4	hg19	CCDS32436.1	.	.	.	.	.	.	.	.	.	.	a	15.56	2.869255	0.51588	.	.	ENSG00000178226	ENST00000268281;ENST00000418068	D;D	0.90324	-2.46;-2.65	4.15	1.84	0.25277	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.85579	0.5729	N	0.22421	0.69	0.51012	D	0.999906	P;D;D	0.57257	0.948;0.979;0.979	P;P;P	0.55303	0.601;0.773;0.773	T	0.80074	-0.1534	9	0.32370	T	0.25	.	2.9529	0.05867	0.6671:0.0:0.1168:0.2161	.	655;650;655	E7EX56;B7ZMK8;Q5K4E3	.;.;POLS2_HUMAN	P	655	ENSP00000268281:L655P;ENSP00000407160:L655P	ENSP00000268281:L655P	L	-	2	0	PRSS36	31059517	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.410000	0.34691	0.697000	0.31718	0.449000	0.29647	CTC	.	.		0.642	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502	
CETP	1071	hgsc.bcm.edu	37	16	57005938	57005938	+	Silent	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:57005938C>T	ENST00000566128.1	+	8	765	c.498C>T	c.(496-498)gaC>gaT	p.D166D	CETP_ENST00000200676.3_Silent_p.D231D|CETP_ENST00000379780.2_Silent_p.D231D|CETP_ENST00000569082.1_3'UTR					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						TTGGGGTGGACATTTCCCTGA	0.597																																					p.D231D		Atlas-SNP	.											.	CETP	50	.	0			c.C693T						.						113.0	92.0	99.0					16																	57005938		2198	4300	6498	SO:0001819	synonymous_variant	1071	exon8			GGTGGACATTTCC	M30185	CCDS10772.1, CCDS67032.1	16q13	2012-10-02			ENSG00000087237	ENSG00000087237		"""BPI fold containing"""	1869	protein-coding gene	gene with protein product	"""BPI fold containing family F"""	118470				3600759, 2334701	Standard	NM_000078		Approved	BPIFF	uc002eki.2	P11597	OTTHUMG00000133279	ENST00000566128.1:c.498C>T	chr16.hg19:g.57005938C>T		131.0	0.0		122.0	35.0	NM_000078		Silent	SNP	ENST00000566128.1	hg19																																																																																				.	.		0.597	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078	
NLRC5	84166	hgsc.bcm.edu	37	16	57063748	57063748	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:57063748A>G	ENST00000262510.6	+	9	2532	c.2307A>G	c.(2305-2307)ctA>ctG	p.L769L	NLRC5_ENST00000436936.1_Silent_p.L769L|NLRC5_ENST00000308149.7_Silent_p.L769L|NLRC5_ENST00000539144.1_Silent_p.L769L	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	769					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				TCCCTCACCTACCACGGCTCC	0.572																																					p.L769L		Atlas-SNP	.											.	NLRC5	186	.	0			c.A2307G						.						103.0	81.0	88.0					16																	57063748		2198	4300	6498	SO:0001819	synonymous_variant	84166	exon8			TCACCTACCACGG	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.2307A>G	chr16.hg19:g.57063748A>G		106.0	0.0		100.0	4.0	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	hg19	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	A	11.11	1.541858	0.27563	.	.	ENSG00000140853	ENST00000538805	.	.	.	5.12	1.99	0.26369	.	.	.	.	.	T	0.24661	0.0598	.	.	.	0.20638	N	0.999874	.	.	.	.	.	.	T	0.22382	-1.0218	4	.	.	.	.	4.0495	0.09788	0.2043:0.0:0.594:0.2017	.	.	.	.	A	522	.	.	T	+	1	0	NLRC5	55621249	0.072000	0.21174	0.102000	0.21198	0.708000	0.40852	0.449000	0.21744	0.137000	0.18759	-0.468000	0.05107	ACC	.	.		0.572	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
CTRL	1506	hgsc.bcm.edu	37	16	67963841	67963841	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:67963841T>C	ENST00000574481.1	-	7	1352	c.791A>G	c.(790-792)aAc>aGc	p.N264S	CTRL_ENST00000576408.1_5'Flank	NM_001907.2	NP_001898.1	P40313	CTRL_HUMAN	chymotrypsin-like	264					digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|urinary_tract(1)	4		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		GTGAGCTCAGTTGTAGGCTAT	0.527																																					p.N264S		Atlas-SNP	.											.	CTRL	11	.	0			c.A791G						.						144.0	133.0	137.0					16																	67963841		2198	4300	6498	SO:0001583	missense	1506	exon7			GCTCAGTTGTAGG		CCDS10852.1	16q22.1	2008-02-05			ENSG00000141086	ENSG00000141086			2524	protein-coding gene	gene with protein product		118888				8268911	Standard	NM_001907		Approved		uc002euw.3	P40313	OTTHUMG00000137552	ENST00000574481.1:c.791A>G	chr16.hg19:g.67963841T>C	ENSP00000458537:p.Asn264Ser	92.0	0.0		97.0	4.0	NM_001907		Missense_Mutation	SNP	ENST00000574481.1	hg19	CCDS10852.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.054839	0.75960	.	.	ENSG00000141086	ENST00000319955	.	.	.	5.55	3.31	0.37934	Peptidase cysteine/serine, trypsin-like (1);	0.815645	0.10574	U	0.658757	T	0.66944	0.2841	L	0.39633	1.23	0.44352	D	0.997249	D	0.71674	0.998	D	0.77557	0.99	T	0.59506	-0.7442	9	0.87932	D	0	.	9.505	0.39042	0.0:0.1453:0.0:0.8547	.	264	P40313	CTRL_HUMAN	S	264	.	ENSP00000322629:N264S	N	-	2	0	CTRL	66521342	1.000000	0.71417	0.269000	0.24586	0.928000	0.56348	4.465000	0.60141	0.405000	0.25532	0.402000	0.26972	AAC	.	.		0.527	CTRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268886.3		
SLC12A4	6560	hgsc.bcm.edu	37	16	67985797	67985797	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:67985797T>C	ENST00000316341.3	-	8	1201	c.1061A>G	c.(1060-1062)gAc>gGc	p.D354G	SLC12A4_ENST00000576616.1_Missense_Mutation_p.D354G|SLC12A4_ENST00000541864.2_Missense_Mutation_p.D323G|SLC12A4_ENST00000422611.2_Missense_Mutation_p.D356G|SLC12A4_ENST00000572010.1_5'Flank|SLC12A4_ENST00000572037.1_Missense_Mutation_p.D306G|SLC12A4_ENST00000338335.3_Missense_Mutation_p.D354G|SLC12A4_ENST00000537830.2_Missense_Mutation_p.D348G	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	354					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	GAAGTAGGGGTCACAGGAGTC	0.587																																					p.D356G		Atlas-SNP	.											.	SLC12A4	81	.	0			c.A1067G						.						120.0	76.0	91.0					16																	67985797		2198	4300	6498	SO:0001583	missense	6560	exon7			TAGGGGTCACAGG		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"""Solute carriers"""	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.1061A>G	chr16.hg19:g.67985797T>C	ENSP00000318557:p.Asp354Gly	136.0	0.0		167.0	7.0	NM_001145962	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	hg19	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.259565	0.80246	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000338335;ENST00000316341	T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.82079	0.4959	M	0.89785	3.06	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.991;0.999;0.985;0.974;0.991	D;P;D;P;P;P	0.87578	0.979;0.792;0.998;0.844;0.743;0.792	D	0.84609	0.0677	10	0.44086	T	0.13	.	14.9987	0.71455	0.0:0.0:0.0:1.0	.	356;354;323;348;354;354	F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;S12A4_HUMAN	G	356;323;348;354;354	ENSP00000395983:D356G;ENSP00000438334:D323G;ENSP00000445962:D348G;ENSP00000343374:D354G;ENSP00000318557:D354G	ENSP00000318557:D354G	D	-	2	0	SLC12A4	66543298	1.000000	0.71417	0.998000	0.56505	0.899000	0.52679	7.997000	0.88414	2.022000	0.59522	0.383000	0.25322	GAC	.	.		0.587	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072	
NOB1	28987	hgsc.bcm.edu	37	16	69788569	69788569	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:69788569T>C	ENST00000268802.5	-	2	153	c.124A>G	c.(124-126)Aca>Gca	p.T42A		NM_014062.1	NP_054781.1	Q9ULX3	NOB1_HUMAN	NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)	42	PINc.				visual perception (GO:0007601)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(2)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CGCCTGCGTGTGGCCTTGTCC	0.627																																					p.T42A		Atlas-SNP	.											.	NOB1	24	.	0			c.A124G						.						73.0	65.0	67.0					16																	69788569		2198	4300	6498	SO:0001583	missense	28987	exon2			TGCGTGTGGCCTT	AB026125	CCDS10884.1	16q22.1	2008-02-05	2006-04-20	2006-04-20	ENSG00000141101	ENSG00000141101			29540	protein-coding gene	gene with protein product	"""nin one binding protein"""	613586	"""PSMD8 binding protein 1"""	PSMD8BP1		16172919	Standard	NM_014062		Approved	NOB1P, ART-4, MST158	uc002exs.4	Q9ULX3	OTTHUMG00000137576	ENST00000268802.5:c.124A>G	chr16.hg19:g.69788569T>C	ENSP00000268802:p.Thr42Ala	63.0	0.0		104.0	5.0	NM_014062	Q7L6B7|Q7M4M4|Q7Z4B5|Q9NWB0	Missense_Mutation	SNP	ENST00000268802.5	hg19	CCDS10884.1	.	.	.	.	.	.	.	.	.	.	T	29.6	5.016757	0.93404	.	.	ENSG00000141101	ENST00000268802	T	0.28454	1.61	4.45	4.45	0.53987	Nucleotide binding protein, PINc (1);	1.464880	0.04777	N	0.429098	T	0.24967	0.0606	N	0.19112	0.55	0.58432	D	0.999998	B	0.11235	0.004	B	0.13407	0.009	T	0.01549	-1.1327	9	.	.	.	.	13.1095	0.59265	0.0:0.0:0.0:1.0	.	42	Q9ULX3	NOB1_HUMAN	A	42	ENSP00000268802:T42A	.	T	-	1	0	NOB1	68346070	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	5.049000	0.64244	1.998000	0.58463	0.482000	0.46254	ACA	.	.		0.627	NOB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268958.2	NM_014062	
ZFHX3	463	hgsc.bcm.edu	37	16	72829897	72829897	+	Silent	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:72829897G>C	ENST00000268489.5	-	9	7356	c.6684C>G	c.(6682-6684)ccC>ccG	p.P2228P	ZFHX3_ENST00000397992.5_Silent_p.P1314P	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2228					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CCGGCGAAGGGGGCCGGGAGT	0.527																																					p.P2228P		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C6684G						.						106.0	105.0	105.0					16																	72829897		2198	4300	6498	SO:0001819	synonymous_variant	463	exon9			CGAAGGGGGCCGG	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.6684C>G	chr16.hg19:g.72829897G>C		143.0	0.0		173.0	68.0	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.		0.527	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
ZNF469	84627	hgsc.bcm.edu	37	16	88494980	88494980	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:88494980T>C	ENST00000437464.1	+	1	1102	c.1102T>C	c.(1102-1104)Ttc>Ctc	p.F368L	ZNF469_ENST00000565624.1_Missense_Mutation_p.F368L	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	368	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						CCCGAGACCCTTCTCTGACAG	0.637																																					p.F368L		Atlas-SNP	.											.	ZNF469	121	.	0			c.T1102C						.						5.0	6.0	6.0					16																	88494980		668	1542	2210	SO:0001583	missense	84627	exon1			AGACCCTTCTCTG	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.1102T>C	chr16.hg19:g.88494980T>C	ENSP00000402343:p.Phe368Leu	74.0	0.0		111.0	5.0	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	hg19	CCDS45544.1	.	.	.	.	.	.	.	.	.	.	T	14.35	2.510235	0.44660	.	.	ENSG00000225614	ENST00000437464	T	0.25414	1.8	4.6	4.6	0.57074	.	.	.	.	.	T	0.16727	0.0402	N	0.19112	0.55	0.26175	N	0.979811	P	0.41673	0.759	B	0.35899	0.213	T	0.08269	-1.0730	9	0.72032	D	0.01	.	11.3612	0.49644	0.0:0.0:0.0:1.0	.	368	Q96JG9	ZN469_HUMAN	L	368	ENSP00000402343:F368L	ENSP00000402343:F368L	F	+	1	0	ZNF469	87022481	1.000000	0.71417	0.991000	0.47740	0.268000	0.26511	2.513000	0.45494	1.706000	0.51276	0.379000	0.24179	TTC	.	.		0.637	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
PIEZO1	9780	hgsc.bcm.edu	37	16	88786816	88786816	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:88786816T>C	ENST00000301015.9	-	41	6172	c.5926A>G	c.(5926-5928)Att>Gtt	p.I1976V	RP5-1142A6.9_ENST00000564984.1_RNA|PIEZO1_ENST00000327397.7_5'Flank	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1976					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						AAGCCAAAAATGATGATGATG	0.602																																					p.I1976V		Atlas-SNP	.											.	PIEZO1	79	.	0			c.A5926G						.						96.0	94.0	94.0					16																	88786816		692	1591	2283	SO:0001583	missense	9780	exon41			CAAAAATGATGAT	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.5926A>G	chr16.hg19:g.88786816T>C	ENSP00000301015:p.Ile1976Val	81.0	0.0		96.0	4.0	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	hg19	CCDS54058.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	15.23|15.23	2.771570|2.771570	0.49680|0.49680	.|.	.|.	ENSG00000103335|ENSG00000103335	ENST00000451779|ENST00000301015	.|T	.|0.25085	.|1.82	5.25|5.25	4.13|4.13	0.48395|0.48395	.|.	.|0.283792	.|0.38837	.|N	.|0.001550	T|T	0.16428|0.16428	0.0395|0.0395	L|L	0.37800|0.37800	1.135|1.135	0.80722|0.80722	D|D	1|1	.|B	.|0.06786	.|0.001	.|B	.|0.11329	.|0.006	T|T	0.04930|0.04930	-1.0917|-1.0917	5|10	.|0.07813	.|T	.|0.8	-28.5959|-28.5959	8.8458|8.8458	0.35170|0.35170	0.0:0.1531:0.0:0.8469|0.0:0.1531:0.0:0.8469	.|.	.|1976	.|Q92508	.|PIEZ1_HUMAN	R|V	1921|1976	.|ENSP00000301015:I1976V	.|ENSP00000301015:I1976V	H|I	-|-	2|1	0|0	FAM38A|FAM38A	87314317|87314317	0.974000|0.974000	0.33945|0.33945	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	0.075000|0.075000	0.14686|0.14686	2.105000|2.105000	0.64084|0.64084	0.454000|0.454000	0.30748|0.30748	CAT|ATT	.	.		0.602	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
ZNF778	197320	hgsc.bcm.edu	37	16	89294115	89294115	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:89294115A>G	ENST00000433976.2	+	6	1667	c.1335A>G	c.(1333-1335)ggA>ggG	p.G445G	RP11-46C24.6_ENST00000563182.1_RNA|ZNF778_ENST00000306502.6_Silent_p.G403G	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	445					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		CTCACACTGGAGAGAAACCAT	0.488																																					p.G473G		Atlas-SNP	.											.	ZNF778	67	.	0			c.A1419G						.						89.0	93.0	91.0					16																	89294115		2194	4299	6493	SO:0001819	synonymous_variant	197320	exon7			CACTGGAGAGAAA	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.1335A>G	chr16.hg19:g.89294115A>G		53.0	0.0		59.0	5.0	NM_001201407	Q08AG0	Silent	SNP	ENST00000433976.2	hg19	CCDS45550.1																																																																																			.	.		0.488	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531	
TCF25	22980	hgsc.bcm.edu	37	16	89972662	89972662	+	Silent	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:89972662G>A	ENST00000263346.8	+	15	1745	c.1689G>A	c.(1687-1689)gaG>gaA	p.E563E	RP11-566K11.7_ENST00000570217.1_RNA|TCF25_ENST00000263347.7_Silent_p.E328E	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	563					heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		TCCTCTCTGAGATCAAGGAAG	0.597																																					p.E563E		Atlas-SNP	.											.	TCF25	61	.	0			c.G1689A						.						57.0	49.0	52.0					16																	89972662		2197	4300	6497	SO:0001819	synonymous_variant	22980	exon15			CTCTGAGATCAAG	AF322111	CCDS10987.1	16q24.3	2008-02-05			ENSG00000141002	ENSG00000141002			29181	protein-coding gene	gene with protein product		612326				12107429, 16574069	Standard	NM_014972		Approved	Nulp1, KIAA1049	uc002fpb.2	Q9BQ70	OTTHUMG00000138986	ENST00000263346.8:c.1689G>A	chr16.hg19:g.89972662G>A		103.0	0.0		92.0	4.0	NM_014972	Q2MK75|Q9UPV3	Silent	SNP	ENST00000263346.8	hg19	CCDS10987.1																																																																																			.	.		0.597	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272875.2	NM_014972	
MYO1C	4641	hgsc.bcm.edu	37	17	1383903	1383903	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:1383903A>G	ENST00000575158.1	-	7	895	c.719T>C	c.(718-720)gTc>gCc	p.V240A	MYO1C_ENST00000361007.2_Missense_Mutation_p.V240A|MYO1C_ENST00000545534.2_Missense_Mutation_p.V251A|MYO1C_ENST00000359786.5_Missense_Mutation_p.V275A|MYO1C_ENST00000438665.2_Missense_Mutation_p.V256A|MYO1C_ENST00000573198.1_5'UTR			Q12965	MYO1E_HUMAN	myosin IC	246	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)	p.Q236fs*17(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GATGGAGGAGACTTTGGCACA	0.602																																					p.V275A		Atlas-SNP	.											.,1	MYO1C	57	.	1	Deletion - Frameshift(1)	liver(1)	c.T824C						.						121.0	109.0	113.0					17																	1383903		2203	4300	6503	SO:0001583	missense	4641	exon7			GAGGAGACTTTGG	X98507	CCDS11003.1, CCDS42226.1, CCDS45562.1	17p13.3	2011-09-27			ENSG00000197879	ENSG00000197879		"""Myosins / Myosin superfamily : Class I"""	7597	protein-coding gene	gene with protein product		606538				9119401	Standard	NM_001080779		Approved	myr2	uc002fsp.3	O00159	OTTHUMG00000090323	ENST00000575158.1:c.719T>C	chr17.hg19:g.1383903A>G	ENSP00000459174:p.Val240Ala	93.0	0.0		79.0	4.0	NM_001080779	Q14778	Missense_Mutation	SNP	ENST00000575158.1	hg19	CCDS11003.1	.	.	.	.	.	.	.	.	.	.	A	19.29	3.799959	0.70567	.	.	ENSG00000197879	ENST00000359786;ENST00000438665;ENST00000535856;ENST00000361007;ENST00000545534;ENST00000535421	D;D;D;D	0.90844	-2.74;-2.74;-2.74;-2.74	5.66	5.66	0.87406	Myosin head, motor domain (2);	0.115086	0.64402	D	0.000016	D	0.90779	0.7105	M	0.70275	2.135	0.80722	D	1	B;B;B	0.18610	0.013;0.029;0.01	B;B;B	0.29077	0.068;0.098;0.041	D	0.88515	0.3092	10	0.66056	D	0.02	.	15.0719	0.72042	1.0:0.0:0.0:0.0	.	251;275;256	B7Z3E5;O00159;O00159-3	.;MYO1C_HUMAN;.	A	275;256;256;240;251;240	ENSP00000352834:V275A;ENSP00000412197:V256A;ENSP00000354283:V240A;ENSP00000437685:V251A	ENSP00000352834:V275A	V	-	2	0	MYO1C	1330653	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	2.161000	0.67846	0.418000	0.28097	GTC	.	.		0.602	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2		
TSR1	55720	hgsc.bcm.edu	37	17	2228075	2228075	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:2228075T>C	ENST00000301364.5	-	13	3148	c.2069A>G	c.(2068-2070)gAc>gGc	p.D690G	SRR_ENST00000344595.5_3'UTR	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	690					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						GACCATTCTGTCTGGATCTAC	0.403																																					p.D690G		Atlas-SNP	.											.	TSR1	57	.	0			c.A2069G						.						98.0	96.0	97.0					17																	2228075		2203	4300	6503	SO:0001583	missense	55720	exon13			ATTCTGTCTGGAT	AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"""TSR1, 20S rRNA accumulation, homolog (yeast)"""			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.2069A>G	chr17.hg19:g.2228075T>C	ENSP00000301364:p.Asp690Gly	124.0	0.0		138.0	6.0	NM_018128	Q8WUY5|Q9NVT0|Q9P2E6	Missense_Mutation	SNP	ENST00000301364.5	hg19	CCDS32525.1	.	.	.	.	.	.	.	.	.	.	T	16.06	3.014693	0.54468	.	.	ENSG00000167721	ENST00000301364	T	0.19105	2.17	5.28	5.28	0.74379	Ribosome biogenesis protein BMS1/TSR1, C-terminal (1);	0.256103	0.46145	D	0.000311	T	0.49201	0.1543	M	0.86178	2.8	0.53688	D	0.999978	D	0.71674	0.998	D	0.74348	0.983	T	0.54715	-0.8252	10	0.54805	T	0.06	-8.3068	12.94	0.58337	0.0:0.0:0.0:1.0	.	690	Q2NL82	TSR1_HUMAN	G	690	ENSP00000301364:D690G	ENSP00000301364:D690G	D	-	2	0	TSR1	2174825	1.000000	0.71417	1.000000	0.80357	0.656000	0.38851	4.719000	0.61937	2.003000	0.58678	0.402000	0.26972	GAC	.	.		0.403	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128	
CLUH	23277	hgsc.bcm.edu	37	17	2604059	2604059	+	Silent	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:2604059G>A	ENST00000570628.2	-	8	1077	c.972C>T	c.(970-972)gcC>gcT	p.A324A	CLUH_ENST00000435359.1_Silent_p.A324A|CLUH_ENST00000538975.1_Silent_p.A324A			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	324					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											CCGCCTGGGGGGCTGTCCAGC	0.657																																					p.A324A		Atlas-SNP	.											.	.	.	.	0			c.C972T						.						40.0	46.0	44.0					17																	2604059		2161	4252	6413	SO:0001819	synonymous_variant	23277	exon8			CTGGGGGGCTGTC	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"""KIAA0664"""	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.972C>T	chr17.hg19:g.2604059G>A		65.0	0.0		71.0	4.0	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Silent	SNP	ENST00000570628.2	hg19	CCDS45572.1																																																																																			.	.		0.657	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	
ATP2A3	489	hgsc.bcm.edu	37	17	3854948	3854948	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:3854948G>C	ENST00000352011.3	-	4	305	c.251C>G	c.(250-252)aCc>aGc	p.T84S	ATP2A3_ENST00000359983.3_Missense_Mutation_p.T84S|ATP2A3_ENST00000397035.3_Missense_Mutation_p.T84S|ATP2A3_ENST00000397043.3_Missense_Mutation_p.T84S|ATP2A3_ENST00000397041.3_Missense_Mutation_p.T84S|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000309890.7_Missense_Mutation_p.T84S			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	84					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		GGCGGTCGTGGTCTCCTCGCC	0.662																																					p.T84S	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.C251G						.						40.0	28.0	32.0					17																	3854948		2202	4300	6502	SO:0001583	missense	489	exon4			GTCGTGGTCTCCT		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.251C>G	chr17.hg19:g.3854948G>C	ENSP00000301387:p.Thr84Ser	222.0	0.0		167.0	103.0	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Missense_Mutation	SNP	ENST00000352011.3	hg19	CCDS11041.1	.	.	.	.	.	.	.	.	.	.	G	8.608	0.888349	0.17540	.	.	ENSG00000074370	ENST00000397043;ENST00000352011;ENST00000359983;ENST00000397041;ENST00000397045;ENST00000309890;ENST00000397035	D;D;D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31;-2.31;-2.31	3.83	3.83	0.44106	ATPase, P-type,  transmembrane domain (1);	0.181563	0.32819	N	0.005615	T	0.77130	0.4085	N	0.19112	0.55	0.44523	D	0.997474	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001;0.001	T	0.72020	-0.4416	10	0.28530	T	0.3	.	12.8645	0.57932	0.0:0.1647:0.8353:0.0	.	84;84;84;84;84;84	Q93084-4;Q93084-2;Q93084;Q93084-6;G3XAE1;Q93084-3	.;.;AT2A3_HUMAN;.;.;.	S	84	ENSP00000380236:T84S;ENSP00000301387:T84S;ENSP00000353072:T84S;ENSP00000380234:T84S;ENSP00000312577:T84S;ENSP00000380229:T84S	ENSP00000312577:T84S	T	-	2	0	ATP2A3	3801697	1.000000	0.71417	0.992000	0.48379	0.977000	0.68977	5.506000	0.66993	2.125000	0.65367	0.514000	0.50259	ACC	.	.		0.662	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
DVL2	1856	hgsc.bcm.edu	37	17	7132947	7132947	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:7132947T>C	ENST00000005340.5	-	6	989	c.707A>G	c.(706-708)cAc>cGc	p.H236R	DVL2_ENST00000574642.1_5'UTR|DVL2_ENST00000575458.1_Missense_Mutation_p.H230R	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	236	Poly-Arg.				canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						TCGCCGCCGGTGGCGCTTAAG	0.632																																					p.H236R		Atlas-SNP	.											.	DVL2	49	.	0			c.A707G						.						52.0	60.0	58.0					17																	7132947		2203	4300	6503	SO:0001583	missense	1856	exon6			CGCCGGTGGCGCT	BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"""Dishevelled homologs"""	3086	protein-coding gene	gene with protein product		602151	"""dishevelled 2 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 2 (Drosophila)"""			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.707A>G	chr17.hg19:g.7132947T>C	ENSP00000005340:p.His236Arg	89.0	0.0		81.0	4.0	NM_004422	D3DTN3|Q53XM0	Missense_Mutation	SNP	ENST00000005340.5	hg19	CCDS11091.1	.	.	.	.	.	.	.	.	.	.	T	9.563	1.119064	0.20877	.	.	ENSG00000004975	ENST00000005340	T	0.04194	3.68	5.0	5.0	0.66597	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.08670	0.0215	N	0.16368	0.405	0.58432	D	0.999999	D;B;B	0.57899	0.981;0.112;0.112	D;B;B	0.69824	0.966;0.023;0.074	T	0.51834	-0.8655	10	0.14656	T	0.56	-18.0085	12.6392	0.56700	0.0:0.0:0.0:1.0	.	143;230;236	B4DM44;B4DLQ0;O14641	.;.;DVL2_HUMAN	R	236	ENSP00000005340:H236R	ENSP00000005340:H236R	H	-	2	0	DVL2	7073671	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	7.514000	0.81750	1.890000	0.54733	0.334000	0.21626	CAC	.	.		0.632	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422	
TP53	7157	hgsc.bcm.edu	37	17	7577557	7577557	+	Missense_Mutation	SNP	A	A	T	rs397516437		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:7577557A>T	ENST00000269305.4	-	7	913	c.724T>A	c.(724-726)Tgc>Agc	p.C242S	TP53_ENST00000420246.2_Missense_Mutation_p.C242S|TP53_ENST00000359597.4_Missense_Mutation_p.C242S|TP53_ENST00000413465.2_Missense_Mutation_p.C242S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.C242S|TP53_ENST00000455263.2_Missense_Mutation_p.C242S	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	242	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:16959974}.|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.C242R(12)|p.C242S(10)|p.0?(8)|p.?(5)|p.N239_C242delNSSC(3)|p.C242G(2)|p.S241del(2)|p.N239_C242>S(1)|p.S241_C242insX(1)|p.C238fs*21(1)|p.C242fs*20(1)|p.C242fs*23(1)|p.C242fs*5(1)|p.N239_C242del(1)|p.Y236_M243delYMCNSSCM(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(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)	CCGCCCATGCAGGAACTGTTA	0.577		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.C242S	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,caecum,carcinoma,0,1	TP53	33396	.	55	Substitution - Missense(24)|Deletion - In frame(10)|Whole gene deletion(8)|Deletion - Frameshift(5)|Unknown(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Complex - deletion inframe(1)	breast(8)|large_intestine(7)|biliary_tract(5)|upper_aerodigestive_tract(4)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|liver(3)|ovary(3)|pancreas(3)|prostate(3)|stomach(2)|oesophagus(2)|lung(2)|urinary_tract(1)	c.T724A						.						138.0	106.0	117.0					17																	7577557		2203	4300	6503	SO:0001583	missense	7157	exon7	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;	CCATGCAGGAACT	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.724T>A	chr17.hg19:g.7577557A>T	ENSP00000269305:p.Cys242Ser	224.0	0.0		129.0	81.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.639501	0.87760	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99914	-7.98;-7.98;-7.98;-7.98;-7.98;-7.98;-7.98;-7.98	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99924	0.9965	M	0.92784	3.345	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;0.999	D	0.95737	0.8780	10	0.87932	D	0	-27.558	12.3101	0.54924	1.0:0.0:0.0:0.0	.	242;242;149;242;242;242	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	S	242;242;242;242;242;242;231;149;110;149	ENSP00000410739:C242S;ENSP00000352610:C242S;ENSP00000269305:C242S;ENSP00000398846:C242S;ENSP00000391127:C242S;ENSP00000391478:C242S;ENSP00000425104:C110S;ENSP00000423862:C149S	ENSP00000269305:C242S	C	-	1	0	TP53	7518282	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.087000	0.94110	2.074000	0.62210	0.379000	0.24179	TGC	.	.		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
CHD3	1107	hgsc.bcm.edu	37	17	7809999	7809999	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:7809999C>A	ENST00000330494.7	+	29	4637	c.4487C>A	c.(4486-4488)tCt>tAt	p.S1496Y	SCARNA21_ENST00000517026.1_RNA|CHD3_ENST00000358181.4_Missense_Mutation_p.S1496Y|CHD3_ENST00000380358.4_Missense_Mutation_p.S1555Y	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1496					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)				GGAGTCATGTCTCTCGTCAAA	0.557																																					p.S1555Y		Atlas-SNP	.											.	CHD3	169	.	0			c.C4664A						.						99.0	95.0	96.0					17																	7809999		2203	4300	6503	SO:0001583	missense	1107	exon29			TCATGTCTCTCGT	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.4487C>A	chr17.hg19:g.7809999C>A	ENSP00000332628:p.Ser1496Tyr	105.0	0.0		78.0	48.0	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	hg19	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.041720	0.55003	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	D;D;D	0.91631	-2.88;-2.82;-2.81	4.69	4.69	0.59074	Domain of unknown function DUF1086 (1);	0.000000	0.44688	D	0.000435	D	0.95971	0.8688	M	0.78637	2.42	0.80722	D	1	D;D;D;D	0.76494	0.998;0.997;0.997;0.999	D;D;D;D	0.87578	0.998;0.994;0.996;0.998	D	0.96542	0.9401	10	0.87932	D	0	-14.2861	17.8077	0.88606	0.0:1.0:0.0:0.0	.	72;1496;1496;1555	B3KWV4;Q12873-2;Q12873;E9PG89	.;.;CHD3_HUMAN;.	Y	1555;1496;1496	ENSP00000369716:S1555Y;ENSP00000350907:S1496Y;ENSP00000332628:S1496Y	ENSP00000332628:S1496Y	S	+	2	0	CHD3	7750724	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.452000	0.66638	2.429000	0.82318	0.313000	0.20887	TCT	.	.		0.557	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273	
DNAH9	1770	hgsc.bcm.edu	37	17	11686973	11686973	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:11686973A>G	ENST00000262442.4	+	40	7797	c.7729A>G	c.(7729-7731)Agc>Ggc	p.S2577G	DNAH9_ENST00000454412.2_Missense_Mutation_p.S2577G	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2577	AAA 3. {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)		GTATGATCGGAGCAAGCTGTC	0.522																																					p.S2577G		Atlas-SNP	.											.	DNAH9	695	.	0			c.A7729G						.						101.0	74.0	83.0					17																	11686973		2203	4300	6503	SO:0001583	missense	1770	exon40			GATCGGAGCAAGC	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.7729A>G	chr17.hg19:g.11686973A>G	ENSP00000262442:p.Ser2577Gly	84.0	0.0		109.0	5.0	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	A	11.37	1.619839	0.28801	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.33865	1.39;1.39	5.37	4.26	0.50523	ATPase, AAA+ type, core (1);	0.200961	0.40302	N	0.001126	T	0.16300	0.0392	N	0.05031	-0.125	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.18808	-1.0325	10	0.23891	T	0.37	.	6.9322	0.24447	0.7731:0.1518:0.0751:0.0	.	2577	Q9NYC9	DYH9_HUMAN	G	2577;2577;1159	ENSP00000262442:S2577G;ENSP00000414874:S2577G	ENSP00000262442:S2577G	S	+	1	0	DNAH9	11627698	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	2.208000	0.42797	0.846000	0.35142	0.523000	0.50628	AGC	.	.		0.522	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
KCNJ12	3768	hgsc.bcm.edu	37	17	21319360	21319360	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:21319360C>T	ENST00000583088.1	+	3	1601	c.706C>T	c.(706-708)Cgg>Tgg	p.R236W	KCNJ12_ENST00000331718.5_Missense_Mutation_p.R236W	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	236					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CATCAAGCCGCGGGTCACCGA	0.637										Prostate(3;0.18)																											p.R236W		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,1	.	.	.	0			c.C706T						.						94.0	72.0	80.0					17																	21319360		2203	4300	6503	SO:0001583	missense	100134444	exon3			AAGCCGCGGGTCA	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.706C>T	chr17.hg19:g.21319360C>T	ENSP00000463778:p.Arg236Trp	190.0	1.0		236.0	23.0	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	hg19	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	C	17.51	3.407256	0.62399	.	.	ENSG00000184185	ENST00000331718	D	0.94497	-3.44	5.32	-8.56	0.00904	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.97284	0.9112	M	0.93898	3.47	0.38797	D	0.955108	D	0.89917	1.0	D	0.75484	0.986	D	0.95584	0.8649	10	0.87932	D	0	.	20.5697	0.99360	0.7808:0.2191:0.0:0.0	.	236	Q14500	IRK12_HUMAN	W	236	ENSP00000328150:R236W	ENSP00000328150:R236W	R	+	1	2	KCNJ12	21259953	0.001000	0.12720	0.203000	0.23512	0.944000	0.59088	-0.033000	0.12246	-0.938000	0.03714	-0.274000	0.10170	CGG	.	.		0.637	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
EFCAB5	374786	hgsc.bcm.edu	37	17	28407894	28407894	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:28407894T>C	ENST00000394835.3	+	17	3513	c.3321T>C	c.(3319-3321)ccT>ccC	p.P1107P	EFCAB5_ENST00000394832.2_Intron|EFCAB5_ENST00000320856.5_Silent_p.P983P	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1107							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						TGGCTCTGCCTCTTCAAGATG	0.433																																					p.P1107P		Atlas-SNP	.											.	EFCAB5	122	.	0			c.T3321C						.						96.0	93.0	94.0					17																	28407894		1883	4112	5995	SO:0001819	synonymous_variant	374786	exon17			TCTGCCTCTTCAA	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"""EF-hand domain containing"""	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.3321T>C	chr17.hg19:g.28407894T>C		101.0	0.0		144.0	6.0	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	hg19	CCDS11254.2																																																																																			.	.		0.433	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
MYO1D	4642	hgsc.bcm.edu	37	17	30965824	30965824	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:30965824T>C	ENST00000318217.5	-	20	2929	c.2625A>G	c.(2623-2625)agA>agG	p.R875R	RP11-220C2.1_ENST00000582272.1_RNA|MYO1D_ENST00000579584.1_Silent_p.R875R|MYO1D_ENST00000394649.4_Silent_p.R787R	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	875	Myosin tail. {ECO:0000255}.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			CAAAAATTGCTCTGTCTTCCA	0.383																																					p.R875R		Atlas-SNP	.											.	MYO1D	93	.	0			c.A2625G						.						180.0	167.0	171.0					17																	30965824		2203	4300	6503	SO:0001819	synonymous_variant	4642	exon20			AATTGCTCTGTCT	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"""Myosins / Myosin superfamily : Class I"""	7598	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 108"""	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.2625A>G	chr17.hg19:g.30965824T>C		164.0	0.0		184.0	8.0	NM_015194	A6H8V3|Q8NHP9	Silent	SNP	ENST00000318217.5	hg19	CCDS32615.1																																																																																			.	.		0.383	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1		
HNF1B	6928	hgsc.bcm.edu	37	17	36104535	36104535	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:36104535A>G	ENST00000225893.4	-	1	702	c.341T>C	c.(340-342)cTc>cCc	p.L114P	HNF1B_ENST00000561193.1_Missense_Mutation_p.L114P|HNF1B_ENST00000560016.1_Missense_Mutation_p.L114P|RP11-115K3.1_ENST00000558143.1_RNA|HNF1B_ENST00000427275.2_Missense_Mutation_p.L114P	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	HNF1 homeobox B	114					anterior/posterior pattern specification (GO:0009952)|branching morphogenesis of an epithelial tube (GO:0048754)|embryonic digestive tract morphogenesis (GO:0048557)|endocrine pancreas development (GO:0031018)|endodermal cell fate specification (GO:0001714)|epithelial cell proliferation (GO:0050673)|genitalia development (GO:0048806)|hepatoblast differentiation (GO:0061017)|hindbrain development (GO:0030902)|inner cell mass cell differentiation (GO:0001826)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|mesonephric duct formation (GO:0072181)|negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis (GO:0061296)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric nephron tubule development (GO:0039020)|pronephros development (GO:0048793)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of endodermal cell fate specification (GO:0042663)|regulation of pronephros size (GO:0035565)|regulation of Wnt signaling pathway (GO:0030111)|response to glucose (GO:0009749)|ureteric bud elongation (GO:0060677)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			CGCCTACCTGAGCATCCGGTC	0.706																																					p.L114P	Colon(71;102 1179 9001 27917 43397)	Atlas-SNP	.											.	HNF1B	61	.	0			c.T341C						.						35.0	39.0	38.0					17																	36104535		2203	4298	6501	SO:0001583	missense	6928	exon1			TACCTGAGCATCC	BC017714	CCDS11324.1, CCDS58538.1	17q12	2014-05-06	2007-08-24	2007-08-24	ENSG00000108753	ENSG00000275410		"""Homeoboxes / HNF class"""	11630	protein-coding gene	gene with protein product		189907	"""transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor"""	TCF2		1677179, 10484768	Standard	NM_000458		Approved	LFB3, VHNF1, HNF1beta, MODY5	uc002hok.4	P35680	OTTHUMG00000188478	ENST00000225893.4:c.341T>C	chr17.hg19:g.36104535A>G	ENSP00000225893:p.Leu114Pro	47.0	0.0		61.0	4.0	NM_001165923	B4DKM3|E0YMJ9	Missense_Mutation	SNP	ENST00000225893.4	hg19	CCDS11324.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.181257	0.57800	.	.	ENSG00000108753	ENST00000225893;ENST00000427275;ENST00000544593;ENST00000539087	D;D	0.99474	-5.97;-5.97	5.24	5.24	0.73138	Hepatocyte nuclear factor 1, N-terminal (1);Lambda repressor-like, DNA-binding (2);	0.199993	0.44483	D	0.000453	D	0.99039	0.9671	M	0.78049	2.395	0.80722	D	1	B;B	0.21381	0.055;0.001	B;B	0.36989	0.238;0.014	D	0.99529	1.0960	10	0.87932	D	0	.	14.4703	0.67512	1.0:0.0:0.0:0.0	.	114;114	E0YMJ6;P35680	.;HNF1B_HUMAN	P	114;114;114;2	ENSP00000225893:L114P;ENSP00000412212:L114P	ENSP00000225893:L114P	L	-	2	0	HNF1B	33178648	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.816000	0.91979	2.203000	0.70933	0.459000	0.35465	CTC	.	.		0.706	HNF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256807.3	NM_000458	
ERBB2	2064	hgsc.bcm.edu	37	17	37868282	37868282	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:37868282A>G	ENST00000269571.5	+	8	1162	c.1003A>G	c.(1003-1005)Agc>Ggc	p.S335G	ERBB2_ENST00000541774.1_Missense_Mutation_p.S320G|ERBB2_ENST00000578199.1_Missense_Mutation_p.S305G|ERBB2_ENST00000584450.1_Missense_Mutation_p.S335G|ERBB2_ENST00000445658.2_Missense_Mutation_p.S59G|ERBB2_ENST00000584601.1_Missense_Mutation_p.S305G|ERBB2_ENST00000406381.2_Missense_Mutation_p.S305G|ERBB2_ENST00000540147.1_Missense_Mutation_p.S305G|ERBB2_ENST00000540042.1_Missense_Mutation_p.S305G			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	335					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|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)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	TGAGAAGTGCAGCAAGCCCTG	0.627		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)																											p.S335G		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	.	ERBB2	429	.	0			c.A1003G						.						131.0	101.0	111.0					17																	37868282		2203	4300	6503	SO:0001583	missense	2064	exon8			AAGTGCAGCAAGC	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1003A>G	chr17.hg19:g.37868282A>G	ENSP00000269571:p.Ser335Gly	92.0	0.0		89.0	4.0	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	hg19	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	A	13.26	2.183264	0.38511	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147;ENST00000540042	T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	5.83	5.83	0.93111	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	.	.	.	.	T	0.44808	0.1311	L	0.31526	0.94	0.33907	D	0.639189	B;P;P;P;B	0.38729	0.37;0.644;0.644;0.559;0.089	B;B;B;B;B	0.34652	0.055;0.098;0.09;0.187;0.021	T	0.54556	-0.8276	9	0.14252	T	0.57	.	9.6526	0.39906	0.9214:0.0:0.0786:0.0	.	59;305;320;335;335	B4DTR1;F5H1T4;P04626-4;P04626;Q9UK79	.;.;.;ERBB2_HUMAN;.	G	305;320;59;335;305;305	ENSP00000385185:S305G;ENSP00000446466:S320G;ENSP00000404047:S59G;ENSP00000269571:S335G;ENSP00000443562:S305G;ENSP00000446382:S305G	ENSP00000269571:S335G	S	+	1	0	ERBB2	35121808	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.657000	0.54474	2.232000	0.73038	0.402000	0.26972	AGC	.	.		0.627	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
ATP6V0A1	535	hgsc.bcm.edu	37	17	40635054	40635054	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:40635054A>G	ENST00000343619.4	+	9	839		c.e9-1		ATP6V0A1_ENST00000264649.6_Splice_Site|ATP6V0A1_ENST00000585525.1_Splice_Site|ATP6V0A1_ENST00000546249.1_Splice_Site|ATP6V0A1_ENST00000537728.1_Splice_Site|ATP6V0A1_ENST00000544137.1_Intron|ATP6V0A1_ENST00000393829.2_Splice_Site	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1						ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|urinary_tract(3)	26		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		CTTATATTCCAGGTTCCGAGC	0.408																																					.		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.717-2A>G						.						69.0	68.0	68.0					17																	40635054		2203	4300	6503	SO:0001630	splice_region_variant	535	exon9			TATTCCAGGTTCC	U73006	CCDS11426.1, CCDS45683.1, CCDS45684.1	17q21	2010-04-21	2006-01-20	2002-05-10	ENSG00000033627	ENSG00000033627		"""ATPases / V-type"""	865	protein-coding gene	gene with protein product		192130	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1A (110/116kD)"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 1"", ""ATPase, H+ transporting, lysosomal V0 subunit A1"""	VPP1, ATP6N1, ATP6N1A		7774924	Standard	NM_001130020		Approved	a1, Vph1, Stv1	uc002hzs.3	Q93050		ENST00000343619.4:c.717-1A>G	chr17.hg19:g.40635054A>G		67.0	0.0		80.0	4.0	NM_001130021	B7Z3B7|Q8N5G7|Q9NSX0	Splice_Site	SNP	ENST00000343619.4	hg19	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.465243	0.84425	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0812	0.81005	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATP6V0A1	37888580	1.000000	0.71417	0.993000	0.49108	0.865000	0.49528	9.339000	0.96797	2.196000	0.70406	0.460000	0.39030	.	.	.		0.408	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020	Intron
ADAM11	4185	hgsc.bcm.edu	37	17	42854589	42854589	+	Silent	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:42854589G>C	ENST00000200557.6	+	21	1906	c.1737G>C	c.(1735-1737)ggG>ggC	p.G579G	ADAM11_ENST00000535346.1_Silent_p.G379G	NM_002390.4	NP_002381.2	O75078	ADA11_HUMAN	ADAM metallopeptidase domain 11	579	Cys-rich.				integrin-mediated signaling pathway (GO:0007229)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Prostate(33;0.0959)				CGGAGCGTGGGAGCTGTGGGC	0.627																																					p.G579G		Atlas-SNP	.											.	ADAM11	118	.	0			c.G1737C						.						54.0	54.0	54.0					17																	42854589		2203	4300	6503	SO:0001819	synonymous_variant	4185	exon21			GCGTGGGAGCTGT	D17390	CCDS11486.1	17q21.3	2014-08-12	2005-08-18		ENSG00000073670			"""ADAM metallopeptidase domain containing"""	189	protein-coding gene	gene with protein product	"""metalloproteinase-like, disintegrin-like, cysteine-rich protein"""	155120	"""a disintegrin and metalloproteinase domain 11"""	MDC		8252040	Standard	XM_005257373		Approved		uc002ihh.3	O75078	OTTHUMG00000179038	ENST00000200557.6:c.1737G>C	chr17.hg19:g.42854589G>C		68.0	0.0		69.0	19.0	NM_002390	Q14808|Q14809|Q14810	Silent	SNP	ENST00000200557.6	hg19	CCDS11486.1																																																																																			.	.		0.627	ADAM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444531.1	NM_002390	
KANSL1	284058	hgsc.bcm.edu	37	17	44109416	44109416	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:44109416T>C	ENST00000262419.6	-	14	3557	c.3087A>G	c.(3085-3087)gaA>gaG	p.E1029E	KANSL1_ENST00000432791.1_Silent_p.E1029E|KANSL1_ENST00000393476.3_Silent_p.E323E|KANSL1_ENST00000574590.1_Silent_p.E1029E|KANSL1_ENST00000572904.1_Silent_p.E1029E|KANSL1_ENST00000575318.1_Silent_p.E965E	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	1029	Sufficient for interaction with KAT8.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CCCTTACCTGTTCATCCAGCC	0.617																																					p.E1029E		Atlas-SNP	.											.	.	.	.	0			c.A3087G						.						56.0	49.0	52.0					17																	44109416		2203	4300	6503	SO:0001819	synonymous_variant	284058	exon14			TACCTGTTCATCC	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.3087A>G	chr17.hg19:g.44109416T>C		82.0	0.0		79.0	4.0	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	hg19	CCDS11503.1																																																																																			.	.		0.617	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
PHB	5245	hgsc.bcm.edu	37	17	47486764	47486764	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:47486764T>C	ENST00000300408.3	-	4	394	c.322A>G	c.(322-324)Acc>Gcc	p.T108A	RP11-81K2.1_ENST00000576461.1_Intron|PHB_ENST00000508009.1_5'UTR|PHB_ENST00000511832.1_Missense_Mutation_p.T108A	NM_001281496.1|NM_001281715.1|NM_002634.2	NP_001268425.1|NP_001268644.1|NP_002625.1	P35232	PHB_HUMAN	prohibitin	108					cellular response to interleukin-6 (GO:0071354)|DNA replication (GO:0006260)|histone deacetylation (GO:0016575)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone receptor signaling pathway (GO:0050847)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|transcription regulatory region DNA binding (GO:0044212)			endometrium(4)|large_intestine(2)|lung(4)	10	all_cancers(4;2.62e-14)|Breast(4;4.21e-29)|all_epithelial(4;6.9e-18)		Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)			CCGATGCTGGTGAAGATGCGA	0.537																																					p.T108A		Atlas-SNP	.											.	PHB	25	.	0			c.A322G						.						89.0	84.0	85.0					17																	47486764		2203	4300	6503	SO:0001583	missense	5245	exon4			TGCTGGTGAAGAT		CCDS11548.1, CCDS62244.1	17q21	2010-11-25			ENSG00000167085	ENSG00000167085			8912	protein-coding gene	gene with protein product		176705				10376528, 8244394	Standard	NM_001281496		Approved	PHB1	uc002iox.1	P35232	OTTHUMG00000134271	ENST00000300408.3:c.322A>G	chr17.hg19:g.47486764T>C	ENSP00000300408:p.Thr108Ala	60.0	0.0		97.0	5.0	NM_002634	B4DY47|Q4VBQ0	Missense_Mutation	SNP	ENST00000300408.3	hg19	CCDS11548.1	.	.	.	.	.	.	.	.	.	.	T	16.81	3.225023	0.58668	.	.	ENSG00000167085	ENST00000300408;ENST00000511832;ENST00000419140;ENST00000504124;ENST00000512041;ENST00000446735;ENST00000434917	D;D;D;D;D;D;D	0.93906	-3.31;-3.31;-3.31;-3.31;-3.31;-3.31;-3.31	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	D	0.90208	0.6939	L	0.40543	1.245	0.80722	D	1	B	0.18013	0.025	B	0.23852	0.049	D	0.87407	0.2373	10	0.51188	T	0.08	.	14.2643	0.66107	0.0:0.0:0.0:1.0	.	108	P35232	PHB_HUMAN	A	108	ENSP00000300408:T108A;ENSP00000425035:T108A;ENSP00000393320:T108A;ENSP00000426433:T108A;ENSP00000422182:T108A;ENSP00000407828:T108A;ENSP00000410680:T108A	ENSP00000300408:T108A	T	-	1	0	PHB	44841763	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.966000	0.87956	1.856000	0.53863	0.379000	0.24179	ACC	.	.		0.537	PHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258826.1	NM_002634	
PHB	5245	hgsc.bcm.edu	37	17	47489105	47489105	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:47489105T>C	ENST00000300408.3	-	3	257	c.185A>G	c.(184-186)cAg>cGg	p.Q62R	RP11-81K2.1_ENST00000576461.1_Intron|PHB_ENST00000508009.1_Intron|PHB_ENST00000511832.1_Missense_Mutation_p.Q62R	NM_001281496.1|NM_001281715.1|NM_002634.2	NP_001268425.1|NP_001268644.1|NP_002625.1	P35232	PHB_HUMAN	prohibitin	62					cellular response to interleukin-6 (GO:0071354)|DNA replication (GO:0006260)|histone deacetylation (GO:0016575)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone receptor signaling pathway (GO:0050847)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|transcription regulatory region DNA binding (GO:0044212)			endometrium(4)|large_intestine(2)|lung(4)	10	all_cancers(4;2.62e-14)|Breast(4;4.21e-29)|all_epithelial(4;6.9e-18)		Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)			AATTGGTTTCTGTACCCACGG	0.502																																					p.Q62R		Atlas-SNP	.											.	PHB	25	.	0			c.A185G						.						98.0	70.0	79.0					17																	47489105		2203	4300	6503	SO:0001583	missense	5245	exon3			GGTTTCTGTACCC		CCDS11548.1, CCDS62244.1	17q21	2010-11-25			ENSG00000167085	ENSG00000167085			8912	protein-coding gene	gene with protein product		176705				10376528, 8244394	Standard	NM_001281496		Approved	PHB1	uc002iox.1	P35232	OTTHUMG00000134271	ENST00000300408.3:c.185A>G	chr17.hg19:g.47489105T>C	ENSP00000300408:p.Gln62Arg	84.0	0.0		89.0	26.0	NM_002634	B4DY47|Q4VBQ0	Missense_Mutation	SNP	ENST00000300408.3	hg19	CCDS11548.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.378621	0.82682	.	.	ENSG00000167085	ENST00000300408;ENST00000511832;ENST00000419140;ENST00000504124;ENST00000512041;ENST00000446735;ENST00000434917	D;D;D;D;D;D;D	0.94376	-3.28;-3.28;-3.28;-3.28;-3.28;-3.28;-3.41	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.94938	0.8363	M	0.87547	2.89	0.80722	D	1	P	0.40909	0.732	B	0.44163	0.443	D	0.95543	0.8614	10	0.87932	D	0	.	15.3327	0.74226	0.0:0.0:0.0:1.0	.	62	P35232	PHB_HUMAN	R	62	ENSP00000300408:Q62R;ENSP00000425035:Q62R;ENSP00000393320:Q62R;ENSP00000426433:Q62R;ENSP00000422182:Q62R;ENSP00000407828:Q62R;ENSP00000410680:Q62R	ENSP00000300408:Q62R	Q	-	2	0	PHB	44844104	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.988000	0.88194	2.095000	0.63458	0.460000	0.39030	CAG	.	.		0.502	PHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258826.1	NM_002634	
ACSF2	80221	hgsc.bcm.edu	37	17	48541615	48541615	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:48541615T>C	ENST00000300441.4	+	10	1279	c.1175T>C	c.(1174-1176)aTc>aCc	p.I392T	ACSF2_ENST00000427954.2_Missense_Mutation_p.I417T|ACSF2_ENST00000541920.1_Missense_Mutation_p.I232T|ACSF2_ENST00000502667.1_Missense_Mutation_p.I379T|ACSF2_ENST00000504392.1_Missense_Mutation_p.I349T	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	392					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			CCAGAGTTGATCCGAGCCATC	0.577																																					p.I392T		Atlas-SNP	.											.	ACSF2	46	.	0			c.T1175C						.						138.0	126.0	130.0					17																	48541615		2203	4300	6503	SO:0001583	missense	80221	exon10			AGTTGATCCGAGC	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"""Acyl-CoA synthetase family"""	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.1175T>C	chr17.hg19:g.48541615T>C	ENSP00000300441:p.Ile392Thr	93.0	0.0		131.0	6.0	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Missense_Mutation	SNP	ENST00000300441.4	hg19	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	T	19.93	3.917982	0.73098	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	4.34	4.34	0.51931	AMP-dependent synthetase/ligase (1);	0.396338	0.26359	N	0.024827	T	0.50154	0.1599	M	0.64676	1.99	0.49130	D	0.99975	P;P;P;P	0.37688	0.605;0.605;0.605;0.605	P;B;P;P	0.45712	0.491;0.388;0.491;0.491	T	0.57093	-0.7870	10	0.87932	D	0	-15.4607	14.0101	0.64490	0.0:0.0:0.0:1.0	.	379;417;349;392	B4DHT5;B4DFQ6;E9PF16;Q96CM8	.;.;.;ACSF2_HUMAN	T	392;232;349;417;379	ENSP00000300441:I392T;ENSP00000437987:I232T;ENSP00000425964:I349T;ENSP00000401831:I417T;ENSP00000421884:I379T	ENSP00000300441:I392T	I	+	2	0	ACSF2	45896614	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	6.350000	0.73017	1.961000	0.56991	0.459000	0.35465	ATC	.	.		0.577	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48598485	48598485	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:48598485A>G	ENST00000323776.5	+	8	1222	c.1060A>G	c.(1060-1062)Agg>Ggg	p.R354G	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.R317G	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			ACCAGCCCAGAGGGACGCTTC	0.557																																					p.R354G		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.A1060G						.						76.0	58.0	64.0					17																	48598485		2203	4300	6503	SO:0001583	missense	84073	exon8			GCCCAGAGGGACG	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.1060A>G	chr17.hg19:g.48598485A>G	ENSP00000323184:p.Arg354Gly	51.0	0.0		57.0	4.0	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	hg19	CCDS32680.2	.	.	.	.	.	.	.	.	.	.	A	12.38	1.919821	0.33908	.	.	ENSG00000136449	ENST00000323776;ENST00000436259	T;T	0.42513	0.97;0.97	5.47	0.295	0.15752	.	0.663614	0.14290	N	0.328982	T	0.23054	0.0557	L	0.27053	0.805	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.09377	0.004;0.004	T	0.15723	-1.0427	10	0.46703	T	0.11	-11.5632	1.3763	0.02221	0.4384:0.2735:0.1554:0.1327	.	317;354	Q8TBZ2;B4DZQ1	MYBPP_HUMAN;.	G	354;317	ENSP00000323184:R354G;ENSP00000397209:R317G	ENSP00000323184:R354G	R	+	1	2	MYCBPAP	45953484	0.273000	0.24181	0.025000	0.17156	0.387000	0.30353	0.679000	0.25291	0.034000	0.15491	0.454000	0.30748	AGG	.	.		0.557	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
ANKFN1	162282	hgsc.bcm.edu	37	17	54428175	54428175	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:54428175T>C	ENST00000318698.2	+	4	281	c.246T>C	c.(244-246)tgT>tgC	p.C82C	ANKFN1_ENST00000566473.2_Silent_p.C82C	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	82										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						TACATCTCTGTCAGTCAAAAA	0.413																																					p.C82C		Atlas-SNP	.											.	ANKFN1	115	.	0			c.T246C						.						110.0	109.0	109.0					17																	54428175		2203	4300	6503	SO:0001819	synonymous_variant	162282	exon4			TCTCTGTCAGTCA	AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"""Ankyrin repeat domain containing"", ""Fibronectin type III domain containing"""	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.246T>C	chr17.hg19:g.54428175T>C		102.0	0.0		106.0	5.0	NM_153228		Silent	SNP	ENST00000318698.2	hg19	CCDS32686.1																																																																																			.	.		0.413	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228	
OR4D2	124538	hgsc.bcm.edu	37	17	56247313	56247313	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:56247313T>C	ENST00000545221.1	+	1	297	c.297T>C	c.(295-297)ggT>ggC	p.G99G		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	99						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(1)|lung(19)|ovary(1)|skin(2)|stomach(1)	26						GCTGCATGGGTCAGATCTTCT	0.527																																					p.G99G		Atlas-SNP	.											.	OR4D2	48	.	0			c.T297C						.						109.0	99.0	102.0					17																	56247313		2203	4300	6503	SO:0001819	synonymous_variant	124538	exon1			CATGGGTCAGATC		CCDS32688.1	17q22	2013-09-23			ENSG00000255713	ENSG00000255713		"""GPCR / Class A : Olfactory receptors"""	8294	protein-coding gene	gene with protein product							Standard	NM_001004707		Approved		uc010wnp.2	P58180	OTTHUMG00000178801	ENST00000545221.1:c.297T>C	chr17.hg19:g.56247313T>C		46.0	0.0		100.0	4.0	NM_001004707	Q6IFN8|Q96R75	Silent	SNP	ENST00000545221.1	hg19	CCDS32688.1																																																																																			.	.		0.527	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1		
MED13	9969	hgsc.bcm.edu	37	17	60028243	60028243	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:60028243A>G	ENST00000397786.2	-	28	6310	c.6234T>C	c.(6232-6234)ccT>ccC	p.P2078P		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	2078					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						AGAACCAGTCAGGTAATGGAC	0.428																																					p.P2078P		Atlas-SNP	.											.	MED13	181	.	0			c.T6234C						.						155.0	141.0	146.0					17																	60028243		1943	4166	6109	SO:0001819	synonymous_variant	9969	exon28			CCAGTCAGGTAAT	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.6234T>C	chr17.hg19:g.60028243A>G		66.0	0.0		84.0	4.0	NM_005121	B2RU05|O60334	Silent	SNP	ENST00000397786.2	hg19	CCDS42366.1																																																																																			.	.		0.428	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
KPNA2	3838	hgsc.bcm.edu	37	17	66038453	66038453	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:66038453T>C	ENST00000537025.2	+	5	1175	c.555T>C	c.(553-555)gcT>gcC	p.A185A	KPNA2_ENST00000330459.3_Silent_p.A185A			P52292	IMA1_HUMAN	karyopherin alpha 2 (RAG cohort 1, importin alpha 1)	185	NLS binding site (major). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|DNA metabolic process (GO:0006259)|NLS-bearing protein import into nucleus (GO:0006607)|regulation of DNA recombination (GO:0000018)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone deacetylase binding (GO:0042826)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|kidney(2)|lung(9)|prostate(1)|urinary_tract(2)	22	all_cancers(12;1.18e-09)		BRCA - Breast invasive adenocarcinoma(8;1.03e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			CTGTCTGGGCTCTAGGAAACA	0.433																																					p.A185A		Atlas-SNP	.											.	KPNA2	55	.	0			c.T555C						.						269.0	273.0	271.0					17																	66038453		2203	4296	6499	SO:0001819	synonymous_variant	3838	exon5			CTGGGCTCTAGGA	U09559	CCDS32713.1	17q24.2	2013-02-14						"""Importins"", ""Armadillo repeat containing"""	6395	protein-coding gene	gene with protein product		600685		RCH1		8016130, 7754385	Standard	NM_002266		Approved	SRP1alpha, IPOA1, QIP2	uc002jgk.3	P52292		ENST00000537025.2:c.555T>C	chr17.hg19:g.66038453T>C		62.0	0.0		71.0	4.0	NM_002266	B9EJD6|Q53YE3|Q9BRU5	Silent	SNP	ENST00000537025.2	hg19	CCDS32713.1																																																																																			.	.		0.433	KPNA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448111.1	NM_002266	
ABCA6	23460	hgsc.bcm.edu	37	17	67092459	67092459	+	Silent	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:67092459G>A	ENST00000284425.2	-	25	3504	c.3330C>T	c.(3328-3330)gtC>gtT	p.V1110V	ABCA6_ENST00000446604.2_5'UTR	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	1110					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					ATATGAAGAAGACAAGAGAAG	0.274																																					p.V1110V		Atlas-SNP	.											.	ABCA6	210	.	0			c.C3330T						.						23.0	27.0	26.0					17																	67092459		2180	4237	6417	SO:0001819	synonymous_variant	23460	exon25			GAAGAAGACAAGA	U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"""ATP binding cassette transporters / subfamily A"""	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.3330C>T	chr17.hg19:g.67092459G>A		64.0	0.0		104.0	5.0	NM_080284	Q6NSH9|Q8N856|Q8WWZ6	Silent	SNP	ENST00000284425.2	hg19	CCDS11683.1																																																																																			.	.		0.274	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284	
KIF19	124602	hgsc.bcm.edu	37	17	72350520	72350520	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:72350520A>G	ENST00000389916.4	+	18	2666	c.2528A>G	c.(2527-2529)gAg>gGg	p.E843G	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	843					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GCTGCCAGTGAGGACAACCTG	0.697																																					p.E843G		Atlas-SNP	.											.	KIF19	102	.	0			c.A2528G						.						11.0	14.0	13.0					17																	72350520		1946	4108	6054	SO:0001583	missense	124602	exon18			CCAGTGAGGACAA	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2528A>G	chr17.hg19:g.72350520A>G	ENSP00000374566:p.Glu843Gly	94.0	0.0		60.0	5.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	hg19	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	A	19.92	3.915684	0.73098	.	.	ENSG00000196169	ENST00000389916	T	0.74632	-0.86	5.06	5.06	0.68205	.	.	.	.	.	T	0.67239	0.2872	L	0.54323	1.7	0.37026	D	0.896437	P	0.39665	0.682	B	0.32980	0.156	T	0.72239	-0.4351	9	0.32370	T	0.25	.	14.5258	0.67887	1.0:0.0:0.0:0.0	.	843	Q2TAC6	KIF19_HUMAN	G	843	ENSP00000374566:E843G	ENSP00000374566:E843G	E	+	2	0	KIF19	69862115	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	5.488000	0.66869	1.915000	0.55452	0.454000	0.30748	GAG	.	.		0.697	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
C17orf77	146723	hgsc.bcm.edu	37	17	72588775	72588775	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:72588775T>C	ENST00000392620.1	+	3	952	c.590T>C	c.(589-591)cTc>cCc	p.L197P	C17orf77_ENST00000328023.2_Missense_Mutation_p.L197P|CD300LD_ENST00000375352.1_5'Flank	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	197						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						TGCACAGGACTCACACCCAGC	0.602																																					p.L197P		Atlas-SNP	.											.	C17orf77	31	.	0			c.T590C						.						89.0	85.0	87.0					17																	72588775		2203	4300	6503	SO:0001583	missense	146723	exon3			CAGGACTCACACC		CCDS32721.1	17q25.1	2006-01-16			ENSG00000182352	ENSG00000182352			26480	protein-coding gene	gene with protein product							Standard	NM_152460		Approved	FLJ31882	uc002jla.1	Q96MU5	OTTHUMG00000067611	ENST00000392620.1:c.590T>C	chr17.hg19:g.72588775T>C	ENSP00000376396:p.Leu197Pro	103.0	0.0		124.0	6.0	NM_152460		Missense_Mutation	SNP	ENST00000392620.1	hg19	CCDS32721.1	.	.	.	.	.	.	.	.	.	.	T	3.951	-0.012295	0.07727	.	.	ENSG00000182352	ENST00000392620;ENST00000328023	T;T	0.57907	0.37;0.37	2.38	2.38	0.29361	.	.	.	.	.	T	0.47192	0.1432	N	0.08118	0	0.09310	N	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.27502	-1.0072	8	.	.	.	.	6.6738	0.23083	0.0:0.0:0.0:1.0	.	197	Q96MU5	CQ077_HUMAN	P	197	ENSP00000376396:L197P;ENSP00000329353:L197P	.	L	+	2	0	C17orf77	70100370	0.001000	0.12720	0.011000	0.14972	0.027000	0.11550	0.157000	0.16402	1.342000	0.45619	0.418000	0.28097	CTC	.	.		0.602	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460	
SPHK1	8877	hgsc.bcm.edu	37	17	74383312	74383312	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:74383312A>G	ENST00000545180.1	+	8	1609	c.800A>G	c.(799-801)cAc>cGc	p.H267R	SPHK1_ENST00000590959.1_Missense_Mutation_p.H281R|SPHK1_ENST00000323374.4_Missense_Mutation_p.H353R|SPHK1_ENST00000392496.3_Missense_Mutation_p.H267R|SPHK1_ENST00000592299.1_Missense_Mutation_p.H267R			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	267					'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	CTGCACTCGCACCTGGGCAGT	0.617																																					p.H353R	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.A1058G						.						62.0	46.0	51.0					17																	74383312		2203	4300	6503	SO:0001583	missense	8877	exon6			ACTCGCACCTGGG	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.800A>G	chr17.hg19:g.74383312A>G	ENSP00000440970:p.His267Arg	62.0	0.0		132.0	6.0	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	hg19	CCDS45785.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.751995	0.89753	.	.	ENSG00000176170	ENST00000545180;ENST00000323374;ENST00000392496;ENST00000543830	T;T;T	0.13196	2.61;2.61;2.61	5.08	5.08	0.68730	.	0.048515	0.85682	D	0.000000	T	0.43255	0.1239	M	0.89968	3.075	0.80722	D	1	D;D;D	0.89917	0.999;0.997;1.0	D;D;D	0.77557	0.988;0.947;0.99	T	0.49153	-0.8969	10	0.27785	T	0.31	-16.2198	14.8579	0.70355	1.0:0.0:0.0:0.0	.	353;281;267	Q9NYA1-2;Q96GK1;Q9NYA1	.;.;SPHK1_HUMAN	R	267;353;267;266	ENSP00000440970:H267R;ENSP00000313681:H353R;ENSP00000376285:H267R	ENSP00000313681:H353R	H	+	2	0	SPHK1	71894907	1.000000	0.71417	0.968000	0.41197	0.881000	0.50899	6.951000	0.75983	1.901000	0.55032	0.460000	0.39030	CAC	.	.		0.617	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972	
RNF213	57674	hgsc.bcm.edu	37	17	78261894	78261894	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:78261894A>G	ENST00000582970.1	+	4	685	c.542A>G	c.(541-543)gAg>gGg	p.E181G	RNF213_ENST00000508628.2_Missense_Mutation_p.E230G|RNF213_ENST00000319921.4_Missense_Mutation_p.E181G|RNF213_ENST00000456466.1_Missense_Mutation_p.E181G	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	181					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GCTTTGGGAGAGGCAGGAGTG	0.687																																					p.E181G		Atlas-SNP	.											.	RNF213	766	.	0			c.A542G						.						19.0	19.0	19.0					17																	78261894		2196	4294	6490	SO:0001583	missense	57674	exon4			TGGGAGAGGCAGG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.542A>G	chr17.hg19:g.78261894A>G	ENSP00000464087:p.Glu181Gly	69.0	0.0		104.0	5.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	A	8.037	0.763092	0.15914	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T;T	0.46819	0.86;0.86	3.78	-6.45	0.01914	.	10.914700	0.00166	N	0.000000	T	0.22437	0.0541	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.07770	-1.0755	10	0.38643	T	0.18	3.1023	2.1781	0.03867	0.5159:0.1395:0.2038:0.1408	.	181	Q9HCF4-2	.	G	181;230;181;181	ENSP00000392123:E181G;ENSP00000324392:E181G	ENSP00000324392:E181G	E	+	2	0	RNF213	75876489	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.297000	0.08276	-1.150000	0.02840	-0.366000	0.07423	GAG	.	.		0.687	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
PTPRM	5797	hgsc.bcm.edu	37	18	8085685	8085685	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:8085685T>C	ENST00000332175.8	+	10	2605	c.1568T>C	c.(1567-1569)gTc>gCc	p.V523A	PTPRM_ENST00000400060.4_Missense_Mutation_p.V523A|PTPRM_ENST00000400053.4_Missense_Mutation_p.V461A|PTPRM_ENST00000444013.1_Missense_Mutation_p.V310A|PTPRM_ENST00000578571.1_3'UTR|PTPRM_ENST00000580170.1_Missense_Mutation_p.V523A	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	523	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				TACAAAGCAGTCAGTTCCTTT	0.388																																					p.V523A		Atlas-SNP	.											.	PTPRM	185	.	0			c.T1568C						.						80.0	78.0	79.0					18																	8085685		2203	4299	6502	SO:0001583	missense	5797	exon10			AAGCAGTCAGTTC	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.1568T>C	chr18.hg19:g.8085685T>C	ENSP00000331418:p.Val523Ala	106.0	0.0		147.0	6.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.326764	0.81690	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.87	5.87	0.94306	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.060088	0.64402	D	0.000003	T	0.56978	0.2022	L	0.42632	1.34	0.58432	D	0.999993	P;P;P	0.40875	0.731;0.507;0.507	P;B;B	0.48552	0.581;0.435;0.435	T	0.55805	-0.8083	10	0.44086	T	0.13	.	16.2806	0.82678	0.0:0.0:0.0:1.0	.	310;523;523	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	A	523;523;461;310	ENSP00000331418:V523A;ENSP00000382933:V523A;ENSP00000382927:V461A;ENSP00000387608:V310A	ENSP00000331418:V523A	V	+	2	0	PTPRM	8075685	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.991000	0.88244	2.248000	0.74166	0.533000	0.62120	GTC	.	.		0.388	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		
DSC3	1825	hgsc.bcm.edu	37	18	28604328	28604328	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:28604328T>C	ENST00000360428.4	-	6	842	c.762A>G	c.(760-762)gaA>gaG	p.E254E	DSC3_ENST00000434452.1_Silent_p.E254E	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	254	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			GTCTACTACTTTCCAAAACTT	0.358																																					p.E254E		Atlas-SNP	.											.	DSC3	225	.	0			c.A762G						.						61.0	66.0	64.0					18																	28604328		2203	4299	6502	SO:0001819	synonymous_variant	1825	exon6			ACTACTTTCCAAA	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.762A>G	chr18.hg19:g.28604328T>C		40.0	0.0		53.0	5.0	NM_024423	A6NN35|Q14200|Q9HAZ9	Silent	SNP	ENST00000360428.4	hg19	CCDS32810.1																																																																																			.	.		0.358	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423	
TRAPPC8	22878	hgsc.bcm.edu	37	18	29432603	29432603	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:29432603T>C	ENST00000283351.4	-	23	3792	c.3457A>G	c.(3457-3459)Aag>Gag	p.K1153E	TRAPPC8_ENST00000582539.1_Missense_Mutation_p.K1099E	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	1153					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						AACTTTCCCTTCTCCCTACTG	0.313																																					p.K1153E		Atlas-SNP	.											.	TRAPPC8	126	.	0			c.A3457G						.						163.0	179.0	173.0					18																	29432603		2203	4300	6503	SO:0001583	missense	22878	exon23			TTCCCTTCTCCCT	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.3457A>G	chr18.hg19:g.29432603T>C	ENSP00000283351:p.Lys1153Glu	68.0	0.0		69.0	4.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	hg19	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	T	13.23	2.175307	0.38413	.	.	ENSG00000153339	ENST00000283351	T	0.19105	2.17	5.78	5.78	0.91487	.	0.137195	0.64402	D	0.000006	T	0.18130	0.0435	L	0.40543	1.245	0.80722	D	1	B	0.22276	0.067	B	0.27380	0.079	T	0.03969	-1.0988	10	0.02654	T	1	.	16.092	0.81098	0.0:0.0:0.0:1.0	.	1153	Q9Y2L5	TPPC8_HUMAN	E	1153	ENSP00000283351:K1153E	ENSP00000283351:K1153E	K	-	1	0	TRAPPC8	27686601	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.370000	0.52372	2.202000	0.70862	0.477000	0.44152	AAG	.	.		0.313	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939	
MBD1	4152	hgsc.bcm.edu	37	18	47801526	47801526	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:47801526T>C	ENST00000591416.1	-	9	1313	c.882A>G	c.(880-882)ccA>ccG	p.P294P	MBD1_ENST00000588937.1_Silent_p.P294P|MBD1_ENST00000269468.5_Silent_p.P294P|MBD1_ENST00000353909.3_Silent_p.P245P|MBD1_ENST00000591535.1_Silent_p.P294P|MBD1_ENST00000339998.6_Silent_p.P294P|MBD1_ENST00000457839.2_Silent_p.P319P|MBD1_ENST00000424334.2_Silent_p.P345P|MBD1_ENST00000349085.2_Silent_p.P294P|MBD1_ENST00000398493.1_Silent_p.P294P|MBD1_ENST00000587605.1_Silent_p.P294P|MBD1_ENST00000269471.5_Silent_p.P294P|MBD1_ENST00000585595.1_Silent_p.P319P|MBD1_ENST00000590208.1_Silent_p.P294P|MBD1_ENST00000347968.3_Silent_p.P294P|MBD1_ENST00000585672.1_Silent_p.P245P|MBD1_ENST00000398488.1_Silent_p.P294P|MBD1_ENST00000382948.5_Silent_p.P294P|MBD1_ENST00000398495.2_Silent_p.P319P|MBD1_ENST00000436910.1_Silent_p.P294P			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1	294	Pro-rich.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						GGGACTGTGATGGGGGTGGTG	0.657																																					p.P319P		Atlas-SNP	.											.	MBD1	228	.	0			c.A957G						.						36.0	44.0	41.0					18																	47801526		2203	4300	6503	SO:0001819	synonymous_variant	4152	exon10			CTGTGATGGGGGT	Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669	ENST00000591416.1:c.882A>G	chr18.hg19:g.47801526T>C		85.0	0.0		95.0	36.0	NM_001204137	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Silent	SNP	ENST00000591416.1	hg19	CCDS11943.1																																																																																			.	.		0.657	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846	
NEDD4L	23327	hgsc.bcm.edu	37	18	56018257	56018257	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:56018257G>A	ENST00000400345.3	+	18	1971	c.1688G>A	c.(1687-1689)cGa>cAa	p.R563Q	NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000357895.5_Missense_Mutation_p.R555Q|NEDD4L_ENST00000456173.2_Missense_Mutation_p.R422Q|NEDD4L_ENST00000256830.9_Missense_Mutation_p.R459Q|NEDD4L_ENST00000256832.7_Missense_Mutation_p.R422Q|NEDD4L_ENST00000456986.1_Missense_Mutation_p.R442Q|NEDD4L_ENST00000382850.4_Missense_Mutation_p.R543Q|NEDD4L_ENST00000431212.2_Missense_Mutation_p.R442Q|NEDD4L_ENST00000356462.6_Missense_Mutation_p.R499Q|NEDD4L_ENST00000586263.1_Missense_Mutation_p.R535Q|NEDD4L_ENST00000435432.2_Missense_Mutation_p.R422Q	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	563	WW 4. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						TTGGATGGCCGAACGTTTTAT	0.423																																					p.R563Q		Atlas-SNP	.											.	NEDD4L	126	.	0			c.G1688A						.						104.0	92.0	96.0					18																	56018257		1859	4086	5945	SO:0001583	missense	23327	exon18			ATGGCCGAACGTT	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"""neural precursor cell expressed, developmentally down-regulated 4-like"""			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.1688G>A	chr18.hg19:g.56018257G>A	ENSP00000383199:p.Arg563Gln	60.0	0.0		96.0	7.0	NM_001144967	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Missense_Mutation	SNP	ENST00000400345.3	hg19	CCDS45872.1	.	.	.	.	.	.	.	.	.	.	G	36	5.924514	0.97110	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000356462;ENST00000256830;ENST00000256832;ENST00000456986;ENST00000357895;ENST00000435432;ENST00000456173;ENST00000431212	D;D;D;D;D;D;D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19;-2.19;-2.19;-2.19;-2.19;-2.19;-2.19	5.57	5.57	0.84162	WW/Rsp5/WWP (6);	0.000000	0.85682	D	0.000000	D	0.93374	0.7887	M	0.76574	2.34	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.997;0.996;0.996;0.998;0.998;1.0;0.996	D;P;P;D;D;D;P	0.72338	0.95;0.634;0.634;0.97;0.915;0.977;0.634	D	0.93251	0.6635	10	0.56958	D	0.05	.	19.5497	0.95312	0.0:0.0:1.0:0.0	.	459;535;555;422;499;563;543	Q96PU5-3;Q96PU5-6;Q96PU5-7;Q3LSM7;Q96PU5-2;Q96PU5;Q96PU5-5	.;.;.;.;.;NED4L_HUMAN;.	Q	563;543;499;459;422;442;555;422;422;442	ENSP00000383199:R563Q;ENSP00000372301:R543Q;ENSP00000348847:R499Q;ENSP00000256830:R459Q;ENSP00000256832:R422Q;ENSP00000411947:R442Q;ENSP00000350569:R555Q;ENSP00000393395:R422Q;ENSP00000405440:R422Q;ENSP00000389406:R442Q	ENSP00000256830:R459Q	R	+	2	0	NEDD4L	54169237	1.000000	0.71417	0.989000	0.46669	0.985000	0.73830	9.120000	0.94369	2.602000	0.87976	0.655000	0.94253	CGA	.	.		0.423	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1		
TMX3	54495	hgsc.bcm.edu	37	18	66377317	66377317	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:66377317T>C	ENST00000299608.2	-	4	522	c.206A>G	c.(205-207)gAg>gGg	p.E69G	TMX3_ENST00000562706.1_Missense_Mutation_p.E69G|TMX3_ENST00000443099.2_Missense_Mutation_p.E69G	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	69	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						GCTTTTCATCTCAAGACCAAC	0.353																																					p.E69G		Atlas-SNP	.											.	TMX3	44	.	0			c.A206G						.						110.0	100.0	103.0					18																	66377317		2203	4300	6503	SO:0001583	missense	54495	exon4			TTCATCTCAAGAC	BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"""Protein disulfide isomerases"""	24718	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 13"""		"""thioredoxin domain containing 10"""	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.206A>G	chr18.hg19:g.66377317T>C	ENSP00000299608:p.Glu69Gly	83.0	0.0		114.0	5.0	NM_019022	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Missense_Mutation	SNP	ENST00000299608.2	hg19	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.269900	0.80469	.	.	ENSG00000166479	ENST00000299608;ENST00000544714;ENST00000443099	T;T;T	0.03860	3.78;3.78;3.78	5.57	5.57	0.84162	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.000000	0.85682	D	0.000000	T	0.20901	0.0503	M	0.78285	2.405	0.80722	D	1	D;D;D	0.76494	0.999;0.983;0.999	D;P;D	0.75020	0.96;0.858;0.985	T	0.00593	-1.1654	10	0.38643	T	0.18	.	14.5486	0.68050	0.0:0.0:0.0:1.0	.	69;69;69	B4DIE3;Q96JJ7-2;Q96JJ7	.;.;TMX3_HUMAN	G	69	ENSP00000299608:E69G;ENSP00000444954:E69G;ENSP00000402605:E69G	ENSP00000299608:E69G	E	-	2	0	TMX3	64528297	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.193000	0.72075	2.116000	0.64780	0.460000	0.39030	GAG	.	.		0.353	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022	
PTPRS	5802	hgsc.bcm.edu	37	19	5258114	5258114	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:5258114T>C	ENST00000587303.1	-	7	719	c.620A>G	c.(619-621)gAg>gGg	p.E207G	PTPRS_ENST00000357368.4_Missense_Mutation_p.E207G|PTPRS_ENST00000588012.1_Missense_Mutation_p.E198G|PTPRS_ENST00000592099.1_Missense_Mutation_p.E198G|PTPRS_ENST00000372412.4_Missense_Mutation_p.E208G|PTPRS_ENST00000353284.2_Missense_Mutation_p.E198G|PTPRS_ENST00000348075.2_Missense_Mutation_p.E198G|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Missense_Mutation_p.E207G			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	207	Ig-like C2-type 2.				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)	GTCGGTTTCCTCACTGCTTTC	0.597																																					p.E207G		Atlas-SNP	.											.	PTPRS	169	.	0			c.A620G						.						116.0	111.0	113.0					19																	5258114		2203	4300	6503	SO:0001583	missense	5802	exon8			GTTTCCTCACTGC	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.620A>G	chr19.hg19:g.5258114T>C	ENSP00000467537:p.Glu207Gly	149.0	0.0		137.0	6.0	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	hg19	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.303899	0.81136	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075;ENST00000355322;ENST00000544524;ENST00000353284	T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37	3.75	3.75	0.43078	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	U	0.000006	T	0.72036	0.3411	L	0.35249	1.045	0.33769	D	0.622812	P;D;P;D;D;P	0.89917	0.911;1.0;0.845;0.994;1.0;0.936	B;D;B;P;D;P	0.97110	0.357;0.999;0.264;0.798;1.0;0.462	T	0.80111	-0.1519	10	0.62326	D	0.03	.	12.6585	0.56801	0.0:0.0:0.0:1.0	.	207;198;198;198;207;224	F8W800;Q13332-7;F5H2T4;Q13332-6;Q13332;Q59FX6	.;.;.;.;PTPRS_HUMAN;.	G	224;208;207;207;207;207;198;207;198;198	ENSP00000361489:E208G;ENSP00000349932:E207G;ENSP00000262963:E207G;ENSP00000269907:E198G;ENSP00000327313:E198G	ENSP00000262963:E207G	E	-	2	0	PTPRS	5209114	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.753000	0.85153	1.589000	0.49982	0.454000	0.30748	GAG	.	.		0.597	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
TRIP10	9322	hgsc.bcm.edu	37	19	6751209	6751209	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:6751209T>C	ENST00000313244.9	+	15	1828	c.1793T>C	c.(1792-1794)gTc>gCc	p.V598A	CTD-3128G10.6_ENST00000594056.1_RNA|TRIP10_ENST00000600428.1_Missense_Mutation_p.V434A|TRIP10_ENST00000596758.1_Missense_Mutation_p.S552P|TRIP10_ENST00000313285.8_Missense_Mutation_p.V542A			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	598	Interaction with ARHGAP17, DAAM1, DIAPH1 and DIAPH2.|Interaction with DNM1 and WASL.|Interaction with PDE6G. {ECO:0000250}.|Interaction with WAS.|Required for interaction with FASLG and localization to lysosomes.|Required for podosome formation.|SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						TACCTCCGAGTCACGCTCAAT	0.612																																					p.V542A		Atlas-SNP	.											.	TRIP10	104	.	0			c.T1625C						.						60.0	67.0	65.0					19																	6751209		2203	4300	6503	SO:0001583	missense	9322	exon14			TCCGAGTCACGCT	AB072596	CCDS12172.1, CCDS74271.1, CCDS74272.1	19p13.3	2008-02-05			ENSG00000125733	ENSG00000125733			12304	protein-coding gene	gene with protein product	"""Cdc42-interacting protein"""	604504	"""salt tolerator"""	STOT		7776974, 9210375, 11294612	Standard	XM_005259683		Approved	STP, HSTP, CIP4	uc002mfr.3	Q15642	OTTHUMG00000150255	ENST00000313244.9:c.1793T>C	chr19.hg19:g.6751209T>C	ENSP00000320117:p.Val598Ala	110.0	0.0		134.0	6.0	NM_004240	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Missense_Mutation	SNP	ENST00000313244.9	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.82|17.82	3.484267|3.484267	0.63962|0.63962	.|.	.|.	ENSG00000125733|ENSG00000125733	ENST00000420690|ENST00000313285;ENST00000313244	.|T;T	.|0.18174	.|2.23;3.08	4.84|4.84	4.84|4.84	0.62591|0.62591	.|Src homology-3 domain (3);	.|0.220353	.|0.37530	.|N	.|0.002051	T|T	0.29061|0.29061	0.0722|0.0722	L|L	0.37850|0.37850	1.14|1.14	0.45946|0.45946	D|D	0.998773|0.998773	D|P;P	0.64830|0.49447	0.994|0.924;0.89	P|P;P	0.59889|0.62298	0.865|0.9;0.496	T|T	0.01661|0.01661	-1.1301|-1.1301	8|10	0.87932|0.72032	D|D	0|0.01	-28.6222|-28.6222	12.6835|12.6835	0.56934|0.56934	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	552|598;542	G5E9U1|Q15642;Q15642-2	.|CIP4_HUMAN;.	P|A	552|542;598	.|ENSP00000320493:V542A;ENSP00000320117:V598A	ENSP00000415493:S552P|ENSP00000320117:V598A	S|V	+|+	1|2	0|0	TRIP10|TRIP10	6702209|6702209	1.000000|1.000000	0.71417|0.71417	0.978000|0.978000	0.43139|0.43139	0.148000|0.148000	0.21650|0.21650	5.542000|5.542000	0.67218|0.67218	2.163000|2.163000	0.67991|0.67991	0.254000|0.254000	0.18369|0.18369	TCA|GTC	.	.		0.612	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2		
INSR	3643	hgsc.bcm.edu	37	19	7152932	7152932	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:7152932T>C	ENST00000302850.5	-	10	2178	c.2036A>G	c.(2035-2037)aAg>aGg	p.K679R	INSR_ENST00000341500.5_Missense_Mutation_p.K679R	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	679	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	CGAGGGCAGCTTCAGCCCTGG	0.542																																					p.K679R		Atlas-SNP	.											.	INSR	265	.	0			c.A2036G						.						63.0	58.0	60.0					19																	7152932		2203	4300	6503	SO:0001583	missense	3643	exon10			GGCAGCTTCAGCC	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.2036A>G	chr19.hg19:g.7152932T>C	ENSP00000303830:p.Lys679Arg	58.0	0.0		67.0	4.0	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	hg19	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	t	13.44	2.237562	0.39598	.	.	ENSG00000171105	ENST00000302850;ENST00000341500	T;T	0.75367	-0.93;-0.93	5.55	5.55	0.83447	Fibronectin, type III (3);	0.000000	0.47852	U	0.000209	T	0.67970	0.2950	L	0.46947	1.48	0.58432	D	0.999995	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.0	T	0.63571	-0.6607	10	0.36615	T	0.2	.	13.6724	0.62434	0.0:0.0:0.0:1.0	.	670;679;679	Q86WY9;P06213-2;P06213	.;.;INSR_HUMAN	R	679	ENSP00000303830:K679R;ENSP00000342838:K679R	ENSP00000303830:K679R	K	-	2	0	INSR	7103932	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	7.477000	0.81069	2.121000	0.65114	0.487000	0.48397	AAG	.	.		0.542	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
MUC16	94025	hgsc.bcm.edu	37	19	9089471	9089471	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:9089471G>C	ENST00000397910.4	-	1	2547	c.2344C>G	c.(2344-2346)Cct>Gct	p.P782A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	782	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ACTCTTTCAGGACTTGTTGCT	0.507																																					p.P782A		Atlas-SNP	.											.	MUC16	4315	.	0			c.C2344G						.						232.0	224.0	227.0					19																	9089471		2020	4191	6211	SO:0001583	missense	94025	exon1			TTTCAGGACTTGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.2344C>G	chr19.hg19:g.9089471G>C	ENSP00000381008:p.Pro782Ala	111.0	0.0		158.0	66.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	0.547	-0.851007	0.02651	.	.	ENSG00000181143	ENST00000397910	T	0.03094	4.05	1.56	-3.12	0.05282	.	.	.	.	.	T	0.01661	0.0053	N	0.03608	-0.345	.	.	.	B	0.15473	0.013	B	0.09377	0.004	T	0.44421	-0.9329	8	0.87932	D	0	.	4.2204	0.10554	0.0:0.2703:0.4022:0.3275	.	782	B5ME49	.	A	782	ENSP00000381008:P782A	ENSP00000381008:P782A	P	-	1	0	MUC16	8950471	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-2.843000	0.00736	-1.645000	0.01515	0.205000	0.17691	CCT	.	.		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SMARCA4	6597	hgsc.bcm.edu	37	19	11099991	11099991	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:11099991A>G	ENST00000429416.3	+	8	1399		c.e8-1		SMARCA4_ENST00000541122.2_Splice_Site|SMARCA4_ENST00000444061.3_Splice_Site|SMARCA4_ENST00000344626.4_Splice_Site|SMARCA4_ENST00000589677.1_Splice_Site|SMARCA4_ENST00000358026.2_Splice_Site|SMARCA4_ENST00000590574.1_Splice_Site|SMARCA4_ENST00000413806.3_Splice_Site|SMARCA4_ENST00000450717.3_Splice_Site	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)				CTCTGCTCCCAGGCTGCAGGC	0.607			"""F, N, Mis"""		NSCLC																																.		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.1119-2A>G						.						82.0	85.0	84.0					19																	11099991		2203	4300	6503	SO:0001630	splice_region_variant	6597	exon7			GCTCCCAGGCTGC	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.1119-1A>G	chr19.hg19:g.11099991A>G		103.0	0.0		123.0	5.0	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Splice_Site	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.009744	0.75046	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	.	.	.	4.42	4.42	0.53409	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.8048	0.57607	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SMARCA4	10960991	1.000000	0.71417	0.989000	0.46669	0.910000	0.53928	7.271000	0.78506	1.871000	0.54225	0.379000	0.24179	.	.	.		0.607	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	Intron
ZNF44	51710	hgsc.bcm.edu	37	19	12383437	12383437	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:12383437A>G	ENST00000356109.5	-	5	1895	c.1777T>C	c.(1777-1779)Tct>Cct	p.S593P	ZNF44_ENST00000355684.5_Missense_Mutation_p.S545P	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	593					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		AGAAGGAAAGAGGGCCAAAAG	0.428																																					p.S593P		Atlas-SNP	.											.	ZNF44	55	.	0			c.T1777C						.						51.0	56.0	54.0					19																	12383437		2196	4300	6496	SO:0001583	missense	51710	exon5			GGAAAGAGGGCCA	X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"""Zinc fingers, C2H2-type"", ""-"""	13110	protein-coding gene	gene with protein product		194542	"""zinc finger protein 58"", ""zinc finger protein 44 (KOX 7)"", ""zinc finger protein 55"""	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.1777T>C	chr19.hg19:g.12383437A>G	ENSP00000348419:p.Ser593Pro	59.0	0.0		76.0	4.0	NM_001164276	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Missense_Mutation	SNP	ENST00000356109.5	hg19	CCDS54223.1	.	.	.	.	.	.	.	.	.	.	A	14.87	2.664520	0.47572	.	.	ENSG00000197857	ENST00000393337;ENST00000356109;ENST00000457673;ENST00000355684	T;T;T	0.18810	2.19;2.2;2.2	1.1	-0.0512	0.13827	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27629	0.0679	M	0.76838	2.35	.	.	.	P;P	0.52577	0.954;0.893	P;P	0.47470	0.548;0.544	T	0.34601	-0.9822	8	0.66056	D	0.02	.	5.2493	0.15514	0.6907:0.0:0.0:0.3093	.	593;545	P15621;F8W7T7	ZNF44_HUMAN;.	P	593;593;545;545	ENSP00000377008:S593P;ENSP00000348419:S593P;ENSP00000347910:S545P	ENSP00000347910:S545P	S	-	1	0	ZNF44	12244437	0.000000	0.05858	0.000000	0.03702	0.876000	0.50452	-3.128000	0.00592	-0.064000	0.13043	0.254000	0.18369	TCT	.	.		0.428	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264	
CACNA1A	773	hgsc.bcm.edu	37	19	13394203	13394203	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:13394203G>A	ENST00000360228.5	-	22	3699	c.3700C>T	c.(3700-3702)Cgc>Tgc	p.R1234C	CACNA1A_ENST00000573710.2_Missense_Mutation_p.R1235C	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1235					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGCACAGGCGGCGAAGGCTG	0.547																																					p.R1235C		Atlas-SNP	.											.	CACNA1A	715	.	0			c.C3703T						.						77.0	84.0	81.0					19																	13394203		2165	4263	6428	SO:0001583	missense	773	exon22			ACAGGCGGCGAAG	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3700C>T	chr19.hg19:g.13394203G>A	ENSP00000353362:p.Arg1234Cys	179.0	0.0		236.0	76.0	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816993	0.50633	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	T	0.42513	0.97	4.92	3.83	0.44106	.	0.063724	0.56097	D	0.000035	T	0.45296	0.1335	L	0.46670	1.46	0.53688	D	0.999979	D;D;D	0.76494	0.959;0.988;0.999	B;P;P	0.50490	0.241;0.576;0.642	T	0.51108	-0.8747	10	0.87932	D	0	.	13.4591	0.61217	0.0:0.0:0.8427:0.1573	.	1235;1238;1234	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	C	1234;1238;1235;1235	ENSP00000353362:R1234C	ENSP00000317661:R1235C	R	-	1	0	CACNA1A	13255203	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.503000	0.53340	2.301000	0.77427	0.561000	0.74099	CGC	.	.		0.547	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
CC2D1A	54862	hgsc.bcm.edu	37	19	14023137	14023137	+	Splice_Site	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:14023137T>C	ENST00000318003.7	+	3	439	c.198T>C	c.(196-198)ggT>ggC	p.G66G	CC2D1A_ENST00000589606.1_Splice_Site_p.G66G	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	66					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)			TACCGCCAGGTCCCTTGCCGA	0.612																																					p.G66G		Atlas-SNP	.											.	CC2D1A	67	.	0			c.T198C						.						39.0	45.0	43.0					19																	14023137		2111	4215	6326	SO:0001630	splice_region_variant	54862	exon3			GCCAGGTCCCTTG	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.197-1T>C	chr19.hg19:g.14023137T>C		62.0	0.0		81.0	4.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Silent	SNP	ENST00000318003.7	hg19	CCDS42512.1																																																																																			.	.		0.612	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	Silent
OR10H2	26538	hgsc.bcm.edu	37	19	15838973	15838973	+	Silent	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:15838973G>A	ENST00000305899.3	+	1	140	c.120G>A	c.(118-120)ctG>ctA	p.L40L		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	40			L -> Q (in dbSNP:rs4569397).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L40L(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					TCACGCTGCTGGGCAACCTGC	0.582																																					p.L40L		Atlas-SNP	.											OR10H2,NS,carcinoma,0,1	OR10H2	59	.	1	Substitution - coding silent(1)	lung(1)	c.G120A						.						227.0	188.0	201.0					19																	15838973		2203	4298	6501	SO:0001819	synonymous_variant	26538	exon1			GCTGCTGGGCAAC	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.120G>A	chr19.hg19:g.15838973G>A		277.0	0.0		363.0	0.0	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	hg19	CCDS12333.1																																																																																			.	.		0.582	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
EPS15L1	58513	hgsc.bcm.edu	37	19	16524615	16524615	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:16524615T>C	ENST00000248070.6	-	13	1374	c.1235A>G	c.(1234-1236)gAg>gGg	p.E412G	EPS15L1_ENST00000597937.1_Missense_Mutation_p.E412G|EPS15L1_ENST00000455140.2_Missense_Mutation_p.E412G|EPS15L1_ENST00000535753.2_Missense_Mutation_p.E412G|EPS15L1_ENST00000594975.1_Missense_Mutation_p.E412G|EPS15L1_ENST00000602009.1_Missense_Mutation_p.E258G	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	412					endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						TCTGATTGCCTCTTCCTTTTC	0.403																																					p.E412G		Atlas-SNP	.											.	EPS15L1	81	.	0			c.A1235G						.						245.0	198.0	214.0					19																	16524615		2203	4300	6503	SO:0001583	missense	58513	exon13			ATTGCCTCTTCCT	AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"""EF-hand domain containing"""	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.1235A>G	chr19.hg19:g.16524615T>C	ENSP00000248070:p.Glu412Gly	214.0	0.0		212.0	9.0	NM_021235	A2RRF3|A5PL29|B4DKA3	Missense_Mutation	SNP	ENST00000248070.6	hg19	CCDS32944.1	.	.	.	.	.	.	.	.	.	.	T	13.11	2.138822	0.37728	.	.	ENSG00000127527	ENST00000455140;ENST00000248070;ENST00000535753	T;D;D	0.83335	1.47;-1.71;-1.71	4.62	3.6	0.41247	.	0.058511	0.64402	D	0.000003	T	0.72914	0.3520	L	0.31926	0.97	0.58432	D	0.999994	B;B;B;B;B;B	0.14438	0.006;0.003;0.01;0.01;0.001;0.001	B;B;B;B;B;B	0.15870	0.014;0.009;0.008;0.01;0.004;0.009	T	0.65026	-0.6268	10	0.36615	T	0.2	.	9.7855	0.40673	0.0:0.0824:0.0:0.9176	.	412;412;411;412;412;412	A8K5P4;A5PL29;A5PKY0;A2RRF3;Q9UBC2;G3V0H2	.;.;.;.;EP15R_HUMAN;.	G	412	ENSP00000393313:E412G;ENSP00000248070:E412G;ENSP00000440103:E412G	ENSP00000248070:E412G	E	-	2	0	EPS15L1	16385615	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	4.099000	0.57755	0.736000	0.32559	-0.378000	0.06908	GAG	.	.		0.403	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235	
FCHO1	23149	hgsc.bcm.edu	37	19	17897403	17897403	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:17897403T>C	ENST00000596536.1	+	27	2730	c.2447T>C	c.(2446-2448)cTc>cCc	p.L816P	FCHO1_ENST00000389133.4_Missense_Mutation_p.L816P|FCHO1_ENST00000595033.1_Missense_Mutation_p.L766P|FCHO1_ENST00000594202.1_Missense_Mutation_p.L816P|FCHO1_ENST00000252771.7_Missense_Mutation_p.L816P|FCHO1_ENST00000597512.1_Missense_Mutation_p.L823P|FCHO1_ENST00000596951.1_Missense_Mutation_p.L816P|FCHO1_ENST00000600676.1_Missense_Mutation_p.L816P|FCHO1_ENST00000539407.1_Missense_Mutation_p.L816P	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	816	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.|Mediates interaction with AGFG1, CALM, DAB2, EPS15, EPS15R, ITSN1 and clathrin.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						GAGAAGCGGCTCACTTGGAGG	0.597																																					p.L816P		Atlas-SNP	.											.	FCHO1	69	.	0			c.T2447C						.						56.0	59.0	58.0					19																	17897403		2203	4300	6503	SO:0001583	missense	23149	exon26			AGCGGCTCACTTG	AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.2447T>C	chr19.hg19:g.17897403T>C	ENSP00000470731:p.Leu816Pro	49.0	0.0		89.0	4.0	NM_001161358	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Missense_Mutation	SNP	ENST00000596536.1	hg19	CCDS32955.1	.	.	.	.	.	.	.	.	.	.	T	14.54	2.564618	0.45694	.	.	ENSG00000130475	ENST00000252771;ENST00000389133;ENST00000539407	T;T;T	0.48836	0.8;0.8;0.8	3.83	3.83	0.44106	Muniscin C-terminal mu homology domain (1);	0.470872	0.18121	N	0.151039	T	0.53206	0.1782	L	0.42245	1.32	0.80722	D	1	D;D	0.56287	0.975;0.969	P;P	0.59761	0.814;0.863	T	0.51694	-0.8673	10	0.49607	T	0.09	-9.159	9.1655	0.37050	0.0:0.0:0.0:1.0	.	816;816	O14526;O14526-2	FCHO1_HUMAN;.	P	816	ENSP00000252771:L816P;ENSP00000373785:L816P;ENSP00000437978:L816P	ENSP00000252771:L816P	L	+	2	0	FCHO1	17758403	0.998000	0.40836	0.615000	0.29064	0.324000	0.28378	5.524000	0.67105	1.761000	0.52028	0.402000	0.26972	CTC	.	.		0.597	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122	
ZNF675	171392	hgsc.bcm.edu	37	19	23837367	23837367	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:23837367T>C	ENST00000359788.4	-	4	536	c.368A>G	c.(367-369)aAg>aGg	p.K123R	ZNF675_ENST00000600313.1_Intron|ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	123					bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				CTTGTGCAACTTACATTCATC	0.294																																					p.K123R		Atlas-SNP	.											.	ZNF675	88	.	0			c.A368G						.						83.0	81.0	82.0					19																	23837367		2203	4298	6501	SO:0001583	missense	171392	exon4			TGCAACTTACATT		CCDS32981.1	19p12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	30768	protein-coding gene	gene with protein product	"""TRAF6 inhibitory zinc finger"""					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.368A>G	chr19.hg19:g.23837367T>C	ENSP00000352836:p.Lys123Arg	102.0	0.0		123.0	5.0	NM_138330	Q8N211	Missense_Mutation	SNP	ENST00000359788.4	hg19	CCDS32981.1	.	.	.	.	.	.	.	.	.	.	.	7.721	0.697156	0.15106	.	.	ENSG00000197372	ENST00000359788	T	0.07114	3.22	1.13	1.13	0.20643	.	.	.	.	.	T	0.12433	0.0302	M	0.84156	2.68	0.09310	N	1	B	0.23937	0.094	B	0.25614	0.062	T	0.20638	-1.0269	9	0.41790	T	0.15	.	6.0138	0.19589	0.0:0.0:0.0:1.0	.	123	Q8TD23	ZN675_HUMAN	R	123	ENSP00000352836:K123R	ENSP00000352836:K123R	K	-	2	0	ZNF675	23629207	0.001000	0.12720	0.002000	0.10522	0.021000	0.10359	0.295000	0.19065	0.469000	0.27268	0.254000	0.18369	AAG	.	.		0.294	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330	
PROSER3	148137	hgsc.bcm.edu	37	19	36252918	36252918	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:36252918A>G	ENST00000544099.1	+	4	374		c.e4-1		C19orf55_ENST00000396908.4_Splice_Site|C19orf55_ENST00000537459.1_Splice_Site|C19orf55_ENST00000536950.1_Splice_Site|C19orf55_ENST00000421853.2_Splice_Site			Q2NL68	PRSR3_HUMAN												cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGATGTTCACAGGTATATAAA	0.527																																					.		Atlas-SNP	.											.	C19orf55	39	.	0			c.312-2A>G						.						31.0	31.0	31.0					19																	36252918		1911	4145	6056	SO:0001630	splice_region_variant	148137	exon4			GTTCACAGGTATA																												ENST00000544099.1:c.312-1A>G	chr19.hg19:g.36252918A>G		70.0	0.0		79.0	5.0	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Splice_Site	SNP	ENST00000544099.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.71	2.913051	0.52439	.	.	ENSG00000167595	ENST00000444637;ENST00000396908;ENST00000301165;ENST00000537459;ENST00000545674	.	.	.	4.78	4.78	0.61160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8688	0.46870	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C19orf55	40944758	0.995000	0.38212	0.989000	0.46669	0.725000	0.41563	4.251000	0.58778	2.124000	0.65301	0.528000	0.53228	.	.	.		0.527	C19orf55-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000398160.2		Intron
PROSER3	148137	hgsc.bcm.edu	37	19	36258938	36258938	+	Splice_Site	SNP	G	G	A	rs398034467|rs5827939		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:36258938G>A	ENST00000396908.4	+	9	1264	c.1191G>A	c.(1189-1191)caG>caA	p.Q397Q	AC002398.13_ENST00000589397.1_RNA|C19orf55_ENST00000544099.1_Silent_p.Q397Q	NM_001039887.2	NP_001034976.2	Q2NL68	PRSR3_HUMAN		398										cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGCTTGCCCAGGGCCGCCCTG	0.731																																					.		Atlas-SNP	.											.,11	C19orf55	39	.	0			c.1190+1G>A						.						1.0	1.0	1.0					19																	36258938		567	1236	1803	SO:0001630	splice_region_variant	148137	exon9			TGCCCAGGGCCGC																												ENST00000396908.4:c.1191+1G>A	chr19.hg19:g.36258938G>A		16.0	0.0		26.0	4.0	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Splice_Site	SNP	ENST00000396908.4	hg19																																																																																				.	.		0.731	C19orf55-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			Silent
ZNF607	84775	hgsc.bcm.edu	37	19	38190282	38190282	+	Silent	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:38190282C>T	ENST00000355202.4	-	5	1345	c.750G>A	c.(748-750)gaG>gaA	p.E250E	CTD-2528L19.4_ENST00000586606.2_Intron|ZNF607_ENST00000395835.3_Silent_p.E249E	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	250					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			CAAAGGGCTTCTCACCAGTGT	0.423																																					p.E250E		Atlas-SNP	.											.	ZNF607	82	.	0			c.G750A						.						51.0	52.0	52.0					19																	38190282		2203	4300	6503	SO:0001819	synonymous_variant	84775	exon5			GGGCTTCTCACCA	AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"""Zinc fingers, C2H2-type"", ""-"""	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.750G>A	chr19.hg19:g.38190282C>T		83.0	0.0		116.0	5.0	NM_032689	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Silent	SNP	ENST00000355202.4	hg19	CCDS33006.1																																																																																			.	.		0.423	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689	
WDR87	83889	hgsc.bcm.edu	37	19	38384513	38384513	+	Silent	SNP	T	T	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:38384513T>A	ENST00000303868.5	-	4	1937	c.1713A>T	c.(1711-1713)acA>acT	p.T571T	WDR87_ENST00000447313.2_Silent_p.T610T	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	571										NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						CATCAAAGGATGTGATGGCAC	0.498																																					p.T571T		Atlas-SNP	.											.	WDR87	191	.	0			c.A1713T						.						29.0	25.0	26.0					19																	38384513		692	1591	2283	SO:0001819	synonymous_variant	83889	exon4			AAAGGATGTGATG	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.1713A>T	chr19.hg19:g.38384513T>A		61.0	0.0		79.0	4.0	NM_031951	Q9BWV9	Silent	SNP	ENST00000303868.5	hg19	CCDS46063.1																																																																																			.	.		0.498	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
ZNF780A	284323	hgsc.bcm.edu	37	19	40589113	40589113	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:40589113T>C	ENST00000595687.2	-	4	250	c.41A>G	c.(40-42)gAc>gGc	p.D14G	ZNF780A_ENST00000455521.1_Missense_Mutation_p.D14G|ZNF780A_ENST00000450241.2_5'UTR|ZNF780A_ENST00000414720.2_Missense_Mutation_p.D30G|ZNF780A_ENST00000594395.1_Missense_Mutation_p.D14G|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000340963.5_Missense_Mutation_p.D14G	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	14	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CTGAGAGAAGTCAATGGCCAC	0.468																																					p.D30G		Atlas-SNP	.											.	ZNF780A	156	.	0			c.A89G						.						96.0	81.0	85.0					19																	40589113		692	1590	2282	SO:0001583	missense	284323	exon5			GAGAAGTCAATGG	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"""Zinc fingers, C2H2-type"", ""-"""	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.41A>G	chr19.hg19:g.40589113T>C	ENSP00000472189:p.Asp14Gly	104.0	0.0		135.0	7.0	NM_001142579	E9PB48|Q6ZN87	Missense_Mutation	SNP	ENST00000595687.2	hg19	CCDS33026.2	.	.	.	.	.	.	.	.	.	.	T	14.85	2.657103	0.47467	.	.	ENSG00000197782	ENST00000443072;ENST00000450241;ENST00000414720;ENST00000455521;ENST00000340963	T;T;T	0.02140	4.43;4.43;4.43	1.65	0.207	0.15214	Krueppel-associated box (4);	.	.	.	.	T	0.04543	0.0124	M	0.83852	2.665	0.25125	N	0.990619	P;B;B	0.36909	0.573;0.245;0.096	B;B;B	0.38842	0.283;0.096;0.211	T	0.22138	-1.0225	9	0.62326	D	0.03	.	4.6707	0.12687	0.0:0.2454:0.0:0.7546	.	14;14;30	E9PB48;O75290;O75290-2	.;Z780A_HUMAN;.	G	14;14;30;14;14	ENSP00000416294:D30G;ENSP00000400997:D14G;ENSP00000341507:D14G	ENSP00000341507:D14G	D	-	2	0	ZNF780A	45280953	0.390000	0.25213	0.355000	0.25773	0.905000	0.53344	1.816000	0.38992	-0.205000	0.10219	0.254000	0.18369	GAC	.	.		0.468	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880	
EGLN2	112398	hgsc.bcm.edu	37	19	41306911	41306911	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:41306911A>G	ENST00000593726.1	+	1	1462	c.434A>G	c.(433-435)gAg>gGg	p.E145G	EGLN2_ENST00000406058.2_Missense_Mutation_p.E145G|EGLN2_ENST00000594140.1_5'Flank|EGLN2_ENST00000303961.4_Missense_Mutation_p.E145G|CTC-490E21.12_ENST00000601627.1_5'Flank|RAB4B-EGLN2_ENST00000594136.1_3'UTR			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	145					cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|intracellular estrogen receptor signaling pathway (GO:0030520)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|positive regulation of protein catabolic process (GO:0045732)|regulation of cell growth (GO:0001558)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-proline 4-dioxygenase activity (GO:0031545)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	CAGGAGGCAGAGCGGGAGGGT	0.692																																					p.E145G		Atlas-SNP	.											.	EGLN2	31	.	0			c.A434G						.						29.0	25.0	26.0					19																	41306911		2200	4297	6497	SO:0001583	missense	112398	exon2			AGGCAGAGCGGGA	AJ310544	CCDS12567.1	19q13.2	2013-08-21	2013-08-21		ENSG00000269858	ENSG00000269858			14660	protein-coding gene	gene with protein product	"""HIF prolyl hydroxylase 1"""	606424	"""EGL nine (C.elegans) homolog 2"", ""egl nine homolog 2 (C. elegans)"""				Standard	NM_080732		Approved	PHD1, HIFPH1	uc002oph.3	Q96KS0		ENST00000593726.1:c.434A>G	chr19.hg19:g.41306911A>G	ENSP00000469686:p.Glu145Gly	179.0	0.0		203.0	11.0	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Missense_Mutation	SNP	ENST00000593726.1	hg19	CCDS12567.1	.	.	.	.	.	.	.	.	.	.	A	10.34	1.323522	0.24080	.	.	ENSG00000171570	ENST00000303961;ENST00000406058	T;T	0.27256	1.68;1.68	4.16	3.13	0.36017	.	0.358142	0.19945	N	0.102543	T	0.12305	0.0299	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22906	-1.0203	10	0.30854	T	0.27	-11.7353	9.2935	0.37802	0.8386:0.0:0.0:0.1614	.	145	Q96KS0	EGLN2_HUMAN	G	145	ENSP00000307080:E145G;ENSP00000385253:E145G	ENSP00000307080:E145G	E	+	2	0	EGLN2	45998751	0.997000	0.39634	0.005000	0.12908	0.529000	0.34654	4.294000	0.59043	0.740000	0.32651	0.482000	0.46254	GAG	.	.		0.692	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1		
CXCL17	284340	hgsc.bcm.edu	37	19	42937936	42937936	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:42937936T>C	ENST00000601181.1	-	2	367	c.152A>G	c.(151-153)gAg>gGg	p.E51G	LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000594688.1_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000593740.2_RNA	NM_198477.1	NP_940879.1	Q6UXB2	VCC1_HUMAN	chemokine (C-X-C motif) ligand 17	51					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|chemotaxis (GO:0006935)	extracellular region (GO:0005576)				large_intestine(2)|skin(1)	3		Prostate(69;0.00899)				ACCTTTGCACTCACATTCTTG	0.567											OREG0025504	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E51G		Atlas-SNP	.											.	CXCL17	8	.	0			c.A152G						.						179.0	148.0	158.0					19																	42937936		2203	4300	6503	SO:0001583	missense	284340	exon2			TTGCACTCACATT		CCDS12608.1	19q13.2	2007-10-15				ENSG00000189377			19232	protein-coding gene	gene with protein product		611387				17201934	Standard	NM_198477		Approved	Dcip1, UNQ473, DMC, VCC1	uc002otu.3	Q6UXB2		ENST00000601181.1:c.152A>G	chr19.hg19:g.42937936T>C	ENSP00000472467:p.Glu51Gly	99.0	0.0	912	111.0	5.0	NM_198477	A8KAC0	Missense_Mutation	SNP	ENST00000601181.1	hg19	CCDS12608.1	.	.	.	.	.	.	.	.	.	.	T	19.70	3.875696	0.72180	.	.	ENSG00000189377	ENST00000341918	.	.	.	4.7	3.61	0.41365	.	0.150264	0.31092	N	0.008275	T	0.33876	0.0878	L	0.29908	0.895	0.31048	N	0.715566	P	0.51351	0.944	P	0.47645	0.553	T	0.38950	-0.9637	9	0.72032	D	0.01	-12.1552	7.1759	0.25744	0.1986:0.0:0.0:0.8014	.	51	Q6UXB2	VCC1_HUMAN	G	51	.	ENSP00000345317:E51G	E	-	2	0	CXCL17	47629776	0.981000	0.34729	1.000000	0.80357	0.995000	0.86356	1.821000	0.39041	2.106000	0.64143	0.443000	0.29094	GAG	.	.		0.567	CXCL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463872.1		
ZNF230	7773	hgsc.bcm.edu	37	19	44511161	44511161	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:44511161A>G	ENST00000429154.2	+	2	160		c.e2-1		ZNF230_ENST00000585632.1_Splice_Site	NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230						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)|large_intestine(2)|lung(10)|skin(1)|stomach(3)|urinary_tract(2)	22		Prostate(69;0.0352)				GGCATTTTCCAGGCACAATTC	0.438																																					.	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											.	ZNF230	44	.	0			.						.						66.0	52.0	56.0					19																	44511161		692	1591	2283	SO:0001630	splice_region_variant	7773	.			TTTTCCAGGCACA	U95044	CCDS33044.1	19q13.31	2013-01-08				ENSG00000159882		"""Zinc fingers, C2H2-type"", ""-"""	13024	protein-coding gene	gene with protein product							Standard	NM_006300		Approved	FDZF2	uc002oyb.1	Q9UIE0		ENST00000429154.2:c.-68-1A>G	chr19.hg19:g.44511161A>G		125.0	0.0		121.0	6.0	.	O15322|Q504X7|Q86W84|Q9P1U6	Splice_Site	SNP	ENST00000429154.2	hg19	CCDS33044.1																																																																																			.	.		0.438	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1		Intron
ZNF284	342909	hgsc.bcm.edu	37	19	44590888	44590888	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:44590888A>G	ENST00000421176.3	+	5	1473	c.1257A>G	c.(1255-1257)agA>agG	p.R419R	RNU6-902P_ENST00000517212.1_RNA|ZNF223_ENST00000591793.1_3'UTR	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	419					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)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				CACATCAGAGAGCCTATAGAG	0.438																																					p.R419R		Atlas-SNP	.											.	ZNF284	38	.	0			c.A1257G						.						135.0	142.0	140.0					19																	44590888		2136	4263	6399	SO:0001819	synonymous_variant	342909	exon5			TCAGAGAGCCTAT	AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"""Zinc fingers, C2H2-type"", ""-"""	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.1257A>G	chr19.hg19:g.44590888A>G		119.0	0.0		117.0	6.0	NM_001037813	Q86WM1	Silent	SNP	ENST00000421176.3	hg19	CCDS46099.1																																																																																			.	.		0.438	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813	
PVRL2	5819	hgsc.bcm.edu	37	19	45375206	45375206	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:45375206C>T	ENST00000252483.5	+	3	575	c.575C>T	c.(574-576)gCc>gTc	p.A192V	PVRL2_ENST00000252485.4_Missense_Mutation_p.A192V	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)	192	Ig-like C2-type 1.				acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		CGCCCACCTGCCCGGATCTCC	0.622																																					p.A192V		Atlas-SNP	.											.	PVRL2	58	.	0			c.C575T						.						38.0	37.0	37.0					19																	45375206		2203	4300	6503	SO:0001583	missense	5819	exon3			CACCTGCCCGGAT	X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.575C>T	chr19.hg19:g.45375206C>T	ENSP00000252483:p.Ala192Val	102.0	0.0		112.0	15.0	NM_002856	A8K5L5|O75455|Q6IBI6|Q96J29	Missense_Mutation	SNP	ENST00000252483.5	hg19	CCDS42576.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737142	0.69304	.	.	ENSG00000130202	ENST00000252483;ENST00000252485	T;T	0.76709	-1.04;-1.04	4.25	4.25	0.50352	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000077	D	0.89687	0.6787	M	0.92923	3.36	0.42513	D	0.992971	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.993	D	0.91776	0.5431	10	0.87932	D	0	.	12.0078	0.53270	0.0:1.0:0.0:0.0	.	192;192	Q92692;Q92692-2	PVRL2_HUMAN;.	V	192	ENSP00000252483:A192V;ENSP00000252485:A192V	ENSP00000252483:A192V	A	+	2	0	PVRL2	50067046	0.937000	0.31787	0.990000	0.47175	0.576000	0.36127	3.927000	0.56499	2.190000	0.69967	0.561000	0.74099	GCC	.	.		0.622	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856	
TPRX1	284355	hgsc.bcm.edu	37	19	48305864	48305864	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:48305864A>G	ENST00000322175.3	-	2	559	c.404T>C	c.(403-405)aTc>aCc	p.I135T	TPRX1_ENST00000535759.1_Missense_Mutation_p.I232T|TPRX1_ENST00000543508.1_Missense_Mutation_p.I135T	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	135	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		tgggcctgggattggggctgg	0.642																																					p.I135T	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.T404C						.						19.0	17.0	18.0					19																	48305864		2047	4026	6073	SO:0001583	missense	284355	exon2			CCTGGGATTGGGG		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.404T>C	chr19.hg19:g.48305864A>G	ENSP00000323455:p.Ile135Thr	108.0	0.0		136.0	6.0	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	hg19	CCDS33066.1	.	.	.	.	.	.	.	.	.	.	a	0	-2.719608	0.00092	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	T;T;T	0.40476	1.03;1.03;1.03	0.383	-0.766	0.11020	.	.	.	.	.	T	0.16385	0.0394	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.08055	0.003	T	0.24728	-1.0152	8	0.11794	T	0.64	.	.	.	.	.	135	Q8N7U7	TPRX1_HUMAN	T	135;232;135	ENSP00000323455:I135T;ENSP00000438832:I232T;ENSP00000438712:I135T	ENSP00000323455:I135T	I	-	2	0	TPRX1	52997676	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-1.564000	0.02152	-0.783000	0.04534	-0.834000	0.03071	ATC	.	.		0.642	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
LIG1	3978	hgsc.bcm.edu	37	19	48665558	48665558	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:48665558T>C	ENST00000263274.7	-	3	487	c.68A>G	c.(67-69)gAg>gGg	p.E23G	LIG1_ENST00000427526.2_Intron|LIG1_ENST00000536218.1_Missense_Mutation_p.E23G|LIG1_ENST00000599165.1_5'UTR	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	23					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|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)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	ATTGGATGCCTCCTTCTCAGG	0.458								Nucleotide excision repair (NER)																													p.E23G		Atlas-SNP	.											.	LIG1	151	.	0			c.A68G						.						193.0	186.0	188.0					19																	48665558		2203	4300	6503	SO:0001583	missense	3978	exon3			GATGCCTCCTTCT		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.68A>G	chr19.hg19:g.48665558T>C	ENSP00000263274:p.Glu23Gly	90.0	0.0		102.0	5.0	NM_000234	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	hg19	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	T	16.79	3.220080	0.58560	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000536218;ENST00000542460	T;T;T	0.56611	0.49;0.45;1.89	4.23	3.1	0.35709	.	0.610961	0.15354	N	0.266809	T	0.40694	0.1127	L	0.60455	1.87	0.27667	N	0.946872	B;B	0.34290	0.447;0.201	B;B	0.26969	0.075;0.039	T	0.21177	-1.0253	10	0.24483	T	0.36	-21.4369	7.1349	0.25523	0.0:0.0:0.2299:0.7701	.	23;23	F5GZ28;P18858	.;DNLI1_HUMAN	G	23;55;23;23	ENSP00000263274:E23G;ENSP00000441531:E23G;ENSP00000445928:E23G	ENSP00000263274:E23G	E	-	2	0	LIG1	53357370	0.953000	0.32496	0.893000	0.35052	0.961000	0.63080	1.800000	0.38833	1.850000	0.53721	0.533000	0.62120	GAG	.	.		0.458	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234	
SCAF1	58506	hgsc.bcm.edu	37	19	50148321	50148321	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:50148321A>G	ENST00000360565.3	+	2	162	c.38A>G	c.(37-39)gAg>gGg	p.E13G		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	13					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		AAGACAGAGGAGTCGGGGGAG	0.612																																					p.E13G		Atlas-SNP	.											.	SCAF1	78	.	0			c.A38G						.						49.0	45.0	46.0					19																	50148321		2203	4300	6503	SO:0001583	missense	58506	exon2			CAGAGGAGTCGGG	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.38A>G	chr19.hg19:g.50148321A>G	ENSP00000353769:p.Glu13Gly	60.0	0.0		85.0	6.0	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	hg19	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	A	8.230	0.804409	0.16467	.	.	ENSG00000126461	ENST00000360565;ENST00000447618	T	0.50548	0.74	4.16	4.16	0.48862	.	0.000000	0.33023	U	0.005369	T	0.50154	0.1599	N	0.19112	0.55	0.29291	N	0.869341	D	0.76494	0.999	D	0.75484	0.986	T	0.47394	-0.9121	10	0.87932	D	0	-25.6664	9.5033	0.39031	1.0:0.0:0.0:0.0	.	13	Q9H7N4	SFR19_HUMAN	G	13	ENSP00000353769:E13G	ENSP00000353769:E13G	E	+	2	0	SCAF1	54840133	1.000000	0.71417	1.000000	0.80357	0.276000	0.26787	2.853000	0.48317	1.743000	0.51761	0.254000	0.18369	GAG	.	.		0.612	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
CEACAM18	729767	hgsc.bcm.edu	37	19	51981947	51981947	+	Splice_Site	SNP	G	G	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:51981947G>C	ENST00000396477.4	+	1	72	c.51G>C	c.(49-51)atG>atC	p.M17I	CEACAM18_ENST00000451626.1_Splice_Site_p.M78I	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	17										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		TCTTCCTCATGGGTAAGAGAT	0.632																																					p.M78I		Atlas-SNP	.											CEACAM18_ENST00000451626,NS,chondrosarcoma,0,1	CEACAM18	96	.	0			c.G234C						.						25.0	27.0	26.0					19																	51981947		1952	4167	6119	SO:0001630	splice_region_variant	729767	exon2			CCTCATGGGTAAG			19q13.41	2013-01-29				ENSG00000213822		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.52+1G>C	chr19.hg19:g.51981947G>C		40.0	0.0		72.0	0.0	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	hg19		.	.	.	.	.	.	.	.	.	.	.	8.544	0.873956	0.17395	.	.	ENSG00000213822	ENST00000451626;ENST00000451086;ENST00000396477	T	0.04758	3.56	2.8	0.459	0.16678	.	.	.	.	.	T	0.02455	0.0075	N	0.08118	0	0.18873	N	0.999987	B	0.10296	0.003	B	0.01281	0.0	T	0.44128	-0.9348	9	0.66056	D	0.02	.	2.992	0.05986	0.1641:0.0:0.5758:0.2601	.	78	A8MTB9	CEA18_HUMAN	I	78;17;17	ENSP00000402203:M78I	ENSP00000379738:M17I	M	+	3	0	CEACAM18	56673759	0.305000	0.24481	0.417000	0.26559	0.127000	0.20565	-0.370000	0.07523	0.200000	0.20447	0.655000	0.94253	ATG	.	.		0.632	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2		Missense_Mutation
KIR2DL3	3804	hgsc.bcm.edu	37	19	55263169	55263169	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:55263169T>C	ENST00000342376.3	+	6	815	c.784T>C	c.(784-786)Ttc>Ctc	p.F262L	KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000541392.1_Intron|KIR2DL3_ENST00000434419.2_Intron	NM_015868.2	NP_056952.2	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	262					immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		cctcctcctcttctttctcct	0.512																																					p.F262L		Atlas-SNP	.											.	KIR2DL3	68	.	0			c.T784C						.						137.0	112.0	121.0					19																	55263169		1408	2560	3968	SO:0001583	missense	3804	exon6			CTCCTCTTCTTTC	L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6331	protein-coding gene	gene with protein product		604938				7749980, 8662091	Standard	XM_006725426		Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000342376.3:c.784T>C	chr19.hg19:g.55263169T>C	ENSP00000342215:p.Phe262Leu	48.0	0.0		116.0	5.0	NM_015868	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	Missense_Mutation	SNP	ENST00000342376.3	hg19	CCDS33107.1	.	.	.	.	.	.	.	.	.	.	T	8.827	0.939009	0.18281	.	.	ENSG00000243772	ENST00000342376	T	0.00455	7.31	0.635	0.635	0.17723	.	.	.	.	.	T	0.00384	0.0012	N	0.25094	0.71	0.09310	N	0.999999	B;P;B;B	0.46395	0.0;0.877;0.001;0.001	B;P;B;B	0.51866	0.001;0.682;0.005;0.005	T	0.57248	-0.7844	8	0.62326	D	0.03	.	.	.	.	.	262;164;262;262	E3NZD7;P43628-2;P43628;E3NZD8	.;.;KI2L3_HUMAN;.	L	262	ENSP00000342215:F262L	ENSP00000342215:F262L	F	+	1	0	KIR2DL3	59954981	0.007000	0.16637	0.061000	0.19648	0.079000	0.17450	-0.023000	0.12456	0.516000	0.28340	0.248000	0.18094	TTC	.	.		0.512	KIR2DL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000141150.1		
NLRP2	55655	hgsc.bcm.edu	37	19	55508725	55508725	+	Missense_Mutation	SNP	C	C	A	rs61735074	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:55508725C>A	ENST00000543010.1	+	12	3063	c.2920C>A	c.(2920-2922)Ctc>Atc	p.L974I	NLRP2_ENST00000339757.7_Missense_Mutation_p.L952I|NLRP2_ENST00000263437.6_Missense_Mutation_p.L971I|NLRP2_ENST00000448584.2_Missense_Mutation_p.L974I|NLRP2_ENST00000537859.1_Missense_Mutation_p.L952I|NLRP2_ENST00000538819.1_Missense_Mutation_p.L950I|NLRP2_ENST00000427260.2_Missense_Mutation_p.L951I|NLRP2_ENST00000391721.4_Missense_Mutation_p.L950I	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	974					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TTGTGAAGACCTCTGCTCTGC	0.542																																					p.L974I		Atlas-SNP	.											.	NLRP2	161	.	0			c.C2920A						.						187.0	157.0	167.0					19																	55508725		2203	4300	6503	SO:0001583	missense	55655	exon12			GAAGACCTCTGCT	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"""Nucleotide-binding domain and leucine rich repeat containing"""	22948	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"""	609364	"""NACHT, leucine rich repeat and PYD containing 2"""	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.2920C>A	chr19.hg19:g.55508725C>A	ENSP00000445135:p.Leu974Ile	232.0	0.0		316.0	156.0	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	C	13.36	2.214248	0.39102	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0;-0.0;-0.0;-0.0;-0.0	3.2	0.921	0.19403	.	.	.	.	.	T	0.70745	0.3259	M	0.65320	2	0.09310	N	1	D;D;D;D;D	0.71674	0.998;0.994;0.994;0.994;0.99	D;D;D;D;D	0.70935	0.971;0.971;0.917;0.971;0.936	T	0.57142	-0.7862	9	0.59425	D	0.04	.	5.7987	0.18401	0.0:0.7173:0.0:0.2827	.	951;952;971;950;974	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	I	974;950;952;974;952;951;950;971	ENSP00000445135:L974I;ENSP00000375601:L950I;ENSP00000344074:L952I;ENSP00000409370:L974I;ENSP00000440601:L952I;ENSP00000402474:L951I;ENSP00000441133:L950I;ENSP00000263437:L971I	ENSP00000263437:L971I	L	+	1	0	NLRP2	60200537	0.195000	0.23338	0.014000	0.15608	0.031000	0.12232	1.773000	0.38563	0.153000	0.19213	0.561000	0.74099	CTC	.	C|0.981;G|0.019		0.542	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
ZNF446	55663	hgsc.bcm.edu	37	19	58989035	58989035	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:58989035T>C	ENST00000594369.1	+	3	755	c.374T>C	c.(373-375)cTc>cCc	p.L125P	ZNF446_ENST00000335841.4_Missense_Mutation_p.L125P|CTD-2619J13.23_ENST00000598051.1_RNA|ZNF446_ENST00000596341.1_Missense_Mutation_p.L125P	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	125					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		CAGGAGGTGCTCCCTGCAGCC	0.602																																					p.L125P		Atlas-SNP	.											.	ZNF446	22	.	0			c.T374C						.						55.0	59.0	58.0					19																	58989035		2203	4300	6503	SO:0001583	missense	55663	exon3			AGGTGCTCCCTGC		CCDS12982.1	19q13.43	2013-01-09				ENSG00000083838		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	21036	protein-coding gene	gene with protein product							Standard	NM_017908		Approved	ZKSCAN20, FLJ20626, ZSCAN52	uc002qsz.3	Q9NWS9		ENST00000594369.1:c.374T>C	chr19.hg19:g.58989035T>C	ENSP00000472802:p.Leu125Pro	106.0	0.0		135.0	6.0	NM_017908		Missense_Mutation	SNP	ENST00000594369.1	hg19	CCDS12982.1	.	.	.	.	.	.	.	.	.	.	T	4.962	0.178769	0.09443	.	.	ENSG00000083838	ENST00000335841;ENST00000540481;ENST00000539679	T	0.06768	3.26	4.35	3.33	0.38152	Transcription regulator SCAN (1);	0.000000	0.32952	N	0.005441	T	0.06416	0.0165	L	0.27053	0.805	0.26798	N	0.969264	B;B;B	0.27450	0.174;0.041;0.179	B;B;B	0.29267	0.1;0.018;0.046	T	0.25572	-1.0128	10	0.66056	D	0.02	-24.4462	7.0245	0.24932	0.0:0.1093:0.0:0.8907	.	125;125;125	F5H201;Q96AF5;Q9NWS9	.;.;ZN446_HUMAN	P	125	ENSP00000336565:L125P	ENSP00000336565:L125P	L	+	2	0	ZNF446	63680847	0.000000	0.05858	0.519000	0.27824	0.073000	0.16967	0.154000	0.16343	0.782000	0.33613	0.402000	0.26972	CTC	.	.		0.602	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908	
C20orf194	25943	hgsc.bcm.edu	37	20	3285095	3285095	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:3285095A>G	ENST00000252032.9	-	21	1841	c.1774T>C	c.(1774-1776)Tat>Cat	p.Y592H	C20orf194_ENST00000498079.1_5'UTR|C20orf194_ENST00000453730.2_Missense_Mutation_p.Y330H	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	592										NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						ACCCCATCATAGAAGGAAATG	0.413																																					p.Y592H		Atlas-SNP	.											.	C20orf194	83	.	0			c.T1774C						.						105.0	100.0	102.0					20																	3285095		1892	4112	6004	SO:0001583	missense	25943	exon21			CATCATAGAAGGA	AL110249	CCDS42851.1	20p13	2012-10-30			ENSG00000088854	ENSG00000088854			17721	protein-coding gene	gene with protein product		614146					Standard	NM_001009984		Approved	DKFZp434N061	uc002wii.3	Q5TEA3	OTTHUMG00000031742	ENST00000252032.9:c.1774T>C	chr20.hg19:g.3285095A>G	ENSP00000252032:p.Tyr592His	69.0	0.0		98.0	4.0	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Missense_Mutation	SNP	ENST00000252032.9	hg19	CCDS42851.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.190935	0.78789	.	.	ENSG00000088854	ENST00000252032;ENST00000453730	T;T	0.42900	1.81;0.96	5.83	5.83	0.93111	.	0.063315	0.64402	D	0.000004	T	0.62792	0.2457	M	0.72894	2.215	0.51482	D	0.99992	D;D	0.76494	0.999;0.999	D;D	0.71656	0.961;0.974	T	0.66578	-0.5888	10	0.87932	D	0	.	13.7216	0.62730	1.0:0.0:0.0:0.0	.	331;592	Q0IIP3;Q5TEA3	.;CT194_HUMAN	H	592;330	ENSP00000252032:Y592H;ENSP00000407229:Y330H	ENSP00000252032:Y592H	Y	-	1	0	C20orf194	3233095	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.441000	0.66569	2.223000	0.72356	0.402000	0.26972	TAT	.	.		0.413	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984	
RASSF2	9770	hgsc.bcm.edu	37	20	4776514	4776514	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:4776514T>C	ENST00000379400.3	-	5	429	c.234A>G	c.(232-234)cgA>cgG	p.R78R	RASSF2_ENST00000379376.2_Silent_p.R78R|RASSF2_ENST00000478553.1_5'Flank	NM_014737.2	NP_055552.1	P50749	RASF2_HUMAN	Ras association (RalGDS/AF-6) domain family member 2	78					bone remodeling (GO:0046849)|cell cycle (GO:0007049)|epidermal growth factor receptor signaling pathway via I-kappaB kinase/NF-kappaB cascade (GO:0038168)|homeostasis of number of cells (GO:0048872)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|ossification (GO:0001503)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|pancreas(2)|prostate(2)|skin(2)	34						ATGGAGGGGGTCGAATGCGTT	0.617																																					p.R78R	Melanoma(158;1891 3343 50738)	Atlas-SNP	.											.	RASSF2	75	.	0			c.A234G						.						138.0	128.0	131.0					20																	4776514		2203	4300	6503	SO:0001819	synonymous_variant	9770	exon5			AGGGGGTCGAATG	D79990	CCDS13083.1	20p13	2011-08-12	2008-02-22		ENSG00000101265	ENSG00000101265			9883	protein-coding gene	gene with protein product	"""centromere protein 34"""	609492				8724849, 15806169	Standard	NM_014737		Approved	KIAA0168, CENP-34	uc002wld.3	P50749	OTTHUMG00000031790	ENST00000379400.3:c.234A>G	chr20.hg19:g.4776514T>C		73.0	0.0		121.0	5.0	NM_014737	A6NIX9|A8K5Z3|Q17S06|Q53HD0|Q6AHZ2|Q8IZA5	Silent	SNP	ENST00000379400.3	hg19	CCDS13083.1																																																																																			.	.		0.617	RASSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077828.1	NM_014737	
ANKEF1	63926	hgsc.bcm.edu	37	20	10032309	10032309	+	Splice_Site	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:10032309A>G	ENST00000378380.3	+	7	1972		c.e7-1		SNAP25-AS1_ENST00000421143.2_RNA|ANKEF1_ENST00000378392.1_Splice_Site|ANKEF1_ENST00000488991.1_Splice_Site|SNAP25-AS1_ENST00000603542.1_RNA	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1								calcium ion binding (GO:0005509)										CTTATTTTACAGAGCTAACGT	0.358																																					.		Atlas-SNP	.											.	.	.	.	0			c.1644-2A>G						.						69.0	66.0	67.0					20																	10032309		2203	4300	6503	SO:0001630	splice_region_variant	63926	exon8			TTTTACAGAGCTA	AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"""EF-hand domain containing"", ""Ankyrin repeat domain containing"""	15803	protein-coding gene	gene with protein product			"""ankyrin repeat domain 5"""	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.1644-1A>G	chr20.hg19:g.10032309A>G		87.0	0.0		98.0	6.0	NM_022096	B3KUQ0|Q9H6Y9	Splice_Site	SNP	ENST00000378380.3	hg19	CCDS13108.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.550589	0.27739	.	.	ENSG00000132623	ENST00000378392;ENST00000378380	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3035	0.82836	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ANKRD5	9980309	1.000000	0.71417	0.907000	0.35723	0.004000	0.04260	8.242000	0.89818	2.299000	0.77371	0.528000	0.53228	.	.	.		0.358	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096	Intron
ZNF133	7692	hgsc.bcm.edu	37	20	18296753	18296753	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:18296753A>G	ENST00000316358.4	+	4	1355	c.1258A>G	c.(1258-1260)Agc>Ggc	p.S420G	ZNF133_ENST00000377671.3_Missense_Mutation_p.S419G|RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000401790.1_Missense_Mutation_p.S420G|ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000538547.1_Missense_Mutation_p.S325G|ZNF133_ENST00000535822.1_Missense_Mutation_p.S325G|ZNF133_ENST00000402618.2_Missense_Mutation_p.S357G|ZNF133_ENST00000396026.3_Missense_Mutation_p.S423G	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	420					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)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						GCACAGCTTCAGCCAGAATTC	0.567																																					p.S419G		Atlas-SNP	.											.	ZNF133	63	.	0			c.A1255G						.						84.0	89.0	87.0					20																	18296753		2203	4300	6503	SO:0001583	missense	7692	exon4			AGCTTCAGCCAGA	AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"""Zinc fingers, C2H2-type"", ""-"""	12917	protein-coding gene	gene with protein product		604075	"""zinc finger protein 150 (pHZ-66)"", ""zinc finger protein 133 (clone pHZ-13)"""	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.1258A>G	chr20.hg19:g.18296753A>G	ENSP00000346090:p.Ser420Gly	70.0	0.0		81.0	4.0	NM_001083330	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Missense_Mutation	SNP	ENST00000316358.4	hg19		.	.	.	.	.	.	.	.	.	.	A	16.70	3.195857	0.58126	.	.	ENSG00000125846	ENST00000377671;ENST00000396026;ENST00000402618;ENST00000401790;ENST00000538547;ENST00000535822;ENST00000316358	T;T;T;T;T;T;T	0.19250	2.16;2.16;3.17;2.16;3.17;3.17;2.16	4.45	3.33	0.38152	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000013	T	0.30417	0.0764	L	0.31476	0.935	0.28358	N	0.920574	D;D;D;P	0.76494	0.999;0.995;0.999;0.925	D;D;D;B	0.72075	0.955;0.924;0.976;0.434	T	0.04128	-1.0975	10	0.66056	D	0.02	-32.8372	10.0274	0.42079	0.831:0.169:0.0:0.0	.	357;423;420;419	B4DIB8;B4DHU7;P52736;P52736-2	.;.;ZN133_HUMAN;.	G	419;423;357;420;325;325;420	ENSP00000366899:S419G;ENSP00000400897:S423G;ENSP00000385279:S357G;ENSP00000383945:S420G;ENSP00000442978:S325G;ENSP00000439427:S325G;ENSP00000346090:S420G	ENSP00000346090:S420G	S	+	1	0	ZNF133	18244753	0.000000	0.05858	0.994000	0.49952	0.975000	0.68041	0.823000	0.27366	1.004000	0.39156	0.459000	0.35465	AGC	.	.		0.567	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434	
NAPB	63908	hgsc.bcm.edu	37	20	23383704	23383704	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:23383704T>C	ENST00000377026.4	-	2	189	c.104A>G	c.(103-105)aAc>aGc	p.N35S	NAPB_ENST00000472855.1_5'UTR|NAPB_ENST00000432543.2_Missense_Mutation_p.N35S|NAPB_ENST00000398425.3_5'UTR	NM_001283018.1|NM_001283020.1|NM_022080.2	NP_001269947.1|NP_001269949.1|NP_071363.1	Q9H115	SNAB_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, beta	35					intracellular protein transport (GO:0006886)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	extracellular vesicular exosome (GO:0070062)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)				endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12	Lung NSC(19;0.0646)|Colorectal(13;0.0993)|all_lung(19;0.143)					TATTCTTGTGTTTCCTCTGAG	0.323																																					p.N35S		Atlas-SNP	.											.	NAPB	22	.	0			c.A104G						.						80.0	75.0	77.0					20																	23383704		2201	4300	6501	SO:0001583	missense	63908	exon2			CTTGTGTTTCCTC	AK022817	CCDS13152.1, CCDS63241.1, CCDS63242.1, CCDS74710.1	20p12.3-p11.21	2008-08-01			ENSG00000125814	ENSG00000125814			15751	protein-coding gene	gene with protein product		611270				8455721	Standard	NM_022080		Approved	SNAP-BETA, SNAPB	uc002wta.3	Q9H115	OTTHUMG00000032062	ENST00000377026.4:c.104A>G	chr20.hg19:g.23383704T>C	ENSP00000366225:p.Asn35Ser	68.0	0.0		92.0	4.0	NM_022080	B4DK44|Q4G0M0|Q4G187|Q5JXF9|Q8N3C4	Missense_Mutation	SNP	ENST00000377026.4	hg19	CCDS13152.1	.	.	.	.	.	.	.	.	.	.	T	3.726	-0.056567	0.07362	.	.	ENSG00000125814	ENST00000377026;ENST00000432543	T;T	0.74842	1.68;-0.88	5.95	5.95	0.96441	Tetratricopeptide-like helical (1);	0.343450	0.33591	N	0.004749	T	0.38480	0.1042	N	0.00315	-1.66	0.80722	D	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.06405	0.001;0.002;0.002	T	0.55354	-0.8154	10	0.02654	T	1	0.4372	15.5971	0.76595	0.0:0.0:0.0:1.0	.	35;35;35	B4DK44;B4DIV0;Q9H115	.;.;SNAB_HUMAN	S	35	ENSP00000366225:N35S;ENSP00000413600:N35S	ENSP00000366225:N35S	N	-	2	0	NAPB	23331704	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.146000	0.50631	2.279000	0.76181	0.533000	0.62120	AAC	.	.		0.323	NAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078317.2	NM_022080	
CBFA2T2	9139	hgsc.bcm.edu	37	20	32212691	32212691	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:32212691G>T	ENST00000346541.3	+	7	1378	c.841G>T	c.(841-843)Ggg>Tgg	p.G281W	CBFA2T2_ENST00000359606.3_Missense_Mutation_p.G291W|CBFA2T2_ENST00000375279.2_Missense_Mutation_p.G281W|CBFA2T2_ENST00000492345.1_Missense_Mutation_p.G252W|CBFA2T2_ENST00000342704.6_Missense_Mutation_p.G272W|CBFA2T2_ENST00000491618.1_3'UTR|CBFA2T2_ENST00000397800.1_Missense_Mutation_p.G252W	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	281					epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						CATGAATCCCGGGGGCCAATT	0.532																																					p.G281W	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-SNP	.											.	CBFA2T2	93	.	0			c.G841T						.						122.0	100.0	108.0					20																	32212691		2203	4300	6503	SO:0001583	missense	9139	exon7			AATCCCGGGGGCC	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"""Zinc fingers, MYND-type"""	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.841G>T	chr20.hg19:g.32212691G>T	ENSP00000262653:p.Gly281Trp	106.0	0.0		151.0	7.0	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Missense_Mutation	SNP	ENST00000346541.3	hg19	CCDS13221.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.760539	0.31137	.	.	ENSG00000078699	ENST00000397803;ENST00000375279;ENST00000342704;ENST00000346541;ENST00000397800;ENST00000359606	T;T;T;T;T	0.45276	0.9;0.91;0.9;0.91;1.49	5.5	4.55	0.56014	.	0.231387	0.38492	N	0.001668	T	0.42743	0.1216	N	0.22421	0.69	0.19300	N	0.999975	D;D	0.61080	0.989;0.989	P;P	0.57960	0.823;0.83	T	0.26087	-1.0113	10	0.66056	D	0.02	-5.192	10.1107	0.42561	0.2103:0.0:0.7897:0.0	.	281;272	O43439;F8W6D7	MTG8R_HUMAN;.	W	55;281;272;281;252;291	ENSP00000364428:G281W;ENSP00000345810:G272W;ENSP00000262653:G281W;ENSP00000380902:G252W;ENSP00000352622:G291W	ENSP00000345810:G272W	G	+	1	0	CBFA2T2	31676352	0.228000	0.23718	0.470000	0.27216	0.003000	0.03518	2.130000	0.42064	1.471000	0.48121	0.650000	0.86243	GGG	.	.		0.532	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999	
GSS	2937	hgsc.bcm.edu	37	20	33530430	33530430	+	Splice_Site	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:33530430T>C	ENST00000216951.2	-	5	450	c.352A>G	c.(352-354)Act>Gct	p.T118A	GSS_ENST00000451957.2_Intron|GSS_ENST00000541098.1_5'UTR	NM_000178.2	NP_000169.1	P48637	GSHB_HUMAN	glutathione synthetase	118					aging (GO:0007568)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|nervous system development (GO:0007399)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to nutrient levels (GO:0031667)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|glutathione binding (GO:0043295)|glutathione synthase activity (GO:0004363)|glycine binding (GO:0016594)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(18;0.035)		Acetylcysteine(DB06151)|Glutathione(DB00143)|Glycine(DB00145)|L-Cysteine(DB00151)	AGGAACACAGTCTGTGGGGAA	0.542																																					p.T118A		Atlas-SNP	.											.	GSS	33	.	0			c.A352G						.						90.0	85.0	87.0					20																	33530430		2203	4300	6503	SO:0001630	splice_region_variant	2937	exon5			ACACAGTCTGTGG		CCDS13245.1	20q11.2	1996-06-18			ENSG00000100983	ENSG00000100983	6.3.2.3		4624	protein-coding gene	gene with protein product		601002				8825653	Standard	NM_000178		Approved		uc002xbg.3	P48637	OTTHUMG00000032315	ENST00000216951.2:c.352-1A>G	chr20.hg19:g.33530430T>C		79.0	0.0		116.0	5.0	NM_000178	B2R697|B6F210|E1P5P9|Q4TTD9	Missense_Mutation	SNP	ENST00000216951.2	hg19	CCDS13245.1	.	.	.	.	.	.	.	.	.	.	T	5.497	0.276732	0.10403	.	.	ENSG00000100983	ENST00000216951	D	0.90444	-2.67	5.77	5.77	0.91146	Glutathione synthase, N-terminal, eukaryotic (1);	0.592570	0.18646	N	0.135159	T	0.82061	0.4955	L	0.33339	1.005	0.80722	D	1	B	0.13145	0.007	B	0.12837	0.008	T	0.72523	-0.4267	10	0.08837	T	0.75	-17.5509	6.3195	0.21208	0.1417:0.0748:0.0:0.7836	.	118	P48637	GSHB_HUMAN	A	118	ENSP00000216951:T118A	ENSP00000216951:T118A	T	-	1	0	GSS	32994091	1.000000	0.71417	0.998000	0.56505	0.926000	0.56050	0.614000	0.24314	2.199000	0.70637	0.533000	0.62120	ACT	.	.		0.542	GSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078821.2		Missense_Mutation
CDH22	64405	hgsc.bcm.edu	37	20	44839091	44839091	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:44839091C>T	ENST00000372262.3	-	6	1541	c.1141G>A	c.(1141-1143)Gtg>Atg	p.V381M	CDH22_ENST00000537909.1_Missense_Mutation_p.V381M|CDH22_ENST00000474438.1_5'UTR	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	381	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				GCCACGCGCACGATCGCCTGG	0.711																																					p.V381M		Atlas-SNP	.											.	CDH22	112	.	0			c.G1141A						.						20.0	19.0	19.0					20																	44839091		2198	4294	6492	SO:0001583	missense	64405	exon7			CGCGCACGATCGC	AF035300	CCDS13395.1	20q13.1	2010-01-26	2009-11-20		ENSG00000149654	ENSG00000149654		"""Cadherins / Major cadherins"""	13251	protein-coding gene	gene with protein product		609920	"""cadherin-like 22"""	C20orf25		8626716	Standard	NM_021248		Approved	dJ998H6.1	uc010ghk.2	Q9UJ99	OTTHUMG00000033073	ENST00000372262.3:c.1141G>A	chr20.hg19:g.44839091C>T	ENSP00000361336:p.Val381Met	89.0	0.0		128.0	58.0	NM_021248	B9EGK7|O43205	Missense_Mutation	SNP	ENST00000372262.3	hg19	CCDS13395.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.721056	0.89205	.	.	ENSG00000149654	ENST00000372262;ENST00000537909	T;T	0.55588	0.51;0.51	4.17	4.17	0.49024	Cadherin (3);Cadherin-like (1);	0.072247	0.56097	D	0.000034	T	0.75788	0.3897	H	0.96142	3.775	0.58432	D	0.999992	D	0.76494	0.999	P	0.60415	0.874	T	0.81920	-0.0712	10	0.87932	D	0	.	9.4414	0.38670	0.0:0.9025:0.0:0.0975	.	381	Q9UJ99	CAD22_HUMAN	M	381	ENSP00000361336:V381M;ENSP00000437790:V381M	ENSP00000361336:V381M	V	-	1	0	CDH22	44272498	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.776000	0.62354	2.171000	0.68590	0.555000	0.69702	GTG	.	.		0.711	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248	
TSHZ2	128553	hgsc.bcm.edu	37	20	51872669	51872669	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:51872669T>C	ENST00000371497.5	+	2	3559	c.2672T>C	c.(2671-2673)cTc>cCc	p.L891P	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Missense_Mutation_p.L888P|TSHZ2_ENST00000603338.2_Missense_Mutation_p.L888P	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	891					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			TTTACGGGACTCTCAATGACC	0.512																																					p.L891P		Atlas-SNP	.											.	TSHZ2	209	.	0			c.T2672C						.						84.0	81.0	82.0					20																	51872669		2203	4300	6503	SO:0001583	missense	128553	exon2			CGGGACTCTCAAT	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	13010	protein-coding gene	gene with protein product		614118	"""chromosome 20 open reading frame 17"", ""zinc finger protein 218"", ""teashirt family zinc finger 2"""	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2672T>C	chr20.hg19:g.51872669T>C	ENSP00000360552:p.Leu891Pro	92.0	0.0		98.0	4.0	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	hg19	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	T	15.99	2.995405	0.54147	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.32753	1.46;1.44	5.67	5.67	0.87782	Homeobox (1);Homeodomain-like (1);	0.060169	0.64402	D	0.000004	T	0.50137	0.1598	L	0.47190	1.495	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.51140	-0.8743	10	0.87932	D	0	-1.7421	15.9017	0.79384	0.0:0.0:0.0:1.0	.	891	Q9NRE2	TSH2_HUMAN	P	891;888;417	ENSP00000360552:L891P;ENSP00000333114:L888P	ENSP00000333114:L888P	L	+	2	0	TSHZ2	51306076	1.000000	0.71417	0.344000	0.25628	0.568000	0.35870	7.693000	0.84214	2.152000	0.67230	0.450000	0.29827	CTC	.	.		0.512	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485	
ZNF217	7764	hgsc.bcm.edu	37	20	52193705	52193705	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:52193705A>G	ENST00000371471.2	-	4	2023	c.1598T>C	c.(1597-1599)gTc>gCc	p.V533A	ZNF217_ENST00000302342.3_Missense_Mutation_p.V533A|RP4-724E16.2_ENST00000424252.1_RNA			O75362	ZN217_HUMAN	zinc finger protein 217	533					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			ATCGTTCTTGACTTCAGCAGC	0.398																																					p.V533A		Atlas-SNP	.											.	ZNF217	227	.	0			c.T1598C						.						113.0	107.0	109.0					20																	52193705		2203	4300	6503	SO:0001583	missense	7764	exon3			TTCTTGACTTCAG	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.1598T>C	chr20.hg19:g.52193705A>G	ENSP00000360526:p.Val533Ala	75.0	0.0		93.0	4.0	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	hg19	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	A	4.692	0.128602	0.08981	.	.	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.09163	3.01;3.01	5.69	-5.58	0.02512	.	1.338680	0.04850	N	0.442196	T	0.07863	0.0197	L	0.33485	1.01	0.09310	N	0.999999	B	0.02656	0.0	B	0.06405	0.002	T	0.39078	-0.9631	10	0.28530	T	0.3	-7.4465	8.1405	0.31080	0.5039:0.1812:0.3149:0.0	.	533	O75362	ZN217_HUMAN	A	533	ENSP00000360526:V533A;ENSP00000304308:V533A	ENSP00000304308:V533A	V	-	2	0	ZNF217	51627112	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-2.380000	0.01066	-0.943000	0.03691	-0.810000	0.03169	GTC	.	.		0.398	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
OSBPL2	9885	hgsc.bcm.edu	37	20	60861769	60861769	+	Splice_Site	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:60861769T>C	ENST00000313733.3	+	11	1327		c.e11+2		OSBPL2_ENST00000358053.2_Splice_Site|OSBPL2_ENST00000439951.2_Splice_Site	NM_144498.1	NP_653081.1	Q9H1P3	OSBL2_HUMAN	oxysterol binding protein-like 2						lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)			TCTGCCCAGGTCTGTGTCCCT	0.662																																					.		Atlas-SNP	.											.	OSBPL2	51	.	0			c.1125+2T>C						.						61.0	54.0	57.0					20																	60861769		2203	4300	6503	SO:0001630	splice_region_variant	9885	exon11			CCCAGGTCTGTGT	AB018315	CCDS13494.1, CCDS13495.1, CCDS63323.1	20q13.3	2008-08-01	2001-11-28		ENSG00000130703	ENSG00000130703		"""Oxysterol binding proteins"""	15761	protein-coding gene	gene with protein product		606731	"""oxysterol-binding protein-like 2"""			10588946, 11861666	Standard	NM_144498		Approved	KIAA0772, ORP-2	uc002yck.1	Q9H1P3	OTTHUMG00000032909	ENST00000313733.3:c.1125+2T>C	chr20.hg19:g.60861769T>C		58.0	0.0		76.0	4.0	NM_144498	A8K736|Q6IBT0|Q9BZB1|Q9Y4B8	Splice_Site	SNP	ENST00000313733.3	hg19	CCDS13495.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.203267	0.79127	.	.	ENSG00000130703	ENST00000358053;ENST00000313733;ENST00000439951	.	.	.	4.82	4.82	0.62117	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6244	0.56622	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	OSBPL2	60295164	1.000000	0.71417	0.968000	0.41197	0.893000	0.52053	7.945000	0.87732	1.812000	0.52913	0.533000	0.62120	.	.	.		0.662	OSBPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080021.1	NM_014835	Intron
ZNF512B	57473	hgsc.bcm.edu	37	20	62614445	62614445	+	Intron	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:62614445T>C	ENST00000450537.1	-	2	56				PRPF6_ENST00000535781.1_Silent_p.D39D|ZNF512B_ENST00000217130.3_Intron			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						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)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CCGCCCGTGATGCAAATGACC	0.577																																					p.D39D		Atlas-SNP	.											.	PRPF6	88	.	0			c.T117C						.						83.0	69.0	74.0					20																	62614445		2203	4300	6503	SO:0001627	intron_variant	24148	exon2			CCGTGATGCAAAT	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.5-15137A>G	chr20.hg19:g.62614445T>C		89.0	0.0		117.0	5.0	NM_012469	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	hg19	CCDS13548.1																																																																																			.	.		0.577	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	
APP	351	hgsc.bcm.edu	37	21	27354754	27354754	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:27354754T>C	ENST00000346798.3	-	9	1160	c.1127A>G	c.(1126-1128)gAc>gGc	p.D376G	APP_ENST00000359726.3_Missense_Mutation_p.D320G|APP_ENST00000357903.3_Missense_Mutation_p.D357G|APP_ENST00000440126.3_Missense_Mutation_p.D352G|APP_ENST00000439274.2_Missense_Mutation_p.D320G|APP_ENST00000348990.5_Missense_Mutation_p.D301G|APP_ENST00000358918.3_Missense_Mutation_p.D376G|APP_ENST00000448388.2_Missense_Mutation_p.D266G|APP_ENST00000354192.3_Missense_Mutation_p.D245G	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	376					adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				GAGATACTTGTCAACGGCATC	0.468																																					p.D376G		Atlas-SNP	.											APP,NS,carcinoma,0,1	APP	90	.	0			c.A1127G						.						91.0	81.0	85.0					21																	27354754		2203	4300	6503	SO:0001583	missense	351	exon9			TACTTGTCAACGG	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"""Endogenous ligands"""	620	protein-coding gene	gene with protein product	"""peptidase nexin-II"""	104760	"""Alzheimer disease"""	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1127A>G	chr21.hg19:g.27354754T>C	ENSP00000284981:p.Asp376Gly	91.0	0.0		94.0	4.0	NM_000484	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Missense_Mutation	SNP	ENST00000346798.3	hg19	CCDS13576.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.2|25.2	4.608698|4.608698	0.87258|0.87258	.|.	.|.	ENSG00000142192|ENSG00000142192	ENST00000346798;ENST00000354192;ENST00000348990;ENST00000357903;ENST00000358918;ENST00000359726;ENST00000448388;ENST00000440126;ENST00000439274|ENST00000448850;ENST00000415997	T;T;T;T;T;T;T;T;T|.	0.72051|.	-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62|.	5.45|5.45	5.45|5.45	0.79879|0.79879	Amyloidogenic glycoprotein, E2 domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.79644|.	0.4481|.	M|M	0.86343|0.86343	2.81|2.81	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.76494|.	0.999;0.998;0.993;0.999;0.991;0.991;0.995|.	D;D;D;D;D;D;D|.	0.76071|.	0.965;0.965;0.987;0.941;0.977;0.977;0.924|.	T|.	0.82438|.	-0.0457|.	10|.	0.87932|.	D|.	0|.	-28.6988|-28.6988	15.3372|15.3372	0.74266|0.74266	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	266;320;352;245;301;357;376|.	E9PEV0;E9PG40;B4DII8;P05067-10;P05067-4;P05067-8;P05067|.	.;.;.;.;.;.;A4_HUMAN|.	G|W	376;245;301;357;376;320;266;352;320|278;110	ENSP00000284981:D376G;ENSP00000346129:D245G;ENSP00000345463:D301G;ENSP00000350578:D357G;ENSP00000351796:D376G;ENSP00000352760:D320G;ENSP00000388538:D266G;ENSP00000387483:D352G;ENSP00000398879:D320G|.	ENSP00000284981:D376G|.	D|X	-|-	2|3	0|0	APP|APP	26276625|26276625	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.937000|0.937000	0.57800|0.57800	5.760000|5.760000	0.68793|0.68793	2.288000|2.288000	0.76882|0.76882	0.533000|0.533000	0.62120|0.62120	GAC|TGA	.	.		0.468	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484	
IGSF5	150084	hgsc.bcm.edu	37	21	41151128	41151128	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:41151128T>C	ENST00000380588.4	+	5	933	c.830T>C	c.(829-831)cTg>cCg	p.L277P	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	277					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)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				ACCATGCTTCTGACGCCGACG	0.478																																					p.L277P		Atlas-SNP	.											.	IGSF5	62	.	0			c.T830C						.						116.0	107.0	110.0					21																	41151128		2203	4300	6503	SO:0001583	missense	150084	exon5			TGCTTCTGACGCC		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.830T>C	chr21.hg19:g.41151128T>C	ENSP00000369962:p.Leu277Pro	103.0	0.0		94.0	4.0	NM_001080444		Missense_Mutation	SNP	ENST00000380588.4	hg19	CCDS33562.1	.	.	.	.	.	.	.	.	.	.	T	14.65	2.598544	0.46318	.	.	ENSG00000183067	ENST00000380588	T	0.10099	2.91	4.24	3.09	0.35607	.	0.398152	0.26038	N	0.026714	T	0.15696	0.0378	L	0.27053	0.805	0.45962	D	0.998788	D	0.69078	0.997	D	0.65573	0.936	T	0.02444	-1.1158	10	0.87932	D	0	-1.6326	6.6193	0.22794	0.0:0.1056:0.0:0.8944	.	277	Q9NSI5	IGSF5_HUMAN	P	277	ENSP00000369962:L277P	ENSP00000369962:L277P	L	+	2	0	IGSF5	40072998	0.960000	0.32886	0.282000	0.24776	0.019000	0.09904	0.317000	0.19487	0.967000	0.38186	0.533000	0.62120	CTG	.	.		0.478	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1		
C2CD2	25966	hgsc.bcm.edu	37	21	43362260	43362260	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:43362260T>C	ENST00000380486.3	-	2	615	c.374A>G	c.(373-375)gAg>gGg	p.E125G		NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	125						cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						GCTCACCTTCTCCTCCGCCGA	0.597																																					p.E125G		Atlas-SNP	.											.	C2CD2	47	.	0			c.A374G						.						10.0	12.0	11.0					21																	43362260		1678	3353	5031	SO:0001583	missense	25966	exon2			ACCTTCTCCTCCG	AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"""TMEM24-like"""		"""chromosome 21 open reading frame 25"""	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.374A>G	chr21.hg19:g.43362260T>C	ENSP00000369853:p.Glu125Gly	161.0	0.0		111.0	6.0	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Missense_Mutation	SNP	ENST00000380486.3	hg19	CCDS42933.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.513290	0.64522	.	.	ENSG00000157617	ENST00000380486	T	0.25414	1.8	4.57	4.57	0.56435	.	0.247937	0.43579	D	0.000557	T	0.39627	0.1085	M	0.69823	2.125	0.38930	D	0.957913	D	0.60575	0.988	P	0.54815	0.761	T	0.33777	-0.9855	10	0.44086	T	0.13	-48.8196	10.6194	0.45470	0.0:0.0:0.0:1.0	.	125	Q9Y426	CU025_HUMAN	G	125	ENSP00000369853:E125G	ENSP00000369853:E125G	E	-	2	0	C2CD2	42235329	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	2.926000	0.48892	2.279000	0.76181	0.533000	0.62120	GAG	.	.		0.597	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	
WDR4	10785	hgsc.bcm.edu	37	21	44282502	44282502	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:44282502A>G	ENST00000398208.2	-	5	515	c.456T>C	c.(454-456)gcT>gcC	p.A152A	WDR4_ENST00000492742.1_5'UTR|WDR4_ENST00000330317.2_Silent_p.A152A	NM_001260474.1|NM_001260475.1|NM_001260476.1|NM_018669.5	NP_001247403.1|NP_001247404.1|NP_001247405.1|NP_061139.2			WD repeat domain 4											haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|ovary(2)	11				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)		CAGGACTCACAGCCTGCATCA	0.607																																					p.A152A		Atlas-SNP	.											.	WDR4	35	.	0			c.T456C						.						26.0	24.0	24.0					21																	44282502		2203	4300	6503	SO:0001819	synonymous_variant	10785	exon5			ACTCACAGCCTGC	AJ243912	CCDS13691.1	21q22.3	2013-01-09			ENSG00000160193	ENSG00000160193		"""WD repeat domain containing"""	12756	protein-coding gene	gene with protein product	"""TRM82 tRNA methyltransferase 82 homolog (S. cerevisiae)"""	605924				12403464	Standard	NM_018669		Approved	TRM82, TRMT82	uc002zci.4	P57081	OTTHUMG00000086826	ENST00000398208.2:c.456T>C	chr21.hg19:g.44282502A>G		41.0	0.0		43.0	4.0	NM_018669		Silent	SNP	ENST00000398208.2	hg19	CCDS13691.1																																																																																			.	.		0.607	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1		
NDUFV3	4731	hgsc.bcm.edu	37	21	44323563	44323563	+	Intron	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:44323563A>G	ENST00000340344.4	+	3	235				NDUFV3_ENST00000354250.2_Silent_p.K147K|NDUFV3_ENST00000460259.1_3'UTR	NM_001001503.1	NP_001001503.1	P56181	NDUV3_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	10				STAD - Stomach adenocarcinoma(101;0.0606)		TGGGTCGGAAAGTGACGTCGC	0.473																																					p.K147K		Atlas-SNP	.											.	NDUFV3	23	.	0			c.A441G						.						118.0	122.0	120.0					21																	44323563		2203	4300	6503	SO:0001627	intron_variant	4731	exon3			TCGGAAAGTGACG		CCDS33572.1, CCDS33573.1	21q22.3	2011-07-04	2002-08-29		ENSG00000160194	ENSG00000160194	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7719	protein-coding gene	gene with protein product	"""complex I 10kDa subunit"""	602184	"""NADH dehydrogenase (ubiquinone) flavoprotein 3 (10kD)"""			9344673	Standard	NM_021075		Approved	CI-10k	uc002zcm.3	P56181	OTTHUMG00000086823	ENST00000340344.4:c.170-5411A>G	chr21.hg19:g.44323563A>G		109.0	0.0		91.0	4.0	NM_021075	A8K0M1|J3KNX7|Q6FGD3|Q8WU60|Q9HCR5	Silent	SNP	ENST00000340344.4	hg19	CCDS33573.1																																																																																			.	.		0.473	NDUFV3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195448.2		
COL18A1	80781	hgsc.bcm.edu	37	21	46899863	46899863	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:46899863T>C	ENST00000359759.4	+	9	2562	c.2541T>C	c.(2539-2541)ggT>ggC	p.G847G	COL18A1_ENST00000355480.5_Silent_p.G612G|COL18A1_ENST00000400337.2_Silent_p.G432G			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	847	Triple-helical region 2 (COL2).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GGGACGTAGGTCCCAAGGGCG	0.672																																					p.G612G		Atlas-SNP	.											.	COL18A1	129	.	0			c.T1836C						.						65.0	79.0	74.0					21																	46899863		2008	4167	6175	SO:0001819	synonymous_variant	80781	exon9			CGTAGGTCCCAAG		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2541T>C	chr21.hg19:g.46899863T>C		67.0	0.0		60.0	4.0	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	hg19																																																																																				.	.		0.672	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
MCM3AP	8888	hgsc.bcm.edu	37	21	47685325	47685325	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:47685325T>C	ENST00000397708.1	-	13	3398	c.3144A>G	c.(3142-3144)gcA>gcG	p.A1048A	MCM3AP_ENST00000291688.1_Silent_p.A1048A			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1048					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					ACGGGGTCAGTGCCAGGACAG	0.647																																					p.A1048A		Atlas-SNP	.											.	MCM3AP	146	.	0			c.A3144G						.						73.0	69.0	71.0					21																	47685325		2203	4300	6503	SO:0001819	synonymous_variant	8888	exon12			GGTCAGTGCCAGG	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.3144A>G	chr21.hg19:g.47685325T>C		78.0	0.0		66.0	4.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	hg19	CCDS13734.1																																																																																			.	.		0.647	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
CLTCL1	8218	hgsc.bcm.edu	37	22	19217362	19217362	+	Splice_Site	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:19217362T>C	ENST00000263200.10	-	11	1853	c.1781A>G	c.(1780-1782)cAg>cGg	p.Q594R	CLTCL1_ENST00000353891.5_Splice_Site_p.Q594R|CLTCL1_ENST00000427926.1_Splice_Site_p.Q594R	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	594	Distal segment.|Heavy chain arm.				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)					GTCACTGACCTGGGGTGCATG	0.537			T	?	ALCL																																p.Q594R		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.A1781G						.						40.0	40.0	40.0					22																	19217362		1993	4180	6173	SO:0001630	splice_region_variant	8218	exon11			CTGACCTGGGGTG		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.1782+1A>G	chr22.hg19:g.19217362T>C		66.0	0.0		93.0	4.0	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	hg19	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.987145	0.74589	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.21543	2.0;2.0;2.0	4.28	4.28	0.50868	Armadillo-type fold (1);	0.072576	0.56097	D	0.000025	T	0.48607	0.1509	M	0.83603	2.65	0.58432	D	0.999998	D;D	0.64830	0.993;0.994	D;D	0.87578	0.968;0.998	T	0.53528	-0.8426	10	0.49607	T	0.09	-15.6511	13.7083	0.62653	0.0:0.0:0.0:1.0	.	594;594	P53675-2;P53675	.;CLH2_HUMAN	R	594	ENSP00000439662:Q594R;ENSP00000445677:Q594R;ENSP00000441158:Q594R	ENSP00000445677:Q594R	Q	-	2	0	CLTCL1	17597362	1.000000	0.71417	1.000000	0.80357	0.465000	0.32709	7.261000	0.78400	1.696000	0.51158	0.528000	0.53228	CAG	.	.		0.537	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	Missense_Mutation
ARVCF	421	hgsc.bcm.edu	37	22	19959474	19959474	+	Silent	SNP	G	G	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:19959474G>T	ENST00000263207.3	-	18	3007	c.2716C>A	c.(2716-2718)Cgg>Agg	p.R906R	ARVCF_ENST00000344269.3_Silent_p.R843R|ARVCF_ENST00000401994.1_Silent_p.R843R|ARVCF_ENST00000406259.1_Silent_p.R900R|ARVCF_ENST00000406522.1_Silent_p.R837R	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	906			R -> Q (in dbSNP:rs165815). {ECO:0000269|PubMed:19690332}.		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					CGCTCCCTCCGGTCCACCGTG	0.637																																					p.R906R		Atlas-SNP	.											.	ARVCF	54	.	0			c.C2716A						.						65.0	63.0	64.0					22																	19959474		2203	4300	6503	SO:0001819	synonymous_variant	421	exon18			CCCTCCGGTCCAC		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"""Armadillo repeat containing"""	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.2716C>A	chr22.hg19:g.19959474G>T		47.0	0.0		88.0	6.0	NM_001670	B7WNV2	Silent	SNP	ENST00000263207.3	hg19	CCDS13771.1																																																																																			.	.		0.637	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
AIFM3	150209	hgsc.bcm.edu	37	22	21328152	21328152	+	Silent	SNP	G	G	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:21328152G>T	ENST00000399167.2	+	4	591	c.351G>T	c.(349-351)gtG>gtT	p.V117V	AIFM3_ENST00000405089.1_Silent_p.V123V|AIFM3_ENST00000440238.2_Silent_p.V117V|AIFM3_ENST00000335375.5_Intron|AIFM3_ENST00000333607.6_Silent_p.V117V|AIFM3_ENST00000399163.2_Silent_p.V117V	NM_144704.2	NP_653305.1	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 3	117	Rieske. {ECO:0000255|PROSITE- ProRule:PRU00628}.				cell redox homeostasis (GO:0045454)|execution phase of apoptosis (GO:0097194)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	21	all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0367)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			CACCCCTGGTGAAAGGTGAGC	0.617																																					p.V123V		Atlas-SNP	.											.	AIFM3	49	.	0			c.G369T						.						35.0	30.0	32.0					22																	21328152		2187	4291	6478	SO:0001819	synonymous_variant	150209	exon4			CCTGGTGAAAGGT	AK094844	CCDS13786.1, CCDS33605.1, CCDS54503.1	22q11.21	2007-05-03			ENSG00000183773	ENSG00000183773			26398	protein-coding gene	gene with protein product						15764604	Standard	NM_144704		Approved	AIFL, FLJ30473		Q96NN9	OTTHUMG00000150804	ENST00000399167.2:c.351G>T	chr22.hg19:g.21328152G>T		63.0	0.0		113.0	34.0	NM_001146288	B7WP37|D3DX37|D3DX38|Q6ZT44|Q8N1V3|Q8N5E0	Silent	SNP	ENST00000399167.2	hg19	CCDS13786.1																																																																																			.	.		0.617	AIFM3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320150.1	NM_144704	
ZNF280B	140883	hgsc.bcm.edu	37	22	22842944	22842944	+	Silent	SNP	T	T	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:22842944T>A	ENST00000406426.1	-	4	1522	c.780A>T	c.(778-780)gcA>gcT	p.A260A	ZNF280B_ENST00000360412.2_Silent_p.A260A			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	260					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TGTCTGTTTTTGCCAATTCAT	0.363																																					p.A260A		Atlas-SNP	.											.	ZNF280B	67	.	0			c.A780T						.						106.0	100.0	102.0					22																	22842944		2203	4300	6503	SO:0001819	synonymous_variant	140883	exon4			TGTTTTTGCCAAT	AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"""zinc finger protein 279"", ""suppressor of hairy wing homolog 2 (Drosophila)"""	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.780A>T	chr22.hg19:g.22842944T>A		81.0	0.0		100.0	17.0	NM_080764		Silent	SNP	ENST00000406426.1	hg19	CCDS13799.1																																																																																			.	.		0.363	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764	
SPECC1L	23384	hgsc.bcm.edu	37	22	24726381	24726381	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:24726381A>G	ENST00000314328.9	+	8	2663	c.2378A>G	c.(2377-2379)gAg>gGg	p.E793G	SPECC1L_ENST00000541492.1_Missense_Mutation_p.E793G|SPECC1L_ENST00000437398.1_Missense_Mutation_p.E793G|SPECC1L-ADORA2A_ENST00000358654.2_Missense_Mutation_p.E793G	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	793					actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						AAAGAATTGGAGGAAATAAAG	0.378																																					p.E793G		Atlas-SNP	.											.	SPECC1L	85	.	0			c.A2378G						.						87.0	91.0	90.0					22																	24726381		2203	4300	6503	SO:0001583	missense	23384	exon7			AATTGGAGGAAAT	AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"""cytokinesis and spindle organization A"", ""cytospin A"""	614140	"""SPECC1-like"""			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.2378A>G	chr22.hg19:g.24726381A>G	ENSP00000325785:p.Glu793Gly	67.0	0.0		82.0	4.0	NM_001145468	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	hg19	CCDS33619.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.829453	0.71258	.	.	ENSG00000100014	ENST00000398280;ENST00000437398;ENST00000314328;ENST00000541492	T;T;T	0.46451	0.87;0.87;0.87	5.94	5.94	0.96194	.	0.097898	0.64402	D	0.000002	T	0.38054	0.1026	L	0.33753	1.03	0.80722	D	1	B;P	0.46987	0.124;0.888	B;P	0.44561	0.031;0.453	T	0.09907	-1.0653	9	.	.	.	-30.0623	15.5759	0.76387	1.0:0.0:0.0:0.0	.	793;793	F5H1H6;Q69YQ0	.;CYTSA_HUMAN	G	821;793;793;793	ENSP00000393363:E793G;ENSP00000325785:E793G;ENSP00000439633:E793G	.	E	+	2	0	SPECC1L	23056381	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.000000	0.93564	2.272000	0.75746	0.459000	0.35465	GAG	.	.		0.378	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330	
MTMR3	8897	hgsc.bcm.edu	37	22	30387534	30387534	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:30387534A>G	ENST00000401950.2	+	7	677	c.335A>G	c.(334-336)aAg>aGg	p.K112R	MTMR3_ENST00000415511.1_3'UTR|MTMR3_ENST00000323630.5_5'UTR|MTMR3_ENST00000351488.3_Missense_Mutation_p.K112R|MTMR3_ENST00000333027.3_Missense_Mutation_p.K112R|MTMR3_ENST00000406629.1_Missense_Mutation_p.K112R	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	112					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			GAGTGGCTGAAGAGACTGAAC	0.413																																					p.K112R		Atlas-SNP	.											.	MTMR3	106	.	0			c.A335G						.						119.0	103.0	108.0					22																	30387534		2203	4300	6503	SO:0001583	missense	8897	exon7			GGCTGAAGAGACT	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.335A>G	chr22.hg19:g.30387534A>G	ENSP00000384651:p.Lys112Arg	68.0	0.0		79.0	5.0	NM_021090	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Missense_Mutation	SNP	ENST00000401950.2	hg19	CCDS13870.1	.	.	.	.	.	.	.	.	.	.	A	12.78	2.040850	0.35989	.	.	ENSG00000100330	ENST00000401950;ENST00000333027;ENST00000445401;ENST00000351488;ENST00000406629	D;D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65;-1.65	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.76630	0.4014	L	0.32530	0.975	0.80722	D	1	P;B;P	0.40302	0.712;0.125;0.712	B;B;B	0.38683	0.279;0.05;0.279	T	0.77270	-0.2650	10	0.40728	T	0.16	.	15.3779	0.74625	1.0:0.0:0.0:0.0	.	112;112;112	Q13615-3;Q13615;Q13615-2	.;MTMR3_HUMAN;.	R	112	ENSP00000384651:K112R;ENSP00000331649:K112R;ENSP00000409063:K112R;ENSP00000307271:K112R;ENSP00000384077:K112R	ENSP00000331649:K112R	K	+	2	0	MTMR3	28717534	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.225000	0.72522	0.533000	0.62120	AAG	.	.		0.413	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090	
MORC2	22880	hgsc.bcm.edu	37	22	31334114	31334114	+	Silent	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:31334114G>A	ENST00000397641.3	-	13	1560	c.1152C>T	c.(1150-1152)atC>atT	p.I384I	MORC2_ENST00000215862.4_Silent_p.I322I|MORC2_ENST00000469915.1_Intron			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	384						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						TACAGTTGTAGATGAACATGC	0.443																																					p.I322I		Atlas-SNP	.											.	MORC2	78	.	0			c.C966T						.						123.0	98.0	107.0					22																	31334114		2203	4300	6503	SO:0001819	synonymous_variant	22880	exon14			GTTGTAGATGAAC	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 1"", ""zinc finger, CW type with coiled-coil domain 1"""	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.1152C>T	chr22.hg19:g.31334114G>A		137.0	0.0		155.0	7.0	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Silent	SNP	ENST00000397641.3	hg19																																																																																				.	.		0.443	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941	
RTCB	51493	hgsc.bcm.edu	37	22	32789991	32789991	+	Splice_Site	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:32789991T>C	ENST00000216038.5	-	10	1278		c.e10-2		RTCB_ENST00000451746.2_Intron	NM_014306.4	NP_055121.1			RNA 2',3'-cyclic phosphate and 5'-OH ligase																		TCCAGTGAGCTGAGGATGCAC	0.403																																					.		Atlas-SNP	.											.	C22orf28	43	.	0			c.1180-2A>G						.						111.0	98.0	102.0					22																	32789991		2203	4300	6503	SO:0001630	splice_region_variant	51493	exon11			GTGAGCTGAGGAT	BC016707	CCDS13905.1	22q12.3	2013-05-22	2013-05-22	2013-05-22	ENSG00000100220	ENSG00000100220	6.5.1.3		26935	protein-coding gene	gene with protein product	"""focal adhesion-associated protein"""	613901	"""chromosome 22 open reading frame 28"""	C22orf28		11042152, 21209330, 21311021	Standard	NM_014306		Approved	HSPC117, FAAP		Q9Y3I0	OTTHUMG00000030300	ENST00000216038.5:c.1180-2A>G	chr22.hg19:g.32789991T>C		56.0	0.0		75.0	4.0	NM_014306		Splice_Site	SNP	ENST00000216038.5	hg19	CCDS13905.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.082258	0.76528	.	.	ENSG00000100220	ENST00000216038	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6325	0.68666	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	C22orf28	31119991	1.000000	0.71417	0.999000	0.59377	0.956000	0.61745	7.885000	0.87282	1.851000	0.53745	0.482000	0.46254	.	.	.		0.403	RTCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075188.3	NM_014306	Intron
BPIFC	254240	hgsc.bcm.edu	37	22	32811918	32811918	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:32811918T>C	ENST00000397452.1	-	15	1495	c.1385A>G	c.(1384-1386)gAt>gGt	p.D462G	BPIFC_ENST00000534972.1_Missense_Mutation_p.D186G|BPIFC_ENST00000300399.3_Missense_Mutation_p.D462G|BPIFC_ENST00000432451.2_Missense_Mutation_p.D219G			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	462						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										AACTTCAATATCTGAATTGAC	0.363																																					p.D462G		Atlas-SNP	.											.	.	.	.	0			c.A1385G						.						87.0	87.0	87.0					22																	32811918		2203	4300	6503	SO:0001583	missense	254240	exon14			TCAATATCTGAAT	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"""BPI fold containing"""	16503	protein-coding gene	gene with protein product		614109	"""bactericidal/permeability-increasing protein-like 2"""	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.1385A>G	chr22.hg19:g.32811918T>C	ENSP00000380594:p.Asp462Gly	68.0	0.0		99.0	4.0	NM_174932	A2RRF1	Missense_Mutation	SNP	ENST00000397452.1	hg19	CCDS13906.1	.	.	.	.	.	.	.	.	.	.	T	15.53	2.860192	0.51482	.	.	ENSG00000184459	ENST00000397452;ENST00000300399;ENST00000534972;ENST00000432451	T;T;T;T	0.08634	3.07;3.07;3.07;3.07	5.5	5.5	0.81552	.	0.649988	0.17083	N	0.187690	T	0.14527	0.0351	M	0.62016	1.91	0.35916	D	0.831468	B;B	0.34103	0.437;0.379	B;B	0.40864	0.342;0.272	T	0.09707	-1.0662	10	0.37606	T	0.19	-8.6693	12.2787	0.54751	0.0:0.0:0.0:1.0	.	219;462	A2RRF1;Q8NFQ6	.;BPIFC_HUMAN	G	462;462;186;219	ENSP00000380594:D462G;ENSP00000300399:D462G;ENSP00000439123:D186G;ENSP00000408920:D219G	ENSP00000300399:D462G	D	-	2	0	BPIFC	31141918	0.010000	0.17322	0.987000	0.45799	0.942000	0.58702	1.682000	0.37628	2.212000	0.71576	0.528000	0.53228	GAT	.	.		0.363	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932	
SSTR3	6753	hgsc.bcm.edu	37	22	37602587	37602587	+	Nonstop_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:37602587T>C	ENST00000328544.3	-	2	1789	c.1256A>G	c.(1255-1257)tAg>tGg	p.*419W	SSTR3_ENST00000402501.1_Nonstop_Mutation_p.*419W	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	0					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)	CCCCAGGCCCTACAGGTAGCT	0.637																																					p.X419W		Atlas-SNP	.											.	SSTR3	42	.	0			c.A1256G						.						42.0	47.0	46.0					22																	37602587		2202	4298	6500	SO:0001578	stop_lost	6753	exon2			AGGCCCTACAGGT		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.1256A>G	chr22.hg19:g.37602587T>C	ENSP00000330138:p.*419Serext*19	58.0	0.0		60.0	5.0	NM_001051	A8K550|Q53ZR7	Missense_Mutation	SNP	ENST00000328544.3	hg19	CCDS13944.1	.	.	.	.	.	.	.	.	.	.	T	8.854	0.945208	0.18356	.	.	ENSG00000183473	ENST00000328544;ENST00000402501	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.7675	0.28988	0.0:0.1619:0.0:0.8381	rs11406761;rs58031140	.	.	.	W	419	.	.	X	-	2	0	SSTR3	35932533	1.000000	0.71417	0.982000	0.44146	0.186000	0.23388	4.076000	0.57591	2.053000	0.61076	0.402000	0.26972	TAG	.	.		0.637	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1		
CYTH4	27128	hgsc.bcm.edu	37	22	37709517	37709517	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:37709517T>C	ENST00000248901.6	+	13	1337	c.1150T>C	c.(1150-1152)Tct>Cct	p.S384P		NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4	384					positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(2)|stomach(1)	15						CGACCTGGTCTCTACTCGGAA	0.587																																					p.S384P		Atlas-SNP	.											.	CYTH4	51	.	0			c.T1150C						.						158.0	132.0	141.0					22																	37709517		2203	4300	6503	SO:0001583	missense	27128	exon13			CTGGTCTCTACTC	AF075458	CCDS13946.1	22q12.3-q13.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000100055	ENSG00000100055		"""Pleckstrin homology (PH) domain containing"""	9505	protein-coding gene	gene with protein product		606514	"""pleckstrin homology, Sec7 and coiled/coil domains 4"", ""pleckstrin homology, Sec7 and coiled-coil domains 4"""	PSCD4		10591208	Standard	NM_013385		Approved	CYT4, cytohesin-4	uc003arf.3	Q9UIA0	OTTHUMG00000150562	ENST00000248901.6:c.1150T>C	chr22.hg19:g.37709517T>C	ENSP00000248901:p.Ser384Pro	129.0	0.0		146.0	6.0	NM_013385	Q5R3F9|Q9UGT6	Missense_Mutation	SNP	ENST00000248901.6	hg19	CCDS13946.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.94|15.94	2.981290|2.981290	0.53827|0.53827	.|.	.|.	ENSG00000100055|ENSG00000100055	ENST00000446506|ENST00000248901;ENST00000404204	.|T	.|0.07216	.|3.21	4.86|4.86	4.86|4.86	0.63082|0.63082	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.14743|0.14743	0.0356|0.0356	M|M	0.70275|0.70275	2.135|2.135	0.51233|0.51233	D|D	0.999912|0.999912	.|P	.|0.36647	.|0.563	.|B	.|0.42555	.|0.391	T|T	0.00899|0.00899	-1.1522|-1.1522	5|10	.|0.59425	.|D	.|0.04	.|.	9.6363|9.6363	0.39809|0.39809	0.0:0.0:0.2993:0.7007|0.0:0.0:0.2993:0.7007	.|.	.|384	.|Q9UIA0	.|CYH4_HUMAN	P|P	136|384;43	.|ENSP00000248901:S384P	.|ENSP00000248901:S384P	L|S	+|+	2|1	0|0	CYTH4|CYTH4	36039463|36039463	0.336000|0.336000	0.24757|0.24757	1.000000|1.000000	0.80357|0.80357	0.957000|0.957000	0.61999|0.61999	0.512000|0.512000	0.22755|0.22755	1.950000|1.950000	0.56595|0.56595	0.402000|0.402000	0.26972|0.26972	CTC|TCT	.	.		0.587	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318917.1		
RANGAP1	5905	hgsc.bcm.edu	37	22	41645369	41645369	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:41645369C>A	ENST00000455915.2	-	14	3128	c.1659G>T	c.(1657-1659)aaG>aaT	p.K553N	RANGAP1_ENST00000356244.3_Missense_Mutation_p.K553N|RANGAP1_ENST00000407260.4_Missense_Mutation_p.K498N|RANGAP1_ENST00000405486.1_Missense_Mutation_p.K553N			P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	553					mitotic cell cycle (GO:0000278)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear pore (GO:0005643)|perinuclear region of cytoplasm (GO:0048471)	Ran GTPase activator activity (GO:0005098)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GTGCAAGGGCCTTGGGGAAAT	0.602																																					p.K553N		Atlas-SNP	.											.	RANGAP1	47	.	0			c.G1659T						.						72.0	60.0	64.0					22																	41645369		2203	4300	6503	SO:0001583	missense	5905	exon15			AAGGGCCTTGGGG	X82260	CCDS14012.1	22q13	2013-01-17			ENSG00000100401	ENSG00000100401			9854	protein-coding gene	gene with protein product		602362	"""segregation distorter homolog (Drosophila)"""	SD		7878053	Standard	NM_002883		Approved	Fug1, KIAA1835	uc003azu.3	P46060	OTTHUMG00000150940	ENST00000455915.2:c.1659G>T	chr22.hg19:g.41645369C>A	ENSP00000401470:p.Lys553Asn	91.0	0.0		99.0	17.0	NM_002883	Q96JJ2	Missense_Mutation	SNP	ENST00000455915.2	hg19	CCDS14012.1	.	.	.	.	.	.	.	.	.	.	C	19.57	3.852060	0.71719	.	.	ENSG00000100401	ENST00000405486;ENST00000356244;ENST00000405383;ENST00000455915;ENST00000407260	T;T;T;T	0.47528	0.84;0.84;0.84;1.3	5.4	5.4	0.78164	Ran-GTPase activating protein 1, C-terminal (3);	0.147294	0.64402	D	0.000013	T	0.61135	0.2323	M	0.72894	2.215	0.47584	D	0.999464	D;P	0.67145	0.996;0.928	D;P	0.63597	0.916;0.74	T	0.59241	-0.7491	10	0.30854	T	0.27	-33.7749	9.5133	0.39091	0.0:0.8375:0.0:0.1625	.	498;553	F8W7I9;P46060	.;RAGP1_HUMAN	N	553;553;553;553;498	ENSP00000385866:K553N;ENSP00000348577:K553N;ENSP00000401470:K553N;ENSP00000385354:K498N	ENSP00000348577:K553N	K	-	3	2	RANGAP1	39975315	0.956000	0.32656	1.000000	0.80357	0.858000	0.48976	1.094000	0.30951	2.515000	0.84797	0.467000	0.42956	AAG	.	.		0.602	RANGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320606.1	NM_002883	
POLDIP3	84271	hgsc.bcm.edu	37	22	42991558	42991558	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:42991558A>G	ENST00000252115.5	-	6	980	c.876T>C	c.(874-876)acT>acC	p.T292T	POLDIP3_ENST00000491021.1_5'UTR|POLDIP3_ENST00000348657.2_Silent_p.T263T|POLDIP3_ENST00000451060.2_Silent_p.T136T|POLDIP3_ENST00000339677.6_Intron	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	292	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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						TGTCCTCCTCAGTGACTCGAG	0.478																																					p.T292T	Ovarian(52;967 1128 5875 19997 42537)	Atlas-SNP	.											.	POLDIP3	58	.	0			c.T876C						.						179.0	140.0	154.0					22																	42991558		2203	4300	6503	SO:0001819	synonymous_variant	84271	exon6			CTCCTCAGTGACT		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.876T>C	chr22.hg19:g.42991558A>G		146.0	0.0		170.0	7.0	NM_032311	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Silent	SNP	ENST00000252115.5	hg19	CCDS14038.1																																																																																			.	.		0.478	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311	
PARVG	64098	hgsc.bcm.edu	37	22	44587943	44587943	+	Silent	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:44587943T>C	ENST00000444313.3	+	8	1003	c.519T>C	c.(517-519)ggT>ggC	p.G173G	PARVG_ENST00000415224.1_Silent_p.G173G|PARVG_ENST00000422871.1_Silent_p.G173G	NM_022141.5	NP_071424.1	Q9HBI0	PARVG_HUMAN	parvin, gamma	173					actin cytoskeleton reorganization (GO:0031532)|cell-matrix adhesion (GO:0007160)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)	17		Ovarian(80;0.024)|all_neural(38;0.0299)				CCAAAAGTGGTCTGAAGTCAG	0.512																																					p.G173G		Atlas-SNP	.											PARVG,NS,carcinoma,0,1	PARVG	41	.	0			c.T519C						.						63.0	68.0	66.0					22																	44587943		2203	4300	6503	SO:0001819	synonymous_variant	64098	exon8			AAGTGGTCTGAAG	AF237772	CCDS14057.1	22q13.31	2013-01-24			ENSG00000138964	ENSG00000138964		"""Parvins"""	14654	protein-coding gene	gene with protein product		608122				11171322	Standard	NM_022141		Approved		uc003bep.4	Q9HBI0	OTTHUMG00000150473	ENST00000444313.3:c.519T>C	chr22.hg19:g.44587943T>C		53.0	0.0		82.0	4.0	NM_001137606	B4DDW5|E7EVM6|Q9BQX5|Q9NSG1	Silent	SNP	ENST00000444313.3	hg19	CCDS14057.1																																																																																			.	.		0.512	PARVG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318238.4	NM_022141	
CELSR1	9620	hgsc.bcm.edu	37	22	46777807	46777807	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:46777807T>C	ENST00000262738.3	-	21	7023	c.7024A>G	c.(7024-7026)Atc>Gtc	p.I2342V		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2342					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CGGTAAATGATGACCAGAGCG	0.726																																					p.I2342V		Atlas-SNP	.											.	CELSR1	242	.	0			c.A7024G						.						17.0	19.0	19.0					22																	46777807		2183	4283	6466	SO:0001583	missense	9620	exon21			AAATGATGACCAG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.7024A>G	chr22.hg19:g.46777807T>C	ENSP00000262738:p.Ile2342Val	80.0	0.0		88.0	4.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	T	5.349	0.249717	0.10130	.	.	ENSG00000075275	ENST00000262738	T	0.07216	3.21	4.89	-9.78	0.00496	Domain of unknown function DUF3497 (1);	0.465341	0.17759	N	0.162948	T	0.04815	0.0130	L	0.39898	1.24	0.31121	N	0.708885	B;B	0.31893	0.345;0.041	B;B	0.33392	0.163;0.097	T	0.16689	-1.0394	10	0.15952	T	0.53	.	9.9564	0.41668	0.0:0.4477:0.2836:0.2686	.	663;2342	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	V	2342	ENSP00000262738:I2342V	ENSP00000262738:I2342V	I	-	1	0	CELSR1	45156471	0.927000	0.31430	0.003000	0.11579	0.013000	0.08279	-0.011000	0.12721	-2.205000	0.00742	-0.388000	0.06559	ATC	.	.		0.726	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
BRD1	23774	hgsc.bcm.edu	37	22	50187702	50187703	+	Missense_Mutation	DNP	CC	CC	AA			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:50187702_50187703CC>AA	ENST00000216267.8	-	6	2824_2825	c.2338_2339GG>TT	c.(2338-2340)GGg>TTg	p.G780L	BRD1_ENST00000342989.5_Missense_Mutation_p.G375L|BRD1_ENST00000404034.1_Missense_Mutation_p.G780L|BRD1_ENST00000457780.2_Missense_Mutation_p.G780L|BRD1_ENST00000404760.1_Missense_Mutation_p.G780L|BRD1_ENST00000542442.1_Missense_Mutation_p.G468L	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	780					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)	p.G780V(1)|p.G375V(1)		endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		CGCCTCCGGCCCCAGCGCAGCT	0.663																																					p.G780V|p.G780W		Atlas-SNP	.											BRD1_ENST00000342989,NS,carcinoma,0,2|.	BRD1	144	.	2	Substitution - Missense(2)	kidney(2)	c.G2339T|c.G2338T						.																																			SO:0001583	missense	23774	exon6			TCCGGCCCCAGCG|CCGGCCCCAGCGC	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.2338_2339delinsAA	chr22.hg19:g.50187702_50187703delinsAA	ENSP00000216267:p.Gly780Leu	67.0	0.0		58.0|57.0	43.0|42.0	NM_014577	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	hg19	CCDS14080.1																																																																																			.	.		0.663	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
MAPK12	6300	hgsc.bcm.edu	37	22	50695539	50695539	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:50695539A>G	ENST00000215659.8	-	4	713	c.398T>C	c.(397-399)cTc>cCc	p.L133P	MAPK12_ENST00000497036.1_5'UTR|MAPK12_ENST00000395780.1_Missense_Mutation_p.L53P	NM_002969.3	NP_002960.2	P53778	MK12_HUMAN	mitogen-activated protein kinase 12	133	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle arrest (GO:0007050)|DNA damage induced protein phosphorylation (GO:0006975)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of peptidase activity (GO:0010952)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	8		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;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CTGGTACACGAGGAACTGGAT	0.662																																					p.L133P		Atlas-SNP	.											.	MAPK12	43	.	0			c.T398C						.						84.0	72.0	76.0					22																	50695539		2203	4300	6503	SO:0001583	missense	6300	exon4			TACACGAGGAACT	U66243	CCDS14089.1	22q13.3	2012-05-08			ENSG00000188130	ENSG00000188130	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6874	protein-coding gene	gene with protein product		602399		SAPK3		9169156	Standard	NM_002969		Approved	ERK6, PRKM12, p38gamma, SAPK-3	uc003bkm.1	P53778	OTTHUMG00000030145	ENST00000215659.8:c.398T>C	chr22.hg19:g.50695539A>G	ENSP00000215659:p.Leu133Pro	98.0	0.0		71.0	4.0	NM_002969	Q14260|Q6IC53|Q99588|Q99672	Missense_Mutation	SNP	ENST00000215659.8	hg19	CCDS14089.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.269694	0.80469	.	.	ENSG00000188130	ENST00000438835;ENST00000395780;ENST00000215659	T;T	0.15487	2.42;2.42	4.71	4.71	0.59529	Serine/threonine-protein kinase-like domain (1);MAP kinase, conserved site (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.25543	U	0.029959	T	0.46658	0.1404	M	0.87971	2.92	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	0.55036	-0.8203	10	0.87932	D	0	-20.3739	13.3024	0.60332	1.0:0.0:0.0:0.0	.	53;133;133	B5MDL5;P53778;F6TXG5	.;MK12_HUMAN;.	P	133;53;133	ENSP00000379126:L53P;ENSP00000215659:L133P	ENSP00000215659:L133P	L	-	2	0	MAPK12	49037666	1.000000	0.71417	0.888000	0.34837	0.817000	0.46193	5.780000	0.68956	1.988000	0.58038	0.402000	0.26972	CTC	.	.		0.662	MAPK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074999.2	NM_002969	
MIOX	55586	hgsc.bcm.edu	37	22	50928027	50928027	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:50928027T>A	ENST00000216075.6	+	9	777	c.703T>A	c.(703-705)Tgc>Agc	p.C235S	MIOX_ENST00000395732.3_Missense_Mutation_p.C235S|MIOX_ENST00000395733.3_Intron	NM_017584.5	NP_060054.4	Q9UGB7	MIOX_HUMAN	myo-inositol oxygenase	235					inositol catabolic process (GO:0019310)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)	aldo-keto reductase (NADP) activity (GO:0004033)|ferric iron binding (GO:0008199)|inositol oxygenase activity (GO:0050113)|NADP binding (GO:0050661)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen (GO:0016701)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	13		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;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCAGCAGCTGTGCAGCCAGCA	0.657																																					p.C235S		Atlas-SNP	.											MIOX,colon,carcinoma,0,1	MIOX	21	.	0			c.T703A						.						23.0	24.0	24.0					22																	50928027		2196	4292	6488	SO:0001583	missense	55586	exon9			CAGCTGTGCAGCC	AF197129	CCDS14092.1	22q13.3	2008-06-11	2005-06-15	2005-06-15	ENSG00000100253	ENSG00000100253			14522	protein-coding gene	gene with protein product	"""kidney-specific protein 32"""	606774	"""aldehyde reductase (aldose reductase) like 6"""	ALDRL6		10944187, 11716759	Standard	NM_017584		Approved		uc003bll.1	Q9UGB7	OTTHUMG00000150207	ENST00000216075.6:c.703T>A	chr22.hg19:g.50928027T>A	ENSP00000216075:p.Cys235Ser	124.0	0.0		128.0	0.0	NM_017584	Q05DJ6|Q5S8C9|Q9BZZ1|Q9UHB8	Missense_Mutation	SNP	ENST00000216075.6	hg19	CCDS14092.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.477193	0.84640	.	.	ENSG00000100253	ENST00000216075;ENST00000395732;ENST00000451761	.	.	.	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.73094	0.3543	M	0.63843	1.955	0.80722	D	1	P;P	0.45283	0.855;0.674	P;P	0.60473	0.875;0.8	T	0.70699	-0.4800	9	0.30078	T	0.28	2.714	13.0331	0.58854	0.0:0.0:0.0:1.0	.	235;235	A6PVH2;Q9UGB7	.;MIOX_HUMAN	S	235;235;215	.	ENSP00000216075:C235S	C	+	1	0	MIOX	49274893	1.000000	0.71417	0.999000	0.59377	0.938000	0.57974	7.608000	0.82898	1.953000	0.56701	0.533000	0.62120	TGC	.	.		0.657	MIOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316835.1	NM_017584	
SHROOM2	357	hgsc.bcm.edu	37	X	9900715	9900715	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:9900715T>C	ENST00000380913.3	+	6	3482	c.3392T>C	c.(3391-3393)gTc>gCc	p.V1131A	SHROOM2_ENST00000493668.1_3'UTR|SHROOM2_ENST00000418909.2_5'UTR	NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	1131					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				AAGGCCACTGTCTGTGAGCGT	0.662																																					p.V1131A		Atlas-SNP	.											.	SHROOM2	139	.	0			c.T3392C						.						62.0	52.0	56.0					X																	9900715		2203	4300	6503	SO:0001583	missense	357	exon6			CCACTGTCTGTGA	X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"""apical protein, Xenopus laevis-like"", ""apical protein-like (Xenopus laevis)"""	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.3392T>C	chrX.hg19:g.9900715T>C	ENSP00000370299:p.Val1131Ala	70.0	0.0		88.0	4.0	NM_001649	B9EIQ7	Missense_Mutation	SNP	ENST00000380913.3	hg19	CCDS14135.1	.	.	.	.	.	.	.	.	.	.	T	1.909	-0.451286	0.04572	.	.	ENSG00000146950	ENST00000380913	T	0.14391	2.51	3.15	1.25	0.21368	.	.	.	.	.	T	0.05135	0.0137	N	0.08118	0	0.34014	D	0.651804	B	0.02656	0.0	B	0.01281	0.0	T	0.44937	-0.9295	9	0.05833	T	0.94	.	7.3423	0.26644	0.0:0.7319:0.1661:0.102	.	1131	Q13796	SHRM2_HUMAN	A	1131	ENSP00000370299:V1131A	ENSP00000370299:V1131A	V	+	2	0	SHROOM2	9860715	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	1.717000	0.37991	-0.156000	0.11079	-0.188000	0.12872	GTC	.	.		0.662	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649	
CDKL5	6792	hgsc.bcm.edu	37	X	18593549	18593549	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:18593549A>G	ENST00000379989.3	+	6	506	c.221A>G	c.(220-222)gAg>gGg	p.E74G	CDKL5_ENST00000379996.3_Missense_Mutation_p.E74G	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	74	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					AACATTGTGGAGTTGAAGGAA	0.393																																					p.E74G		Atlas-SNP	.											.	CDKL5	124	.	0			c.A221G						.						182.0	167.0	172.0					X																	18593549		2203	4300	6503	SO:0001583	missense	6792	exon5			TTGTGGAGTTGAA	Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"""Cyclin-dependent kinases"""	11411	protein-coding gene	gene with protein product		300203	"""serine/threonine kinase 9"""	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.221A>G	chrX.hg19:g.18593549A>G	ENSP00000369325:p.Glu74Gly	105.0	0.0		97.0	5.0	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Missense_Mutation	SNP	ENST00000379989.3	hg19	CCDS14186.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.986496	0.74589	.	.	ENSG00000008086	ENST00000379996;ENST00000379989	T;T	0.42513	0.97;0.97	5.69	5.69	0.88448	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	0.85682	D	0.000000	T	0.53351	0.1791	L	0.31845	0.965	0.53005	D	0.999966	D	0.71674	0.998	D	0.71870	0.975	T	0.55811	-0.8082	10	0.59425	D	0.04	-21.4508	14.8699	0.70448	1.0:0.0:0.0:0.0	.	74	O76039	CDKL5_HUMAN	G	74	ENSP00000369332:E74G;ENSP00000369325:E74G	ENSP00000369325:E74G	E	+	2	0	CDKL5	18503470	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.339000	0.96797	1.893000	0.54813	0.486000	0.48141	GAG	.	.		0.393	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159	
PTCHD1	139411	hgsc.bcm.edu	37	X	23411677	23411677	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:23411677T>C	ENST00000379361.4	+	3	2902	c.2042T>C	c.(2041-2043)gTc>gCc	p.V681A		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	681					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						AAGTTCATCGTCTTCAATCCG	0.483																																					p.V681A		Atlas-SNP	.											.	PTCHD1	213	.	0			c.T2042C						.						91.0	82.0	85.0					X																	23411677		2203	4300	6503	SO:0001583	missense	139411	exon3			TCATCGTCTTCAA	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.2042T>C	chrX.hg19:g.23411677T>C	ENSP00000368666:p.Val681Ala	74.0	0.0		113.0	5.0	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Missense_Mutation	SNP	ENST00000379361.4	hg19	CCDS35215.2	.	.	.	.	.	.	.	.	.	.	T	14.08	2.429925	0.43122	.	.	ENSG00000165186	ENST00000379361	D	0.88509	-2.39	5.34	5.34	0.76211	.	0.059808	0.64402	D	0.000002	D	0.84606	0.5509	L	0.34521	1.04	0.41461	D	0.988041	B	0.23937	0.094	B	0.32149	0.141	T	0.80369	-0.1411	10	0.25106	T	0.35	.	14.3778	0.66889	0.0:0.0:0.0:1.0	.	681	Q96NR3	PTHD1_HUMAN	A	681	ENSP00000368666:V681A	ENSP00000368666:V681A	V	+	2	0	PTCHD1	23321598	1.000000	0.71417	0.986000	0.45419	0.997000	0.91878	7.694000	0.84235	1.775000	0.52247	0.430000	0.28490	GTC	.	.		0.483	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495	
POLA1	5422	hgsc.bcm.edu	37	X	24741325	24741325	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:24741325A>G	ENST00000379059.3	+	11	1138	c.1123A>G	c.(1123-1125)Agc>Ggc	p.S375G	POLA1_ENST00000379068.3_Missense_Mutation_p.S381G	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	375					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	GACCCATGTGAGCTGTTGTGT	0.383																																					p.S375G		Atlas-SNP	.											.	POLA1	117	.	0			c.A1123G						.						224.0	205.0	211.0					X																	24741325		2203	4300	6503	SO:0001583	missense	5422	exon11			CATGTGAGCTGTT		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"""DNA polymerases"""	9173	protein-coding gene	gene with protein product		312040	"""polymerase (DNA directed), alpha"", ""polymerase (DNA directed), alpha 1"", ""N syndrome (mental retardation, malformations, chromosome breakage)"""	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.1123A>G	chrX.hg19:g.24741325A>G	ENSP00000368349:p.Ser375Gly	139.0	0.0		178.0	8.0	NM_016937	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	hg19	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	A	18.52	3.641159	0.67244	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.12672	2.66;2.66	5.25	5.25	0.73442	DNA-directed DNA polymerase, family B, exonuclease domain (1);	0.040115	0.85682	D	0.000000	T	0.51991	0.1707	H	0.96861	3.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.69281	-0.5186	10	0.87932	D	0	-9.3184	14.239	0.65945	1.0:0.0:0.0:0.0	.	381;375	A6NMQ1;P09884	.;DPOLA_HUMAN	G	381;375	ENSP00000368358:S381G;ENSP00000368349:S375G	ENSP00000368349:S375G	S	+	1	0	POLA1	24651246	1.000000	0.71417	1.000000	0.80357	0.369000	0.29798	8.673000	0.91186	1.939000	0.56221	0.486000	0.48141	AGC	.	.		0.383	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937	
POLA1	5422	hgsc.bcm.edu	37	X	24844595	24844595	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:24844595C>T	ENST00000379059.3	+	32	3610	c.3595C>T	c.(3595-3597)Cag>Tag	p.Q1199*	POLA1_ENST00000379068.3_Nonsense_Mutation_p.Q1205*	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	1199					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	TGAGCAGCTGCAGAAACAGGA	0.468																																					p.Q1199X		Atlas-SNP	.											.	POLA1	117	.	0			c.C3595T						.						114.0	74.0	87.0					X																	24844595		2203	4300	6503	SO:0001587	stop_gained	5422	exon32			CAGCTGCAGAAAC		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"""DNA polymerases"""	9173	protein-coding gene	gene with protein product		312040	"""polymerase (DNA directed), alpha"", ""polymerase (DNA directed), alpha 1"", ""N syndrome (mental retardation, malformations, chromosome breakage)"""	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.3595C>T	chrX.hg19:g.24844595C>T	ENSP00000368349:p.Gln1199*	77.0	0.0		73.0	4.0	NM_016937	Q86UQ7	Nonsense_Mutation	SNP	ENST00000379059.3	hg19	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	C	42	9.569633	0.99207	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	.	.	.	5.69	4.8	0.61643	.	0.111512	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.9983	14.2989	0.66334	0.3139:0.6861:0.0:0.0	.	.	.	.	X	1205;1199	.	ENSP00000368349:Q1199X	Q	+	1	0	POLA1	24754516	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.980000	0.49321	2.407000	0.81776	0.529000	0.55759	CAG	.	.		0.468	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937	
XK	7504	hgsc.bcm.edu	37	X	37553772	37553772	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:37553772T>C	ENST00000378616.3	+	2	682	c.479T>C	c.(478-480)gTc>gCc	p.V160A	TM4SF2_ENST00000465127.1_Intron	NM_021083.2	NP_066569.1	P51811	XK_HUMAN	X-linked Kx blood group	160					amino acid transport (GO:0006865)|transport (GO:0006810)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15		all_lung(315;0.175)				TACATAAGTGTCATGCAGCAG	0.483																																					p.V160A		Atlas-SNP	.											.	XK	48	.	0			c.T479C						.						68.0	50.0	56.0					X																	37553772		2200	4296	6496	SO:0001583	missense	7504	exon2			TAAGTGTCATGCA	Z32684	CCDS14241.1	Xp21.1	2014-07-19	2014-06-18		ENSG00000047597	ENSG00000047597		"""Blood group antigens"""	12811	protein-coding gene	gene with protein product	"""Kx antigen"", ""McLeod syndrome"""	314850	"""Kell blood group precursor (McLeod phenotype)"", ""XK, Kell blood group complex subunit (McLeod syndrome)"", ""neuroacanthocytosis"", ""neurocanthocytosis"""	NA, NAC		8004674, 11761473	Standard	NM_021083		Approved	XKR1, Kx, X1k	uc004ddq.3	P51811	OTTHUMG00000033171	ENST00000378616.3:c.479T>C	chrX.hg19:g.37553772T>C	ENSP00000367879:p.Val160Ala	100.0	0.0		115.0	5.0	NM_021083	Q4TTN6|Q8IUK6|Q9UC77	Missense_Mutation	SNP	ENST00000378616.3	hg19	CCDS14241.1	.	.	.	.	.	.	.	.	.	.	T	11.49	1.653096	0.29425	.	.	ENSG00000047597	ENST00000378616	T	0.66995	-0.24	6.04	3.72	0.42706	.	0.565552	0.19027	N	0.124642	T	0.64382	0.2593	M	0.72894	2.215	0.34753	D	0.73195	B	0.12013	0.005	B	0.20955	0.032	T	0.63902	-0.6532	10	0.31617	T	0.26	-3.2206	11.3662	0.49673	0.0:0.0841:0.0:0.9159	.	160	P51811	XK_HUMAN	A	160	ENSP00000367879:V160A	ENSP00000367879:V160A	V	+	2	0	XK	37438711	0.835000	0.29415	0.001000	0.08648	0.370000	0.29829	4.857000	0.62939	0.384000	0.24942	0.417000	0.27973	GTC	.	.		0.483	XK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080875.1	NM_021083	
ZNF674	641339	hgsc.bcm.edu	37	X	46401522	46401522	+	Start_Codon_SNP	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:46401522T>C	ENST00000523374.1	-	3	211	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	ZNF674_ENST00000414387.2_Start_Codon_SNP_p.M1V	NM_001039891.2|NM_001146291.1|NM_001190417.1	NP_001034980.1|NP_001139763.1|NP_001177346.1	Q2M3X9	ZN674_HUMAN	zinc finger protein 674	1					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)	2						GACATGGCCATCTTGTTGTGC	0.373																																					p.M1V		Atlas-SNP	.											.	ZNF674	3	.	0			c.A1G						.						86.0	82.0	83.0					X																	46401522		2173	4276	6449	SO:0001582	initiator_codon_variant	641339	exon3			TGGCCATCTTGTT	AY971607	CCDS48099.1, CCDS55406.1	Xp11.3	2013-01-08	2010-09-15		ENSG00000251192	ENSG00000251192		"""Zinc fingers, C2H2-type"", ""-"""	17625	protein-coding gene	gene with protein product		300573		MRX92		16385466	Standard	NM_001039891		Approved	ZNF673B	uc004dgr.3	Q2M3X9	OTTHUMG00000021420	ENST00000523374.1:c.1A>G	chrX.hg19:g.46401522T>C	ENSP00000429148:p.Met1Val	38.0	0.0		78.0	4.0	NM_001146291	B4DHE2|E9PHQ4	Missense_Mutation	SNP	ENST00000523374.1	hg19	CCDS48099.1	.	.	.	.	.	.	.	.	.	.	t	7.074	0.568893	0.13560	.	.	ENSG00000251192	ENST00000523374;ENST00000414387;ENST00000518708	T;T;T	0.00792	5.69;5.69;5.69	2.53	2.53	0.30540	Krueppel-associated box (1);	.	.	.	.	T	0.00724	0.0024	.	.	.	0.09310	N	1	B;B;B	0.28233	0.204;0.001;0.204	B;B;B	0.17979	0.02;0.001;0.02	T	0.48636	-0.9018	8	0.72032	D	0.01	.	6.147	0.20291	0.0:0.0:0.0:1.0	.	1;1;1	E9PHQ4;E5RHV3;Q2M3X9	.;.;ZN674_HUMAN	V	1	ENSP00000429148:M1V;ENSP00000428248:M1V;ENSP00000429646:M1V	ENSP00000428248:M1V	M	-	1	0	ZNF674	46286466	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	0.180000	0.16860	1.243000	0.43853	0.381000	0.24937	ATG	.	.		0.373	ZNF674-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056357.2	NM_001039891	Missense_Mutation
ZNF41	7592	hgsc.bcm.edu	37	X	47307869	47307869	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:47307869T>C	ENST00000377065.4	-	5	1939	c.1300A>G	c.(1300-1302)Acg>Gcg	p.T434A	ZNF41_ENST00000397050.2_Missense_Mutation_p.T444A|ZNF41_ENST00000465311.1_5'Flank|ZNF41_ENST00000313116.7_Missense_Mutation_p.T434A	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	476					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				TTCTCTCCCGTGTGGATTCTC	0.433																																					p.T434A		Atlas-SNP	.											.	ZNF41	71	.	0			c.A1300G						.						114.0	105.0	108.0					X																	47307869		2203	4300	6503	SO:0001583	missense	7592	exon5			CTCCCGTGTGGAT	X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"""Zinc fingers, C2H2-type"", ""-"""	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.1300A>G	chrX.hg19:g.47307869T>C	ENSP00000366265:p.Thr434Ala	54.0	0.0		63.0	4.0	NM_007130	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Missense_Mutation	SNP	ENST00000377065.4	hg19	CCDS14279.1	.	.	.	.	.	.	.	.	.	.	T	18.16	3.561575	0.65538	.	.	ENSG00000147124	ENST00000313116;ENST00000377065;ENST00000397050	T;T;T	0.26518	1.73;1.73;1.73	3.58	3.58	0.41010	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36338	N	0.002655	T	0.24661	0.0598	N	0.03948	-0.315	0.32078	N	0.593589	D;D;D;D;D	0.63880	0.992;0.992;0.984;0.992;0.993	D;D;D;D;D	0.76575	0.979;0.979;0.967;0.979;0.988	T	0.30090	-0.9990	10	0.87932	D	0	.	9.74	0.40413	0.0:0.0:0.0:1.0	.	434;436;444;468;476	P51814-6;P51814-2;P51814-3;P51814-5;P51814	.;.;.;.;ZNF41_HUMAN	A	434;434;444	ENSP00000315173:T434A;ENSP00000366265:T434A;ENSP00000380243:T444A	ENSP00000315173:T434A	T	-	1	0	ZNF41	47192813	1.000000	0.71417	0.998000	0.56505	0.962000	0.63368	5.119000	0.64679	1.655000	0.50712	0.486000	0.48141	ACG	.	.		0.433	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380	
IQSEC2	23096	hgsc.bcm.edu	37	X	53264288	53264288	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:53264288T>C	ENST00000375368.5	-	14	3750	c.3550A>G	c.(3550-3552)Agc>Ggc	p.S1184G	IQSEC2_ENST00000396435.3_Missense_Mutation_p.S1194G|IQSEC2_ENST00000375365.2_3'UTR			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	1184	Pro-rich.				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)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						GGCCTCTGGCTCTTGTACTCC	0.652																																					p.S1194G		Atlas-SNP	.											.	IQSEC2	195	.	0			c.A3580G						.						32.0	31.0	31.0					X																	53264288		692	1591	2283	SO:0001583	missense	23096	exon15			TCTGGCTCTTGTA	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"""mental retardation, X-linked 1 (non-dysmorphic)"""	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.3550A>G	chrX.hg19:g.53264288T>C	ENSP00000364517:p.Ser1184Gly	47.0	0.0		68.0	4.0	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	hg19		.	.	.	.	.	.	.	.	.	.	T	1.025	-0.683714	0.03353	.	.	ENSG00000124313	ENST00000396435;ENST00000375368	T;T	0.43294	0.95;0.95	2.06	2.06	0.26882	.	0.114198	0.64402	N	0.000015	T	0.15782	0.0380	N	0.03608	-0.345	0.22521	N	0.999021	B	0.16396	0.017	B	0.16289	0.015	T	0.08371	-1.0725	10	0.48119	T	0.1	.	2.4407	0.04493	0.0:0.181:0.2965:0.5225	.	1194	Q5JU85-2	.	G	1194;1184	ENSP00000379712:S1194G;ENSP00000364517:S1184G	ENSP00000364517:S1184G	S	-	1	0	IQSEC2	53281013	1.000000	0.71417	0.998000	0.56505	0.207000	0.24258	1.070000	0.30653	1.069000	0.40788	0.235000	0.17854	AGC	.	.		0.652	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345	
WNK3	65267	hgsc.bcm.edu	37	X	54263832	54263832	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:54263832A>G	ENST00000375159.2	-	19	4166	c.4167T>C	c.(4165-4167)aaT>aaC	p.N1389N	WNK3_ENST00000375169.3_Silent_p.N1342N|WNK3_ENST00000354646.2_Silent_p.N1389N			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1389					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						AAGTTTTTGGATTTTGTGTGG	0.358																																					p.N1389N		Atlas-SNP	.											.	WNK3	218	.	0			c.T4167C						.						95.0	88.0	90.0					X																	54263832		2203	4300	6503	SO:0001819	synonymous_variant	65267	exon20			TTTTGGATTTTGT	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"""protein kinase, lysine deficient 3"""	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.4167T>C	chrX.hg19:g.54263832A>G		49.0	0.0		41.0	4.0	NM_020922	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Silent	SNP	ENST00000375159.2	hg19	CCDS14357.1																																																																																			.	.		0.358	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922	
USP51	158880	hgsc.bcm.edu	37	X	55514365	55514365	+	Silent	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:55514365A>G	ENST00000500968.3	-	2	1090	c.1008T>C	c.(1006-1008)tgT>tgC	p.C336C	USP51_ENST00000586165.1_5'UTR	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	336					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						CCTTTGTCTCACAGGTTGATT	0.373																																					p.C336C		Atlas-SNP	.											.	USP51	71	.	0			c.T1008C						.						100.0	98.0	99.0					X																	55514365		2203	4300	6503	SO:0001819	synonymous_variant	158880	exon2			TGTCTCACAGGTT	BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"""Ubiquitin-specific peptidases"""	23086	protein-coding gene	gene with protein product			"""ubiquitin specific protease 51"""			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.1008T>C	chrX.hg19:g.55514365A>G		98.0	0.0		114.0	5.0	NM_201286	Q8IWJ8	Silent	SNP	ENST00000500968.3	hg19	CCDS14370.1																																																																																			.	.		0.373	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2	NM_201286	
GPR174	84636	hgsc.bcm.edu	37	X	78427231	78427231	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:78427231T>C	ENST00000276077.1	+	1	763	c.727T>C	c.(727-729)Ttt>Ctt	p.F243L		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						CCTAATTTGCTTTGCACCTTA	0.383										HNSCC(63;0.18)																											p.F243L		Atlas-SNP	.											.	GPR174	79	.	0			c.T727C						.						108.0	99.0	102.0					X																	78427231		2203	4300	6503	SO:0001583	missense	84636	exon1			ATTTGCTTTGCAC	AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"""GPCR / Class A : Orphans"""	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.727T>C	chrX.hg19:g.78427231T>C	ENSP00000276077:p.Phe243Leu	101.0	0.0		86.0	4.0	NM_032553	Q2M3F7	Missense_Mutation	SNP	ENST00000276077.1	hg19	CCDS14443.1	.	.	.	.	.	.	.	.	.	.	t	20.7	4.040197	0.75732	.	.	ENSG00000147138	ENST00000276077	T	0.72615	-0.67	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.84320	0.5446	M	0.83223	2.63	0.58432	D	0.999993	D	0.89917	1.0	D	0.97110	1.0	D	0.86664	0.1906	10	0.87932	D	0	.	12.8586	0.57901	0.0:0.0:0.0:1.0	.	243	Q9BXC1	GP174_HUMAN	L	243	ENSP00000276077:F243L	ENSP00000276077:F243L	F	+	1	0	GPR174	78313887	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.802000	0.85969	1.716000	0.51395	0.397000	0.26171	TTT	.	.		0.383	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553	
CHM	1121	hgsc.bcm.edu	37	X	85282510	85282510	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:85282510A>G	ENST00000357749.2	-	2	130	c.101T>C	c.(100-102)gTt>gCt	p.V34A	CHM_ENST00000358786.4_Missense_Mutation_p.V34A|CHM_ENST00000537751.1_Intron|CHM_ENST00000467744.2_5'UTR	NM_000390.2	NP_000381.1	P24386	RAE1_HUMAN	choroideremia (Rab escort protein 1)	34					blood vessel development (GO:0001568)|protein geranylgeranylation (GO:0018344)|protein targeting to membrane (GO:0006612)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytosol (GO:0005829)|Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|prostate(1)	20		all_lung(315;5.41e-06)				AACATGCAGAACTCTCCGGCC	0.328																																					p.V34A		Atlas-SNP	.											.	CHM	57	.	0			c.T101C						.						66.0	58.0	61.0					X																	85282510		2203	4300	6503	SO:0001583	missense	1121	exon2			TGCAGAACTCTCC	X78121	CCDS14454.1, CCDS48139.1	Xq21.1-q21.3	2014-09-17			ENSG00000188419	ENSG00000188419			1940	protein-coding gene	gene with protein product		300390		TCD, DXS540		1373238	Standard	XM_006724615		Approved	REP-1	uc004eet.3	P24386	OTTHUMG00000021937	ENST00000357749.2:c.101T>C	chrX.hg19:g.85282510A>G	ENSP00000350386:p.Val34Ala	92.0	0.0		124.0	5.0	NM_001145414	A1L4D2|O43732	Missense_Mutation	SNP	ENST00000357749.2	hg19	CCDS14454.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.038231	0.75617	.	.	ENSG00000188419	ENST00000357749;ENST00000358786	T;T	0.81078	-1.45;-1.45	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.89955	0.6865	M	0.90650	3.135	0.80722	D	1	P;P	0.43973	0.823;0.656	P;P	0.56474	0.799;0.749	D	0.91743	0.5406	10	0.87932	D	0	-11.761	14.2794	0.66200	1.0:0.0:0.0:0.0	.	34;34	A1L4D2;P24386	.;RAE1_HUMAN	A	34	ENSP00000350386:V34A;ENSP00000362228:V34A	ENSP00000350386:V34A	V	-	2	0	CHM	85169166	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	6.769000	0.74985	1.750000	0.51863	0.356000	0.21956	GTT	.	.		0.328	CHM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057396.3	NM_000390	
TAF7L	54457	hgsc.bcm.edu	37	X	100524209	100524209	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:100524209T>C	ENST00000372907.3	-	13	1372	c.1361A>G	c.(1360-1362)gAa>gGa	p.E454G	TAF7L_ENST00000372905.2_Missense_Mutation_p.E294G|TAF7L_ENST00000324762.6_Missense_Mutation_p.E294G|TAF7L_ENST00000356784.1_Missense_Mutation_p.E368G	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	454					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						CTGCAACTGTTCCTGTAGGGA	0.433																																					p.E454G	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.A1361G						.						169.0	151.0	157.0					X																	100524209		2203	4300	6503	SO:0001583	missense	54457	exon13			AACTGTTCCTGTA	AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"""cancer/testis antigen 40"""	300314	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"""	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.1361A>G	chrX.hg19:g.100524209T>C	ENSP00000361998:p.Glu454Gly	70.0	0.0		100.0	4.0	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	hg19	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.547717	0.45383	.	.	ENSG00000102387	ENST00000372907;ENST00000372905;ENST00000324762;ENST00000356784	T;T;T;T	0.29142	2.11;1.58;1.58;1.63	4.48	4.48	0.54585	.	0.687962	0.12318	N	0.479575	T	0.45637	0.1352	M	0.75615	2.305	0.22240	N	0.999268	D;P	0.54207	0.965;0.944	P;P	0.51016	0.656;0.526	T	0.36915	-0.9728	10	0.66056	D	0.02	-2.3587	11.4937	0.50396	0.0:0.0:0.0:1.0	.	454;294	Q5H9L4;Q5H9L4-3	TAF7L_HUMAN;.	G	454;294;294;368	ENSP00000361998:E454G;ENSP00000361996:E294G;ENSP00000320283:E294G;ENSP00000349235:E368G	ENSP00000320283:E294G	E	-	2	0	TAF7L	100410865	0.996000	0.38824	0.002000	0.10522	0.057000	0.15508	3.401000	0.52601	1.566000	0.49654	0.417000	0.27973	GAA	.	.		0.433	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2		
TCEAL6	158931	hgsc.bcm.edu	37	X	101395774	101395774	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:101395774T>C	ENST00000372774.3	-	3	779	c.530A>G	c.(529-531)gAc>gGc	p.D177G	TCEAL6_ENST00000372773.1_Missense_Mutation_p.D177G	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						CACCCCGTTGTCCCCTTGGGC	0.507																																					p.D177G		Atlas-SNP	.											.	TCEAL6	27	.	0			c.A530G						.						19.0	18.0	19.0					X																	101395774		2197	4274	6471	SO:0001583	missense	158931	exon3			CCGTTGTCCCCTT	BC071675	CCDS43978.1	Xq22.1	2014-03-21			ENSG00000204071	ENSG00000204071			24553	protein-coding gene	gene with protein product						16221301	Standard	NM_001006938		Approved	WEX2	uc004eiq.3	Q6IPX3	OTTHUMG00000022050	ENST00000372774.3:c.530A>G	chrX.hg19:g.101395774T>C	ENSP00000361860:p.Asp177Gly	62.0	0.0		163.0	11.0	NM_001006938	Q5H9J8	Missense_Mutation	SNP	ENST00000372774.3	hg19	CCDS43978.1	.	.	.	.	.	.	.	.	.	.	A	0.755	-0.771235	0.02951	.	.	ENSG00000204071	ENST00000372774;ENST00000372773	T;T	0.23147	1.92;1.92	2.82	-3.23	0.05109	.	0.272209	0.20313	N	0.094788	T	0.11836	0.0288	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08186	-1.0734	10	0.48119	T	0.1	.	3.3698	0.07216	0.1211:0.4969:0.222:0.1599	.	177	Q6IPX3-2	.	G	177	ENSP00000361860:D177G;ENSP00000361859:D177G	ENSP00000361859:D177G	D	-	2	0	TCEAL6	101282430	0.001000	0.12720	0.010000	0.14722	0.828000	0.46876	-1.039000	0.03550	-1.000000	0.03438	-0.742000	0.03525	GAC	.	.		0.507	TCEAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057609.1	NM_001006938	
TCEAL6	158931	hgsc.bcm.edu	37	X	101395778	101395778	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	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	60.0	0.0		155.0	17.0	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	
COL4A6	1288	hgsc.bcm.edu	37	X	107448673	107448673	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:107448673A>G	ENST00000372216.4	-	11	786	c.686T>C	c.(685-687)gTc>gCc	p.V229A	COL4A6_ENST00000334504.7_Missense_Mutation_p.V228A|COL4A6_ENST00000538570.1_Missense_Mutation_p.V228A|COL4A6_ENST00000394872.2_Intron|COL4A6_ENST00000545689.1_Missense_Mutation_p.V228A	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	229	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						GTTTACCTTGACTCCTTTCTC	0.393									Alport syndrome with Diffuse Leiomyomatosis																												p.V229A	Melanoma(87;1895 1945 2589 7165)	Atlas-SNP	.											.	COL4A6	270	.	0			c.T686C						.						165.0	165.0	165.0					X																	107448673		2203	4300	6503	SO:0001583	missense	1288	exon11	Familial Cancer Database		ACCTTGACTCCTT	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"""Collagens"""	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.686T>C	chrX.hg19:g.107448673A>G	ENSP00000361290:p.Val229Ala	59.0	0.0		99.0	5.0	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Missense_Mutation	SNP	ENST00000372216.4	hg19	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	A	10.83	1.462002	0.26248	.	.	ENSG00000197565	ENST00000372216;ENST00000334504;ENST00000541389;ENST00000545689;ENST00000538570	D;D;D;D	0.94897	-3.55;-3.55;-3.55;-3.55	4.97	-1.77	0.07982	.	.	.	.	.	T	0.82268	0.5000	N	0.05534	-0.03	0.26412	N	0.97625	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.09377	0.004;0.004;0.002;0.004	T	0.70554	-0.4840	9	0.10902	T	0.67	.	4.0947	0.09985	0.4061:0.0:0.4004:0.1935	.	228;228;229;228	F5H851;F5H3Q5;Q14031;Q14031-2	.;.;CO4A6_HUMAN;.	A	229;228;228;228;228	ENSP00000361290:V229A;ENSP00000334733:V228A;ENSP00000443707:V228A;ENSP00000445236:V228A	ENSP00000334733:V228A	V	-	2	0	COL4A6	107335329	0.885000	0.30320	0.989000	0.46669	0.933000	0.57130	-0.249000	0.08842	-0.297000	0.08934	-0.360000	0.07572	GTC	.	.		0.393	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2		
RBMXL3	139804	hgsc.bcm.edu	37	X	114424452	114424452	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:114424452C>T	ENST00000424776.3	+	1	490	c.448C>T	c.(448-450)Cgc>Tgc	p.R150C	LRCH2_ENST00000317135.8_Intron|LRCH2_ENST00000538422.1_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	150							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						GCCCAGGAAGCGCGGGCCGCC	0.721																																					p.R150C		Atlas-SNP	.											.	RBMXL3	83	.	0			c.C448T						.						4.0	6.0	5.0					X																	114424452		608	1426	2034	SO:0001583	missense	139804	exon1			AGGAAGCGCGGGC	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.448C>T	chrX.hg19:g.114424452C>T	ENSP00000417451:p.Arg150Cys	14.0	0.0		10.0	8.0	NM_001145346	B4DXC0	Missense_Mutation	SNP	ENST00000424776.3	hg19	CCDS55478.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.828794	0.32329	.	.	ENSG00000175718	ENST00000424776	T	0.04360	3.64	1.26	-0.00448	0.14022	.	.	.	.	.	T	0.03739	0.0106	L	0.45352	1.415	0.19300	N	0.999975	B	0.29232	0.238	B	0.09377	0.004	T	0.41142	-0.9525	9	0.87932	D	0	.	2.0251	0.03517	0.3989:0.3103:0.0:0.2908	.	150	Q8N7X1	RMXL3_HUMAN	C	150	ENSP00000417451:R150C	ENSP00000417451:R150C	R	+	1	0	RBMXL3	114330708	0.016000	0.18221	0.003000	0.11579	0.001000	0.01503	-1.352000	0.02619	-0.071000	0.12886	-0.625000	0.03995	CGC	.	.		0.721	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
GRIA3	2892	hgsc.bcm.edu	37	X	122336608	122336608	+	Intron	SNP	C	C	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:122336608C>G	ENST00000371251.1	+	2	320				GRIA3_ENST00000371266.1_Missense_Mutation_p.A130G|GRIA3_ENST00000371256.5_Intron|GRIA3_ENST00000479118.1_Intron|GRIA3_ENST00000541091.1_Intron|GRIA3_ENST00000264357.5_Intron|GRIA3_ENST00000542149.1_Intron|GRIA3_ENST00000371264.3_Missense_Mutation_p.A130G			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3						glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	GGTGGGCCCGCCAAAACTGGG	0.502																																					p.A130G		Atlas-SNP	.											.	GRIA3	386	.	0			c.C389G						.																																			SO:0001627	intron_variant	2892	exon3			GGCCCGCCAAAAC	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4573	protein-coding gene	gene with protein product		305915	"""glutamate receptor, ionotrophic, AMPA 3"""	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.268+16766C>G	chrX.hg19:g.122336608C>G		51.0	0.0		82.0	5.0	NM_001256743	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Missense_Mutation	SNP	ENST00000371251.1	hg19	CCDS14604.1	.	.	.	.	.	.	.	.	.	.	C	14.15	2.450610	0.43531	.	.	ENSG00000125675	ENST00000371266;ENST00000371264	.	.	.	4.06	1.29	0.21616	.	.	.	.	.	T	0.28134	0.0694	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.28138	-1.0053	7	0.87932	D	0	.	3.503	0.07680	0.0:0.5445:0.2109:0.2445	.	130	Q4TT43	.	G	130	.	ENSP00000360311:A130G	A	+	2	0	GRIA3	122164289	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.326000	0.07965	0.146000	0.19002	0.538000	0.68166	GCC	.	.		0.502	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828	
GPC4	2239	hgsc.bcm.edu	37	X	132438856	132438856	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:132438856T>C	ENST00000370828.3	-	7	1713	c.1189A>G	c.(1189-1191)Aag>Gag	p.K397E	GPC4_ENST00000535467.1_Missense_Mutation_p.K327E	NM_001448.2	NP_001439.2	O75487	GPC4_HUMAN	glypican 4	397					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;0.000127)					CAGAATTTCTTGGCCTGTTTC	0.423																																					p.K397E		Atlas-SNP	.											.	GPC4	58	.	0			c.A1189G						.						217.0	176.0	190.0					X																	132438856		2203	4300	6503	SO:0001583	missense	2239	exon7			ATTTCTTGGCCTG	AF030186	CCDS14637.1	Xq26.1	2008-02-05			ENSG00000076716	ENSG00000076716		"""Proteoglycans / Cell Surface : Glypicans"""	4452	protein-coding gene	gene with protein product	"""glypican proteoglycan 4"""	300168				9787072	Standard	NM_001448		Approved	K-glypican	uc004exc.1	O75487	OTTHUMG00000022434	ENST00000370828.3:c.1189A>G	chrX.hg19:g.132438856T>C	ENSP00000359864:p.Lys397Glu	76.0	0.0		84.0	4.0	NM_001448	B2R6J7|B4E2C0|Q6ZMA6|Q96L43|Q9NU08|Q9UJN1|Q9UPD9	Missense_Mutation	SNP	ENST00000370828.3	hg19	CCDS14637.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.065833	0.76187	.	.	ENSG00000076716	ENST00000370828;ENST00000536418;ENST00000535467	T;T	0.53640	0.61;0.61	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.55497	0.1924	M	0.82716	2.605	0.80722	D	1	B	0.25521	0.128	B	0.31869	0.137	T	0.59847	-0.7377	10	0.72032	D	0.01	-13.423	13.1714	0.59599	0.0:0.0:0.0:1.0	.	397	O75487	GPC4_HUMAN	E	397;391;327	ENSP00000359864:K397E;ENSP00000444959:K327E	ENSP00000359864:K397E	K	-	1	0	GPC4	132266522	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.635000	0.83286	1.702000	0.51228	0.481000	0.45027	AAG	.	.		0.423	GPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058338.1	NM_001448	
ZNF449	203523	hgsc.bcm.edu	37	X	134481371	134481371	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:134481371A>G	ENST00000339249.4	+	2	468	c.328A>G	c.(328-330)Aga>Gga	p.R110G	ZNF449_ENST00000370760.3_Missense_Mutation_p.R110G|ZNF449_ENST00000370761.3_Missense_Mutation_p.R110G	NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	110	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				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(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					AGACTTACAGAGAGAACTTGA	0.473																																					p.R110G		Atlas-SNP	.											.	ZNF449	68	.	0			c.A328G						.						67.0	59.0	61.0					X																	134481371		2203	4300	6503	SO:0001583	missense	203523	exon2			TTACAGAGAGAAC	AY280801	CCDS14649.1	Xq26.3	2013-01-09			ENSG00000173275	ENSG00000173275		"""-"", ""Zinc fingers, C2H2-type"""	21039	protein-coding gene	gene with protein product		300627					Standard	NM_152695		Approved	ZSCAN19, FLJ23614	uc004eys.3	Q6P9G9	OTTHUMG00000022478	ENST00000339249.4:c.328A>G	chrX.hg19:g.134481371A>G	ENSP00000339585:p.Arg110Gly	60.0	0.0		76.0	4.0	NM_152695	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Missense_Mutation	SNP	ENST00000339249.4	hg19	CCDS14649.1	.	.	.	.	.	.	.	.	.	.	A	12.80	2.045253	0.36085	.	.	ENSG00000173275	ENST00000370761;ENST00000339249;ENST00000370760	T;T;T	0.04706	3.57;3.57;3.57	4.6	3.4	0.38934	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.000000	0.47455	D	0.000229	T	0.09379	0.0231	N	0.21545	0.675	0.31957	N	0.608961	D;D;B	0.76494	0.999;0.999;0.001	D;D;B	0.85130	0.997;0.996;0.008	T	0.05649	-1.0872	10	0.87932	D	0	.	7.2429	0.26106	0.7767:0.2233:0.0:0.0	.	110;110;110	Q6P9G9;Q6P9G9-2;Q6P9G9-3	ZN449_HUMAN;.;.	G	110	ENSP00000359797:R110G;ENSP00000339585:R110G;ENSP00000359796:R110G	ENSP00000339585:R110G	R	+	1	2	ZNF449	134309037	0.954000	0.32549	1.000000	0.80357	0.981000	0.71138	0.498000	0.22530	0.835000	0.34877	0.481000	0.45027	AGA	.	.		0.473	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695	
HMGB3	3149	hgsc.bcm.edu	37	X	150155773	150155773	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:150155773A>G	ENST00000325307.7	+	4	559	c.463A>G	c.(463-465)Aag>Gag	p.K155E	HMGB3_ENST00000448905.2_Missense_Mutation_p.K155E	NM_005342.2	NP_005333.2	O15347	HMGB3_HUMAN	high mobility group box 3	155					DNA recombination (GO:0006310)|multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(2)|lung(2)|skin(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					GAAGTATGAGAAGGTAAGGTG	0.493																																					p.K155E		Atlas-SNP	.											.	HMGB3	27	.	0			c.A463G						.						50.0	46.0	48.0					X																	150155773		2203	4300	6503	SO:0001583	missense	3149	exon4			TATGAGAAGGTAA	AF274572	CCDS35428.1	Xq28	2011-07-01	2011-04-05	2002-08-16	ENSG00000029993	ENSG00000029993		"""High-mobility group / Canonical"""	5004	protein-coding gene	gene with protein product	"""non-histone chromosomal protein"""	300193	"""high-mobility group (nonhistone chromosomal) protein 4"", ""high-mobility group box 3"""	HMG4		9598312	Standard	XM_005274665		Approved	HMG2A, MGC90319	uc004fep.3	O15347	OTTHUMG00000024162	ENST00000325307.7:c.463A>G	chrX.hg19:g.150155773A>G	ENSP00000359393:p.Lys155Glu	54.0	0.0		83.0	4.0	NM_005342	O95556|Q6NS40	Missense_Mutation	SNP	ENST00000325307.7	hg19	CCDS35428.1	.	.	.	.	.	.	.	.	.	.	a	29.6	5.018090	0.93404	.	.	ENSG00000029993	ENST00000419110;ENST00000325307;ENST00000455596;ENST00000448905	D;D;D;D	0.98150	-4.75;-4.75;-4.75;-4.75	5.05	5.05	0.67936	High mobility group, HMG1/HMG2, subgroup (1);High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	D	0.000000	D	0.98065	0.9362	M	0.73753	2.245	0.58432	D	0.999993	P	0.49961	0.93	P	0.58820	0.846	D	0.97957	1.0335	10	0.44086	T	0.13	.	13.0733	0.59074	1.0:0.0:0.0:0.0	.	155	O15347	HMGB3_HUMAN	E	155	ENSP00000410354:K155E;ENSP00000359393:K155E;ENSP00000405601:K155E;ENSP00000442758:K155E	ENSP00000359393:K155E	K	+	1	0	HMGB3	149906431	1.000000	0.71417	0.998000	0.56505	0.952000	0.60782	5.753000	0.68736	1.678000	0.50952	0.430000	0.28490	AAG	.	.		0.493	HMGB3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060867.1	NM_005342	
F8	2157	hgsc.bcm.edu	37	X	154088732	154088732	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:154088732A>G	ENST00000360256.4	-	25	7075	c.6875T>C	c.(6874-6876)cTc>cCc	p.L2292P	F8_ENST00000330287.6_Missense_Mutation_p.L157P	NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	2292	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CTGAAAAAAGAGAGTCCACTG	0.408																																					p.L2292P		Atlas-SNP	.											.	F8	646	.	0			c.T6875C						.						129.0	124.0	126.0					X																	154088732		2203	4300	6503	SO:0001583	missense	2157	exon25			AAAAAGAGAGTCC	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"""Factor VIIIF8B"", ""hemophilia A"""	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.6875T>C	chrX.hg19:g.154088732A>G	ENSP00000353393:p.Leu2292Pro	72.0	0.0		77.0	4.0	NM_000132	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	hg19	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	a	8.464	0.856006	0.17106	.	.	ENSG00000185010	ENST00000330287;ENST00000360256	D;D	0.98207	-4.79;-4.79	5.47	-1.42	0.08913	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.789610	0.12244	N	0.486278	D	0.90442	0.7007	N	0.02973	-0.45	0.23101	N	0.998298	B;B	0.13594	0.008;0.001	B;B	0.13407	0.009;0.002	D	0.84433	0.0578	10	0.22109	T	0.4	0.0413	4.7331	0.12975	0.5281:0.0:0.3332:0.1387	.	2292;157	P00451;Q14286	FA8_HUMAN;.	P	157;2292	ENSP00000327895:L157P;ENSP00000353393:L2292P	ENSP00000327895:L157P	L	-	2	0	F8	153741926	0.182000	0.23173	0.024000	0.17045	0.952000	0.60782	0.513000	0.22770	-0.684000	0.05183	0.441000	0.28932	CTC	.	.		0.408	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4		
F8	2157	hgsc.bcm.edu	37	X	154157276	154157276	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:154157276C>T	ENST00000360256.4	-	14	4989	c.4789G>A	c.(4789-4791)Gaa>Aaa	p.E1597K		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1597	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TTCCACTCTTCTTTTGGTATC	0.423																																					p.E1597K		Atlas-SNP	.											.	F8	646	.	0			c.G4789A	GRCh37	CI080940	F8	I		.						171.0	170.0	170.0					X																	154157276		2203	4300	6503	SO:0001583	missense	2157	exon14			ACTCTTCTTTTGG	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"""Factor VIIIF8B"", ""hemophilia A"""	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.4789G>A	chrX.hg19:g.154157276C>T	ENSP00000353393:p.Glu1597Lys	116.0	0.0		136.0	7.0	NM_000132	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	hg19	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	c	7.861	0.726083	0.15439	.	.	ENSG00000185010	ENST00000360256	D	0.99176	-5.52	5.38	2.68	0.31781	.	0.532899	0.21047	N	0.081071	D	0.96506	0.8860	L	0.43701	1.375	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	D	0.90812	0.4702	10	0.29301	T	0.29	-2.2032	7.2414	0.26098	0.0:0.7141:0.0:0.2859	.	1597	P00451	FA8_HUMAN	K	1597	ENSP00000353393:E1597K	ENSP00000353393:E1597K	E	-	1	0	F8	153810470	0.721000	0.28007	0.003000	0.11579	0.373000	0.29922	0.485000	0.22324	0.149000	0.19098	-0.250000	0.11733	GAA	.	.		0.423	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4		
MT-ATP8	4509	hgsc.bcm.edu	37	M	8430	8430	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrM:8430T>C	ENST00000361851.1	+	1	65	c.65T>C	c.(64-66)cTc>cCc	p.L22P	MT-TR_ENST00000387439.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-ND3_ENST00000361227.2_5'Flank|MT-ND4_ENST00000361381.2_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TD_ENST00000387419.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TK_ENST00000387421.1_RNA			P03928	ATP8_HUMAN	mitochondrially encoded ATP synthase 8	22					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)										TACACTATTCCTCATCACCCA	0.373																																					p.L22P		Atlas-SNP	.											.	.	.	.	0			c.T65C						.																																			SO:0001583	missense	0	exon1			TATTCCTCATCAC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000228253	ENSG00000228253		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	7415	protein-coding gene	gene with protein product		516070	"""ATP synthase 8"""	MTATP8			Standard			Approved	ATP8, A6L		P03928		ENST00000361851.1:c.65T>C	chrM.hg19:g.8430T>C	ENSP00000355265:p.Leu22Pro	69.0	0.0		7.0	7.0	ENST00000361851	Q34771	Missense_Mutation	SNP	ENST00000361851.1	hg19																																																																																				.	.		0.373	MT-ATP8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024030	
MT-ND5	4540	hgsc.bcm.edu	37	M	13595	13595	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrM:13595G>A	ENST00000361567.2	+	1	1259	c.1259G>A	c.(1258-1260)aGc>aAc	p.S420N	MT-TT_ENST00000387460.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TE_ENST00000387459.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TP_ENST00000387461.2_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	420					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						CTCCCTGACAAGCGCCTATAG	0.463																																					p.S420N		Atlas-SNP	.											.	.	.	.	0			c.G1259A						.																																			SO:0001583	missense	0	exon1			TGACAAGCGCCTA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1259G>A	chrM.hg19:g.13595G>A	ENSP00000354813:p.Ser420Asn	92.0	0.0		17.0	12.0	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.		0.463	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
SMC1B	27127	hgsc.bcm.edu	37	22	45789663	45789663	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:45789663delT	ENST00000357450.4	-	9	1395	c.1396delA	c.(1396-1398)acafs	p.T466fs	SMC1B_ENST00000404354.3_Frame_Shift_Del_p.T466fs	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	466					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)		CTTGATTTTGTTTTTTCAATT	0.323																																					p.T466fs		Atlas-INDEL	.											.	SMC1B	215	.	0			c.1397delC						.						83.0	73.0	76.0					22																	45789663		1817	4074	5891	SO:0001589	frameshift_variant	27127	exon9			.	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.1396delA	chr22.hg19:g.45789663delT	ENSP00000350036:p.Thr466fs	122.0	0.0		183.0	14.0	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Frame_Shift_Del	DEL	ENST00000357450.4	hg19	CCDS43027.1																																																																																			.	.		0.323	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
OR8A1	390275	hgsc.bcm.edu	37	11	124440280	124440280	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:124440280delA	ENST00000284287.3	+	1	388	c.316delA	c.(316-318)aaafs	p.K106fs		NM_001005194.1	NP_001005194.1	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A, member 1	106					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			haematopoietic_and_lymphoid_tissue(1)|lung(16)|ovary(2)|prostate(1)|skin(2)	22		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		TGTGTCAGAGAAAAACATCAT	0.478																																					p.E105fs		Atlas-INDEL	.											.	OR8A1	61	.	0			c.315delG						.						182.0	163.0	170.0					11																	124440280		2201	4299	6500	SO:0001589	frameshift_variant	390275	exon1			.	BK004495	CCDS31712.1	11q24.2	2012-08-09			ENSG00000196119	ENSG00000196119		"""GPCR / Class A : Olfactory receptors"""	8469	protein-coding gene	gene with protein product							Standard	NM_001005194		Approved	OST025	uc010san.2	Q8NGG7	OTTHUMG00000165923	ENST00000284287.3:c.316delA	chr11.hg19:g.124440280delA	ENSP00000284287:p.Lys106fs	123.0	0.0		190.0	13.0	NM_001005194	Q6IEW7|Q96RC6	Frame_Shift_Del	DEL	ENST00000284287.3	hg19	CCDS31712.1																																																																																			.	.		0.478	OR8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387062.1	NM_001005194	
GZMM	3004	hgsc.bcm.edu	37	19	549133	549133	+	Frame_Shift_Del	DEL	C	C	-	rs373974834		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:549133delC	ENST00000264553.3	+	4	598	c.560delC	c.(559-561)tccfs	p.S187fs		NM_001258351.1|NM_005317.3	NP_001245280.1|NP_005308	P51124	GRAM_HUMAN	granzyme M (lymphocyte met-ase 1)	187	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|membrane (GO:0016020)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|large_intestine(1)|prostate(1)	3		all_cancers(10;1.94e-35)|all_epithelial(18;5.94e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)		GGCAGCCTCTCCCCCAGCATG	0.706																																					p.S187fs		Atlas-INDEL	.											.	GZMM	11	.	0			c.559delT						.						12.0	9.0	10.0					19																	549133		2157	4212	6369	SO:0001589	frameshift_variant	3004	exon4			.		CCDS12031.1, CCDS74240.1	19p13.3	2008-07-16				ENSG00000197540			4712	protein-coding gene	gene with protein product	"""lymphocyte met-ase 1"""	600311				8119738	Standard	NM_005317		Approved	MET1, LMET1	uc002low.2	P51124		ENST00000264553.3:c.560delC	chr19.hg19:g.549133delC	ENSP00000264553:p.Ser187fs	137.0	0.0		154.0	10.0	NM_005317		Frame_Shift_Del	DEL	ENST00000264553.3	hg19	CCDS12031.1																																																																																			.	.		0.706	GZMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451895.2	NM_005317	
OR7C2	26658	hgsc.bcm.edu	37	19	15052711	15052711	+	Frame_Shift_Del	DEL	C	C	-	rs201572109		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:15052711delC	ENST00000248072.3	+	1	411	c.411delC	c.(409-411)aacfs	p.N137fs		NM_012377.1	NP_036509.1	O60412	OR7C2_HUMAN	olfactory receptor, family 7, subfamily C, member 2	137						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(8)|ovary(2)|skin(2)	15	Ovarian(108;0.203)					TCATCATGAACCCCCGGCTCT	0.542																																					p.N137fs		Atlas-INDEL	.											.	OR7C2	50	.	0			c.410delA						.						134.0	129.0	131.0					19																	15052711		2203	4300	6503	SO:0001589	frameshift_variant	26658	exon1			.	U86255	CCDS12320.1	19p13.1	2012-08-09				ENSG00000127529		"""GPCR / Class A : Olfactory receptors"""	8374	protein-coding gene	gene with protein product				OR7C3			Standard	NM_012377		Approved	OR19-18	uc010xoc.2	O60412		ENST00000248072.3:c.411delC	chr19.hg19:g.15052711delC	ENSP00000248072:p.Asn137fs	190.0	0.0		202.0	14.0	NM_012377	O43881|Q6IFP9	Frame_Shift_Del	DEL	ENST00000248072.3	hg19	CCDS12320.1																																																																																			.	.		0.542	OR7C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466281.1		
ARNT	405	hgsc.bcm.edu	37	1	150789283	150789283	+	Frame_Shift_Del	DEL	G	G	-	rs587670365		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:150789283delG	ENST00000358595.5	-	18	1983	c.1783delC	c.(1783-1785)cggfs	p.R595fs	ARNT_ENST00000505755.1_Frame_Shift_Del_p.R580fs|ARNT_ENST00000354396.2_Frame_Shift_Del_p.R595fs|ARNT_ENST00000515192.1_Frame_Shift_Del_p.R581fs	NM_001197325.1|NM_001668.3|NM_178427.2	NP_001184254.1|NP_001659.1|NP_848514.1	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	595					cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCTGCCGGCCGGGGGGTAGGA	0.527			T	ETV6	AML																																p.R595fs		Atlas-INDEL	.		Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	.	ARNT	68	.	0			c.1784delG						.						83.0	83.0	83.0					1																	150789283		2203	4300	6503	SO:0001589	frameshift_variant	405	exon18			.	AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437		"""Basic helix-loop-helix proteins"""	700	protein-coding gene	gene with protein product		126110					Standard	NM_001668		Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000358595.5:c.1783delC	chr1.hg19:g.150789283delG	ENSP00000351407:p.Arg595fs	123.0	0.0		213.0	14.0	NM_001668	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	Frame_Shift_Del	DEL	ENST00000358595.5	hg19	CCDS970.1																																																																																			.	.		0.527	ARNT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084741.2		
PPP3CB	5532	hgsc.bcm.edu	37	10	75230481	75230481	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:75230481delA	ENST00000360663.5	-	8	1057	c.946delT	c.(946-948)tcgfs	p.S316fs	PPP3CB_ENST00000342558.3_Frame_Shift_Del_p.S316fs|PPP3CB_ENST00000394829.2_Frame_Shift_Del_p.S316fs|PPP3CB_ENST00000394822.2_Frame_Shift_Del_p.S334fs|PPP3CB_ENST00000545874.1_Frame_Shift_Del_p.S230fs|PPP3CB_ENST00000394828.2_Frame_Shift_Del_p.S316fs|PPP3CB_ENST00000495897.1_5'UTR			P16298	PP2BB_HUMAN	protein phosphatase 3, catalytic subunit, beta isozyme	316					axon extension (GO:0048675)|calcium ion-dependent exocytosis (GO:0017156)|cellular response to drug (GO:0035690)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|innate immune response (GO:0045087)|learning (GO:0007612)|locomotion involved in locomotory behavior (GO:0031987)|memory (GO:0007613)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of transcription, DNA-templated (GO:0045893)|protein dephosphorylation (GO:0006470)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)|social behavior (GO:0035176)|T cell activation (GO:0042110)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	calcineurin complex (GO:0005955)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein phosphatase 2B binding (GO:0030346)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(7)|skin(1)|urinary_tract(1)	22	Prostate(51;0.0119)					TTAGGTGCCGAAAAAATTGTT	0.264																																					p.S316fs		Atlas-INDEL	.											PPP3CB,caecum,carcinoma,0,1	PPP3CB	68	.	0			c.947delC						.						79.0	79.0	79.0					10																	75230481		2202	4298	6500	SO:0001589	frameshift_variant	5532	exon8			.	M29551	CCDS7328.1, CCDS44436.1, CCDS44437.1	10q22.2	2010-03-17	2010-03-05		ENSG00000107758	ENSG00000107758	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9315	protein-coding gene	gene with protein product	"""calcineurin A beta"", ""protein phosphatase 2B, catalytic subunit, beta isoform"""	114106	"""protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform (calcineurin A beta)"", ""protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform"""	CALNB		1659808, 2558868	Standard	XM_005269944		Approved	CALNA2, CNA2, PP2Bbeta	uc001juf.3	P16298	OTTHUMG00000018472	ENST00000360663.5:c.946delT	chr10.hg19:g.75230481delA	ENSP00000353881:p.Ser316fs	127.0	0.0		165.0	10.0	NM_001142354	P16299|Q5F2F9|Q8N1F0|Q8N3W4	Frame_Shift_Del	DEL	ENST00000360663.5	hg19	CCDS7328.1																																																																																			.	.		0.264	PPP3CB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048669.1	NM_021132	
SF3A3	10946	hgsc.bcm.edu	37	1	38442595	38442595	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:38442595delA	ENST00000373019.4	-	12	1921	c.966delT	c.(964-966)tttfs	p.F322fs	SF3A3_ENST00000489537.1_5'Flank|SF3A3_ENST00000448721.2_Frame_Shift_Del_p.F269fs	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	322					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GGGCTTCTAGAAAAGCAATGT	0.403																																					p.L323X		Atlas-INDEL	.											.	SF3A3	37	.	0			c.967delC						.						142.0	144.0	143.0					1																	38442595		2201	4300	6501	SO:0001589	frameshift_variant	10946	exon12			.	U08815	CCDS428.1	1p34.3	2012-06-07	2002-08-29		ENSG00000183431	ENSG00000183431			10767	protein-coding gene	gene with protein product		605596	"""splicing factor 3a, subunit 3, 60kD"""			7816610, 8022796	Standard	NM_006802		Approved	SF3a60, SAP61, PRP9, PRPF9	uc001cci.3	Q12874	OTTHUMG00000004438	ENST00000373019.4:c.966delT	chr1.hg19:g.38442595delA	ENSP00000362110:p.Phe322fs	170.0	0.0		209.0	14.0	NM_006802	D3DPT5|Q15460|Q5VT87	Frame_Shift_Del	DEL	ENST00000373019.4	hg19	CCDS428.1																																																																																			.	.		0.403	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802	
RXRB	6257	hgsc.bcm.edu	37	6	33166144	33166144	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:33166144delG	ENST00000374680.3	-	3	792	c.581delC	c.(580-582)cctfs	p.P195fs	RXRB_ENST00000374685.4_Frame_Shift_Del_p.P195fs|RXRB_ENST00000413614.2_Frame_Shift_Del_p.P99fs|SLC39A7_ENST00000374675.3_5'Flank|RNY4P10_ENST00000365571.1_RNA|RXRB_ENST00000544186.1_Intron|SLC39A7_ENST00000374677.3_5'Flank	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	195	Modulating. {ECO:0000250}.|Pro-rich.				cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	GCCACCTGGAGGGGGTGGACA	0.612																																					p.P194fs		Atlas-INDEL	.											.	RXRB	34	.	0			c.582delT						.						108.0	129.0	122.0					6																	33166144		1508	2707	4215	SO:0001589	frameshift_variant	6257	exon3			.	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"""Nuclear hormone receptors"""	10478	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 2"""	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.581delC	chr6.hg19:g.33166144delG	ENSP00000363812:p.Pro195fs	101.0	0.0		137.0	11.0	NM_021976	P28703|Q59G65|Q5JP92|Q5STQ1	Frame_Shift_Del	DEL	ENST00000374680.3	hg19	CCDS4768.1																																																																																			.	.		0.612	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976	
FBXO28	23219	hgsc.bcm.edu	37	1	224345442	224345442	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:224345442delA	ENST00000366862.5	+	5	1144	c.1101delA	c.(1099-1101)agafs	p.R367fs	FBXO28_ENST00000424254.2_3'UTR	NM_015176.3	NP_055991.1	Q9NVF7	FBX28_HUMAN	F-box protein 28	367										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(2)|skin(1)	10	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.0363)		TTCGGAATAGAAAGTAAATTG	0.448																																					p.R367fs		Atlas-INDEL	.											.	FBXO28	34	.	0			c.1100delG						.						39.0	43.0	41.0					1																	224345442		2203	4300	6503	SO:0001589	frameshift_variant	23219	exon5			.	AK001628	CCDS1539.1, CCDS44320.1	1q42.12	2011-08-12			ENSG00000143756	ENSG00000143756		"""F-boxes /  ""other"""""	29046	protein-coding gene	gene with protein product	"""centromere protein 30"""	609100				9455484	Standard	NM_015176		Approved	FLJ10766, KIAA0483, Fbx28, CENP-30	uc001hoh.3	Q9NVF7	OTTHUMG00000037495	ENST00000366862.5:c.1101delA	chr1.hg19:g.224345442delA	ENSP00000355827:p.Arg367fs	47.0	0.0		124.0	10.0	NM_015176	E9PEM8|O75070	Frame_Shift_Del	DEL	ENST00000366862.5	hg19	CCDS1539.1																																																																																			.	.		0.448	FBXO28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091283.2	NM_015176	
ADAMTS8	11095	hgsc.bcm.edu	37	11	130297563	130297563	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:130297563delC	ENST00000257359.6	-	1	1325	c.619delG	c.(619-621)gccfs	p.A207fs		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	207					negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		CTACTCGTGGCCCCCAGGGGC	0.667																																					p.A207fs		Atlas-INDEL	.											.	ADAMTS8	172	.	0			c.620delC						.						20.0	30.0	27.0					11																	130297563		2179	4267	6446	SO:0001589	frameshift_variant	11095	exon1			.	AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	224	protein-coding gene	gene with protein product		605175	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8"""			10438512	Standard	NM_007037		Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.619delG	chr11.hg19:g.130297563delC	ENSP00000257359:p.Ala207fs	83.0	0.0		166.0	10.0	NM_007037	Q9NZS0	Frame_Shift_Del	DEL	ENST00000257359.6	hg19	CCDS41732.1																																																																																			.	.		0.667	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037	
NAPSA	9476	hgsc.bcm.edu	37	19	50868809	50868809	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:50868809delC	ENST00000253719.2	-	1	278	c.70delG	c.(70-72)gccfs	p.A24fs	NR1H2_ENST00000600978.1_Intron|CTB-191K22.6_ENST00000597049.1_RNA|NR1H2_ENST00000542413.1_Intron	NM_004851.1	NP_004842.1	O96009	NAPSA_HUMAN	napsin A aspartic peptidase	24					membrane protein proteolysis (GO:0033619)|proteolysis (GO:0006508)|surfactant homeostasis (GO:0043129)	alveolar lamellar body (GO:0097208)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)|peptidase activity (GO:0008233)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)		ATCAGTGTGGCCCCGGAAGGC	0.592																																					p.A24fs		Atlas-INDEL	.											.	NAPSA	38	.	0			c.71delC						.						67.0	60.0	62.0					19																	50868809		2203	4300	6503	SO:0001589	frameshift_variant	9476	exon1			.	AF090386	CCDS12794.1	19q13.33	2011-08-25				ENSG00000131400			13395	protein-coding gene	gene with protein product	"""kidney-derived aspartic protease-like protein"""	605631					Standard	NM_004851		Approved	NAP1, NAPA, Kdap, KAP	uc002prx.3	O96009		ENST00000253719.2:c.70delG	chr19.hg19:g.50868809delC	ENSP00000253719:p.Ala24fs	71.0	0.0		170.0	13.0	NM_004851	Q8WWD9	Frame_Shift_Del	DEL	ENST00000253719.2	hg19	CCDS12794.1																																																																																			.	.		0.592	NAPSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464714.1	NM_004851	
SUPT7L	9913	hgsc.bcm.edu	37	2	27883855	27883855	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:27883855delA	ENST00000337768.5	-	3	984	c.415delT	c.(415-417)tatfs	p.Y139fs	SUPT7L_ENST00000404798.2_Intron|SLC4A1AP_ENST00000326019.6_5'Flank|SUPT7L_ENST00000405491.1_Frame_Shift_Del_p.Y137fs|SUPT7L_ENST00000406540.1_Frame_Shift_Del_p.Y137fs|SUPT7L_ENST00000464789.2_Frame_Shift_Del_p.Y137fs	NM_001282729.1|NM_014860.1	NP_001269658.1|NP_055675.1	O94864	ST65G_HUMAN	suppressor of Ty 7 (S. cerevisiae)-like	139					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|maintenance of protein location in nucleus (GO:0051457)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)					cctTACCGATAAAAGTCACTC	0.463																																					p.Y139fs		Atlas-INDEL	.											.	SUPT7L	36	.	0			c.416delA						.						75.0	75.0	75.0					2																	27883855		1978	4161	6139	SO:0001589	frameshift_variant	9913	exon3			.	AF197954	CCDS42667.1, CCDS62885.1, CCDS62886.1	2p23.3	2008-02-05			ENSG00000119760	ENSG00000119760			30632	protein-coding gene	gene with protein product		612762				9872452, 11564863	Standard	NM_001282732		Approved	STAF65, gamma, KIAA0764, SPT7L	uc002rli.1	O94864	OTTHUMG00000151947	ENST00000337768.5:c.415delT	chr2.hg19:g.27883855delA	ENSP00000336750:p.Tyr139fs	175.0	0.0		157.0	10.0	NM_014860	B4E3W3|Q6IB21|Q9H2T6	Frame_Shift_Del	DEL	ENST00000337768.5	hg19	CCDS42667.1																																																																																			.	.		0.463	SUPT7L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324568.1	NM_014860	
GLB1L3	112937	hgsc.bcm.edu	37	11	134152001	134152001	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:134152001delG	ENST00000431683.2	+	5	514	c.514delG	c.(514-516)gggfs	p.G173fs	GLB1L3_ENST00000389887.5_Frame_Shift_Del_p.G173fs	NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	173					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		GATGGACCTCGGGGGCTTGCC	0.537																																					p.L171fs		Atlas-INDEL	.											.	GLB1L3	102	.	0			c.513delC						.						40.0	39.0	39.0					11																	134152001		2200	4297	6497	SO:0001589	frameshift_variant	112937	exon5			.		CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.514delG	chr11.hg19:g.134152001delG	ENSP00000396615:p.Gly173fs	142.0	0.0		202.0	14.0	NM_001080407	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Frame_Shift_Del	DEL	ENST00000431683.2	hg19	CCDS44780.1																																																																																			.	.		0.537	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416	
RCOR2	283248	hgsc.bcm.edu	37	11	63679557	63679557	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:63679557delG	ENST00000301459.4	-	12	1739	c.1352delC	c.(1351-1353)ccgfs	p.P451fs	RCOR2_ENST00000473926.2_5'UTR	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	451	Pro-rich.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						CCTCAGCAGCGGGGGTGGCTG	0.706																																					p.P451fs		Atlas-INDEL	.											.	RCOR2	43	.	0			c.1353delG						.						4.0	5.0	5.0					11																	63679557		1770	3514	5284	SO:0001589	frameshift_variant	283248	exon12			.	BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.1352delC	chr11.hg19:g.63679557delG	ENSP00000301459:p.Pro451fs	142.0	0.0		153.0	10.0	NM_173587	Q96FP3	Frame_Shift_Del	DEL	ENST00000301459.4	hg19	CCDS8052.1																																																																																			.	.		0.706	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587	
MRPL16	54948	hgsc.bcm.edu	37	11	59575183	59575183	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:59575183delA	ENST00000300151.4	-	3	474	c.261delT	c.(259-261)tttfs	p.F87fs		NM_017840.3	NP_060310.1	Q9NX20	RM16_HUMAN	mitochondrial ribosomal protein L16	87					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|liver(1)|lung(8)	11						CCAAGATTGCAAAATTGCCTT	0.418																																					p.A88fs		Atlas-INDEL	.											.	MRPL16	25	.	0			c.262delG						.						269.0	282.0	278.0					11																	59575183		2201	4295	6496	SO:0001589	frameshift_variant	54948	exon3			.	AF183428	CCDS7976.1	11q12.1	2012-09-13			ENSG00000166902	ENSG00000166902		"""Mitochondrial ribosomal proteins / large subunits"""	14476	protein-coding gene	gene with protein product		611829					Standard	NM_017840		Approved	FLJ20484, PNAS-111	uc001noh.2	Q9NX20	OTTHUMG00000167410	ENST00000300151.4:c.261delT	chr11.hg19:g.59575183delA	ENSP00000300151:p.Phe87fs	170.0	0.0		216.0	13.0	NM_017840	Q9BYD0|Q9HB70	Frame_Shift_Del	DEL	ENST00000300151.4	hg19	CCDS7976.1																																																																																			.	.		0.418	MRPL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394521.1	NM_017840	
DNM3	26052	hgsc.bcm.edu	37	1	172356459	172356459	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:172356459delC	ENST00000355305.5	+	19	2420	c.2263delC	c.(2263-2265)cccfs	p.P757fs	DNM3_ENST00000358155.4_Frame_Shift_Del_p.P751fs|DNM3_ENST00000367731.1_Frame_Shift_Del_p.P747fs			Q9UQ16	DYN3_HUMAN	dynamin 3	757					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						CACTCCGGCACCCCCTCCAGT	0.587																																					p.A748fs		Atlas-INDEL	.											.	DNM3	85	.	0			c.2244delA						.						28.0	31.0	30.0					1																	172356459		2053	4188	6241	SO:0001589	frameshift_variant	26052	exon19			.	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"""Pleckstrin homology (PH) domain containing"""	29125	protein-coding gene	gene with protein product	"""Dyna III"""	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.2263delC	chr1.hg19:g.172356459delC	ENSP00000347457:p.Pro757fs	100.0	0.0		143.0	12.0	NM_015569	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Frame_Shift_Del	DEL	ENST00000355305.5	hg19																																																																																				.	.		0.587	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569	
PCDHB5	26167	hgsc.bcm.edu	37	5	140515047	140515047	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:140515047delA	ENST00000231134.5	+	1	248	c.31delA	c.(31-33)aaafs	p.K11fs		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	11					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AACGCCACAGAAAAGGCAAGT	0.448																																					p.Q10fs		Atlas-INDEL	.											.	PCDHB5	184	.	0			c.30delG						.						97.0	86.0	90.0					5																	140515047		2203	4300	6503	SO:0001589	frameshift_variant	26167	exon1			.	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"""Cadherins / Protocadherins : Clustered"""	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.31delA	chr5.hg19:g.140515047delA	ENSP00000231134:p.Lys11fs	200.0	0.0		229.0	14.0	NM_015669	Q549F4|Q9UFU9	Frame_Shift_Del	DEL	ENST00000231134.5	hg19	CCDS4247.1																																																																																			.	.		0.448	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669	
RLTPR	146206	hgsc.bcm.edu	37	16	67688777	67688777	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:67688777delG	ENST00000334583.6	+	32	4007	c.3679delG	c.(3679-3681)gggfs	p.G1228fs	RLTPR_ENST00000545661.1_Frame_Shift_Del_p.G1192fs	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	1228					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		CCGAGGCAGCGGGGGTGCCGA	0.587																																					p.S1226fs		Atlas-INDEL	.											.	RLTPR	124	.	0			c.3678delC						.						42.0	51.0	48.0					16																	67688777		2167	4263	6430	SO:0001589	frameshift_variant	146206	exon32			.	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"""RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein"", ""leucine rich repeat containing 16C"""	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.3679delG	chr16.hg19:g.67688777delG	ENSP00000334958:p.Gly1228fs	121.0	0.0		141.0	13.0	NM_001013838	B8X2Z3	Frame_Shift_Del	DEL	ENST00000334583.6	hg19	CCDS45513.1																																																																																			.	.		0.587	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838	
KIF15	56992	hgsc.bcm.edu	37	3	44882704	44882704	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:44882704delA	ENST00000326047.4	+	29	3708	c.3559delA	c.(3559-3561)aaafs	p.K1187fs	KIF15_ENST00000425755.1_Frame_Shift_Del_p.K822fs	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	1187					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)		CAGAGAAGTCAAAAATGCTGA	0.368																																					p.V1186fs		Atlas-INDEL	.											.	KIF15	103	.	0			c.3558delC						.						61.0	66.0	64.0					3																	44882704		2203	4300	6503	SO:0001589	frameshift_variant	56992	exon29			.	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.3559delA	chr3.hg19:g.44882704delA	ENSP00000324020:p.Lys1187fs	94.0	0.0		127.0	11.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Frame_Shift_Del	DEL	ENST00000326047.4	hg19	CCDS33744.1																																																																																			.	.		0.368	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2		
UGDH	7358	hgsc.bcm.edu	37	4	39515764	39515764	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:39515764delT	ENST00000316423.6	-	3	545	c.203delA	c.(202-204)aatfs	p.N68fs	UGDH_ENST00000501493.2_Frame_Shift_Del_p.N68fs|UGDH_ENST00000515398.1_5'UTR|UGDH_ENST00000507089.1_5'UTR|UGDH_ENST00000506179.1_Frame_Shift_Del_p.N68fs	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	68					cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)			breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						AAAAAAAAGATTTTTTCCTCG	0.308																																					p.N68fs		Atlas-INDEL	.											.	UGDH	52	.	0			c.204delT						.						63.0	75.0	71.0					4																	39515764		2201	4289	6490	SO:0001589	frameshift_variant	7358	exon3			.	AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	"""UDP-glucose dehydrogenase"""			9737970, 10575217	Standard	NM_003359		Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.203delA	chr4.hg19:g.39515764delT	ENSP00000319501:p.Asn68fs	134.0	0.0		155.0	10.0	NM_001184700	B3KUU2|B4DN25|O60589	Frame_Shift_Del	DEL	ENST00000316423.6	hg19	CCDS3455.1																																																																																			.	.		0.308	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359	
EHBP1L1	254102	hgsc.bcm.edu	37	11	65351025	65351025	+	Frame_Shift_Del	DEL	T	T	-	rs559675386		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:65351025delT	ENST00000309295.4	+	9	3147	c.2882delT	c.(2881-2883)gttfs	p.V961fs		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	961						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						GAGATGAAGGTTTTAGAGTCT	0.552																																					p.V961fs		Atlas-INDEL	.											.	EHBP1L1	64	.	0			c.2881delG						.						23.0	24.0	24.0					11																	65351025		1832	4082	5914	SO:0001589	frameshift_variant	254102	exon9			.	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.2882delT	chr11.hg19:g.65351025delT	ENSP00000312671:p.Val961fs	115.0	0.0		190.0	13.0	NM_001099409	Q8TB89|Q9H7M7	Frame_Shift_Del	DEL	ENST00000309295.4	hg19	CCDS44649.1																																																																																			.	.		0.552	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
ROS1	6098	hgsc.bcm.edu	37	6	117683915	117683915	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:117683915delC	ENST00000368508.3	-	21	3430	c.3232delG	c.(3232-3234)gtgfs	p.V1078fs	ROS1_ENST00000368507.3_Frame_Shift_Del_p.V1073fs|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1078	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		TTTGTTAACACCCCATTTTCA	0.348			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																p.V1078fs		Atlas-INDEL	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	ROS1	728	.	0			c.3233delT						.						117.0	123.0	121.0					6																	117683915		2203	4300	6503	SO:0001589	frameshift_variant	6098	exon21			.	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.3232delG	chr6.hg19:g.117683915delC	ENSP00000357494:p.Val1078fs	131.0	0.0		165.0	10.0	NM_002944	Q15368|Q5TDB5	Frame_Shift_Del	DEL	ENST00000368508.3	hg19	CCDS5116.1																																																																																			.	.		0.348	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
RPF1	80135	hgsc.bcm.edu	37	1	84945079	84945079	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:84945079delG	ENST00000370654.5	+	1	130	c.115delG	c.(115-117)gggfs	p.G39fs	RPF1_ENST00000370656.1_Frame_Shift_Del_p.G39fs	NM_025065.6	NP_079341.2	Q9H9Y2	RPF1_HUMAN	ribosome production factor 1 homolog (S. cerevisiae)	39					rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			breast(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(2)|prostate(1)	14						GACGGAAAACGGGGTCCAACC	0.557																																					p.N38fs		Atlas-INDEL	.											.	RPF1	31	.	0			c.114delC						.						29.0	34.0	32.0					1																	84945079		2203	4300	6503	SO:0001589	frameshift_variant	80135	exon1			.	AF322053	CCDS695.1	1p22.3	2009-09-25	2009-09-25	2009-09-25	ENSG00000117133	ENSG00000117133			30350	protein-coding gene	gene with protein product	"""RNA processing factor 1"", ""ribosome production factor 1"""		"""brix domain containing 5"""	BXDC5		11864606	Standard	NM_025065		Approved		uc001djv.4	Q9H9Y2	OTTHUMG00000009857	ENST00000370654.5:c.115delG	chr1.hg19:g.84945079delG	ENSP00000359688:p.Gly39fs	136.0	0.0		155.0	10.0	NM_025065	Q5VSK7|Q6AHX1|Q8WXZ8	Frame_Shift_Del	DEL	ENST00000370654.5	hg19	CCDS695.1																																																																																			.	.		0.557	RPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027238.1	NM_025065	
MCHR2	84539	hgsc.bcm.edu	37	6	100395834	100395834	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:100395834delT	ENST00000281806.2	-	3	510	c.196delA	c.(196-198)acafs	p.T66fs	MCHR2_ENST00000369212.2_Frame_Shift_Del_p.T66fs	NM_001040179.1	NP_001035269.1	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	66						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	39		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		TCAGGGACTGTTTTTTTCCTG	0.413																																					p.T66fs		Atlas-INDEL	.											.	MCHR2	97	.	0			c.197delC						.						57.0	60.0	59.0					6																	100395834		2203	4300	6503	SO:0001589	frameshift_variant	84539	exon3			.	AF347063	CCDS5044.1	6q16	2012-08-08	2006-02-15	2006-02-15	ENSG00000152034	ENSG00000152034		"""GPCR / Class A : MCH receptors"""	20867	protein-coding gene	gene with protein product		606111	"""G protein-coupled receptor 145"""	GPR145		11355873, 11274220	Standard	NM_032503		Approved	SLT, MCH2, MCH2R	uc003pqi.1	Q969V1	OTTHUMG00000015270	ENST00000281806.2:c.196delA	chr6.hg19:g.100395834delT	ENSP00000281806:p.Thr66fs	149.0	0.0		184.0	13.0	NM_001040179	B3KVW4|E1P5D7|Q5VTV7|Q6Q377|Q9BXA8	Frame_Shift_Del	DEL	ENST00000281806.2	hg19	CCDS5044.1																																																																																			.	.		0.413	MCHR2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041620.2	NM_032503	
GLI3	2737	hgsc.bcm.edu	37	7	42006102	42006102	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:42006102delC	ENST00000395925.3	-	15	2653	c.2569delG	c.(2569-2571)gccfs	p.A857fs	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	857					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|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)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						CTCAGGTAGGCCGAGCTGATG	0.662									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.A857fs		Atlas-INDEL	.											.	GLI3	312	.	0			c.2570delC						.						34.0	35.0	35.0					7																	42006102		2202	4300	6502	SO:0001589	frameshift_variant	2737	exon15	Familial Cancer Database	;	.		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.2569delG	chr7.hg19:g.42006102delC	ENSP00000379258:p.Ala857fs	145.0	0.0		154.0	10.0	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Frame_Shift_Del	DEL	ENST00000395925.3	hg19	CCDS5465.1																																																																																			.	.		0.662	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
AIM1	202	hgsc.bcm.edu	37	6	106967727	106967727	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:106967727delG	ENST00000369066.3	+	2	1907	c.1420delG	c.(1420-1422)gggfs	p.G474fs		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		ACCCGCTCCTGGGGATGTTCC	0.488																																					p.P473fs		Atlas-INDEL	.											.	AIM1	161	.	0			c.1419delT						.						93.0	97.0	95.0					6																	106967727		2203	4300	6503	SO:0001589	frameshift_variant	202	exon2			.	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.1420delG	chr6.hg19:g.106967727delG	ENSP00000358062:p.Gly474fs	134.0	0.0		183.0	11.0	NM_001624	Q6P2P0|Q9BTM3	Frame_Shift_Del	DEL	ENST00000369066.3	hg19	CCDS34506.1																																																																																			.	.		0.488	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
ERCC1	2067	hgsc.bcm.edu	37	19	45916842	45916842	+	Intron	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:45916842delT	ENST00000300853.3	-	9	1435				ERCC1_ENST00000591636.1_Intron|ERCC1_ENST00000013807.5_Frame_Shift_Del_p.K312fs|ERCC1_ENST00000588738.1_Intron|ERCC1_ENST00000589165.1_Intron|ERCC1_ENST00000423698.2_Intron|ERCC1_ENST00000340192.7_Intron	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1						cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|male gonad development (GO:0008584)|mitotic recombination (GO:0006312)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|oogenesis (GO:0048477)|post-embryonic hemopoiesis (GO:0035166)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|replicative cell aging (GO:0001302)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to sucrose (GO:0009744)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)|syncytium formation (GO:0006949)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	cytoplasm (GO:0005737)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|skin(1)	15		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)		tcTTTGGTTCTTTTTTCACCT	0.512								Nucleotide excision repair (NER)																													p.E313fs		Atlas-INDEL	.											.	ERCC1	46	.	0			c.937delG						.						122.0	127.0	125.0					19																	45916842		2203	4300	6503	SO:0001627	intron_variant	2067	exon8			.		CCDS12662.1, CCDS12663.1, CCDS54279.1	19q13.32	2014-03-07	2014-03-07			ENSG00000012061			3433	protein-coding gene	gene with protein product		126380	"""excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)"""			6462228	Standard	NM_001983		Approved	RAD10	uc002pbs.2	P07992		ENST00000300853.3:c.843+92A>-	chr19.hg19:g.45916842delT		132.0	0.0		166.0	10.0	NM_202001	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Frame_Shift_Del	DEL	ENST00000300853.3	hg19	CCDS12662.1																																																																																			.	.		0.512	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983	
DMBX1	127343	hgsc.bcm.edu	37	1	46976722	46976722	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:46976722delC	ENST00000360032.3	+	3	463	c.449delC	c.(448-450)gccfs	p.A150fs	DMBX1_ENST00000371956.4_Frame_Shift_Del_p.A155fs	NM_172225.1	NP_757379.1			diencephalon/mesencephalon homeobox 1											endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)					AAGGCCGAGGCCCCCACTCCA	0.647																																					p.A155fs		Atlas-INDEL	.											.	DMBX1	50	.	0			c.463delG						.						52.0	63.0	59.0					1																	46976722		2203	4300	6503	SO:0001589	frameshift_variant	127343	exon3			.	AB037699	CCDS536.1	1p34.1	2011-06-20	2004-03-29	2004-03-30	ENSG00000197587	ENSG00000197587		"""Homeoboxes / PRD class"""	19026	protein-coding gene	gene with protein product		607410	"""orthodenticle homolog 3 (Drosophila)"""	OTX3			Standard	NM_147192		Approved	PAXB	uc001cpx.3	Q8NFW5	OTTHUMG00000007982	ENST00000360032.3:c.449delC	chr1.hg19:g.46976722delC	ENSP00000353132:p.Ala150fs	165.0	0.0		198.0	14.0	NM_147192		Frame_Shift_Del	DEL	ENST00000360032.3	hg19	CCDS536.1																																																																																			.	.		0.647	DMBX1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021895.1		
SMYD5	10322	hgsc.bcm.edu	37	2	73452036	73452036	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:73452036delA	ENST00000389501.4	+	11	1028	c.983delA	c.(982-984)gaafs	p.E328fs		NM_006062.2	NP_006053.2	Q6GMV2	SMYD5_HUMAN	SMYD family member 5	328	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13						TCCTTTCCAGAAAACAACTTC	0.483																																					p.E328fs		Atlas-INDEL	.											.	SMYD5	58	.	0			c.982delG						.						125.0	107.0	113.0					2																	73452036		2203	4300	6503	SO:0001589	frameshift_variant	10322	exon11			.	U50383	CCDS33221.2	2p12	2007-02-09	2003-05-14	2003-05-16	ENSG00000135632	ENSG00000135632		"""Zinc fingers, MYND-type"""	16258	protein-coding gene	gene with protein product			"""retinoic acid induced 15"""	RAI15		8754834	Standard	NM_006062		Approved	RRG1, NN8-4AG, ZMYND23	uc002siw.2	Q6GMV2	OTTHUMG00000150482	ENST00000389501.4:c.983delA	chr2.hg19:g.73452036delA	ENSP00000374152:p.Glu328fs	131.0	0.0		133.0	11.0	NM_006062	D6W5H3|Q13558	Frame_Shift_Del	DEL	ENST00000389501.4	hg19	CCDS33221.2																																																																																			.	.		0.483	SMYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318301.1	NM_006062	
USP13	8975	hgsc.bcm.edu	37	3	179501906	179501906	+	Frame_Shift_Del	DEL	T	T	-	rs34456126		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:179501906delT	ENST00000263966.3	+	21	3040	c.2569delT	c.(2569-2571)tttfs	p.F857fs	USP13_ENST00000496897.1_Frame_Shift_Del_p.F792fs	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	857	USP.				autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			CTACATGTACTTTTACCGCAG	0.378																																					p.Y856fs		Atlas-INDEL	.											.	USP13	117	.	0			c.2568delC						.						119.0	124.0	122.0					3																	179501906		2203	4300	6503	SO:0001589	frameshift_variant	8975	exon21			.	U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"""Ubiquitin-specific peptidases"""	12611	protein-coding gene	gene with protein product		603591	"""ubiquitin specific protease 13 (isopeptidase T-3)"""			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.2569delT	chr3.hg19:g.179501906delT	ENSP00000263966:p.Phe857fs	179.0	0.0		166.0	10.0	NM_003940	A8K2S3|B4DYF3|D3DNS2|Q96B25	Frame_Shift_Del	DEL	ENST00000263966.3	hg19	CCDS3235.1																																																																																			.	.		0.378	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1		
MAPK11	5600	hgsc.bcm.edu	37	22	50704089	50704089	+	Splice_Site	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:50704089delC	ENST00000330651.6	-	10	863	c.763delG	c.(763-765)gcc>cc	p.A255fs	MAPK11_ENST00000495277.1_5'Flank	NM_002751.5	NP_002742.3	Q15759	MK11_HUMAN	mitogen-activated protein kinase 11	255	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|gene expression (GO:0010467)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|lung(4)	6		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;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Regorafenib(DB08896)	TATGTCCGGGCCTGGGGGCAC	0.632																																					p.A255fs	GBM(9;634 739 50668)	Atlas-INDEL	.											.	MAPK11	23	.	0			c.764delC						.						27.0	31.0	30.0					22																	50704089		2203	4299	6502	SO:0001630	splice_region_variant	5600	exon10			.	Y14440	CCDS14090.1	22q13.33	2011-06-09			ENSG00000185386	ENSG00000185386	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6873	protein-coding gene	gene with protein product		602898		PRKM11		9218798	Standard	NM_002751		Approved	p38-2, p38Beta, SAPK2	uc003bkr.3	Q15759	OTTHUMG00000150226	ENST00000330651.6:c.763-1G>-	chr22.hg19:g.50704089delC		135.0	0.0		148.0	10.0	NM_002751	A8K730|B0LPG1|B7Z630|E7ETQ1|L7RT27|O00284|O15472|Q2XNF2	Frame_Shift_Del	DEL	ENST00000330651.6	hg19	CCDS14090.1																																																																																			.	.		0.632	MAPK11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316900.1		Frame_Shift_Del
ARHGEF12	23365	hgsc.bcm.edu	37	11	120346091	120346091	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:120346091delA	ENST00000397843.2	+	33	3318	c.3152delA	c.(3151-3153)caafs	p.Q1051fs	ARHGEF12_ENST00000356641.3_Frame_Shift_Del_p.Q1032fs|ARHGEF12_ENST00000532993.1_Frame_Shift_Del_p.Q948fs	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	1051	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		GTATTGTTACAAAAGCAGGAT	0.368			T	MLL	AML																																p.Q1051fs		Atlas-INDEL	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.3151delC						.						180.0	163.0	169.0					11																	120346091		1917	4122	6039	SO:0001589	frameshift_variant	23365	exon33			.	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"""Rho guanine nucleotide exchange factors"""	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.3152delA	chr11.hg19:g.120346091delA	ENSP00000380942:p.Gln1051fs	126.0	0.0		228.0	14.0	NM_015313	O15086|Q6P526	Frame_Shift_Del	DEL	ENST00000397843.2	hg19	CCDS41727.1																																																																																			.	.		0.368	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313	
ADORA1	134	hgsc.bcm.edu	37	1	203134406	203134406	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:203134406delC	ENST00000367236.4	+	3	1280	c.359delC	c.(358-360)accfs	p.T120fs	ADORA1_ENST00000472535.1_3'UTR|ADORA1_ENST00000337894.4_Frame_Shift_Del_p.T120fs|ADORA1_ENST00000309502.3_Frame_Shift_Del_p.T120fs|ADORA1_ENST00000367235.1_3'UTR	NM_001048230.1	NP_001041695.1	P30542	AA1R_HUMAN	adenosine A1 receptor	120					activation of MAPKK activity (GO:0000186)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cognition (GO:0050890)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood pressure (GO:0045776)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heart contraction (GO:0045822)|negative regulation of hormone secretion (GO:0046888)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of mucus secretion (GO:0070256)|negative regulation of neurotrophin production (GO:0032900)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of vasodilation (GO:0045908)|nervous system development (GO:0007399)|phagocytosis (GO:0006909)|positive regulation of blood pressure (GO:0045777)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of nucleoside transport (GO:0032244)|positive regulation of peptide secretion (GO:0002793)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of protein dephosphorylation (GO:0035307)|protein targeting to membrane (GO:0006612)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of glomerular filtration (GO:0003093)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|relaxation of vascular smooth muscle (GO:0060087)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|temperature homeostasis (GO:0001659)	asymmetric synapse (GO:0032279)|axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled adenosine receptor activity (GO:0001609)|phospholipase C activity (GO:0004629)|purine nucleoside binding (GO:0001883)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(9)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25					Adenosine(DB00640)|Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Gabapentin(DB00996)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Theobromine(DB01412)|Theophylline(DB00277)	ATGGTGGTGACCCCCCGGAGG	0.652																																					p.T120fs		Atlas-INDEL	.											.	ADORA1	62	.	0			c.358delA						.						33.0	40.0	38.0					1																	203134406		2203	4300	6503	SO:0001589	frameshift_variant	134	exon3			.	BC026340	CCDS1434.1	1q32.1	2012-08-08			ENSG00000163485	ENSG00000163485		"""GPCR / Class A : Adenosine receptors"""	262	protein-coding gene	gene with protein product		102775				1662665, 2541503	Standard	NM_001048230		Approved	RDC7	uc001gzf.1	P30542	OTTHUMG00000042125	ENST00000367236.4:c.359delC	chr1.hg19:g.203134406delC	ENSP00000356205:p.Thr120fs	65.0	0.0		146.0	10.0	NM_001048230	A6NFY5|A6NGP4|A8K1L3|B3KXQ4|D2CGD0|Q6FHK3|Q8TAM8	Frame_Shift_Del	DEL	ENST00000367236.4	hg19	CCDS1434.1																																																																																			.	.		0.652	ADORA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100273.1	NM_000674	
SNX24	28966	hgsc.bcm.edu	37	5	122272475	122272475	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:122272475delA	ENST00000261369.4	+	2	292	c.107delA	c.(106-108)gaafs	p.E36fs	SNX24_ENST00000511211.1_3'UTR|SNX24_ENST00000513881.1_Frame_Shift_Del_p.E36fs|SNX24_ENST00000506996.1_Frame_Shift_Del_p.E36fs|SNX24_ENST00000395451.4_Frame_Shift_Del_p.E69fs	NM_014035.2	NP_054754.1	Q9Y343	SNX24_HUMAN	sorting nexin 24	36	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			lung(5)	5		Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)		CATTTTGTTGAAAAGAGATAC	0.294																																					p.E36fs		Atlas-INDEL	.											.	SNX24	14	.	0			c.106delG						.						129.0	117.0	121.0					5																	122272475		2203	4299	6502	SO:0001589	frameshift_variant	28966	exon2			.	AF139461	CCDS4132.1	5q23.2	2008-03-11	2007-08-15		ENSG00000064652	ENSG00000064652		"""Sorting nexins"""	21533	protein-coding gene	gene with protein product						12461558	Standard	NM_014035		Approved	SBBI31	uc011cwo.2	Q9Y343	OTTHUMG00000128913	ENST00000261369.4:c.107delA	chr5.hg19:g.122272475delA	ENSP00000261369:p.Glu36fs	142.0	0.0		180.0	13.0	NM_014035	Q6UY33	Frame_Shift_Del	DEL	ENST00000261369.4	hg19	CCDS4132.1																																																																																			.	.		0.294	SNX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250885.2	NM_014035	
SLC25A13	10165	hgsc.bcm.edu	37	7	95906607	95906607	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:95906607delT	ENST00000265631.5	-	3	249	c.113delA	c.(112-114)aatfs	p.N38fs	SLC25A13_ENST00000542654.1_De_novo_Start_OutOfFrame|SLC25A13_ENST00000416240.2_Frame_Shift_Del_p.N38fs			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	38					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)			breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	GACAAAGTCATTGGGGGACAT	0.343																																					p.N38fs		Atlas-INDEL	.											.	SLC25A13	131	.	0			c.114delT						.						53.0	50.0	51.0					7																	95906607		2202	4299	6501	SO:0001589	frameshift_variant	10165	exon3			.	AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"""Solute carriers"", ""EF-hand domain containing"""	10983	protein-coding gene	gene with protein product	"""mitochondrial aspartate glutamate carrier 2"""	603859	"""solute carrier family 25, member 13 (citrin)"""	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.113delA	chr7.hg19:g.95906607delT	ENSP00000265631:p.Asn38fs	76.0	0.0		151.0	10.0	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Frame_Shift_Del	DEL	ENST00000265631.5	hg19	CCDS5645.1																																																																																			.	.		0.343	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251	
FZD6	8323	hgsc.bcm.edu	37	8	104330820	104330820	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:104330820delT	ENST00000358755.4	+	3	497	c.180delT	c.(178-180)catfs	p.H60fs	FZD6_ENST00000522566.1_Frame_Shift_Del_p.H60fs|FZD6_ENST00000540287.1_Intron|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	87.0	0.0		125.0	11.0	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	
KIF15	56992	hgsc.bcm.edu	37	3	44879844	44879844	+	Frame_Shift_Del	DEL	G	G	-	rs369445825		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:44879844delG	ENST00000326047.4	+	27	3398	c.3249delG	c.(3247-3249)tcgfs	p.S1083fs	KIF15_ENST00000425755.1_Frame_Shift_Del_p.S718fs	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	1083					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)		AAAAACACTCGGGGCTGCTGC	0.517																																					p.S1083fs		Atlas-INDEL	.											KIF15,NS,carcinoma,0,1	KIF15	103	.	0			c.3248delC						.						52.0	56.0	54.0					3																	44879844		2203	4300	6503	SO:0001589	frameshift_variant	56992	exon27			.	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.3249delG	chr3.hg19:g.44879844delG	ENSP00000324020:p.Ser1083fs	153.0	0.0		159.0	10.0	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Frame_Shift_Del	DEL	ENST00000326047.4	hg19	CCDS33744.1																																																																																			.	.		0.517	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2		
GPR63	81491	hgsc.bcm.edu	37	6	97246738	97246738	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:97246738delT	ENST00000229955.3	-	2	1215	c.870delA	c.(868-870)aaafs	p.K290fs	GPR63_ENST00000417980.1_Frame_Shift_Del_p.K290fs	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	290						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		TGAGACCCAGTTTGCTGGCCT	0.463																																					p.L291fs		Atlas-INDEL	.											.	GPR63	60	.	0			c.871delC						.						89.0	85.0	86.0					6																	97246738		2203	4300	6503	SO:0001589	frameshift_variant	81491	exon2			.	AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"""GPCR / Class A : Orphans"""	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.870delA	chr6.hg19:g.97246738delT	ENSP00000229955:p.Lys290fs	102.0	0.0		124.0	10.0	NM_030784	Q9UJH3	Frame_Shift_Del	DEL	ENST00000229955.3	hg19	CCDS5036.1																																																																																			.	.		0.463	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2		
SCG5	6447	hgsc.bcm.edu	37	15	32936003	32936003	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:32936003delC	ENST00000300175.4	+	2	320	c.210delC	c.(208-210)ggcfs	p.G70fs	SCG5_ENST00000413748.2_Frame_Shift_Del_p.G70fs|SCG5_ENST00000497208.1_Frame_Shift_Del_p.G70fs|SCG5_ENST00000494364.1_Frame_Shift_Del_p.G70fs	NM_001144757.1	NP_001138229.1	P05408	7B2_HUMAN	secretogranin V (7B2 protein)	70					intracellular protein transport (GO:0006886)|neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|regulation of hormone secretion (GO:0046883)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	enzyme inhibitor activity (GO:0004857)|GTP binding (GO:0005525)|unfolded protein binding (GO:0051082)			lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	6		all_lung(180;7.32e-08)		all cancers(64;6.48e-17)|Epithelial(43;1.23e-11)|GBM - Glioblastoma multiforme(186;1.39e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0212)		ATCTTGTGGGCCCCCAGAGCA	0.443																																					p.G70fs		Atlas-INDEL	.											.	SCG5	13	.	0			c.209delG						.						36.0	35.0	35.0					15																	32936003		1862	4105	5967	SO:0001589	frameshift_variant	6447	exon2			.	Y00757	CCDS45207.1, CCDS45208.1	15q13-q14	2006-03-20	2006-03-20	2006-03-20	ENSG00000166922	ENSG00000166922			10816	protein-coding gene	gene with protein product	"""prohormone convertase chaperone"""	173120	"""secretory granule, neuroendocrine protein 1 (7B2 protein)"""	SGNE1		8162254, 12646671	Standard	NM_003020		Approved	7B2, SgV	uc001zha.2	P05408	OTTHUMG00000159447	ENST00000300175.4:c.210delC	chr15.hg19:g.32936003delC	ENSP00000300175:p.Gly70fs	141.0	0.0		152.0	11.0	NM_003020	P01164|Q6FHD0|Q9BS38	Frame_Shift_Del	DEL	ENST00000300175.4	hg19	CCDS45207.1																																																																																			.	.		0.443	SCG5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355438.1	NM_003020	
TENM1	10178	hgsc.bcm.edu	37	X	123697625	123697625	+	Intron	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:123697625delA	ENST00000371130.3	-	13	2327				TENM1_ENST00000422452.2_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1						immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GTAGTGAGCTAAAAGGGAGGG	0.343																																					.		Atlas-INDEL	.											.	.	.	.	0			c.2264-2T>-						.						53.0	48.0	50.0					X																	123697625		2203	4299	6502	SO:0001627	intron_variant	10178	exon14			.	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.2264-3T>-	chrX.hg19:g.123697625delA		144.0	0.0		193.0	15.0	NM_001163278	B2RTR5|Q5JZ17	Splice_Site	DEL	ENST00000371130.3	hg19	CCDS14609.1																																																																																			.	.		0.343	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
CAMSAP3	57662	hgsc.bcm.edu	37	19	7672746	7672746	+	Intron	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:7672746delC	ENST00000160298.4	+	5	722				CAMSAP3_ENST00000446248.2_Frame_Shift_Del_p.P233fs	NM_020902.1	NP_065953.1	Q9P1Y5	CAMP3_HUMAN	calmodulin regulated spectrin-associated protein family, member 3						epithelial cell-cell adhesion (GO:0090136)|microtubule anchoring (GO:0034453)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of organelle organization (GO:0033043)|zonula adherens maintenance (GO:0045218)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)|zonula adherens (GO:0005915)	microtubule minus-end binding (GO:0051011)			cervix(1)|endometrium(7)|kidney(3)|lung(6)|urinary_tract(2)	19						GGGGAGCAAACCCCCCATGGT	0.657																																					p.K231fs		Atlas-INDEL	.											.	CAMSAP3	131	.	0			c.693delA						.						23.0	26.0	25.0					19																	7672746		1919	4116	6035	SO:0001627	intron_variant	57662	exon6			.	AB040976	CCDS42489.1, CCDS45947.1	19p13.3-p13.2	2014-06-12	2011-08-18	2011-08-18		ENSG00000076826			29307	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 80"""	612685	"""KIAA1543"""	KIAA1543		11318610, 10819331, 19041755, 19508979	Standard	NM_001080429		Approved	Nezha, PPP1R80	uc002mgu.4	Q9P1Y5		ENST00000160298.4:c.622-266C>-	chr19.hg19:g.7672746delC		253.0	0.0		306.0	19.0	NM_001080429	Q8NDF1	Frame_Shift_Del	DEL	ENST00000160298.4	hg19	CCDS42489.1																																																																																			.	.		0.657	CAMSAP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459300.1	XM_048362	
FAM186A	121006	hgsc.bcm.edu	37	12	50747194	50747194	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:50747194delG	ENST00000327337.5	-	4	3420	c.3421delC	c.(3421-3423)cagfs	p.Q1141fs	FAM186A_ENST00000543111.1_Frame_Shift_Del_p.Q1141fs|FAM186A_ENST00000543096.1_5'Flank	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1141																	CCTTGAACCTGGGTCTGCTGA	0.632																																					p.Q1141fs	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-INDEL	.											.	FAM186A	181	.	0			c.3422delA						.						26.0	23.0	24.0					12																	50747194		692	1591	2283	SO:0001589	frameshift_variant	121006	exon4			.		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.3421delC	chr12.hg19:g.50747194delG	ENSP00000329995:p.Gln1141fs	105.0	0.0		146.0	11.0	NM_001145475		Frame_Shift_Del	DEL	ENST00000327337.5	hg19	CCDS44878.1																																																																																			.	.		0.632	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
PYROXD2	84795	hgsc.bcm.edu	37	10	100152700	100152700	+	Splice_Site	DEL	T	T	-	rs554216343		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:100152700delT	ENST00000370575.4	-	9	974	c.926delA	c.(925-927)aag>ag	p.K309fs	MIR1287_ENST00000408492.1_RNA|PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	309							oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						GCCGTTCACCTTTTCAGTGAA	0.542																																					p.K309fs		Atlas-INDEL	.											.	PYROXD2	43	.	0			c.927delG						.						96.0	84.0	88.0					10																	100152700		2203	4300	6503	SO:0001630	splice_region_variant	84795	exon9			.	AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 33"""	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.927+1A>-	chr10.hg19:g.100152700delT		218.0	0.0		156.0	10.0	NM_032709	D3DR61|Q5TAA9|Q9BRQ1	Frame_Shift_Del	DEL	ENST00000370575.4	hg19	CCDS7474.1																																																																																			.	.		0.542	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709	Frame_Shift_Del
KRCC1	51315	hgsc.bcm.edu	37	2	88327573	88327573	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:88327573delT	ENST00000347055.3	-	4	903	c.510delA	c.(508-510)aaafs	p.K170fs		NM_016618.1	NP_057702.1	Q9NPI7	KRCC1_HUMAN	lysine-rich coiled-coil 1	170	Lys-rich.									cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	7						CCTCCTCTGATTTTTCTCTGC	0.428																																					p.S171fs		Atlas-INDEL	.											.	KRCC1	25	.	0			c.511delT						.						120.0	121.0	121.0					2																	88327573		2203	4300	6503	SO:0001589	frameshift_variant	51315	exon4			.	AF208845	CCDS2000.1	2p11.2	2008-02-05			ENSG00000172086	ENSG00000172086			28039	protein-coding gene	gene with protein product						12477932	Standard	XM_005264360		Approved	FLJ22333	uc002sso.1	Q9NPI7	OTTHUMG00000130315	ENST00000347055.3:c.510delA	chr2.hg19:g.88327573delT	ENSP00000340083:p.Lys170fs	238.0	0.0		354.0	24.0	NM_016618	Q3B7J7	Frame_Shift_Del	DEL	ENST00000347055.3	hg19	CCDS2000.1																																																																																			.	.		0.428	KRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252664.1	NM_016618	
OPN3	23596	hgsc.bcm.edu	37	1	241757938	241757938	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:241757938delG	ENST00000366554.2	-	4	1107	c.1001delC	c.(1000-1002)cctfs	p.P334fs	KMO_ENST00000366557.4_3'UTR|OPN3_ENST00000331838.5_Frame_Shift_Del_p.P255fs|KMO_ENST00000366559.4_3'UTR|OPN3_ENST00000469376.1_5'UTR	NM_014322.2	NP_055137.2	Q9H1Y3	OPN3_HUMAN	opsin 3	334					detection of light stimulus (GO:0009583)|detection of visible light (GO:0009584)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(1)|large_intestine(5)|lung(5)	11	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			GTCTTTAGCAGGCCTCTGGCA	0.463																																					p.P334fs		Atlas-INDEL	.											.	OPN3	28	.	0			c.1002delT						.						103.0	105.0	105.0					1																	241757938		2203	4300	6503	SO:0001589	frameshift_variant	23596	exon4			.	AF140242	CCDS31072.1	1q43	2014-06-13	2008-04-16		ENSG00000054277	ENSG00000054277		"""GPCR / Class A : Opsin receptors"""	14007	protein-coding gene	gene with protein product	"""panopsin"", ""protein phosphatase 1, regulatory subunit 116"""	606695	"""encephalopsin"""	ECPN		10234000, 11401433	Standard	NM_014322		Approved	ERO, NMO-1, encephalopsin, PPP1R116	uc001hza.3	Q9H1Y3	OTTHUMG00000039691	ENST00000366554.2:c.1001delC	chr1.hg19:g.241757938delG	ENSP00000355512:p.Pro334fs	115.0	0.0		175.0	11.0	NM_014322	Q8IX08|Q9Y344	Frame_Shift_Del	DEL	ENST00000366554.2	hg19	CCDS31072.1																																																																																			.	.		0.463	OPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095713.1	NM_014322	
PDP1	54704	hgsc.bcm.edu	37	8	94934597	94934597	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:94934597delA	ENST00000297598.4	+	2	579	c.310delA	c.(310-312)aaafs	p.K104fs	PDP1_ENST00000517764.1_Frame_Shift_Del_p.K104fs|PDP1_ENST00000396200.3_Frame_Shift_Del_p.K129fs|PDP1_ENST00000520728.1_Frame_Shift_Del_p.K104fs	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	104					cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						ATTTGACGGCAAAAATGTCAG	0.448																																					p.G128fs		Atlas-INDEL	.											.	PDP1	97	.	0			c.384delC						.						108.0	111.0	110.0					8																	94934597		2203	4300	6503	SO:0001589	frameshift_variant	54704	exon3			.	AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9279	protein-coding gene	gene with protein product		605993	"""protein phosphatase 2C, magnesium-dependent, catalytic subunit"""	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.310delA	chr8.hg19:g.94934597delA	ENSP00000297598:p.Lys104fs	144.0	0.0		200.0	13.0	NM_001161780	B3KX71|J3KPU0|Q5U5K1	Frame_Shift_Del	DEL	ENST00000297598.4	hg19	CCDS6259.1																																																																																			.	.		0.448	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444	
C2orf71	388939	hgsc.bcm.edu	37	2	29294038	29294038	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:29294038delG	ENST00000331664.5	-	1	3089	c.3090delC	c.(3088-3090)cccfs	p.P1030fs		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1030	Pro-rich.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CAGGTGGGCTGGGGGGCGTCT	0.667																																					p.S1031fs		Atlas-INDEL	.											.	C2orf71	146	.	0			c.3091delA						.						29.0	35.0	33.0					2																	29294038		1942	4118	6060	SO:0001589	frameshift_variant	388939	exon1			.		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3090delC	chr2.hg19:g.29294038delG	ENSP00000332809:p.Pro1030fs	213.0	0.0		232.0	14.0	NM_001029883		Frame_Shift_Del	DEL	ENST00000331664.5	hg19	CCDS42669.1																																																																																			.	.		0.667	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
PIK3C3	5289	hgsc.bcm.edu	37	18	39593452	39593452	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:39593452delA	ENST00000262039.4	+	11	1303	c.1217delA	c.(1216-1218)gaafs	p.E406fs	PIK3C3_ENST00000398870.3_Frame_Shift_Del_p.E343fs	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	406	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						CTCAAATATGAAAATTTTGAT	0.308										TSP Lung(28;0.18)																											p.E406fs	NSCLC(37;552 1060 2683 16430 37914)	Atlas-INDEL	.											.	PIK3C3	138	.	0			c.1216delG						.						79.0	86.0	84.0					18																	39593452		2203	4298	6501	SO:0001589	frameshift_variant	5289	exon11			.	Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"""phosphoinositide-3-kinase, class 3"""			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.1217delA	chr18.hg19:g.39593452delA	ENSP00000262039:p.Glu406fs	215.0	0.0		256.0	16.0	NM_002647	Q15134	Frame_Shift_Del	DEL	ENST00000262039.4	hg19	CCDS11920.1																																																																																			.	.		0.308	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647	
GMPPA	29926	hgsc.bcm.edu	37	2	220369963	220369963	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:220369963delG	ENST00000358215.3	+	8	1003	c.634delG	c.(634-636)ggcfs	p.G212fs	GMPPA_ENST00000373917.3_Frame_Shift_Del_p.G212fs|GMPPA_ENST00000373908.1_Frame_Shift_Del_p.G212fs|GMPPA_ENST00000341142.3_Frame_Shift_Del_p.G212fs|GMPPA_ENST00000313597.5_Frame_Shift_Del_p.G212fs|AC053503.11_ENST00000429882.1_RNA	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	212					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		GGACTCACCAGGCTTGTGGCC	0.587																																					p.P211fs		Atlas-INDEL	.											.	GMPPA	50	.	0			c.633delA						.						66.0	66.0	66.0					2																	220369963		2203	4300	6503	SO:0001589	frameshift_variant	29926	exon8			.	AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.634delG	chr2.hg19:g.220369963delG	ENSP00000350949:p.Gly212fs	144.0	0.0		165.0	11.0	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Frame_Shift_Del	DEL	ENST00000358215.3	hg19	CCDS2441.1																																																																																			.	.		0.587	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335	
BCL11A	53335	hgsc.bcm.edu	37	2	60688969	60688969	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:60688969delG	ENST00000335712.6	-	4	1305	c.1078delC	c.(1078-1080)ctcfs	p.L360fs	BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000537768.1_Intron|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000356842.4_Frame_Shift_Del_p.L360fs|BCL11A_ENST00000538214.1_Frame_Shift_Del_p.L326fs|BCL11A_ENST00000358510.4_Frame_Shift_Del_p.L326fs	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	360	Pro-rich.				B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			AGAGGAGGGAGGGGGGGCGTC	0.632			T	IGH@	B-CLL																																p.L360fs		Atlas-INDEL	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	BCL11A	298	.	0			c.1079delT						.						39.0	48.0	44.0					2																	60688969		2198	4297	6495	SO:0001589	frameshift_variant	53335	exon4			.	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"""Zinc fingers, C2H2-type"""	13221	protein-coding gene	gene with protein product		606557	"""ecotropic viral integration site 9"""	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.1078delC	chr2.hg19:g.60688969delG	ENSP00000338774:p.Leu360fs	141.0	0.0		191.0	13.0	NM_022893	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Frame_Shift_Del	DEL	ENST00000335712.6	hg19	CCDS1862.1																																																																																			.	.		0.632	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893	
DNAH17	8632	hgsc.bcm.edu	37	17	76482378	76482378	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:76482378delG	ENST00000585328.1	-	45	7138	c.7014delC	c.(7012-7014)cccfs	p.P2338fs	DNAH17_ENST00000389840.5_Frame_Shift_Del_p.P2329fs|RP11-559N14.5_ENST00000588565.1_RNA|DNAH17_ENST00000586052.1_5'UTR|RP11-559N14.5_ENST00000585969.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2329					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(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			ACAGCTCCCTGGGGGAGTCGG	0.627																																					p.R2344fs		Atlas-INDEL	.											.	DNAH17	347	.	0			c.7030delA						.						46.0	52.0	50.0					17																	76482378		2078	4197	6275	SO:0001589	frameshift_variant	8632	exon45			.	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.7014delC	chr17.hg19:g.76482378delG	ENSP00000465516:p.Pro2338fs	84.0	0.0		181.0	11.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Frame_Shift_Del	DEL	ENST00000585328.1	hg19																																																																																				.	.		0.627	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
MAP7D3	79649	hgsc.bcm.edu	37	X	135314194	135314194	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:135314194delG	ENST00000316077.9	-	8	1142	c.922delC	c.(922-924)cagfs	p.Q308fs	MAP7D3_ENST00000370663.5_Frame_Shift_Del_p.Q290fs|MAP7D3_ENST00000370661.1_Frame_Shift_Del_p.Q273fs	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	308					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)					ACATTCACCTGGGGGGGTGCA	0.532																																					p.Q308fs		Atlas-INDEL	.											.	MAP7D3	102	.	0			c.923delA						.						179.0	175.0	176.0					X																	135314194		2042	4171	6213	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.922delC	chrX.hg19:g.135314194delG	ENSP00000318086:p.Gln308fs	130.0	0.0		135.0	11.0	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Frame_Shift_Del	DEL	ENST00000316077.9	hg19	CCDS44004.1																																																																																			.	.		0.532	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2		
ITGAM	3684	hgsc.bcm.edu	37	16	31308914	31308914	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:31308914delC	ENST00000287497.8	+	13	1511	c.1436delC	c.(1435-1437)gccfs	p.A479fs	ITGAM_ENST00000544665.3_Frame_Shift_Del_p.A479fs			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	479					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						CTCATCGGGGCCCCCCATTAC	0.677																																					p.A479fs		Atlas-INDEL	.											.	ITGAM	137	.	0			c.1435delG						.						67.0	75.0	72.0					16																	31308914		2193	4295	6488	SO:0001589	frameshift_variant	3684	exon13			.	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"""CD molecules"", ""Complement system"", ""Integrins"""	6149	protein-coding gene	gene with protein product		120980	"""integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"""	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.1436delC	chr16.hg19:g.31308914delC	ENSP00000287497:p.Ala479fs	149.0	0.0		208.0	13.0	NM_000632	Q4VAK0|Q4VAK1|Q4VAK2	Frame_Shift_Del	DEL	ENST00000287497.8	hg19	CCDS45470.1																																																																																			.	.		0.677	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632	
FKBP4	2288	hgsc.bcm.edu	37	12	2907011	2907011	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:2907011delC	ENST00000001008.4	+	3	554	c.367delC	c.(367-369)cccfs	p.P124fs	RP4-816N1.6_ENST00000547834.1_RNA|RP4-816N1.7_ENST00000547042.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	124	PPIase FKBP-type 1. {ECO:0000255|PROSITE- ProRule:PRU00277}.				androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			TCCAAAGATTCCCCCCAATGC	0.552																																					p.I122fs		Atlas-INDEL	.											.	FKBP4	29	.	0			c.366delT						.						161.0	136.0	145.0					12																	2907011		2203	4300	6503	SO:0001589	frameshift_variant	2288	exon3			.	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"""Tetratricopeptide (TTC) repeat domain containing"""	3720	protein-coding gene	gene with protein product		600611	"""FK506-binding protein 4 (59kD)"""			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.367delC	chr12.hg19:g.2907011delC	ENSP00000001008:p.Pro124fs	154.0	0.0		154.0	11.0	NM_002014	D3DUQ1|Q9UCP1|Q9UCV7	Frame_Shift_Del	DEL	ENST00000001008.4	hg19	CCDS8512.1																																																																																			.	.		0.552	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1		
GIMAP2	26157	hgsc.bcm.edu	37	7	150390266	150390266	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:150390266delT	ENST00000223293.5	+	3	986	c.892delT	c.(892-894)tttfs	p.F298fs		NM_015660.2	NP_056475.1	Q9UG22	GIMA2_HUMAN	GTPase, IMAP family member 2	298						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	GTP binding (GO:0005525)			kidney(1)|large_intestine(1)|lung(8)|skin(2)|urinary_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTGCAATTTGTTTTGTTGCTT	0.313																																					p.L297fs		Atlas-INDEL	.											.	GIMAP2	39	.	0			c.891delG						.						112.0	103.0	106.0					7																	150390266		2203	4299	6502	SO:0001589	frameshift_variant	26157	exon3			.	AL110151	CCDS5905.1	7q36.1	2014-04-04			ENSG00000106560	ENSG00000106560		"""GTPases, IMAP"""	21789	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 12"""	608085				15474311	Standard	NM_015660		Approved	DKFZp586D0824, HIMAP2, IMAP2, IAN12	uc003who.3	Q9UG22	OTTHUMG00000157488	ENST00000223293.5:c.892delT	chr7.hg19:g.150390266delT	ENSP00000223293:p.Phe298fs	79.0	0.0		155.0	10.0	NM_015660	Q96L25	Frame_Shift_Del	DEL	ENST00000223293.5	hg19	CCDS5905.1																																																																																			.	.		0.313	GIMAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348948.1	NM_015660	
SMARCA1	6594	hgsc.bcm.edu	37	X	128649751	128649751	+	Frame_Shift_Del	DEL	C	C	-	rs139862410	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:128649751delC	ENST00000371122.4	-	5	672	c.543delG	c.(541-543)gggfs	p.G181fs	SMARCA1_ENST00000371121.3_Frame_Shift_Del_p.G181fs|SMARCA1_ENST00000478420.1_5'UTR|SMARCA1_ENST00000371123.1_Frame_Shift_Del_p.G181fs	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	181					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						CTCTCAGTGGCCCCCCTTTCA	0.348																																					p.P182fs		Atlas-INDEL	.											.	SMARCA1	126	.	0			c.544delC						.						70.0	66.0	67.0					X																	128649751		2203	4300	6503	SO:0001589	frameshift_variant	6594	exon5			.	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.543delG	chrX.hg19:g.128649751delC	ENSP00000360163:p.Gly181fs	153.0	0.0		212.0	13.0	NM_139035	Q5JV41|Q5JV42	Frame_Shift_Del	DEL	ENST00000371122.4	hg19	CCDS14612.1																																																																																			.	.		0.348	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069	
TULP2	7288	hgsc.bcm.edu	37	19	49400644	49400644	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:49400644delC	ENST00000221399.3	-	3	186	c.42delG	c.(40-42)gggfs	p.G14fs	NUCB1_ENST00000405315.4_5'Flank|NUCB1_ENST00000407032.1_5'Flank	NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	14					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		CGAGCTCATGCCCCAGGATGC	0.597																																					p.H15fs		Atlas-INDEL	.											.	TULP2	60	.	0			c.43delC						.						134.0	94.0	107.0					19																	49400644		2203	4300	6503	SO:0001589	frameshift_variant	7288	exon3			.	U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"""cancer/testis antigen 65"""	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.42delG	chr19.hg19:g.49400644delC	ENSP00000221399:p.Gly14fs	124.0	0.0		153.0	10.0	NM_003323	Q8TC50	Frame_Shift_Del	DEL	ENST00000221399.3	hg19	CCDS12739.1																																																																																			.	.		0.597	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323	
HDDC2	51020	hgsc.bcm.edu	37	6	125621689	125621689	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:125621689delT	ENST00000398153.2	-	2	243	c.201delA	c.(199-201)aaafs	p.K67fs	HDDC2_ENST00000368377.4_Frame_Shift_Del_p.K67fs|HDDC2_ENST00000608284.1_Frame_Shift_Del_p.K67fs|HDDC2_ENST00000608295.1_Frame_Shift_Del_p.K67fs	NM_016063.2	NP_057147.2	Q7Z4H3	HDDC2_HUMAN	HD domain containing 2	67	HD.					extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|lung(4)	6			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0186)		CTTACCGGTCTTTGTTAAGAC	0.483																																					p.D68fs		Atlas-INDEL	.											.	HDDC2	21	.	0			c.202delG						.						91.0	97.0	95.0					6																	125621689		1980	4165	6145	SO:0001589	frameshift_variant	51020	exon2			.	AF151888	CCDS43503.1	6q13-q24.3	2008-02-05	2005-08-22	2005-08-22	ENSG00000111906	ENSG00000111906			21078	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 74"""	C6orf74		10810093	Standard	NM_016063		Approved	CGI-130, dJ167O5.2	uc003qaa.1	Q7Z4H3	OTTHUMG00000015506	ENST00000398153.2:c.201delA	chr6.hg19:g.125621689delT	ENSP00000381220:p.Lys67fs	154.0	0.0		178.0	11.0	NM_016063	Q5TDQ4|Q6NZ49|Q9BTT2|Q9BV31|Q9Y3D1	Frame_Shift_Del	DEL	ENST00000398153.2	hg19	CCDS43503.1																																																																																			.	.		0.483	HDDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472493.1	NM_016063	
SDCCAG3	10807	hgsc.bcm.edu	37	9	139303504	139303504	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:139303504delT	ENST00000357365.3	-	3	365	c.236delA	c.(235-237)aagfs	p.K79fs	PMPCA_ENST00000371720.1_5'Flank|SDCCAG3_ENST00000298537.7_Intron|SDCCAG3_ENST00000371725.3_Intron|PMPCA_ENST00000371717.3_5'Flank|PMPCA_ENST00000399219.3_5'Flank	NM_001039707.1	NP_001034796.1	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	79						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)		ACATTTCCCCTTTCCATAGCC	0.453																																					p.K79fs		Atlas-INDEL	.											.	SDCCAG3	41	.	0			c.237delG						.						133.0	139.0	137.0					9																	139303504		1938	4146	6084	SO:0001589	frameshift_variant	10807	exon3			.	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.236delA	chr9.hg19:g.139303504delT	ENSP00000349929:p.Lys79fs	127.0	0.0		151.0	10.0	NM_001039707	A6NCP1|O60525|Q5SXN1|Q5SXN2|Q5SXN3|Q5SXN4|Q5SXN8|Q6V704|Q9NVY5	Frame_Shift_Del	DEL	ENST00000357365.3	hg19	CCDS43904.1																																																																																			.	.		0.453	SDCCAG3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055060.2	NM_006643	
RAB6A	5870	hgsc.bcm.edu	37	11	73431914	73431914	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:73431914delT	ENST00000336083.3	-	3	615	c.160delA	c.(160-162)actfs	p.T54fs	RP11-456I15.2_ENST00000538624.1_RNA|RAB6A_ENST00000310653.6_Frame_Shift_Del_p.T54fs|RAB6A_ENST00000541588.1_Frame_Shift_Del_p.T54fs|RAB6A_ENST00000536566.1_Frame_Shift_Del_p.T21fs	NM_198896.1	NP_942599.1	P20340	RAB6A_HUMAN	RAB6A, member RAS oncogene family	54					antigen processing and presentation (GO:0019882)|early endosome to Golgi transport (GO:0034498)|GTP catabolic process (GO:0006184)|minus-end-directed organelle transport along microtubule (GO:0072385)|peptidyl-cysteine methylation (GO:0018125)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|protein domain specific binding (GO:0019904)			large_intestine(2)|lung(2)	4						AAGTACATAGTTTTTGATAAA	0.328																																					p.T54fs		Atlas-INDEL	.											.	RAB6A	17	.	0			c.161delC						.						115.0	112.0	113.0					11																	73431914		2199	4293	6492	SO:0001589	frameshift_variant	5870	exon3			.	AF130986	CCDS8223.1, CCDS8224.1, CCDS58155.1, CCDS58156.1	11q13.3	2008-08-08			ENSG00000175582	ENSG00000175582		"""RAB, member RAS oncogene"""	9786	protein-coding gene	gene with protein product		179513		RAB6			Standard	NM_001243718		Approved		uc001ouf.3	P20340	OTTHUMG00000134308	ENST00000336083.3:c.160delA	chr11.hg19:g.73431914delT	ENSP00000336850:p.Thr54fs	74.0	0.0		160.0	12.0	NM_002869	A8K133|B7Z772|F5H668|Q1W5D8|Q5U0A8|Q9UBE4	Frame_Shift_Del	DEL	ENST00000336083.3	hg19	CCDS8224.1																																																																																			.	.		0.328	RAB6A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259241.2		
REST	5978	hgsc.bcm.edu	37	4	57798156	57798156	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:57798156delA	ENST00000309042.7	+	4	3446	c.3132delA	c.(3130-3132)agafs	p.R1044fs		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	1044	Interaction with RCOR1.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|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)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					AATCTAGCAGAAAAAATGCAA	0.448																																					p.R1044fs		Atlas-INDEL	.											REST,right_lower_lobe,carcinoma,0,1	REST	104	.	0			c.3131delG						.						71.0	67.0	68.0					4																	57798156		2203	4300	6503	SO:0001589	frameshift_variant	5978	exon4			.	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.3132delA	chr4.hg19:g.57798156delA	ENSP00000311816:p.Arg1044fs	145.0	0.0		166.0	10.0	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Frame_Shift_Del	DEL	ENST00000309042.7	hg19	CCDS3509.1																																																																																			.	.		0.448	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
KIAA1919	91749	hgsc.bcm.edu	37	6	111587466	111587466	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:111587466delT	ENST00000368847.4	+	4	1054	c.701delT	c.(700-702)cttfs	p.L234fs		NM_153369.2	NP_699200.2	Q5TF39	NAGT1_HUMAN	KIAA1919	234					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			large_intestine(3)|lung(2)|ovary(4)|skin(3)	12		all_cancers(87;2.35e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.055)|all cancers(137;0.0871)|Epithelial(106;0.0884)		CTTTGTCTCCTTTTTCTGTTC	0.378																																					p.L234fs		Atlas-INDEL	.											.	KIAA1919	54	.	0			c.700delC						.						109.0	99.0	102.0					6																	111587466		2203	4300	6503	SO:0001589	frameshift_variant	91749	exon4			.	BC036115	CCDS5090.1	6q22	2013-10-02			ENSG00000173214	ENSG00000173214			21053	protein-coding gene	gene with protein product							Standard	NM_153369		Approved	MGC33953, MFSD4B	uc003puv.4	Q5TF39	OTTHUMG00000015372	ENST00000368847.4:c.701delT	chr6.hg19:g.111587466delT	ENSP00000357840:p.Leu234fs	129.0	0.0		176.0	11.0	NM_153369	A8K9M0|Q8IYB6|Q96PW9|Q9P0D6	Frame_Shift_Del	DEL	ENST00000368847.4	hg19	CCDS5090.1																																																																																			.	.		0.378	KIAA1919-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041827.1	NM_153369	
PYGM	5837	hgsc.bcm.edu	37	11	64521090	64521090	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:64521090delC	ENST00000164139.3	-	11	1702	c.1304delG	c.(1303-1305)ggcfs	p.G435fs	PYGM_ENST00000377432.3_Frame_Shift_Del_p.G347fs|PYGM_ENST00000462303.1_5'Flank	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	435					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTTCACTGCGCCCTCCTCCAC	0.662																																					p.G435fs		Atlas-INDEL	.											.	PYGM	77	.	0			c.1305delC						.						45.0	31.0	35.0					11																	64521090		2199	4295	6494	SO:0001589	frameshift_variant	5837	exon11			.		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"""Glycogen phosphorylases"""	9726	protein-coding gene	gene with protein product	"""McArdle syndrome"", ""glycogen storage disease type V"", ""glycogen phosphorylase, muscle form"""	608455	"""phosphorylase, glycogen; muscle"""				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.1304delG	chr11.hg19:g.64521090delC	ENSP00000164139:p.Gly435fs	116.0	0.0		150.0	10.0	NM_005609	A0AVK1|A6NDY6	Frame_Shift_Del	DEL	ENST00000164139.3	hg19	CCDS8079.1																																																																																			.	.		0.662	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609	
WAPAL	23063	hgsc.bcm.edu	37	10	88232474	88232474	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:88232474delA	ENST00000298767.5	-	6	2260	c.1788delT	c.(1786-1788)tttfs	p.F596fs	WAPAL_ENST00000263070.7_5'Flank	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	596	Mediates interaction with the cohesin complex.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						CAGGAGCCTTAAAAACTCCAT	0.348																																					p.K597fs		Atlas-INDEL	.											.	WAPAL	81	.	0			c.1789delA						.						123.0	110.0	114.0					10																	88232474		2203	4300	6503	SO:0001589	frameshift_variant	23063	exon6			.	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"""friend of EBNA2"""	610754	"""KIAA0261"""	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.1788delT	chr10.hg19:g.88232474delA	ENSP00000298767:p.Phe596fs	141.0	0.0		130.0	12.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Frame_Shift_Del	DEL	ENST00000298767.5	hg19	CCDS7375.1																																																																																			.	.		0.348	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045	
FGD6	55785	hgsc.bcm.edu	37	12	95501402	95501402	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:95501402delA	ENST00000343958.4	-	12	3493	c.3270delT	c.(3268-3270)tttfs	p.F1090fs	FGD6_ENST00000549499.1_Frame_Shift_Del_p.F1090fs|FGD6_ENST00000546711.1_Frame_Shift_Del_p.F1090fs	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	1090	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						CTTCTTTGAGAAAAACCTGAT	0.398																																					p.L1091fs		Atlas-INDEL	.											.	FGD6	127	.	0			c.3271delC						.						127.0	117.0	121.0					12																	95501402		2203	4300	6503	SO:0001589	frameshift_variant	55785	exon12			.	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.3270delT	chr12.hg19:g.95501402delA	ENSP00000344446:p.Phe1090fs	109.0	0.0		126.0	13.0	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Frame_Shift_Del	DEL	ENST00000343958.4	hg19	CCDS31878.1																																																																																			.	.		0.398	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351	
LRRC36	55282	hgsc.bcm.edu	37	16	67360810	67360810	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:67360810delG	ENST00000329956.6	+	1	64	c.45delG	c.(43-45)ctgfs	p.L15fs	LRRC36_ENST00000563303.1_Intron|KCTD19_ENST00000304372.5_5'Flank	NM_018296.5	NP_060766.5	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36	15										endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	24		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)		TTCGCCGCCTGGGGGCGCTGA	0.692											OREG0023877	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L15fs		Atlas-INDEL	.											.	LRRC36	68	.	0			c.44delT						.						13.0	16.0	15.0					16																	67360810		2181	4277	6458	SO:0001589	frameshift_variant	55282	exon1			.	BC026156	CCDS32467.1, CCDS58474.1	16q22.1	2008-02-05				ENSG00000159708			25615	protein-coding gene	gene with protein product						12477932	Standard	NM_001161575		Approved	FLJ11004	uc002esv.3	Q1X8D7		ENST00000329956.6:c.45delG	chr16.hg19:g.67360810delG	ENSP00000329943:p.Leu15fs	96.0	0.0	1098	109.0	11.0	NM_018296	A4FTV6|A6NDE9|A8K8E6|Q7Z5K5	Frame_Shift_Del	DEL	ENST00000329956.6	hg19	CCDS32467.1																																																																																			.	.		0.692	LRRC36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421770.1	NM_018296	
DSG3	1830	hgsc.bcm.edu	37	18	29054359	29054359	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:29054359delT	ENST00000257189.4	+	15	2460	c.2377delT	c.(2377-2379)tttfs	p.F793fs		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	793					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			GGACTCCTACTTTTCTCAGGT	0.373																																					p.Y792fs		Atlas-INDEL	.											.	DSG3	172	.	0			c.2376delC						.						129.0	135.0	133.0					18																	29054359		2203	4300	6503	SO:0001589	frameshift_variant	1830	exon15			.	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.2377delT	chr18.hg19:g.29054359delT	ENSP00000257189:p.Phe793fs	134.0	0.0		142.0	10.0	NM_001944	A8K2V2	Frame_Shift_Del	DEL	ENST00000257189.4	hg19	CCDS11898.1																																																																																			.	.		0.373	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
CHPT1	56994	hgsc.bcm.edu	37	12	102107976	102107976	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:102107976delG	ENST00000229266.3	+	2	617	c.382delG	c.(382-384)gggfs	p.G128fs	CHPT1_ENST00000550385.1_3'UTR|CHPT1_ENST00000549872.1_Frame_Shift_Del_p.G128fs	NM_020244.2	NP_064629.2	Q8WUD6	CHPT1_HUMAN	choline phosphotransferase 1	128					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	diacylglycerol binding (GO:0019992)|diacylglycerol cholinephosphotransferase activity (GO:0004142)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						TTCCCCTTTAGGGGAGCTCTT	0.383																																					p.L127fs		Atlas-INDEL	.											.	CHPT1	27	.	0			c.381delA						.						134.0	143.0	140.0					12																	102107976		2203	4300	6503	SO:0001589	frameshift_variant	56994	exon2			.		CCDS9086.1	12q	2010-07-08				ENSG00000111666	2.7.8.2		17852	protein-coding gene	gene with protein product	"""phosphatidylcholine synthesizing enzyme"""					10893425	Standard	NM_020244		Approved	CPT1	uc001tin.3	Q8WUD6		ENST00000229266.3:c.382delG	chr12.hg19:g.102107976delG	ENSP00000229266:p.Gly128fs	125.0	0.0		175.0	11.0	NM_020244	B3KQM2|Q7Z7H0|Q7Z7H1|Q7Z7H2|Q8IWQ4|Q8IWQ5|Q8WYI4|Q9NRQ6|Q9NRQ7|Q9Y6M6	Frame_Shift_Del	DEL	ENST00000229266.3	hg19	CCDS9086.1																																																																																			.	.		0.383	CHPT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409173.1	NM_020244	
CARD9	64170	hgsc.bcm.edu	37	9	139266450	139266450	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:139266450delG	ENST00000371732.5	-	2	246	c.81delC	c.(79-81)cccfs	p.P27fs	CARD9_ENST00000315908.7_Frame_Shift_Del_p.P27fs|CARD9_ENST00000371734.3_Frame_Shift_Del_p.P27fs	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	27	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)	p.P27P(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		TGATGCGTGAGGGGTCGATGA	0.622																																					p.S28fs		Atlas-INDEL	.											.	CARD9	47	.	1	Substitution - coding silent(1)	kidney(1)	c.82delT						.						155.0	118.0	130.0					9																	139266450		2203	4300	6503	SO:0001589	frameshift_variant	64170	exon2			.	AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925	ENST00000371732.5:c.81delC	chr9.hg19:g.139266450delG	ENSP00000360797:p.Pro27fs	146.0	0.0		174.0	11.0	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Frame_Shift_Del	DEL	ENST00000371732.5	hg19	CCDS6997.1																																																																																			.	.		0.622	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
DOCK7	85440	hgsc.bcm.edu	37	1	63114152	63114152	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:63114152delT	ENST00000340370.5	-	5	470	c.453delA	c.(451-453)aaafs	p.K151fs	DOCK7_ENST00000404627.2_Frame_Shift_Del_p.K151fs|DOCK7_ENST00000251157.5_Frame_Shift_Del_p.K151fs	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	151					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						TTGGCAAACCTTTTTGCCTTT	0.289																																					p.G152fs		Atlas-INDEL	.											.	DOCK7	184	.	0			c.454delG						.						40.0	33.0	35.0					1																	63114152		2196	4290	6486	SO:0001589	frameshift_variant	85440	exon5			.		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.453delA	chr1.hg19:g.63114152delT	ENSP00000340742:p.Lys151fs	145.0	0.0		160.0	10.0	NM_001272002	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Frame_Shift_Del	DEL	ENST00000340370.5	hg19	CCDS30734.1																																																																																			.	.		0.289	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
DDX18	8886	hgsc.bcm.edu	37	2	118579744	118579744	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:118579744delA	ENST00000263239.2	+	7	1101	c.973delA	c.(973-975)aaafs	p.K325fs	DDX18_ENST00000474694.1_3'UTR	NM_006773.3	NP_006764.3	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	325	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ATTTATGTATAAAAACCTGCA	0.348																																					p.Y324X		Atlas-INDEL	.											.	DDX18	79	.	0			c.972delT						.						129.0	125.0	126.0					2																	118579744		2203	4300	6503	SO:0001589	frameshift_variant	8886	exon7			.	X98743	CCDS2120.1	2q21.2	2008-02-05	2003-06-13		ENSG00000088205	ENSG00000088205		"""DEAD-boxes"""	2741	protein-coding gene	gene with protein product		606355	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 18 (Myc-regulated)"""			8861962	Standard	NM_006773		Approved	MrDb	uc002tlh.1	Q9NVP1	OTTHUMG00000058521	ENST00000263239.2:c.973delA	chr2.hg19:g.118579744delA	ENSP00000263239:p.Lys325fs	177.0	0.0		229.0	14.0	NM_006773	Q6GTZ9|Q6IAU4|Q92732|Q9BQB7	Frame_Shift_Del	DEL	ENST00000263239.2	hg19	CCDS2120.1																																																																																			.	.		0.348	DDX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129632.3	NM_006773	
ARHGAP11A	9824	hgsc.bcm.edu	37	15	32929175	32929176	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:32929175_32929176delAT	ENST00000361627.3	+	12	2923_2924	c.2201_2202delAT	c.(2200-2202)aatfs	p.N735fs	ARHGAP11A_ENST00000543522.1_Frame_Shift_Del_p.N546fs|ARHGAP11A_ENST00000565905.1_Frame_Shift_Del_p.N546fs	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	735					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		GATAAACTAAATAATAAATTAA	0.356																																					p.734_734del	Colon(45;757 1134 30003 36652)	Atlas-INDEL	.											.	ARHGAP11A	84	.	0			c.2200_2201del						.																																			SO:0001589	frameshift_variant	9824	exon12			.	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"""Rho GTPase activating proteins"""	15783	protein-coding gene	gene with protein product	"""GAP (1-12)"""	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.2201_2202delAT	chr15.hg19:g.32929175_32929176delAT	ENSP00000355090:p.Asn735fs	47.0	0.0		63.0	11.0	NM_014783	B4DZN9|Q6PI96|Q9Y3S6	Frame_Shift_Del	DEL	ENST00000361627.3	hg19	CCDS10028.1																																																																																			.	.		0.356	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783	
SLC28A1	9154	hgsc.bcm.edu	37	15	85431063	85431063	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:85431063delG	ENST00000286749.3	+	2	162	c.72delG	c.(70-72)atgfs	p.M24fs	SLC28A1_ENST00000338602.2_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000538177.1_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000394573.1_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000537703.1_5'UTR|SLC28A1_ENST00000537624.1_Frame_Shift_Del_p.M24fs|SLC28A1_ENST00000537216.1_Frame_Shift_Del_p.M24fs			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	24					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	TGGAGAACATGGGGGCTGATT	0.567																																					p.M24fs		Atlas-INDEL	.											.	SLC28A1	118	.	0			c.71delT						.						172.0	155.0	161.0					15																	85431063		2203	4299	6502	SO:0001589	frameshift_variant	9154	exon3			.	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.72delG	chr15.hg19:g.85431063delG	ENSP00000286749:p.Met24fs	161.0	0.0		190.0	12.0	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Frame_Shift_Del	DEL	ENST00000286749.3	hg19	CCDS10334.1																																																																																			.	.		0.567	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
LMNB2	84823	hgsc.bcm.edu	37	19	2432473	2432473	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:2432473delC	ENST00000582871.1	-	9	1557	c.1471delG	c.(1471-1473)gagfs	p.E492fs	LMNB2_ENST00000325327.3_Frame_Shift_Del_p.E512fs|LMNB2_ENST00000475819.1_5'Flank	NM_032737.3	NP_116126.3	Q03252	LMNB2_HUMAN	lamin B2	492	LTD.|Tail.					lamin filament (GO:0005638)|nuclear inner membrane (GO:0005637)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		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)		GCGATCTCCTCCCCCTCCAAG	0.632																																					p.E511fs		Atlas-INDEL	.											.	LMNB2	40	.	0			c.1532delA						.						309.0	228.0	255.0					19																	2432473		2203	4300	6503	SO:0001589	frameshift_variant	84823	exon9			.	M94362	CCDS12090.1, CCDS12090.2	19p13.3	2013-01-16			ENSG00000176619	ENSG00000176619		"""Intermediate filaments type V, lamins"""	6638	protein-coding gene	gene with protein product		150341		LMN2		1630457	Standard	NM_032737		Approved		uc002lvy.4	Q03252	OTTHUMG00000150626	ENST00000582871.1:c.1471delG	chr19.hg19:g.2432473delC	ENSP00000462730:p.Glu492fs	124.0	0.0		165.0	10.0	NM_032737	O75292|Q14734|Q96DF6	Frame_Shift_Del	DEL	ENST00000582871.1	hg19																																																																																				.	.		0.632	LMNB2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032737	
ANO2	57101	hgsc.bcm.edu	37	12	5721863	5721863	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:5721863delC	ENST00000356134.5	-	21	2120	c.2049delG	c.(2047-2049)gggfs	p.G683fs	ANO2_ENST00000546188.1_Frame_Shift_Del_p.G683fs|ANO2_ENST00000327087.8_Frame_Shift_Del_p.G682fs	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	687					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						TCAACTGCTTCCCCAACATGA	0.507																																					p.K683fs		Atlas-INDEL	.											.	ANO2	309	.	0			c.2047delA						.						76.0	77.0	77.0					12																	5721863		1942	4156	6098	SO:0001589	frameshift_variant	57101	exon20			.	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.2049delG	chr12.hg19:g.5721863delC	ENSP00000348453:p.Gly683fs	114.0	0.0		161.0	11.0	NM_020373	C4N787|Q9H847	Frame_Shift_Del	DEL	ENST00000356134.5	hg19																																																																																				.	.		0.507	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373	
SLC16A5	9121	hgsc.bcm.edu	37	17	73094135	73094135	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:73094135delC	ENST00000450736.2	+	3	617	c.202delC	c.(202-204)cccfs	p.P68fs	SLC16A5_ENST00000538213.2_Frame_Shift_Del_p.P108fs|SLC16A5_ENST00000580123.1_Frame_Shift_Del_p.P68fs|SLC16A5_ENST00000329783.4_Frame_Shift_Del_p.P68fs|SLC16A5_ENST00000585293.1_3'UTR			O15375	MOT6_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 5	68					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	all_lung(278;0.226)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Pyruvic acid(DB00119)	TCCCACAGGGCCCCTGTGCAG	0.652																																					p.G67fs		Atlas-INDEL	.											.	SLC16A5	80	.	0			c.201delG						.						50.0	50.0	50.0					17																	73094135		2203	4300	6503	SO:0001589	frameshift_variant	9121	exon4			.	U59299	CCDS11713.1	17q25.1	2013-07-18	2013-07-18		ENSG00000170190	ENSG00000170190		"""Solute carriers"""	10926	protein-coding gene	gene with protein product		603879	"""solute carrier family 16 (monocarboxylic acid transporters), member 5"", ""solute carrier family 16, member 5 (monocarboxylic acid transporter 6)"""			9425115	Standard	NM_004695		Approved	MCT5, MCT6	uc002jmr.4	O15375	OTTHUMG00000179277	ENST00000450736.2:c.202delC	chr17.hg19:g.73094135delC	ENSP00000390564:p.Pro68fs	147.0	0.0		225.0	15.0	NM_001271765	B4E288	Frame_Shift_Del	DEL	ENST00000450736.2	hg19	CCDS11713.1																																																																																			.	.		0.652	SLC16A5-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445547.1	NM_004695	
ITFG1	81533	hgsc.bcm.edu	37	16	47347686	47347686	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:47347686delT	ENST00000320640.6	-	9	1079	c.851delA	c.(850-852)aatfs	p.N284fs	Y_RNA_ENST00000410835.1_RNA|RP11-474B12.1_ENST00000564739.1_RNA|ITFG1_ENST00000544001.2_Frame_Shift_Del_p.N171fs|ITFG1_ENST00000568047.1_5'Flank	NM_030790.3	NP_110417.2	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1	284						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	19		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)				CTTTTGGCAATTTTTATCTTC	0.338																																					p.N284fs		Atlas-INDEL	.											.	ITFG1	49	.	0			c.852delT						.						114.0	101.0	106.0					16																	47347686		2202	4300	6502	SO:0001589	frameshift_variant	81533	exon9			.	AF503339	CCDS10728.1	16q12.1	2008-02-05			ENSG00000129636	ENSG00000129636			30697	protein-coding gene	gene with protein product	"""T cell immunomodulatory protein"""	611803				12598909	Standard	NM_030790		Approved	CDA08, TIP	uc002eet.3	Q8TB96	OTTHUMG00000133103	ENST00000320640.6:c.851delA	chr16.hg19:g.47347686delT	ENSP00000319918:p.Asn284fs	93.0	0.0		146.0	10.0	NM_030790	Q96SR4|Q9BRE2|Q9H2V9	Frame_Shift_Del	DEL	ENST00000320640.6	hg19	CCDS10728.1																																																																																			.	.		0.338	ITFG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256768.3	NM_030790	
RGL3	57139	hgsc.bcm.edu	37	19	11526663	11526663	+	Frame_Shift_Del	DEL	A	A	-	rs151155820	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:11526663delA	ENST00000380456.3	-	5	650	c.587delT	c.(586-588)ttgfs	p.L196fs	RGL3_ENST00000393423.3_Frame_Shift_Del_p.L196fs	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	196	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						AGCCTCCTCCAAAAAATCTTC	0.582																																					p.L196fs	GBM(174;751 2067 17998 27979 33959)	Atlas-INDEL	.											.	RGL3	100	.	0			c.588delG						.						130.0	145.0	140.0					19																	11526663		2203	4300	6503	SO:0001589	frameshift_variant	57139	exon5			.	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.587delT	chr19.hg19:g.11526663delA	ENSP00000369823:p.Leu196fs	118.0	0.0		155.0	11.0	NM_001035223	B5ME84|B7ZL22|Q0P6G0	Frame_Shift_Del	DEL	ENST00000380456.3	hg19	CCDS32910.1																																																																																			.	.		0.582	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867	
ANXA13	312	hgsc.bcm.edu	37	8	124748069	124748069	+	Intron	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:124748069delC	ENST00000419625.1	-	1	88				ANXA13_ENST00000262219.6_Frame_Shift_Del_p.D22fs	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13						cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			GGTTGGGAGTCCCCTTTAGGC	0.512																																					p.D22fs		Atlas-INDEL	.											.	ANXA13	38	.	0			c.65delA						.						140.0	140.0	140.0					8																	124748069		2203	4300	6503	SO:0001627	intron_variant	312	exon2			.	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"""Annexins"""	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.15+1490G>-	chr8.hg19:g.124748069delC		147.0	0.0		142.0	11.0	NM_001003954	Q9BQR5	Frame_Shift_Del	DEL	ENST00000419625.1	hg19	CCDS47917.1																																																																																			.	.		0.512	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306	
MICALL1	85377	hgsc.bcm.edu	37	22	38321985	38321985	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:38321985delC	ENST00000215957.6	+	8	1526	c.1400delC	c.(1399-1401)accfs	p.T467fs		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	467	Pro-rich.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					TACGGCATCACCCCTACCAGC	0.682																																					p.T467fs		Atlas-INDEL	.											.	MICALL1	53	.	0			c.1399delA						.						31.0	37.0	35.0					22																	38321985		2202	4299	6501	SO:0001589	frameshift_variant	85377	exon8			.	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"""molecule interacting with Rab13"""					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.1400delC	chr22.hg19:g.38321985delC	ENSP00000215957:p.Thr467fs	212.0	0.0		237.0	16.0	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Frame_Shift_Del	DEL	ENST00000215957.6	hg19	CCDS13961.1																																																																																			.	.		0.682	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386	
OSBPL8	114882	hgsc.bcm.edu	37	12	76780366	76780366	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:76780366delT	ENST00000261183.3	-	13	1906	c.1427delA	c.(1426-1428)aagfs	p.K476fs	OSBPL8_ENST00000393250.4_Frame_Shift_Del_p.K434fs|OSBPL8_ENST00000393249.2_Frame_Shift_Del_p.K434fs	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	476					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						TACCTTTGGCTTTTTATAGAA	0.279																																					p.K476fs		Atlas-INDEL	.											.	OSBPL8	86	.	0			c.1428delG						.						55.0	62.0	59.0					12																	76780366		2200	4278	6478	SO:0001589	frameshift_variant	114882	exon13			.	AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16396	protein-coding gene	gene with protein product		606736				1735225, 17991739	Standard	NM_020841		Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.1427delA	chr12.hg19:g.76780366delT	ENSP00000261183:p.Lys476fs	143.0	0.0		229.0	16.0	NM_020841	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	Frame_Shift_Del	DEL	ENST00000261183.3	hg19	CCDS31862.1																																																																																			.	.		0.279	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406357.1	NM_020841	
NCSTN	23385	hgsc.bcm.edu	37	1	160318871	160318871	+	Frame_Shift_Del	DEL	C	C	-	rs200450922		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:160318871delC	ENST00000294785.5	+	3	398	c.273delC	c.(271-273)aacfs	p.N91fs	NCSTN_ENST00000392212.4_Frame_Shift_Del_p.N71fs|NCSTN_ENST00000535857.1_Frame_Shift_Del_p.N91fs|NCSTN_ENST00000368063.1_Frame_Shift_Del_p.N71fs|NCSTN_ENST00000368065.4_5'Flank	NM_015331.2	NP_056146.1	Q92542	NICA_HUMAN	nicastrin	91					amyloid precursor protein catabolic process (GO:0042987)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)|proteolysis (GO:0006508)|T cell proliferation (GO:0042098)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(2)	34	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			ATGGCCCCAACCCCCCTTACA	0.478																																					p.N91fs		Atlas-INDEL	.											.	NCSTN	64	.	0			c.272delA						.																																			SO:0001589	frameshift_variant	23385	exon3			.	AF240468	CCDS1203.1	1q22-q23	2014-09-17			ENSG00000162736	ENSG00000162736			17091	protein-coding gene	gene with protein product		605254				9039502, 10993067	Standard	XM_005245053		Approved	KIAA0253, APH2	uc001fvx.3	Q92542	OTTHUMG00000033110	ENST00000294785.5:c.273delC	chr1.hg19:g.160318871delC	ENSP00000294785:p.Asn91fs	145.0	0.0		268.0	17.0	NM_015331	Q5T207|Q5T208|Q86VV5	Frame_Shift_Del	DEL	ENST00000294785.5	hg19	CCDS1203.1																																																																																			.	.		0.478	NCSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080622.1	NM_015331	
ARMC9	80210	hgsc.bcm.edu	37	2	232123766	232123766	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:232123766delT	ENST00000349938.4	+	11	1171	c.977delT	c.(976-978)attfs	p.I326fs	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	326						extracellular vesicular exosome (GO:0070062)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		AAGGATTTGATTTTGGGGAGT	0.438																																					p.I326fs		Atlas-INDEL	.											.	ARMC9	129	.	0			c.976delA						.						144.0	134.0	138.0					2																	232123766		2203	4300	6503	SO:0001589	frameshift_variant	80210	exon11			.	BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931		"""Armadillo repeat containing"""	20730	protein-coding gene	gene with protein product						11347906	Standard	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.977delT	chr2.hg19:g.232123766delT	ENSP00000258417:p.Ile326fs	157.0	0.0		185.0	13.0	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Frame_Shift_Del	DEL	ENST00000349938.4	hg19	CCDS2484.1																																																																																			.	.		0.438	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139	
HEATR3	55027	hgsc.bcm.edu	37	16	50106592	50106592	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:50106592delT	ENST00000299192.7	+	5	780	c.589delT	c.(589-591)tttfs	p.F197fs	HEATR3_ENST00000285767.4_Frame_Shift_Del_p.F111fs	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	197				F -> L (in Ref. 1; AAP97710). {ECO:0000305}.						cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						TTTAAGTAGGTTTCCTACCAA	0.343																																					p.R196fs		Atlas-INDEL	.											.	HEATR3	59	.	0			c.588delG						.						193.0	180.0	184.0					16																	50106592		2198	4300	6498	SO:0001589	frameshift_variant	55027	exon5			.	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.589delT	chr16.hg19:g.50106592delT	ENSP00000299192:p.Phe197fs	157.0	0.0		153.0	11.0	NM_182922	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Frame_Shift_Del	DEL	ENST00000299192.7	hg19	CCDS10739.1																																																																																			.	.		0.343	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922	
EIF4G3	8672	hgsc.bcm.edu	37	1	21181509	21181509	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:21181509delC	ENST00000264211.8	-	20	3421	c.3227delG	c.(3226-3228)ggafs	p.G1076fs	EIF4G3_ENST00000374935.3_Frame_Shift_Del_p.G796fs|EIF4G3_ENST00000374937.3_Frame_Shift_Del_p.G1082fs|EIF4G3_ENST00000400422.1_Frame_Shift_Del_p.G1076fs|EIF4G3_ENST00000602326.1_Frame_Shift_Del_p.G1082fs|EIF4G3_ENST00000536266.1_Frame_Shift_Del_p.G680fs|EIF4G3_ENST00000537738.1_Frame_Shift_Del_p.G566fs	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	1076					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	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)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		GCTGCCTTTTCCCCAGCTGCC	0.458																																					p.G1112fs		Atlas-INDEL	.											.	EIF4G3	300	.	0			c.3336delA						.						233.0	195.0	208.0					1																	21181509		2203	4300	6503	SO:0001589	frameshift_variant	8672	exon24			.	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.3227delG	chr1.hg19:g.21181509delC	ENSP00000264211:p.Gly1076fs	90.0	0.0		103.0	10.0	NM_001198801	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Frame_Shift_Del	DEL	ENST00000264211.8	hg19	CCDS214.1																																																																																			.	.		0.458	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760	
IAH1	285148	hgsc.bcm.edu	37	2	9628363	9628363	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:9628363delA	ENST00000497473.1	+	6	689	c.652delA	c.(652-654)aaafs	p.K219fs	IAH1_ENST00000470914.1_Frame_Shift_Del_p.K106fs|IAH1_ENST00000545602.1_Frame_Shift_Del_p.K106fs|IAH1_ENST00000482918.1_Frame_Shift_Del_p.K106fs|IAH1_ENST00000489468.1_3'UTR	NM_001039613.1	NP_001034702.1	Q2TAA2	IAH1_HUMAN	isoamyl acetate-hydrolyzing esterase 1 homolog (S. cerevisiae)	219					lipid catabolic process (GO:0016042)	extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on ester bonds (GO:0016788)			breast(1)|large_intestine(2)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTTGATAGAGAAAAAGGTCTC	0.433																																					p.E217fs		Atlas-INDEL	.											.	IAH1	12	.	0			c.651delG						.						146.0	132.0	136.0					2																	9628363		1867	4112	5979	SO:0001589	frameshift_variant	285148	exon6			.	BC111025	CCDS42651.1	2p25.1	2010-08-05			ENSG00000134330	ENSG00000134330			27696	protein-coding gene	gene with protein product						12477932	Standard	XR_426950		Approved		uc002qzr.3	Q2TAA2	OTTHUMG00000159076	ENST00000497473.1:c.652delA	chr2.hg19:g.9628363delA	ENSP00000417580:p.Lys219fs	152.0	0.0		159.0	10.0	NM_001039613	B4DMV3	Frame_Shift_Del	DEL	ENST00000497473.1	hg19	CCDS42651.1																																																																																			.	.		0.433	IAH1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353192.1	NM_001039613	
BMPR2	659	hgsc.bcm.edu	37	2	203407121	203407121	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:203407121delG	ENST00000374580.4	+	10	1903	c.1364delG	c.(1363-1365)aggfs	p.R455fs	BMPR2_ENST00000374574.2_Frame_Shift_Del_p.R455fs	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	455	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						CTCGTGTCTAGGGAAAAACAG	0.418																																					p.R455fs		Atlas-INDEL	.											.	BMPR2	142	.	0			c.1363delA						.						51.0	50.0	50.0					2																	203407121		2203	4300	6503	SO:0001589	frameshift_variant	659	exon10			.	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"""primary pulmonary hypertension 1"""	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.1364delG	chr2.hg19:g.203407121delG	ENSP00000363708:p.Arg455fs	138.0	0.0		162.0	10.0	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Frame_Shift_Del	DEL	ENST00000374580.4	hg19	CCDS33361.1																																																																																			.	.		0.418	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204	
SYT14	255928	hgsc.bcm.edu	37	1	210329212	210329212	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:210329212delA	ENST00000472886.1	+	7	1325	c.1311delA	c.(1309-1311)atafs	p.I437fs	SYT14_ENST00000534859.1_Frame_Shift_Del_p.I437fs|SYT14_ENST00000367015.1_Frame_Shift_Del_p.I399fs|SYT14_ENST00000399639.2_Frame_Shift_Del_p.I437fs|SYT14_ENST00000271745.7_3'UTR|SYT14_ENST00000537238.1_Frame_Shift_Del_p.I399fs|SYT14_ENST00000422431.1_Frame_Shift_Del_p.I482fs|SYT14_ENST00000367019.1_Frame_Shift_Del_p.I437fs			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	437	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cell death (GO:0008219)	integral component of membrane (GO:0016021)	phospholipid binding (GO:0005543)			endometrium(4)|large_intestine(11)|lung(17)|ovary(1)|prostate(1)|skin(3)	37				OV - Ovarian serous cystadenocarcinoma(81;0.085)		CAGAAGTGATAAAAGGCAGCC	0.393																																					p.I482fs		Atlas-INDEL	.											.	SYT14	89	.	0			c.1445delT						.						69.0	68.0	68.0					1																	210329212		2203	4300	6503	SO:0001589	frameshift_variant	255928	exon8			.	AK091517	CCDS31014.1, CCDS53470.1, CCDS58058.1	1q32.2	2013-01-21			ENSG00000143469	ENSG00000143469		"""Synaptotagmins"""	23143	protein-coding gene	gene with protein product		610949					Standard	NM_001256006		Approved	sytXIV, FLJ34198	uc001hhs.5	Q8NB59	OTTHUMG00000036652	ENST00000472886.1:c.1311delA	chr1.hg19:g.210329212delA	ENSP00000418901:p.Ile437fs	132.0	0.0		253.0	16.0	NM_001146264	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Frame_Shift_Del	DEL	ENST00000472886.1	hg19	CCDS31014.1																																																																																			.	.		0.393	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262	
MCM3	4172	hgsc.bcm.edu	37	6	52147525	52147525	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:52147525delT	ENST00000229854.7	-	3	402	c.326delA	c.(325-327)aagfs	p.K109fs	MCM3_ENST00000596288.1_Frame_Shift_Del_p.K154fs|MCM3_ENST00000419835.2_Frame_Shift_Del_p.K63fs			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	109					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					GGAGACGTGCTTGGAGCCAAA	0.532																																					p.K154fs		Atlas-INDEL	.											.	MCM3	63	.	0			c.462delG						.						97.0	97.0	97.0					6																	52147525		2203	4300	6503	SO:0001589	frameshift_variant	4172	exon3			.	X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"""minichromosome maintenance deficient (S. cerevisiae) 3"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"""			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.326delA	chr6.hg19:g.52147525delT	ENSP00000229854:p.Lys109fs	132.0	0.0		162.0	10.0	NM_002388	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Frame_Shift_Del	DEL	ENST00000229854.7	hg19																																																																																				.	.		0.532	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1		
PTPRT	11122	hgsc.bcm.edu	37	20	41306553	41306553	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:41306553delC	ENST00000373187.1	-	7	1105	c.1106delG	c.(1105-1107)ggtfs	p.G369fs	PTPRT_ENST00000373190.1_Frame_Shift_Del_p.G369fs|PTPRT_ENST00000373193.3_Frame_Shift_Del_p.G369fs|PTPRT_ENST00000373184.1_Frame_Shift_Del_p.G369fs|PTPRT_ENST00000356100.2_Frame_Shift_Del_p.G369fs|PTPRT_ENST00000373201.1_Frame_Shift_Del_p.G369fs|PTPRT_ENST00000373198.4_Frame_Shift_Del_p.G369fs			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	369	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				CGGTCCCGTACCCCCCTCACC	0.547																																					p.G369fs		Atlas-INDEL	.											.	PTPRT	372	.	0			c.1107delT						.						96.0	96.0	96.0					20																	41306553		1937	4139	6076	SO:0001589	frameshift_variant	11122	exon7			.	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1106delG	chr20.hg19:g.41306553delC	ENSP00000362283:p.Gly369fs	125.0	0.0		177.0	12.0	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Frame_Shift_Del	DEL	ENST00000373187.1	hg19	CCDS42874.1																																																																																			.	.		0.547	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1		
UST	10090	hgsc.bcm.edu	37	6	149340329	149340329	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:149340329delT	ENST00000367463.4	+	6	839	c.736delT	c.(736-738)tttfs	p.F246fs		NM_005715.2	NP_005706.1	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase	246					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(2)	12		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		CCCCAGGTTATTTTACATCAT	0.463																																					p.L245fs		Atlas-INDEL	.											.	UST	42	.	0			c.735delA						.						179.0	169.0	172.0					6																	149340329		2203	4300	6503	SO:0001589	frameshift_variant	10090	exon6			.	AB020316	CCDS5213.1	6q25.1	2008-02-05			ENSG00000111962	ENSG00000111962		"""Sulfotransferases, membrane-bound"""	17223	protein-coding gene	gene with protein product		610752				10187838	Standard	NM_005715		Approved	2OST	uc003qmg.3	Q9Y2C2	OTTHUMG00000016135	ENST00000367463.4:c.736delT	chr6.hg19:g.149340329delT	ENSP00000356433:p.Phe246fs	125.0	0.0		174.0	11.0	NM_005715	B2RCX6	Frame_Shift_Del	DEL	ENST00000367463.4	hg19	CCDS5213.1																																																																																			.	.		0.463	UST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043363.1	NM_005715	
NRXN2	9379	hgsc.bcm.edu	37	11	64375286	64375286	+	Frame_Shift_Del	DEL	G	G	-	rs369377520		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:64375286delG	ENST00000377551.1	-	22	4732	c.4521delC	c.(4519-4521)cccfs	p.P1507fs	NRXN2_ENST00000409571.1_Frame_Shift_Del_p.P1500fs|NRXN2_ENST00000377559.3_Frame_Shift_Del_p.P1437fs|NRXN2_ENST00000301894.2_Frame_Shift_Del_p.P461fs|NRXN2_ENST00000265459.6_Frame_Shift_Del_p.P1507fs			Q9P2S2	NRX2A_HUMAN	neurexin 2	1507					adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)	p.T1508fs*82(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						CGTCGTCCGTGGGGGGGAGGC	0.697																																					p.T1508fs		Atlas-INDEL	.											.,3	NRXN2	247	.	1	Insertion - Frameshift(1)	ovary(1)	c.4522delA						.						37.0	33.0	34.0					11																	64375286		2190	4293	6483	SO:0001589	frameshift_variant	9379	exon23			.		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"""neurexin II"""	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.4521delC	chr11.hg19:g.64375286delG	ENSP00000366774:p.Pro1507fs	102.0	0.0		145.0	12.0	NM_015080	A7E2C1|Q9Y2D6	Frame_Shift_Del	DEL	ENST00000377551.1	hg19	CCDS8077.1																																																																																			.	.		0.697	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080	
KRTAP25-1	100131902	hgsc.bcm.edu	37	21	31661691	31661691	+	Frame_Shift_Del	DEL	A	A	-	rs8127420	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:31661691delA	ENST00000416044.1	-	1	141	c.118delT	c.(118-120)tccfs	p.S40fs		NM_001128598.1	NP_001122070.1	Q3LHN0	KR251_HUMAN	keratin associated protein 25-1	40			S -> P (in dbSNP:rs8127420).			intermediate filament (GO:0005882)				breast(1)	1						CAGGTCCTGGACACAAAATTC	0.403																																					p.S40fs		Atlas-INDEL	.											.	KRTAP25-1	13	.	0			c.119delC						.						131.0	124.0	126.0					21																	31661691		692	1591	2283	SO:0001589	frameshift_variant	100131902	exon1			.		CCDS46640.1	21q22.1	2010-10-18	2008-02-26	2008-04-22	ENSG00000232263	ENSG00000232263		"""Keratin associated proteins"""	34003	protein-coding gene	gene with protein product							Standard	NM_001128598		Approved	KAP25.1	uc010glr.1	Q3LHN0	OTTHUMG00000125482	ENST00000416044.1:c.118delT	chr21.hg19:g.31661691delA	ENSP00000398619:p.Ser40fs	183.0	0.0		154.0	12.0	NM_001128598		Frame_Shift_Del	DEL	ENST00000416044.1	hg19	CCDS46640.1																																																																																			.	.		0.403	KRTAP25-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246805.1	NM_001128598	
NEXN	91624	hgsc.bcm.edu	37	1	78408251	78408251	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:78408251delA	ENST00000334785.7	+	13	1949	c.1765delA	c.(1765-1767)aaafs	p.K589fs	NEXN_ENST00000457030.1_Frame_Shift_Del_p.K575fs|NEXN_ENST00000480732.2_3'UTR|NEXN_ENST00000330010.8_Frame_Shift_Del_p.K525fs|FUBP1_ENST00000489495.1_5'Flank	NM_144573.3	NP_653174.3			nexilin (F actin binding protein)											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				Colorectal(170;0.114)		GAAGCCTCTTAAAAACACATC	0.438																																					p.L588fs		Atlas-INDEL	.											.	NEXN	77	.	0			c.1764delT						.						100.0	98.0	99.0					1																	78408251		1893	4103	5996	SO:0001589	frameshift_variant	91624	exon13			.	AK057954	CCDS41351.1, CCDS53335.1	1p31.1	2014-09-17			ENSG00000162614	ENSG00000162614		"""Immunoglobulin superfamily / I-set domain containing"""	29557	protein-coding gene	gene with protein product		613121				12053183, 8227983	Standard	NM_144573		Approved	nexilin, NELIN	uc001dic.4	Q0ZGT2	OTTHUMG00000040533	ENST00000334785.7:c.1765delA	chr1.hg19:g.78408251delA	ENSP00000333938:p.Lys589fs	120.0	0.0		138.0	10.0	NM_144573		Frame_Shift_Del	DEL	ENST00000334785.7	hg19	CCDS41351.1																																																																																			.	.		0.438	NEXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097549.1	NM_144573	
CRISP2	7180	hgsc.bcm.edu	37	6	49660494	49660494	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:49660494delT	ENST00000339139.4	-	10	960	c.724delA	c.(724-726)attfs	p.I242fs		NM_001142407.2|NM_001142408.2|NM_001142417.2|NM_001142435.2|NM_001261822.1|NM_003296.3	NP_001135879.1|NP_001135880.1|NP_001135889.1|NP_001135907.1|NP_001248751.1|NP_003287.1	P16562	CRIS2_HUMAN	cysteine-rich secretory protein 2	242					single organismal cell-cell adhesion (GO:0016337)	extracellular space (GO:0005615)				kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	19	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			AATCAGTAAATTTTGTTCTCA	0.398																																					p.I242fs		Atlas-INDEL	.											.	CRISP2	53	.	0			c.725delT						.						167.0	146.0	153.0					6																	49660494		2203	4300	6503	SO:0001589	frameshift_variant	7180	exon10			.	X95239	CCDS4928.1	6p12.3	2009-03-12	2003-09-03	2003-09-05	ENSG00000124490	ENSG00000124490			12024	protein-coding gene	gene with protein product	"""cancer/testis antigen 36"""	187430	"""testis specific protein 1 (probe H4-1 p3-1)"""	GAPDL5, TPX1		2613236, 8665901	Standard	NM_003296		Approved	CRISP-2, CT36	uc003ozo.3	P16562	OTTHUMG00000014822	ENST00000339139.4:c.724delA	chr6.hg19:g.49660494delT	ENSP00000339155:p.Ile242fs	97.0	0.0		136.0	10.0	NM_001142408	A8K8M0|Q53FF2|Q5U8Z9|Q7Z7B2	Frame_Shift_Del	DEL	ENST00000339139.4	hg19	CCDS4928.1																																																																																			.	.		0.398	CRISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040870.2	NM_003296	
FBXO4	26272	hgsc.bcm.edu	37	5	41927229	41927229	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:41927229delT	ENST00000281623.3	+	2	360	c.304delT	c.(304-306)tttfs	p.F102fs	FBXO4_ENST00000296812.2_Frame_Shift_Del_p.F102fs|FBXO4_ENST00000509134.1_Frame_Shift_Del_p.F102fs	NM_012176.2	NP_036308.1	Q9UKT5	FBX4_HUMAN	F-box protein 4	102	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|telomere maintenance (GO:0000723)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(11)|prostate(1)|stomach(1)|urinary_tract(2)	27		Lung NSC(810;4.15e-05)|Breast(839;0.00093)|Ovarian(839;0.00965)|Myeloproliferative disorder(839;0.0255)|all_neural(839;0.0604)				GTGGAGATACTTTTTGTTGAG	0.378																																					p.Y101fs		Atlas-INDEL	.											.	FBXO4	42	.	0			c.303delC						.						183.0	180.0	181.0					5																	41927229		2203	4300	6503	SO:0001589	frameshift_variant	26272	exon2			.	AF129534	CCDS3938.1, CCDS3939.1, CCDS75238.1	5p12	2008-02-05	2004-06-15		ENSG00000151876	ENSG00000151876		"""F-boxes /  ""other"""""	13583	protein-coding gene	gene with protein product		609090	"""F-box only protein 4"""			10531035, 10531037	Standard	NM_033484		Approved	FBX4	uc003jmq.3	Q9UKT5	OTTHUMG00000094799	ENST00000281623.3:c.304delT	chr5.hg19:g.41927229delT	ENSP00000281623:p.Phe102fs	134.0	0.0		192.0	12.0	NM_033484	Q68CU8|Q86VT8|Q9UK98	Frame_Shift_Del	DEL	ENST00000281623.3	hg19	CCDS3938.1																																																																																			.	.		0.378	FBXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211614.1		
ATAD3A	55210	hgsc.bcm.edu	37	1	1463179	1463179	+	Frame_Shift_Del	DEL	G	G	-	rs200868669		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:1463179delG	ENST00000378755.5	+	14	1680	c.1586delG	c.(1585-1587)cggfs	p.R529fs	ATAD3A_ENST00000378756.3_Frame_Shift_Del_p.R481fs|ATAD3A_ENST00000536055.1_Frame_Shift_Del_p.R402fs	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	529					cell growth (GO:0016049)|negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		CAGGAGGAACGGGAGCGCCTG	0.582																																					p.R529fs		Atlas-INDEL	.											.	ATAD3A	35	.	0			c.1585delC						.						110.0	114.0	112.0					1																	1463179		2203	4300	6503	SO:0001589	frameshift_variant	55210	exon14			.	AK025865	CCDS31.1, CCDS53259.1, CCDS53260.1	1p36.33	2010-04-21		2007-02-08	ENSG00000197785	ENSG00000197785		"""ATPases / AAA-type"""	25567	protein-coding gene	gene with protein product		612316				12477932	Standard	NM_018188		Approved	FLJ10709	uc001afz.2	Q9NVI7	OTTHUMG00000000575	ENST00000378755.5:c.1586delG	chr1.hg19:g.1463179delG	ENSP00000368030:p.Arg529fs	219.0	0.0		166.0	10.0	NM_018188	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Frame_Shift_Del	DEL	ENST00000378755.5	hg19	CCDS31.1																																																																																			.	.		0.582	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188	
TRPM8	79054	hgsc.bcm.edu	37	2	234879010	234879010	+	Frame_Shift_Del	DEL	C	C	-	rs201204922		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:234879010delC	ENST00000324695.4	+	17	2335	c.2295delC	c.(2293-2295)cacfs	p.H765fs	TRPM8_ENST00000433712.2_Intron	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	765					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	CGGTGCCACACCCCCCCGAGC	0.577																																					p.H765fs		Atlas-INDEL	.											.,2	TRPM8	146	.	0			c.2294delA						.						309.0	295.0	300.0					2																	234879010		2203	4300	6503	SO:0001589	frameshift_variant	79054	exon17			.	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.2295delC	chr2.hg19:g.234879010delC	ENSP00000323926:p.His765fs	189.0	0.0		242.0	15.0	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Frame_Shift_Del	DEL	ENST00000324695.4	hg19	CCDS33407.1																																																																																			.	.		0.577	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
DNAH12	201625	hgsc.bcm.edu	37	3	57357612	57357612	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:57357612delT	ENST00000351747.2	-	48	7590	c.7410delA	c.(7408-7410)aaafs	p.K2470fs	DNAH12_ENST00000344804.4_Frame_Shift_Del_p.K103fs	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	2470	AAA 4. {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						TTTTCCCTAGTTTGTCAGTTA	0.333																																					p.L2471X		Atlas-INDEL	.											.	DNAH12	182	.	0			c.7411delC						.						198.0	177.0	183.0					3																	57357612		692	1591	2283	SO:0001589	frameshift_variant	201625	exon48			.	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.7410delA	chr3.hg19:g.57357612delT	ENSP00000295937:p.Lys2470fs	119.0	0.0		161.0	10.0	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Frame_Shift_Del	DEL	ENST00000351747.2	hg19																																																																																				.	.		0.333	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
DNAH7	56171	hgsc.bcm.edu	37	2	196673531	196673531	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:196673531delA	ENST00000312428.6	-	53	10058	c.9958delT	c.(9958-9960)tgtfs	p.C3320fs		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3320					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						AGCCATGTACAAAGGTTGGCA	0.423																																					p.C3320fs		Atlas-INDEL	.											.	DNAH7	512	.	0			c.9959delG						.						92.0	84.0	86.0					2																	196673531		1888	4124	6012	SO:0001589	frameshift_variant	56171	exon53			.	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.9958delT	chr2.hg19:g.196673531delA	ENSP00000311273:p.Cys3320fs	120.0	0.0		138.0	12.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Frame_Shift_Del	DEL	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.423	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
TMEM59	9528	hgsc.bcm.edu	37	1	54506473	54506473	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:54506473delA	ENST00000234831.5	-	6	912	c.663delT	c.(661-663)tttfs	p.F221fs	TMEM59_ENST00000371341.1_Frame_Shift_Del_p.F90fs|TMEM59_ENST00000371348.1_Frame_Shift_Del_p.F90fs|TMEM59_ENST00000371344.1_Frame_Shift_Del_p.F90fs	NM_004872.3	NP_004863.2	Q9BXS4	TMM59_HUMAN	transmembrane protein 59	221					autophagy (GO:0006914)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of protein glycosylation in Golgi (GO:0090285)|negative regulation of protein processing (GO:0010955)|positive regulation of autophagy (GO:0010508)	extracellular vesicular exosome (GO:0070062)|Golgi cis cisterna (GO:0000137)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)			kidney(3)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7						CATCTTCAAGAAAATTCCTGT	0.343																																					p.L222fs		Atlas-INDEL	.											.	TMEM59	28	.	0			c.664delC						.						103.0	104.0	104.0					1																	54506473		2203	4300	6503	SO:0001589	frameshift_variant	9528	exon6			.	AF047439	CCDS586.1	1p32.3	2008-05-14	2005-07-22	2005-07-22	ENSG00000116209	ENSG00000116209			1239	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 8"""	C1orf8		9653160	Standard	NM_004872		Approved	HSPC001	uc001cwp.3	Q9BXS4	OTTHUMG00000008437	ENST00000234831.5:c.663delT	chr1.hg19:g.54506473delA	ENSP00000234831:p.Phe221fs	186.0	0.0		190.0	13.0	NM_004872	B3KQL7|O75393|Q4VBP9|Q5T705|Q96KX7	Frame_Shift_Del	DEL	ENST00000234831.5	hg19	CCDS586.1																																																																																			.	.		0.343	TMEM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023254.2	NM_004872	
UNK	85451	hgsc.bcm.edu	37	17	73808634	73808634	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:73808634delA	ENST00000589666.1	+	4	700	c.590delA	c.(589-591)gaafs	p.E197fs	UNK_ENST00000293218.3_Frame_Shift_Del_p.E273fs	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	197							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCCATGATAGAAAAGATCCTC	0.617																																					p.E197fs		Atlas-INDEL	.											.	UNK	87	.	0			c.589delG						.						40.0	46.0	44.0					17																	73808634		2054	4201	6255	SO:0001589	frameshift_variant	85451	exon4			.	AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"""Zinc fingers, CCCH-type domain containing"""	29369	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 5"", ""zinc finger CCCH-type containing 5"", ""unkempt homolog (Drosophila)"""	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.590delA	chr17.hg19:g.73808634delA	ENSP00000464893:p.Glu197fs	84.0	0.0		155.0	11.0	NM_001080419		Frame_Shift_Del	DEL	ENST00000589666.1	hg19	CCDS45778.2																																																																																			.	.		0.617	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419	
DSG3	1830	hgsc.bcm.edu	37	18	29055783	29055783	+	Frame_Shift_Del	DEL	A	A	-	rs552614590		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:29055783delA	ENST00000257189.4	+	16	2643	c.2560delA	c.(2560-2562)aaafs	p.K855fs		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	855					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ACCCAAATTTAAAAAACTTGC	0.488																																					p.F853fs		Atlas-INDEL	.											.	DSG3	172	.	0			c.2559delT						.						98.0	98.0	98.0					18																	29055783		2203	4300	6503	SO:0001589	frameshift_variant	1830	exon16			.	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.2560delA	chr18.hg19:g.29055783delA	ENSP00000257189:p.Lys855fs	165.0	0.0		192.0	12.0	NM_001944	A8K2V2	Frame_Shift_Del	DEL	ENST00000257189.4	hg19	CCDS11898.1																																																																																			.	.		0.488	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
C2orf43	60526	hgsc.bcm.edu	37	2	20901391	20901391	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:20901391delC	ENST00000237822.3	-	6	804	c.725delG	c.(724-726)ggcfs	p.G242fs	C2orf43_ENST00000381090.3_Frame_Shift_Del_p.G242fs|C2orf43_ENST00000403006.2_Frame_Shift_Del_p.G112fs|C2orf43_ENST00000440866.2_Frame_Shift_Del_p.A164fs|C2orf43_ENST00000435420.2_Frame_Shift_Del_p.G194fs|C2orf43_ENST00000541941.1_Frame_Shift_Del_p.G112fs	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	242										endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATTTCTTGGCCCCCAAGGTA	0.323																																					p.G242fs		Atlas-INDEL	.											.	C2orf43	28	.	0			c.726delC						.						240.0	234.0	236.0					2																	20901391		2203	4300	6503	SO:0001589	frameshift_variant	60526	exon6			.	AK025473	CCDS1702.1, CCDS62864.1, CCDS74488.1, CCDS74489.1	2p24.1	2014-02-07			ENSG00000118961	ENSG00000118961			26145	protein-coding gene	gene with protein product		613570				17135363, 24357060	Standard	NM_001282723		Approved	FLJ21820	uc002rec.3	Q9H6V9	OTTHUMG00000122097	ENST00000237822.3:c.725delG	chr2.hg19:g.20901391delC	ENSP00000237822:p.Gly242fs	158.0	0.0		176.0	11.0	NM_021925	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Frame_Shift_Del	DEL	ENST00000237822.3	hg19	CCDS1702.1																																																																																			.	.		0.323	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1	NM_021925	
FSTL4	23105	hgsc.bcm.edu	37	5	132553042	132553042	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:132553042delT	ENST00000265342.7	-	13	1736	c.1487delA	c.(1486-1488)aatfs	p.N496fs	CTB-49A3.2_ENST00000502776.1_RNA|CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	496						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTGGGTTGCATTTTTTTCTCT	0.493																																					p.N496fs		Atlas-INDEL	.											.	FSTL4	74	.	0			c.1488delT						.						87.0	85.0	86.0					5																	132553042		2203	4300	6503	SO:0001589	frameshift_variant	23105	exon13			.	AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.1487delA	chr5.hg19:g.132553042delT	ENSP00000265342:p.Asn496fs	150.0	0.0		167.0	11.0	NM_015082	Q8TBU0|Q9UPU1	Frame_Shift_Del	DEL	ENST00000265342.7	hg19	CCDS34238.1																																																																																			.	.		0.493	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786	
TOP3B	8940	hgsc.bcm.edu	37	22	22318323	22318323	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:22318323delG	ENST00000398793.2	-	11	1610	c.1176delC	c.(1174-1176)cccfs	p.P392fs	TOP3B_ENST00000357179.5_Frame_Shift_Del_p.P392fs|TOP3B_ENST00000413067.2_Frame_Shift_Del_p.P121fs	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	392					chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		CAGACTTCATGGGGGTGATGG	0.607																																					p.M393X		Atlas-INDEL	.											.	TOP3B	107	.	0			c.1177delA						.						80.0	76.0	77.0					22																	22318323		2203	4300	6503	SO:0001589	frameshift_variant	8940	exon11			.	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.1176delC	chr22.hg19:g.22318323delG	ENSP00000381773:p.Pro392fs	103.0	0.0		139.0	10.0	NM_003935	A0M8Q3|Q9BUP5	Frame_Shift_Del	DEL	ENST00000398793.2	hg19	CCDS13797.1																																																																																			.	.		0.607	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935	
GRAMD1C	54762	hgsc.bcm.edu	37	3	113595052	113595052	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:113595052delA	ENST00000358160.4	+	5	896	c.404delA	c.(403-405)gaafs	p.E135fs	GRAMD1C_ENST00000479212.1_3'UTR|GRAMD1C_ENST00000452134.2_5'UTR	NM_017577.4	NP_060047.3	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	135	GRAM.					integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	26						ATGACCAAGGAAAAAACTGCT	0.294																																					p.E135fs		Atlas-INDEL	.											.	GRAMD1C	71	.	0			c.403delG						.						101.0	107.0	105.0					3																	113595052		2203	4300	6503	SO:0001589	frameshift_variant	54762	exon5			.		CCDS33826.1, CCDS54625.1	3q13.31	2005-11-02			ENSG00000178075	ENSG00000178075			25252	protein-coding gene	gene with protein product						12975309	Standard	NM_017577		Approved	DKFZp434C0328	uc003eaq.4	Q8IYS0	OTTHUMG00000159340	ENST00000358160.4:c.404delA	chr3.hg19:g.113595052delA	ENSP00000350881:p.Glu135fs	164.0	0.0		196.0	12.0	NM_017577	A8K9Y1|A8KA99|Q6AW94|Q6UWN1|Q8N6S0|Q9UF46	Frame_Shift_Del	DEL	ENST00000358160.4	hg19	CCDS33826.1																																																																																			.	.		0.294	GRAMD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354733.1	NM_017577	
PIK3R1	5295	hgsc.bcm.edu	37	5	67575562	67575565	+	Splice_Site	DEL	GTTT	GTTT	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	GTTT	GTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:67575562_67575565delGTTT	ENST00000521381.1	+	5	1250		c.e5+1		PIK3R1_ENST00000396611.1_Splice_Site|PIK3R1_ENST00000274335.5_Splice_Site|PIK3R1_ENST00000521657.1_Splice_Site	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)						B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|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)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	TTAGCTCCAGGTTTGTTTTTTCTC	0.397			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																											p.212_212del		Atlas-Indel,Pindel	.		Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	.	PIK3R1	869	.	2	Whole gene deletion(1)|Unknown(1)	large_intestine(1)|lung(1)	c.634_634del						.																																			SO:0001630	splice_region_variant	5295	exon5			.	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.634+1GTTT>-	chr5.hg19:g.67575566_67575569delGTTT		127.0	0.0		159.0	34.0	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Frame_Shift_Del	DEL	ENST00000521381.1	hg19	CCDS3993.1																																																																																			.	.		0.397	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	Intron
NEK8	284086	hgsc.bcm.edu	37	17	27064915	27064915	+	Frame_Shift_Del	DEL	C	C	-	rs371295223		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:27064915delC	ENST00000268766.6	+	7	1002	c.968delC	c.(967-969)accfs	p.T323fs	AC010761.6_ENST00000584779.1_RNA	NM_178170.2	NP_835464.1	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	323					organ morphogenesis (GO:0009887)|regulation of hippo signaling (GO:0035330)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|primary cilium (GO:0072372)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Lung NSC(42;0.0158)					GGGCTGGGCACCCCCCTGCGG	0.667																																					p.T323fs	NSCLC(6;19 293 14866 25253 49845)	Atlas-INDEL	.											.	NEK8	76	.	0			c.967delA						.						43.0	49.0	47.0					17																	27064915		2203	4298	6501	SO:0001589	frameshift_variant	284086	exon7			.	AY267371	CCDS32597.1	17q11.1	2012-11-15	2012-11-15			ENSG00000160602			13387	protein-coding gene	gene with protein product		609799	"""NIMA (never in mitosis gene a)- related kinase 8"""			18199800	Standard	NM_178170		Approved	NPHP9	uc002hcp.3	Q86SG6		ENST00000268766.6:c.968delC	chr17.hg19:g.27064915delC	ENSP00000268766:p.Thr323fs	80.0	0.0		116.0	10.0	NM_178170	A6NIC5|Q14CL7|Q2M1S6|Q8NDH1	Frame_Shift_Del	DEL	ENST00000268766.6	hg19	CCDS32597.1																																																																																			.	.		0.667	NEK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446467.2		
EPHA10	284656	hgsc.bcm.edu	37	1	38185112	38185112	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:38185112delG	ENST00000373048.4	-	15	2729	c.2730delC	c.(2728-2730)cccfs	p.P910fs	EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000540011.1_Intron|EPHA10_ENST00000330210.7_Frame_Shift_Del_p.P405fs|EPHA10_ENST00000427468.2_Frame_Shift_Del_p.P910fs	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	910					ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GGGCACACTTGGGGGGCTCTG	0.612																																					p.K911fs		Atlas-INDEL	.											.	EPHA10	120	.	0			c.2731delA						.						37.0	45.0	43.0					1																	38185112		2056	4173	6229	SO:0001589	frameshift_variant	284656	exon15			.	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2730delC	chr1.hg19:g.38185112delG	ENSP00000362139:p.Pro910fs	186.0	0.0		216.0	13.0	NM_001099439	A4FU89|J3KPB5|Q6NW42	Frame_Shift_Del	DEL	ENST00000373048.4	hg19	CCDS41305.1																																																																																			.	.		0.612	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
RARS2	57038	hgsc.bcm.edu	37	6	88279277	88279277	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:88279277delT	ENST00000369536.5	-	2	113	c.68delA	c.(67-69)aacfs	p.N23fs		NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	23					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)		TGTGATCAAGTTTTCTGGTGG	0.323																																					p.N23fs		Atlas-INDEL	.											.	RARS2	61	.	0			c.69delC						.						113.0	116.0	115.0					6																	88279277		2203	4300	6503	SO:0001589	frameshift_variant	57038	exon2			.	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.68delA	chr6.hg19:g.88279277delT	ENSP00000358549:p.Asn23fs	139.0	0.0		161.0	10.0	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Frame_Shift_Del	DEL	ENST00000369536.5	hg19	CCDS5011.1																																																																																			.	.		0.323	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320	
ALG10B	144245	hgsc.bcm.edu	37	12	38714025	38714025	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:38714025delT	ENST00000308742.4	+	3	748	c.432delT	c.(430-432)tatfs	p.Y144fs	AC117372.1_ENST00000401168.2_RNA|ALG10B_ENST00000551464.1_Intron	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	144					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)			breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				CAACACTTTATTTTTTTAACT	0.318																																					p.Y144fs		Atlas-INDEL	.											.	ALG10B	58	.	0			c.431delA						.						68.0	74.0	72.0					12																	38714025		2203	4295	6498	SO:0001589	frameshift_variant	144245	exon3			.	AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"""potassium channel regulator 1"", ""dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"""		"""asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"""				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.432delT	chr12.hg19:g.38714025delT	ENSP00000310120:p.Tyr144fs	317.0	0.0		405.0	25.0	NM_001013620	B2RPF4	Frame_Shift_Del	DEL	ENST00000308742.4	hg19	CCDS31772.1																																																																																			.	.		0.318	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620	
ADCK4	79934	hgsc.bcm.edu	37	19	41220518	41220518	+	Frame_Shift_Del	DEL	C	C	-	rs113871093	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:41220518delC	ENST00000324464.3	-	2	321	c.20delG	c.(19-21)ggcfs	p.G7fs	ADCK4_ENST00000243583.6_Frame_Shift_Del_p.G7fs|ITPKC_ENST00000263370.2_5'Flank|ADCK4_ENST00000450541.1_Frame_Shift_Del_p.G7fs	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	7						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)	p.G7fs*69(2)		NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			CCGAAGTAGGCCCCCCACCTT	0.642																																					p.G7fs		Atlas-INDEL	.											.	ADCK4	92	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.21delC						.						34.0	39.0	37.0					19																	41220518		2203	4300	6503	SO:0001589	frameshift_variant	79934	exon2			.	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.20delG	chr19.hg19:g.41220518delC	ENSP00000315118:p.Gly7fs	155.0	0.0		169.0	12.0	NM_001142555	Q8TAJ1|Q9HA52	Frame_Shift_Del	DEL	ENST00000324464.3	hg19	CCDS12562.1																																																																																			.	.		0.642	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
RNF145	153830	hgsc.bcm.edu	37	5	158585835	158585835	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:158585835delG	ENST00000424310.2	-	11	2194	c.1835delC	c.(1834-1836)ccafs	p.P612fs	RNF145_ENST00000518284.1_5'UTR|RNF145_ENST00000519865.1_Frame_Shift_Del_p.P612fs|RNF145_ENST00000274542.2_Frame_Shift_Del_p.P640fs|RNF145_ENST00000520638.1_Frame_Shift_Del_p.P626fs|RNF145_ENST00000521606.2_Frame_Shift_Del_p.P629fs|RNF145_ENST00000518802.1_Frame_Shift_Del_p.P642fs	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	612						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTCCTGGCCTGGGGGTTCAGT	0.512																																					p.P642fs		Atlas-INDEL	.											.	RNF145	110	.	0			c.1926delA						.						93.0	86.0	88.0					5																	158585835		2203	4300	6503	SO:0001589	frameshift_variant	153830	exon11			.	BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"""RING-type (C3HC4) zinc fingers"""	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.1835delC	chr5.hg19:g.158585835delG	ENSP00000409064:p.Pro612fs	168.0	0.0		210.0	15.0	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Frame_Shift_Del	DEL	ENST00000424310.2	hg19	CCDS56390.1																																																																																			.	.		0.512	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726	
UBQLN3	50613	hgsc.bcm.edu	37	11	5529234	5529234	+	Frame_Shift_Del	DEL	G	G	-	rs141131818	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:5529234delG	ENST00000311659.4	-	2	1702	c.1555delC	c.(1555-1557)cgtfs	p.R519fs	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_5'Flank|HBG2_ENST00000380252.1_5'Flank|AC104389.28_ENST00000415970.1_RNA	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	519										NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCAGGGCACGGGGGTTTGCC	0.577																																					p.R519fs	Ovarian(72;684 1260 12332 41642 52180)	Atlas-INDEL	.											.	UBQLN3	107	.	0			c.1556delG						.						54.0	55.0	55.0					11																	5529234		2201	4297	6498	SO:0001589	frameshift_variant	50613	exon2			.	AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"""Ubiquilin family"""	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.1555delC	chr11.hg19:g.5529234delG	ENSP00000347997:p.Arg519fs	128.0	0.0		180.0	11.0	NM_017481	Q9NRE0	Frame_Shift_Del	DEL	ENST00000311659.4	hg19	CCDS7758.1																																																																																			.	.		0.577	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481	
CHD1	1105	hgsc.bcm.edu	37	5	98207855	98207855	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:98207855delC	ENST00000284049.3	-	27	3910	c.3761delG	c.(3760-3762)ggcfs	p.G1254fs	CHD1_ENST00000511067.1_5'Flank	NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1254					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)	ATCTTCTTTGCCCCAGTCTAT	0.368																																					p.G1254fs		Atlas-INDEL	.											.	CHD1	137	.	0			c.3762delC						.						109.0	108.0	109.0					5																	98207855		2203	4300	6503	SO:0001589	frameshift_variant	1105	exon27			.	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.3761delG	chr5.hg19:g.98207855delC	ENSP00000284049:p.Gly1254fs	128.0	0.0		181.0	11.0	NM_001270	Q17RZ3	Frame_Shift_Del	DEL	ENST00000284049.3	hg19	CCDS34204.1																																																																																			.	.		0.368	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
PIGA	5277	hgsc.bcm.edu	37	X	15339659	15339659	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:15339659delC	ENST00000333590.4	-	6	1508	c.1424delG	c.(1423-1425)ggtfs	p.G475fs	PIGA_ENST00000482148.1_5'UTR|PIGA_ENST00000428964.1_Frame_Shift_Del_p.G160fs|PIGA_ENST00000542278.1_Frame_Shift_Del_p.G241fs	NM_002641.3	NP_002632.1	P37287	PIGA_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class A	475					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)					ATTATTCTCACCCCCTCTTTT	0.383																																					p.G475fs		Atlas-INDEL	.											.	PIGA	34	.	0			c.1425delT						.						90.0	91.0	91.0					X																	15339659		2203	4300	6503	SO:0001589	frameshift_variant	5277	exon6			.	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.1424delG	chrX.hg19:g.15339659delC	ENSP00000369820:p.Gly475fs	138.0	0.0		176.0	12.0	NM_002641	B4E0V2|Q16025|Q16250	Frame_Shift_Del	DEL	ENST00000333590.4	hg19	CCDS14165.1																																																																																			.	.		0.383	PIGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055854.1	NM_002641	
HNRNPDL	9987	hgsc.bcm.edu	37	4	83348625	83348625	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:83348625delT	ENST00000295470.5	-	4	1042	c.867delA	c.(865-867)aaafs	p.K289fs	HNRNPDL_ENST00000349655.4_Frame_Shift_Del_p.K170fs|HNRNPDL_ENST00000514511.1_5'UTR|HNRNPDL_ENST00000502762.1_Frame_Shift_Del_p.K289fs|HNRNPDL_ENST00000602300.1_Frame_Shift_Del_p.K170fs	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like	289	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										TTTCTAACAATTTTTTTACTG	0.289																																					p.L290fs		Atlas-INDEL	.											.	HNRPDL	35	.	0			c.868delT						.						74.0	75.0	75.0					4																	83348625		2202	4299	6501	SO:0001589	frameshift_variant	9987	exon4			.	D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"""RNA binding motif (RRM) containing"""	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299	ENST00000295470.5:c.867delA	chr4.hg19:g.83348625delT	ENSP00000295470:p.Lys289fs	121.0	0.0		183.0	12.0	NM_031372	Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Frame_Shift_Del	DEL	ENST00000295470.5	hg19	CCDS3593.1																																																																																			.	.		0.289	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463	
PLCG2	5336	hgsc.bcm.edu	37	16	81939079	81939079	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:81939079delG	ENST00000359376.3	+	15	1648	c.1434delG	c.(1432-1434)cagfs	p.Q478fs		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	478					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						ACAAGCAACAGGGGGAGCTGT	0.577																																					p.Q478fs		Atlas-INDEL	.											.	PLCG2	276	.	0			c.1433delA						.						71.0	77.0	75.0					16																	81939079		2041	4196	6237	SO:0001589	frameshift_variant	5336	exon15			.		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.1434delG	chr16.hg19:g.81939079delG	ENSP00000352336:p.Gln478fs	172.0	0.0		235.0	16.0	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Frame_Shift_Del	DEL	ENST00000359376.3	hg19	CCDS42204.1																																																																																			.	.		0.577	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
PREX1	57580	hgsc.bcm.edu	37	20	47256419	47256419	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:47256419delT	ENST00000371941.3	-	30	3811	c.3789delA	c.(3787-3789)aaafs	p.K1263fs	PREX1_ENST00000496915.1_5'Flank|PREX1_ENST00000396220.1_Frame_Shift_Del_p.K1263fs	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1263					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)			TACACTCTTCTTTCTGTTTAA	0.552																																					p.E1264fs		Atlas-INDEL	.											.	PREX1	441	.	0			c.3790delG						.						124.0	125.0	125.0					20																	47256419		2203	4300	6503	SO:0001589	frameshift_variant	57580	exon30			.	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.3789delA	chr20.hg19:g.47256419delT	ENSP00000361009:p.Lys1263fs	131.0	0.0		183.0	11.0	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Frame_Shift_Del	DEL	ENST00000371941.3	hg19	CCDS13410.1																																																																																			.	.		0.552	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
MYO6	4646	hgsc.bcm.edu	37	6	76558143	76558143	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:76558143delA	ENST00000369977.3	+	11	1112	c.973delA	c.(973-975)aaafs	p.K326fs	MYO6_ENST00000369981.3_Frame_Shift_Del_p.K326fs|MYO6_ENST00000369985.4_Frame_Shift_Del_p.K326fs|MYO6_ENST00000369975.1_Frame_Shift_Del_p.K326fs	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	326	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		CACGGCTATGAAAAAAATTGG	0.413																																					p.M324fs		Atlas-INDEL	.											.	MYO6	124	.	0			c.972delG						.						140.0	141.0	141.0					6																	76558143		2203	4300	6503	SO:0001589	frameshift_variant	4646	exon11			.	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"""Myosins / Myosin superfamily : Class VI"""	7605	protein-coding gene	gene with protein product		600970	"""deafness, autosomal recessive 37"""	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.973delA	chr6.hg19:g.76558143delA	ENSP00000358994:p.Lys326fs	141.0	0.0		178.0	11.0	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Frame_Shift_Del	DEL	ENST00000369977.3	hg19	CCDS34487.1																																																																																			.	.		0.413	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999	
ITIH5	80760	hgsc.bcm.edu	37	10	7605064	7605064	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:7605064delC	ENST00000256861.6	-	14	2889	c.2811delG	c.(2809-2811)gggfs	p.G937fs	ITIH5_ENST00000397146.2_Intron|ITIH5_ENST00000446830.2_Frame_Shift_Del_p.G718fs|ITIH5_ENST00000298441.6_Frame_Shift_Del_p.G723fs	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	0					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						CCTGGACATTCCCCGGCCAAG	0.542																																					p.G937fs		Atlas-INDEL	.											.	ITIH5	343	.	0			c.2811delA						.						188.0	180.0	183.0					10																	7605064		2203	4300	6503	SO:0001589	frameshift_variant	80760	exon15			.			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.2811delG	chr10.hg19:g.7605064delC	ENSP00000256861:p.Gly937fs	172.0	0.0		172.0	11.0	NM_030569	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Frame_Shift_Del	DEL	ENST00000256861.6	hg19																																																																																				.	.		0.542	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
PHOX2A	401	hgsc.bcm.edu	37	11	71950817	71950817	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:71950817delG	ENST00000298231.5	-	3	1002	c.831delC	c.(829-831)cccfs	p.P277fs	PHOX2A_ENST00000544057.1_5'Flank	NM_005169.3	NP_005160.2	O14813	PHX2A_HUMAN	paired-like homeobox 2a	277					dopaminergic neuron differentiation (GO:0071542)|locus ceruleus development (GO:0021703)|midbrain development (GO:0030901)|noradrenergic neuron differentiation (GO:0003357)|oculomotor nerve formation (GO:0021623)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of respiratory gaseous exchange (GO:0043576)|somatic motor neuron differentiation (GO:0021523)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)|trochlear nerve formation (GO:0021642)	nuclear chromatin (GO:0000790)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)	5						TCTTCAGGGCGGGGCCGGGCT	0.697																																					p.A278fs		Atlas-INDEL	.											.	PHOX2A	14	.	0			c.832delG						.						5.0	7.0	6.0					11																	71950817		1982	3943	5925	SO:0001589	frameshift_variant	401	exon3			.	AF022722	CCDS8214.1	11q13.4	2014-09-04	2007-07-12	2003-02-14	ENSG00000165462	ENSG00000165462		"""Homeoboxes / PRD class"""	691	protein-coding gene	gene with protein product		602753	"""aristaless (Drosophila) homeobox, aristaless homeobox (Drosophila), fibrosis of extraocular muscles, congenital, 2, autosomal recessive"", ""paired-like (aristaless) homeobox 2a"""	ARIX, FEOM2		8661014, 11600883	Standard	NM_005169		Approved	PMX2A, CFEOM2	uc001osh.4	O14813	OTTHUMG00000167899	ENST00000298231.5:c.831delC	chr11.hg19:g.71950817delG	ENSP00000298231:p.Pro277fs	108.0	0.0		181.0	14.0	NM_005169	A8K3N0|Q8IVZ2	Frame_Shift_Del	DEL	ENST00000298231.5	hg19	CCDS8214.1																																																																																			.	.		0.697	PHOX2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396885.1	NM_005169	
PUM1	9698	hgsc.bcm.edu	37	1	31532353	31532353	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:31532353delG	ENST00000257075.5	-	2	154	c.61delC	c.(61-63)cacfs	p.H21fs	PUM1_ENST00000423018.2_Frame_Shift_Del_p.H21fs|PUM1_ENST00000373742.2_Frame_Shift_Del_p.H57fs|PUM1_ENST00000426105.2_Frame_Shift_Del_p.H21fs|PUM1_ENST00000373747.3_Frame_Shift_Del_p.H21fs|PUM1_ENST00000373741.4_Frame_Shift_Del_p.H57fs|PUM1_ENST00000440538.2_Frame_Shift_Del_p.H21fs|PUM1_ENST00000424085.2_Frame_Shift_Del_p.H21fs	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	21					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)		TGTTTCAGGTGGGGGCTGAAA	0.473																																					p.H21fs		Atlas-INDEL	.											.	PUM1	107	.	0			c.62delA						.						95.0	98.0	97.0					1																	31532353		2203	4300	6503	SO:0001589	frameshift_variant	9698	exon2			.	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.61delC	chr1.hg19:g.31532353delG	ENSP00000257075:p.His21fs	97.0	0.0		129.0	11.0	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Frame_Shift_Del	DEL	ENST00000257075.5	hg19	CCDS338.1																																																																																			.	.		0.473	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1		
ZNF562	54811	hgsc.bcm.edu	37	19	9767254	9767254	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:9767254delA	ENST00000448622.1	-	5	479	c.317delT	c.(316-318)ttgfs	p.L106fs	ZNF562_ENST00000453372.2_Frame_Shift_Del_p.L106fs|ZNF562_ENST00000453792.2_Frame_Shift_Del_p.L37fs|ZNF562_ENST00000590155.1_Frame_Shift_Del_p.L106fs|ZNF562_ENST00000587392.1_Intron|ZNF562_ENST00000537617.1_5'UTR|ZNF562_ENST00000293648.4_Frame_Shift_Del_p.L34fs|ZNF562_ENST00000541032.1_Frame_Shift_Del_p.L69fs	NM_001130031.1|NM_001130032.1	NP_001123503.1|NP_001123504.1	Q6V9R5	ZN562_HUMAN	zinc finger protein 562	106	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	17						TTGATTCTTCAAAAAACCCTG	0.373																																					p.L106fs		Atlas-INDEL	.											.	ZNF562	72	.	0			c.318delG						.						145.0	142.0	143.0					19																	9767254		2203	4300	6503	SO:0001589	frameshift_variant	54811	exon5			.	AK000086	CCDS12217.1, CCDS45956.1, CCDS74280.1	19p13.2	2013-09-20			ENSG00000171466	ENSG00000171466		"""Zinc fingers, C2H2-type"", ""-"""	25950	protein-coding gene	gene with protein product							Standard	NM_001130031		Approved	FLJ20079	uc010xks.2	Q6V9R5	OTTHUMG00000180205	ENST00000448622.1:c.317delT	chr19.hg19:g.9767254delA	ENSP00000411784:p.Leu106fs	168.0	0.0		228.0	14.0	NM_001130032	Q32MN2|Q9NXS5	Frame_Shift_Del	DEL	ENST00000448622.1	hg19	CCDS45956.1																																																																																			.	.		0.373	ZNF562-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450239.1	NM_017656	
CDKL2	8999	hgsc.bcm.edu	37	4	76523281	76523281	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:76523281delT	ENST00000429927.2	-	8	1703	c.1000delA	c.(1000-1002)agafs	p.R334fs	CDKL2_ENST00000307465.4_Frame_Shift_Del_p.R334fs	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	334					sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			AGTGTTTTTCTTTCTTCAACT	0.244																																					p.R334fs		Atlas-INDEL	.											CDKL2,NS,carcinoma,0,1	CDKL2	58	.	0			c.1001delG						.						37.0	37.0	37.0					4																	76523281		2201	4276	6477	SO:0001589	frameshift_variant	8999	exon8			.	U35146	CCDS3570.1	4q21.21	2011-11-04			ENSG00000138769	ENSG00000138769		"""Cyclin-dependent kinases"""	1782	protein-coding gene	gene with protein product		603442				9000130	Standard	NM_003948		Approved	P56, KKIAMRE	uc003hiq.3	Q92772	OTTHUMG00000130103	ENST00000429927.2:c.1000delA	chr4.hg19:g.76523281delT	ENSP00000412365:p.Arg334fs	118.0	0.0		173.0	11.0	NM_003948	B2R695	Frame_Shift_Del	DEL	ENST00000429927.2	hg19	CCDS3570.1																																																																																			.	.		0.244	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948	
FPGT-TNNI3K	100526835	hgsc.bcm.edu	37	1	74930365	74930365	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:74930365delA	ENST00000370899.3	+	24	2508	c.2471delA	c.(2470-2472)gaafs	p.E824fs	TNNI3K_ENST00000326637.3_Intron|TNNI3K_ENST00000370891.2_Intron|FPGT-TNNI3K_ENST00000557284.2_Intron	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough																		GTGTACACAGAAACTCTTAAG	0.388																																					p.E824fs		Atlas-INDEL	.											.	.	.	.	0			c.2470delG						.						20.0	19.0	19.0					1																	74930365		876	1990	2866	SO:0001589	frameshift_variant	100526835	exon24			.			1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.2471delA	chr1.hg19:g.74930365delA	ENSP00000359936:p.Glu824fs	105.0	0.0		120.0	10.0	NM_001199327		Frame_Shift_Del	DEL	ENST00000370899.3	hg19																																																																																				.	.		0.388	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3		
EML5	161436	hgsc.bcm.edu	37	14	89087164	89087164	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:89087164delA	ENST00000380664.5	-	37	5284	c.5285delT	c.(5284-5286)ttafs	p.L1763fs	EML5_ENST00000352093.5_Frame_Shift_Del_p.L1725fs|EML5_ENST00000554922.1_Frame_Shift_Del_p.L1771fs|EML5_ENST00000553320.1_5'Flank			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	1763						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						ACTCACTAGTAAAATGATAAA	0.378																																					p.L1770fs		Atlas-INDEL	.											.	EML5	141	.	0			c.5310delA						.						103.0	93.0	96.0					14																	89087164		1859	4114	5973	SO:0001589	frameshift_variant	161436	exon38			.	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.5285delT	chr14.hg19:g.89087164delA	ENSP00000370039:p.Leu1763fs	171.0	0.0		201.0	14.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Frame_Shift_Del	DEL	ENST00000380664.5	hg19	CCDS45148.1																																																																																			.	.		0.378	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
HDLBP	3069	hgsc.bcm.edu	37	2	242194991	242194991	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:242194991delT	ENST00000391975.1	-	8	1105	c.878delA	c.(877-879)aagfs	p.K294fs	HDLBP_ENST00000427183.2_Intron|HDLBP_ENST00000310931.4_Frame_Shift_Del_p.K294fs|HDLBP_ENST00000391976.2_Frame_Shift_Del_p.K294fs	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	294	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		TGTAGTCTTCTTTTTCTAAAT	0.502																																					p.K293fs		Atlas-INDEL	.											.	HDLBP	118	.	0			c.879delG						.						105.0	97.0	99.0					2																	242194991		2203	4300	6503	SO:0001589	frameshift_variant	3069	exon8			.		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"""vigilin"""	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.878delA	chr2.hg19:g.242194991delT	ENSP00000375836:p.Lys294fs	115.0	0.0		207.0	13.0	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Frame_Shift_Del	DEL	ENST00000391975.1	hg19	CCDS2547.1																																																																																			.	.		0.502	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346	
CELF5	60680	hgsc.bcm.edu	37	19	3290263	3290263	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:3290263delC	ENST00000292672.2	+	11	1258	c.1221delC	c.(1219-1221)ctcfs	p.L407fs	CELF5_ENST00000541430.2_Intron	NM_021938.3	NP_068757.2	Q8N6W0	CELF5_HUMAN	CUGBP, Elav-like family member 5	407	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						TCTACCACCTCCCCCAGGAGT	0.572																																					p.L407fs		Atlas-INDEL	.											.	CELF5	32	.	0			c.1220delT						.						88.0	77.0	81.0					19																	3290263		2203	4300	6503	SO:0001589	frameshift_variant	60680	exon11			.	AF248649	CCDS12106.1, CCDS54197.1	19p13	2013-02-12	2010-02-19	2010-02-19		ENSG00000161082		"""RNA binding motif (RRM) containing"""	14058	protein-coding gene	gene with protein product		612680	"""Bruno (Drosophila) -like 5, RNA binding protein"", ""bruno-like 5, RNA binding protein (Drosophila)"""	BRUNOL5		10893231	Standard	NM_001172673		Approved		uc002lxm.3	Q8N6W0		ENST00000292672.2:c.1221delC	chr19.hg19:g.3290263delC	ENSP00000292672:p.Leu407fs	268.0	0.0		315.0	19.0	NM_021938	D6W614|O75253|Q59GP2|Q86VW6|Q9BZC0|Q9NR86	Frame_Shift_Del	DEL	ENST00000292672.2	hg19	CCDS12106.1																																																																																			.	.		0.572	CELF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452574.1	NM_021938	
PTK7	5754	hgsc.bcm.edu	37	6	43100230	43100230	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:43100230delC	ENST00000230419.4	+	7	1254	c.1033delC	c.(1033-1035)cccfs	p.P346fs	PTK7_ENST00000471863.1_Frame_Shift_Del_p.P346fs|PTK7_ENST00000352931.2_Frame_Shift_Del_p.P346fs|PTK7_ENST00000349241.2_Frame_Shift_Del_p.P346fs|PTK7_ENST00000345201.2_Frame_Shift_Del_p.P346fs|PTK7_ENST00000481273.1_Frame_Shift_Del_p.P354fs	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	346	Ig-like C2-type 4.				actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			GACCTGCCTTCCCCCCAAGGG	0.617																																					p.L352fs		Atlas-INDEL	.											.	PTK7	101	.	0			c.1056delT						.						61.0	63.0	62.0					6																	43100230		2203	4300	6503	SO:0001589	frameshift_variant	5754	exon7			.	AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9618	protein-coding gene	gene with protein product		601890	"""PTK7 protein tyrosine kinase 7"""			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.1033delC	chr6.hg19:g.43100230delC	ENSP00000230419:p.Pro346fs	155.0	0.0		166.0	15.0	NM_001270398	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Frame_Shift_Del	DEL	ENST00000230419.4	hg19	CCDS4884.1																																																																																			.	.		0.617	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2		
USH2A	7399	hgsc.bcm.edu	37	1	216062051	216062051	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:216062051delG	ENST00000307340.3	-	41	8326	c.7940delC	c.(7939-7941)cctfs	p.P2647fs	USH2A_ENST00000366943.2_Frame_Shift_Del_p.P2647fs|RP5-1111A8.3_ENST00000414995.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2647	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GGGGTGGGTAGGGGGTTGCCA	0.507										HNSCC(13;0.011)																											p.P2647fs		Atlas-INDEL	.											.	USH2A	1168	.	0			c.7941delT						.						74.0	81.0	79.0					1																	216062051		2203	4300	6503	SO:0001589	frameshift_variant	7399	exon41			.	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.7940delC	chr1.hg19:g.216062051delG	ENSP00000305941:p.Pro2647fs	99.0	0.0		171.0	11.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Frame_Shift_Del	DEL	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.507	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
AHDC1	27245	hgsc.bcm.edu	37	1	27876439	27876439	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	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	238.0	0.0		249.0	18.0	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		
TRAPPC11	60684	hgsc.bcm.edu	37	4	184596365	184596365	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:184596365delA	ENST00000334690.6	+	7	911	c.709delA	c.(709-711)aaafs	p.K237fs	TRAPPC11_ENST00000357207.4_Frame_Shift_Del_p.K237fs|TRAPPC11_ENST00000511409.1_3'UTR|RNU6-335P_ENST00000364563.1_RNA	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	237					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)											CAGTGAGTTGAAACAAGATAC	0.264																																					p.L236fs		Atlas-INDEL	.											.	.	.	.	0			c.708delG						.						47.0	50.0	49.0					4																	184596365		2199	4288	6487	SO:0001589	frameshift_variant	60684	exon7			.		CCDS34112.1, CCDS47166.1	4q35.1	2011-12-12	2011-12-12	2011-12-12	ENSG00000168538	ENSG00000168538		"""Trafficking protein particle complex"""	25751	protein-coding gene	gene with protein product	"""gryzun homolog (Drosophila)"", ""foie gras homolog (zebrafish)"""	614138	"""chromosome 4 open reading frame 41"""	C4orf41		19942856, 21525244	Standard	NM_021942		Approved	FLJ12716, gry, foigr	uc003ivx.3	Q7Z392	OTTHUMG00000160673	ENST00000334690.6:c.709delA	chr4.hg19:g.184596365delA	ENSP00000335371:p.Lys237fs	155.0	0.0		131.0	11.0	NM_021942	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Frame_Shift_Del	DEL	ENST00000334690.6	hg19	CCDS34112.1																																																																																			.	.		0.264	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942	
KIF13A	63971	hgsc.bcm.edu	37	6	17852235	17852235	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:17852235delA	ENST00000259711.6	-	7	638	c.533delT	c.(532-534)ttgfs	p.L178fs	KIF13A_ENST00000378843.2_Frame_Shift_Del_p.L178fs|KIF13A_ENST00000378826.2_Frame_Shift_Del_p.L178fs|KIF13A_ENST00000378816.5_Frame_Shift_Del_p.L178fs|KIF13A_ENST00000378814.5_Frame_Shift_Del_p.L178fs	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	178	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			ATATGGTCCCAAAACTTTATG	0.353																																					p.L178fs		Atlas-INDEL	.											.	KIF13A	276	.	0			c.534delG						.						51.0	48.0	49.0					6																	17852235		1819	4075	5894	SO:0001589	frameshift_variant	63971	exon7			.	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.533delT	chr6.hg19:g.17852235delA	ENSP00000259711:p.Leu178fs	128.0	0.0		184.0	16.0	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Frame_Shift_Del	DEL	ENST00000259711.6	hg19	CCDS47381.1																																																																																			.	.		0.353	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
SPATS2	65244	hgsc.bcm.edu	37	12	49878388	49878388	+	Frame_Shift_Del	DEL	T	T	-	rs141171093	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:49878388delT	ENST00000553127.1	+	5	554	c.41delT	c.(40-42)attfs	p.I14fs	SPATS2_ENST00000552918.1_Frame_Shift_Del_p.I14fs|SPATS2_ENST00000321898.6_Frame_Shift_Del_p.I14fs			Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2	14						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|prostate(1)|urinary_tract(4)	21						TCAGGATTCATTTTTGATTTG	0.388																																					p.I14fs		Atlas-INDEL	.											.	SPATS2	43	.	0			c.40delA						.						109.0	98.0	102.0					12																	49878388		2203	4300	6503	SO:0001589	frameshift_variant	65244	exon4			.	AK023179	CCDS31794.1	12q13.12	2009-06-12							18650	protein-coding gene	gene with protein product		611667				11944913, 17989879	Standard	NM_023071		Approved	SPATA10, SCR59, FLJ13117	uc001rud.2	Q86XZ4		ENST00000553127.1:c.41delT	chr12.hg19:g.49878388delT	ENSP00000448228:p.Ile14fs	151.0	0.0		165.0	14.0	NM_023071	A8K8G9|Q9H7D4|Q9H8Y7|Q9H8Z8	Frame_Shift_Del	DEL	ENST00000553127.1	hg19	CCDS31794.1																																																																																			.	.		0.388	SPATS2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404023.1	NM_023071	
EML3	256364	hgsc.bcm.edu	37	11	62379012	62379012	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:62379012delC	ENST00000394773.2	-	2	386	c.79delG	c.(79-81)gagfs	p.E27fs	ROM1_ENST00000278833.3_5'Flank|EML3_ENST00000278845.4_Frame_Shift_Del_p.E27fs|ROM1_ENST00000534093.1_5'Flank|EML3_ENST00000494176.2_5'UTR|EML3_ENST00000529309.1_Frame_Shift_Del_p.E27fs|EML3_ENST00000531557.1_5'Flank	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	27						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						ATCTCCTGCTCCTGCACCCGA	0.642																																					p.E27fs		Atlas-INDEL	.											.	EML3	61	.	0			c.80delA						.						27.0	29.0	28.0					11																	62379012		2202	4299	6501	SO:0001589	frameshift_variant	256364	exon2			.	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"""WD repeat domain containing"""	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.79delG	chr11.hg19:g.62379012delC	ENSP00000378254:p.Glu27fs	119.0	0.0		256.0	17.0	NM_153265	Q6ZQW7|Q8NA55	Frame_Shift_Del	DEL	ENST00000394773.2	hg19	CCDS8023.2																																																																																			.	.		0.642	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265	
GARNL3	84253	hgsc.bcm.edu	37	9	130107748	130107748	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:130107748delA	ENST00000373387.4	+	16	1775	c.1423delA	c.(1423-1425)aaafs	p.K476fs	GARNL3_ENST00000435213.2_Frame_Shift_Del_p.K454fs|GARNL3_ENST00000314904.5_Frame_Shift_Del_p.K476fs	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	476					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						AGGGATCTGTAAAAAAGAGGT	0.363																																					p.C474X		Atlas-INDEL	.											.	GARNL3	83	.	0			c.1422delT						.						95.0	94.0	94.0					9																	130107748		2203	4300	6503	SO:0001589	frameshift_variant	84253	exon16			.	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 3"""			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.1423delA	chr9.hg19:g.130107748delA	ENSP00000362485:p.Lys476fs	140.0	0.0		162.0	13.0	NM_032293	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Frame_Shift_Del	DEL	ENST00000373387.4	hg19	CCDS6869.2																																																																																			.	.		0.363	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293	
TMEM2	23670	hgsc.bcm.edu	37	9	74327107	74327107	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:74327107delT	ENST00000377044.4	-	16	3200	c.2661delA	c.(2659-2661)aaafs	p.K887fs	TMEM2_ENST00000377066.5_Frame_Shift_Del_p.K824fs	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	887					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		TTGGCACATATTTTTTGAAAG	0.418																																					p.Y888fs		Atlas-INDEL	.											.	TMEM2	112	.	0			c.2662delT						.						136.0	125.0	129.0					9																	74327107		2203	4300	6503	SO:0001589	frameshift_variant	23670	exon16			.		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.2661delA	chr9.hg19:g.74327107delT	ENSP00000366243:p.Lys887fs	185.0	0.0		197.0	12.0	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Frame_Shift_Del	DEL	ENST00000377044.4	hg19	CCDS6638.1																																																																																			.	.		0.418	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
PARP14	54625	hgsc.bcm.edu	37	3	122399784	122399784	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:122399784delC	ENST00000474629.2	+	1	320	c.54delC	c.(52-54)gacfs	p.D18fs		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	18					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)		GGGGCCCCGACCCCCCGAAGA	0.682																																					p.D18fs		Atlas-INDEL	.											.	PARP14	242	.	0			c.53delA						.						17.0	21.0	20.0					3																	122399784		1861	4092	5953	SO:0001589	frameshift_variant	54625	exon1			.	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.54delC	chr3.hg19:g.122399784delC	ENSP00000418194:p.Asp18fs	137.0	0.0		141.0	10.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Frame_Shift_Del	DEL	ENST00000474629.2	hg19	CCDS46894.1																																																																																			.	.		0.682	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
CCDC138	165055	hgsc.bcm.edu	37	2	109492664	109492664	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:109492664delG	ENST00000295124.4	+	15	2013	c.1953delG	c.(1951-1953)ctgfs	p.L651fs	CCDC138_ENST00000412964.2_3'UTR	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	651										endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						TGTTCAATCTGGGTTTAACAA	0.338																																					p.L651fs		Atlas-INDEL	.											.	CCDC138	49	.	0			c.1952delT						.						80.0	80.0	80.0					2																	109492664		2203	4300	6503	SO:0001589	frameshift_variant	165055	exon15			.	AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.1953delG	chr2.hg19:g.109492664delG	ENSP00000295124:p.Leu651fs	157.0	0.0		199.0	12.0	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Frame_Shift_Del	DEL	ENST00000295124.4	hg19	CCDS2080.1																																																																																			.	.		0.338	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978	
LCN15	389812	hgsc.bcm.edu	37	9	139656669	139656669	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:139656669delT	ENST00000316144.5	-	5	515	c.491delA	c.(490-492)aagfs	p.K164fs	LCN15_ENST00000482511.1_5'UTR	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15	164			K -> E (in dbSNP:rs2297722).		lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						CATCATGTCCTTGGGGAGCCC	0.647																																					p.K164fs		Atlas-INDEL	.											.	LCN15	11	.	0			c.492delG						.						18.0	19.0	19.0					9																	139656669		2190	4295	6485	SO:0001589	frameshift_variant	389812	exon5			.		CCDS7006.1	9q34.3	2011-10-24			ENSG00000177984	ENSG00000177984		"""Lipocalins"""	33777	protein-coding gene	gene with protein product							Standard	NM_203347		Approved	UNQ2541, PRO6093	uc004cjd.3	Q6UWW0	OTTHUMG00000020943	ENST00000316144.5:c.491delA	chr9.hg19:g.139656669delT	ENSP00000313833:p.Lys164fs	167.0	0.0		226.0	14.0	NM_203347		Frame_Shift_Del	DEL	ENST00000316144.5	hg19	CCDS7006.1																																																																																			.	.		0.647	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347	
TBC1D17	79735	hgsc.bcm.edu	37	19	50386052	50386052	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:50386052delG	ENST00000221543.5	+	8	1129	c.830delG	c.(829-831)cggfs	p.R277fs	TBC1D17_ENST00000535102.2_Frame_Shift_Del_p.R244fs	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	277	Required for interaction with OPTN.				autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)			NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		ACCGTGGAGCGGGGCCCTCCA	0.682																																					p.R277fs		Atlas-INDEL	.											.	TBC1D17	39	.	0			c.829delC						.						19.0	22.0	21.0					19																	50386052		2201	4296	6497	SO:0001589	frameshift_variant	79735	exon8			.	AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.830delG	chr19.hg19:g.50386052delG	ENSP00000221543:p.Arg277fs	143.0	0.0		181.0	11.0	NM_024682	B4DT12|B9A6L8|F5H1W7	Frame_Shift_Del	DEL	ENST00000221543.5	hg19	CCDS12785.1																																																																																			.	.		0.682	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682	
MDK	4192	hgsc.bcm.edu	37	11	46404272	46404272	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:46404272delC	ENST00000405308.2	+	4	809	c.380delC	c.(379-381)accfs	p.T127fs	MDK_ENST00000407067.1_Frame_Shift_Del_p.T127fs|MDK_ENST00000395565.1_Frame_Shift_Del_p.T127fs|MDK_ENST00000395566.4_Frame_Shift_Del_p.T127fs|MDK_ENST00000533283.1_3'UTR|MDK_ENST00000395569.4_Frame_Shift_Del_p.T71fs|MDK_ENST00000359803.3_Frame_Shift_Del_p.T127fs	NM_001270550.1	NP_001257479.1	P21741	MK_HUMAN	midkine (neurite growth-promoting factor 2)	127					adrenal gland development (GO:0030325)|behavioral fear response (GO:0001662)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cerebellar granular layer development (GO:0021681)|cerebral cortex development (GO:0021987)|defecation (GO:0030421)|dentate gyrus development (GO:0021542)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of cell division (GO:0051781)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of behavior (GO:0050795)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to wounding (GO:0009611)|short-term memory (GO:0007614)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			lung(1)	1				GBM - Glioblastoma multiforme(35;0.0252)|Lung(87;0.14)		AAGCCCTGCACCCCCAAGACC	0.657																																					p.T127fs		Atlas-INDEL	.											.	MDK	4	.	0			c.379delA						.						49.0	37.0	41.0					11																	46404272		2200	4298	6498	SO:0001589	frameshift_variant	4192	exon4			.		CCDS7919.1, CCDS59226.1	11p11.2	2008-07-18			ENSG00000110492	ENSG00000110492			6972	protein-coding gene	gene with protein product		162096		NEGF2		8406506	Standard	NM_002391		Approved	MK, FLJ27379	uc001nco.4	P21741	OTTHUMG00000150315	ENST00000405308.2:c.380delC	chr11.hg19:g.46404272delC	ENSP00000385451:p.Thr127fs	252.0	0.0		289.0	19.0	NM_001012333	Q2LEK4|Q9UCC7	Frame_Shift_Del	DEL	ENST00000405308.2	hg19	CCDS7919.1																																																																																			.	.		0.657	MDK-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317546.2	NM_001012334	
KDM1A	23028	hgsc.bcm.edu	37	1	23376988	23376988	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:23376988delT	ENST00000356634.3	+	3	775	c.626delT	c.(625-627)gttfs	p.V209fs	RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Frame_Shift_Del_p.V229fs|KDM1A_ENST00000542151.1_Frame_Shift_Del_p.V229fs	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	209	SWIRM. {ECO:0000255|PROSITE- ProRule:PRU00247}.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|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)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						ACCCAGAAGGTTTTTCTTTTC	0.408																																					p.V229fs		Atlas-INDEL	.											.	KDM1A	49	.	0			c.685delG						.						120.0	116.0	118.0					1																	23376988		2203	4300	6503	SO:0001589	frameshift_variant	23028	exon4			.	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"""Chromatin-modifying enzymes / K-demethylases"""	29079	protein-coding gene	gene with protein product		609132	"""amine oxidase (flavin containing) domain 2"", ""lysine (K)-specific demethylase 1"""	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.626delT	chr1.hg19:g.23376988delT	ENSP00000349049:p.Val209fs	117.0	0.0		146.0	13.0	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Frame_Shift_Del	DEL	ENST00000356634.3	hg19	CCDS30627.1																																																																																			.	.		0.408	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013	
CAP2	10486	hgsc.bcm.edu	37	6	17543332	17543332	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:17543332delG	ENST00000229922.2	+	11	1699	c.1167delG	c.(1165-1167)gtgfs	p.V389fs	CAP2_ENST00000489374.1_Frame_Shift_Del_p.V277fs|CAP2_ENST00000465994.1_Frame_Shift_Del_p.V325fs|CAP2_ENST00000378990.2_Frame_Shift_Del_p.V363fs|CAP2_ENST00000493172.1_Frame_Shift_Del_p.V129fs	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	389	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			ACAATGTGGTGGGCATTGTGG	0.433																																					p.V389fs		Atlas-INDEL	.											.	CAP2	61	.	0			c.1166delT						.						167.0	165.0	166.0					6																	17543332		2203	4300	6503	SO:0001589	frameshift_variant	10486	exon11			.	BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.1167delG	chr6.hg19:g.17543332delG	ENSP00000229922:p.Val389fs	138.0	0.0		173.0	12.0	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Frame_Shift_Del	DEL	ENST00000229922.2	hg19	CCDS4539.1																																																																																			.	.		0.433	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2		
EHBP1	23301	hgsc.bcm.edu	37	2	63176136	63176136	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:63176136delA	ENST00000263991.5	+	14	2742	c.2260delA	c.(2260-2262)aaafs	p.K755fs	EHBP1_ENST00000405015.3_Frame_Shift_Del_p.K720fs|EHBP1_ENST00000354487.3_Frame_Shift_Del_p.K720fs|EHBP1_ENST00000405289.1_Frame_Shift_Del_p.K720fs|EHBP1_ENST00000431489.1_Frame_Shift_Del_p.K720fs	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	755			K -> Q (in dbSNP:rs17432615).			cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			ATCTCCTATCAAAAAAACAAG	0.373																																					p.I753fs		Atlas-INDEL	.											.	EHBP1	127	.	0			c.2259delC						.						42.0	46.0	45.0					2																	63176136		2202	4299	6501	SO:0001589	frameshift_variant	23301	exon14			.	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.2260delA	chr2.hg19:g.63176136delA	ENSP00000263991:p.Lys755fs	163.0	0.0		177.0	12.0	NM_015252	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Frame_Shift_Del	DEL	ENST00000263991.5	hg19	CCDS1872.1																																																																																			.	.		0.373	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252	
ATP13A2	23400	hgsc.bcm.edu	37	1	17312998	17312998	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:17312998delC	ENST00000326735.8	-	28	3398	c.3365delG	c.(3364-3366)ggtfs	p.G1122fs	RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Intron|ATP13A2_ENST00000452699.1_Frame_Shift_Del_p.G1117fs			Q9NQ11	AT132_HUMAN	ATPase type 13A2	1122					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		GGTGACCAGACCCAGCAGCAG	0.677																																					p.G1122fs		Atlas-INDEL	.											.	ATP13A2	85	.	0			c.3366delT						.						48.0	53.0	51.0					1																	17312998		2203	4299	6502	SO:0001589	frameshift_variant	23400	exon28			.	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.3365delG	chr1.hg19:g.17312998delC	ENSP00000327214:p.Gly1122fs	165.0	0.0		170.0	11.0	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Frame_Shift_Del	DEL	ENST00000326735.8	hg19	CCDS175.1																																																																																			.	.		0.677	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
ABHD3	171586	hgsc.bcm.edu	37	18	19263929	19263929	+	Intron	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:19263929delA	ENST00000289119.2	-	4	649				RP11-13N13.6_ENST00000578583.1_RNA|ABHD3_ENST00000580981.1_Intron|ABHD3_ENST00000579875.1_Intron|ABHD3_ENST00000578270.1_Intron|MIR320C1_ENST00000408566.1_RNA	NM_138340.4	NP_612213.2	Q8WU67	ABHD3_HUMAN	abhydrolase domain containing 3							integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(2)	10						CCACACATCTAAAAACCAGGA	0.313																																					.		Atlas-INDEL	.											.	ABHD3	32	.	0			c.510-2T>-						.						79.0	88.0	85.0					18																	19263929		2203	4296	6499	SO:0001627	intron_variant	171586	exon5			.	AK024880	CCDS32802.1	18q11.1	2011-02-16			ENSG00000158201	ENSG00000158201		"""Abhydrolase domain containing"""	18718	protein-coding gene	gene with protein product		612197					Standard	NM_138340		Approved	LABH3	uc002ktl.2	Q8WU67		ENST00000289119.2:c.510-3T>-	chr18.hg19:g.19263929delA		181.0	0.0		213.0	13.0	NM_138340	B0YIV0|B7Z5C2|O43411	Splice_Site	DEL	ENST00000289119.2	hg19	CCDS32802.1																																																																																			.	.		0.313	ABHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444757.1		
TNS3	64759	hgsc.bcm.edu	37	7	47333390	47333390	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:47333390delA	ENST00000398879.1	-	25	4079	c.3713delT	c.(3712-3714)ttgfs	p.L1238fs	TNS3_ENST00000311160.9_Frame_Shift_Del_p.L1238fs|TNS3_ENST00000355730.3_Frame_Shift_Del_p.L998fs			Q68CZ2	TENS3_HUMAN	tensin 3	1238	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						ACACTCGATCAAAAAGTGCCG	0.438																																					p.L1238fs		Atlas-INDEL	.											.	TNS3	140	.	0			c.3714delG						.						93.0	90.0	91.0					7																	47333390		1902	4114	6016	SO:0001589	frameshift_variant	64759	exon25			.	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"""SH2 domain containing"""	21616	protein-coding gene	gene with protein product	"""tumor endothelial marker 6"""	606825	"""tensin-like SH2 domain-containing 1"""	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.3713delT	chr7.hg19:g.47333390delA	ENSP00000381854:p.Leu1238fs	92.0	0.0		108.0	10.0	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Frame_Shift_Del	DEL	ENST00000398879.1	hg19	CCDS5506.2																																																																																			.	.		0.438	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748	
TTC1	7265	hgsc.bcm.edu	37	5	159476629	159476629	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:159476629delA	ENST00000231238.5	+	6	760	c.650delA	c.(649-651)gaafs	p.E217fs	TTC1_ENST00000520274.1_3'UTR|TTC1_ENST00000522793.1_Frame_Shift_Del_p.E217fs	NM_001282500.1|NM_003314.1	NP_001269429.1|NP_003305.1	Q99614	TTC1_HUMAN	tetratricopeptide repeat domain 1	217					protein folding (GO:0006457)	peroxisomal membrane (GO:0005778)	unfolded protein binding (GO:0051082)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(1)|prostate(1)|skin(1)	12	Renal(175;0.00196)	all_hematologic(541;0.00014)|Breast(839;0.0101)|all_neural(177;0.0281)|Medulloblastoma(196;0.0425)|Lung NSC(249;0.119)|all_lung(500;0.163)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	Epithelial(171;8.37e-05)|all cancers(165;0.000694)|OV - Ovarian serous cystadenocarcinoma(192;0.0402)		TCTATATTAGAAAAAGATCCA	0.358																																					p.E217fs		Atlas-INDEL	.											.	TTC1	26	.	0			c.649delG						.						51.0	54.0	53.0					5																	159476629		2203	4300	6503	SO:0001589	frameshift_variant	7265	exon6			.	U46570	CCDS4348.1	5q32-q33.2	2013-01-10			ENSG00000113312	ENSG00000113312		"""Tetratricopeptide (TTC) repeat domain containing"""	12391	protein-coding gene	gene with protein product		601963				8836031	Standard	NM_003314		Approved	TPR1	uc003lxu.3	Q99614	OTTHUMG00000130326	ENST00000231238.5:c.650delA	chr5.hg19:g.159476629delA	ENSP00000231238:p.Glu217fs	96.0	0.0		139.0	12.0	NM_003314	B2RCT2|D3DQJ8|Q9BVT3	Frame_Shift_Del	DEL	ENST00000231238.5	hg19	CCDS4348.1																																																																																			.	.		0.358	TTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252675.3	NM_003314	
DNAH7	56171	hgsc.bcm.edu	37	2	196799425	196799426	+	Frame_Shift_Del	DEL	CG	CG	-	rs372668189|rs199987634		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:196799425_196799426delCG	ENST00000312428.6	-	21	3460_3461	c.3360_3361delCG	c.(3358-3363)agcgaafs	p.SE1120fs		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1120	Stem. {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						ACCTCTCCTTCGCTGCTCTTCA	0.401																																					p.1121_1121del		Atlas-Indel,Pindel	.											.	DNAH7	512	.	0			c.3361_3362del						.																																			SO:0001589	frameshift_variant	56171	exon21			.	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.3360_3361delCG	chr2.hg19:g.196799425_196799426delCG	ENSP00000311273:p.Ser1120fs	208.0	0.0		221.0	48.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Frame_Shift_Del	DEL	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.401	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
SYNE2	23224	hgsc.bcm.edu	37	14	64518666	64518666	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:64518666delT	ENST00000344113.4	+	48	8247	c.8035delT	c.(8035-8037)tttfs	p.F2679fs	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Frame_Shift_Del_p.F2712fs|SYNE2_ENST00000358025.3_Frame_Shift_Del_p.F2679fs	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2679					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)		CAAGCATGGATTTTCTGTTTT	0.433																																					p.G2678fs		Atlas-INDEL	.											.	SYNE2	577	.	0			c.8034delA						.						91.0	91.0	91.0					14																	64518666		1907	4118	6025	SO:0001589	frameshift_variant	23224	exon48			.	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.8035delT	chr14.hg19:g.64518666delT	ENSP00000341781:p.Phe2679fs	153.0	0.0		186.0	12.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Frame_Shift_Del	DEL	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.433	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
APC	324	hgsc.bcm.edu	37	5	112176345	112176345	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:112176345delA	ENST00000457016.1	+	16	5434	c.5054delA	c.(5053-5055)gaafs	p.E1685fs	APC_ENST00000508376.2_Frame_Shift_Del_p.E1685fs|APC_ENST00000257430.4_Frame_Shift_Del_p.E1685fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1685	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|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 apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GGTGAATTTGAAAAACGAGAT	0.438		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.E1685fs	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-INDEL	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	APC	4158	.	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.5053delG						.						58.0	58.0	58.0					5																	112176345		2202	4300	6502	SO:0001589	frameshift_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	.	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.5054delA	chr5.hg19:g.112176345delA	ENSP00000413133:p.Glu1685fs	104.0	0.0		114.0	11.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	hg19	CCDS4107.1																																																																																			.	.		0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
VIPR1	7433	hgsc.bcm.edu	37	3	42576497	42576497	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:42576497delC	ENST00000325123.4	+	11	1154	c.1041delC	c.(1039-1041)atcfs	p.I347fs	VIPR1-AS1_ENST00000602176.1_RNA|VIPR1-AS1_ENST00000596630.1_RNA|VIPR1_ENST00000543411.1_Frame_Shift_Del_p.I299fs|VIPR1-AS1_ENST00000601312.1_RNA|VIPR1-AS1_ENST00000452639.3_RNA|VIPR1-AS1_ENST00000600342.1_RNA|VIPR1-AS1_ENST00000610022.1_RNA|VIPR1-AS1_ENST00000593611.1_RNA|VIPR1_ENST00000433647.1_Frame_Shift_Del_p.I306fs|VIPR1-AS1_ENST00000608869.1_RNA|VIPR1-AS1_ENST00000593621.1_RNA|VIPR1-AS1_ENST00000598837.1_RNA|VIPR1_ENST00000438259.2_Frame_Shift_Del_p.I137fs	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	347					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)		TCCTGCTGATCCCCCTGTTTG	0.527																																					p.I347fs		Atlas-INDEL	.											.	VIPR1	45	.	0			c.1040delT						.						169.0	136.0	147.0					3																	42576497		2203	4300	6503	SO:0001589	frameshift_variant	7433	exon11			.	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.1041delC	chr3.hg19:g.42576497delC	ENSP00000327246:p.Ile347fs	179.0	0.0		198.0	14.0	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Frame_Shift_Del	DEL	ENST00000325123.4	hg19	CCDS2698.1																																																																																			.	.		0.527	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624	
FBXL18	80028	hgsc.bcm.edu	37	7	5540757	5540757	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:5540757delG	ENST00000382368.3	-	3	1266	c.1143delC	c.(1141-1143)tccfs	p.S381fs	FBXL18_ENST00000453700.3_Frame_Shift_Del_p.S381fs	NM_024963.4	NP_079239.3	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	381									FBXL18/RNF216(2)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		GGTTGCAGCAGGACGCCACCA	0.692																																					p.C382fs		Atlas-INDEL	.											.	FBXL18	99	.	0			c.1144delT						.						18.0	26.0	23.0					7																	5540757		2170	4266	6436	SO:0001589	frameshift_variant	80028	exon3			.	AK057042	CCDS43546.1	7p22.2	2011-06-09			ENSG00000155034	ENSG00000155034		"""F-boxes / Leucine-rich repeats"""	21874	protein-coding gene	gene with protein product		609084					Standard	NM_024963		Approved	FLJ11467, Fbl18	uc003son.4	Q96ME1	OTTHUMG00000151832	ENST00000382368.3:c.1143delC	chr7.hg19:g.5540757delG	ENSP00000371805:p.Ser381fs	170.0	0.0		153.0	10.0	NM_024963	Q9BR90|Q9BTC7|Q9HAK7	Frame_Shift_Del	DEL	ENST00000382368.3	hg19	CCDS43546.1																																																																																			.	.		0.692	FBXL18-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324093.1	NM_024963	
ZNF148	7707	hgsc.bcm.edu	37	3	124952718	124952718	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:124952718delT	ENST00000360647.4	-	9	1337	c.852delA	c.(850-852)aaafs	p.K284fs	ZNF148_ENST00000485866.1_Frame_Shift_Del_p.K284fs|ZNF148_ENST00000497929.1_5'UTR|ZNF148_ENST00000492394.1_Frame_Shift_Del_p.K284fs|ZNF148_ENST00000544464.1_Intron|ZNF148_ENST00000468369.1_Intron|ZNF148_ENST00000484491.1_Frame_Shift_Del_p.K284fs|SLC12A8_ENST00000423114.2_Intron	NM_021964.2	NP_068799.2	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	284					cellular defense response (GO:0006968)|gamete generation (GO:0007276)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein complex assembly (GO:0006461)|substantia nigra development (GO:0021762)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)	28						ATCTATTTAGTTTTTTGTCAT	0.383																																					p.L285X		Atlas-INDEL	.											.	ZNF148	84	.	0			c.853delC						.						86.0	86.0	86.0					3																	124952718		2203	4300	6503	SO:0001589	frameshift_variant	7707	exon9			.	U09851	CCDS3031.1	3q21.2	2013-01-08	2006-06-13		ENSG00000163848	ENSG00000163848		"""Zinc fingers, C2H2-type"""	12933	protein-coding gene	gene with protein product		601897	"""zinc finger protein 148 (pHZ-52)"""			7557990, 9925940	Standard	NM_021964		Approved	BERF-1, ZBP-89, BFCOL1, HT-BETA, ZFP148, pHZ-52	uc003ehx.4	Q9UQR1	OTTHUMG00000159448	ENST00000360647.4:c.852delA	chr3.hg19:g.124952718delT	ENSP00000353863:p.Lys284fs	100.0	0.0		130.0	10.0	NM_021964	D3DN27|O00389|O43591|Q58EY5|Q6PJ98	Frame_Shift_Del	DEL	ENST00000360647.4	hg19	CCDS3031.1																																																																																			.	.		0.383	ZNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355452.4	NM_021964	
CKM	1158	hgsc.bcm.edu	37	19	45811713	45811713	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:45811713delC	ENST00000221476.3	-	6	905	c.731delG	c.(730-732)ggcfs	p.G244fs		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	244	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|phosphocreatine biosynthetic process (GO:0046314)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.N245fs*17(1)		cervix(1)|endometrium(1)|large_intestine(8)|lung(3)|prostate(2)|skin(2)	17		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)	CTTCATGTTGCCCCCCTTCTC	0.577																																					p.G244fs		Atlas-INDEL	.											.,1	CKM	40	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.732delC						.						119.0	96.0	104.0					19																	45811713		2203	4300	6503	SO:0001589	frameshift_variant	1158	exon6			.	M14780	CCDS12659.1	19q13.32	2012-10-02			ENSG00000104879	ENSG00000104879	2.7.3.2		1994	protein-coding gene	gene with protein product		123310		CKMM			Standard	NM_001824		Approved		uc002pbd.4	P06732		ENST00000221476.3:c.731delG	chr19.hg19:g.45811713delC	ENSP00000221476:p.Gly244fs	104.0	0.0		162.0	12.0	NM_001824	Q96QL9	Frame_Shift_Del	DEL	ENST00000221476.3	hg19	CCDS12659.1																																																																																			.	.		0.577	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1		
EFHC1	114327	hgsc.bcm.edu	37	6	52343943	52343943	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:52343943delG	ENST00000371068.5	+	8	1490	c.1387delG	c.(1387-1389)gggfs	p.G464fs	EFHC1_ENST00000538167.1_Frame_Shift_Del_p.G445fs|EFHC1_ENST00000433625.2_Frame_Shift_Del_p.G373fs	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	464	DM10 3. {ECO:0000255|PROSITE- ProRule:PRU00665}.					axoneme (GO:0005930)|neuronal cell body (GO:0043025)	calcium ion binding (GO:0005509)|protein C-terminus binding (GO:0008022)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	27	Lung NSC(77;0.109)					TGGTATCATTGGGGGCAAGTA	0.458																																					p.I462fs		Atlas-INDEL	.											.	EFHC1	68	.	0			c.1386delT						.						159.0	146.0	150.0					6																	52343943		2203	4300	6503	SO:0001589	frameshift_variant	114327	exon8			.	AK001328	CCDS4942.1, CCDS55021.1	6p12.3	2014-02-04			ENSG00000096093	ENSG00000096093		"""EF-hand domain containing"""	16406	protein-coding gene	gene with protein product	"""myoclonin-1"""	608815	"""epilepsy, juvenile myoclonic 1"""	EJM1, EJM		15258581	Standard	NM_018100		Approved	FLJ10466	uc003pap.4	Q5JVL4	OTTHUMG00000014848	ENST00000371068.5:c.1387delG	chr6.hg19:g.52343943delG	ENSP00000360107:p.Gly464fs	131.0	0.0		151.0	12.0	NM_018100	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Frame_Shift_Del	DEL	ENST00000371068.5	hg19	CCDS4942.1																																																																																			.	.		0.458	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100	
TMEM87A	25963	hgsc.bcm.edu	37	15	42512286	42512286	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:42512286delT	ENST00000389834.4	-	16	1715	c.1451delA	c.(1450-1452)aagfs	p.K484fs	RP11-546B15.1_ENST00000563846.1_RNA|TMEM87A_ENST00000448392.1_Frame_Shift_Del_p.K423fs	NM_015497.3	NP_056312.2	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A	484						integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		CATAGGCTCCTTTTGTTCATC	0.308																																					p.K484fs		Atlas-INDEL	.											.	TMEM87A	56	.	0			c.1452delG						.						110.0	119.0	116.0					15																	42512286		2203	4299	6502	SO:0001589	frameshift_variant	25963	exon16			.	AF132733	CCDS32205.1, CCDS45243.1, CCDS66742.1	15q15.1	2005-10-30				ENSG00000103978			24522	protein-coding gene	gene with protein product						12477932	Standard	XM_005254287		Approved	DKFZP564G2022	uc021sjr.1	Q8NBN3		ENST00000389834.4:c.1451delA	chr15.hg19:g.42512286delT	ENSP00000374484:p.Lys484fs	141.0	0.0		198.0	12.0	NM_015497	Q6NT77|Q8NCA4|Q9BS46|Q9P103|Q9Y3Y7	Frame_Shift_Del	DEL	ENST00000389834.4	hg19	CCDS32205.1																																																																																			.	.		0.308	TMEM87A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420482.2	NM_015497	
PIEZO1	9780	hgsc.bcm.edu	37	16	88780815	88780815	+	IGR	DEL	C	C	-	rs573239956		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:88780815delC	ENST00000301015.9	-	0	8072				MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000453996.2_Frame_Shift_Del_p.G374fs|CTU2_ENST00000567949.1_Frame_Shift_Del_p.G445fs|CTU2_ENST00000378384.3_Frame_Shift_Del_p.G287fs|CTU2_ENST00000312060.5_Frame_Shift_Del_p.G374fs	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						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						TGGTGAAGGGCCCCCGGGATG	0.662																																					p.G374fs		Atlas-INDEL	.											.	CTU2	66	.	0			c.1121delG						.						64.0	80.0	75.0					16																	88780815		2193	4293	6486	SO:0001628	intergenic_variant	348180	exon11			.	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		chr16.hg19:g.88780815delC		162.0	0.0		192.0	12.0	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Frame_Shift_Del	DEL	ENST00000301015.9	hg19	CCDS54058.1																																																																																			.	.		0.662	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
PPOX	5498	hgsc.bcm.edu	37	1	161140731	161140731	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:161140731delA	ENST00000367999.4	+	12	1549	c.1283delA	c.(1282-1284)caafs	p.Q428fs	PPOX_ENST00000544598.1_Frame_Shift_Del_p.Q136fs|PPOX_ENST00000432542.2_Intron|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000495483.1_Intron|PPOX_ENST00000352210.5_Frame_Shift_Del_p.Q428fs|B4GALT3_ENST00000470882.1_5'Flank	NM_001122764.1	NP_001116236.1	P50336	PPOX_HUMAN	protoporphyrinogen oxidase	428					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)			GGTCACTGGCAAAAACTAGGT	0.478																																					p.Q428fs		Atlas-INDEL	.											.	PPOX	34	.	0			c.1282delC						.						124.0	127.0	126.0					1																	161140731		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.1283delA	chr1.hg19:g.161140731delA	ENSP00000356978:p.Gln428fs	92.0	0.0		129.0	10.0	NM_001122764	D3DVG0|Q5VTW8	Frame_Shift_Del	DEL	ENST00000367999.4	hg19	CCDS1221.1																																																																																			.	.		0.478	PPOX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082993.1	NM_000309	
MUTYH	4595	hgsc.bcm.edu	37	1	45797094	45797094	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:45797094delC	ENST00000372098.3	-	13	1445	c.1312delG	c.(1312-1314)gagfs	p.E438fs	MUTYH_ENST00000372100.5_Frame_Shift_Del_p.E424fs|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000355498.2_Frame_Shift_Del_p.E413fs|MUTYH_ENST00000372104.1_Frame_Shift_Del_p.E413fs|MUTYH_ENST00000456914.2_Frame_Shift_Del_p.E413fs|MUTYH_ENST00000488731.2_Frame_Shift_Del_p.E108fs|MUTYH_ENST00000354383.6_Frame_Shift_Del_p.E414fs|MUTYH_ENST00000450313.1_Frame_Shift_Del_p.E441fs|MUTYH_ENST00000372115.3_Frame_Shift_Del_p.E427fs|MUTYH_ENST00000528332.2_Frame_Shift_Del_p.E122fs|MUTYH_ENST00000372110.3_Frame_Shift_Del_p.E428fs|MUTYH_ENST00000529984.1_Frame_Shift_Del_p.E108fs|MUTYH_ENST00000448481.1_Frame_Shift_Del_p.E424fs|MUTYH_ENST00000528013.2_Frame_Shift_Del_p.E427fs			Q9UIF7	MUTYH_HUMAN	mutY homolog	438	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					TCACTTACCTCCCCAAGGTGC	0.602			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																												p.E441fs		Atlas-INDEL	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.1322delA						.						46.0	48.0	48.0					1																	45797094		2203	4300	6503	SO:0001589	frameshift_variant	4595	exon13	Familial Cancer Database	MAP, MYH-associated polyposis	.	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"""mutY (E. coli) homolog"", ""mutY homolog (E. coli)"""			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.1312delG	chr1.hg19:g.45797094delC	ENSP00000361170:p.Glu438fs	140.0	0.0		159.0	12.0	NM_001128425	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Frame_Shift_Del	DEL	ENST00000372098.3	hg19	CCDS520.1																																																																																			.	.		0.602	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222	
SMPD4	55627	hgsc.bcm.edu	37	2	130910956	130910956	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:130910956delT	ENST00000409031.1	-	18	3226	c.2078delA	c.(2077-2079)aagfs	p.K693fs	SMPD4_ENST00000443958.2_Frame_Shift_Del_p.K357fs|SMPD4_ENST00000473720.1_5'Flank|SMPD4_ENST00000339679.7_Frame_Shift_Del_p.K551fs|SMPD4_ENST00000426662.2_Frame_Shift_Del_p.K329fs|SMPD4_ENST00000452225.2_Frame_Shift_Del_p.K434fs|SMPD4_ENST00000453750.1_Frame_Shift_Del_p.K442fs|SMPD4_ENST00000351288.6_Frame_Shift_Del_p.K664fs|SMPD4_ENST00000431183.2_Frame_Shift_Del_p.K591fs	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	654				L -> Q (in Ref. 2; BAA91567). {ECO:0000305}.	cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	GGGGAGTTGCTTTTTTCCATT	0.617																																					p.K693fs		Atlas-INDEL	.											.	SMPD4	67	.	0			c.2079delG						.						81.0	68.0	72.0					2																	130910956		2203	4300	6503	SO:0001589	frameshift_variant	55627	exon18			.	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.2078delA	chr2.hg19:g.130910956delT	ENSP00000386531:p.Lys693fs	156.0	0.0		194.0	12.0	NM_017951	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Frame_Shift_Del	DEL	ENST00000409031.1	hg19	CCDS42751.1																																																																																			.	.		0.617	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751	
SCN7A	6332	hgsc.bcm.edu	37	2	167313428	167313428	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:167313428delT	ENST00000409855.1	-	10	1368	c.1242delA	c.(1240-1242)aaafs	p.K414fs		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	414					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	TCTGTTGAAATTTTGGTTCAA	0.313																																					p.F415fs		Atlas-INDEL	.											.	SCN7A	410	.	0			c.1243delT						.						56.0	52.0	53.0					2																	167313428		1794	4048	5842	SO:0001589	frameshift_variant	6332	exon10			.	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.1242delA	chr2.hg19:g.167313428delT	ENSP00000386796:p.Lys414fs	169.0	0.0		194.0	12.0	NM_002976		Frame_Shift_Del	DEL	ENST00000409855.1	hg19	CCDS46442.1																																																																																			.	.		0.313	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
RNF44	22838	hgsc.bcm.edu	37	5	175956599	175956599	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:175956599delC	ENST00000274811.4	-	9	1585	c.1061delG	c.(1060-1062)ggtfs	p.G354fs	RNF44_ENST00000537487.1_Frame_Shift_Del_p.G273fs|RNF44_ENST00000509404.1_5'Flank	NM_014901.4	NP_055716.1	Q7L0R7	RNF44_HUMAN	ring finger protein 44	354							zinc ion binding (GO:0008270)			endometrium(2)|lung(3)|prostate(1)|skin(1)|stomach(1)	8	all_cancers(89;0.0029)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTTGGTGAGACCCCGGGGCTT	0.667																																					p.G354fs		Atlas-INDEL	.											.	RNF44	33	.	0			c.1062delT						.						68.0	63.0	65.0					5																	175956599		2203	4300	6503	SO:0001589	frameshift_variant	22838	exon9			.	AB029023	CCDS4404.1	5q35.3	2013-01-09			ENSG00000146083	ENSG00000146083		"""RING-type (C3HC4) zinc fingers"""	19180	protein-coding gene	gene with protein product						10470851	Standard	NM_014901		Approved	KIAA1100	uc003mek.1	Q7L0R7	OTTHUMG00000130664	ENST00000274811.4:c.1061delG	chr5.hg19:g.175956599delC	ENSP00000274811:p.Gly354fs	164.0	0.0		181.0	11.0	NM_014901	B4DYE0|Q8ND05|Q9UPQ2	Frame_Shift_Del	DEL	ENST00000274811.4	hg19	CCDS4404.1																																																																																			.	.		0.667	RNF44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253156.2		
ACSBG2	81616	hgsc.bcm.edu	37	19	6183239	6183239	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:6183239delG	ENST00000586696.1	+	10	1554	c.1278delG	c.(1276-1278)tcgfs	p.S426fs	ACSBG2_ENST00000252669.5_Frame_Shift_Del_p.S426fs|ACSBG2_ENST00000588304.1_Frame_Shift_Del_p.S376fs|ACSBG2_ENST00000591741.1_3'UTR|ACSBG2_ENST00000591403.1_Frame_Shift_Del_p.S426fs|ACSBG2_ENST00000588485.1_Frame_Shift_Del_p.S239fs			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	426					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GTGAGAGCTCGGGACCCCACA	0.547																																					p.S426fs		Atlas-INDEL	.											.	ACSBG2	83	.	0			c.1277delC						.						68.0	70.0	69.0					19																	6183239		2203	4300	6503	SO:0001589	frameshift_variant	81616	exon10			.		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"""Acyl-CoA synthetase family"""	24174	protein-coding gene	gene with protein product	"""bubblegum related protein"""	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.1278delG	chr19.hg19:g.6183239delG	ENSP00000465589:p.Ser426fs	138.0	0.0		170.0	11.0	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Frame_Shift_Del	DEL	ENST00000586696.1	hg19	CCDS12159.1																																																																																			.	.		0.547	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924	
SPATA7	55812	hgsc.bcm.edu	37	14	88883150	88883150	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:88883150delA	ENST00000393545.4	+	5	623	c.334delA	c.(334-336)aaafs	p.K112fs	SPATA7_ENST00000356583.5_Frame_Shift_Del_p.K80fs|SPATA7_ENST00000556553.1_Frame_Shift_Del_p.K80fs|SPATA7_ENST00000045347.7_Frame_Shift_Del_p.K112fs	NM_018418.4	NP_060888.2	Q9P0W8	SPAT7_HUMAN	spermatogenesis associated 7	112					response to stimulus (GO:0050896)|visual perception (GO:0007601)					cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	18						AGCCAATTATAAAAATAATTC	0.289																																					p.Y111X		Atlas-INDEL	.											.	SPATA7	58	.	0			c.333delT						.						46.0	50.0	49.0					14																	88883150		2199	4294	6493	SO:0001589	frameshift_variant	55812	exon5			.	AF144487	CCDS9883.1, CCDS32132.1	14q31.3	2011-02-17				ENSG00000042317			20423	protein-coding gene	gene with protein product		609868	"""Leber congenital amaurosis 3"""	LCA3		9799089, 19268277	Standard	NM_018418		Approved	HSD3	uc001xwq.3	Q9P0W8		ENST00000393545.4:c.334delA	chr14.hg19:g.88883150delA	ENSP00000377176:p.Lys112fs	174.0	0.0		163.0	10.0	NM_018418	Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7	Frame_Shift_Del	DEL	ENST00000393545.4	hg19	CCDS9883.1																																																																																			.	.		0.289	SPATA7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410172.1		
INPP5J	27124	hgsc.bcm.edu	37	22	31524051	31524051	+	Intron	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:31524051delG	ENST00000331075.5	+	7	1948				INPP5J_ENST00000405300.1_Intron|INPP5J_ENST00000412277.2_Intron|INPP5J_ENST00000404453.1_Intron|INPP5J_ENST00000401755.1_5'UTR|INPP5J_ENST00000400294.2_Intron|INPP5J_ENST00000404390.3_Intron|INPP5J_ENST00000402238.1_Intron	NM_001284285.1	NP_001271214.1	Q15735	PI5PA_HUMAN	inositol polyphosphate-5-phosphatase J						inositol phosphate metabolic process (GO:0043647)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	12						AGGACCAGGTGGGGTCCTTGT	0.587																																					.		Atlas-INDEL	.											.	INPP5J	94	.	0			c.795+2G>-						.						45.0	46.0	46.0					22																	31524051		2082	4199	6281	SO:0001627	intron_variant	27124	exon7			.	U45975	CCDS46687.1, CCDS63453.1, CCDS63454.1, CCDS63455.1, CCDS74847.1	22q12.2	2008-09-09	2008-09-09	2008-09-09	ENSG00000185133	ENSG00000185133			8956	protein-coding gene	gene with protein product		606481	"""phosphatidylinositol (4,5) bisphosphate 5-phosphatase, A"""	PIB5PA		10591208	Standard	NM_001284287		Approved	INPP5	uc003aju.4	Q15735	OTTHUMG00000151206	ENST00000331075.5:c.1899+3G>-	chr22.hg19:g.31524051delG		122.0	0.0		154.0	11.0	NM_001002837	B3KS54|Q32M61|Q6ZTH6|Q8N902|Q9UDT9	Splice_Site	DEL	ENST00000331075.5	hg19																																																																																				.	.		0.587	INPP5J-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000321784.1	NM_001002837	
ASUN	55726	hgsc.bcm.edu	37	12	27067353	27067353	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:27067353delA	ENST00000261191.7	-	12	1943	c.1407delT	c.(1405-1407)tttfs	p.F469fs	ASUN_ENST00000539625.1_Frame_Shift_Del_p.F368fs	NM_018164.2	NP_060634.2	Q9NVM9	ASUN_HUMAN	asunder spermatogenesis regulator	469					centrosome localization (GO:0051642)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|protein localization to nuclear envelope (GO:0090435)|regulation of fertilization (GO:0080154)|regulation of mitotic cell cycle (GO:0007346)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											CTTGCATGTTAAAAATGGTGG	0.323																																					p.N470fs		Atlas-INDEL	.											.	.	.	.	0			c.1408delA						.						140.0	140.0	140.0					12																	27067353		2203	4300	6503	SO:0001589	frameshift_variant	55726	exon12			.	AK001222	CCDS8708.1	12p12.3	2013-05-08	2013-05-08	2011-12-09	ENSG00000064102	ENSG00000064102			20174	protein-coding gene	gene with protein product	"""spermatogenesis associated 30"""	615079	"""chromosome 12 open reading frame 11"", ""asunder, spermatogenesis regulator homolog (Drosphila)"""	C12orf11		12414650, 19357193, 23097494	Standard	NM_018164		Approved	FLJ10637, NET48, Mat89Bb, SPATA30	uc001rhk.4	Q9NVM9	OTTHUMG00000169193	ENST00000261191.7:c.1407delT	chr12.hg19:g.27067353delA	ENSP00000261191:p.Phe469fs	131.0	0.0		173.0	12.0	NM_018164	B4DNK1|Q86WE2|Q96HM2|Q9BTX2|Q9NTB6|Q9NVM5	Frame_Shift_Del	DEL	ENST00000261191.7	hg19	CCDS8708.1																																																																																			.	.		0.323	ASUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402819.1	NM_018164	
GATAD2A	54815	hgsc.bcm.edu	37	19	19609429	19609429	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:19609429delC	ENST00000360315.3	+	8	1414	c.1102delC	c.(1102-1104)cccfs	p.P369fs	GATAD2A_ENST00000404158.1_Frame_Shift_Del_p.P369fs|GATAD2A_ENST00000358713.3_Frame_Shift_Del_p.P369fs|GATAD2A_ENST00000537887.1_5'UTR|GATAD2A_ENST00000429563.2_Frame_Shift_Del_p.P196fs|GATAD2A_ENST00000252577.5_Frame_Shift_Del_p.P369fs	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	369	CR2; histone tail-binding.				anterior neuropore closure (GO:0021506)|blood vessel development (GO:0001568)|DNA methylation (GO:0006306)|embryonic body morphogenesis (GO:0010172)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|neural fold formation (GO:0001842)|programmed cell death (GO:0012501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|NuRD complex (GO:0016581)	protein binding, bridging (GO:0030674)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13						CCCACCCAAGCCCCCAGCCCC	0.637																																					p.K367fs		Atlas-INDEL	.											.	GATAD2A	81	.	0			c.1101delG						.						38.0	39.0	39.0					19																	19609429		2203	4300	6503	SO:0001589	frameshift_variant	54815	exon8			.	AL390164	CCDS12402.2	19p13.11	2013-01-25			ENSG00000167491	ENSG00000167491		"""GATA zinc finger domain containing"""	29989	protein-coding gene	gene with protein product	"""p66 alpha"""	614997				12183469	Standard	NM_017660		Approved	p66alpha	uc010xqt.2	Q86YP4	OTTHUMG00000152541	ENST00000360315.3:c.1102delC	chr19.hg19:g.19609429delC	ENSP00000353463:p.Pro369fs	210.0	0.0		279.0	17.0	NM_017660	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Frame_Shift_Del	DEL	ENST00000360315.3	hg19	CCDS12402.2																																																																																			.	.		0.637	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660	
ATP5A1	498	hgsc.bcm.edu	37	18	43666170	43666170	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:43666170delA	ENST00000398752.6	-	10	1459	c.1338delT	c.(1336-1338)tttfs	p.F446fs	ATP5A1_ENST00000590665.1_Frame_Shift_Del_p.F424fs|ATP5A1_ENST00000593152.2_Frame_Shift_Del_p.F396fs|ATP5A1_ENST00000282050.2_Frame_Shift_Del_p.F446fs	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	446					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						CGAACTGGGCAAAAGCAGCAA	0.473																																					p.A447fs		Atlas-INDEL	.											.	ATP5A1	52	.	0			c.1339delG						.						94.0	87.0	89.0					18																	43666170		2203	4300	6503	SO:0001589	frameshift_variant	498	exon10			.	D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	823	protein-coding gene	gene with protein product		164360	"""ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2"", ""ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"""	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.1338delT	chr18.hg19:g.43666170delA	ENSP00000381736:p.Phe446fs	141.0	0.0		209.0	13.0	NM_004046	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Frame_Shift_Del	DEL	ENST00000398752.6	hg19	CCDS11927.1																																																																																			.	.		0.473	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046	
LGALS4	3960	hgsc.bcm.edu	37	19	39294528	39294528	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:39294528delG	ENST00000307751.4	-	5	959	c.482delC	c.(481-483)ccgfs	p.P161fs	LGALS4_ENST00000597803.1_5'Flank	NM_006149.3	NP_006140.1	P56470	LEG4_HUMAN	lectin, galactoside-binding, soluble, 4	161					cell adhesion (GO:0007155)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17	all_cancers(60;1.02e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			TGGCATCATCGGGGGTCCCTG	0.582																																					p.P161fs		Atlas-INDEL	.											.	LGALS4	39	.	0			c.483delG						.						46.0	47.0	47.0					19																	39294528		2203	4300	6503	SO:0001589	frameshift_variant	3960	exon5			.		CCDS12521.1	19q13.2	2014-03-19	2008-07-25		ENSG00000171747	ENSG00000171747		"""Lectins, galactoside-binding"""	6565	protein-coding gene	gene with protein product	"""galectin 4"""	602518				8063692	Standard	NM_006149		Approved	GAL4	uc002ojg.3	P56470	OTTHUMG00000182608	ENST00000307751.4:c.482delC	chr19.hg19:g.39294528delG	ENSP00000302100:p.Pro161fs	93.0	0.0		129.0	10.0	NM_006149		Frame_Shift_Del	DEL	ENST00000307751.4	hg19	CCDS12521.1																																																																																			.	.		0.582	LGALS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462641.1	NM_006149	
NUB1	51667	hgsc.bcm.edu	37	7	151052912	151052912	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:151052912delA	ENST00000355851.4	+	6	551	c.474delA	c.(472-474)ctafs	p.L158fs	NUB1_ENST00000413040.2_Frame_Shift_Del_p.L182fs|NUB1_ENST00000568733.1_Frame_Shift_Del_p.L182fs|NUB1_ENST00000566856.1_Frame_Shift_Del_p.L158fs|NUB1_ENST00000477666.1_3'UTR	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	158					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		TGCTTGAACTAAAACAATCTG	0.398																																					p.L182fs		Atlas-INDEL	.											.	NUB1	31	.	0			c.545delT						.						56.0	50.0	52.0					7																	151052912		1853	4109	5962	SO:0001589	frameshift_variant	51667	exon6			.	AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"""NEDD8 ultimate buster-1"""	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.474delA	chr7.hg19:g.151052912delA	ENSP00000348110:p.Leu158fs	113.0	0.0		176.0	11.0	NM_016118	O95422|Q75MR9|Q8IX22|Q9BXR2	Frame_Shift_Del	DEL	ENST00000355851.4	hg19																																																																																				.	.		0.398	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118	
AIRE	326	hgsc.bcm.edu	37	21	45707420	45707420	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:45707420delC	ENST00000291582.5	+	4	611	c.484delC	c.(484-486)cccfs	p.P163fs		NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	163					humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		GAAGGCCAAGCCCCCCAAGAA	0.716									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy																												p.K161fs		Atlas-INDEL	.											.	AIRE	61	.	0			c.483delG						.																																			SO:0001589	frameshift_variant	326	exon4	Familial Cancer Database	APECED	.	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"""Zinc fingers, PHD-type"""	360	protein-coding gene	gene with protein product	"""autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"""	607358	"""autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"""	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.484delC	chr21.hg19:g.45707420delC	ENSP00000291582:p.Pro163fs	347.0	0.0		263.0	17.0	NM_000383	B2RP50|O43922|O43932|O75745	Frame_Shift_Del	DEL	ENST00000291582.5	hg19	CCDS13706.1																																																																																			.	.		0.716	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2		
ZNF516	9658	hgsc.bcm.edu	37	18	74153203	74153203	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:74153203delG	ENST00000443185.2	-	3	2125	c.1808delC	c.(1807-1809)ccafs	p.P603fs	ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	603					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(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		TTGCTCACCTGGTGCAGGTTC	0.647																																					p.P603fs		Atlas-INDEL	.											.	ZNF516	102	.	0			c.1809delA						.						8.0	10.0	9.0					18																	74153203		1957	4040	5997	SO:0001589	frameshift_variant	9658	exon3			.	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.1808delC	chr18.hg19:g.74153203delG	ENSP00000394757:p.Pro603fs	106.0	0.0		134.0	10.0	NM_014643		Frame_Shift_Del	DEL	ENST00000443185.2	hg19																																																																																				.	.		0.647	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
ATP9A	10079	hgsc.bcm.edu	37	20	50307291	50307291	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:50307291delC	ENST00000338821.5	-	8	974	c.710delG	c.(709-711)ggafs	p.G237fs	ATP9A_ENST00000311637.5_Intron|ATP9A_ENST00000402822.1_Intron	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	237					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GGTAAAAGTTCCCACGAAGTT	0.458																																					p.G237fs		Atlas-INDEL	.											.	ATP9A	135	.	0			c.711delA						.						203.0	181.0	189.0					20																	50307291		2203	4300	6503	SO:0001589	frameshift_variant	10079	exon8			.	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"""ATPases / P-type"""	13540	protein-coding gene	gene with protein product		609126	"""ATPase, Class II, type 9A"""			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.710delG	chr20.hg19:g.50307291delC	ENSP00000342481:p.Gly237fs	120.0	0.0		156.0	11.0	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Frame_Shift_Del	DEL	ENST00000338821.5	hg19	CCDS33489.1																																																																																			.	.		0.458	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045	
PSMD12	5718	hgsc.bcm.edu	37	17	65340878	65340878	+	Frame_Shift_Del	DEL	A	A	-	rs142928637		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:65340878delA	ENST00000356126.3	-	9	1034	c.927delT	c.(925-927)tttfs	p.F309fs	PSMD12_ENST00000357146.4_Frame_Shift_Del_p.F289fs	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	309	PCI.				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)					CCATTGTGGTAAAAAGCTTTA	0.323																																					p.T310fs		Atlas-INDEL	.											.	PSMD12	32	.	0			c.928delA						.						53.0	52.0	52.0					17																	65340878		2203	4300	6503	SO:0001589	frameshift_variant	5718	exon9			.	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.927delT	chr17.hg19:g.65340878delA	ENSP00000348442:p.Phe309fs	215.0	0.0		258.0	16.0	NM_002816	A6NP15|Q53HA2|Q6P053	Frame_Shift_Del	DEL	ENST00000356126.3	hg19	CCDS11669.1																																																																																			.	.		0.323	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871	
UFSP1	402682	hgsc.bcm.edu	37	7	100486590	100486590	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:100486590delG	ENST00000388761.2	-	1	749	c.303delC	c.(301-303)cccfs	p.P101fs		NM_001015072.3	NP_001015072.2	Q6NVU6	UFSP1_HUMAN	UFM1-specific peptidase 1 (non-functional)	101						extracellular vesicular exosome (GO:0070062)	thiolester hydrolase activity (GO:0016790)|UFM1 hydrolase activity (GO:0071567)			lung(1)|stomach(1)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)					GTAGTTCACTGGGGCTTTTTG	0.587																																					p.S102fs		Atlas-INDEL	.											.	UFSP1	8	.	0			c.304delA						.						88.0	92.0	91.0					7																	100486590		2203	4300	6503	SO:0001589	frameshift_variant	402682	exon1			.	AF312032	CCDS34710.1	7q22.1	2008-03-25			ENSG00000176125	ENSG00000176125			33821	protein-coding gene	gene with protein product		611481				17182609, 18321862	Standard	NM_001015072		Approved	UFSP	uc003uxc.4	Q6NVU6	OTTHUMG00000159662	ENST00000388761.2:c.303delC	chr7.hg19:g.100486590delG	ENSP00000373413:p.Pro101fs	131.0	0.0		171.0	11.0	NM_001015072	A4D2E4|A8K8V2|B6ZDG6|Q9BXP6	Frame_Shift_Del	DEL	ENST00000388761.2	hg19	CCDS34710.1																																																																																			.	.		0.587	UFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356751.1	NM_001015072	
WFDC3	140686	hgsc.bcm.edu	37	20	44416474	44416474	+	Splice_Site	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:44416474delC	ENST00000243938.4	-	4	442		c.e4+1		WFDC3_ENST00000372630.2_Intron|WFDC3_ENST00000481847.1_Splice_Site|WFDC3_ENST00000372632.2_Intron	NM_080614.1	NP_542181.1	Q8IUB2	WFDC3_HUMAN	WAP four-disulfide core domain 3							extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|large_intestine(3)|prostate(1)	5		Myeloproliferative disorder(115;0.0122)				GCGTTTCTTACCCAGCTTCTG	0.433																																					.		Atlas-INDEL	.											.	WFDC3	18	.	0			c.358+2G>-						.						173.0	134.0	147.0					20																	44416474		2203	4300	6503	SO:0001630	splice_region_variant	140686	exon5			.	AL050348	CCDS33478.1	20q13.12	2013-01-21			ENSG00000124116	ENSG00000124116		"""WAP four-disulfide core domain containing"""	15957	protein-coding gene	gene with protein product						12206714, 10680116	Standard	NM_080614		Approved	dJ447F3.3, WAP14	uc002xpf.1	Q8IUB2	OTTHUMG00000032614	ENST00000243938.4:c.358+1G>-	chr20.hg19:g.44416474delC		197.0	0.0		217.0	14.0	NM_080614	A6PVF2|Q0P6A5|Q3T1C5|Q8TC52|Q9BQP3|Q9BQP4	Splice_Site	DEL	ENST00000243938.4	hg19	CCDS33478.1																																																																																			.	.		0.433	WFDC3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316858.1		Intron
NCOA6	23054	hgsc.bcm.edu	37	20	33329681	33329681	+	Frame_Shift_Del	DEL	T	T	-	rs148955887		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:33329681delT	ENST00000374796.2	-	12	6949	c.4379delA	c.(4378-4380)aagfs	p.K1460fs	NCOA6_ENST00000359003.2_Frame_Shift_Del_p.K1460fs			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1460					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						CTGCCCATCCTTTTTGGACTG	0.448																																					p.K1460fs		Atlas-INDEL	.											.	NCOA6	219	.	0			c.4380delG						.						104.0	96.0	99.0					20																	33329681		2203	4300	6503	SO:0001589	frameshift_variant	23054	exon11			.	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.4379delA	chr20.hg19:g.33329681delT	ENSP00000363929:p.Lys1460fs	166.0	0.0		197.0	12.0	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Frame_Shift_Del	DEL	ENST00000374796.2	hg19	CCDS13241.1																																																																																			.	.		0.448	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071	
AHSA1	10598	hgsc.bcm.edu	37	14	77929054	77929054	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:77929054delA	ENST00000216479.3	+	4	584	c.424delA	c.(424-426)aaafs	p.K142fs	AHSA1_ENST00000535854.2_Frame_Shift_Del_p.K142fs|AHSA1_ENST00000555457.1_Intron	NM_012111.2	NP_036243.1	O95433	AHSA1_HUMAN	AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast)	142					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)		AGAAGGGGTGAAACTTCTAAG	0.438																																					p.V141fs		Atlas-INDEL	.											.	AHSA1	24	.	0			c.423delG						.						125.0	117.0	120.0					14																	77929054		2203	4300	6503	SO:0001589	frameshift_variant	10598	exon4			.	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.424delA	chr14.hg19:g.77929054delA	ENSP00000216479:p.Lys142fs	120.0	0.0		157.0	10.0	NM_012111	B2R9L2|B4DUR9|Q96IL6|Q9P060	Frame_Shift_Del	DEL	ENST00000216479.3	hg19	CCDS9863.1																																																																																			.	.		0.438	AHSA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414017.1	NM_012111	
PATZ1	23598	hgsc.bcm.edu	37	22	31723029	31723029	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:31723029delC	ENST00000266269.5	-	5	2541	c.1912delG	c.(1912-1914)gacfs	p.D638fs	PATZ1_ENST00000405309.3_3'UTR|PATZ1_ENST00000351933.4_Frame_Shift_Del_p.D592fs|RP3-400N23.6_ENST00000440456.1_RNA	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	638					male gonad development (GO:0008584)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)		EWSR1/PATZ1(2)	NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	12						GGGCCCAGGTCCCCCAGGGGG	0.567																																					p.D638fs		Atlas-INDEL	.											.	PATZ1	24	.	0			c.1913delA						.						72.0	79.0	77.0					22																	31723029		2203	4300	6503	SO:0001589	frameshift_variant	23598	exon5			.	AL096880	CCDS13894.1, CCDS13895.1, CCDS13896.1, CCDS46691.1	22q12.2	2013-01-09	2006-09-19	2006-09-19	ENSG00000100105	ENSG00000100105		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	13071	protein-coding gene	gene with protein product		605165	"""zinc finger protein 278"""	ZNF278		10591208, 18241078, 18401526	Standard	NM_014323		Approved	MAZR, dJ400N23, ZBTB19, ZSG, RIAZ, PATZ	uc003akq.3	Q9HBE1	OTTHUMG00000151254	ENST00000266269.5:c.1912delG	chr22.hg19:g.31723029delC	ENSP00000266269:p.Asp638fs	126.0	0.0		183.0	13.0	NM_014323	Q9HBE2|Q9HBE3|Q9P1A9|Q9UDU0|Q9Y529	Frame_Shift_Del	DEL	ENST00000266269.5	hg19	CCDS13894.1																																																																																			.	.		0.567	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321932.1	NM_032052	
PLOD2	5352	hgsc.bcm.edu	37	3	145806385	145806385	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:145806385delA	ENST00000360060.3	-	9	1170	c.993delT	c.(991-993)tttfs	p.F331fs	RP11-274H2.2_ENST00000480247.1_RNA|PLOD2_ENST00000282903.5_Frame_Shift_Del_p.F331fs|PLOD2_ENST00000494950.1_Frame_Shift_Del_p.F276fs|PLOD2_ENST00000461497.1_5'Flank	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	331					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)	TGTTATGAATAAAAAGTTTAA	0.284																																					p.I332fs		Atlas-INDEL	.											.	PLOD2	81	.	0			c.994delA						.						57.0	56.0	56.0					3																	145806385		2201	4296	6497	SO:0001589	frameshift_variant	5352	exon9			.	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.993delT	chr3.hg19:g.145806385delA	ENSP00000353170:p.Phe331fs	110.0	0.0		162.0	12.0	NM_182943	B3KWS3|Q59ED2|Q8N170	Frame_Shift_Del	DEL	ENST00000360060.3	hg19	CCDS3131.1																																																																																			.	.		0.284	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935	
AMN	81693	hgsc.bcm.edu	37	14	103390126	103390126	+	Frame_Shift_Del	DEL	C	C	-	rs119478058		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:103390126delC	ENST00000299155.5	+	2	155	c.122delC	c.(121-123)accfs	p.T41fs		NM_030943.3	NP_112205.2	Q9BXJ7	AMNLS_HUMAN	amnion associated transmembrane protein	41			T -> I (in RH-MGA1; dbSNP:rs28939377). {ECO:0000269|PubMed:12590260}.		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)	CAGAACCGGACCCCGTGCGCC	0.706																																					p.T41fs		Atlas-INDEL	.											.	AMN	13	.	0			c.121delA	GRCh37	CM030407	AMN	M	rs119478058	.						29.0	36.0	34.0					14																	103390126		2203	4298	6501	SO:0001589	frameshift_variant	81693	exon2			.	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.122delC	chr14.hg19:g.103390126delC	ENSP00000299155:p.Thr41fs	104.0	0.0		150.0	11.0	NM_030943	Q6UX83	Frame_Shift_Del	DEL	ENST00000299155.5	hg19	CCDS9977.1																																																																																			.	.		0.706	AMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415704.1		
B3GALT4	8705	hgsc.bcm.edu	37	6	33245843	33245843	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:33245843delT	ENST00000451237.1	+	1	927	c.647delT	c.(646-648)gttfs	p.V216fs		NM_003782.3	NP_003773.1	O96024	B3GT4_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	216					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	ganglioside galactosyltransferase activity (GO:0047915)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|urinary_tract(2)	13						GGAGGCCAGGTTTTGCACAGC	0.637																																					p.V216fs		Atlas-INDEL	.											.	B3GALT4	30	.	0			c.646delG						.						71.0	72.0	72.0					6																	33245843		2203	4300	6503	SO:0001589	frameshift_variant	8705	exon1			.	Y15061	CCDS34425.1	6p21.3	2013-02-19			ENSG00000235863	ENSG00000235863		"""Beta 3-glycosyltransferases"""	919	protein-coding gene	gene with protein product		603095				9582303	Standard	NM_003782		Approved	beta3Gal-T4, GalT4	uc003odr.3	O96024	OTTHUMG00000031100	ENST00000451237.1:c.647delT	chr6.hg19:g.33245843delT	ENSP00000390784:p.Val216fs	135.0	0.0		154.0	10.0	NM_003782		Frame_Shift_Del	DEL	ENST00000451237.1	hg19	CCDS34425.1																																																																																			.	.		0.637	B3GALT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076162.2		
LAMA5	3911	hgsc.bcm.edu	37	20	60928262	60928262	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:60928262delG	ENST00000252999.3	-	3	562	c.496delC	c.(496-498)cggfs	p.R166fs	RP11-157P1.5_ENST00000487421.1_RNA|RP11-157P1.5_ENST00000456721.2_RNA|LAMA5_ENST00000370692.3_Frame_Shift_Del_p.R166fs|RP11-157P1.5_ENST00000477848.1_RNA|LAMA5_ENST00000370677.3_Frame_Shift_Del_p.R166fs|RP11-157P1.5_ENST00000478167.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	166	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			AGGTCCGGCCGGGGTGAGTTG	0.672																																					p.R166fs		Atlas-INDEL	.											.	LAMA5	268	.	0			c.497delG						.						41.0	38.0	39.0					20																	60928262		2182	4282	6464	SO:0001589	frameshift_variant	3911	exon3			.	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.496delC	chr20.hg19:g.60928262delG	ENSP00000252999:p.Arg166fs	137.0	0.0		178.0	11.0	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Frame_Shift_Del	DEL	ENST00000252999.3	hg19	CCDS33502.1																																																																																			.	.		0.672	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
PAFAH1B1	5048	hgsc.bcm.edu	37	17	2569341	2569341	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:2569341delT	ENST00000397195.5	+	4	600	c.149delT	c.(148-150)cttfs	p.L51fs	PAFAH1B1_ENST00000572915.2_Intron	NM_000430.3	NP_000421.1			platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa)											endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(1)|skin(1)	11						TATGCTGGTCTTTTGGAAAAA	0.244																																					p.L50fs		Atlas-INDEL	.											.	PAFAH1B1	26	.	0			c.148delC						.						13.0	14.0	13.0					17																	2569341		2093	4168	6261	SO:0001589	frameshift_variant	5048	exon4			.	L25107	CCDS32528.1	17p13.3	2014-04-04	2010-02-10		ENSG00000007168	ENSG00000007168		"""WD repeat domain containing"""	8574	protein-coding gene	gene with protein product	"""lissencephaly-1"""	601545	"""platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit (45kD)"", ""Miller-Dieker syndrome chromosome region"", ""platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa"", ""platelet-activating factor acetylhydrolase, isoform Ib, subunit 1 (45kDa)"""	MDCR, MDS		8355785, 9063735	Standard	NM_000430		Approved	LIS1, PAFAH	uc002fuw.4	P43034	OTTHUMG00000177574	ENST00000397195.5:c.149delT	chr17.hg19:g.2569341delT	ENSP00000380378:p.Leu51fs	123.0	0.0		112.0	12.0	NM_000430		Frame_Shift_Del	DEL	ENST00000397195.5	hg19	CCDS32528.1																																																																																			.	.		0.244	PAFAH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437797.2	NM_000430	
IGSF1	3547	hgsc.bcm.edu	37	X	130417076	130417076	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:130417076delT	ENST00000361420.3	-	6	909	c.830delA	c.(829-831)aatfs	p.N277fs	IGSF1_ENST00000370904.1_Frame_Shift_Del_p.N268fs|IGSF1_ENST00000370903.3_Frame_Shift_Del_p.N277fs|IGSF1_ENST00000370910.1_Frame_Shift_Del_p.N268fs			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	277	Ig-like C2-type 3.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						ATTTGCCTCATTTTTTATTGT	0.398																																					p.N277fs		Atlas-INDEL	.											.	IGSF1	231	.	0			c.831delT						.						113.0	97.0	103.0					X																	130417076		2203	4300	6503	SO:0001589	frameshift_variant	3547	exon6			.	AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.830delA	chrX.hg19:g.130417076delT	ENSP00000355010:p.Asn277fs	226.0	0.0		249.0	16.0	NM_001555	B5MEG2|H9KV64|O15070|Q9NTC8	Frame_Shift_Del	DEL	ENST00000361420.3	hg19	CCDS14629.1																																																																																			.	.		0.398	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1		
CASKIN1	57524	hgsc.bcm.edu	37	16	2239271	2239271	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:2239271delG	ENST00000343516.6	-	5	546	c.454delC	c.(454-456)ctgfs	p.L152fs		NM_020764.3	NP_065815.1	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	152					signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|liver(1)|lung(7)|ovary(4)|prostate(5)|skin(3)	28						GCCAGGTCCAGGGGCGTCTTC	0.667																																					p.L152fs		Atlas-INDEL	.											.	CASKIN1	130	.	0			c.455delT						.						40.0	51.0	47.0					16																	2239271		2077	4196	6273	SO:0001589	frameshift_variant	57524	exon5			.	AF451977	CCDS42103.1	16p13.3	2013-01-10				ENSG00000167971		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	20879	protein-coding gene	gene with protein product		612184				12040031	Standard	NM_020764		Approved	KIAA1306, ANKS5A	uc010bsg.1	Q8WXD9		ENST00000343516.6:c.454delC	chr16.hg19:g.2239271delG	ENSP00000345436:p.Leu152fs	98.0	0.0		165.0	11.0	NM_020764	Q9P2P0	Frame_Shift_Del	DEL	ENST00000343516.6	hg19	CCDS42103.1																																																																																			.	.		0.667	CASKIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435055.1	NM_020764	
DHX33	56919	hgsc.bcm.edu	37	17	5353579	5353579	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:5353579delC	ENST00000225296.3	-	10	1872	c.1672delG	c.(1672-1674)gatfs	p.D558fs	DHX33_ENST00000433302.3_Frame_Shift_Del_p.D334fs	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	558					positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GTCATGTGATCCCCCTCGCTG	0.542																																					p.D558fs		Atlas-INDEL	.											.	DHX33	41	.	0			c.1673delA						.						151.0	152.0	152.0					17																	5353579		2203	4300	6503	SO:0001589	frameshift_variant	56919	exon10			.	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"""DEAH-boxes"""	16718	protein-coding gene	gene with protein product		614405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"""	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.1672delG	chr17.hg19:g.5353579delC	ENSP00000225296:p.Asp558fs	173.0	0.0		147.0	11.0	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Frame_Shift_Del	DEL	ENST00000225296.3	hg19	CCDS11072.1																																																																																			.	.		0.542	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
TLE3	7090	hgsc.bcm.edu	37	15	70358457	70358457	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:70358457delG	ENST00000558939.1	-	7	1850	c.473delC	c.(472-474)ccafs	p.P158fs	TLE3_ENST00000559191.1_Intron|TLE3_ENST00000442299.2_Frame_Shift_Del_p.P158fs|TLE3_ENST00000440567.3_Frame_Shift_Del_p.P151fs|TLE3_ENST00000557907.1_Frame_Shift_Del_p.P158fs|TLE3_ENST00000451782.2_Frame_Shift_Del_p.P158fs|TLE3_ENST00000558379.1_Frame_Shift_Del_p.P158fs|TLE3_ENST00000317509.8_Frame_Shift_Del_p.P158fs|TLE3_ENST00000560589.1_Frame_Shift_Del_p.P102fs|TLE3_ENST00000558201.1_Frame_Shift_Del_p.P164fs|TLE3_ENST00000559048.1_Frame_Shift_Del_p.P163fs|TLE3_ENST00000557997.1_Frame_Shift_Del_p.P158fs|TLE3_ENST00000560939.1_Frame_Shift_Del_p.P163fs|TLE3_ENST00000559929.1_Frame_Shift_Del_p.P168fs|TLE3_ENST00000539550.1_Frame_Shift_Del_p.P102fs	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	158	Gly/Pro-rich.				Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CCCTGTCACTGGGGGGATTCC	0.667																																					p.P158fs		Atlas-INDEL	.											.	TLE3	104	.	0			c.474delA						.						22.0	25.0	24.0					15																	70358457		1948	4153	6101	SO:0001589	frameshift_variant	7090	exon7			.	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.473delC	chr15.hg19:g.70358457delG	ENSP00000452871:p.Pro158fs	161.0	0.0		226.0	14.0	NM_001105192	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Frame_Shift_Del	DEL	ENST00000558939.1	hg19	CCDS45293.1																																																																																			.	.		0.667	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
IGSF22	283284	hgsc.bcm.edu	37	11	18741308	18741308	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:18741308delC	ENST00000513874.1	-	7	790	c.651delG	c.(649-651)gggfs	p.G217fs	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	217	Lys-rich.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						TCCTGAGCAGCCCCCGAAAGT	0.522																																					p.L218fs		Atlas-INDEL	.											.	IGSF22	211	.	0			c.652delC						.						150.0	151.0	151.0					11																	18741308		1889	4112	6001	SO:0001589	frameshift_variant	283284	exon7			.	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.651delG	chr11.hg19:g.18741308delC	ENSP00000421191:p.Gly217fs	141.0	0.0		191.0	13.0	NM_173588	A6NNA0|D6RGV7	Frame_Shift_Del	DEL	ENST00000513874.1	hg19	CCDS41625.2																																																																																			.	.		0.522	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
ILDR1	286676	hgsc.bcm.edu	37	3	121712685	121712685	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:121712685delG	ENST00000344209.5	-	7	1037	c.911delC	c.(910-912)cctfs	p.P304fs	ILDR1_ENST00000393631.1_Frame_Shift_Del_p.P215fs|ILDR1_ENST00000273691.3_Frame_Shift_Del_p.P260fs|ILDR1_ENST00000462014.1_Frame_Shift_Del_p.P272fs|ILDR1_ENST00000460554.1_5'UTR	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	304					positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		TTTGAGGTCAGGGGGCAGAGG	0.582																																					p.P304fs		Atlas-INDEL	.											ILDR1_ENST00000344209,NS,carcinoma,0,2	ILDR1	120	.	0			c.912delT						.						80.0	76.0	77.0					3																	121712685		2203	4300	6503	SO:0001589	frameshift_variant	286676	exon7			.	BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"""deafness, autosomal recessive 42"""	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.911delC	chr3.hg19:g.121712685delG	ENSP00000345667:p.Pro304fs	128.0	0.0		155.0	11.0	NM_001199799	Q6ZP61|Q7Z578	Frame_Shift_Del	DEL	ENST00000344209.5	hg19	CCDS56271.1																																																																																			.	.		0.582	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924	
DMTF1	9988	hgsc.bcm.edu	37	7	86813845	86813845	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:86813845delA	ENST00000394703.5	+	13	1516	c.953delA	c.(952-954)gaafs	p.E318fs	DMTF1_ENST00000414194.2_Frame_Shift_Del_p.E52fs|DMTF1_ENST00000432937.2_Frame_Shift_Del_p.E230fs|DMTF1_ENST00000331242.7_Frame_Shift_Del_p.E318fs|DMTF1_ENST00000413276.2_Frame_Shift_Del_p.E318fs	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	318	HTH myb-type. {ECO:0000255|PROSITE- ProRule:PRU00625}.|Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Required for DNA-binding. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					ACCCGCTCAGAAAAGCAATGT	0.488																																					p.E318fs		Atlas-INDEL	.											.	DMTF1	48	.	0			c.952delG						.						121.0	98.0	106.0					7																	86813845		2203	4300	6503	SO:0001589	frameshift_variant	9988	exon11			.	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"""cyclin D-binding Myb-like protein"""	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.953delA	chr7.hg19:g.86813845delA	ENSP00000378193:p.Glu318fs	74.0	0.0		193.0	12.0	NM_001142327	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Frame_Shift_Del	DEL	ENST00000394703.5	hg19	CCDS5601.1																																																																																			.	.		0.488	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145	
MYH15	22989	hgsc.bcm.edu	37	3	108205276	108205276	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:108205276delG	ENST00000273353.3	-	11	1085	c.1029delC	c.(1027-1029)gccfs	p.A343fs		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	343	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TTACTTCTGTGGCCAGCAATT	0.448																																					p.T344fs		Atlas-INDEL	.											.	MYH15	223	.	0			c.1030delA						.						88.0	84.0	85.0					3																	108205276		1893	4133	6026	SO:0001589	frameshift_variant	22989	exon11			.	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1029delC	chr3.hg19:g.108205276delG	ENSP00000273353:p.Ala343fs	162.0	0.0		159.0	10.0	NM_014981		Frame_Shift_Del	DEL	ENST00000273353.3	hg19	CCDS43127.1																																																																																			.	.		0.448	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
PM20D2	135293	hgsc.bcm.edu	37	6	89864571	89864571	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:89864571delA	ENST00000275072.4	+	4	957	c.862delA	c.(862-864)aaafs	p.K289fs		NM_001010853.1	NP_001010853.1	Q8IYS1	P20D2_HUMAN	peptidase M20 domain containing 2	289						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|skin(1)	12		all_cancers(76;9.47e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00813)		AGTTTTGACCAAAAAGGCAGA	0.358																																					p.T287fs		Atlas-INDEL	.											.	PM20D2	30	.	0			c.861delC						.						88.0	93.0	91.0					6																	89864571		2203	4300	6503	SO:0001589	frameshift_variant	135293	exon4			.	BC035036	CCDS34499.1	6q15	2014-07-14	2007-11-14	2007-11-14	ENSG00000146281	ENSG00000146281			21408	protein-coding gene	gene with protein product	"""&#946;-alanyl-lysine dipeptidase"""	615913	"""aminoacylase 1-like 2"""	ACY1L2		24891507	Standard	NM_001010853		Approved	bA63L7.3	uc003pmz.4	Q8IYS1	OTTHUMG00000015193	ENST00000275072.4:c.862delA	chr6.hg19:g.89864571delA	ENSP00000275072:p.Lys289fs	178.0	0.0		213.0	13.0	NM_001010853	B4DYJ2|Q5T7J9|Q6MZV2|Q86XD9	Frame_Shift_Del	DEL	ENST00000275072.4	hg19	CCDS34499.1																																																																																			.	.		0.358	PM20D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041477.1	NM_001010853	
T	6862	hgsc.bcm.edu	37	6	166579270	166579270	+	Frame_Shift_Del	DEL	C	C	-	rs2305089	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:166579270delC	ENST00000296946.2	-	4	998	c.530delG	c.(529-531)ggtfs	p.G177fs	T_ENST00000366871.3_Frame_Shift_Del_p.G177fs	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	177			G -> D (in dbSNP:rs2305089). {ECO:0000269|PubMed:15489334}.		anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		GCGCTGTGGACCCCCAACTCT	0.537									Chordoma, Familial Clustering of																												p.G177fs		Atlas-INDEL	.											.	T	77	.	0			c.531delT						.						325.0	283.0	297.0					6																	166579270		2203	4300	6503	SO:0001589	frameshift_variant	6862	exon4	Familial Cancer Database		.	AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"""T-boxes"""	11515	protein-coding gene	gene with protein product		601397	"""T brachyury (mouse) homolog"""			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.530delG	chr6.hg19:g.166579270delC	ENSP00000296946:p.Gly177fs	192.0	0.0		154.0	10.0	NM_001270484	E7ERD6|Q4KMP4	Frame_Shift_Del	DEL	ENST00000296946.2	hg19	CCDS5290.1																																																																																			.	.		0.537	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181	
UACA	55075	hgsc.bcm.edu	37	15	70959454	70959454	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:70959454delT	ENST00000322954.6	-	16	3754	c.3569delA	c.(3568-3570)aagfs	p.K1190fs	UACA_ENST00000560441.1_Frame_Shift_Del_p.K1175fs|UACA_ENST00000379983.2_Frame_Shift_Del_p.K1177fs|UACA_ENST00000539319.1_Frame_Shift_Del_p.K1081fs	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1190					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TTCTTCTTCCTTTTCTCTCAA	0.373																																					p.K1190fs		Atlas-INDEL	.											.	UACA	235	.	0			c.3570delG						.						147.0	141.0	143.0					15																	70959454		2199	4297	6496	SO:0001589	frameshift_variant	55075	exon16			.	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.3569delA	chr15.hg19:g.70959454delT	ENSP00000314556:p.Lys1190fs	136.0	0.0		156.0	10.0	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Frame_Shift_Del	DEL	ENST00000322954.6	hg19	CCDS10235.1																																																																																			.	.		0.373	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		
WDR46	9277	hgsc.bcm.edu	37	6	33247088	33247088	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:33247088delC	ENST00000374617.4	-	15	2154	c.1798delG	c.(1798-1800)gccfs	p.A600fs	B3GALT4_ENST00000606990.1_Intron	NM_001164267.1|NM_005452.5	NP_001157739.1|NP_005443.3	O15213	WDR46_HUMAN	WD repeat domain 46	600							poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	20						GATGGCCGGGCCCCCGTGGGC	0.617																																					p.A600fs		Atlas-INDEL	.											.	WDR46	43	.	0			c.1799delC						.						88.0	96.0	93.0					6																	33247088		2203	4300	6503	SO:0001589	frameshift_variant	9277	exon15			.	Z97184	CCDS4772.1	6p21.3	2013-01-09	2005-05-31	2005-05-31	ENSG00000227057	ENSG00000227057		"""WD repeat domain containing"""	13923	protein-coding gene	gene with protein product		611440	"""chromosome 6 open reading frame 11"""	C6orf11		9545376, 9521053	Standard	NM_005452		Approved	BING4, UTP7	uc003ods.3	O15213	OTTHUMG00000031192	ENST00000374617.4:c.1798delG	chr6.hg19:g.33247088delC	ENSP00000363746:p.Ala600fs	139.0	0.0		159.0	10.0	NM_005452	A6NDP5|Q5HYZ0|Q5STK5|Q5STR3	Frame_Shift_Del	DEL	ENST00000374617.4	hg19	CCDS4772.1																																																																																			.	.		0.617	WDR46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076382.2	NM_005452	
SEC16B	89866	hgsc.bcm.edu	37	1	177901668	177901668	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:177901668delC	ENST00000308284.6	-	24	3058	c.2969delG	c.(2968-2970)ggafs	p.G990fs	SEC16B_ENST00000495165.1_5'UTR|RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	990					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						CGCAGCTGCTCCCCCGCTGGA	0.657																																					p.G990fs		Atlas-INDEL	.											.	SEC16B	92	.	0			c.2970delA						.						11.0	15.0	14.0					1																	177901668		2021	4112	6133	SO:0001589	frameshift_variant	89866	exon24			.	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2969delG	chr1.hg19:g.177901668delC	ENSP00000308339:p.Gly990fs	117.0	0.0		213.0	13.0	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Frame_Shift_Del	DEL	ENST00000308284.6	hg19	CCDS44281.1																																																																																			.	.		0.657	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
NLRC4	58484	hgsc.bcm.edu	37	2	32449804	32449804	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:32449804delT	ENST00000404025.2	-	10	3301	c.2813delA	c.(2812-2814)aacfs	p.N938fs	NLRC4_ENST00000402280.1_Frame_Shift_Del_p.N938fs|NLRC4_ENST00000342905.6_Frame_Shift_Del_p.N273fs|NLRC4_ENST00000360906.5_Frame_Shift_Del_p.N938fs			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	938					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					CTGCTGGAAGTTTTTCAGAGG	0.348																																					p.N938fs		Atlas-INDEL	.											NLRC4_ENST00000404025,NS,carcinoma,0,1	NLRC4	165	.	0			c.2814delC						.						53.0	55.0	54.0					2																	32449804		2203	4300	6503	SO:0001589	frameshift_variant	58484	exon9			.	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"""Nucleotide-binding domain and leucine rich repeat containing"""	16412	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4"", ""NOD-like receptor C4"""	606831	"""caspase recruitment domain family, member 12"""	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.2813delA	chr2.hg19:g.32449804delT	ENSP00000385090:p.Asn938fs	77.0	0.0		102.0	11.0	NM_001199139	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Frame_Shift_Del	DEL	ENST00000404025.2	hg19	CCDS33174.1																																																																																			.	.		0.348	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209	
KCNQ5	56479	hgsc.bcm.edu	37	6	73787512	73787512	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:73787512delT	ENST00000370398.1	+	5	929	c.820delT	c.(820-822)tttfs	p.F274fs	KCNQ5_ENST00000355635.3_Frame_Shift_Del_p.F274fs|KCNQ5_ENST00000370392.1_Frame_Shift_Del_p.F274fs|KCNQ5_ENST00000355194.4_Frame_Shift_Del_p.F274fs|KCNQ5_ENST00000402622.2_Frame_Shift_Del_p.F274fs|KCNQ5_ENST00000342056.2_Frame_Shift_Del_p.F274fs|KCNQ5_ENST00000403813.2_Frame_Shift_Del_p.F274fs|KCNQ5_ENST00000414165.2_Frame_Shift_Del_p.F274fs	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	274					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)	GTACATAGGATTTTTGGTTCT	0.353																																					p.G273fs	GBM(142;1375 1859 14391 23261 44706)	Atlas-INDEL	.											.	KCNQ5	153	.	0			c.819delA						.						137.0	116.0	123.0					6																	73787512		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.820delT	chr6.hg19:g.73787512delT	ENSP00000359425:p.Phe274fs	107.0	0.0		140.0	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																																																																																			.	.		0.353	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842	
DDX46	9879	hgsc.bcm.edu	37	5	134109494	134109494	+	Frame_Shift_Del	DEL	A	A	-	rs35026423		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:134109494delA	ENST00000354283.4	+	5	691	c.556delA	c.(556-558)aaafs	p.K187fs	DDX46_ENST00000452510.2_Frame_Shift_Del_p.K187fs			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	187					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGGAGAACTGAAAAAGGAAAT	0.373																																					p.L185fs	Colon(13;391 453 4901 21675 24897)	Atlas-INDEL	.											.	DDX46	77	.	0			c.555delG						.						131.0	131.0	131.0					5																	134109494		2203	4300	6503	SO:0001589	frameshift_variant	9879	exon5			.		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"""DEAD-boxes"""	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.556delA	chr5.hg19:g.134109494delA	ENSP00000346236:p.Lys187fs	118.0	0.0		172.0	12.0	NM_014829	O94894|Q96EI0|Q9Y658	Frame_Shift_Del	DEL	ENST00000354283.4	hg19	CCDS34240.1																																																																																			.	.		0.373	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829	
C1orf74	148304	hgsc.bcm.edu	37	1	209956336	209956336	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:209956336delG	ENST00000294811.1	-	2	900	c.644delC	c.(643-645)ccafs	p.P215fs		NM_152485.2	NP_689698.1	Q96LT6	CA074_HUMAN	chromosome 1 open reading frame 74	215										endometrium(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	15				OV - Ovarian serous cystadenocarcinoma(81;0.0328)		GAGCAGGATTGGGGGTTGACC	0.502																																					p.P215fs		Atlas-INDEL	.											.	C1orf74	30	.	0			c.645delA						.						85.0	94.0	91.0					1																	209956336		2203	4300	6503	SO:0001589	frameshift_variant	148304	exon2			.	AK057807	CCDS1491.1	1q32.2	2008-02-05			ENSG00000162757	ENSG00000162757			26319	protein-coding gene	gene with protein product						12477932	Standard	NM_152485		Approved	FLJ25078	uc001hhp.1	Q96LT6	OTTHUMG00000036483	ENST00000294811.1:c.644delC	chr1.hg19:g.209956336delG	ENSP00000294811:p.Pro215fs	101.0	0.0		175.0	11.0	NM_152485		Frame_Shift_Del	DEL	ENST00000294811.1	hg19	CCDS1491.1																																																																																			.	.		0.502	C1orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088745.1	NM_152485	
PBRM1	55193	hgsc.bcm.edu	37	3	52712558	52712558	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:52712558delC	ENST00000296302.7	-	2	195	c.194delG	c.(193-195)ggcfs	p.G65fs	PBRM1_ENST00000410007.1_Frame_Shift_Del_p.G65fs|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.G65fs|PBRM1_ENST00000409114.3_Frame_Shift_Del_p.G65fs|PBRM1_ENST00000409057.1_Frame_Shift_Del_p.G65fs|PBRM1_ENST00000409767.1_Frame_Shift_Del_p.G65fs|PBRM1_ENST00000337303.4_Frame_Shift_Del_p.G65fs|PBRM1_ENST00000394830.3_Frame_Shift_Del_p.G65fs			Q86U86	PB1_HUMAN	polybromo 1	65	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.			G -> S (in Ref. 4; AAI15011). {ECO:0000305}.	chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GAGAAGTCTGCCCTGTTCATC	0.443			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																p.G65fs		Atlas-INDEL	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.195delC						.						139.0	127.0	131.0					3																	52712558		2203	4300	6503	SO:0001589	frameshift_variant	55193	exon3			.	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.194delG	chr3.hg19:g.52712558delC	ENSP00000296302:p.Gly65fs	130.0	0.0		149.0	10.0	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	hg19																																																																																				.	.		0.443	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
COL8A1	1295	hgsc.bcm.edu	37	3	99513597	99513597	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:99513597delC	ENST00000261037.3	+	5	1232	c.852delC	c.(850-852)ggcfs	p.G284fs	COL8A1_ENST00000273342.4_Frame_Shift_Del_p.G284fs	NM_001850.4	NP_001841.2	P27658	CO8A1_HUMAN	collagen, type VIII, alpha 1	284	Triple-helical region (COL1).				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen type VIII trimer (GO:0005591)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(15)|skin(5)|upper_aerodigestive_tract(1)	27						GGCCCCAGGGCCCCCTGGGAA	0.657																																					p.G284fs		Atlas-INDEL	.											.	COL8A1	68	.	0			c.851delG						.						18.0	25.0	22.0					3																	99513597		2174	4284	6458	SO:0001589	frameshift_variant	1295	exon5			.	AF170702	CCDS2934.1	3q11.1-q13.2	2013-01-16			ENSG00000144810	ENSG00000144810		"""Collagens"""	2215	protein-coding gene	gene with protein product		120251	"""chromosome 3 open reading frame 7"""	C3orf7		2029894	Standard	NM_001850		Approved	MGC9568	uc003dth.2	P27658	OTTHUMG00000148669	ENST00000261037.3:c.852delC	chr3.hg19:g.99513597delC	ENSP00000261037:p.Gly284fs	56.0	0.0		89.0	10.0	NM_001850	D3DN42|Q53XI6|Q96D07	Frame_Shift_Del	DEL	ENST00000261037.3	hg19	CCDS2934.1																																																																																			.	.		0.657	COL8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309001.1	NM_001850	
HERC6	55008	hgsc.bcm.edu	37	4	89326115	89326115	+	Frame_Shift_Del	DEL	A	A	-	rs369850043		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:89326115delA	ENST00000264346.7	+	9	1239	c.1180delA	c.(1180-1182)aaafs	p.K394fs	HERC6_ENST00000380265.5_Frame_Shift_Del_p.K394fs	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	394					hematopoietic progenitor cell differentiation (GO:0002244)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		GATAGCAGTGAAAAGAAGAAG	0.433																																					p.V393fs		Atlas-INDEL	.											.	HERC6	104	.	0			c.1179delG						.						139.0	131.0	133.0					4																	89326115		1845	4104	5949	SO:0001589	frameshift_variant	55008	exon9			.	AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"""hect domain and RLD 6"""				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.1180delA	chr4.hg19:g.89326115delA	ENSP00000264346:p.Lys394fs	129.0	0.0		166.0	10.0	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Frame_Shift_Del	DEL	ENST00000264346.7	hg19	CCDS47098.1																																																																																			.	.		0.433	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2		
FAM186A	121006	hgsc.bcm.edu	37	12	50746097	50746097	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:50746097delA	ENST00000327337.5	-	4	4517	c.4518delT	c.(4516-4518)cttfs	p.L1507fs	FAM186A_ENST00000543111.1_Frame_Shift_Del_p.L1507fs|FAM186A_ENST00000543096.1_5'Flank	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1507																	GAGGGATGAGAAGGATCCCCA	0.662																																					p.L1507fs	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-INDEL	.											.	FAM186A	181	.	0			c.4519delC						.						7.0	1.0	4.0					12																	50746097		163	193	356	SO:0001589	frameshift_variant	121006	exon4			.		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.4518delT	chr12.hg19:g.50746097delA	ENSP00000329995:p.Leu1507fs	125.0	0.0		171.0	11.0	NM_001145475		Frame_Shift_Del	DEL	ENST00000327337.5	hg19	CCDS44878.1																																																																																			.	.		0.662	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
ASH1L	55870	hgsc.bcm.edu	37	1	155408163	155408163	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:155408163delT	ENST00000368346.3	-	5	6422	c.5783delA	c.(5782-5784)aagfs	p.K1928fs	ASH1L_ENST00000392403.3_Frame_Shift_Del_p.K1928fs			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1928					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)			TGGCTTCTGCTTTTTTCTGGT	0.368																																					p.K1928fs		Atlas-INDEL	.											.	ASH1L	279	.	0			c.5784delG						.						144.0	139.0	141.0					1																	155408163		2203	4300	6503	SO:0001589	frameshift_variant	55870	exon5			.	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.5783delA	chr1.hg19:g.155408163delT	ENSP00000357330:p.Lys1928fs	84.0	0.0		164.0	12.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Frame_Shift_Del	DEL	ENST00000368346.3	hg19																																																																																				.	.		0.368	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
HES1	3280	hgsc.bcm.edu	37	3	193854479	193854479	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:193854479delT	ENST00000232424.3	+	2	418	c.182delT	c.(181-183)attfs	p.I61fs		NM_005524.3	NP_005515.1	P30042	ES1_HUMAN	hes family bHLH transcription factor 1	0						mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6	all_cancers(143;7.3e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;3.65e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;1.48e-05)		AAAACACTGATTTTGGATGCT	0.388																																					p.I61fs		Atlas-INDEL	.											.	HES1	23	.	0			c.181delA						.						68.0	73.0	71.0					3																	193854479		2203	4300	6503	SO:0001589	frameshift_variant	3280	exon2			.	L19314	CCDS3305.1	3q28-q29	2013-10-17	2013-10-17	2003-01-10	ENSG00000114315	ENSG00000114315		"""Basic helix-loop-helix proteins"""	5192	protein-coding gene	gene with protein product		139605	"""hairy homolog (Drosophila)"", ""hairy and enhancer of split 1, (Drosophila)"""	HRY		8020957	Standard	NM_005524		Approved	FLJ20408, HES-1, Hes1, bHLHb39	uc003ftq.2	Q14469	OTTHUMG00000155984	ENST00000232424.3:c.182delT	chr3.hg19:g.193854479delT	ENSP00000232424:p.Ile61fs	155.0	0.0		220.0	14.0	NM_005524	A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507	Frame_Shift_Del	DEL	ENST00000232424.3	hg19	CCDS3305.1																																																																																			.	.		0.388	HES1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342632.1		
LRRFIP1	9208	hgsc.bcm.edu	37	2	238647924	238647924	+	Intron	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:238647924delG	ENST00000392000.4	+	5	366				LRRFIP1_ENST00000289175.6_Intron|LRRFIP1_ENST00000308482.9_Frame_Shift_Del_p.R202fs|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)		GCCTCCTCCAGGGCCAGCTCG	0.662																																					p.R202fs		Atlas-INDEL	.											.	LRRFIP1	171	.	0			c.604delA						.						8.0	10.0	9.0					2																	238647924		1546	3553	5099	SO:0001627	intron_variant	9208	exon11			.	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.250-9083G>-	chr2.hg19:g.238647924delG		121.0	0.0		166.0	11.0	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Frame_Shift_Del	DEL	ENST00000392000.4	hg19	CCDS46552.1																																																																																			.	.		0.662	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
LPIN3	64900	hgsc.bcm.edu	37	20	39977799	39977799	+	Frame_Shift_Del	DEL	C	C	-	rs559175371	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:39977799delC	ENST00000373257.3	+	5	716	c.625delC	c.(625-627)cccfs	p.P210fs		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	210					fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				TGGCGAGTGGCCCCCCCAGGC	0.537													CCCCCCC|CCCCCCC|CCCCCC|deletion	3	0.000599042	0.0	0.0	5008	,	,		17869	0.0		0.003	False		,,,				2504	0.0				p.W208fs		Atlas-INDEL	.											.	LPIN3	69	.	0			c.624delG						.			6,0,4258		0,0,6,0,0,2126	70.0	71.0	71.0			-1.4	0.0	20		72	6,2,8246		0,0,6,0,2,4119	no	codingComplex	LPIN3	NM_022896.1		0,0,12,0,2,6245	A1A1,A1A2,A1R,A2A2,A2R,RR		0.0969,0.1407,0.1118			39977799	12,2,12504	2203	4300	6503	SO:0001589	frameshift_variant	64900	exon5			.	AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793			14451	protein-coding gene	gene with protein product		605520	"""lipin 3-like"""	LIPN3L		11138012	Standard	XM_005260515		Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.625delC	chr20.hg19:g.39977799delC	ENSP00000362354:p.Pro210fs	130.0	0.0		158.0	10.0	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Frame_Shift_Del	DEL	ENST00000373257.3	hg19	CCDS33469.1																																																																																			.	.		0.537	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896	
PSRC1	84722	hgsc.bcm.edu	37	1	109824582	109824582	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:109824582delG	ENST00000438534.2	-	4	316	c.178delC	c.(178-180)cagfs	p.Q60fs	PSRC1_ENST00000369909.2_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369904.3_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369903.2_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000369907.3_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000409138.2_Frame_Shift_Del_p.Q60fs|PSRC1_ENST00000409267.1_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	105.0	0.0		168.0	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	
UBA3	9039	hgsc.bcm.edu	37	3	69117114	69117114	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:69117114delA	ENST00000361055.4	-	6	447	c.393delT	c.(391-393)tttfs	p.F131fs	UBA3_ENST00000349511.4_Frame_Shift_Del_p.F117fs|UBA3_ENST00000540295.1_Intron|UBA3_ENST00000415609.2_Frame_Shift_Del_p.F90fs	NM_003968.3	NP_003959.3	Q8TBC4	UBA3_HUMAN	ubiquitin-like modifier activating enzyme 3	131					cellular protein modification process (GO:0006464)|endomitotic cell cycle (GO:0007113)|protein neddylation (GO:0045116)|proteolysis (GO:0006508)|regulation of cell cycle (GO:0051726)	cytosol (GO:0005829)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|NEDD8 activating enzyme activity (GO:0019781)|protein heterodimerization activity (GO:0046982)			endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	19		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.98e-05)|Epithelial(33;0.000363)|LUSC - Lung squamous cell carcinoma(21;0.012)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.206)|Kidney(39;0.241)		TGTCATTTAGAAATTCTGCAG	0.269																																					p.L132X		Atlas-INDEL	.											.	UBA3	43	.	0			c.394delC						.						55.0	61.0	59.0					3																	69117114		2203	4297	6500	SO:0001589	frameshift_variant	9039	exon6			.	AB012190	CCDS2909.1, CCDS2910.1	3p14.1	2013-09-26	2007-11-30	2007-11-30	ENSG00000144744	ENSG00000144744		"""Ubiquitin-like modifier activating enzymes"""	12470	protein-coding gene	gene with protein product	"""NEDD8-activating enzyme E1 catalytic subunit"", ""NEDD8-activating enzyme E1 subunit 2"""	603172	"""ubiquitin-activating enzyme E1C (homologous to yeast UBA3)"", ""ubiquitin-activating enzyme E1C (UBA3 homolog, yeast)"""	UBE1C		9694792	Standard	NM_003968		Approved	hUba3, NAE2	uc003dno.3	Q8TBC4	OTTHUMG00000154325	ENST00000361055.4:c.393delT	chr3.hg19:g.69117114delA	ENSP00000354340:p.Phe131fs	167.0	0.0		208.0	13.0	NM_003968	A6NLB5|A8K027|O76088|Q9NTU3	Frame_Shift_Del	DEL	ENST00000361055.4	hg19	CCDS2909.1																																																																																			.	.		0.269	UBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334839.1	NM_198195	
HERC5	51191	hgsc.bcm.edu	37	4	89407334	89407334	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:89407334delT	ENST00000264350.3	+	14	1959	c.1806delT	c.(1804-1806)aatfs	p.N602fs	HERC5_ENST00000508159.1_Frame_Shift_Del_p.N240fs	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	602					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		ACCGTCTCAATTTTTTTGTAG	0.348																																					p.N602fs	Esophageal Squamous(39;887 1012 34045 50514)	Atlas-INDEL	.											.	HERC5	114	.	0			c.1805delA						.						129.0	132.0	131.0					4																	89407334		2203	4300	6503	SO:0001589	frameshift_variant	51191	exon14			.	AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"""hect domain and RLD 5"""			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.1806delT	chr4.hg19:g.89407334delT	ENSP00000264350:p.Asn602fs	130.0	0.0		163.0	15.0	NM_016323	B2RTQ1|Q69G20	Frame_Shift_Del	DEL	ENST00000264350.3	hg19	CCDS3630.1																																																																																			.	.		0.348	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323	
ATP12A	479	hgsc.bcm.edu	37	13	25280558	25280558	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:25280558delC	ENST00000381946.3	+	15	2293	c.2126delC	c.(2125-2127)tccfs	p.S709fs	RNY1P7_ENST00000384743.1_RNA|ATP12A_ENST00000218548.6_Frame_Shift_Del_p.S715fs			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	709					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		GCCCGGACATCCCCCCAGCAG	0.567																																					p.S715fs	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-INDEL	.											.	ATP12A	172	.	0			c.2143delT						.						114.0	87.0	96.0					13																	25280558		2203	4300	6503	SO:0001589	frameshift_variant	479	exon15			.	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.2126delC	chr13.hg19:g.25280558delC	ENSP00000371372:p.Ser709fs	222.0	0.0		190.0	12.0	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Frame_Shift_Del	DEL	ENST00000381946.3	hg19	CCDS31948.1																																																																																			.	.		0.567	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
SCN10A	6336	hgsc.bcm.edu	37	3	38739704	38739704	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:38739704delG	ENST00000449082.2	-	27	5006	c.5007delC	c.(5005-5007)cccfs	p.P1669fs		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1669					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	TGTTGAGGATGGGGCTGAGGA	0.597																																					p.I1670fs		Atlas-INDEL	.											.	SCN10A	359	.	0			c.5008delA						.						77.0	80.0	79.0					3																	38739704		2203	4300	6503	SO:0001589	frameshift_variant	6336	exon27			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.5007delC	chr3.hg19:g.38739704delG	ENSP00000390600:p.Pro1669fs	162.0	0.0		186.0	13.0	NM_006514	A6NDQ1	Frame_Shift_Del	DEL	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.		0.597	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
CCDC93	54520	hgsc.bcm.edu	37	2	118735578	118735578	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:118735578delT	ENST00000376300.2	-	8	786	c.649delA	c.(649-651)atgfs	p.M217fs	CCDC93_ENST00000319432.5_Frame_Shift_Del_p.M216fs|CCDC93_ENST00000460781.1_5'UTR	NM_019044.4	NP_061917.3	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	217										breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2)	29						ACCTTCTCCATTTTGCTCTGG	0.398																																					p.M217fs		Atlas-INDEL	.											.	CCDC93	70	.	0			c.650delT						.						166.0	139.0	148.0					2																	118735578		2203	4300	6503	SO:0001589	frameshift_variant	54520	exon8			.	BC028609	CCDS2121.2	2q14.1	2008-02-05			ENSG00000125633	ENSG00000125633			25611	protein-coding gene	gene with protein product						12477932	Standard	NM_019044		Approved	FLJ10996	uc002tlj.3	Q567U6	OTTHUMG00000058517	ENST00000376300.2:c.649delA	chr2.hg19:g.118735578delT	ENSP00000365477:p.Met217fs	145.0	0.0		147.0	10.0	NM_019044	A8K3V7|Q4LE78|Q53TJ2|Q8TBX5|Q9H6R5|Q9NV15	Frame_Shift_Del	DEL	ENST00000376300.2	hg19	CCDS2121.2																																																																																			.	.		0.398	CCDC93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000129615.1	NM_019044	
ENTPD6	955	hgsc.bcm.edu	37	20	25187773	25187773	+	Frame_Shift_Del	DEL	G	G	-	rs369864358		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:25187773delG	ENST00000376652.4	+	3	279	c.116delG	c.(115-117)cggfs	p.R39fs	ENTPD6_ENST00000433259.2_Frame_Shift_Del_p.R39fs|ENTPD6_ENST00000354989.5_Frame_Shift_Del_p.R22fs|ENTPD6_ENST00000360031.2_Frame_Shift_Del_p.R38fs			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	39					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						GGGAGCCTGCGGGTGGCGAAG	0.607																																					p.R39fs		Atlas-INDEL	.											.	ENTPD6	57	.	0			c.115delC						.						55.0	56.0	56.0					20																	25187773		2203	4300	6503	SO:0001589	frameshift_variant	955	exon3			.	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"""interleukin 6 signal transducer-2"""	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.116delG	chr20.hg19:g.25187773delG	ENSP00000365840:p.Arg39fs	100.0	0.0		129.0	10.0	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Frame_Shift_Del	DEL	ENST00000376652.4	hg19	CCDS13170.1																																																																																			.	.		0.607	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2		
C6orf1	221491	hgsc.bcm.edu	37	6	34214570	34214570	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:34214570delG	ENST00000476320.1	-	5	883	c.201delC	c.(199-201)cccfs	p.P67fs	C6orf1_ENST00000413013.2_Frame_Shift_Del_p.P47fs|C6orf1_ENST00000481533.1_Frame_Shift_Del_p.P67fs|C6orf1_ENST00000468145.1_Frame_Shift_Del_p.P67fs|C6orf1_ENST00000335352.3_Frame_Shift_Del_p.P47fs|C6orf1_ENST00000394990.4_Frame_Shift_Del_p.P67fs	NM_001008703.1	NP_001008703.1	Q86T20	CF001_HUMAN	chromosome 6 open reading frame 1	67						extracellular region (GO:0005576)				endometrium(1)|prostate(1)	2		Ovarian(999;0.0228)		BRCA - Breast invasive adenocarcinoma(397;1.11e-10)		GGTGGGGCAAGGGGGTCAGGT	0.652											OREG0017364	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L68fs		Atlas-INDEL	.											.	C6orf1	6	.	0			c.202delT						.						36.0	36.0	36.0					6																	34214570		2202	4300	6502	SO:0001589	frameshift_variant	221491	exon5			.	AY062936	CCDS4790.1, CCDS75433.1	6p21.3	2011-12-12			ENSG00000186577	ENSG00000186577			1340	protein-coding gene	gene with protein product		611419				10036196	Standard	NM_178508		Approved	LBH, MGC57858	uc003ojh.3	Q86T20	OTTHUMG00000159754	ENST00000476320.1:c.201delC	chr6.hg19:g.34214570delG	ENSP00000417604:p.Pro67fs	116.0	0.0	846	153.0	10.0	NM_001008704	A8K299	Frame_Shift_Del	DEL	ENST00000476320.1	hg19	CCDS4790.1																																																																																			.	.		0.652	C6orf1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357175.1	NM_178508	
NOS1AP	9722	hgsc.bcm.edu	37	1	162312409	162312409	+	Intron	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:162312409delT	ENST00000361897.5	+	6	855				NOS1AP_ENST00000530878.1_Intron|MIR556_ENST00000384996.1_RNA	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein						regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			TTAGCTCATCTTTTTTATTAC	0.353																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.						36.0	33.0	34.0					1																	162312409		1551	3556	5107	SO:0001627	intron_variant	693141	.			.	AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"""C-terminal PDZ domain ligand of neuronal nitric oxide synthase"""	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.454-1216T>-	chr1.hg19:g.162312409delT		103.0	0.0		176.0	13.0	.	B7ZLF5|O43564|Q3T551|Q5VU95	RNA	DEL	ENST00000361897.5	hg19	CCDS1237.1																																																																																			.	.		0.353	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697	
SRRT	51593	hgsc.bcm.edu	37	7	100485681	100485681	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:100485681delC	ENST00000347433.4	+	18	2503	c.2345delC	c.(2344-2346)accfs	p.T782fs	SRRT_ENST00000432932.1_Frame_Shift_Del_p.T777fs|SRRT_ENST00000457580.2_Frame_Shift_Del_p.T778fs|SRRT_ENST00000388793.4_Frame_Shift_Del_p.T781fs			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	782	Pro-rich.				cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CCAGGTTTGACCCCAGGACTC	0.617																																					p.T782fs		Atlas-INDEL	.											.	SRRT	108	.	0			c.2344delA						.						47.0	52.0	50.0					7																	100485681		2203	4300	6503	SO:0001589	frameshift_variant	51593	exon18			.		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"""arsenite resistance protein"""	614469	"""serrate RNA effector molecule homolog (Arabidopsis)"""			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.2345delC	chr7.hg19:g.100485681delC	ENSP00000314491:p.Thr782fs	137.0	0.0		165.0	10.0	NM_015908	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Frame_Shift_Del	DEL	ENST00000347433.4	hg19	CCDS34709.1																																																																																			.	.		0.617	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908	
SPINK6	404203	hgsc.bcm.edu	37	5	147593496	147593496	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:147593496delC	ENST00000325630.2	+	3	361	c.105delC	c.(103-105)gacfs	p.D35fs		NM_001195290.1|NM_205841.3	NP_001182219.1|NP_995313.2	Q6UWN8	ISK6_HUMAN	serine peptidase inhibitor, Kazal type 6	35	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGTTCCAGGACCCCAAGGTCT	0.468																																					p.D35fs		Atlas-INDEL	.											.	SPINK6	8	.	0			c.104delA						.						136.0	110.0	119.0					5																	147593496		2203	4300	6503	SO:0001589	frameshift_variant	404203	exon3			.	AY358716	CCDS34268.1	5q32	2011-08-31	2005-08-17		ENSG00000178172	ENSG00000178172		"""Serine peptidase inhibitors, Kazal type"""	29486	protein-coding gene	gene with protein product	"""protease inhibitor H"""	615868	"""serine protease inhibitor, Kazal type 6"""			15060002	Standard	NM_205841		Approved	MGC21394, UNQ844, BUSI2	uc021yff.1	Q6UWN8	OTTHUMG00000163425	ENST00000325630.2:c.105delC	chr5.hg19:g.147593496delC	ENSP00000324870:p.Asp35fs	149.0	0.0		159.0	10.0	NM_205841	E0X656|Q8N5P0	Frame_Shift_Del	DEL	ENST00000325630.2	hg19	CCDS34268.1																																																																																			.	.		0.468	SPINK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373332.1	NM_205841	
FAM221B	392307	hgsc.bcm.edu	37	9	35825746	35825746	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:35825746delG	ENST00000423537.2	-	2	682	c.413delC	c.(412-414)ccafs	p.P138fs	TMEM8B_ENST00000377996.1_Intron	NM_001012446.3	NP_001012448.2	A6H8Z2	F221B_HUMAN	family with sequence similarity 221, member B	138										endometrium(2)|kidney(1)|lung(4)	7						CCTTGTCCATGGGACCTCATT	0.498											OREG0019180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P138fs		Atlas-INDEL	.											.	FAM221B	38	.	0			c.414delA						.						206.0	195.0	198.0					9																	35825746		1905	4140	6045	SO:0001589	frameshift_variant	392307	exon2			.	BX648702	CCDS43799.1, CCDS43799.2	9p13.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000204930	ENSG00000204930			30762	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 128"""	C9orf128			Standard	NM_001012446		Approved		uc010mlc.2	A6H8Z2	OTTHUMG00000019880	ENST00000423537.2:c.413delC	chr9.hg19:g.35825746delG	ENSP00000415299:p.Pro138fs	109.0	0.0	858	140.0	11.0	NM_001012446	Q5TCW2	Frame_Shift_Del	DEL	ENST00000423537.2	hg19	CCDS43799.2																																																																																			.	.		0.498	FAM221B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355861.1	NM_001012446	
ARHGEF26	26084	hgsc.bcm.edu	37	3	153847453	153847453	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:153847453delA	ENST00000356448.4	+	4	1498	c.1214delA	c.(1213-1215)gaafs	p.E405fs	ARHGEF26_ENST00000465093.1_Frame_Shift_Del_p.E405fs|ARHGEF26_ENST00000465817.1_Frame_Shift_Del_p.E405fs	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	405					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						AAGTCAGATGAAAAAATTGTG	0.398																																					p.E405fs	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-INDEL	.											.	ARHGEF26	158	.	0			c.1213delG						.						100.0	93.0	95.0					3																	153847453		1855	4128	5983	SO:0001589	frameshift_variant	26084	exon4			.	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.1214delA	chr3.hg19:g.153847453delA	ENSP00000348828:p.Glu405fs	182.0	0.0		232.0	17.0	NM_015595	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Frame_Shift_Del	DEL	ENST00000356448.4	hg19	CCDS46938.1																																																																																			.	.		0.398	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595	
ZNF324B	388569	hgsc.bcm.edu	37	19	58967548	58967548	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:58967548delT	ENST00000336614.4	+	4	1344	c.1237delT	c.(1237-1239)tttfs	p.F413fs	ZNF324B_ENST00000391696.1_Frame_Shift_Del_p.F403fs|ZNF324B_ENST00000545523.1_Frame_Shift_Del_p.F413fs	NM_207395.2	NP_997278.2	Q6AW86	Z324B_HUMAN	zinc finger protein 324B	413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		CTCCTCGCTCTTTTTGCACCA	0.657																																					p.L412fs		Atlas-INDEL	.											.	ZNF324B	58	.	0			c.1236delC						.						49.0	51.0	50.0					19																	58967548		2203	4300	6503	SO:0001589	frameshift_variant	388569	exon4			.	AK127750	CCDS33138.1	19q13.43	2013-01-08				ENSG00000249471		"""Zinc fingers, C2H2-type"", ""-"""	33107	protein-coding gene	gene with protein product							Standard	NM_207395		Approved	FLJ45850	uc002qsv.1	Q6AW86		ENST00000336614.4:c.1237delT	chr19.hg19:g.58967548delT	ENSP00000337473:p.Phe413fs	139.0	0.0		226.0	14.0	NM_207395	B2RTZ6|Q6ZMX8|Q6ZS42	Frame_Shift_Del	DEL	ENST00000336614.4	hg19	CCDS33138.1																																																																																			.	.		0.657	ZNF324B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467038.1	NM_207395	
RIT2	6014	hgsc.bcm.edu	37	18	40323632	40323632	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:40323632delA	ENST00000326695.5	-	5	651	c.480delT	c.(478-480)tttfs	p.F160fs	RIT2_ENST00000589109.1_3'UTR|RIT2_ENST00000590910.1_3'UTR	NM_002930.2	NP_002921.1	Q99578	RIT2_HUMAN	Ras-like without CAAX 2	160					neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.F160fs*18(1)		endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CAGAGGTCTCAAAAAAACCAC	0.383																																					p.E161fs		Atlas-INDEL	.											.,1	RIT2	56	.	1	Deletion - Frameshift(1)	lung(1)	c.481delG						.						73.0	75.0	74.0					18																	40323632		2203	4300	6503	SO:0001589	frameshift_variant	6014	exon5			.	BC018060	CCDS11921.1, CCDS62431.1	18q12.3	2014-05-09	2002-09-11	2002-09-13	ENSG00000152214	ENSG00000152214			10017	protein-coding gene	gene with protein product		609592	"""Ric (Drosophila)-like, expressed in neurons"""	RIN		8824319, 8918462	Standard	NM_002930		Approved	RIBA	uc002lav.4	Q99578	OTTHUMG00000132611	ENST00000326695.5:c.480delT	chr18.hg19:g.40323632delA	ENSP00000321805:p.Phe160fs	101.0	0.0		116.0	10.0	NM_002930	B2R9L1|O15295|Q8TD69|Q8WVF6|Q92964	Frame_Shift_Del	DEL	ENST00000326695.5	hg19	CCDS11921.1																																																																																			.	.		0.383	RIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255852.1	NM_002930	
TFIP11	24144	hgsc.bcm.edu	37	22	26902743	26902743	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:26902743delT	ENST00000407690.1	-	5	644	c.361delA	c.(361-363)acgfs	p.T121fs	TFIP11_ENST00000496523.1_5'Flank|TFIP11_ENST00000407148.1_Frame_Shift_Del_p.T121fs|TFIP11_ENST00000407431.1_Frame_Shift_Del_p.T121fs|TFIP11_ENST00000405938.1_Frame_Shift_Del_p.T121fs	NM_012143.2	NP_036275.1	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	121					biomineral tissue development (GO:0031214)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|spliceosomal complex disassembly (GO:0000390)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	DNA binding (GO:0003677)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25						GAGACTACCGTTTTTAGCTTC	0.463																																					p.T121fs		Atlas-INDEL	.											.	TFIP11	72	.	0			c.362delC						.						115.0	107.0	110.0					22																	26902743		2203	4300	6503	SO:0001589	frameshift_variant	24144	exon6			.	AL050258	CCDS13838.1	22q12.1	2013-01-28			ENSG00000100109	ENSG00000100109		"""G patch domain containing"""	17165	protein-coding gene	gene with protein product		612747				10806191, 11230166	Standard	NM_012143		Approved	TIP39, DKFZP434B194, Spp382	uc003acs.2	Q9UBB9	OTTHUMG00000150883	ENST00000407690.1:c.361delA	chr22.hg19:g.26902743delT	ENSP00000384421:p.Thr121fs	103.0	0.0		140.0	10.0	NM_001008697	O95908|Q20WL0|Q5H8V8|Q9UGV7|Q9Y2Q8	Frame_Shift_Del	DEL	ENST00000407690.1	hg19	CCDS13838.1																																																																																			.	.		0.463	TFIP11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320750.1	NM_001008697	
FER1L6	654463	hgsc.bcm.edu	37	8	125029888	125029888	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:125029888delA	ENST00000522917.1	+	16	2149	c.1943delA	c.(1942-1944)gaafs	p.E648fs	FER1L6-AS1_ENST00000518567.1_RNA|FER1L6_ENST00000399018.1_Frame_Shift_Del_p.E648fs	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	648						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TCTGAAGCAGAAAAAAAGCCC	0.343																																					p.E648fs		Atlas-INDEL	.											.	FER1L6	268	.	0			c.1942delG						.						87.0	84.0	85.0					8																	125029888		1808	4068	5876	SO:0001589	frameshift_variant	654463	exon16			.	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"""fer-1-like 6 (C. elegans)"""				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.1943delA	chr8.hg19:g.125029888delA	ENSP00000428280:p.Glu648fs	104.0	0.0		101.0	11.0	NM_001039112		Frame_Shift_Del	DEL	ENST00000522917.1	hg19	CCDS43767.1																																																																																			.	.		0.343	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
DHX36	170506	hgsc.bcm.edu	37	3	154010423	154010423	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:154010423delA	ENST00000496811.1	-	15	1811	c.1731delT	c.(1729-1731)tttfs	p.F577fs	DHX36_ENST00000308361.6_Frame_Shift_Del_p.F577fs|DHX36_ENST00000329463.5_Frame_Shift_Del_p.F563fs|DHX36_ENST00000544526.1_Frame_Shift_Del_p.F563fs	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	577	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TCTGAGTATCAAAATGCGTCT	0.378																																					p.D578fs		Atlas-INDEL	.											.	DHX36	98	.	0			c.1732delG						.						229.0	217.0	221.0					3																	154010423		2203	4300	6503	SO:0001589	frameshift_variant	170506	exon15			.	AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"""DEAH-boxes"""	14410	protein-coding gene	gene with protein product		612767	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"""	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.1731delT	chr3.hg19:g.154010423delA	ENSP00000417078:p.Phe577fs	196.0	0.0		203.0	13.0	NM_020865	B2RB00|Q70JU3|Q8IYE5|Q9P240	Frame_Shift_Del	DEL	ENST00000496811.1	hg19	CCDS3171.1																																																																																			.	.		0.378	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865	
INO80D	54891	hgsc.bcm.edu	37	2	206892990	206892990	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:206892990delT	ENST00000403263.1	-	6	1547	c.1143delA	c.(1141-1143)aaafs	p.K381fs	Y_RNA_ENST00000384656.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	381					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						GGTGCTTATATTTCTGCTGAA	0.498																																					p.Y382fs		Atlas-INDEL	.											.	INO80D	134	.	0			c.1144delT						.						73.0	71.0	72.0					2																	206892990		1891	4117	6008	SO:0001589	frameshift_variant	54891	exon6			.		CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933		"""INO80 complex subunits"""	25997	protein-coding gene	gene with protein product						16230350	Standard	NM_017759		Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.1143delA	chr2.hg19:g.206892990delT	ENSP00000384198:p.Lys381fs	116.0	0.0		132.0	10.0	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Frame_Shift_Del	DEL	ENST00000403263.1	hg19	CCDS46500.1																																																																																			.	.		0.498	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759	
ZNFX1	57169	hgsc.bcm.edu	37	20	47896879	47896879	+	5'Flank	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:47896879delT	ENST00000396105.1	-	0	0				SNORD12B_ENST00000410433.1_RNA|SNORD12_ENST00000391002.1_RNA|ZFAS1_ENST00000417721.1_RNA|ZFAS1_ENST00000326677.5_RNA|ZFAS1_ENST00000450535.1_RNA|ZFAS1_ENST00000428008.1_RNA|ZFAS1_ENST00000458653.1_RNA|ZFAS1_ENST00000371743.3_RNA|ZNFX1_ENST00000371754.4_5'Flank|ZNFX1_ENST00000371752.1_5'Flank|SNORD12C_ENST00000386307.1_RNA|ZFAS1_ENST00000441722.1_RNA	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1								metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ATGACTTAGCTTTTTTCCCCG	0.438																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.						121.0	93.0	101.0					20																	47896879		1568	3582	5150	SO:0001631	upstream_gene_variant	100113393	.			.	AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696		chr20.hg19:g.47896879delT	Exception_encountered	214.0	0.0		213.0	13.0	.	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	RNA	DEL	ENST00000396105.1	hg19	CCDS13417.1																																																																																			.	.		0.438	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035	
RGPD6	729540	hgsc.bcm.edu	37	2	111292773	111292773	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:111292773delC	ENST00000329516.3	-	20	3266	c.3190delG	c.(3190-3192)gtafs	p.V1064fs		NM_001123363.3	NP_001116835.1	Q99666	RGPD5_HUMAN	RANBP2-like and GRIP domain containing 6	1064	RanBD1 1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)											AATAGTTTTACCCCCTGTGAA	0.393																																					p.V1064fs		Atlas-INDEL	.											.	RGPD5	1	.	0			c.3191delT						.																																			SO:0001589	frameshift_variant	84220	exon20			.	AK056675	CCDS46388.1, CCDS42729.1	2q13	2013-01-10			ENSG00000183054	ENSG00000183054		"""Tetratricopeptide (TTC) repeat domain containing"""	32419	protein-coding gene	gene with protein product		612709				15710750, 15815621, 9480752	Standard	NM_001037866		Approved	RGP6	uc021vly.1	Q99666	OTTHUMG00000153196	ENST00000329516.3:c.3190delG	chr2.hg19:g.111292773delC	ENSP00000330842:p.Val1064fs	99.0	0.0		132.0	10.0	NM_005054	Q53QN2|Q53T03|Q59GM7|Q9H0B2	Frame_Shift_Del	DEL	ENST00000329516.3	hg19	CCDS46388.1																																																																																			.	.		0.393	RGPD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330029.5	NM_001123363	
ADCY10	55811	hgsc.bcm.edu	37	1	167806547	167806547	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:167806547delT	ENST00000367851.4	-	22	3201	c.3017delA	c.(3016-3018)aagfs	p.K1006fs	ADCY10_ENST00000367848.1_Frame_Shift_Del_p.K914fs|ADCY10_ENST00000545172.1_Frame_Shift_Del_p.K853fs	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	1006					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						CAAGATAAGCTTTTCTTCAGC	0.378																																					p.K1006fs		Atlas-INDEL	.											.	ADCY10	175	.	0			c.3018delG						.						82.0	84.0	84.0					1																	167806547		2203	4300	6503	SO:0001589	frameshift_variant	55811	exon22			.	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.3017delA	chr1.hg19:g.167806547delT	ENSP00000356825:p.Lys1006fs	98.0	0.0		181.0	11.0	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Frame_Shift_Del	DEL	ENST00000367851.4	hg19	CCDS1265.1																																																																																			.	.		0.378	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417	
OR4K17	390436	hgsc.bcm.edu	37	14	20586015	20586015	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:20586015delT	ENST00000315543.4	+	1	450	c.450delT	c.(448-450)gctfs	p.A150fs		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|skin(3)	21	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)		TCTCCATGGCTTTTGACAGAT	0.433																																					p.A150fs		Atlas-INDEL	.											.	OR4K17	58	.	0			c.449delC						.						167.0	144.0	152.0					14																	20586015		2203	4300	6503	SO:0001589	frameshift_variant	390436	exon1			.		CCDS32030.1	14q11.2	2013-09-23			ENSG00000176230	ENSG00000176230		"""GPCR / Class A : Olfactory receptors"""	15355	protein-coding gene	gene with protein product							Standard	NM_001004715		Approved		uc001vwo.1	Q8NGC6	OTTHUMG00000170783	ENST00000315543.4:c.450delT	chr14.hg19:g.20586015delT	ENSP00000319197:p.Ala150fs	146.0	0.0		176.0	11.0	NM_001004715	Q6IF12	Frame_Shift_Del	DEL	ENST00000315543.4	hg19	CCDS32030.1																																																																																			.	.		0.433	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1		
VWA5A	4013	hgsc.bcm.edu	37	11	123994945	123994945	+	Splice_Site	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:123994945delT	ENST00000456829.2	+	11	1417	c.1166delT	c.(1165-1167)ctt>ct	p.L389fs	VWA5A_ENST00000361352.5_Splice_Site_p.L389fs|VWA5A_ENST00000392748.1_Splice_Site_p.L389fs|VWA5A_ENST00000392744.4_Splice_Site_p.L405fs|VWA5A_ENST00000360334.4_Intron|VWA5A_ENST00000449321.1_Splice_Site_p.L389fs	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	389	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.									autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						TTTGTATAGCTTTTTGTCTTT	0.348																																					p.L389fs		Atlas-INDEL	.											.	VWA5A	102	.	0			c.1165delC						.						96.0	90.0	92.0					11																	123994945		2201	4299	6500	SO:0001630	splice_region_variant	4013	exon10			.	AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"""loss of heterozygosity, 11, chromosomal region 2, gene A"""	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.1165-1T>-	chr11.hg19:g.123994945delT		121.0	0.0		230.0	14.0	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Frame_Shift_Del	DEL	ENST00000456829.2	hg19	CCDS8444.1																																																																																			.	.		0.348	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622	Frame_Shift_Del
TTN	7273	hgsc.bcm.edu	37	2	179614678	179614678	+	Intron	DEL	A	A	-	rs201544975		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:179614678delA	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000360870.5_Frame_Shift_Del_p.L4150fs|TTN_ENST00000342992.6_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin						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)			AATATCAGACAAAAATACAAA	0.358																																					p.L4150fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.12450delG						.						77.0	82.0	80.0					2																	179614678		2203	4297	6500	SO:0001627	intron_variant	7273	exon46			.	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.10360+3172T>-	chr2.hg19:g.179614678delA		196.0	0.0		220.0	14.0	NM_133379	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																																																																																				.	.		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KIF19	124602	hgsc.bcm.edu	37	17	72338849	72338849	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:72338849delC	ENST00000389916.4	+	4	450	c.312delC	c.(310-312)ggcfs	p.G104fs		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	104	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						TTGCCTATGGCCCCACAGGTA	0.587																																					p.G104fs		Atlas-INDEL	.											.	KIF19	102	.	0			c.311delG						.						137.0	105.0	116.0					17																	72338849		2203	4300	6503	SO:0001589	frameshift_variant	124602	exon4			.	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.312delC	chr17.hg19:g.72338849delC	ENSP00000374566:p.Gly104fs	132.0	0.0		163.0	10.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Frame_Shift_Del	DEL	ENST00000389916.4	hg19	CCDS32718.2																																																																																			.	.		0.587	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
SERPINA9	327657	hgsc.bcm.edu	37	14	94933604	94933604	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:94933604delA	ENST00000380365.3	-	3	822	c.744delT	c.(742-744)tttfs	p.F248fs	SERPINA9_ENST00000546329.1_Frame_Shift_Del_p.F230fs|RP11-349I1.2_ENST00000536735.1_RNA|SERPINA9_ENST00000448305.2_Frame_Shift_Del_p.F168fs|SERPINA9_ENST00000298845.7_Frame_Shift_Del_p.F166fs|SERPINA9_ENST00000539349.1_5'Flank|SERPINA9_ENST00000424550.2_Frame_Shift_Del_p.F117fs|SERPINA9_ENST00000337425.5_Frame_Shift_Del_p.F266fs			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	248					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		TATCCACCCCAAAAGCGAACT	0.517																																					p.G267fs		Atlas-INDEL	.											.	SERPINA9	105	.	0			c.799delG						.						70.0	69.0	69.0					14																	94933604		2010	4184	6194	SO:0001589	frameshift_variant	327657	exon3			.	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.744delT	chr14.hg19:g.94933604delA	ENSP00000369723:p.Phe248fs	114.0	0.0		165.0	13.0	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Frame_Shift_Del	DEL	ENST00000380365.3	hg19																																																																																				.	.		0.517	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
KIF2A	3796	hgsc.bcm.edu	37	5	61643927	61643927	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:61643927delA	ENST00000401507.3	+	3	523	c.212delA	c.(211-213)gaafs	p.E71fs	KIF2A_ENST00000506857.1_Frame_Shift_Del_p.E44fs|KIF2A_ENST00000407818.3_Frame_Shift_Del_p.E71fs|KIF2A_ENST00000381103.2_Frame_Shift_Del_p.E51fs|KIF2A_ENST00000509663.2_Intron	NM_001243953.1|NM_004520.4	NP_001230882.1|NP_004511.2	O00139	KIF2A_HUMAN	kinesin heavy chain member 2A	71	Globular. {ECO:0000255}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|nervous system development (GO:0007399)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	15		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		CCTGATGAAGAAATTGAACCC	0.403																																					p.E71fs		Atlas-INDEL	.											.	KIF2A	69	.	0			c.211delG						.						139.0	137.0	138.0					5																	61643927		2203	4300	6503	SO:0001589	frameshift_variant	3796	exon3			.	BC031828	CCDS3980.2, CCDS47216.1, CCDS58949.1	5q12-q13	2008-02-05	2006-09-26	2006-09-26	ENSG00000068796	ENSG00000068796		"""Kinesins"""	6318	protein-coding gene	gene with protein product		602591	"""kinesin heavy chain member 2"""	KIF2		9177777	Standard	NM_001098511		Approved	HK2	uc003jsz.4	O00139	OTTHUMG00000097755	ENST00000401507.3:c.212delA	chr5.hg19:g.61643927delA	ENSP00000385622:p.Glu71fs	123.0	0.0		170.0	11.0	NM_001243953	A5YM42|A5YM54|B4DY54|D3DW97|E9PB70|Q7Z5I3|Q8N5Q7	Frame_Shift_Del	DEL	ENST00000401507.3	hg19	CCDS3980.2																																																																																			.	.		0.403	KIF2A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317989.1	NM_004520	
ZC3H18	124245	hgsc.bcm.edu	37	16	88691079	88691079	+	Frame_Shift_Del	DEL	C	C	-	rs540178633		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:88691079delC	ENST00000301011.5	+	12	2168	c.1968delC	c.(1966-1968)gtcfs	p.V656fs	ZC3H18_ENST00000452588.2_Frame_Shift_Del_p.V680fs	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	656	Ser-rich.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CTGCTCCTGTCCCCGAGCCCA	0.692																																					p.V656fs	Ovarian(121;375 2276 20373 38669)	Atlas-INDEL	.											.	ZC3H18	90	.	0			c.1967delT						.						46.0	65.0	59.0					16																	88691079		2198	4300	6498	SO:0001589	frameshift_variant	124245	exon12			.	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"""Zinc fingers, CCCH-type domain containing"""	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.1968delC	chr16.hg19:g.88691079delC	ENSP00000301011:p.Val656fs	123.0	0.0		209.0	14.0	NM_144604	Q96DG4|Q96MP7	Frame_Shift_Del	DEL	ENST00000301011.5	hg19	CCDS10967.1																																																																																			.	.		0.692	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604	
MYO15A	51168	hgsc.bcm.edu	37	17	18051452	18051452	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:18051452delC	ENST00000205890.5	+	31	6957	c.6619delC	c.(6619-6621)cccfs	p.P2208fs	snoU13_ENST00000459354.1_RNA	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2208	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.|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)					CCGCACCTTACCCCCGACCCA	0.647																																					p.L2206fs		Atlas-INDEL	.											.	MYO15A	268	.	0			c.6618delA						.						38.0	42.0	41.0					17																	18051452		2028	4177	6205	SO:0001589	frameshift_variant	51168	exon30			.	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.6619delC	chr17.hg19:g.18051452delC	ENSP00000205890:p.Pro2208fs	148.0	0.0		202.0	13.0	NM_016239	B4DFC7	Frame_Shift_Del	DEL	ENST00000205890.5	hg19	CCDS42271.1																																																																																			.	.		0.647	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
CHEK2	11200	hgsc.bcm.edu	37	22	29099532	29099532	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:29099532delT	ENST00000405598.1	-	9	1060	c.869delA	c.(868-870)aacfs	p.N290fs	CHEK2_ENST00000402731.1_Frame_Shift_Del_p.N290fs|CHEK2_ENST00000403642.1_Frame_Shift_Del_p.N199fs|CHEK2_ENST00000544772.1_Frame_Shift_Del_p.N69fs|CHEK2_ENST00000328354.6_Frame_Shift_Del_p.N290fs|CHEK2_ENST00000382578.1_Frame_Shift_Del_p.N199fs|CHEK2_ENST00000382580.2_Frame_Shift_Del_p.N333fs|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000404276.1_Frame_Shift_Del_p.N290fs|CHEK2_ENST00000464581.1_5'UTR|CHEK2_ENST00000382566.1_Intron|CHEK2_ENST00000348295.3_Frame_Shift_Del_p.N290fs			O96017	CHK2_HUMAN	checkpoint kinase 2	290	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						ATCAAAAAAGTTTTTAATCTT	0.333			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.N333fs		Atlas-INDEL	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	.	CHEK2	438	.	0			c.999delC						.						16.0	18.0	17.0					22																	29099532		2197	4295	6492	SO:0001589	frameshift_variant	11200	exon9			.	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.869delA	chr22.hg19:g.29099532delT	ENSP00000386087:p.Asn290fs	84.0	0.0		131.0	10.0	NM_001005735	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Frame_Shift_Del	DEL	ENST00000405598.1	hg19	CCDS13843.1																																																																																			.	.		0.333	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735	
MACROD1	28992	hgsc.bcm.edu	37	11	63767024	63767024	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:63767024delG	ENST00000255681.6	-	7	861	c.795delC	c.(793-795)cccfs	p.P265fs	OTUB1_ENST00000535715.1_Intron	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1	265	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						TGGAGATGCAGGGGAACGCCT	0.716																																					p.C266fs		Atlas-INDEL	.											.	MACROD1	17	.	0			c.796delT						.						13.0	15.0	14.0					11																	63767024		2189	4284	6473	SO:0001589	frameshift_variant	28992	exon7			.	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.795delC	chr11.hg19:g.63767024delG	ENSP00000255681:p.Pro265fs	92.0	0.0		154.0	11.0	NM_014067	Q9UH96	Frame_Shift_Del	DEL	ENST00000255681.6	hg19	CCDS8056.1																																																																																			.	.		0.716	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
WHSC1	7468	hgsc.bcm.edu	37	4	1957786	1957786	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:1957786delT	ENST00000382895.3	+	17	3183	c.2752delT	c.(2752-2754)ttcfs	p.F918fs	WHSC1_ENST00000382892.2_Frame_Shift_Del_p.F918fs|WHSC1_ENST00000482415.2_3'UTR|WHSC1_ENST00000382891.5_Frame_Shift_Del_p.F918fs|WHSC1_ENST00000382888.3_Frame_Shift_Del_p.F266fs|WHSC1_ENST00000508803.1_Frame_Shift_Del_p.F918fs	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	918	PWWP 2. {ECO:0000255|PROSITE- ProRule:PRU00162}.				anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		GATTGGAGAATTCCCTGTGTT	0.473			T	IGH@	MM																																p.E917fs		Atlas-INDEL	.		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	WHSC1	180	.	0			c.2751delA						.						148.0	175.0	166.0					4																	1957786		2203	4300	6503	SO:0001589	frameshift_variant	7468	exon15			.	AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"""Zinc fingers, PHD-type"""	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.2752delT	chr4.hg19:g.1957786delT	ENSP00000372351:p.Phe918fs	129.0	0.0		169.0	11.0	NM_133335	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Frame_Shift_Del	DEL	ENST00000382895.3	hg19	CCDS33940.1																																																																																			.	.		0.473	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330	
CACNA1G	8913	hgsc.bcm.edu	37	17	48704048	48704048	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:48704048delC	ENST00000359106.5	+	38	7070	c.7070delC	c.(7069-7071)tccfs	p.S2357fs	CACNA1G_ENST00000514717.1_Frame_Shift_Del_p.S2207fs|CACNA1G_ENST00000507510.2_Frame_Shift_Del_p.S2312fs|CACNA1G_ENST00000512389.1_Frame_Shift_Del_p.S2253fs|CACNA1G_ENST00000513964.1_Frame_Shift_Del_p.S2219fs|CACNA1G_ENST00000510115.1_Frame_Shift_Del_p.S2278fs|CACNA1G_ENST00000503485.1_Frame_Shift_Del_p.S2230fs|CACNA1G_ENST00000515765.1_Frame_Shift_Del_p.S2301fs|CACNA1G_ENST00000429973.2_Frame_Shift_Del_p.S2246fs|CACNA1G_ENST00000502264.1_Frame_Shift_Del_p.S2286fs|CACNA1G_ENST00000510366.1_Frame_Shift_Del_p.S2212fs|CACNA1G_ENST00000515165.1_Frame_Shift_Del_p.S2264fs|CACNA1G_ENST00000360761.4_Frame_Shift_Del_p.S2241fs|CACNA1G_ENST00000352832.5_Frame_Shift_Del_p.S2230fs|CACNA1G_ENST00000507336.1_Frame_Shift_Del_p.S2346fs|CACNA1G_ENST00000514181.1_Frame_Shift_Del_p.S2239fs|CACNA1G_ENST00000514079.1_Frame_Shift_Del_p.S2271fs|CACNA1G_ENST00000507609.1_Frame_Shift_Del_p.S2257fs|CACNA1G_ENST00000505165.1_Frame_Shift_Del_p.S2185fs|CACNA1G_ENST00000358244.5_Frame_Shift_Del_p.S2151fs|CACNA1G_ENST00000513689.2_Frame_Shift_Del_p.S2267fs|CACNA1G_ENST00000507896.1_Frame_Shift_Del_p.S2174fs|CTB-22K21.2_ENST00000502435.1_RNA|CACNA1G_ENST00000442258.2_Frame_Shift_Del_p.S2223fs|CACNA1G_ENST00000354983.4_Frame_Shift_Del_p.S2323fs|CACNA1G_ENST00000515411.1_Frame_Shift_Del_p.S2294fs	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	2357					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GCCTCGCCCTCCCCAAAGAAA	0.632											OREG0024569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S2357fs		Atlas-INDEL	.											.	CACNA1G	659	.	0			c.7069delT						.						57.0	63.0	61.0					17																	48704048		1984	4143	6127	SO:0001589	frameshift_variant	8913	exon38			.	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.7070delC	chr17.hg19:g.48704048delC	ENSP00000352011:p.Ser2357fs	151.0	0.0	956	156.0	12.0	NM_018896	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Frame_Shift_Del	DEL	ENST00000359106.5	hg19	CCDS45730.1																																																																																			.	.		0.632	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
OAS3	4940	hgsc.bcm.edu	37	12	113402157	113402157	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:113402157delT	ENST00000228928.7	+	11	2526	c.2347delT	c.(2347-2349)tttfs	p.F783fs	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	783	OAS domain 3.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						CATCTGTTCATTTTTGAAGGA	0.512																																					p.S782fs		Atlas-INDEL	.											.	OAS3	63	.	0			c.2346delA						.						49.0	50.0	50.0					12																	113402157		1875	4106	5981	SO:0001589	frameshift_variant	4940	exon11			.	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.2347delT	chr12.hg19:g.113402157delT	ENSP00000228928:p.Phe783fs	172.0	0.0		180.0	12.0	NM_006187	Q2HJ14|Q9H3P5	Frame_Shift_Del	DEL	ENST00000228928.7	hg19	CCDS44981.1																																																																																			.	.		0.512	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
ANKFY1	51479	hgsc.bcm.edu	37	17	4076695	4076695	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:4076695delC	ENST00000341657.4	-	21	3003	c.2968delG	c.(2968-2970)gttfs	p.V990fs	CYB5D2_ENST00000573984.1_Intron|ANKFY1_ENST00000574367.1_Frame_Shift_Del_p.V991fs|ANKFY1_ENST00000570535.1_Frame_Shift_Del_p.V1032fs	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	990					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						GTCAGGAGAACCCGGATGTTG	0.582																																					p.V1032fs		Atlas-INDEL	.											.	ANKFY1	81	.	0			c.3095delT						.						69.0	78.0	75.0					17																	4076695		1981	4155	6136	SO:0001589	frameshift_variant	51479	exon21			.	AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"""Zinc fingers, FYVE domain containing"", ""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.2968delG	chr17.hg19:g.4076695delC	ENSP00000343362:p.Val990fs	150.0	0.0		151.0	11.0	NM_001257999	A8KA65|Q5RKV4|Q9ULG5	Frame_Shift_Del	DEL	ENST00000341657.4	hg19																																																																																				.	.		0.582	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376	
TRRAP	8295	hgsc.bcm.edu	37	7	98575870	98575870	+	Frame_Shift_Del	DEL	A	A	-	rs56341061		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:98575870delA	ENST00000359863.4	+	56	8610	c.8401delA	c.(8401-8403)aaafs	p.K2802fs	TRRAP_ENST00000355540.3_Frame_Shift_Del_p.K2784fs|TRRAP_ENST00000446306.3_Frame_Shift_Del_p.K2784fs	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2802	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GGATAAAGCCAAAAAAGAACA	0.388																																					p.A2800fs		Atlas-INDEL	.											.	TRRAP	863	.	0			c.8400delC						.						142.0	139.0	140.0					7																	98575870		2203	4300	6503	SO:0001589	frameshift_variant	8295	exon56			.	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.8401delA	chr7.hg19:g.98575870delA	ENSP00000352925:p.Lys2802fs	127.0	0.0		258.0	17.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Frame_Shift_Del	DEL	ENST00000359863.4	hg19	CCDS59066.1																																																																																			.	.		0.388	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
PLEKHA7	144100	hgsc.bcm.edu	37	11	16816462	16816462	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:16816462delT	ENST00000355661.3	-	18	2523	c.2513delA	c.(2512-2514)aatfs	p.N838fs	PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000448080.2_Frame_Shift_Del_p.N838fs|PLEKHA7_ENST00000531066.1_Frame_Shift_Del_p.N838fs			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	838					epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)	p.N838fs*61(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						CTCACCCGGATTTTTTACTGA	0.498																																					p.N838fs		Atlas-INDEL	.											.	PLEKHA7	120	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2514delT						.						154.0	151.0	152.0					11																	16816462		2200	4294	6494	SO:0001589	frameshift_variant	144100	exon18			.	BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689		"""Pleckstrin homology (PH) domain containing"""	27049	protein-coding gene	gene with protein product		612686				12477932	Standard	NM_175058		Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000355661.3:c.2513delA	chr11.hg19:g.16816462delT	ENSP00000347883:p.Asn838fs	121.0	0.0		140.0	10.0	NM_175058	B4DK33|B4DWC3|Q86VZ7	Frame_Shift_Del	DEL	ENST00000355661.3	hg19	CCDS31434.1																																																																																			.	.		0.498	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058	
CEBPZ	10153	hgsc.bcm.edu	37	2	37455194	37455194	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:37455194delT	ENST00000234170.5	-	2	1287	c.1142delA	c.(1141-1143)aagfs	p.K381fs		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	381					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				AAGAAGAGCCTTTTCTTCCTC	0.418																																					p.K381fs		Atlas-INDEL	.											.	CEBPZ	68	.	0			c.1143delG						.						103.0	108.0	106.0					2																	37455194		2203	4300	6503	SO:0001589	frameshift_variant	10153	exon2			.	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.1142delA	chr2.hg19:g.37455194delT	ENSP00000234170:p.Lys381fs	105.0	0.0		159.0	10.0	NM_005760	Q8NE75	Frame_Shift_Del	DEL	ENST00000234170.5	hg19	CCDS1787.1																																																																																			.	.		0.418	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760	
PCDHB12	56124	hgsc.bcm.edu	37	5	140588664	140588664	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:140588664delG	ENST00000239450.2	+	1	374	c.185delG	c.(184-186)cggfs	p.R62fs	PCDHB12_ENST00000541609.1_Intron	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	62	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGTCTTCGCGGGGGGCTCGG	0.512																																					p.R62fs		Atlas-INDEL	.											PCDHB12,caecum,carcinoma,0,2	PCDHB12	179	.	0			c.184delC						.						83.0	94.0	90.0					5																	140588664		2203	4300	6503	SO:0001589	frameshift_variant	56124	exon1			.	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.185delG	chr5.hg19:g.140588664delG	ENSP00000239450:p.Arg62fs	115.0	0.0		162.0	11.0	NM_018932	B4DDU1	Frame_Shift_Del	DEL	ENST00000239450.2	hg19	CCDS4254.1																																																																																			.	.		0.512	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
AGTR1	185	hgsc.bcm.edu	37	3	148459417	148459417	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:148459417delA	ENST00000497524.1	+	2	986	c.595delA	c.(595-597)aaafs	p.K199fs	AGTR1_ENST00000418473.2_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000475347.1_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000542281.1_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000474935.1_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000404754.2_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000402260.1_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000349243.3_Frame_Shift_Del_p.K199fs|AGTR1_ENST00000461609.1_Frame_Shift_Del_p.K199fs	NM_009585.3	NP_033611.1	P30556	AGTR1_HUMAN	angiotensin II receptor, type 1	199					angiotensin-activated signaling pathway (GO:0038166)|calcium-mediated signaling (GO:0019722)|cell chemotaxis (GO:0060326)|G-protein coupled receptor signaling pathway (GO:0007186)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|phospholipase C-activating angiotensin-activated signaling pathway (GO:0086097)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of phospholipase A2 activity (GO:0032430)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|renin-angiotensin regulation of aldosterone production (GO:0002018)|Rho protein signal transduction (GO:0007266)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	angiotensin type I receptor activity (GO:0001596)|angiotensin type II receptor activity (GO:0004945)|bradykinin receptor binding (GO:0031711)|protein heterodimerization activity (GO:0046982)			breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30			LUSC - Lung squamous cell carcinoma(72;0.127)|Lung(72;0.152)		Azilsartan medoxomil(DB08822)|Candesartan(DB00796)|Eprosartan(DB00876)|Forasartan(DB01342)|Irbesartan(DB01029)|Losartan(DB00678)|Olmesartan(DB00275)|Saprisartan(DB01347)|Tasosartan(DB01349)|Telmisartan(DB00966)|Valsartan(DB00177)	GGGCCTGACCAAAAATATACT	0.378																																					p.T233fs		Atlas-INDEL	.											.	AGTR1	63	.	0			c.699delC						.						65.0	71.0	69.0					3																	148459417		2199	4299	6498	SO:0001589	frameshift_variant	185	exon4			.	M87290	CCDS3137.1	3q24	2012-08-08	2002-02-20		ENSG00000144891	ENSG00000144891		"""GPCR / Class A : Angiotensin receptors"""	336	protein-coding gene	gene with protein product		106165	"""angiotensin receptor 1B"""	AGTR1B		1550596	Standard	NM_009585		Approved	AT1, AT2R1, AGTR1A, AT2R1A, HAT1R, AG2S, AT2R1B, AT1B	uc003ewh.4	P30556	OTTHUMG00000159503	ENST00000497524.1:c.595delA	chr3.hg19:g.148459417delA	ENSP00000419422:p.Lys199fs	136.0	0.0		164.0	11.0	NM_031850	Q13725|Q8TBK4	Frame_Shift_Del	DEL	ENST00000497524.1	hg19	CCDS3137.1																																																																																			.	.		0.378	AGTR1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355807.1		
BCAR3	8412	hgsc.bcm.edu	37	1	94140264	94140264	+	Frame_Shift_Del	DEL	G	G	-	rs141721897		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:94140264delG	ENST00000370244.1	-	4	511	c.223delC	c.(223-225)cacfs	p.H75fs	BCAR3_ENST00000370243.1_Frame_Shift_Del_p.H75fs|BCAR3_ENST00000260502.6_Frame_Shift_Del_p.H75fs	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	75					lens morphogenesis in camera-type eye (GO:0002089)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	25		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		GATTTGGAGTGGGGGAGGGTG	0.557																																					p.H75fs		Atlas-INDEL	.											.	BCAR3	62	.	0			c.224delA						.						68.0	63.0	65.0					1																	94140264		2203	4300	6503	SO:0001589	frameshift_variant	8412	exon2			.	U92715	CCDS745.1, CCDS58010.1	1p22.1	2013-02-14			ENSG00000137936	ENSG00000137936		"""SH2 domain containing"""	973	protein-coding gene	gene with protein product		604704				9582273	Standard	NM_001261408		Approved	NSP2, SH2D3B	uc001dpz.4	O75815	OTTHUMG00000010301	ENST00000370244.1:c.223delC	chr1.hg19:g.94140264delG	ENSP00000359264:p.His75fs	120.0	0.0		156.0	10.0	NM_001261409	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Frame_Shift_Del	DEL	ENST00000370244.1	hg19	CCDS745.1																																																																																			.	.		0.557	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1		
STT3B	201595	hgsc.bcm.edu	37	3	31661295	31661295	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:31661295delA	ENST00000295770.2	+	9	1509	c.1300delA	c.(1300-1302)aaafs	p.K434fs	STT3B_ENST00000453168.1_3'UTR	NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	434					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						GTTCTGCATCAAAAATATCAA	0.333																																					p.I433fs		Atlas-INDEL	.											.,1	STT3B	52	.	0			c.1299delC						.						159.0	139.0	146.0					3																	31661295		2203	4300	6503	SO:0001589	frameshift_variant	201595	exon9			.	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.1300delA	chr3.hg19:g.31661295delA	ENSP00000295770:p.Lys434fs	129.0	0.0		159.0	10.0	NM_178862	Q96JZ4|Q96KY7	Frame_Shift_Del	DEL	ENST00000295770.2	hg19	CCDS2650.1																																																																																			.	.		0.333	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862	
HFM1	164045	hgsc.bcm.edu	37	1	91844032	91844032	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:91844032delT	ENST00000370425.3	-	10	1262	c.1164delA	c.(1162-1164)aaafs	p.K388fs	HFM1_ENST00000370424.3_Frame_Shift_Del_p.K67fs|HFM1_ENST00000294696.5_De_novo_Start_OutOfFrame	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	388	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TGCTATCCCATTTTTCCTAGA	0.318																																					p.W389fs		Atlas-INDEL	.											.	HFM1	188	.	0			c.1165delT						.						88.0	85.0	86.0					1																	91844032		2203	4300	6503	SO:0001589	frameshift_variant	164045	exon10			.	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.1164delA	chr1.hg19:g.91844032delT	ENSP00000359454:p.Lys388fs	129.0	0.0		187.0	12.0	NM_001017975	B1B0B6|Q8N9Q0	Frame_Shift_Del	DEL	ENST00000370425.3	hg19	CCDS30769.2																																																																																			.	.		0.318	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
MYBPHL	343263	hgsc.bcm.edu	37	1	109837772	109837772	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:109837772delG	ENST00000357155.1	-	7	1064	c.1015delC	c.(1015-1017)ctafs	p.L339fs	MYBPHL_ENST00000477962.1_5'UTR	NM_001010985.2|NM_001265613.1	NP_001010985.2|NP_001252542.1	A2RUH7	MBPHL_HUMAN	myosin binding protein H-like	339	Ig-like C2-type 2.									central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(2)	14		all_lung(203;0.00519)|all_epithelial(167;0.00575)|Lung NSC(277;0.00822)		Colorectal(144;0.0306)|Lung(183;0.0681)|COAD - Colon adenocarcinoma(174;0.117)|Epithelial(280;0.197)|all cancers(265;0.225)		GCCTCCCCTAGGGGGTTCACC	0.577																																					p.L339fs		Atlas-INDEL	.											.	MYBPHL	28	.	0			c.1016delT						.						103.0	94.0	97.0					1																	109837772		2203	4300	6503	SO:0001589	frameshift_variant	343263	exon7			.	AK129834	CCDS30793.1	1p13	2013-02-11			ENSG00000221986	ENSG00000221986		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	30434	protein-coding gene	gene with protein product							Standard	NM_001010985		Approved		uc001dxk.1	A2RUH7	OTTHUMG00000012002	ENST00000357155.1:c.1015delC	chr1.hg19:g.109837772delG	ENSP00000349678:p.Leu339fs	184.0	0.0		205.0	15.0	NM_001010985	B7ZME5|Q5T2Z7	Frame_Shift_Del	DEL	ENST00000357155.1	hg19	CCDS30793.1																																																																																			.	.		0.577	MYBPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033197.1	NM_001010985	
AXL	558	hgsc.bcm.edu	37	19	41725374	41725374	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:41725374delC	ENST00000301178.4	+	1	267	c.77delC	c.(76-78)gccfs	p.A26fs	CTD-2195B23.3_ENST00000598541.1_RNA|AXL_ENST00000359092.3_Frame_Shift_Del_p.A26fs	NM_001278599.1|NM_021913.3	NP_001265528.1|NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase	26	Interaction with GAS6.				apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interferon-alpha (GO:0035457)|cellular response to lipopolysaccharide (GO:0071222)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte homeostasis (GO:0034101)|forebrain cell migration (GO:0021885)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|natural killer cell differentiation (GO:0001779)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of tumor necrosis factor production (GO:0032720)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein kinase B signaling (GO:0051897)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|phosphatidylserine binding (GO:0001786)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	48						GCGTGCATGGCCCCCAGGGGT	0.701																																					p.A26fs		Atlas-INDEL	.											.	AXL	126	.	0			c.76delG						.						12.0	16.0	14.0					19																	41725374		2192	4287	6479	SO:0001589	frameshift_variant	558	exon1			.	M76125	CCDS12574.1, CCDS12575.1, CCDS62677.1	19q13.1	2013-02-11				ENSG00000167601	2.7.10.1	"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	905	protein-coding gene	gene with protein product		109135				1656220	Standard	NM_021913		Approved	UFO, JTK11	uc010ehj.3	P30530		ENST00000301178.4:c.77delC	chr19.hg19:g.41725374delC	ENSP00000301178:p.Ala26fs	279.0	0.0		222.0	14.0	NM_021913	Q8N5L2|Q9UD27	Frame_Shift_Del	DEL	ENST00000301178.4	hg19	CCDS12575.1																																																																																			.	.		0.701	AXL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463323.2		
CBFA2T2	9139	hgsc.bcm.edu	37	20	32207380	32207380	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:32207380delC	ENST00000346541.3	+	5	1042	c.505delC	c.(505-507)cccfs	p.P169fs	CBFA2T2_ENST00000359606.3_Frame_Shift_Del_p.P179fs|CBFA2T2_ENST00000375279.2_Frame_Shift_Del_p.P169fs|CBFA2T2_ENST00000492345.1_Frame_Shift_Del_p.P140fs|CBFA2T2_ENST00000342704.6_Frame_Shift_Del_p.P160fs|CBFA2T2_ENST00000491618.1_3'UTR|CBFA2T2_ENST00000344201.3_Frame_Shift_Del_p.P140fs|CBFA2T2_ENST00000397800.1_Frame_Shift_Del_p.P140fs|CBFA2T2_ENST00000397798.2_Frame_Shift_Del_p.P140fs	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	169	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						CACAAACTTTCCCCTTCGTCC	0.348																																					p.F168fs	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-INDEL	.											.	CBFA2T2	93	.	0			c.504delT						.						88.0	90.0	90.0					20																	32207380		2203	4300	6503	SO:0001589	frameshift_variant	9139	exon5			.	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"""Zinc fingers, MYND-type"""	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.505delC	chr20.hg19:g.32207380delC	ENSP00000262653:p.Pro169fs	95.0	0.0		143.0	10.0	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Frame_Shift_Del	DEL	ENST00000346541.3	hg19	CCDS13221.1																																																																																			.	.		0.348	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999	
USP34	9736	hgsc.bcm.edu	37	2	61507429	61507429	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:61507429delA	ENST00000398571.2	-	39	5282	c.5206delT	c.(5206-5208)tggfs	p.W1736fs		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1736					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			CATAACAACCAAAAATACTCT	0.244																																					p.W1736fs		Atlas-INDEL	.											.	USP34	334	.	0			c.5207delG						.						55.0	55.0	55.0					2																	61507429		1793	4046	5839	SO:0001589	frameshift_variant	9736	exon39			.	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.5206delT	chr2.hg19:g.61507429delA	ENSP00000381577:p.Trp1736fs	176.0	0.0		195.0	13.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Frame_Shift_Del	DEL	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.		0.244	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
SF1	7536	hgsc.bcm.edu	37	11	64540917	64540917	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:64540917delG	ENST00000377390.3	-	3	558	c.221delC	c.(220-222)cctfs	p.P74fs	SF1_ENST00000377387.1_Frame_Shift_Del_p.P199fs|SF1_ENST00000433274.2_Frame_Shift_Del_p.P48fs|SF1_ENST00000227503.9_Frame_Shift_Del_p.P74fs|SF1_ENST00000334944.5_Frame_Shift_Del_p.P74fs|SF1_ENST00000422298.2_Intron|SF1_ENST00000377394.3_Frame_Shift_Del_p.P74fs	NM_004630.3	NP_004621.2	Q15637	SF01_HUMAN	splicing factor 1	74					Leydig cell differentiation (GO:0033327)|male sex determination (GO:0030238)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of steroid biosynthetic process (GO:0050810)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribosome (GO:0005840)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.P74fs*63(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	31						CTCAGGGTTAGGGGGGATGCC	0.453																																					p.P199fs		Atlas-INDEL	.											.	SF1	124	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.597delT						.						80.0	69.0	73.0					11																	64540917		2201	4297	6498	SO:0001589	frameshift_variant	7536	exon3			.	D26120	CCDS8080.1, CCDS8081.1, CCDS31599.1, CCDS44642.1, CCDS44642.2, CCDS53660.1, CCDS53661.1	11q13	2014-09-17	2001-12-19	2002-01-11	ENSG00000168066	ENSG00000168066		"""Zinc fingers, CCHC domain containing"""	12950	protein-coding gene	gene with protein product		601516	"""zinc finger protein 162"""	ZNF162		7912130, 9573336	Standard	NM_201997		Approved	ZFM1, ZCCHC25	uc001oaz.2	Q15637	OTTHUMG00000066833	ENST00000377390.3:c.221delC	chr11.hg19:g.64540917delG	ENSP00000366607:p.Pro74fs	93.0	0.0		166.0	10.0	NM_001178030	B7Z1Q1|C9JJE2|Q14818|Q14819|Q15913|Q8IY00|Q92744|Q92745|Q969H7|Q9BW01|Q9UEI0	Frame_Shift_Del	DEL	ENST00000377390.3	hg19	CCDS31599.1																																																																																			.	.		0.453	SF1-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143242.1	NM_004630	
ADHFE1	137872	hgsc.bcm.edu	37	8	67359569	67359569	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:67359569delA	ENST00000396623.3	+	7	652	c.621delA	c.(619-621)gtafs	p.V207fs	ADHFE1_ENST00000379385.4_Frame_Shift_Del_p.V207fs|ADHFE1_ENST00000415254.1_Frame_Shift_Del_p.V159fs|ADHFE1_ENST00000496501.1_3'UTR	NM_144650.2	NP_653251.2	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	207					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|molecular hydrogen transport (GO:0015993)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacid-oxoacid transhydrogenase activity (GO:0047988)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	29		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			ACTTGAAAGTAAAAATTGGTA	0.318																																					p.V207fs		Atlas-INDEL	.											.	ADHFE1	83	.	0			c.620delT						.						62.0	67.0	65.0					8																	67359569		2203	4300	6503	SO:0001589	frameshift_variant	137872	exon7			.	AK056992	CCDS6190.2	8q12.3	2013-05-21			ENSG00000147576	ENSG00000147576	1.1.99.24	"""Alcohol dehydrogenases"""	16354	protein-coding gene	gene with protein product	"""hydroxyacid-oxoacid transhydrogenase"""	611083				12592711	Standard	NM_144650		Approved	ADHFe1, FLJ32430	uc003xwb.4	Q8IWW8	OTTHUMG00000150215	ENST00000396623.3:c.621delA	chr8.hg19:g.67359569delA	ENSP00000379865:p.Val207fs	138.0	0.0		151.0	10.0	NM_144650	B4DTJ8|Q49A19|Q68CI7|Q6P2B6|Q96MF9	Frame_Shift_Del	DEL	ENST00000396623.3	hg19	CCDS6190.2																																																																																			.	.		0.318	ADHFE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316867.3	NM_144650	
RADIL	55698	hgsc.bcm.edu	37	7	4841575	4841575	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:4841575delG	ENST00000399583.3	-	12	2738	c.2551delC	c.(2551-2553)ctgfs	p.L851fs	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Frame_Shift_Del_p.L611fs	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	851	Pro-rich.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CTGGGAGCCAGGGGGCAGCTC	0.697																																					p.L851fs		Atlas-INDEL	.											.	RADIL	110	.	0			c.2552delT						.						6.0	7.0	6.0					7																	4841575		1508	3379	4887	SO:0001589	frameshift_variant	55698	exon12			.	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2551delC	chr7.hg19:g.4841575delG	ENSP00000382492:p.Leu851fs	87.0	0.0		128.0	10.0	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Frame_Shift_Del	DEL	ENST00000399583.3	hg19	CCDS43544.1																																																																																			.	.		0.697	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
PHF3	23469	hgsc.bcm.edu	37	6	64395267	64395267	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:64395267delA	ENST00000262043.3	+	4	1984	c.1644delA	c.(1642-1644)agafs	p.R548fs	PHF3_ENST00000509330.1_Frame_Shift_Del_p.R548fs|PHF3_ENST00000393387.1_Frame_Shift_Del_p.R548fs			Q92576	PHF3_HUMAN	PHD finger protein 3	548					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			TCAAAGTCAGAAAAAAACAAA	0.333																																					p.R548fs	GBM(135;136 1820 29512 34071 46235)	Atlas-INDEL	.											.	PHF3	191	.	0			c.1643delG						.						51.0	54.0	53.0					6																	64395267		2203	4298	6501	SO:0001589	frameshift_variant	23469	exon3			.	AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"""Zinc fingers, PHD-type"""	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.1644delA	chr6.hg19:g.64395267delA	ENSP00000262043:p.Arg548fs	162.0	0.0		182.0	11.0	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Frame_Shift_Del	DEL	ENST00000262043.3	hg19	CCDS4966.1																																																																																			.	.		0.333	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2		
EFCAB7	84455	hgsc.bcm.edu	37	1	64034025	64034025	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:64034025delA	ENST00000371088.4	+	12	1788	c.1542delA	c.(1540-1542)ccafs	p.P514fs	EFCAB7_ENST00000461039.1_3'UTR	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	514							calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						AATGCAAGCCAAAAATTAAAG	0.348																																					p.P514fs		Atlas-INDEL	.											.	EFCAB7	45	.	0			c.1541delC						.						80.0	76.0	77.0					1																	64034025		2203	4300	6503	SO:0001589	frameshift_variant	84455	exon12			.	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.1542delA	chr1.hg19:g.64034025delA	ENSP00000360129:p.Pro514fs	100.0	0.0		143.0	10.0	NM_032437	Q658P0|Q96B95|Q96JM6	Frame_Shift_Del	DEL	ENST00000371088.4	hg19	CCDS30737.1																																																																																			.	.		0.348	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
NUCB2	4925	hgsc.bcm.edu	37	11	17332420	17332420	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:17332420delA	ENST00000529010.1	+	7	751	c.532delA	c.(532-534)aaafs	p.K179fs	NUCB2_ENST00000458064.2_Frame_Shift_Del_p.K179fs|NUCB2_ENST00000323688.6_Frame_Shift_Del_p.K179fs	NM_005013.2	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2	179						cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						TGAAGAATTTAAAAAATATGA	0.279																																					p.F177fs		Atlas-INDEL	.											.	NUCB2	31	.	0			c.531delT						.						67.0	67.0	67.0					11																	17332420		1800	4032	5832	SO:0001589	frameshift_variant	4925	exon7			.	AF052642	CCDS41623.1	11p15.1	2013-01-10						"""EF-hand domain containing"""	8044	protein-coding gene	gene with protein product		608020				7811391	Standard	NM_005013		Approved	NEFA	uc001mmw.3	P80303		ENST00000529010.1:c.532delA	chr11.hg19:g.17332420delA	ENSP00000436455:p.Lys179fs	130.0	0.0		157.0	11.0	NM_005013	A8K642|D3DQX5|Q8NFT5	Frame_Shift_Del	DEL	ENST00000529010.1	hg19	CCDS41623.1																																																																																			.	.		0.279	NUCB2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387614.2	NM_005013	
WWP1	11059	hgsc.bcm.edu	37	8	87454970	87454970	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:87454970delT	ENST00000517970.1	+	18	2268	c.1961delT	c.(1960-1962)cttfs	p.L654fs	WWP1_ENST00000341922.2_Frame_Shift_Del_p.L524fs|WWP1_ENST00000349423.2_Frame_Shift_Del_p.L436fs|WWP1_ENST00000265428.4_Frame_Shift_Del_p.L654fs	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	654	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						CCAGACCATCTTTCATACTTC	0.338																																					p.L654fs		Atlas-INDEL	.											.	WWP1	97	.	0			c.1960delC						.						128.0	118.0	121.0					8																	87454970		2203	4300	6503	SO:0001589	frameshift_variant	11059	exon18			.	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.1961delT	chr8.hg19:g.87454970delT	ENSP00000427793:p.Leu654fs	143.0	0.0		165.0	12.0	NM_007013	O00307|Q5YLC1|Q96BP4	Frame_Shift_Del	DEL	ENST00000517970.1	hg19	CCDS6242.1																																																																																			.	.		0.338	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013	
MB21D1	115004	hgsc.bcm.edu	37	6	74161746	74161746	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:74161746delG	ENST00000370315.3	-	1	253	c.159delC	c.(157-159)cccfs	p.P53fs	MB21D1_ENST00000370318.1_Frame_Shift_Del_p.P53fs	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	53					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						ACTTCCTGGCGGGGCCGAACT	0.716																																					p.A54fs		Atlas-INDEL	.											.	MB21D1	33	.	0			c.160delG						.						4.0	5.0	5.0					6																	74161746		1997	3978	5975	SO:0001589	frameshift_variant	115004	exon1			.	BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"""chromosome 6 open reading frame 150"""	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.159delC	chr6.hg19:g.74161746delG	ENSP00000359339:p.Pro53fs	145.0	0.0		179.0	12.0	NM_138441	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Frame_Shift_Del	DEL	ENST00000370315.3	hg19	CCDS4978.1																																																																																			.	.		0.716	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441	
CCDC59	29080	hgsc.bcm.edu	37	12	82746994	82746994	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:82746994delT	ENST00000256151.7	-	4	1073	c.662delA	c.(661-663)aagfs	p.K221fs	CCDC59_ENST00000548126.1_5'UTR	NM_014167.4	NP_054886.2	Q9P031	TAP26_HUMAN	coiled-coil domain containing 59	221					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)	5						TGGTTGGCCCTTTTTAGTCTT	0.343																																					p.K221fs		Atlas-INDEL	.											.	CCDC59	17	.	0			c.663delG						.						162.0	150.0	154.0					12																	82746994		2203	4298	6501	SO:0001589	frameshift_variant	29080	exon4			.	AF213377	CCDS9023.1	12q21.31	2007-10-17				ENSG00000133773			25005	protein-coding gene	gene with protein product						16630564, 12882447	Standard	NM_014167		Approved	HSPC128, TAP26, BR22	uc001szp.4	Q9P031		ENST00000256151.7:c.662delA	chr12.hg19:g.82746994delT	ENSP00000256151:p.Lys221fs	163.0	0.0		190.0	12.0	NM_014167	Q9H2V5|Q9NW62	Frame_Shift_Del	DEL	ENST00000256151.7	hg19	CCDS9023.1																																																																																			.	.		0.343	CCDC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408186.1	NM_014167	
WDSUB1	151525	hgsc.bcm.edu	37	2	160092653	160092653	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:160092653delT	ENST00000409990.3	-	11	1578	c.1322delA	c.(1321-1323)aagfs	p.K442fs	WDSUB1_ENST00000359774.4_Frame_Shift_Del_p.K442fs|WDSUB1_ENST00000409124.1_Frame_Shift_Del_p.K395fs|WDSUB1_ENST00000358147.4_Frame_Shift_Del_p.K350fs|WDSUB1_ENST00000392796.3_Frame_Shift_Del_p.K442fs	NM_001128213.1	NP_001121685	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain containing 1	442	U-box.						ubiquitin-protein transferase activity (GO:0004842)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|stomach(3)	16						TGTACGTTTCTTTTTGCTGAT	0.373																																					p.K441fs		Atlas-INDEL	.											.	WDSUB1	39	.	0			c.1323delG						.						112.0	101.0	104.0					2																	160092653		2203	4300	6503	SO:0001589	frameshift_variant	151525	exon11			.	AK093494	CCDS2208.1	2q24.2	2013-01-28	2006-02-17	2005-03-25	ENSG00000196151	ENSG00000196151		"""WD repeat domain containing"", ""Sterile alpha motif (SAM) domain containing"", ""U-box domain containing"""	26697	protein-coding gene	gene with protein product			"""WD repeat and SAM domain containing 1"", ""WD repeat, SAM and U-box domain containing 1"""	WDSAM1		12477932	Standard	NM_152528		Approved	UBOX6, FLJ36175	uc002ual.4	Q8N9V3	OTTHUMG00000132028	ENST00000409990.3:c.1322delA	chr2.hg19:g.160092653delT	ENSP00000387078:p.Lys442fs	110.0	0.0		148.0	11.0	NM_152528	Q53TI9|Q8N6N8	Frame_Shift_Del	DEL	ENST00000409990.3	hg19	CCDS2208.1																																																																																			.	.		0.373	WDSUB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333339.1	NM_152528	
KANSL1L	151050	hgsc.bcm.edu	37	2	211018375	211018375	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:211018375delT	ENST00000281772.9	-	2	1195	c.932delA	c.(931-933)aatfs	p.N311fs	KANSL1L_ENST00000452086.1_Frame_Shift_Del_p.N311fs|KANSL1L_ENST00000457374.1_Frame_Shift_Del_p.N311fs|KANSL1L_ENST00000429908.2_5'Flank|KANSL1L_ENST00000418791.1_Frame_Shift_Del_p.N311fs	NM_152519.2	NP_689732.2	A0AUZ9	KAL1L_HUMAN	KAT8 regulatory NSL complex subunit 1-like	311						histone acetyltransferase complex (GO:0000123)											TGCAAAGCCATTTTTTGCATC	0.408																																					p.N311fs		Atlas-INDEL	.											.	.	.	.	0			c.933delT						.						176.0	165.0	169.0					2																	211018375		2203	4300	6503	SO:0001589	frameshift_variant	151050	exon2			.	AK074441	CCDS33370.1	2q34	2012-02-20	2012-02-20	2012-02-20	ENSG00000144445	ENSG00000144445			26310	protein-coding gene	gene with protein product	"""KIAA1267-like"""	613833	"""chromosome 2 open reading frame 67"""	C2orf67		12477932	Standard	NM_152519		Approved	FLJ23861, FLJ32349, MSL1v2, KIAA1267L	uc002vds.3	A0AUZ9	OTTHUMG00000154697	ENST00000281772.9:c.932delA	chr2.hg19:g.211018375delT	ENSP00000281772:p.Asn311fs	205.0	0.0		257.0	16.0	NM_152519	B7ZLN1|I6L9A8|Q53TV8|Q53TW3|Q6IS05|Q8TCI1|Q96MI0|Q9UFC3	Frame_Shift_Del	DEL	ENST00000281772.9	hg19	CCDS33370.1																																																																																			.	.		0.408	KANSL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336633.3	NM_152519	
TTN	7273	hgsc.bcm.edu	37	2	179483342	179483342	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:179483342delT	ENST00000591111.1	-	201	42236	c.42012delA	c.(42010-42012)aaafs	p.K14004fs	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.K6705fs|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.K13077fs|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000604956.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.K6772fs|TTN_ENST00000589042.1_Frame_Shift_Del_p.K15645fs|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Frame_Shift_Del_p.K6580fs|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589907.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14004	Ig-like 95.				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)			ATCCTTCTGCTTTTCCATGTT	0.363																																					p.A15646fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.46936delG						.						175.0	160.0	165.0					2																	179483342		1829	4074	5903	SO:0001589	frameshift_variant	7273	exon251			.	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.42012delA	chr2.hg19:g.179483342delT	ENSP00000465570:p.Lys14004fs	83.0	0.0		129.0	12.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.		0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
EIF4G1	1981	hgsc.bcm.edu	37	3	184039824	184039824	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:184039824delC	ENST00000346169.2	+	10	1723	c.1452delC	c.(1450-1452)ctcfs	p.L484fs	EIF4G1_ENST00000350481.5_Frame_Shift_Del_p.L320fs|EIF4G1_ENST00000392537.2_Frame_Shift_Del_p.L397fs|EIF4G1_ENST00000435046.2_Frame_Shift_Del_p.L288fs|EIF4G1_ENST00000411531.1_Frame_Shift_Del_p.L444fs|EIF4G1_ENST00000342981.4_Frame_Shift_Del_p.L484fs|EIF4G1_ENST00000382330.3_Frame_Shift_Del_p.L491fs|EIF4G1_ENST00000319274.6_Frame_Shift_Del_p.L484fs|EIF4G1_ENST00000352767.3_Frame_Shift_Del_p.L491fs|EIF4G1_ENST00000441154.1_Frame_Shift_Del_p.L320fs|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000434061.2_Frame_Shift_Del_p.L288fs|EIF4G1_ENST00000414031.1_Frame_Shift_Del_p.L444fs|EIF4G1_ENST00000427845.1_Frame_Shift_Del_p.L397fs|EIF4G1_ENST00000424196.1_Frame_Shift_Del_p.L491fs	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	484					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)			AGGAACTGCTCCCCCCAGAGA	0.537																																					p.L491fs		Atlas-INDEL	.											.	EIF4G1	151	.	0			c.1472delT						.						63.0	64.0	64.0					3																	184039824		2203	4300	6503	SO:0001589	frameshift_variant	1981	exon10			.	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.1452delC	chr3.hg19:g.184039824delC	ENSP00000316879:p.Leu484fs	177.0	0.0		224.0	16.0	NM_001194947	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Frame_Shift_Del	DEL	ENST00000346169.2	hg19	CCDS3259.1																																																																																			.	.		0.537	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37508625	37508625	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:37508625delA	ENST00000602533.1	+	34	3916	c.3817delA	c.(3817-3819)aaafs	p.K1273fs	ANKRD30A_ENST00000361713.1_Frame_Shift_Del_p.K1273fs|ANKRD30A_ENST00000374660.1_Frame_Shift_Del_p.K1392fs			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1329					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						ACTACAAAGCAAAAATATGTG	0.343																																					p.S1272fs		Atlas-INDEL	.											.	ANKRD30A	448	.	0			c.3816delC						.						53.0	48.0	50.0					10																	37508625		1854	4093	5947	SO:0001589	frameshift_variant	91074	exon34			.	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.3817delA	chr10.hg19:g.37508625delA	ENSP00000473551:p.Lys1273fs	135.0	0.0		199.0	12.0	NM_052997	Q5W025	Frame_Shift_Del	DEL	ENST00000602533.1	hg19																																																																																				.	.		0.343	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
AK7	122481	hgsc.bcm.edu	37	14	96937927	96937927	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:96937927delA	ENST00000267584.4	+	13	1514	c.1470delA	c.(1468-1470)gcafs	p.A490fs		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	490	Adenylate kinase.				axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		ATGATCAAGCAAAAGACCTGT	0.303																																					p.A490fs		Atlas-INDEL	.											.	AK7	69	.	0			c.1469delC						.						90.0	86.0	87.0					14																	96937927		2203	4300	6503	SO:0001589	frameshift_variant	122481	exon13			.	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"""Adenylate kinases"""	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.1470delA	chr14.hg19:g.96937927delA	ENSP00000267584:p.Ala490fs	107.0	0.0		162.0	13.0	NM_152327	Q8IYP6	Frame_Shift_Del	DEL	ENST00000267584.4	hg19	CCDS9945.1																																																																																			.	.		0.303	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1		
SUGP2	10147	hgsc.bcm.edu	37	19	19136181	19136181	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:19136181delA	ENST00000601879.1	-	3	1273	c.976delT	c.(976-978)tcafs	p.S326fs	SUGP2_ENST00000456085.2_Frame_Shift_Del_p.S95fs|SUGP2_ENST00000452918.2_Frame_Shift_Del_p.S326fs|SUGP2_ENST00000600377.1_Frame_Shift_Del_p.S340fs|SUGP2_ENST00000598202.1_5'Flank|SUGP2_ENST00000337018.6_Frame_Shift_Del_p.S326fs			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	326					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						CCAAATCTTGAAAAAACATCA	0.393																																					p.S326X		Atlas-INDEL	.											.	SUGP2	107	.	0			c.977delC						.						71.0	77.0	75.0					19																	19136181		2203	4300	6503	SO:0001589	frameshift_variant	10147	exon3			.	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"""G patch domain containing"""	18641	protein-coding gene	gene with protein product		607993	"""splicing factor, arginine/serine-rich 14"""	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.976delT	chr19.hg19:g.19136181delA	ENSP00000472286:p.Ser326fs	102.0	0.0		159.0	10.0	NM_014884	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Frame_Shift_Del	DEL	ENST00000601879.1	hg19	CCDS12392.1																																																																																			.	.		0.393	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392	
TOP3A	7156	hgsc.bcm.edu	37	17	18217965	18217965	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	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	151.0	0.0		216.0	15.0	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		
FANCM	57697	hgsc.bcm.edu	37	14	45654537	45654537	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:45654537delT	ENST00000267430.5	+	18	4718	c.4633delT	c.(4633-4635)tttfs	p.F1545fs	FANCM_ENST00000555013.1_3'UTR|FANCM_ENST00000542564.2_Frame_Shift_Del_p.F1519fs	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1545					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						ATTACTTGACTTTTTAAATGA	0.269								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.D1544fs		Atlas-INDEL	.											.	FANCM	225	.	0			c.4632delC						.						62.0	63.0	63.0					14																	45654537		2203	4292	6495	SO:0001589	frameshift_variant	57697	exon18	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.4633delT	chr14.hg19:g.45654537delT	ENSP00000267430:p.Phe1545fs	153.0	0.0		188.0	13.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Frame_Shift_Del	DEL	ENST00000267430.5	hg19	CCDS32070.1																																																																																			.	.		0.269	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
C11orf30	56946	hgsc.bcm.edu	37	11	76162945	76162945	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:76162945delG	ENST00000529032.1	+	2	114	c.114delG	c.(112-114)cagfs	p.Q38fs	C11orf30_ENST00000533988.1_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000334736.3_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000524490.1_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000343878.3_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000533248.1_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000525919.1_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000524767.1_Frame_Shift_Del_p.Q38fs|C11orf30_ENST00000525959.1_3'UTR|C11orf30_ENST00000525038.1_Frame_Shift_Del_p.Q38fs			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	38	ENT. {ECO:0000255|PROSITE- ProRule:PRU00476}.|Interaction with BRCA2.				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						TTCGGGCACAGGGGGATCTCA	0.333																																					p.Q38fs		Atlas-INDEL	.											.	C11orf30	123	.	0			c.113delA						.						38.0	39.0	39.0					11																	76162945		2200	4292	6492	SO:0001589	frameshift_variant	56946	exon3			.	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.114delG	chr11.hg19:g.76162945delG	ENSP00000432327:p.Gln38fs	88.0	0.0		173.0	12.0	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Frame_Shift_Del	DEL	ENST00000529032.1	hg19	CCDS8244.1																																																																																			.	.		0.333	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193	
NUP205	23165	hgsc.bcm.edu	37	7	135311045	135311045	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:135311045delG	ENST00000285968.6	+	33	4755	c.4729delG	c.(4729-4731)gggfs	p.G1577fs		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1577					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)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	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)	p.V1578fs*1(1)		breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						GCTAAGATCAGGGGTGATTGT	0.448																																					p.S1576fs		Atlas-INDEL	.											.	NUP205	198	.	1	Deletion - Frameshift(1)	lung(1)	c.4728delA						.						124.0	114.0	117.0					7																	135311045		2203	4300	6503	SO:0001589	frameshift_variant	23165	exon33			.	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.4729delG	chr7.hg19:g.135311045delG	ENSP00000285968:p.Gly1577fs	91.0	0.0		129.0	10.0	NM_015135	A6H8X3|Q86YC1	Frame_Shift_Del	DEL	ENST00000285968.6	hg19	CCDS34759.1																																																																																			.	.		0.448	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1		
NDRG3	57446	hgsc.bcm.edu	37	20	35310974	35310974	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:35310974delT	ENST00000349004.1	-	7	472	c.391delA	c.(391-393)agcfs	p.S131fs	NDRG3_ENST00000373773.3_Frame_Shift_Del_p.S36fs|NDRG3_ENST00000540765.1_Frame_Shift_Del_p.S27fs|NDRG3_ENST00000373803.2_Frame_Shift_Del_p.S131fs|NDRG3_ENST00000359675.2_Frame_Shift_Del_p.S119fs	NM_032013.3	NP_114402.1	Q9UGV2	NDRG3_HUMAN	NDRG family member 3	131					cell differentiation (GO:0030154)|negative regulation of cell growth (GO:0030308)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12		Myeloproliferative disorder(115;0.00878)				CCAATGATGCTTTTCAGGCTG	0.453																																					p.S131fs		Atlas-INDEL	.											.	NDRG3	32	.	0			c.392delG						.						171.0	135.0	147.0					20																	35310974		2203	4300	6503	SO:0001589	frameshift_variant	57446	exon7			.	AL031662	CCDS13284.1, CCDS13285.1	20q11.21-q11.23	2008-07-28			ENSG00000101079	ENSG00000101079			14462	protein-coding gene	gene with protein product		605273				10831399, 17998568	Standard	NM_032013		Approved		uc002xfw.3	Q9UGV2	OTTHUMG00000032398	ENST00000349004.1:c.391delA	chr20.hg19:g.35310974delT	ENSP00000345292:p.Ser131fs	135.0	0.0		211.0	16.0	NM_032013	A2A2S8|E1P5U7|E1P5U8|Q5TH32|Q96PL8|Q96SM2|Q9BXY7|Q9H3N7|Q9H411|Q9H8J6	Frame_Shift_Del	DEL	ENST00000349004.1	hg19	CCDS13285.1																																																																																			.	.		0.453	NDRG3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079053.2		
RPGR	6103	hgsc.bcm.edu	37	X	38146456	38146456	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:38146456delT	ENST00000339363.3	-	14	2578	c.2411delA	c.(2410-2412)aatfs	p.N804fs	RPGR_ENST00000378505.2_Frame_Shift_Del_p.N599fs|RPGR_ENST00000338898.3_3'UTR|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000342811.3_Frame_Shift_Del_p.N599fs|RPGR_ENST00000309513.3_Frame_Shift_Del_p.N537fs|RPGR_ENST00000318842.7_Frame_Shift_Del_p.N599fs			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator	804	Glu-rich.				cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						ctctattccatttccttttga	0.413																																					p.N599fs		Atlas-INDEL	.											.	RPGR	175	.	0			c.1797delT						.						79.0	58.0	65.0					X																	38146456		2202	4300	6502	SO:0001589	frameshift_variant	6103	exon15			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2411delA	chrX.hg19:g.38146456delT	ENSP00000343671:p.Asn804fs	116.0	0.0		181.0	11.0	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Frame_Shift_Del	DEL	ENST00000339363.3	hg19																																																																																				.	.		0.413	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
ANKHD1	54882	hgsc.bcm.edu	37	5	139905676	139905676	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:139905676delA	ENST00000360839.2	+	26	4742	c.4588delA	c.(4588-4590)aaafs	p.K1531fs	ANKHD1-EIF4EBP3_ENST00000532219.1_Frame_Shift_Del_p.K1531fs|SNORD45_ENST00000363181.1_RNA|ANKHD1_ENST00000544120.1_5'Flank|ANKHD1_ENST00000297183.6_Frame_Shift_Del_p.K1531fs	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1531						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTGTTTGGGAAAAAAAGGGC	0.423																																					p.G1529fs		Atlas-INDEL	.											ANKHD1-EIF4EBP3,colon,carcinoma,0,2	ANKHD1	233	.	0			c.4587delG						.						133.0	145.0	141.0					5																	139905676		2203	4300	6503	SO:0001589	frameshift_variant	54882	exon26			.	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"""Ankyrin repeat domain containing"""	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.4588delA	chr5.hg19:g.139905676delA	ENSP00000354085:p.Lys1531fs	111.0	0.0		134.0	10.0	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Frame_Shift_Del	DEL	ENST00000360839.2	hg19	CCDS4225.1																																																																																			.	.		0.423	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747	
GOSR1	9527	hgsc.bcm.edu	37	17	28849276	28849276	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:28849276delT	ENST00000225724.5	+	9	705	c.633delT	c.(631-633)cgtfs	p.R211fs	GOSR1_ENST00000581721.1_Frame_Shift_Del_p.R197fs|GOSR1_ENST00000451249.2_Frame_Shift_Del_p.R209fs|GOSR1_ENST00000467337.2_Frame_Shift_Del_p.R146fs	NM_001007024.1|NM_001007025.1|NM_004871.2	NP_001007025.1|NP_001007026.1|NP_004862.1	O95249	GOSR1_HUMAN	golgi SNAP receptor complex member 1	211					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			endometrium(2)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	12						CCAAAGATCGTTTTCCTGCTG	0.463																																					p.R211fs		Atlas-INDEL	.											.	GOSR1	25	.	0			c.632delG						.						281.0	311.0	300.0					17																	28849276		2203	4300	6503	SO:0001589	frameshift_variant	9527	exon9			.	AF047438	CCDS11258.1, CCDS45643.1, CCDS45644.1	17q11	2011-04-15			ENSG00000108587	ENSG00000108587			4430	protein-coding gene	gene with protein product	"""golgi integral membrane protein 2"""	604026				8638159, 9653160, 15004235	Standard	XM_005258072		Approved	GOS28, P28, GS28, GOS-28, GOLIM2	uc002hfe.3	O95249	OTTHUMG00000132796	ENST00000225724.5:c.633delT	chr17.hg19:g.28849276delT	ENSP00000225724:p.Arg211fs	147.0	0.0		177.0	12.0	NM_004871	J3KST5|O75392	Frame_Shift_Del	DEL	ENST00000225724.5	hg19	CCDS11258.1																																																																																			.	.		0.463	GOSR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256208.2		
SLFN12L	100506736	hgsc.bcm.edu	37	17	33806378	33806378	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:33806378delT	ENST00000260908.7	-	2	968	c.851delA	c.(850-852)aatfs	p.N284fs	SLFN12L_ENST00000449046.1_Frame_Shift_Del_p.N315fs|SLFN12L_ENST00000361112.4_Frame_Shift_Del_p.N313fs|RP11-686D22.9_ENST00000587076.1_RNA	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	121.0	0.0		189.0	12.0	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	
SCG2	7857	hgsc.bcm.edu	37	2	224462280	224462280	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:224462280delG	ENST00000305409.2	-	2	1953	c.1721delC	c.(1720-1722)ccgfs	p.P574fs		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.P574Q(1)		NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		ATCATTCTTCGGGGGCCCCAC	0.493																																					p.P574fs		Atlas-INDEL	.											.	SCG2	99	.	1	Substitution - Missense(1)	lung(1)	c.1722delG						.						84.0	85.0	85.0					2																	224462280		2203	4300	6503	SO:0001589	frameshift_variant	7857	exon2			.	M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"""secretoneurin"", ""chromogranin C"""	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.1721delC	chr2.hg19:g.224462280delG	ENSP00000304133:p.Pro574fs	187.0	0.0		249.0	15.0	NM_003469	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Frame_Shift_Del	DEL	ENST00000305409.2	hg19	CCDS2457.1																																																																																			.	.		0.493	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469	
SLC44A3	126969	hgsc.bcm.edu	37	1	95356749	95356749	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:95356749delA	ENST00000271227.6	+	13	1648	c.1546delA	c.(1546-1548)aaafs	p.K516fs	SLC44A3_ENST00000529450.1_Frame_Shift_Del_p.K483fs|SLC44A3_ENST00000467909.1_Frame_Shift_Del_p.K468fs|SLC44A3_ENST00000532427.1_Frame_Shift_Del_p.K436fs|SLC44A3_ENST00000527077.1_Frame_Shift_Del_p.K448fs|SLC44A3_ENST00000446120.2_Frame_Shift_Del_p.K480fs|SLC44A3_ENST00000530397.1_3'UTR	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	516					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	AGATGCATTCAAAATCTTGTC	0.313																																					p.F515fs		Atlas-INDEL	.											.	SLC44A3	109	.	0			c.1545delC						.						102.0	111.0	108.0					1																	95356749		2203	4300	6503	SO:0001589	frameshift_variant	126969	exon13			.	BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"""Solute carriers"""	28689	protein-coding gene	gene with protein product			"""solute carrier family, member 3"""			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.1546delA	chr1.hg19:g.95356749delA	ENSP00000271227:p.Lys516fs	150.0	0.0		189.0	12.0	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Frame_Shift_Del	DEL	ENST00000271227.6	hg19	CCDS44176.1																																																																																			.	.		0.313	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369	
ZNF366	167465	hgsc.bcm.edu	37	5	71739993	71739993	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:71739993delC	ENST00000318442.5	-	5	2315	c.1825delG	c.(1825-1827)gagfs	p.E609fs	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	609	Interaction with CTBP1.|Interaction with NRIP1.				negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TGGGCACTCTCCCCGTCTGAC	0.657																																					p.E609fs		Atlas-INDEL	.											.	ZNF366	108	.	0			c.1826delA						.						59.0	70.0	66.0					5																	71739993		2203	4299	6502	SO:0001589	frameshift_variant	167465	exon5			.	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"""Zinc fingers, C2H2-type"""	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.1825delG	chr5.hg19:g.71739993delC	ENSP00000313158:p.Glu609fs	122.0	0.0		141.0	10.0	NM_152625	Q5HYI9|Q7RTV4	Frame_Shift_Del	DEL	ENST00000318442.5	hg19	CCDS4015.1																																																																																			.	.		0.657	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3		
GPC5	2262	hgsc.bcm.edu	37	13	92345489	92345489	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:92345489delT	ENST00000377067.3	+	3	746	c.374delT	c.(373-375)cttfs	p.L125fs		NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	125					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				ACCAGTATACTTTTTTGCAGT	0.413																																					p.L125fs		Atlas-INDEL	.											.	GPC5	140	.	0			c.373delC						.						89.0	94.0	92.0					13																	92345489		2203	4300	6503	SO:0001589	frameshift_variant	2262	exon3			.	AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"""Proteoglycans / Cell Surface : Glypicans"""	4453	protein-coding gene	gene with protein product	"""glypican proteoglycan 5"""	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.374delT	chr13.hg19:g.92345489delT	ENSP00000366267:p.Leu125fs	162.0	0.0		166.0	10.0	NM_004466	B2R726|O60436|Q9BX27	Frame_Shift_Del	DEL	ENST00000377067.3	hg19	CCDS9468.1																																																																																			.	.		0.413	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466	
REL	5966	hgsc.bcm.edu	37	2	61147771	61147771	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:61147771delA	ENST00000295025.8	+	10	1401	c.1081delA	c.(1081-1083)aaafs	p.K362fs	REL_ENST00000394479.3_Frame_Shift_Del_p.K330fs	NM_002908.2	NP_002899.1	Q04864	REL_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog	362					cytokine production (GO:0001816)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of neuron death (GO:1901215)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(3)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	16	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			AAGATACTTCAAAAAAGGTAT	0.318			A		Hodgkin Lymphoma																																p.F360fs		Atlas-INDEL	.		Dom	yes		2	2p13-p12	5966	v-rel reticuloendotheliosis viral oncogene homolog (avian)		L	.	REL	48	.	0			c.1080delC						.						34.0	38.0	37.0					2																	61147771		2202	4295	6497	SO:0001589	frameshift_variant	5966	exon10			.	M11595	CCDS1864.1, CCDS74515.1	2p13-p12	2013-07-09	2013-07-09		ENSG00000162924	ENSG00000162924			9954	protein-coding gene	gene with protein product		164910				1577270	Standard	XM_005264470		Approved	I-Rel, c-Rel	uc002sam.1	Q04864	OTTHUMG00000129418	ENST00000295025.8:c.1081delA	chr2.hg19:g.61147771delA	ENSP00000295025:p.Lys362fs	153.0	0.0		213.0	13.0	NM_002908	Q17RU2|Q2PNZ7|Q6LDY0	Frame_Shift_Del	DEL	ENST00000295025.8	hg19	CCDS1864.1																																																																																			.	.		0.318	REL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251576.3	NM_002908	
EXD3	54932	hgsc.bcm.edu	37	9	140268006	140268006	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:140268006delG	ENST00000340951.4	-	4	361	c.166delC	c.(166-168)ctgfs	p.L56fs	EXD3_ENST00000342129.4_5'UTR|EXD3_ENST00000479452.1_Frame_Shift_Del_p.L56fs|EXD3_ENST00000475006.1_5'UTR	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0	Pro-rich.									NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						AGCCCGGCCAGGGGGTCGTCC	0.662																																					p.L56fs		Atlas-INDEL	.											.	EXD3	86	.	0			c.167delT						.						7.0	9.0	8.0					9																	140268006		1855	4043	5898	SO:0001589	frameshift_variant	54932	exon4			.		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.166delC	chr9.hg19:g.140268006delG	ENSP00000340474:p.Leu56fs	151.0	0.0		183.0	11.0	NM_017820	Q6P1M1|Q8IXT8	Frame_Shift_Del	DEL	ENST00000340951.4	hg19	CCDS48066.1																																																																																			.	.		0.662	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
CDH23	64072	hgsc.bcm.edu	37	10	73326586	73326586	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:73326586delC	ENST00000224721.6	+	6	537	c.532delC	c.(532-534)cccfs	p.P179fs	CDH23_ENST00000398809.4_Frame_Shift_Del_p.P174fs|CDH23_ENST00000461841.3_Frame_Shift_Del_p.P219fs|CDH23_ENST00000398842.3_Frame_Shift_Del_p.P174fs|CDH23_ENST00000299366.7_Frame_Shift_Del_p.P219fs	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	174	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CTCCTTCCAGCCCCCCTCCCA	0.612																																					p.Q172fs		Atlas-INDEL	.											.	CDH23	365	.	0			c.516delG						.						47.0	51.0	49.0					10																	73326586		2028	4188	6216	SO:0001589	frameshift_variant	64072	exon7			.	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.532delC	chr10.hg19:g.73326586delC	ENSP00000224721:p.Pro179fs	128.0	0.0		120.0	10.0	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Frame_Shift_Del	DEL	ENST00000224721.6	hg19																																																																																				.	.		0.612	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
EPHA10	284656	hgsc.bcm.edu	37	1	38184055	38184055	+	Frame_Shift_Del	DEL	C	C	-	rs78757428	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:38184055delC	ENST00000373048.4	-	17	3015	c.3016delG	c.(3016-3018)gtgfs	p.V1006fs	EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000540011.1_3'UTR|EPHA10_ENST00000330210.7_Frame_Shift_Del_p.V501fs|EPHA10_ENST00000427468.2_Frame_Shift_Del_p.V1006fs	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	1006					ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)	p.V1007M(2)		NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CACACCTGCACCCCCTGGCCC	0.662																																					p.V1006fs		Atlas-INDEL	.											.	EPHA10	120	.	2	Substitution - Missense(2)	stomach(2)	c.3017delT						.						68.0	76.0	74.0					1																	38184055		2042	4175	6217	SO:0001589	frameshift_variant	284656	exon17			.	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.3016delG	chr1.hg19:g.38184055delC	ENSP00000362139:p.Val1006fs	169.0	0.0		230.0	15.0	NM_001099439	A4FU89|J3KPB5|Q6NW42	Frame_Shift_Del	DEL	ENST00000373048.4	hg19	CCDS41305.1																																																																																			.	.		0.662	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
CEP76	79959	hgsc.bcm.edu	37	18	12678387	12678387	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:12678387delT	ENST00000262127.2	-	10	1569	c.1344delA	c.(1342-1344)aaafs	p.K448fs	CEP76_ENST00000423709.2_Frame_Shift_Del_p.K373fs|PSMG2_ENST00000585331.2_Intron|PSMG2_ENST00000589405.1_Intron	NM_024899.2	NP_079175.2	Q8TAP6	CEP76_HUMAN	centrosomal protein 76kDa	448					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						GGTACAGTGGTTTGGGCTGTT	0.348																																					p.P449fs		Atlas-INDEL	.											.	CEP76	45	.	0			c.1345delC						.						122.0	118.0	120.0					18																	12678387		2203	4300	6503	SO:0001589	frameshift_variant	79959	exon10			.	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.1344delA	chr18.hg19:g.12678387delT	ENSP00000262127:p.Lys448fs	134.0	0.0		154.0	10.0	NM_024899	B0YJB2|B4DXG5|B4DZW1|Q658N5|Q9H9U7	Frame_Shift_Del	DEL	ENST00000262127.2	hg19	CCDS11861.1																																																																																			.	.		0.348	CEP76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254611.1	NM_024899	
APC	324	hgsc.bcm.edu	37	5	112164604	112164604	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:112164604delA	ENST00000457016.1	+	14	2058	c.1678delA	c.(1678-1680)aaafs	p.K561fs	APC_ENST00000508376.2_Frame_Shift_Del_p.K561fs|APC_ENST00000257430.4_Frame_Shift_Del_p.K561fs|CTC-554D6.1_ENST00000520401.1_Frame_Shift_Del_p.V55fs			P25054	APC_HUMAN	adenomatous polyposis coli	561	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|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 apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TGTAAATAGTAAAAAGACGTT	0.303		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.S559fs	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-INDEL	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	APC	4158	.	1	Unknown(1)	skin(1)	c.1677delT						.						124.0	134.0	131.0					5																	112164604		2202	4300	6502	SO:0001589	frameshift_variant	324	exon15	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	.	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1678delA	chr5.hg19:g.112164604delA	ENSP00000413133:p.Lys561fs	203.0	0.0		239.0	16.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	hg19	CCDS4107.1																																																																																			.	.		0.303	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
SLC3A1	6519	hgsc.bcm.edu	37	2	44502687	44502687	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:44502687delA	ENST00000260649.6	+	1	89	c.13delA	c.(13-15)aaafs	p.K5fs	SLC3A1_ENST00000410056.3_Frame_Shift_Del_p.K5fs|SLC3A1_ENST00000409229.3_Frame_Shift_Del_p.K5fs|SLC3A1_ENST00000409387.1_Frame_Shift_Del_p.K5fs|SLC3A1_ENST00000409741.1_Frame_Shift_Del_p.K5fs	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	5					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	GGCTGAAGATAAAAGCAAGAG	0.488																																					p.D4fs		Atlas-INDEL	.											.	SLC3A1	62	.	0			c.12delT						.						58.0	57.0	58.0					2																	44502687		2203	4300	6503	SO:0001589	frameshift_variant	6519	exon1			.		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"""Solute carriers"""	11025	protein-coding gene	gene with protein product		104614	"""solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"""			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.13delA	chr2.hg19:g.44502687delA	ENSP00000260649:p.Lys5fs	169.0	0.0		246.0	15.0	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Frame_Shift_Del	DEL	ENST00000260649.6	hg19	CCDS1819.1																																																																																			.	.		0.488	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341	
SCAF11	9169	hgsc.bcm.edu	37	12	46328022	46328022	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:46328022delA	ENST00000369367.3	-	8	802	c.569delT	c.(568-570)ttcfs	p.F190fs	SCAF11_ENST00000549162.1_5'UTR|SCAF11_ENST00000419565.2_Frame_Shift_Del_p.F190fs	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	190					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						CATATTGGAGAAAAAATTTCT	0.303																																					p.F190fs		Atlas-INDEL	.											.	SCAF11	145	.	0			c.570delC						.						47.0	45.0	46.0					12																	46328022		1790	4055	5845	SO:0001589	frameshift_variant	9169	exon8			.	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"""RING-type (C3HC4) zinc fingers"""	10784	protein-coding gene	gene with protein product		603668	"""splicing factor, arginine/serine-rich 2, interacting protein"", ""serine/arginine-rich splicing factor 2, interacting protein"""	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.569delT	chr12.hg19:g.46328022delA	ENSP00000358374:p.Phe190fs	118.0	0.0		171.0	11.0	NM_004719	A6NEU9|A6NLW5|Q8IW59	Frame_Shift_Del	DEL	ENST00000369367.3	hg19	CCDS8748.2																																																																																			.	.		0.303	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719	
DDX53	168400	hgsc.bcm.edu	37	X	23020376	23020376	+	IGR	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:23020376delG	ENST00000327968.5	+	0	2118				RP11-40F8.2_ENST00000455399.1_lincRNA	NM_182699.3	NP_874358.2	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53							nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|RNA binding (GO:0003723)			breast(2)|endometrium(5)|kidney(4)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	35						cacgtgccatgggggtttatC	0.313																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			.	AY039237	CCDS35214.1	Xp22.13	2009-03-25			ENSG00000184735	ENSG00000184735		"""DEAD-boxes"""	20083	protein-coding gene	gene with protein product	"""cancer associated gene"", ""cancer/testis antigen 26"""						Standard	NM_182699		Approved	CAGE, CT26	uc004daj.3	Q86TM3	OTTHUMG00000021248		chrX.hg19:g.23020376delG		188.0	0.0		229.0	14.0	.	Q0D2N2|Q6NVV4	RNA	DEL	ENST00000327968.5	hg19	CCDS35214.1																																																																																			.	.		0.313	DDX53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056043.1	NM_182699	
TRAF5	7188	hgsc.bcm.edu	37	1	211526743	211526743	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:211526743delC	ENST00000261464.5	+	2	216	c.162delC	c.(160-162)aacfs	p.N54fs	TRAF5_ENST00000427925.2_Frame_Shift_Del_p.N54fs|TRAF5_ENST00000367004.3_Frame_Shift_Del_p.N54fs|TRAF5_ENST00000462410.1_3'UTR|TRAF5_ENST00000336184.2_Frame_Shift_Del_p.N54fs	NM_001033910.2	NP_001029082.1	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	54					apoptotic process (GO:0006915)|positive regulation of cell proliferation (GO:0008284)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	CD40 receptor complex (GO:0035631)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)	signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		TGCTTCACAACCCCCACCAGA	0.572																																					p.N54fs		Atlas-INDEL	.											.	TRAF5	64	.	0			c.161delA						.																																			SO:0001589	frameshift_variant	7188	exon2			.	AB000509	CCDS1497.1	1q32	2008-02-05			ENSG00000082512	ENSG00000082512		"""RING-type (C3HC4) zinc fingers"""	12035	protein-coding gene	gene with protein product		602356				9126477	Standard	NM_001033910		Approved	RNF84	uc001hii.3	O00463	OTTHUMG00000036997	ENST00000261464.5:c.162delC	chr1.hg19:g.211526743delC	ENSP00000261464:p.Asn54fs	82.0	0.0		158.0	10.0	NM_001033910	B4DIS9|B4E0A2|Q6FHY1	Frame_Shift_Del	DEL	ENST00000261464.5	hg19	CCDS1497.1																																																																																			.	.		0.572	TRAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089825.1	NM_004619	
UBAC1	10422	hgsc.bcm.edu	37	9	138845578	138845578	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:138845578delT	ENST00000371756.3	-	3	498	c.281delA	c.(280-282)aagfs	p.K94fs		NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	94	Ubiquitin-like.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		TGGAGCACGCTTTTTTATCAA	0.408																																					p.K94fs	NSCLC(78;973 1398 27381 29552 42415)	Atlas-INDEL	.											.	UBAC1	40	.	0			c.282delG						.						85.0	79.0	81.0					9																	138845578		2203	4300	6503	SO:0001589	frameshift_variant	10422	exon3			.	AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"""ubiquitin associated domain containing 1"""	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.281delA	chr9.hg19:g.138845578delT	ENSP00000360821:p.Lys94fs	116.0	0.0		120.0	10.0	NM_016172	O75500|Q9UMW7	Frame_Shift_Del	DEL	ENST00000371756.3	hg19	CCDS35177.1																																																																																			.	.		0.408	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172	
MAN2B1	4125	hgsc.bcm.edu	37	19	12760238	12760238	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:12760238delC	ENST00000456935.2	-	19	2312	c.2272delG	c.(2272-2274)gatfs	p.D758fs	CTD-2192J16.22_ENST00000597692.1_5'Flank|MAN2B1_ENST00000221363.4_Frame_Shift_Del_p.D757fs	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	758					cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GGTCGATAATCCCGCCTGGGG	0.522																																					p.D758fs		Atlas-INDEL	.											.	MAN2B1	91	.	0			c.2273delA						.						53.0	42.0	46.0					19																	12760238		2203	4300	6503	SO:0001589	frameshift_variant	4125	exon19			.		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.2272delG	chr19.hg19:g.12760238delC	ENSP00000395473:p.Asp758fs	152.0	0.0		216.0	18.0	NM_000528	G5E928|O15330|Q16680|Q93094|Q9BW13	Frame_Shift_Del	DEL	ENST00000456935.2	hg19	CCDS32919.1																																																																																			.	.		0.522	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
RALGAPA2	57186	hgsc.bcm.edu	37	20	20493319	20493319	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:20493319delA	ENST00000202677.7	-	32	4701	c.4694delT	c.(4693-4695)ttgfs	p.L1565fs		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	1565					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						ATTTTGGCGCAAAATGACCTC	0.473																																					p.L1565fs		Atlas-INDEL	.											.	RALGAPA2	274	.	0			c.4695delG						.						135.0	126.0	129.0					20																	20493319		1925	4143	6068	SO:0001589	frameshift_variant	57186	exon32			.	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 74"""	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.4694delT	chr20.hg19:g.20493319delA	ENSP00000202677:p.Leu1565fs	148.0	0.0		187.0	13.0	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Frame_Shift_Del	DEL	ENST00000202677.7	hg19	CCDS46584.1																																																																																			.	.		0.473	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343	
PFAS	5198	hgsc.bcm.edu	37	17	8172524	8172524	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:8172524delC	ENST00000314666.6	+	28	4092	c.3959delC	c.(3958-3960)tccfs	p.S1320fs	PFAS_ENST00000545834.1_Frame_Shift_Del_p.S896fs	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1320					'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)	p.S1320F(1)		central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	CTGACCACCTCCCCCTGGCTC	0.622																																					p.S1320fs		Atlas-INDEL	.											.	PFAS	91	.	1	Substitution - Missense(1)	large_intestine(1)	c.3958delT						.						41.0	41.0	41.0					17																	8172524		2203	4300	6503	SO:0001589	frameshift_variant	5198	exon28			.	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"""FGAR amidotransferase"""	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.3959delC	chr17.hg19:g.8172524delC	ENSP00000313490:p.Ser1320fs	144.0	0.0		114.0	11.0	NM_012393	A6H8V8	Frame_Shift_Del	DEL	ENST00000314666.6	hg19	CCDS11136.1																																																																																			.	.		0.622	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2		
FZD8	8325	hgsc.bcm.edu	37	10	35929138	35929138	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:35929138delC	ENST00000374694.1	-	1	1224	c.1220delG	c.(1219-1221)ggcfs	p.G407fs	MIR4683_ENST00000579659.1_RNA	NM_031866.2	NP_114072.1	Q9H461	FZD8_HUMAN	frizzled class receptor 8	407					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|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(3)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	11						GCTGGCCATGCCGAAGAAGTA	0.642																																					p.G407fs		Atlas-INDEL	.											.	FZD8	41	.	0			c.1221delC						.						57.0	56.0	57.0					10																	35929138		2203	4300	6503	SO:0001589	frameshift_variant	8325	exon1			.	AB043703	CCDS7192.1	10p11.2	2014-01-29	2014-01-29		ENSG00000177283	ENSG00000177283		"""GPCR / Class F : Frizzled receptors"""	4046	protein-coding gene	gene with protein product		606146	"""frizzled (Drosophila) homolog 8"", ""frizzled homolog 8 (Drosophila)"", ""frizzled 8, seven transmembrane spanning receptor"", ""frizzled family receptor 8"""			11295046	Standard	NM_031866		Approved		uc001iyz.1	Q9H461	OTTHUMG00000017956	ENST00000374694.1:c.1220delG	chr10.hg19:g.35929138delC	ENSP00000363826:p.Gly407fs	61.0	0.0		117.0	10.0	NM_031866		Frame_Shift_Del	DEL	ENST00000374694.1	hg19	CCDS7192.1																																																																																			.	.		0.642	FZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047575.2	NM_031866	
LAMA3	3909	hgsc.bcm.edu	37	18	21399914	21399914	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:21399914delT	ENST00000313654.9	+	19	2498	c.2257delT	c.(2257-2259)tttfs	p.F753fs	LAMA3_ENST00000399516.3_Frame_Shift_Del_p.F753fs	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	753					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)					TCCGCTGGCATTTCCTGAGTT	0.473																																					p.A752fs		Atlas-INDEL	.											.	LAMA3	397	.	0			c.2256delA						.						119.0	117.0	118.0					18																	21399914		1954	4136	6090	SO:0001589	frameshift_variant	3909	exon19			.	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.2257delT	chr18.hg19:g.21399914delT	ENSP00000324532:p.Phe753fs	199.0	0.0		312.0	20.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Frame_Shift_Del	DEL	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.		0.473	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
CCDC38	120935	hgsc.bcm.edu	37	12	96292465	96292465	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:96292465delT	ENST00000344280.3	-	6	971	c.414delA	c.(412-414)aaafs	p.K138fs	SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	138										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTGCTATGTCTTTTTCAAACT	0.373																																					p.D139fs		Atlas-INDEL	.											.	CCDC38	45	.	0			c.415delG						.						158.0	142.0	148.0					12																	96292465		2203	4300	6503	SO:0001589	frameshift_variant	120935	exon6			.	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.414delA	chr12.hg19:g.96292465delT	ENSP00000345470:p.Lys138fs	285.0	0.0		313.0	19.0	NM_182496	Q8N835	Frame_Shift_Del	DEL	ENST00000344280.3	hg19	CCDS9056.1																																																																																			.	.		0.373	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
TRIP10	9322	hgsc.bcm.edu	37	19	6750606	6750606	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:6750606delC	ENST00000313244.9	+	14	1654	c.1619delC	c.(1618-1620)tccfs	p.S540fs	CTD-3128G10.6_ENST00000594056.1_RNA|TRIP10_ENST00000600428.1_Frame_Shift_Del_p.S376fs|TRIP10_ENST00000596758.1_Frame_Shift_Del_p.S484fs|TRIP10_ENST00000313285.8_Frame_Shift_Del_p.S484fs			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	540	Interaction with DNM1 and WASL.|Interaction with DNM2 and WASL. {ECO:0000250}.|Interaction with PDE6G. {ECO:0000250}.|Required for interaction with FASLG and localization to lysosomes.|Required for podosome formation.|SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						GAACCCACATCCCCCATAGGT	0.547																																					p.S484fs		Atlas-INDEL	.											.	TRIP10	104	.	0			c.1450delT						.																																			SO:0001589	frameshift_variant	9322	exon13			.	AB072596	CCDS12172.1, CCDS74271.1, CCDS74272.1	19p13.3	2008-02-05			ENSG00000125733	ENSG00000125733			12304	protein-coding gene	gene with protein product	"""Cdc42-interacting protein"""	604504	"""salt tolerator"""	STOT		7776974, 9210375, 11294612	Standard	XM_005259683		Approved	STP, HSTP, CIP4	uc002mfr.3	Q15642	OTTHUMG00000150255	ENST00000313244.9:c.1619delC	chr19.hg19:g.6750606delC	ENSP00000320117:p.Ser540fs	189.0	0.0		216.0	15.0	NM_004240	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Frame_Shift_Del	DEL	ENST00000313244.9	hg19																																																																																				.	.		0.547	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2		
ACTN1	87	hgsc.bcm.edu	37	14	69345708	69345708	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:69345708delG	ENST00000193403.6	-	19	2742	c.2359delC	c.(2359-2361)cagfs	p.Q787fs	ACTN1_ENST00000376839.3_Intron|ACTN1_ENST00000538545.2_Intron|ACTN1_ENST00000394419.4_Frame_Shift_Del_p.Q787fs|ACTN1_ENST00000438964.2_Intron	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	787	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GCGAGTACCTGGGGGTCGTTG	0.582																																					p.Q787fs		Atlas-INDEL	.											.	ACTN1	77	.	0			c.2360delA						.						198.0	197.0	197.0					14																	69345708		2203	4300	6503	SO:0001589	frameshift_variant	87	exon19			.	M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"""EF-hand domain containing"""	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.2359delC	chr14.hg19:g.69345708delG	ENSP00000193403:p.Gln787fs	147.0	0.0		176.0	11.0	NM_001102	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Frame_Shift_Del	DEL	ENST00000193403.6	hg19	CCDS9792.1																																																																																			.	.		0.582	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102	
CREBRF	153222	hgsc.bcm.edu	37	5	172537584	172537584	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:172537584delA	ENST00000296953.2	+	6	1796	c.1477delA	c.(1477-1479)aaafs	p.K494fs	CREBRF_ENST00000540014.1_Frame_Shift_Del_p.K496fs	NM_153607.2	NP_705835.2	Q8IUR6	CRERF_HUMAN	CREB3 regulatory factor	494					negative regulation of endoplasmic reticulum unfolded protein response (GO:1900102)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular transport (GO:0032388)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein transport (GO:0051222)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TCCAAATCCTAAAAAACTCCT	0.403																																					p.P492fs		Atlas-INDEL	.											.	.	.	.	0			c.1476delT						.						80.0	81.0	81.0					5																	172537584		2203	4300	6503	SO:0001589	frameshift_variant	153222	exon6			.	AY139008	CCDS34293.1, CCDS54948.1	5q35.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164463	ENSG00000164463			24050	protein-coding gene	gene with protein product	"""luman/CREB3 recruitment factor"""		"""chromosome 5 open reading frame 41"""	C5orf41		18391022	Standard	NM_153607		Approved	LRF	uc003mch.3	Q8IUR6	OTTHUMG00000163322	ENST00000296953.2:c.1477delA	chr5.hg19:g.172537584delA	ENSP00000296953:p.Lys494fs	143.0	0.0		161.0	10.0	NM_153607	B3DFH2|B3KW49|D3DQM2|F5GXN3|Q5HYG4|Q5HYK0|Q86YR3|Q8IZG1	Frame_Shift_Del	DEL	ENST00000296953.2	hg19	CCDS34293.1																																																																																			.	.		0.403	CREBRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372667.1	NM_153607	
MYT1L	23040	hgsc.bcm.edu	37	2	1795691	1795691	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:1795691delT	ENST00000399161.2	-	25	4256	c.3509delA	c.(3508-3510)aatfs	p.N1170fs	MYT1L_ENST00000407844.1_Frame_Shift_Del_p.N168fs|MYT1L_ENST00000428368.2_Frame_Shift_Del_p.N1168fs	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1170					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		TAGGGCTTTATTTTCTGGACT	0.378																																					p.N1168fs		Atlas-INDEL	.											.	MYT1L	241	.	0			c.3504delT						.						120.0	106.0	111.0					2																	1795691		1832	4081	5913	SO:0001589	frameshift_variant	23040	exon25			.	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"""Zinc fingers, C2HC-type containing"""	7623	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 1"""	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.3509delA	chr2.hg19:g.1795691delT	ENSP00000382114:p.Asn1170fs	126.0	0.0		160.0	11.0	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Frame_Shift_Del	DEL	ENST00000399161.2	hg19																																																																																				.	.		0.378	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025	
IL1R2	7850	hgsc.bcm.edu	37	2	102636130	102636130	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:102636130delA	ENST00000332549.3	+	5	773	c.544delA	c.(544-546)aaafs	p.K182fs	IL1R2_ENST00000441002.1_Frame_Shift_Del_p.K182fs|IL1R2_ENST00000393414.2_Frame_Shift_Del_p.K182fs	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	182	Ig-like C2-type 2.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						AGACAATGAGAAATTTCTAAG	0.398																																					p.E181fs	Pancreas(106;189 1628 2302 5133 12295)	Atlas-INDEL	.											.	IL1R2	58	.	0			c.543delG						.						80.0	75.0	77.0					2																	102636130		2203	4300	6503	SO:0001589	frameshift_variant	7850	exon5			.	X59770	CCDS2054.1, CCDS58719.1	2q12	2013-01-11			ENSG00000115590	ENSG00000115590		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5994	protein-coding gene	gene with protein product		147811		IL1RB		10191101, 1833184	Standard	NM_004633		Approved	CD121b	uc002tbm.3	P27930	OTTHUMG00000130695	ENST00000332549.3:c.544delA	chr2.hg19:g.102636130delA	ENSP00000330959:p.Lys182fs	129.0	0.0		178.0	11.0	NM_004633	D3DVJ5|Q6LCE6|Q9UE68	Frame_Shift_Del	DEL	ENST00000332549.3	hg19	CCDS2054.1																																																																																			.	.		0.398	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633	
ESF1	51575	hgsc.bcm.edu	37	20	13695562	13695562	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:13695562delT	ENST00000202816.1	-	14	2622	c.2515delA	c.(2515-2517)acafs	p.T839fs		NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	839	Lys-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						AACTGCTCTGTTTTGGTTTTT	0.294																																					p.T839fs		Atlas-INDEL	.											.	ESF1	77	.	0			c.2516delC						.						105.0	99.0	101.0					20																	13695562		2203	4300	6503	SO:0001589	frameshift_variant	51575	exon14			.		CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 6"""	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.2515delA	chr20.hg19:g.13695562delT	ENSP00000202816:p.Thr839fs	96.0	0.0		149.0	10.0	NM_001276380	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Frame_Shift_Del	DEL	ENST00000202816.1	hg19	CCDS13117.1																																																																																			.	.		0.294	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649	
TMEM173	340061	hgsc.bcm.edu	37	5	138857961	138857961	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:138857961delT	ENST00000330794.4	-	6	986	c.653delA	c.(652-654)aacfs	p.N218fs	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	218	c-di-GMP-binding domain (CBD).				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GAAGCGAATGTTGGGGTCAGC	0.542																																					p.N218fs		Atlas-Indel,Pindel	.											.	TMEM173	19	.	0			c.654delC						.						137.0	123.0	128.0					5																	138857961		2203	4300	6503	SO:0001589	frameshift_variant	340061	exon6			.		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.653delA	chr5.hg19:g.138857961delT	ENSP00000331288:p.Asn218fs	170.0	0.0		151.0	43.0	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Frame_Shift_Del	DEL	ENST00000330794.4	hg19	CCDS4215.1																																																																																			.	.		0.542	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282	
COL9A3	1299	hgsc.bcm.edu	37	20	61458146	61458146	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:61458146delG	ENST00000343916.3	+	15	769	c.766delG	c.(766-768)gggfs	p.G256fs		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	256	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)					AGGGCCGCCTGGGATCCCAGG	0.667																																					p.P255fs		Atlas-INDEL	.											.	COL9A3	70	.	0			c.765delT						.						36.0	35.0	35.0					20																	61458146		2200	4298	6498	SO:0001589	frameshift_variant	1299	exon15			.	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.766delG	chr20.hg19:g.61458146delG	ENSP00000341640:p.Gly256fs	85.0	0.0		134.0	10.0	NM_001853	Q13681|Q9H4G9|Q9UPE2	Frame_Shift_Del	DEL	ENST00000343916.3	hg19	CCDS13505.1																																																																																			.	.		0.667	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853	
CPO	130749	hgsc.bcm.edu	37	2	207833909	207833909	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:207833909delG	ENST00000272852.3	+	9	920	c.874delG	c.(874-876)gggfs	p.G292fs		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	292						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		TGCCTCATCAGGGTCTTCAAG	0.443																																					p.S291fs		Atlas-INDEL	.											.	CPO	42	.	0			c.873delA						.						121.0	122.0	121.0					2																	207833909		2203	4300	6503	SO:0001589	frameshift_variant	130749	exon9			.		CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"""metallocarboxypeptidase O"", ""metallocarboxypeptidase C"""	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.874delG	chr2.hg19:g.207833909delG	ENSP00000272852:p.Gly292fs	119.0	0.0		148.0	10.0	NM_173077	Q2M277|Q7RTW7	Frame_Shift_Del	DEL	ENST00000272852.3	hg19	CCDS2372.1																																																																																			.	.		0.443	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077	
SEC14L4	284904	hgsc.bcm.edu	37	22	30887947	30887947	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:30887947delC	ENST00000255858.7	-	10	868	c.785delG	c.(784-786)ggtfs	p.G262fs	SEC14L4_ENST00000381982.3_Frame_Shift_Del_p.G262fs|RP4-539M6.14_ENST00000610156.1_RNA|SEC14L4_ENST00000392772.2_Frame_Shift_Del_p.G208fs|RP4-539M6.14_ENST00000442126.1_RNA|SEC14L4_ENST00000540456.1_Frame_Shift_Del_p.G247fs	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	262	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	GGGCACCTCACCCCCATAGTT	0.617																																					p.G262fs		Atlas-INDEL	.											.	SEC14L4	43	.	0			c.786delT						.						64.0	57.0	59.0					22																	30887947		2203	4300	6503	SO:0001589	frameshift_variant	284904	exon10			.	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.785delG	chr22.hg19:g.30887947delC	ENSP00000255858:p.Gly262fs	118.0	0.0		158.0	10.0	NM_001161368	A5D6W7|A6NCV4	Frame_Shift_Del	DEL	ENST00000255858.7	hg19	CCDS13878.1																																																																																			.	.		0.617	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977	
MYOM3	127294	hgsc.bcm.edu	37	1	24394840	24394840	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:24394840delA	ENST00000374434.3	-	26	3330	c.3168delT	c.(3166-3168)tttfs	p.F1056fs	MYOM3_ENST00000338909.5_5'Flank|MYOM3_ENST00000329601.7_Frame_Shift_Del_p.F1056fs|MYOM3_ENST00000330966.7_Frame_Shift_Del_p.F1057fs|RP11-293P20.4_ENST00000429191.1_RNA|RP11-293P20.2_ENST00000439239.2_RNA	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	1056						M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		TCTCTCGGTCAAAATTGATTT	0.488																																					p.D1057fs		Atlas-INDEL	.											.	MYOM3	131	.	0			c.3169delG						.						210.0	203.0	205.0					1																	24394840		1902	4108	6010	SO:0001589	frameshift_variant	127294	exon26			.	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.3168delT	chr1.hg19:g.24394840delA	ENSP00000363557:p.Phe1056fs	147.0	0.0		165.0	10.0	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Frame_Shift_Del	DEL	ENST00000374434.3	hg19	CCDS41281.1																																																																																			.	.		0.488	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
HAGHL	84264	hgsc.bcm.edu	37	16	777988	777988	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:777988delG	ENST00000341413.4	+	3	410	c.129delG	c.(127-129)gagfs	p.E43fs	NARFL_ENST00000562862.1_5'Flank|HAGHL_ENST00000564537.1_Frame_Shift_Del_p.E43fs|HAGHL_ENST00000561546.1_Frame_Shift_Del_p.E43fs|HAGHL_ENST00000564545.1_Intron|HAGHL_ENST00000549114.1_Frame_Shift_Del_p.E43fs|HAGHL_ENST00000389703.3_Frame_Shift_Del_p.E43fs|CCDC78_ENST00000293889.6_5'Flank			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like	43							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				TGGGCCGGGAGGGGGTGTCTC	0.687																																					p.E43fs	Pancreas(46;538 1326 12403 32360)	Atlas-INDEL	.											.	HAGHL	18	.	0			c.128delA						.						26.0	32.0	30.0					16																	777988		2191	4290	6481	SO:0001589	frameshift_variant	84264	exon2			.	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"""hydroxyacyl glutathione hydrolase-like"""			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.129delG	chr16.hg19:g.777988delG	ENSP00000341952:p.Glu43fs	217.0	0.0		246.0	15.0	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Frame_Shift_Del	DEL	ENST00000341413.4	hg19																																																																																				.	.		0.687	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304	
ZNF195	7748	hgsc.bcm.edu	37	11	3392251	3392251	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:3392251delT	ENST00000399602.4	-	3	306	c.180delA	c.(178-180)aaafs	p.K60fs	ZNF195_ENST00000005082.9_Frame_Shift_Del_p.K60fs|ZNF195_ENST00000527386.1_5'UTR|ZNF195_ENST00000526601.1_Frame_Shift_Del_p.K64fs|ZNF195_ENST00000438262.2_Frame_Shift_Del_p.K64fs|ZNF195_ENST00000528796.1_Frame_Shift_Del_p.K60fs|ZNF195_ENST00000429541.2_Frame_Shift_Del_p.K64fs|ZNF195_ENST00000343338.7_Frame_Shift_Del_p.K64fs|ZNF195_ENST00000354599.6_Frame_Shift_Del_p.K60fs|AC123788.1_ENST00000581561.1_RNA	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	60	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)	17		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		TCCAGGGCTCTTTTCGTTGCT	0.498																																					p.E65fs		Atlas-INDEL	.											.	ZNF195	77	.	0			c.193delG						.						159.0	163.0	162.0					11																	3392251		2170	4280	6450	SO:0001589	frameshift_variant	7748	exon4			.		CCDS41604.1, CCDS44521.1, CCDS44522.1, CCDS55736.1, CCDS55737.1, CCDS58111.1	11p15.5	2013-01-08			ENSG00000005801	ENSG00000005801		"""Zinc fingers, C2H2-type"", ""-"""	12986	protein-coding gene	gene with protein product		602187				9344677	Standard	NM_001130520		Approved		uc001lxt.3	O14628	OTTHUMG00000011694	ENST00000399602.4:c.180delA	chr11.hg19:g.3392251delT	ENSP00000382511:p.Lys60fs	88.0	0.0		125.0	10.0	NM_001256824	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Frame_Shift_Del	DEL	ENST00000399602.4	hg19	CCDS44522.1																																																																																			.	.		0.498	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2		
TK1	7083	hgsc.bcm.edu	37	17	76170874	76170874	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:76170874delG	ENST00000301634.7	-	7	909	c.671delC	c.(670-672)ccafs	p.P224fs	TK1_ENST00000588734.1_Frame_Shift_Del_p.P257fs|TK1_ENST00000405273.1_Frame_Shift_Del_p.P224fs|TK1_ENST00000590862.1_Intron	NM_003258.4	NP_003249.3	P04183	KITH_HUMAN	thymidine kinase 1, soluble	224					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|digestive tract development (GO:0048565)|DNA replication (GO:0006260)|fetal process involved in parturition (GO:0060138)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to copper ion (GO:0046688)|response to cortisol (GO:0051414)|response to nutrient levels (GO:0031667)|response to toxic substance (GO:0009636)|skeletal muscle cell proliferation (GO:0014856)|small molecule metabolic process (GO:0044281)|thymidine metabolic process (GO:0046104)	cytosol (GO:0005829)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|nucleoside kinase activity (GO:0019206)|thymidine kinase activity (GO:0004797)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|urinary_tract(2)	4			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.0804)|Lung(188;0.23)		Trifluridine(DB00432)|Zidovudine(DB00495)	AATCTGCTGTGGGGCAAAGAG	0.652																																					p.P224fs		Atlas-INDEL	.											.	TK1	23	.	0			c.672delA						.						41.0	38.0	39.0					17																	76170874		2202	4300	6502	SO:0001589	frameshift_variant	7083	exon7			.		CCDS11754.1	17q23.2-q25.3	2012-10-02			ENSG00000167900	ENSG00000167900	2.7.1.21		11830	protein-coding gene	gene with protein product		188300					Standard	NM_003258		Approved		uc002juw.2	P04183	OTTHUMG00000150674	ENST00000301634.7:c.671delC	chr17.hg19:g.76170874delG	ENSP00000301634:p.Pro224fs	116.0	0.0		173.0	11.0	NM_003258	B2RC58|Q969V0|Q9UMG9	Frame_Shift_Del	DEL	ENST00000301634.7	hg19	CCDS11754.1																																																																																			.	.		0.652	TK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319577.1	NM_003258	
MTRF1L	54516	hgsc.bcm.edu	37	6	153315778	153315778	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:153315778delC	ENST00000367233.5	-	4	556	c.557delG	c.(556-558)ggtfs	p.G186fs	MTRF1L_ENST00000464135.1_5'UTR|MTRF1L_ENST00000367230.1_Frame_Shift_Del_p.G150fs|MTRF1L_ENST00000367231.5_Frame_Shift_Del_p.G186fs	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	186						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)		GGCTTCTGAACCCCCAATGCT	0.413																																					p.G186fs		Atlas-INDEL	.											.	MTRF1L	21	.	0			c.558delT						.						92.0	91.0	91.0					6																	153315778		2203	4300	6503	SO:0001589	frameshift_variant	54516	exon4			.	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.557delG	chr6.hg19:g.153315778delC	ENSP00000356202:p.Gly186fs	123.0	0.0		121.0	10.0	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Frame_Shift_Del	DEL	ENST00000367233.5	hg19	CCDS5243.1																																																																																			.	.		0.413	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041	
CDC23	8697	hgsc.bcm.edu	37	5	137537124	137537124	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:137537124delT	ENST00000394886.2	-	5	459	c.429delA	c.(427-429)aaafs	p.K143fs		NM_004661.3	NP_004652.2	Q9UJX2	CDC23_HUMAN	cell division cycle 23	143					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of exit from mitosis (GO:0007096)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(6)|prostate(2)|skin(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TCACTTGTCCTTTTTCCAGGG	0.373																																					p.G144fs		Atlas-INDEL	.											.	CDC23	46	.	0			c.430delG						.						77.0	76.0	77.0					5																	137537124		2203	4300	6503	SO:0001589	frameshift_variant	8697	exon5			.	AF053977	CCDS4200.2	5q31	2013-01-17	2013-01-17		ENSG00000094880	ENSG00000094880		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1724	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 8"""	603462	"""CDC23 (cell division cycle 23, yeast, homolog)"", ""cell division cycle 23 homolog (S. cerevisiae)"""			9790767	Standard	NM_004661		Approved	APC8, ANAPC8, CUT23	uc003lcl.3	Q9UJX2	OTTHUMG00000129198	ENST00000394886.2:c.429delA	chr5.hg19:g.137537124delT	ENSP00000378350:p.Lys143fs	108.0	0.0		147.0	10.0	NM_004661	A8K6E5|B4E3A2|B7WP05|D3DQB7|O75433|Q53FN2|Q9BS73	Frame_Shift_Del	DEL	ENST00000394886.2	hg19	CCDS4200.2																																																																																			.	.		0.373	CDC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251275.2		
DOCK1	1793	hgsc.bcm.edu	37	10	129242484	129242484	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:129242484delC	ENST00000280333.6	+	50	5400	c.5291delC	c.(5290-5292)tccfs	p.S1764fs		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1764					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		TCACCGTCCTCCCAGCAAACA	0.572																																					p.S1764fs		Atlas-INDEL	.											.	DOCK1	188	.	0			c.5290delT						.						87.0	101.0	96.0					10																	129242484		2089	4209	6298	SO:0001589	frameshift_variant	1793	exon50			.	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.5291delC	chr10.hg19:g.129242484delC	ENSP00000280333:p.Ser1764fs	99.0	0.0		139.0	10.0	NM_001380	A9Z1Z5	Frame_Shift_Del	DEL	ENST00000280333.6	hg19																																																																																				.	.		0.572	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
ADAR	103	hgsc.bcm.edu	37	1	154561054	154561054	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:154561054delT	ENST00000368474.4	-	10	3057	c.2858delA	c.(2857-2859)aagfs	p.K953fs	ADAR_ENST00000292205.5_Frame_Shift_Del_p.K996fs|ADAR_ENST00000368471.3_Frame_Shift_Del_p.K658fs	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	953	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		TGACACAGTCTTTTTTATTTG	0.443																																					p.K953fs		Atlas-INDEL	.											.	ADAR	113	.	0			c.2859delG						.						133.0	131.0	131.0					1																	154561054		2203	4300	6503	SO:0001589	frameshift_variant	103	exon10			.	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"""interferon-induced protein 4"""	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.2858delA	chr1.hg19:g.154561054delT	ENSP00000357459:p.Lys953fs	59.0	0.0		156.0	10.0	NM_001111	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Frame_Shift_Del	DEL	ENST00000368474.4	hg19	CCDS1071.1																																																																																			.	.		0.443	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111	
TEP1	7011	hgsc.bcm.edu	37	14	20846338	20846338	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:20846338delC	ENST00000262715.5	-	39	5606	c.5566delG	c.(5566-5568)gttfs	p.V1857fs	TEP1_ENST00000556935.1_Frame_Shift_Del_p.V1749fs|TEP1_ENST00000545983.1_Frame_Shift_Del_p.V195fs	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1857					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		ACAGCCACAACCCCCCCAGGC	0.627																																					p.V1856fs		Atlas-INDEL	.											.	TEP1	224	.	0			c.5567delT						.						63.0	70.0	68.0					14																	20846338		2203	4300	6503	SO:0001589	frameshift_variant	7011	exon39			.		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.5566delG	chr14.hg19:g.20846338delC	ENSP00000262715:p.Val1857fs	154.0	0.0		174.0	13.0	NM_007110	A0AUV9	Frame_Shift_Del	DEL	ENST00000262715.5	hg19	CCDS9548.1																																																																																			.	.		0.627	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
NUP155	9631	hgsc.bcm.edu	37	5	37309279	37309279	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:37309279delT	ENST00000231498.3	-	24	2922	c.2719delA	c.(2719-2721)attfs	p.I907fs	NUP155_ENST00000513532.1_Frame_Shift_Del_p.I843fs|NUP155_ENST00000502533.1_5'UTR|NUP155_ENST00000381843.2_Frame_Shift_Del_p.I848fs	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	166.0	0.0		150.0	11.0	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	
KDM1B	221656	hgsc.bcm.edu	37	6	18197380	18197380	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:18197380delT	ENST00000297792.5	+	9	843	c.666delT	c.(664-666)tatfs	p.Y222fs	KDM1B_ENST00000397244.1_Frame_Shift_Del_p.Y222fs|KDM1B_ENST00000546309.2_Intron|KDM1B_ENST00000388870.2_Frame_Shift_Del_p.Y354fs			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	354					DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						GAATACTGTATTTTATGACCA	0.463																																					p.Y222fs		Atlas-INDEL	.											.	KDM1B	58	.	0			c.665delA						.						126.0	112.0	116.0					6																	18197380		2203	4300	6503	SO:0001589	frameshift_variant	221656	exon9			.	AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097		"""Chromatin-modifying enzymes / K-demethylases"""	21577	protein-coding gene	gene with protein product		613081	"""amine oxidase, flavin containing 1"", ""chromosome 6 open reading frame 193"", ""amine oxidase (flavin containing) domain 1"""	C6orf193, AOF1		19407342, 19727073	Standard	NM_153042		Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.666delT	chr6.hg19:g.18197380delT	ENSP00000297792:p.Tyr222fs	196.0	0.0		159.0	10.0	NM_153042	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	Frame_Shift_Del	DEL	ENST00000297792.5	hg19	CCDS34343.1																																																																																			.	.		0.463	KDM1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277080.1	NM_153042	
ZFHX3	463	hgsc.bcm.edu	37	16	72993684	72993684	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:72993684delC	ENST00000268489.5	-	2	1033	c.361delG	c.(361-363)gacfs	p.D121fs	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	121					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CTCTCCTCGTCCCCCTCCTCA	0.687																																					p.D121fs		Atlas-INDEL	.											.	ZFHX3	404	.	0			c.362delA						.						31.0	32.0	32.0					16																	72993684		2198	4300	6498	SO:0001589	frameshift_variant	463	exon2			.	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.361delG	chr16.hg19:g.72993684delC	ENSP00000268489:p.Asp121fs	166.0	0.0		179.0	14.0	NM_006885	D3DWS8|O15101|Q13719	Frame_Shift_Del	DEL	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.		0.687	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
CKAP2L	150468	hgsc.bcm.edu	37	2	113520086	113520086	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:113520086delT	ENST00000302450.6	-	2	176	c.98delA	c.(97-99)aacfs	p.N33fs	CKAP2L_ENST00000481732.1_5'UTR|CKAP2L_ENST00000541405.1_5'UTR	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	33						centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	28						TCACTTGGTGTTTTGGCTCTT	0.413																																					p.N33fs		Atlas-INDEL	.											.	CKAP2L	54	.	0			c.99delC						.						196.0	161.0	173.0					2																	113520086		2203	4300	6503	SO:0001589	frameshift_variant	150468	exon2			.	AL832036	CCDS2100.1	2q13	2008-02-05			ENSG00000169607	ENSG00000169607			26877	protein-coding gene	gene with protein product						12477932	Standard	NM_152515		Approved	FLJ40629	uc002tie.2	Q8IYA6	OTTHUMG00000131313	ENST00000302450.6:c.98delA	chr2.hg19:g.113520086delT	ENSP00000305204:p.Asn33fs	83.0	0.0		156.0	10.0	NM_152515	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Frame_Shift_Del	DEL	ENST00000302450.6	hg19	CCDS2100.1																																																																																			.	.		0.413	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515	
ADAM33	80332	hgsc.bcm.edu	37	20	3650236	3650236	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:3650236delG	ENST00000356518.2	-	20	2530	c.2289delC	c.(2287-2289)cccfs	p.P763fs	ADAM33_ENST00000350009.2_Frame_Shift_Del_p.P737fs|ADAM33_ENST00000466620.1_5'UTR|ADAM33_ENST00000379861.4_Frame_Shift_Del_p.P763fs	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	763					proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|skin(3)	29						CCAACTCCATGGGGTGAACGC	0.647																																					p.M764fs		Atlas-INDEL	.											.	ADAM33	76	.	0			c.2290delA						.						21.0	21.0	21.0					20																	3650236		2202	4296	6498	SO:0001589	frameshift_variant	80332	exon20			.	AL117415, AB055891	CCDS13058.1, CCDS63219.1	20p13	2010-04-06	2005-08-18		ENSG00000149451	ENSG00000149451		"""ADAM metallopeptidase domain containing"""	15478	protein-coding gene	gene with protein product		607114	"""a disintegrin and metalloproteinase domain 33"", ""chromosome 20 open reading frame 153"""	C20orf153		11814695	Standard	XM_005260843		Approved	DKFZp434K0521, dJ964F7.1	uc002wit.3	Q9BZ11	OTTHUMG00000031758	ENST00000356518.2:c.2289delC	chr20.hg19:g.3650236delG	ENSP00000348912:p.Pro763fs	120.0	0.0		161.0	10.0	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Frame_Shift_Del	DEL	ENST00000356518.2	hg19	CCDS13058.1																																																																																			.	.		0.647	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220	
LEPR	3953	hgsc.bcm.edu	37	1	66064394	66064394	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:66064394delG	ENST00000349533.6	+	8	1086	c.901delG	c.(901-903)gggfs	p.G301fs	LEPR_ENST00000371060.3_Frame_Shift_Del_p.G301fs|LEPR_ENST00000406510.3_Intron|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000371059.3_Frame_Shift_Del_p.G301fs|LEPR_ENST00000344610.8_Frame_Shift_Del_p.G301fs|LEPR_ENST00000371058.1_Frame_Shift_Del_p.G301fs	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					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)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		TATACTTCCTGGGTCTTCGTA	0.453																																					p.P300fs		Atlas-INDEL	.											.	LEPR	284	.	0			c.900delT						.						113.0	109.0	110.0					1																	66064394		2203	4300	6503	SO:0001589	frameshift_variant	3953	exon8			.	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.901delG	chr1.hg19:g.66064394delG	ENSP00000330393:p.Gly301fs	179.0	0.0		205.0	15.0	NM_002303	Q6FHL5	Frame_Shift_Del	DEL	ENST00000349533.6	hg19	CCDS631.1																																																																																			.	.		0.453	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
CAPN3	825	hgsc.bcm.edu	37	15	42698130	42698130	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:42698130delA	ENST00000397163.3	+	15	2008	c.1789delA	c.(1789-1791)aaafs	p.K598fs	CAPN3_ENST00000356316.3_Intron|CAPN3_ENST00000397200.4_Frame_Shift_Del_p.K86fs|CAPN3_ENST00000318023.7_Intron|CAPN3_ENST00000349748.3_Intron|CAPN3_ENST00000569136.1_5'UTR|CAPN3_ENST00000561817.1_Intron|CAPN3_ENST00000357568.3_Intron|CAPN3_ENST00000337571.4_Intron|CAPN3_ENST00000397204.4_5'UTR|RP11-164J13.1_ENST00000495723.1_RNA	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	598	Linker.				apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		GCAGAAAAAGAAAAAAACCAA	0.418																																					p.K596fs		Atlas-INDEL	.											.,1	CAPN3	172	.	0			c.1788delG						.						176.0	189.0	185.0					15																	42698130		1919	4131	6050	SO:0001589	frameshift_variant	825	exon15			.	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"""EF-hand domain containing"""	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.1789delA	chr15.hg19:g.42698130delA	ENSP00000380349:p.Lys598fs	110.0	0.0		156.0	11.0	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Frame_Shift_Del	DEL	ENST00000397163.3	hg19	CCDS45245.1																																																																																			.	.		0.418	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1		
ANXA8L1	728113	hgsc.bcm.edu	37	10	47169805	47169805	+	Frame_Shift_Del	DEL	G	G	-	rs2670516		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:47169805delG	ENST00000359178.4	-	2	215	c.94delC	c.(94-96)caafs	p.Q32fs	ANXA8L1_ENST00000414655.2_Intron|ANXA8L1_ENST00000545298.1_Frame_Shift_Del_p.Q32fs|ANXA8L1_ENST00000358140.4_Frame_Shift_Del_p.Q32fs	NM_001098845.1	NP_001092315	Q5T2P8	AXA81_HUMAN	annexin A8-like 1	32							calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)			large_intestine(1)|lung(1)	2						TTCATGGCTTGGTAGAGGGTC	0.592																																					p.K32fs		Atlas-INDEL	.											.	ANXA8	3	.	0			c.95delA						.						27.0	1.0	11.0					10																	47169805		831	1279	2110	SO:0001589	frameshift_variant	653145	exon2			.		CCDS73097.1, CCDS73098.1, CCDS73099.1	10q11.22	2014-06-19			ENSG00000150165			"""Annexins"""	23334	protein-coding gene	gene with protein product			"""annexin A8-like 2"""	ANXA8L2			Standard	NM_001098845		Approved	bA301J7.3, bA145E20.2		Q5T2P8	OTTHUMG00000018114	ENST00000359178.4:c.94delC	chr10.hg19:g.47169805delG	ENSP00000352101:p.Gln32fs	1.0	0.0		17.0	10.0	NM_001271702	A6NDE6|B4DKI1	Frame_Shift_Del	DEL	ENST00000359178.4	hg19	CCDS41511.1																																																																																			.	.		0.592	ANXA8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047843.1		
ZNF106	64397	hgsc.bcm.edu	37	15	42742679	42742679	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:42742679delT	ENST00000263805.4	-	2	2048	c.1722delA	c.(1720-1722)aaafs	p.K574fs	ZNF106_ENST00000565380.1_Intron|ZNF106_ENST00000565611.1_Intron	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	574					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										TCAAAGACCCTTTTTCAGATT	0.388																																					p.G575fs		Atlas-INDEL	.											.	ZFP106	117	.	0			c.1723delG						.						115.0	114.0	114.0					15																	42742679		2203	4299	6502	SO:0001589	frameshift_variant	64397	exon2			.	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"""Zinc fingers, C2H2-type"""	12886	protein-coding gene	gene with protein product	"""SH3-domain binding protein 3"""		"""zinc finger protein 106 homolog (mouse)"""	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.1722delA	chr15.hg19:g.42742679delT	ENSP00000263805:p.Lys574fs	128.0	0.0		155.0	10.0	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Frame_Shift_Del	DEL	ENST00000263805.4	hg19	CCDS32208.1																																																																																			.	.		0.388	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
FAM200B	285550	hgsc.bcm.edu	37	4	15689819	15689819	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:15689819delT	ENST00000422728.2	+	2	2057	c.1219delT	c.(1219-1221)tttfs	p.F408fs	FAM200B_ENST00000504137.1_Intron	NM_001145191.1	NP_001138663.1	P0CF97	F200B_HUMAN	family with sequence similarity 200, member B	408							nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)	2						tgagattcacttttttctcat	0.313																																					p.H406fs		Atlas-INDEL	.											.	FAM200B	56	.	0			c.1218delC						.						32.0	26.0	28.0					4																	15689819		692	1589	2281	SO:0001589	frameshift_variant	285550	exon2			.	BC048993	CCDS47028.1	4p15.32	2014-04-02			ENSG00000237765	ENSG00000237765			27740	protein-coding gene	gene with protein product	"""chromosome 4 open reading frame 53"""						Standard	NM_001145191		Approved	C4orf53	uc003gof.4	P0CF97	OTTHUMG00000160279	ENST00000422728.2:c.1219delT	chr4.hg19:g.15689819delT	ENSP00000393017:p.Phe408fs	136.0	0.0		153.0	10.0	NM_001145191		Frame_Shift_Del	DEL	ENST00000422728.2	hg19	CCDS47028.1																																																																																			.	.		0.313	FAM200B-005	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360100.1	NM_001145191	
MBD5	55777	hgsc.bcm.edu	37	2	149247480	149247480	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:149247480delA	ENST00000407073.1	+	12	4577	c.3580delA	c.(3580-3582)aaafs	p.K1195fs	MBD5_ENST00000404807.1_Frame_Shift_Del_p.K1428fs	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1195					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		CCACACATCCAAAAAACAGTG	0.488																																					p.S1193fs		Atlas-INDEL	.											.,1	MBD5	164	.	0			c.3579delC						.						95.0	99.0	98.0					2																	149247480		2203	4300	6503	SO:0001589	frameshift_variant	55777	exon12			.	AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.3580delA	chr2.hg19:g.149247480delA	ENSP00000386049:p.Lys1195fs	121.0	0.0		166.0	11.0	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Frame_Shift_Del	DEL	ENST00000407073.1	hg19	CCDS33302.1																																																																																			.	.		0.488	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2		
MAD1L1	8379	hgsc.bcm.edu	37	7	2274931	2274931	+	5'Flank	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:2274931delC	ENST00000406869.1	-	0	0				FTSJ2_ENST00000242257.8_Frame_Shift_Del_p.G189fs|MAD1L1_ENST00000399654.2_5'Flank|MAD1L1_ENST00000402746.1_5'Flank|FTSJ2_ENST00000486040.1_5'UTR|FTSJ2_ENST00000407040.1_Frame_Shift_Del_p.G95fs|MAD1L1_ENST00000265854.7_5'Flank|FTSJ2_ENST00000440306.2_3'UTR			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)						mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)				central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		AAAGGAATGTCCCCCCAGGTT	0.547																																					p.T190fs		Atlas-INDEL	.											.	FTSJ2	22	.	0			c.568delA						.						87.0	80.0	82.0					7																	2274931		2203	4300	6503	SO:0001631	upstream_gene_variant	29960	exon3			.	U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"""MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"""			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493		chr7.hg19:g.2274931delC	Exception_encountered	154.0	0.0		179.0	17.0	NM_013393	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Frame_Shift_Del	DEL	ENST00000406869.1	hg19	CCDS43539.1																																																																																			.	.		0.547	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550	
PIGN	23556	hgsc.bcm.edu	37	18	59752471	59752471	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:59752471delA	ENST00000357637.5	-	26	2812	c.2397delT	c.(2395-2397)tttfs	p.F799fs	PIGN_ENST00000400334.3_Frame_Shift_Del_p.F799fs	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	799					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				TTCCAGTTCCAAAAAATGCTG	0.303																																					p.G800fs		Atlas-INDEL	.											.	PIGN	62	.	0			c.2398delG						.						31.0	28.0	29.0					18																	59752471		1717	3847	5564	SO:0001589	frameshift_variant	23556	exon26			.	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"""Phosphatidylinositol glycan anchor biosynthesis"""	8967	protein-coding gene	gene with protein product		606097	"""phosphatidylinositol glycan, class N"""			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.2397delT	chr18.hg19:g.59752471delA	ENSP00000350263:p.Phe799fs	154.0	0.0		190.0	12.0	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Frame_Shift_Del	DEL	ENST00000357637.5	hg19	CCDS45879.1																																																																																			.	.		0.303	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37505286	37505286	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:37505286delA	ENST00000602533.1	+	32	2978	c.2879delA	c.(2878-2880)caafs	p.Q960fs	ANKRD30A_ENST00000361713.1_Frame_Shift_Del_p.Q960fs|ANKRD30A_ENST00000374660.1_Frame_Shift_Del_p.Q1079fs			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	277.0	0.0		363.0	25.0	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	
KRTAP5-2	440021	hgsc.bcm.edu	37	11	1619161	1619161	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:1619161delC	ENST00000412090.1	-	1	363	c.320delG	c.(319-321)ggcfs	p.G107fs	KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA	NM_001004325.1	NP_001004325.1	Q701N4	KRA52_HUMAN	keratin associated protein 5-2	107	6 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				large_intestine(1)|lung(2)|skin(1)	4		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		AGAACCACAGCCCCCCTTGGA	0.657																																					p.G107fs		Atlas-INDEL	.											.	KRTAP5-2	38	.	0			c.321delC						.						85.0	110.0	101.0					11																	1619161		2201	4299	6500	SO:0001589	frameshift_variant	440021	exon1			.	AB126071	CCDS31331.1	11p15.5	2008-02-05				ENSG00000205867		"""Keratin associated proteins"""	23597	protein-coding gene	gene with protein product						15144888	Standard	NM_001004325		Approved	KRTAP5.2, KRTAP5-8	uc001ltv.3	Q701N4		ENST00000412090.1:c.320delG	chr11.hg19:g.1619161delC	ENSP00000400041:p.Gly107fs	180.0	0.0		238.0	15.0	NM_001004325	A9JTZ1	Frame_Shift_Del	DEL	ENST00000412090.1	hg19	CCDS31331.1																																																																																			.	.		0.657	KRTAP5-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384775.1	NM_001004325	
PTPRN2	5799	hgsc.bcm.edu	37	7	157926551	157926551	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:157926551delC	ENST00000389418.4	-	9	1383	c.1374delG	c.(1372-1374)gggfs	p.G458fs	PTPRN2_ENST00000404321.2_Frame_Shift_Del_p.G481fs|PTPRN2_ENST00000409483.1_Frame_Shift_Del_p.G420fs|PTPRN2_ENST00000389416.4_Frame_Shift_Del_p.G441fs|PTPRN2_ENST00000389413.3_Frame_Shift_Del_p.G458fs	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	458					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GCGGCTGCTGCCCCAGCAGAT	0.617																																					p.Q459fs		Atlas-INDEL	.											.	PTPRN2	243	.	0			c.1375delC						.						51.0	57.0	55.0					7																	157926551		2203	4300	6503	SO:0001589	frameshift_variant	5799	exon9			.	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.1374delG	chr7.hg19:g.157926551delC	ENSP00000374069:p.Gly458fs	97.0	0.0		128.0	10.0	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Frame_Shift_Del	DEL	ENST00000389418.4	hg19	CCDS5947.1																																																																																			.	.		0.617	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
SLC14A1	6563	hgsc.bcm.edu	37	18	43329808	43329808	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:43329808delA	ENST00000321925.4	+	10	1294	c.1062delA	c.(1060-1062)acafs	p.T354fs	RP11-116O18.3_ENST00000586213.1_RNA|SLC14A1_ENST00000402943.2_Frame_Shift_Del_p.T249fs|SLC14A1_ENST00000589700.1_3'UTR|SLC14A1_ENST00000591541.1_Frame_Shift_Del_p.T58fs|SLC14A1_ENST00000502059.2_Frame_Shift_Del_p.T246fs|SLC14A1_ENST00000436407.3_Frame_Shift_Del_p.T410fs|SLC14A1_ENST00000415427.3_Frame_Shift_Del_p.T410fs|SLC14A1_ENST00000535474.1_Frame_Shift_Del_p.T222fs|SLC14A1_ENST00000586142.1_Frame_Shift_Del_p.T354fs	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	354					transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						TCATGACCACAAAAAATTCCA	0.468																																					p.T410fs		Atlas-INDEL	.											.	SLC14A1	84	.	0			c.1229delC						.						145.0	134.0	138.0					18																	43329808		2203	4300	6503	SO:0001589	frameshift_variant	6563	exon9			.	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"""Blood group antigens"", ""Solute carriers"""	10918	protein-coding gene	gene with protein product		613868	"""Kidd blood group"", ""solute carrier family 14 (urea transporter), member 1"""	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.1062delA	chr18.hg19:g.43329808delA	ENSP00000318546:p.Thr354fs	198.0	0.0		248.0	15.0	NM_001146037	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Frame_Shift_Del	DEL	ENST00000321925.4	hg19	CCDS11925.1																																																																																			.	.		0.468	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865	
CHFR	55743	hgsc.bcm.edu	37	12	133418144	133418144	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:133418144delT	ENST00000432561.2	-	18	2064	c.1991delA	c.(1990-1992)aacfs	p.N664fs	CHFR_ENST00000537522.1_Frame_Shift_Del_p.N286fs|CHFR_ENST00000266880.7_Frame_Shift_Del_p.N663fs|CHFR_ENST00000443047.2_Frame_Shift_Del_p.N572fs|CHFR_ENST00000450056.2_Frame_Shift_Del_p.N652fs|CHFR_ENST00000541341.1_Frame_Shift_Del_p.N91fs|CHFR_ENST00000315585.7_Frame_Shift_Del_p.N623fs|CHFR_ENST00000541837.2_5'UTR			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	664					mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		GGATGCTTAGTTTTTGAACCT	0.433																																					p.N664fs		Atlas-INDEL	.											.	CHFR	83	.	0			c.1992delC						.						137.0	136.0	136.0					12																	133418144		2203	4300	6503	SO:0001589	frameshift_variant	55743	exon18			.	AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"""RING-type (C3HC4) zinc fingers"""	20455	protein-coding gene	gene with protein product		605209	"""checkpoint with forkhead and ring finger domains"""			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.1991delA	chr12.hg19:g.133418144delT	ENSP00000392395:p.Asn664fs	160.0	0.0		123.0	10.0	NM_001161344	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Frame_Shift_Del	DEL	ENST00000432561.2	hg19	CCDS53849.1																																																																																			.	.		0.433	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397130.2		
POLG	5428	hgsc.bcm.edu	37	15	89860003	89860003	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:89860003delT	ENST00000268124.5	-	23	4032	c.3699delA	c.(3697-3699)aaafs	p.K1233fs	FANCI_ENST00000300027.8_3'UTR|POLG_ENST00000442287.2_Frame_Shift_Del_p.K1233fs|FANCI_ENST00000310775.7_3'UTR	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	1233					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			GCTGGCTTCGTTTTTCCAAGG	0.507								DNA polymerases (catalytic subunits)																													p.R1234fs	Colon(73;648 1203 11348 18386 27782)	Atlas-INDEL	.											.	POLG	75	.	0			c.3700delC						.						105.0	98.0	100.0					15																	89860003		2200	4299	6499	SO:0001589	frameshift_variant	5428	exon23			.	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"""DNA polymerases"""	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.3699delA	chr15.hg19:g.89860003delT	ENSP00000268124:p.Lys1233fs	192.0	0.0		168.0	11.0	NM_001126131	Q8NFM2|Q92515	Frame_Shift_Del	DEL	ENST00000268124.5	hg19	CCDS10350.1																																																																																			.	.		0.507	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693	
CKMT2	1160	hgsc.bcm.edu	37	5	80552810	80552810	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:80552810delG	ENST00000424301.2	+	7	984	c.746delG	c.(745-747)aggfs	p.R249fs	CKMT2-AS1_ENST00000501927.2_RNA|CKMT2_ENST00000437669.1_Frame_Shift_Del_p.R249fs|CKMT2-AS1_ENST00000500148.2_RNA|CKMT2_ENST00000254035.4_Frame_Shift_Del_p.R249fs|CKMT2-AS1_ENST00000512287.1_RNA|CKMT2-AS1_ENST00000503483.2_RNA|CKMT2-AS1_ENST00000511495.1_RNA|CKMT2-AS1_ENST00000505295.1_RNA|CKMT2-AS1_ENST00000502041.2_RNA	NM_001825.2	NP_001816.2	P17540	KCRS_HUMAN	creatine kinase, mitochondrial 2 (sarcomeric)	249	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(4)|urinary_tract(1)	17		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	CCAGATGCCAGGGGAATCTGG	0.468																																					p.R249fs		Atlas-INDEL	.											.	CKMT2	44	.	0			c.745delA						.						112.0	105.0	108.0					5																	80552810		2203	4300	6503	SO:0001589	frameshift_variant	1160	exon7			.		CCDS4053.1	5q14.1	2013-09-20			ENSG00000131730	ENSG00000131730	2.7.3.2		1996	protein-coding gene	gene with protein product		123295				2324105	Standard	NM_001825		Approved	SMTCK	uc003khd.4	P17540	OTTHUMG00000119013	ENST00000424301.2:c.746delG	chr5.hg19:g.80552810delG	ENSP00000404203:p.Arg249fs	185.0	0.0		206.0	15.0	NM_001825	Q6ICS8|Q8N1E1	Frame_Shift_Del	DEL	ENST00000424301.2	hg19	CCDS4053.1																																																																																			.	.		0.468	CKMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369600.1	NM_001825	
SH2D2A	9047	hgsc.bcm.edu	37	1	156786488	156786488	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:156786488delG	ENST00000368199.3	-	1	166	c.13delC	c.(13-15)ctgfs	p.L5fs	NTRK1_ENST00000392302.2_Intron|SH2D2A_ENST00000495306.1_5'UTR|SH2D2A_ENST00000392306.2_Frame_Shift_Del_p.L5fs|SH2D2A_ENST00000368198.3_5'UTR	NM_001161443.1|NM_001161444.1|NM_003975.3	NP_001154915.1|NP_001154916.1|NP_003966.2	Q9NP31	SH22A_HUMAN	SH2 domain containing 2A	5					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|large_intestine(2)|lung(15)	18	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ATCTGGGCCAGGGGGAACTCC	0.582																																					p.L5fs		Atlas-INDEL	.											.	SH2D2A	78	.	0			c.14delT						.						90.0	85.0	87.0					1																	156786488		2203	4300	6503	SO:0001589	frameshift_variant	9047	exon1			.	AJ000553	CCDS1159.1, CCDS53380.1, CCDS53381.1	1q21	2013-02-14	2010-04-21		ENSG00000027869	ENSG00000027869		"""SH2 domain containing"""	10821	protein-coding gene	gene with protein product	"""T lymphocyte specific adaptor protein"", ""T cell specific adapter protein TSAd"", ""T cell specific adpater protein TSAd"""	604514	"""SH2 domain protein 2A"""			9468509	Standard	NM_003975		Approved	TSAd, F2771	uc009wsh.2	Q9NP31	OTTHUMG00000041305	ENST00000368199.3:c.13delC	chr1.hg19:g.156786488delG	ENSP00000357182:p.Leu5fs	83.0	0.0		156.0	10.0	NM_003975	O43817|Q5UBZ1|Q5VZS4|Q5VZS5|Q9UPA7	Frame_Shift_Del	DEL	ENST00000368199.3	hg19	CCDS1159.1																																																																																			.	.		0.582	SH2D2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098982.1	NM_003975	
MYCBP2	23077	hgsc.bcm.edu	37	13	77798633	77798633	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:77798633delA	ENST00000544440.2	-	20	2795	c.2778delT	c.(2776-2778)tttfs	p.F926fs	MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000357337.6_Frame_Shift_Del_p.F926fs|MYCBP2_ENST00000407578.2_Frame_Shift_Del_p.F964fs					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		GCCCATAACCAAATGTATAGA	0.353																																					p.G965fs		Atlas-INDEL	.											.	MYCBP2	1029	.	0			c.2893delG						.						117.0	111.0	113.0					13																	77798633		2203	4300	6503	SO:0001589	frameshift_variant	23077	exon20			.	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.2778delT	chr13.hg19:g.77798633delA	ENSP00000444596:p.Phe926fs	218.0	0.0		157.0	11.0	NM_015057		Frame_Shift_Del	DEL	ENST00000544440.2	hg19																																																																																				.	.		0.353	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
RAB11FIP3	9727	hgsc.bcm.edu	37	16	538888	538888	+	Frame_Shift_Del	DEL	G	G	-	rs139898544	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:538888delG	ENST00000262305.4	+	5	1541	c.1153delG	c.(1153-1155)gggfs	p.G386fs	RAB11FIP3_ENST00000450428.1_Frame_Shift_Del_p.G90fs|RAB11FIP3_ENST00000457159.1_Frame_Shift_Del_p.G386fs	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	386					cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.G385R(1)		breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				CACGGTGATCGGGGGCGAGGA	0.602																																					p.I384fs	Melanoma(160;2366 2595 4474 8099)	Atlas-INDEL	.											.	RAB11FIP3	31	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.1152delC						.						89.0	77.0	81.0					16																	538888		2202	4300	6502	SO:0001589	frameshift_variant	9727	exon5			.	AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565		"""EF-hand domain containing"""	17224	protein-coding gene	gene with protein product		608738				9734811, 11481332	Standard	NM_014700		Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.1153delG	chr16.hg19:g.538888delG	ENSP00000262305:p.Gly386fs	117.0	0.0		140.0	12.0	NM_014700	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Frame_Shift_Del	DEL	ENST00000262305.4	hg19	CCDS32351.1																																																																																			.	.		0.602	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700	
SHOX2	6474	hgsc.bcm.edu	37	3	157820545	157820545	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:157820545delA	ENST00000425436.3	-	2	502	c.477delT	c.(475-477)tttfs	p.F159fs	SHOX2_ENST00000483851.2_Frame_Shift_Del_p.F159fs|SHOX2_ENST00000554685.1_5'UTR|SHOX2_ENST00000389589.4_Frame_Shift_Del_p.F183fs|SHOX2_ENST00000441443.2_Frame_Shift_Del_p.F30fs|SHOX2_ENST00000490689.2_Frame_Shift_Del_p.F30fs	NM_001163678.1|NM_006884.3	NP_001157150.1|NP_006875.2	O60902	SHOX2_HUMAN	short stature homeobox 2	159					cardiac atrium morphogenesis (GO:0003209)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte development (GO:0002063)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint morphogenesis (GO:0060272)|heart development (GO:0007507)|heart valve development (GO:0003170)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of axonogenesis (GO:0050772)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of chondrocyte differentiation (GO:0032330)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(10)|skin(3)|upper_aerodigestive_tract(1)	20			Lung(72;0.00318)|LUSC - Lung squamous cell carcinoma(72;0.0043)			GGGTCTCGTCAAAAAGCCTCT	0.582																																					p.D184fs		Atlas-INDEL	.											.	SHOX2	84	.	0			c.550delG						.						165.0	134.0	145.0					3																	157820545		2203	4300	6503	SO:0001589	frameshift_variant	6474	exon3			.	AJ002368	CCDS33884.1, CCDS43164.1, CCDS33884.2, CCDS54664.1	3q25.32	2011-06-20			ENSG00000168779	ENSG00000168779		"""Homeoboxes / PRD class"""	10854	protein-coding gene	gene with protein product		602504				9482898, 9466998	Standard	NM_006884		Approved	SHOT, OG12X, OG12	uc003fbs.3	O60902	OTTHUMG00000158755	ENST00000425436.3:c.477delT	chr3.hg19:g.157820545delA	ENSP00000398704:p.Phe159fs	212.0	0.0		230.0	14.0	NM_003030	O60465|O60467|O60903	Frame_Shift_Del	DEL	ENST00000425436.3	hg19	CCDS43164.1																																																																																			.	.		0.582	SHOX2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352057.2		
ZCWPW1	55063	hgsc.bcm.edu	37	7	99998706	99998706	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:99998706delC	ENST00000398027.2	-	18	2125	c.1878delG	c.(1876-1878)gggfs	p.G626fs	ZCWPW1_ENST00000324725.6_Frame_Shift_Del_p.G455fs|ZCWPW1_ENST00000490721.1_Frame_Shift_Del_p.G455fs|ZCWPW1_ENST00000360951.4_3'UTR	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	626							zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CCCCGCTCTGCCCCAGCTCTC	0.607																																					p.Q627fs		Atlas-INDEL	.											.	ZCWPW1	41	.	0			c.1879delC						.						48.0	52.0	51.0					7																	99998706		2054	4204	6258	SO:0001589	frameshift_variant	55063	exon18			.	AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"""zinc finger, CW-type with PWWP domain 1"""			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.1878delG	chr7.hg19:g.99998706delC	ENSP00000381109:p.Gly626fs	95.0	0.0		207.0	13.0	NM_017984	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Frame_Shift_Del	DEL	ENST00000398027.2	hg19	CCDS43623.1																																																																																			.	.		0.607	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984	
LACE1	246269	hgsc.bcm.edu	37	6	108668193	108668193	+	Splice_Site	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:108668193delT	ENST00000368977.4	+	3	551	c.365delT	c.(364-366)ctt>ct	p.L122fs		NM_145315.3	NP_660358.2	Q8WV93	LACE1_HUMAN	lactation elevated 1	122						mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.S124fs*55(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)		AATTTGCAGCTTTTTTCAAGG	0.343																																					p.L122fs		Atlas-INDEL	.											.,1	LACE1	30	.	1	Insertion - Frameshift(1)	upper_aerodigestive_tract(1)	c.364delC						.						103.0	105.0	104.0					6																	108668193		2203	4300	6503	SO:0001630	splice_region_variant	246269	exon3			.	AF520418	CCDS5067.1	6q22.1	2006-11-10			ENSG00000135537	ENSG00000135537			16411	protein-coding gene	gene with protein product	"""ATPase family gene 1 homolog (S. cerevisiae)"""					12079282	Standard	XM_005266885		Approved	AFG1	uc003psj.3	Q8WV93	OTTHUMG00000015324	ENST00000368977.4:c.364-1T>-	chr6.hg19:g.108668193delT		124.0	0.0		142.0	10.0	NM_145315	Q8N6A3	Frame_Shift_Del	DEL	ENST00000368977.4	hg19	CCDS5067.1																																																																																			.	.		0.343	LACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041719.4	NM_145315	Frame_Shift_Del
ZFP64	55734	hgsc.bcm.edu	37	20	50713933	50713933	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:50713933delG	ENST00000361387.2	-	7	1015	c.955delC	c.(955-957)cgcfs	p.R319fs	ZFP64_ENST00000371523.4_Frame_Shift_Del_p.R100fs|ZFP64_ENST00000371518.2_Frame_Shift_Del_p.R319fs|ZFP64_ENST00000477786.1_5'UTR	NM_199427.2	NP_955459.2	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	276					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CTGAGATGGCGGTCCAAGTCT	0.408																																					p.R319fs		Atlas-INDEL	.											.	ZFP64	240	.	0			c.956delG						.						267.0	266.0	267.0					20																	50713933		2203	4300	6503	SO:0001589	frameshift_variant	55734	exon7			.	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000361387.2:c.955delC	chr20.hg19:g.50713933delG	ENSP00000355179:p.Arg319fs	131.0	0.0		179.0	11.0	NM_199427	Q9NTS7|Q9NVH4	Frame_Shift_Del	DEL	ENST00000361387.2	hg19	CCDS13439.1																																																																																			.	.		0.408	ZFP64-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079743.2	NM_018197	
PNPLA7	375775	hgsc.bcm.edu	37	9	140356679	140356679	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:140356679delG	ENST00000277531.4	-	30	3708	c.3522delC	c.(3520-3522)cccfs	p.P1174fs	NSMF_ENST00000392812.4_5'Flank|NSMF_ENST00000265663.7_5'Flank|NSMF_ENST00000371473.3_5'Flank|PNPLA7_ENST00000371457.1_Frame_Shift_Del_p.P780fs|NSMF_ENST00000371475.3_5'Flank|PNPLA7_ENST00000406427.1_Frame_Shift_Del_p.P1199fs|NSMF_ENST00000371474.3_5'Flank|PNPLA7_ENST00000492278.1_5'UTR|NSMF_ENST00000371472.2_5'Flank|NSMF_ENST00000437259.1_5'Flank	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	1174					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		AGCTGTCGATGGGGGGGCGCA	0.652																																					p.I1200fs		Atlas-INDEL	.											.	PNPLA7	124	.	0			c.3598delA						.						46.0	43.0	44.0					9																	140356679		2203	4298	6501	SO:0001589	frameshift_variant	375775	exon31			.	AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"""Patatin-like phospholipase domain containing"""	24768	protein-coding gene	gene with protein product		612122	"""chromosome 9 open reading frame 111"""	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.3522delC	chr9.hg19:g.140356679delG	ENSP00000277531:p.Pro1174fs	165.0	0.0		166.0	10.0	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Frame_Shift_Del	DEL	ENST00000277531.4	hg19	CCDS7045.1																																																																																			.	.		0.652	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
EIF4G3	8672	hgsc.bcm.edu	37	1	21306905	21306905	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:21306905delG	ENST00000264211.8	-	4	441	c.247delC	c.(247-249)caafs	p.Q84fs	EIF4G3_ENST00000356916.3_Frame_Shift_Del_p.Q95fs|EIF4G3_ENST00000374935.3_Frame_Shift_Del_p.Q84fs|EIF4G3_ENST00000374937.3_Frame_Shift_Del_p.Q91fs|EIF4G3_ENST00000400422.1_Frame_Shift_Del_p.Q84fs|EIF4G3_ENST00000602326.1_Frame_Shift_Del_p.Q91fs|EIF4G3_ENST00000374927.4_Frame_Shift_Del_p.Q84fs	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	84					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	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)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		GGATATTGTTGGGGGGGCCCA	0.443																																					p.Q94fs		Atlas-INDEL	.											.	EIF4G3	300	.	0			c.281delA						.						23.0	27.0	26.0					1																	21306905		2203	4300	6503	SO:0001589	frameshift_variant	8672	exon10			.	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.247delC	chr1.hg19:g.21306905delG	ENSP00000264211:p.Gln84fs	117.0	0.0		192.0	12.0	NM_001198803	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Frame_Shift_Del	DEL	ENST00000264211.8	hg19	CCDS214.1																																																																																			.	.		0.443	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760	
PCDHA7	56141	hgsc.bcm.edu	37	5	140214086	140214086	+	Frame_Shift_Del	DEL	A	A	-	rs532311058		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:140214086delA	ENST00000525929.1	+	1	118	c.118delA	c.(118-120)aaafs	p.K40fs	PCDHA7_ENST00000378125.3_Frame_Shift_Del_p.K40fs|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	40	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGAGGAGGCTAAACATGGCAA	0.622																																					p.A39fs	NSCLC(160;258 2013 5070 22440 28951)	Atlas-INDEL	.											.	PCDHA7	367	.	0			c.117delT						.						58.0	71.0	66.0					5																	140214086		2203	4300	6503	SO:0001589	frameshift_variant	56141	exon1			.	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"""Cadherins / Protocadherins : Clustered"""	8673	other	complex locus constituent	"""KIAA0345-like 7"", ""ortholog to mouse CNR4"""	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.118delA	chr5.hg19:g.140214086delA	ENSP00000436426:p.Lys40fs	155.0	0.0		182.0	11.0	NM_031852	O75282	Frame_Shift_Del	DEL	ENST00000525929.1	hg19	CCDS54918.1																																																																																			.	.		0.622	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910	
UTP15	84135	hgsc.bcm.edu	37	5	72874641	72874641	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:72874641delT	ENST00000296792.4	+	10	1365	c.1110delT	c.(1108-1110)catfs	p.H370fs	UTP15_ENST00000508491.1_Frame_Shift_Del_p.H351fs|UTP15_ENST00000543251.1_Frame_Shift_Del_p.H180fs	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	370					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		ATCTGAAACATTTTCGGATCT	0.358																																					p.H370fs		Atlas-INDEL	.											.	UTP15	30	.	0			c.1109delA						.						120.0	123.0	122.0					5																	72874641		2203	4300	6503	SO:0001589	frameshift_variant	84135	exon10			.	AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"""WD repeat domain containing"""	25758	protein-coding gene	gene with protein product			"""UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"""			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.1110delT	chr5.hg19:g.72874641delT	ENSP00000296792:p.His370fs	128.0	0.0		147.0	10.0	NM_032175	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Frame_Shift_Del	DEL	ENST00000296792.4	hg19	CCDS34186.1																																																																																			.	.		0.358	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175	
ATG4C	84938	hgsc.bcm.edu	37	1	63284957	63284957	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:63284957delA	ENST00000317868.4	+	5	883	c.676delA	c.(676-678)aaafs	p.K227fs	ATG4C_ENST00000371120.3_Frame_Shift_Del_p.K227fs	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	227					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|protein targeting to membrane (GO:0006612)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)		ATG4C/FBXO38(2)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(3)|ovary(1)|prostate(2)	19						GAAGTCTGGGAAAAAAGCAGG	0.368																																					p.G225fs		Atlas-INDEL	.											.	ATG4C	96	.	0			c.675delG						.						86.0	86.0	86.0					1																	63284957		2203	4300	6503	SO:0001589	frameshift_variant	84938	exon5			.	AK027773	CCDS623.1	1p31.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000125703	ENSG00000125703			16040	protein-coding gene	gene with protein product		611339	"""AUT (S. cerevisiae)-like 1, cysteine endopeptidase; AUT-like 1, cysteine endopeptidase (S. cerevisiae)"", ""APG4 autophagy 4 homolog C (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog C (S. cerevisiae)"""	AUTL1, APG4C		12446702	Standard	NM_032852		Approved	FLJ14867, AUTL3	uc001dau.3	Q96DT6	OTTHUMG00000009142	ENST00000317868.4:c.676delA	chr1.hg19:g.63284957delA	ENSP00000322159:p.Lys227fs	157.0	0.0		177.0	11.0	NM_178221	A6NLR8|D3DQ58|Q96K04	Frame_Shift_Del	DEL	ENST00000317868.4	hg19	CCDS623.1																																																																																			.	.		0.368	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852	
SARDH	1757	hgsc.bcm.edu	37	9	136559454	136559454	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:136559454delC	ENST00000371872.4	-	15	2104	c.1847delG	c.(1846-1848)ggcfs	p.G616fs	SARDH_ENST00000371868.1_Frame_Shift_Del_p.G44fs|SARDH_ENST00000439388.1_Frame_Shift_Del_p.G616fs|SARDH_ENST00000422262.2_Frame_Shift_Del_p.G448fs	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	616					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		ACTCTCGGTGCCCCCACGGTG	0.677																																					p.G616fs		Atlas-INDEL	.											.	SARDH	112	.	0			c.1848delC						.						41.0	33.0	36.0					9																	136559454		1923	3716	5639	SO:0001589	frameshift_variant	1757	exon15			.		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1847delG	chr9.hg19:g.136559454delC	ENSP00000360938:p.Gly616fs	225.0	0.0		273.0	17.0	NM_001134707	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Frame_Shift_Del	DEL	ENST00000371872.4	hg19	CCDS6978.1																																																																																			.	.		0.677	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
DYNC1LI1	51143	hgsc.bcm.edu	37	3	32611883	32611883	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:32611883delG	ENST00000273130.4	-	2	278	c.175delC	c.(175-177)cgcfs	p.R59fs	DYNC1LI1_ENST00000432458.2_Frame_Shift_Del_p.R59fs	NM_016141.3	NP_057225.2	Q9Y6G9	DC1L1_HUMAN	dynein, cytoplasmic 1, light intermediate chain 1	59					microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(1)|lung(3)|ovary(1)	7						GAGCGCGAGCGGGTGGAGACC	0.731																																					p.R59fs		Atlas-INDEL	.											.	DYNC1LI1	23	.	0			c.176delG						.						23.0	23.0	23.0					3																	32611883		2195	4294	6489	SO:0001589	frameshift_variant	51143	exon2			.	AF078849	CCDS2654.1	3p23	2013-01-18	2005-11-25	2005-11-25	ENSG00000144635	ENSG00000144635		"""Cytoplasmic dyneins"""	18745	protein-coding gene	gene with protein product		615890	"""dynein, cytoplasmic, light intermediate polypeptide 1"""	DNCLI1		16260502	Standard	NM_016141		Approved		uc003cfb.4	Q9Y6G9	OTTHUMG00000130750	ENST00000273130.4:c.175delC	chr3.hg19:g.32611883delG	ENSP00000273130:p.Arg59fs	135.0	0.0		180.0	11.0	NM_016141	A2RRG7|Q53HC8|Q53HK7	Frame_Shift_Del	DEL	ENST00000273130.4	hg19	CCDS2654.1																																																																																			.	.		0.731	DYNC1LI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253250.1	NM_016141	
UTP11L	51118	hgsc.bcm.edu	37	1	38483393	38483393	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:38483393delA	ENST00000373014.4	+	3	240	c.179delA	c.(178-180)gaafs	p.E60fs	UTP11L_ENST00000488453.1_3'UTR|UTP11L_ENST00000537711.1_Frame_Shift_Del_p.E60fs	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	136.0	0.0		188.0	15.0	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	
OR2L5	81466	hgsc.bcm.edu	37	1	248186140	248186140	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:248186140delG	ENST00000355281.1	+	1	891	c.891delG	c.(889-891)atgfs	p.M297fs	OR2L13_ENST00000366478.2_Intron	NM_001258284.1	NP_001245213.1	Q8NG80	OR2L5_HUMAN	olfactory receptor, family 2, subfamily L, member 5	297						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)										AGGAGGTGATGGGGGCCCTGA	0.478																																					p.M297fs		Atlas-INDEL	.											.	.	.	.	0			c.890delT						.																																			SO:0001589	frameshift_variant	81466	exon1			.		CCDS58068.1	1q44	2012-08-09		2004-03-10	ENSG00000197454	ENSG00000197454		"""GPCR / Class A : Olfactory receptors"""	15011	protein-coding gene	gene with protein product				OR2L11, OR2L5P			Standard	NM_001258284		Approved		uc031psy.1	Q8NG80	OTTHUMG00000040194	ENST00000355281.1:c.891delG	chr1.hg19:g.248186140delG	ENSP00000347428:p.Met297fs	108.0	0.0		162.0	12.0	NM_001258284	Q6IF04	Frame_Shift_Del	DEL	ENST00000355281.1	hg19	CCDS58068.1																																																																																			.	.		0.478	OR2L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096851.1		
CLIP4	79745	hgsc.bcm.edu	37	2	29383293	29383293	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:29383293delG	ENST00000320081.5	+	12	1749	c.1494delG	c.(1492-1494)ctgfs	p.L498fs	CLIP4_ENST00000401617.2_Frame_Shift_Del_p.L391fs|CLIP4_ENST00000401605.1_Frame_Shift_Del_p.L498fs|CLIP4_ENST00000404424.1_Frame_Shift_Del_p.L498fs	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	498										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					GACAGAGACTGGGCACCATTA	0.423																																					p.L498fs		Atlas-INDEL	.											.	CLIP4	69	.	0			c.1493delT						.						121.0	113.0	116.0					2																	29383293		2203	4300	6503	SO:0001589	frameshift_variant	79745	exon12			.	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"""Ankyrin repeat domain containing"""	26108	protein-coding gene	gene with protein product			"""restin-like 2"""	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.1494delG	chr2.hg19:g.29383293delG	ENSP00000327009:p.Leu498fs	133.0	0.0		166.0	11.0	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Frame_Shift_Del	DEL	ENST00000320081.5	hg19	CCDS1770.1																																																																																			.	.		0.423	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692	
JAKMIP2	9832	hgsc.bcm.edu	37	5	147021317	147021317	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:147021317delT	ENST00000265272.5	-	8	1702	c.1235delA	c.(1234-1236)aagfs	p.K412fs	JAKMIP2_ENST00000333010.6_Frame_Shift_Del_p.K370fs|JAKMIP2_ENST00000507386.1_Frame_Shift_Del_p.K412fs	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	412						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGGATGAGCTTTTCTCGGTC	0.378																																					p.K412fs		Atlas-INDEL	.											.	JAKMIP2	154	.	0			c.1236delG						.						166.0	158.0	161.0					5																	147021317		2203	4300	6503	SO:0001589	frameshift_variant	9832	exon8			.	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.1235delA	chr5.hg19:g.147021317delT	ENSP00000265272:p.Lys412fs	148.0	0.0		175.0	12.0	NM_001270934	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Frame_Shift_Del	DEL	ENST00000265272.5	hg19	CCDS4285.1																																																																																			.	.		0.378	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	
RPRD1B	58490	hgsc.bcm.edu	37	20	36676769	36676769	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:36676769delA	ENST00000373433.4	+	3	703	c.301delA	c.(301-303)aaafs	p.K102fs		NM_021215.3	NP_067038.1	Q9NQG5	RPR1B_HUMAN	regulation of nuclear pre-mRNA domain containing 1B	102	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.				dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle process (GO:0010564)|transcription, DNA-templated (GO:0006351)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)	12						TGAAGGCTGTAAAAAACCTTT	0.388																																					p.C100X		Atlas-INDEL	.											.	RPRD1B	25	.	0			c.300delT						.						96.0	82.0	87.0					20																	36676769		2203	4300	6503	SO:0001589	frameshift_variant	58490	exon3			.	AL109823	CCDS13301.1	20q11.21-q12	2012-02-09	2008-08-15	2008-07-28	ENSG00000101413	ENSG00000101413			16209	protein-coding gene	gene with protein product		614694	"""chromosome 20 open reading frame 77"""	C20orf77		22231121	Standard	NM_021215		Approved	dJ1057B20.2, DKFZp434P0735, CREPT, FLJ44520, NET60	uc002xho.4	Q9NQG5	OTTHUMG00000032434	ENST00000373433.4:c.301delA	chr20.hg19:g.36676769delA	ENSP00000362532:p.Lys102fs	157.0	0.0		155.0	12.0	NM_021215	Q1WDE7|Q6PKF4	Frame_Shift_Del	DEL	ENST00000373433.4	hg19	CCDS13301.1																																																																																			.	.		0.388	RPRD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079142.2	NM_021215	
DEPDC7	91614	hgsc.bcm.edu	37	11	33050250	33050250	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:33050250delA	ENST00000241051.3	+	4	786	c.694delA	c.(694-696)aaafs	p.K232fs	DEPDC7_ENST00000311388.3_Frame_Shift_Del_p.K223fs	NM_001077242.1	NP_001070710.1	Q96QD5	DEPD7_HUMAN	DEP domain containing 7	232					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17						GGCTGTACCTAAAATTCCTCA	0.428																																					p.P231fs		Atlas-INDEL	.											.	DEPDC7	94	.	0			c.693delT						.						106.0	101.0	103.0					11																	33050250		1922	4140	6062	SO:0001589	frameshift_variant	91614	exon4			.		CCDS41632.1, CCDS41633.1	11p13	2006-03-24			ENSG00000121690	ENSG00000121690			29899	protein-coding gene	gene with protein product		612294				10568747	Standard	NM_001077242		Approved		uc001mub.3	Q96QD5	OTTHUMG00000166242	ENST00000241051.3:c.694delA	chr11.hg19:g.33050250delA	ENSP00000241051:p.Lys232fs	132.0	0.0		166.0	10.0	NM_001077242	G5E941|Q8N602|Q8NCU9|Q9UGK5	Frame_Shift_Del	DEL	ENST00000241051.3	hg19	CCDS41632.1																																																																																			.	.		0.428	DEPDC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388655.1	NM_139160	
ESYT1	23344	hgsc.bcm.edu	37	12	56525317	56525317	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:56525317delG	ENST00000394048.5	+	6	1035	c.771delG	c.(769-771)gtgfs	p.V257fs	ESYT1_ENST00000267113.4_Frame_Shift_Del_p.V257fs|RP11-603J24.5_ENST00000550947.1_RNA|ESYT1_ENST00000541590.1_Frame_Shift_Del_p.V257fs|RP11-603J24.5_ENST00000549438.1_RNA	NM_001184796.1|NM_015292.2	NP_001171725.1|NP_056107.1	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	257	Glycerophospholipid-binding barrel-like domain. {ECO:0000250}.				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						TTCCCTTCGTGGGGGCTGTGT	0.537																																					p.V257fs		Atlas-INDEL	.											.	ESYT1	84	.	0			c.770delT						.						160.0	164.0	162.0					12																	56525317		2203	4300	6503	SO:0001589	frameshift_variant	23344	exon6			.	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.771delG	chr12.hg19:g.56525317delG	ENSP00000377612:p.Val257fs	168.0	0.0		193.0	12.0	NM_015292	A0FGR7|A8K2S2|O94848|Q6PJN4|Q9H6J1|Q9H6W2|Q9Y416	Frame_Shift_Del	DEL	ENST00000394048.5	hg19	CCDS8904.1																																																																																			.	.		0.537	ESYT1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407906.1	NM_015292	
PGAP1	80055	hgsc.bcm.edu	37	2	197737220	197737220	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:197737220delT	ENST00000354764.4	-	18	1787	c.1673delA	c.(1672-1674)aacfs	p.N559fs	PGAP1_ENST00000409475.1_Frame_Shift_Del_p.N559fs	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	559					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						ATGGGTATTGTTTTCTGGTTG	0.333																																					p.N558fs		Atlas-INDEL	.											.	PGAP1	84	.	0			c.1674delC						.						101.0	101.0	101.0					2																	197737220		2203	4300	6503	SO:0001589	frameshift_variant	80055	exon18			.		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"""GPI inositol-deacylase"""	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.1673delA	chr2.hg19:g.197737220delT	ENSP00000346809:p.Asn559fs	138.0	0.0		171.0	11.0	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Frame_Shift_Del	DEL	ENST00000354764.4	hg19	CCDS2318.1																																																																																			.	.		0.333	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989	
CD97	976	hgsc.bcm.edu	37	19	14508727	14508727	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:14508727delC	ENST00000242786.5	+	8	879	c.799delC	c.(799-801)cccfs	p.P268fs	CD97_ENST00000357355.3_Frame_Shift_Del_p.P219fs|CD97_ENST00000358600.3_Frame_Shift_Del_p.P175fs	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	268					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CTGGACCCCGCCCCCTGGAGT	0.607																																					p.P266fs		Atlas-INDEL	.											.	CD97	86	.	0			c.798delG						.						6.0	9.0	8.0					19																	14508727		1874	3927	5801	SO:0001589	frameshift_variant	976	exon8			.		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	1711	protein-coding gene	gene with protein product	"""leukocyte antigen CD97"", ""seven-span transmembrane protein"", ""seven-transmembrane, heterodimeric receptor associated with inflammation"", ""seven transmembrane helix receptor"""	601211	"""CD97 antigen"""			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.799delC	chr19.hg19:g.14508727delC	ENSP00000242786:p.Pro268fs	149.0	0.0		197.0	13.0	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Frame_Shift_Del	DEL	ENST00000242786.5	hg19	CCDS32929.1																																																																																			.	.		0.607	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481	
MLKL	197259	hgsc.bcm.edu	37	16	74725195	74725195	+	Frame_Shift_Del	DEL	T	T	-	rs56247416	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:74725195delT	ENST00000308807.7	-	4	1165	c.702delA	c.(700-702)aaafs	p.K234fs	MLKL_ENST00000306247.7_Intron	NM_152649.2	NP_689862.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						CAGCCTGGAGTTTTTTGAATA	0.438																																					p.L235fs		Atlas-INDEL	.											.	MLKL	51	.	0			c.703delC						.						255.0	264.0	261.0					16																	74725195		2198	4300	6498	SO:0001589	frameshift_variant	197259	exon4			.	AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000308807.7:c.702delA	chr16.hg19:g.74725195delT	ENSP00000308351:p.Lys234fs	139.0	0.0		161.0	12.0	NM_152649		Frame_Shift_Del	DEL	ENST00000308807.7	hg19	CCDS32487.1																																																																																			.	.		0.438	MLKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436403.3	NM_152649	
ABI3BP	25890	hgsc.bcm.edu	37	3	100585744	100585744	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:100585744delT	ENST00000284322.5	-	10	1097	c.988delA	c.(988-990)atcfs	p.I330fs	ABI3BP_ENST00000495063.1_Frame_Shift_Del_p.I330fs|ABI3BP_ENST00000471714.1_Frame_Shift_Del_p.I330fs	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	330					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						CGTGCTGAGATTTTTTCAACC	0.368																																					p.I330fs		Atlas-INDEL	.											.	ABI3BP	305	.	0			c.989delT						.						113.0	104.0	107.0					3																	100585744		1832	4086	5918	SO:0001589	frameshift_variant	25890	exon10			.	AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"""Fibronectin type III domain containing"""	17265	protein-coding gene	gene with protein product	"""target of Nesh-SH3"""	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.988delA	chr3.hg19:g.100585744delT	ENSP00000284322:p.Ile330fs	136.0	0.0		147.0	11.0	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Frame_Shift_Del	DEL	ENST00000284322.5	hg19	CCDS46880.1																																																																																			.	.		0.368	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1		
EPHA3	2042	hgsc.bcm.edu	37	3	89259454	89259454	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:89259454delA	ENST00000336596.2	+	3	823	c.598delA	c.(598-600)aaafs	p.K201fs	EPHA3_ENST00000494014.1_Frame_Shift_Del_p.K201fs|EPHA3_ENST00000452448.2_Frame_Shift_Del_p.K201fs	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	201	Cys-rich.|Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				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)		AGTATACTTCAAAAAGTGCCC	0.448										TSP Lung(6;0.00050)																											p.F199fs		Atlas-INDEL	.											.	EPHA3	501	.	0			c.597delC						.						144.0	132.0	136.0					3																	89259454		2203	4300	6503	SO:0001589	frameshift_variant	2042	exon3			.	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.598delA	chr3.hg19:g.89259454delA	ENSP00000337451:p.Lys201fs	202.0	0.0		283.0	17.0	NM_005233	Q9H2V3|Q9H2V4	Frame_Shift_Del	DEL	ENST00000336596.2	hg19	CCDS2922.1																																																																																			.	.		0.448	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
ATP13A5	344905	hgsc.bcm.edu	37	3	193002803	193002803	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:193002803delA	ENST00000342358.4	-	27	3243	c.3126delT	c.(3124-3126)tttfs	p.F1042fs	ATP13A5_ENST00000495496.1_5'UTR	NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	1042						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		TGGTGGTCTCAAAACTTAAAA	0.388																																					p.E1043fs		Atlas-INDEL	.											.	ATP13A5	171	.	0			c.3127delG						.						123.0	128.0	127.0					3																	193002803		2203	4300	6503	SO:0001589	frameshift_variant	344905	exon27			.	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"""ATPases / P-type"""	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.3126delT	chr3.hg19:g.193002803delA	ENSP00000341942:p.Phe1042fs	153.0	0.0		190.0	12.0	NM_198505	Q6UWS4|Q6ZWL0	Frame_Shift_Del	DEL	ENST00000342358.4	hg19	CCDS33914.1																																																																																			.	.		0.388	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
SLC43A1	8501	hgsc.bcm.edu	37	11	57259093	57259093	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:57259093delT	ENST00000278426.3	-	10	1380	c.1025delA	c.(1024-1026)aatfs	p.N342fs	SLC43A1_ENST00000533515.1_5'UTR|SLC43A1_ENST00000528450.1_Frame_Shift_Del_p.N342fs	NM_003627.5	NP_003618.1			solute carrier family 43 (amino acid system L transporter), member 1											breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	19						TTGCTGTTCATTTGTCTCTGT	0.637											OREG0020651	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N342fs		Atlas-INDEL	.											.	SLC43A1	48	.	0			c.1026delT						.						135.0	117.0	123.0					11																	57259093		2201	4296	6497	SO:0001589	frameshift_variant	8501	exon10			.	AF045584	CCDS7958.1	11q12.1	2013-07-17	2013-07-17	2003-09-12	ENSG00000149150	ENSG00000149150		"""Solute carriers"""	9225	protein-coding gene	gene with protein product		603733	"""prostate cancer overexpressed gene 1"""	POV1		9255310, 9722952	Standard	NM_003627		Approved	R00504, PB39	uc001nkk.3	O75387	OTTHUMG00000167030	ENST00000278426.3:c.1025delA	chr11.hg19:g.57259093delT	ENSP00000278426:p.Asn342fs	130.0	0.0	1021	161.0	10.0	NM_001198810		Frame_Shift_Del	DEL	ENST00000278426.3	hg19	CCDS7958.1																																																																																			.	.		0.637	SLC43A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392541.1	NM_003627	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204419065	204419065	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:204419065delG	ENST00000367187.3	-	14	2703	c.2147delC	c.(2146-2148)ccafs	p.P717fs	PIK3C2B_ENST00000424712.2_Frame_Shift_Del_p.P717fs	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	717	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00041, ECO:0000255|PROSITE- ProRule:PRU00880}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			GCTCCCCGGTGGGGGGATGGG	0.617																																					p.P716fs		Atlas-INDEL	.											.	PIK3C2B	142	.	0			c.2148delA						.						25.0	28.0	27.0					1																	204419065		2203	4300	6503	SO:0001589	frameshift_variant	5287	exon14			.	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.2147delC	chr1.hg19:g.204419065delG	ENSP00000356155:p.Pro717fs	122.0	0.0		214.0	14.0	NM_002646	O95666|Q5SW99	Frame_Shift_Del	DEL	ENST00000367187.3	hg19	CCDS1446.1																																																																																			.	.		0.617	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
PARVA	55742	hgsc.bcm.edu	37	11	12499491	12499491	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:12499491delT	ENST00000550549.1	+	4	444	c.395delT	c.(394-396)cttfs	p.L132fs	PARVA_ENST00000334956.8_Frame_Shift_Del_p.L172fs|PARVA_ENST00000539723.1_Frame_Shift_Del_p.L132fs|PARVA_ENST00000538608.1_Frame_Shift_Del_p.L79fs			Q9NVD7	PARVA_HUMAN	parvin, alpha	132	CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|actin-mediated cell contraction (GO:0070252)|cell junction assembly (GO:0034329)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|heterotypic cell-cell adhesion (GO:0034113)|outflow tract septum morphogenesis (GO:0003148)|regulation of cell shape (GO:0008360)|smooth muscle cell chemotaxis (GO:0071670)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)	11				Epithelial(150;0.00624)		CTGCAGAAGCTTTTCGGTAGG	0.403																																					p.L172fs		Atlas-INDEL	.											.	PARVA	27	.	0			c.514delC						.						175.0	171.0	173.0					11																	12499491		1926	4126	6052	SO:0001589	frameshift_variant	55742	exon4			.	AF237771	CCDS44541.1, CCDS44541.2	11p15.3	2014-06-13	2005-05-26		ENSG00000197702	ENSG00000197702		"""Parvins"""	14652	protein-coding gene	gene with protein product		608120	"""matrix-remodelling associated 2"""	MXRA2		11171322	Standard	NM_018222		Approved	FLJ12254, FLJ10793	uc001mki.4	Q9NVD7	OTTHUMG00000165778	ENST00000550549.1:c.395delT	chr11.hg19:g.12499491delT	ENSP00000447198:p.Leu132fs	133.0	0.0		173.0	11.0	NM_018222	Q96C85|Q9HA48	Frame_Shift_Del	DEL	ENST00000550549.1	hg19																																																																																				.	.		0.403	PARVA-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018222	
JPH4	84502	hgsc.bcm.edu	37	14	24040276	24040276	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:24040276delG	ENST00000397118.3	-	6	2566	c.1664delC	c.(1663-1665)ccgfs	p.P555fs	RP11-66N24.3_ENST00000555968.1_RNA|JPH4_ENST00000544177.1_Frame_Shift_Del_p.P220fs|JPH4_ENST00000356300.4_Frame_Shift_Del_p.P555fs|AP1G2_ENST00000308724.5_5'Flank	NM_032452.2	NP_115828.2	Q96JJ6	JPH4_HUMAN	junctophilin 4	555					calcium ion transport into cytosol (GO:0060402)|learning (GO:0007612)|neuromuscular process controlling balance (GO:0050885)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic plasticity (GO:0048167)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)				endometrium(1)|large_intestine(2)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		GGCCCTCAGCGGGGGCAGGGG	0.677																																					p.P555fs		Atlas-INDEL	.											.	JPH4	64	.	0			c.1665delG						.						52.0	57.0	56.0					14																	24040276		2203	4300	6503	SO:0001589	frameshift_variant	84502	exon5			.	AB058734	CCDS9603.1	14q11	2004-05-28	2004-05-28	2004-05-28	ENSG00000092051	ENSG00000092051			20156	protein-coding gene	gene with protein product			"""junctophilin like 1"""	JPHL1		11347906	Standard	NM_032452		Approved	KIAA1831	uc001wkr.2	Q96JJ6	OTTHUMG00000028769	ENST00000397118.3:c.1664delC	chr14.hg19:g.24040276delG	ENSP00000380307:p.Pro555fs	127.0	0.0		167.0	11.0	NM_001146028	D3DS53|Q8ND44|Q96DQ0	Frame_Shift_Del	DEL	ENST00000397118.3	hg19	CCDS9603.1																																																																																			.	.		0.677	JPH4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413853.1	NM_032452	
UBR2	23304	hgsc.bcm.edu	37	6	42637938	42637938	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:42637938delA	ENST00000372899.1	+	35	4248	c.3990delA	c.(3988-3990)atafs	p.I1330fs	UBR2_ENST00000372883.3_3'UTR|UBR2_ENST00000372901.1_Frame_Shift_Del_p.I1330fs	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1330					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			GTGTTCCCATAATGTGTTGGG	0.418																																					p.I1330fs		Atlas-INDEL	.											.	UBR2	134	.	0			c.3989delT						.						147.0	124.0	132.0					6																	42637938		2203	4300	6503	SO:0001589	frameshift_variant	23304	exon35			.	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.3990delA	chr6.hg19:g.42637938delA	ENSP00000361990:p.Ile1330fs	136.0	0.0		155.0	10.0	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Frame_Shift_Del	DEL	ENST00000372899.1	hg19	CCDS4870.1																																																																																			.	.		0.418	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
PHYH	5264	hgsc.bcm.edu	37	10	13336580	13336580	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:13336580delT	ENST00000263038.4	-	4	320	c.262delA	c.(262-264)atcfs	p.I88fs	PHYH_ENST00000396920.3_Frame_Shift_Del_p.I69fs|PHYH_ENST00000396913.2_5'UTR	NM_006214.3	NP_006205.1	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase	88					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|isoprenoid metabolic process (GO:0006720)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|electron carrier activity (GO:0009055)|L-ascorbic acid binding (GO:0031418)|metal ion binding (GO:0046872)|phytanoyl-CoA dioxygenase activity (GO:0048244)			NS(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	25		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	TTTCTGCAGATTTTTTCAAAC	0.433																																					p.I88fs		Atlas-INDEL	.											.	PHYH	50	.	0			c.263delT						.						112.0	103.0	106.0					10																	13336580		2203	4300	6503	SO:0001589	frameshift_variant	5264	exon4			.		CCDS7097.1, CCDS41489.1	10p13	2010-04-27	2006-01-09		ENSG00000107537	ENSG00000107537	1.14.11.18		8940	protein-coding gene	gene with protein product	"""Refsum disease"", ""phytanoyl-CoA dioxygenase"""	602026	"""phytanoyl-CoA hydroxylase (Refsum disease)"", ""phytanoyl-CoA hydroxylase"""			9326939	Standard	XM_005252469		Approved	PAHX, RD, PHYH1	uc001imf.3	O14832	OTTHUMG00000017693	ENST00000263038.4:c.262delA	chr10.hg19:g.13336580delT	ENSP00000263038:p.Ile88fs	157.0	0.0		166.0	10.0	NM_006214	A8MTS8|B1ALH5	Frame_Shift_Del	DEL	ENST00000263038.4	hg19	CCDS7097.1																																																																																			.	.		0.433	PHYH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046845.2		
TUB	7275	hgsc.bcm.edu	37	11	8117161	8117161	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:8117161delG	ENST00000299506.2	+	5	663	c.514delG	c.(514-516)gggfs	p.G173fs	TUB_ENST00000534099.1_Frame_Shift_Del_p.G179fs|TUB_ENST00000305253.4_Frame_Shift_Del_p.G228fs	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	173					multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403)			breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		GGCAGCTGGTGGGGGCGAACG	0.642																																					p.G226fs		Atlas-INDEL	.											.	TUB	71	.	0			c.678delT						.						22.0	24.0	23.0					11																	8117161		2197	4292	6489	SO:0001589	frameshift_variant	7275	exon6			.	U54644	CCDS7786.1, CCDS7787.1	11p15.5	2013-08-06	2013-08-06		ENSG00000166402	ENSG00000166402			12406	protein-coding gene	gene with protein product		601197	"""tubby (mouse) homolog"", ""tubby homolog (mouse)"""			8612280	Standard	NM_003320		Approved	rd5	uc001mfy.3	P50607	OTTHUMG00000165690	ENST00000299506.2:c.514delG	chr11.hg19:g.8117161delG	ENSP00000299506:p.Gly173fs	174.0	0.0		216.0	13.0	NM_003320	D3DQU4|O00293|Q6B007	Frame_Shift_Del	DEL	ENST00000299506.2	hg19	CCDS7787.1																																																																																			.	.		0.642	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	NM_003320	
YTHDC2	64848	hgsc.bcm.edu	37	5	112917159	112917159	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:112917159delT	ENST00000161863.4	+	25	3613	c.3400delT	c.(3400-3402)tttfs	p.F1134fs		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1134					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GCATAGCTTATTTTTACGCCG	0.388																																					p.L1133fs		Atlas-INDEL	.											.	YTHDC2	118	.	0			c.3399delA						.						110.0	104.0	106.0					5																	112917159		2202	4300	6502	SO:0001589	frameshift_variant	64848	exon25			.	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.3400delT	chr5.hg19:g.112917159delT	ENSP00000161863:p.Phe1134fs	178.0	0.0		246.0	15.0	NM_022828	B2RP66	Frame_Shift_Del	DEL	ENST00000161863.4	hg19	CCDS4113.1																																																																																			.	.		0.388	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
VASH2	79805	hgsc.bcm.edu	37	1	213146180	213146180	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:213146180delC	ENST00000517399.1	+	5	756	c.756delC	c.(754-756)gtcfs	p.V252fs	VASH2_ENST00000366965.2_Frame_Shift_Del_p.V208fs|VASH2_ENST00000366966.2_Frame_Shift_Del_p.V187fs|VASH2_ENST00000366968.4_Frame_Shift_Del_p.V187fs|VASH2_ENST00000366967.2_Frame_Shift_Del_p.V148fs|VASH2_ENST00000366964.3_Frame_Shift_Del_p.V110fs|VASH2_ENST00000271776.4_3'UTR			Q86V25	VASH2_HUMAN	vasohibin 2	252					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)	cytoplasm (GO:0005737)				endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(81;0.00479)|all cancers(67;0.00844)|GBM - Glioblastoma multiforme(131;0.0496)|Epithelial(68;0.0986)		GGCTGTACGTCCCCCATGAGC	0.488																																					p.V208fs		Atlas-INDEL	.											.	VASH2	55	.	0			c.623delT						.						112.0	100.0	104.0					1																	213146180		2203	4300	6503	SO:0001589	frameshift_variant	79805	exon4			.	AK022567	CCDS1511.1, CCDS44315.1, CCDS44316.1, CCDS73026.1	1q23	2008-02-05			ENSG00000143494	ENSG00000143494			25723	protein-coding gene	gene with protein product		610471				16528006	Standard	XR_247041		Approved	FLJ12505	uc001hjw.3	Q86V25	OTTHUMG00000036925	ENST00000517399.1:c.756delC	chr1.hg19:g.213146180delC	ENSP00000428324:p.Val252fs	153.0	0.0		243.0	17.0	NM_024749	B4DYZ5|Q2VT46|Q5VTE7|Q5VTE9|Q7Z6E3|Q8IZ24|Q9H9W5	Frame_Shift_Del	DEL	ENST00000517399.1	hg19	CCDS1511.1																																																																																			.	.		0.488	VASH2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381686.1	NM_024749	
RGS11	8786	hgsc.bcm.edu	37	16	323531	323531	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:323531delC	ENST00000397770.3	-	8	549	c.532delG	c.(532-534)gacfs	p.D178fs	RGS11_ENST00000359740.5_Frame_Shift_Del_p.D167fs|RGS11_ENST00000316163.5_Frame_Shift_Del_p.D157fs|RGS11_ENST00000397768.3_Frame_Shift_Del_p.D178fs			O94810	RGS11_HUMAN	regulator of G-protein signaling 11	178					G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|lung(4)|ovary(1)|pancreas(1)	8		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				ACCAGCCTGTCCCCCTTGCTG	0.711																																					p.D178fs		Atlas-INDEL	.											.	RGS11	29	.	0			c.533delA						.						27.0	24.0	25.0					16																	323531		2156	4260	6416	SO:0001589	frameshift_variant	8786	exon8			.	AF035153	CCDS10403.1, CCDS42088.1, CCDS66884.1	16p13.3	2008-07-28	2007-08-14		ENSG00000076344	ENSG00000076344		"""Regulators of G-protein signaling"""	9993	protein-coding gene	gene with protein product		603895	"""regulator of G-protein signalling 11"""			9789084	Standard	NM_001286486		Approved		uc002cgj.1	O94810	OTTHUMG00000064893	ENST00000397770.3:c.532delG	chr16.hg19:g.323531delC	ENSP00000380876:p.Asp178fs	201.0	0.0		197.0	13.0	NM_183337	O75883|Q4TT71|Q4TT72	Frame_Shift_Del	DEL	ENST00000397770.3	hg19	CCDS42088.1																																																																																			.	.		0.711	RGS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139325.2		
SENP7	57337	hgsc.bcm.edu	37	3	101090875	101090875	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:101090875delA	ENST00000394095.2	-	7	826	c.773delT	c.(772-774)ttafs	p.L258fs	SENP7_ENST00000314261.7_Frame_Shift_Del_p.L192fs|SENP7_ENST00000348610.3_Frame_Shift_Del_p.L225fs|SENP7_ENST00000394094.2_Frame_Shift_Del_p.L193fs|SENP7_ENST00000394091.1_Frame_Shift_Del_p.L94fs|SENP7_ENST00000358203.3_Frame_Shift_Del_p.L94fs	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	258						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						ATCAGATATTAAAAGAGAAAT	0.323																																					p.L258fs		Atlas-INDEL	.											.	SENP7	170	.	0			c.774delA						.						97.0	93.0	95.0					3																	101090875		2203	4300	6503	SO:0001589	frameshift_variant	57337	exon7			.		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"""SUMO1/sentrin specific protease 7"""			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.773delT	chr3.hg19:g.101090875delA	ENSP00000377655:p.Leu258fs	109.0	0.0		166.0	10.0	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Frame_Shift_Del	DEL	ENST00000394095.2	hg19	CCDS2941.2																																																																																			.	.		0.323	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
ZNF330	27309	hgsc.bcm.edu	37	4	142154925	142154925	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:142154925delG	ENST00000262990.4	+	10	973	c.745delG	c.(745-747)gggfs	p.G249fs	ZNF330_ENST00000421169.2_Frame_Shift_Del_p.G189fs	NM_014487.4	NP_055302.1	Q9Y3S2	ZN330_HUMAN	zinc finger protein 330	249						chromosome, centromeric region (GO:0000775)|midbody (GO:0030496)|nucleolus (GO:0005730)	metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	14	all_hematologic(180;0.162)					TGGAGCTTCTGGGTATGATGC	0.453																																					p.S248fs		Atlas-INDEL	.											.	ZNF330	31	.	0			c.744delT						.						131.0	120.0	123.0					4																	142154925		2203	4300	6503	SO:0001589	frameshift_variant	27309	exon10			.	AJ006591	CCDS3754.1	4q31.21	2008-05-15			ENSG00000109445	ENSG00000109445		"""Zinc fingers, C2H2-type"""	15462	protein-coding gene	gene with protein product		609550				11528117, 10593942	Standard	NM_001292002		Approved	NOA36, HSA6591	uc003iiq.4	Q9Y3S2	OTTHUMG00000133413	ENST00000262990.4:c.745delG	chr4.hg19:g.142154925delG	ENSP00000262990:p.Gly249fs	199.0	0.0		161.0	12.0	NM_014487	B2RDA3	Frame_Shift_Del	DEL	ENST00000262990.4	hg19	CCDS3754.1																																																																																			.	.		0.453	ZNF330-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257271.2	NM_014487	
GPCPD1	56261	hgsc.bcm.edu	37	20	5550794	5550794	+	Splice_Site	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:5550794delT	ENST00000379019.4	-	12	1360	c.1148delA	c.(1147-1149)aag>ag	p.K384fs	GPCPD1_ENST00000481038.1_5'UTR	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	384	GP-PDE.				glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)	glycerophosphocholine phosphodiesterase activity (GO:0047389)|starch binding (GO:2001070)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)	16						TCAACGTACCTTTTTCATAGT	0.303																																					p.K383fs		Atlas-INDEL	.											.	GPCPD1	52	.	0			c.1149delG						.						78.0	75.0	76.0					20																	5550794		2203	4300	6503	SO:0001630	splice_region_variant	56261	exon12			.		CCDS13090.1	20p12.3	2011-01-25			ENSG00000125772	ENSG00000125772			26957	protein-coding gene	gene with protein product		614124				10718198, 20576599	Standard	NM_019593		Approved	KIAA1434, GDE5, GDPD6	uc002wme.4	Q9NPB8	OTTHUMG00000031806	ENST00000379019.4:c.1149+1A>-	chr20.hg19:g.5550794delT		128.0	0.0		280.0	17.0	NM_019593	D3DW06|Q9BQL8|Q9NUX0	Frame_Shift_Del	DEL	ENST00000379019.4	hg19	CCDS13090.1																																																																																			.	.		0.303	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077869.1	NM_019593	Frame_Shift_Del
DDX12P	440081	hgsc.bcm.edu	37	12	9574420	9574420	+	IGR	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:9574420delA								RP13-735L24.1 (24207 upstream) : SNORA75 (23233 downstream)																							TCACCACAGGAAAACTCCACC	0.607																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.						22.0	19.0	20.0					12																	9574420		692	1577	2269	SO:0001628	intergenic_variant	440081	.			.																													chr12.hg19:g.9574420delA		222.0	0.0		258.0	16.0	.		RNA	DEL		hg19																																																																																				.	.	0	0.607								
RGS6	9628	hgsc.bcm.edu	37	14	72985093	72985093	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:72985093delC	ENST00000553530.1	+	15	1333	c.1126delC	c.(1126-1128)cccfs	p.P376fs	RGS6_ENST00000553525.1_Frame_Shift_Del_p.P376fs|RGS6_ENST00000554782.1_Frame_Shift_Del_p.P237fs|RGS6_ENST00000407322.4_Frame_Shift_Del_p.P376fs|RGS6_ENST00000404301.2_Frame_Shift_Del_p.P376fs|RGS6_ENST00000406236.4_Frame_Shift_Del_p.P376fs|RGS6_ENST00000402788.2_Frame_Shift_Del_p.P376fs|RGS6_ENST00000556437.1_Frame_Shift_Del_p.P376fs|RGS6_ENST00000555571.1_Frame_Shift_Del_p.P376fs|RGS6_ENST00000434263.2_Frame_Shift_Del_p.P307fs|RGS6_ENST00000355512.6_Frame_Shift_Del_p.P376fs|RGS6_ENST00000343854.6_Frame_Shift_Del_p.P339fs	NM_001204417.1|NM_001204418.1|NM_001204420.1|NM_001204421.1|NM_001204422.1|NM_004296.5	NP_001191346.1|NP_001191347.1|NP_001191349.1|NP_001191350.1|NP_001191351.1|NP_004287.3	P49758	RGS6_HUMAN	regulator of G-protein signaling 6	376	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neuron differentiation (GO:0045666)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		TAAGAAACAACCCCTACAGGA	0.522																																					p.Q375fs	Ovarian(143;1926 2468 21071 48641)	Atlas-INDEL	.											.	RGS6	92	.	0			c.1125delA						.						74.0	74.0	74.0					14																	72985093		2203	4300	6503	SO:0001589	frameshift_variant	9628	exon15			.	AF073920	CCDS9808.1, CCDS55924.1, CCDS73655.1	14q24.3	2008-07-28	2007-08-14			ENSG00000182732		"""Regulators of G-protein signaling"""	10002	protein-coding gene	gene with protein product		603894	"""regulator of G-protein signalling 6"""			10083744, 14734556	Standard	NM_004296		Approved		uc010ttn.2	P49758		ENST00000553530.1:c.1126delC	chr14.hg19:g.72985093delC	ENSP00000452331:p.Pro376fs	110.0	0.0		171.0	14.0	NM_001204424	C9JE95|F8W7W5|O75576|O75577|Q7Z4K3|Q7Z4K4|Q7Z4K5|Q7Z4K6|Q8TE13|Q8TE14|Q8TE15|Q8TE16|Q8TE17|Q8TE18|Q8TE19|Q8TE20|Q8TE21|Q8TE22|Q9UDS8|Q9UDT0|Q9Y245|Q9Y647	Frame_Shift_Del	DEL	ENST00000553530.1	hg19	CCDS9808.1																																																																																			.	.		0.522	RGS6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413033.2		
ENTPD5	957	hgsc.bcm.edu	37	14	74443074	74443074	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:74443074delC	ENST00000334696.6	-	9	914	c.595delG	c.(595-597)gacfs	p.D199fs	ENTPD5_ENST00000557325.1_Frame_Shift_Del_p.D199fs	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	199					'de novo' posttranslational protein folding (GO:0051084)|ATP metabolic process (GO:0046034)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|positive regulation of glycolytic process (GO:0045821)|protein N-linked glycosylation (GO:0006487)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	guanosine-diphosphatase activity (GO:0004382)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(234;0.00394)		CCCCCTAGGTCCAAGGTCCCC	0.537																																					p.D199fs		Atlas-INDEL	.											.	ENTPD5	26	.	0			c.596delA						.						103.0	88.0	93.0					14																	74443074		2203	4300	6503	SO:0001589	frameshift_variant	957	exon9			.	AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097			3367	protein-coding gene	gene with protein product		603162	"""proto-oncogene CPH"""	CD39L4, PCPH		9271669, 9676430	Standard	NM_001249		Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000334696.6:c.595delG	chr14.hg19:g.74443074delC	ENSP00000335246:p.Asp199fs	109.0	0.0		147.0	10.0	NM_001249	A1L4C5|Q96RX0	Frame_Shift_Del	DEL	ENST00000334696.6	hg19	CCDS9825.1																																																																																			.	.		0.537	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249	
PTS	5805	hgsc.bcm.edu	37	11	112101391	112101391	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:112101391delA	ENST00000280362.3	+	4	308	c.229delA	c.(229-231)aaafs	p.K78fs	PTS_ENST00000524931.1_Frame_Shift_Del_p.K10fs|PTS_ENST00000525803.1_Intron	NM_000317.2	NP_000308.1	Q03393	PTPS_HUMAN	6-pyruvoyltetrahydropterin synthase	78					cellular amino acid metabolic process (GO:0006520)|central nervous system development (GO:0007417)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)|tetrahydrobiopterin biosynthetic process (GO:0006729)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	6-pyruvoyltetrahydropterin synthase activity (GO:0003874)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(1)|large_intestine(1)	2		all_cancers(61;2.51e-14)|all_epithelial(67;1.64e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.27e-06)|BRCA - Breast invasive adenocarcinoma(274;1.43e-06)|all cancers(92;2.1e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0519)		GGCTGATCTCAAAAAATATAT	0.408																																					p.L76fs		Atlas-INDEL	.											.	PTS	7	.	0			c.228delC						.						180.0	183.0	182.0					11																	112101391		2201	4297	6498	SO:0001589	frameshift_variant	5805	exon4			.	U63382	CCDS8359.1	11q22.3	2014-04-01				ENSG00000150787	4.2.3.12		9689	protein-coding gene	gene with protein product		612719				8188266	Standard	NM_000317		Approved	PTPS	uc001pnj.4	Q03393		ENST00000280362.3:c.229delA	chr11.hg19:g.112101391delA	ENSP00000280362:p.Lys78fs	82.0	0.0		136.0	10.0	NM_000317	B0YJ87|Q8WVG8	Frame_Shift_Del	DEL	ENST00000280362.3	hg19	CCDS8359.1																																																																																			.	.		0.408	PTS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393541.1	NM_000317	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103158325	103158325	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:103158325delA	ENST00000375735.2	+	75	11230	c.11086delA	c.(11086-11088)aaafs	p.K3696fs	DYNC2H1_ENST00000398093.3_Frame_Shift_Del_p.K3703fs|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	3696	AAA 6. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TTTTGCATGTAAAACTCTGGG	0.333																																					p.C3702X		Atlas-INDEL	.											.	DYNC2H1	246	.	0			c.11106delT						.						90.0	87.0	88.0					11																	103158325		1848	4091	5939	SO:0001589	frameshift_variant	79659	exon76			.	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.11086delA	chr11.hg19:g.103158325delA	ENSP00000364887:p.Lys3696fs	185.0	0.0		230.0	15.0	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Frame_Shift_Del	DEL	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.333	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
INF2	64423	hgsc.bcm.edu	37	14	105174185	105174185	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:105174185delC	ENST00000392634.4	+	8	1693	c.1581delC	c.(1579-1581)agcfs	p.S527fs	INF2_ENST00000330634.7_Frame_Shift_Del_p.S527fs	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	527					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.V530fs*50(1)		large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		GCACCTGCAGCCCCCCCGTGG	0.716																																					p.S527fs		Atlas-Indel,Pindel	.											.,1	INF2	148	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1580delG						.						14.0	16.0	15.0					14																	105174185		1937	4086	6023	SO:0001589	frameshift_variant	64423	exon8			.	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.1581delC	chr14.hg19:g.105174185delC	ENSP00000376410:p.Ser527fs	128.0	0.0		144.0	13.0	NM_001031714	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Frame_Shift_Del	DEL	ENST00000392634.4	hg19	CCDS9989.2																																																																																			.	.		0.716	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489	
DMXL1	1657	hgsc.bcm.edu	37	5	118450216	118450216	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:118450216delT	ENST00000311085.8	+	6	624	c.544delT	c.(544-546)tttfs	p.F183fs	DMXL1_ENST00000539542.1_Frame_Shift_Del_p.F183fs	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	183										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		AGATGGAGAATTTTTTGCCAC	0.299																																					p.E181fs		Atlas-INDEL	.											.	DMXL1	268	.	0			c.543delA						.						53.0	55.0	54.0					5																	118450216		2197	4293	6490	SO:0001589	frameshift_variant	1657	exon6			.	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.544delT	chr5.hg19:g.118450216delT	ENSP00000309690:p.Phe183fs	220.0	0.0		275.0	17.0	NM_005509		Frame_Shift_Del	DEL	ENST00000311085.8	hg19	CCDS4125.1																																																																																			.	.		0.299	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
NPR1	4881	hgsc.bcm.edu	37	1	153654991	153654991	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:153654991delA	ENST00000368680.3	+	5	1661	c.1189delA	c.(1189-1191)aaafs	p.K397fs		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	397					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	AGGATACCTGAAAATTGATAG	0.483																																					p.L396fs	Pancreas(141;1349 1870 15144 15830 40702)	Atlas-INDEL	.											.	NPR1	104	.	0			c.1188delG						.						124.0	103.0	110.0					1																	153654991		2203	4300	6503	SO:0001589	frameshift_variant	4881	exon5			.	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"""guanylate cyclase A"""	108960	"""atrionatriuretic peptide receptor A"", ""natriuretic peptide receptor A"""	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.1189delA	chr1.hg19:g.153654991delA	ENSP00000357669:p.Lys397fs	77.0	0.0		182.0	11.0	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Frame_Shift_Del	DEL	ENST00000368680.3	hg19	CCDS1051.1																																																																																			.	.		0.483	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906	
SPEM1	374768	hgsc.bcm.edu	37	17	7324238	7324238	+	Frame_Shift_Del	DEL	C	C	-	rs377239691		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:7324238delC	ENST00000323675.3	+	3	269	c.244delC	c.(244-246)cccfs	p.P83fs	RP11-104H15.7_ENST00000575310.1_RNA	NM_199339.2	NP_955371.2	Q8N4L4	SPEM1_HUMAN	spermatid maturation 1	83					sperm individualization (GO:0007291)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	12		Prostate(122;0.173)				GCAGACCCAGCCCCCTAAGAA	0.597																																					p.Q81fs		Atlas-INDEL	.											.	SPEM1	41	.	0			c.243delG						.						121.0	129.0	126.0					17																	7324238		2045	4185	6230	SO:0001589	frameshift_variant	374768	exon3			.	AK097400	CCDS42254.1	17p13.1	2011-12-12	2008-02-04	2008-02-04	ENSG00000181323	ENSG00000181323			32429	protein-coding gene	gene with protein product		615116	"""chromosome 17 open reading frame 83"""	C17orf83		17426145, 20558241, 21184802	Standard	NM_199339		Approved	FLJ40081	uc002ggv.3	Q8N4L4		ENST00000323675.3:c.244delC	chr17.hg19:g.7324238delC	ENSP00000315554:p.Pro83fs	165.0	0.0		119.0	11.0	NM_199339		Frame_Shift_Del	DEL	ENST00000323675.3	hg19	CCDS42254.1																																																																																			.	.		0.597	SPEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440932.1	NM_199339	
RTTN	25914	hgsc.bcm.edu	37	18	67801730	67801730	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:67801730delA	ENST00000255674.6	-	23	3219	c.2933delT	c.(2932-2934)ttgfs	p.L978fs	RTTN_ENST00000437017.1_Frame_Shift_Del_p.L978fs|RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	978					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				GGAAACAGGCAAACTGAAGAC	0.323																																					p.L978fs		Atlas-INDEL	.											.	RTTN	184	.	0			c.2934delG						.						81.0	74.0	76.0					18																	67801730		1827	4073	5900	SO:0001589	frameshift_variant	25914	exon23			.	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.2933delT	chr18.hg19:g.67801730delA	ENSP00000255674:p.Leu978fs	119.0	0.0		142.0	10.0	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Frame_Shift_Del	DEL	ENST00000255674.6	hg19	CCDS42443.1																																																																																			.	.		0.323	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630	
HGS	9146	hgsc.bcm.edu	37	17	79660963	79660963	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:79660963delC	ENST00000329138.4	+	11	1039	c.904delC	c.(904-906)cccfs	p.P303fs		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	303	Interaction with SNX1. {ECO:0000250}.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141)	metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			CTCCTCAGCGCCCCCCGCCAG	0.652																																					p.A301fs		Atlas-INDEL	.											.	HGS	54	.	0			c.903delG						.						31.0	35.0	34.0					17																	79660963		2203	4300	6503	SO:0001589	frameshift_variant	9146	exon11			.	D84064	CCDS11784.1	17q25	2009-04-29				ENSG00000185359		"""Zinc fingers, FYVE domain containing"""	4897	protein-coding gene	gene with protein product		604375				9407053, 9630564	Standard	NM_004712		Approved	Hrs, ZFYVE8, Vps27	uc002kbg.3	O14964		ENST00000329138.4:c.904delC	chr17.hg19:g.79660963delC	ENSP00000331201:p.Pro303fs	117.0	0.0		158.0	10.0	NM_004712	Q9NR36	Frame_Shift_Del	DEL	ENST00000329138.4	hg19	CCDS11784.1																																																																																			.	.		0.652	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712	
CUL3	8452	hgsc.bcm.edu	37	2	225368413	225368413	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:225368413delT	ENST00000264414.4	-	9	1671	c.1333delA	c.(1333-1335)agtfs	p.S445fs	CUL3_ENST00000344951.4_Frame_Shift_Del_p.S379fs|CUL3_ENST00000409777.1_Frame_Shift_Del_p.S421fs|CUL3_ENST00000409096.1_Frame_Shift_Del_p.S421fs	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	445					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TCAGAAACACTTTTATTTGTG	0.313																																					p.S451fs		Atlas-INDEL	.											.	CUL3	96	.	0			c.1352delG						.						128.0	115.0	119.0					2																	225368413		2202	4299	6501	SO:0001589	frameshift_variant	8452	exon9			.	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.1333delA	chr2.hg19:g.225368413delT	ENSP00000264414:p.Ser445fs	128.0	0.0		154.0	10.0	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Frame_Shift_Del	DEL	ENST00000264414.4	hg19	CCDS2462.1																																																																																			.	.		0.313	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2		
PLCB1	23236	hgsc.bcm.edu	37	20	8130989	8130989	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:8130989delT	ENST00000338037.6	+	2	175	c.148delT	c.(148-150)tttfs	p.F52fs	PLCB1_ENST00000378641.3_Frame_Shift_Del_p.F52fs|PLCB1_ENST00000378637.2_Frame_Shift_Del_p.F52fs	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	52					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)	p.F50I(1)		NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						CCCTCAGGGATTTTTCTTTTA	0.308																																					p.L49fs		Atlas-INDEL	.											.	PLCB1	394	.	1	Substitution - Missense(1)	skin(1)	c.147delG						.						78.0	78.0	78.0					20																	8130989		2203	4292	6495	SO:0001589	frameshift_variant	23236	exon2			.	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.148delT	chr20.hg19:g.8130989delT	ENSP00000338185:p.Phe52fs	124.0	0.0		181.0	11.0	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Frame_Shift_Del	DEL	ENST00000338037.6	hg19	CCDS13102.1																																																																																			.	.		0.308	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		
EPB41L4A	64097	hgsc.bcm.edu	37	5	111545590	111545590	+	Splice_Site	DEL	T	T	-	rs34402942		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:111545590delT	ENST00000261486.5	-	13	1453	c.1177delA	c.(1177-1179)agc>gc	p.S393fs	EPB41L4A_ENST00000507810.1_5'UTR|CTC-459M5.2_ENST00000506875.1_RNA|CTC-459M5.2_ENST00000505825.1_RNA	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	393						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		TTCACTGACCTTTTTACTGGT	0.313																																					p.S393fs		Atlas-INDEL	.											.	EPB41L4A	130	.	0			c.1178delG						.						191.0	175.0	180.0					5																	111545590		1819	4083	5902	SO:0001630	splice_region_variant	64097	exon13			.	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.1178+1A>-	chr5.hg19:g.111545590delT		89.0	0.0		152.0	10.0	NM_022140	A4FUI6	Frame_Shift_Del	DEL	ENST00000261486.5	hg19	CCDS43350.1																																																																																			.	.		0.313	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		Frame_Shift_Del
UTP23	84294	hgsc.bcm.edu	37	8	117783923	117783923	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:117783923delA	ENST00000309822.2	+	3	693	c.592delA	c.(592-594)aaafs	p.K198fs	UTP23_ENST00000517820.1_Intron|UTP23_ENST00000357148.3_Intron|UTP23_ENST00000520733.1_Intron	NM_032334.2	NP_115710.2	Q9BRU9	UTP23_HUMAN	UTP23, small subunit (SSU) processome component, homolog (yeast)	198					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	12						AAAGCGCAAGAAAATAAGTGG	0.363																																					p.K197fs		Atlas-INDEL	.											.	UTP23	38	.	0			c.591delG						.						55.0	57.0	56.0					8																	117783923		2203	4300	6503	SO:0001589	frameshift_variant	84294	exon3			.		CCDS6320.1	8q24.11	2008-06-12	2008-06-12	2008-06-12		ENSG00000147679			28224	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 53"""	C8orf53		16769905	Standard	NM_032334		Approved	MGC14595	uc003yoc.3	Q9BRU9		ENST00000309822.2:c.592delA	chr8.hg19:g.117783923delA	ENSP00000308332:p.Lys198fs	129.0	0.0		151.0	10.0	NM_032334	B2RE25|Q96NJ8	Frame_Shift_Del	DEL	ENST00000309822.2	hg19	CCDS6320.1																																																																																			.	.		0.363	UTP23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381173.1	NM_032334	
DGKE	8526	hgsc.bcm.edu	37	17	54926133	54926133	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:54926133delG	ENST00000284061.3	+	6	1145	c.965delG	c.(964-966)tggfs	p.W322fs		NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	322	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|phospholipid biosynthetic process (GO:0008654)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25	Breast(9;3.59e-07)					ACATTGGGTTGGGGTACAGGT	0.413																																					p.W322fs		Atlas-INDEL	.											.	DGKE	47	.	0			c.964delT						.						137.0	132.0	133.0					17																	54926133		2203	4300	6503	SO:0001589	frameshift_variant	8526	exon6			.	U49379	CCDS11590.1	17q22	2008-07-18	2002-08-29			ENSG00000153933	2.7.1.107		2852	protein-coding gene	gene with protein product		601440	"""diacylglycerol kinase, epsilon (64kD)"""			8626589, 10051413	Standard	NM_003647		Approved	DAGK6, DGK	uc002iur.3	P52429		ENST00000284061.3:c.965delG	chr17.hg19:g.54926133delG	ENSP00000284061:p.Trp322fs	158.0	0.0		193.0	12.0	NM_003647	Q8TBM4|Q9UKQ3	Frame_Shift_Del	DEL	ENST00000284061.3	hg19	CCDS11590.1																																																																																			.	.		0.413	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647	
SENP5	205564	hgsc.bcm.edu	37	3	196626588	196626588	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:196626588delA	ENST00000323460.5	+	3	1814	c.1565delA	c.(1564-1566)gaafs	p.E522fs	SENP5_ENST00000419026.1_Frame_Shift_Del_p.E12fs|SENP5_ENST00000445299.2_Frame_Shift_Del_p.E522fs	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	522					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-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;0.004)		CCACTCAGTGAAAAAGAAGTC	0.303																																					p.E522fs	Ovarian(47;891 1095 11174 13858 51271)	Atlas-INDEL	.											.	SENP5	68	.	0			c.1564delG						.						91.0	99.0	96.0					3																	196626588		2202	4298	6500	SO:0001589	frameshift_variant	205564	exon3			.	BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"""SUMO1/sentrin specific protease 5"""			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.1565delA	chr3.hg19:g.196626588delA	ENSP00000327197:p.Glu522fs	190.0	0.0		175.0	11.0	NM_152699	B4DY82|Q96SA5	Frame_Shift_Del	DEL	ENST00000323460.5	hg19	CCDS3322.1																																																																																			.	.		0.303	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699	
LIMK1	3984	hgsc.bcm.edu	37	7	73523283	73523283	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:73523283delG	ENST00000336180.2	+	10	1252	c.1201delG	c.(1201-1203)gggfs	p.G401fs	LIMK1_ENST00000538333.3_Frame_Shift_Del_p.G367fs|LIMK1_ENST00000418310.1_Frame_Shift_Del_p.G431fs	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	401	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)	CAAGTTCATCGGGGTGCTCTA	0.602																																					p.I400fs		Atlas-INDEL	.											.	LIMK1	55	.	0			c.1200delC						.						123.0	95.0	104.0					7																	73523283		2203	4300	6503	SO:0001589	frameshift_variant	3984	exon10			.	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.1201delG	chr7.hg19:g.73523283delG	ENSP00000336740:p.Gly401fs	85.0	0.0		211.0	14.0	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Frame_Shift_Del	DEL	ENST00000336180.2	hg19	CCDS5563.1																																																																																			.	.		0.602	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314	
HIVEP3	59269	hgsc.bcm.edu	37	1	42050249	42050249	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:42050249delT	ENST00000372583.1	-	4	1105	c.220delA	c.(220-222)acgfs	p.T74fs	HIVEP3_ENST00000429157.2_Frame_Shift_Del_p.T74fs|HIVEP3_ENST00000372584.1_Frame_Shift_Del_p.T74fs|HIVEP3_ENST00000247584.5_Frame_Shift_Del_p.T74fs	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	74					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TGCTGGCCCGTTTTCTCCTGA	0.632																																					p.T74fs		Atlas-INDEL	.											.	HIVEP3	235	.	0			c.221delC						.						90.0	106.0	100.0					1																	42050249		2203	4300	6503	SO:0001589	frameshift_variant	59269	exon4			.	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.220delA	chr1.hg19:g.42050249delT	ENSP00000361664:p.Thr74fs	126.0	0.0		179.0	12.0	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Frame_Shift_Del	DEL	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.		0.632	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
OAF	220323	hgsc.bcm.edu	37	11	120097608	120097608	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:120097608delG	ENST00000328965.4	+	3	963	c.450delG	c.(448-450)cagfs	p.Q150fs	OAF_ENST00000531220.1_Frame_Shift_Del_p.Q34fs	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	150						extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(5)	6		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)		ACTTCAGCCAGGGGGCCCTGC	0.627																																					p.Q150fs		Atlas-INDEL	.											.	OAF	12	.	0			c.449delA						.						67.0	60.0	62.0					11																	120097608		2203	4300	6503	SO:0001589	frameshift_variant	220323	exon3			.	BC047726	CCDS8430.1	11q23.3	2010-11-23			ENSG00000184232	ENSG00000184232			28752	protein-coding gene	gene with protein product						12477932	Standard	NM_178507		Approved	MGC52117	uc001pxb.3	Q86UD1	OTTHUMG00000166139	ENST00000328965.4:c.450delG	chr11.hg19:g.120097608delG	ENSP00000332613:p.Gln150fs	75.0	0.0		146.0	11.0	NM_178507		Frame_Shift_Del	DEL	ENST00000328965.4	hg19	CCDS8430.1																																																																																			.	.		0.627	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507	
MBD5	55777	hgsc.bcm.edu	37	2	149243489	149243489	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:149243489delC	ENST00000407073.1	+	11	4021	c.3024delC	c.(3022-3024)aacfs	p.N1008fs	MBD5_ENST00000404807.1_Frame_Shift_Del_p.N1241fs	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1008					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		CTAACAATAACCCCATGGCTT	0.443																																					p.N1008fs		Atlas-INDEL	.											.	MBD5	164	.	0			c.3023delA						.						107.0	113.0	111.0					2																	149243489		2203	4300	6503	SO:0001589	frameshift_variant	55777	exon11			.	AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.3024delC	chr2.hg19:g.149243489delC	ENSP00000386049:p.Asn1008fs	155.0	0.0		204.0	13.0	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Frame_Shift_Del	DEL	ENST00000407073.1	hg19	CCDS33302.1																																																																																			.	.		0.443	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2		
SNTB1	6641	hgsc.bcm.edu	37	8	121823695	121823695	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:121823695delC	ENST00000395601.3	-	2	803	c.389delG	c.(388-390)ggcfs	p.G130fs	RP11-713M15.2_ENST00000605955.1_RNA|SNTB1_ENST00000519177.1_5'UTR|SNTB1_ENST00000517992.1_Frame_Shift_Del_p.G130fs	NM_021021.3	NP_066301.1	Q13884	SNTB1_HUMAN	syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1)	130	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.|PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|protein complex (GO:0043234)|synapse (GO:0045202)				NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(6)	24	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			GTTCTCCTTGCCCCCCTTGAT	0.637																																					p.G130fs		Atlas-INDEL	.											.	SNTB1	54	.	0			c.390delC						.						59.0	60.0	60.0					8																	121823695		2203	4300	6503	SO:0001589	frameshift_variant	6641	exon1			.	AF028828	CCDS6334.1	8q23-q24	2013-01-10	2002-08-29		ENSG00000172164	ENSG00000172164		"""Pleckstrin homology (PH) domain containing"""	11168	protein-coding gene	gene with protein product	"""tax interaction protein 43"""	600026	"""syntrophin, beta 1 (dystrophin-associated protein A1, 59kD, basic component 1)"""	SNT2B1		8183929, 9482110	Standard	NM_021021		Approved	59-DAP, A1B, BSYN2, TIP-43, SNT2	uc010mdg.3	Q13884	OTTHUMG00000165041	ENST00000395601.3:c.389delG	chr8.hg19:g.121823695delC	ENSP00000378965:p.Gly130fs	166.0	0.0		243.0	15.0	NM_021021	A8K9E0|O14912|Q4KMG8	Frame_Shift_Del	DEL	ENST00000395601.3	hg19	CCDS6334.1																																																																																			.	.		0.637	SNTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381535.1	NM_021021	
PLSCR5	389158	hgsc.bcm.edu	37	3	146311885	146311885	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:146311885delT	ENST00000443512.1	-	4	1278	c.275delA	c.(274-276)aacfs	p.N92fs	PLSCR5_ENST00000482567.1_Frame_Shift_Del_p.N80fs|PLSCR5_ENST00000492200.1_Frame_Shift_Del_p.N92fs	NM_001085420.1	NP_001078889.1	A0PG75	PLS5_HUMAN	phospholipid scramblase family, member 5	92										endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						TCCCAAGCTGTTTTTAATCTC	0.348																																					p.N92fs		Atlas-INDEL	.											.	PLSCR5	35	.	0			c.276delC						.						116.0	113.0	114.0					3																	146311885		1832	4087	5919	SO:0001589	frameshift_variant	389158	exon4			.	AY436642	CCDS46931.1	3q24	2004-06-28			ENSG00000231213	ENSG00000231213			19952	protein-coding gene	gene with protein product							Standard	NM_001085420		Approved		uc010hvc.3	A0PG75	OTTHUMG00000159437	ENST00000443512.1:c.275delA	chr3.hg19:g.146311885delT	ENSP00000390111:p.Asn92fs	111.0	0.0		138.0	10.0	NM_001085420	B2RXK5	Frame_Shift_Del	DEL	ENST00000443512.1	hg19	CCDS46931.1																																																																																			.	.		0.348	PLSCR5-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355365.1	XM_371670	
ANKRD7	56311	hgsc.bcm.edu	37	7	117876139	117876139	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:117876139delA	ENST00000265224.4	+	4	668	c.513delA	c.(511-513)ccafs	p.P171fs	ANKRD7_ENST00000357099.4_Frame_Shift_Del_p.P191fs|ANKRD7_ENST00000433239.1_Frame_Shift_Del_p.P118fs|ANKRD7_ENST00000477532.1_3'UTR|ANKRD7_ENST00000417525.1_Frame_Shift_Del_p.P118fs	NM_019644.3	NP_062618.2	Q92527	ANKR7_HUMAN	ankyrin repeat domain 7	171					male gonad development (GO:0008584)	nucleus (GO:0005634)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)	29						ACAATAATCCAAAAATGGTAA	0.274																																					p.P171fs		Atlas-INDEL	.											.	ANKRD7	44	.	0			c.512delC						.						77.0	79.0	79.0					7																	117876139		1797	4070	5867	SO:0001589	frameshift_variant	56311	exon4			.	D78334	CCDS43638.1	7q31	2013-01-10			ENSG00000106013	ENSG00000106013		"""Ankyrin repeat domain containing"""	18588	protein-coding gene	gene with protein product	"""testis-specific ankyrin motif containing protein"""	610731				8812458	Standard	NM_019644		Approved	TSA806	uc003vji.3	Q92527	OTTHUMG00000156960	ENST00000265224.4:c.513delA	chr7.hg19:g.117876139delA	ENSP00000265224:p.Pro171fs	110.0	0.0		159.0	11.0	NM_019644	B4DYF5|Q96QN1|Q9UDM3	Frame_Shift_Del	DEL	ENST00000265224.4	hg19	CCDS43638.1																																																																																			.	.		0.274	ANKRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346826.1	NM_001077708	
SLC25A22	79751	hgsc.bcm.edu	37	11	799358	799358	+	5'Flank	DEL	G	G	-	rs11820580	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:799358delG	ENST00000320230.5	-	0	0				PIDD_ENST00000411829.2_Frame_Shift_Del_p.P877fs|PIDD_ENST00000347755.5_Frame_Shift_Del_p.P894fs|SLC25A22_ENST00000531214.1_5'Flank	NM_001191061.1|NM_024698.5	NP_001177990.1|NP_078974.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22						L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CAGGCAGAGCGGGGTCCTTGG	0.672																																					p.A895fs	Colon(93;848 1468 3270 23355 49636)	Atlas-INDEL	.											.	PIDD	76	.	0			c.2683delG						.						44.0	48.0	47.0					11																	799358		2202	4295	6497	SO:0001631	upstream_gene_variant	55367	exon16			.	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"""Solute carriers"""	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310		chr11.hg19:g.799358delG	Exception_encountered	204.0	0.0		208.0	13.0	NM_145886	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Frame_Shift_Del	DEL	ENST00000320230.5	hg19	CCDS7715.1																																																																																			.	.		0.672	SLC25A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257107.2		
UNC80	285175	hgsc.bcm.edu	37	2	210682639	210682639	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:210682639delC	ENST00000439458.1	+	11	1736	c.1656delC	c.(1654-1656)gacfs	p.D552fs	UNC80_ENST00000272845.6_Frame_Shift_Del_p.D552fs	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	552					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						ACCTGCCGGACCCCTCCAACA	0.562																																					p.D552fs		Atlas-INDEL	.											.	UNC80	280	.	0			c.1655delA						.						38.0	44.0	43.0					2																	210682639		692	1591	2283	SO:0001589	frameshift_variant	285175	exon11			.	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.1656delC	chr2.hg19:g.210682639delC	ENSP00000391088:p.Asp552fs	108.0	0.0		152.0	10.0	NM_032504	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Frame_Shift_Del	DEL	ENST00000439458.1	hg19	CCDS46504.1																																																																																			.	.		0.562	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
FBXL12	54850	hgsc.bcm.edu	37	19	9922291	9922291	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:9922291delG	ENST00000247977.4	-	3	503	c.262delC	c.(262-264)cagfs	p.Q88fs	FBXL12_ENST00000586469.1_Frame_Shift_Del_p.P63fs|FBXL12_ENST00000592067.1_3'UTR|FBXL12_ENST00000586651.1_3'UTR|FBXL12_ENST00000589626.1_3'UTR|FBXL12_ENST00000591009.1_Frame_Shift_Del_p.Q35fs|FBXL12_ENST00000585379.1_Frame_Shift_Del_p.Q35fs|FBXL12_ENST00000588922.1_3'UTR	NM_017703.1	NP_060173.1	Q9NXK8	FXL12_HUMAN	F-box and leucine-rich repeat protein 12	88					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)		p.Q88fs*7(1)		endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(2)	10						GGGGACAACTGGGGGGCCTGG	0.632																																					p.Q88fs		Atlas-INDEL	.											.	FBXL12	17	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.263delA						.						42.0	48.0	46.0					19																	9922291		2202	4295	6497	SO:0001589	frameshift_variant	54850	exon3			.	AK000195	CCDS12218.1	19p13.2	2011-06-09				ENSG00000127452		"""F-boxes / Leucine-rich repeats"""	13611	protein-coding gene	gene with protein product		609079				10531037	Standard	XM_005259964		Approved	FLJ20188, Fbl12	uc002mme.3	Q9NXK8		ENST00000247977.4:c.262delC	chr19.hg19:g.9922291delG	ENSP00000247977:p.Gln88fs	120.0	0.0		175.0	11.0	NM_017703	B3KSJ8|Q9H5K4	Frame_Shift_Del	DEL	ENST00000247977.4	hg19	CCDS12218.1																																																																																			.	.		0.632	FBXL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450265.1	NM_017703	
PCSK2	5126	hgsc.bcm.edu	37	20	17208071	17208071	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:17208071delG	ENST00000262545.2	+	1	436	c.121delG	c.(121-123)gggfs	p.G42fs	PCSK2_ENST00000377899.1_Frame_Shift_Del_p.G23fs|PCSK2_ENST00000536609.1_Frame_Shift_Del_p.G42fs	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	42					cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	GTTGCATAAAGGGGGAGAGGA	0.532																																					p.K40fs		Atlas-INDEL	.											.	PCSK2	112	.	0			c.120delA						.						81.0	72.0	75.0					20																	17208071		2203	4300	6503	SO:0001589	frameshift_variant	5126	exon1			.	AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"""neuroendocrine convertase 2"", ""KEX2-like endoprotease 2"""	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.121delG	chr20.hg19:g.17208071delG	ENSP00000262545:p.Gly42fs	186.0	0.0		205.0	14.0	NM_002594	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Frame_Shift_Del	DEL	ENST00000262545.2	hg19	CCDS13125.1																																																																																			.	.		0.532	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594	
HIAT1	64645	hgsc.bcm.edu	37	1	100542770	100542770	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:100542770delT	ENST00000370152.3	+	9	1077	c.941delT	c.(940-942)attfs	p.I314fs	RP4-714D9.2_ENST00000432294.1_RNA	NM_033055.2	NP_149044.2	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1	314					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|skin(1)	16		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)		AAGAACACCATTTTACTGGGT	0.269																																					p.I314fs		Atlas-INDEL	.											.	HIAT1	46	.	0			c.940delA						.						95.0	99.0	98.0					1																	100542770		2203	4299	6502	SO:0001589	frameshift_variant	64645	exon9			.	AK096669	CCDS763.1	1p21.3	2008-02-05			ENSG00000156875	ENSG00000156875			23363	protein-coding gene	gene with protein product						9299464	Standard	NM_033055		Approved	DKFZP564L0864	uc001dst.3	Q96MC6	OTTHUMG00000010755	ENST00000370152.3:c.941delT	chr1.hg19:g.100542770delT	ENSP00000359171:p.Ile314fs	131.0	0.0		194.0	12.0	NM_033055	Q6P2N7|Q8N8K2|Q8NBV3|Q96NY0|Q9NT25	Frame_Shift_Del	DEL	ENST00000370152.3	hg19	CCDS763.1																																																																																			.	.		0.269	HIAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029657.1	NM_033055	
DNMT3A	1788	hgsc.bcm.edu	37	2	25505341	25505341	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:25505341delG	ENST00000264709.3	-	4	754	c.417delC	c.(415-417)cccfs	p.P139fs	DNMT3A_ENST00000406659.3_Frame_Shift_Del_p.P139fs|DNMT3A_ENST00000321117.5_Frame_Shift_Del_p.P139fs	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	139					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCCCTCCTTGGGGGTGCAGC	0.667			"""Mis, F, N, S"""		AML																																p.K140fs		Atlas-INDEL	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.418delA						.						20.0	23.0	22.0					2																	25505341		2202	4300	6502	SO:0001589	frameshift_variant	1788	exon4			.		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.417delC	chr2.hg19:g.25505341delG	ENSP00000264709:p.Pro139fs	121.0	0.0		158.0	12.0	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Frame_Shift_Del	DEL	ENST00000264709.3	hg19	CCDS33157.1																																																																																			.	.		0.667	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552	
HDLBP	3069	hgsc.bcm.edu	37	2	242170362	242170362	+	Intron	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:242170362delA	ENST00000391975.1	-	25	3516				HDLBP_ENST00000427183.2_Intron|HDLBP_ENST00000310931.4_Intron|HDLBP_ENST00000391976.2_Intron	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein						cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		TCCTGGGGCTAAAAAAGGAGA	0.507																																					.		Atlas-INDEL	.											.	HDLBP	118	.	0			c.3289-2T>-						.						83.0	75.0	78.0					2																	242170362		2203	4300	6503	SO:0001627	intron_variant	3069	exon26			.		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"""vigilin"""	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.3289-3T>-	chr2.hg19:g.242170362delA		118.0	0.0		149.0	11.0	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Splice_Site	DEL	ENST00000391975.1	hg19	CCDS2547.1																																																																																			.	.		0.507	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346	
KIF21A	55605	hgsc.bcm.edu	37	12	39688246	39688246	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:39688246delC	ENST00000361418.5	-	38	5020	c.5005delG	c.(5005-5007)gaafs	p.E1669fs	KIF21A_ENST00000361961.3_Frame_Shift_Del_p.E1656fs|KIF21A_ENST00000544797.2_Frame_Shift_Del_p.E1632fs|KIF21A_ENST00000541463.2_Frame_Shift_Del_p.E1616fs|KIF21A_ENST00000395670.3_Frame_Shift_Del_p.E1670fs			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1669					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)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				GCAATATCTTCCCCCAGATCT	0.363																																					p.E1669fs		Atlas-INDEL	.											.	KIF21A	238	.	0			c.5006delA						.						123.0	113.0	116.0					12																	39688246		2203	4300	6503	SO:0001589	frameshift_variant	55605	exon38			.	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"""Kinesins"", ""WD repeat domain containing"""	19349	protein-coding gene	gene with protein product		608283	"""fibrosis of the extraocular muscles, congenital, 1"""	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.5005delG	chr12.hg19:g.39688246delC	ENSP00000354878:p.Glu1669fs	199.0	0.0		193.0	13.0	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Frame_Shift_Del	DEL	ENST00000361418.5	hg19	CCDS53776.1																																																																																			.	.		0.363	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641	
FASTKD1	79675	hgsc.bcm.edu	37	2	170387133	170387133	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:170387133delT	ENST00000453153.2	-	14	2752	c.2406delA	c.(2404-2406)aaafs	p.K802fs	FASTKD1_ENST00000495505.1_5'UTR|FASTKD1_ENST00000453929.2_Frame_Shift_Del_p.K759fs	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	802	RAP. {ECO:0000255|PROSITE- ProRule:PRU00619}.				cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						CCAAATGTCGTTTTTTCATAG	0.338																																					p.R803fs		Atlas-INDEL	.											.	FASTKD1	86	.	0			c.2407delC						.						151.0	163.0	159.0					2																	170387133		2203	4300	6503	SO:0001589	frameshift_variant	79675	exon14			.	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.2406delA	chr2.hg19:g.170387133delT	ENSP00000400513:p.Lys802fs	230.0	0.0		285.0	20.0	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Frame_Shift_Del	DEL	ENST00000453153.2	hg19	CCDS33318.1																																																																																			.	.		0.338	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
TDG	6996	hgsc.bcm.edu	37	12	104370720	104370720	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:104370720delT	ENST00000392872.3	+	2	282	c.48delT	c.(46-48)gctfs	p.A16fs	TDG_ENST00000544861.1_Intron|TDG_ENST00000266775.9_Frame_Shift_Del_p.A12fs	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	16					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		AAGCTCAAGCTTTTTATACGT	0.388								Base excision repair (BER), DNA glycosylases																													p.A16fs		Atlas-INDEL	.											.	TDG	43	.	0			c.47delC						.						53.0	51.0	52.0					12																	104370720		2203	4300	6503	SO:0001589	frameshift_variant	6996	exon2			.	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"""G/T mismatch-specific thymine DNA glycosylase"""	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.48delT	chr12.hg19:g.104370720delT	ENSP00000376611:p.Ala16fs	160.0	0.0		195.0	12.0	NM_003211	Q8IUZ6|Q8IZM3	Frame_Shift_Del	DEL	ENST00000392872.3	hg19	CCDS9095.1																																																																																			.	.		0.388	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		
ASH1L	55870	hgsc.bcm.edu	37	1	155450361	155450361	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:155450361delG	ENST00000368346.3	-	3	2939	c.2300delC	c.(2299-2301)cctfs	p.P767fs	ASH1L_ENST00000392403.3_Frame_Shift_Del_p.P767fs			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	767					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)			TACAAATGAAGGGGGTCCAAT	0.383																																					p.P767fs		Atlas-INDEL	.											.	ASH1L	279	.	0			c.2301delT						.						134.0	137.0	136.0					1																	155450361		2203	4300	6503	SO:0001589	frameshift_variant	55870	exon3			.	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.2300delC	chr1.hg19:g.155450361delG	ENSP00000357330:p.Pro767fs	141.0	0.0		282.0	17.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Frame_Shift_Del	DEL	ENST00000368346.3	hg19																																																																																				.	.		0.383	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
TBC1D1	23216	hgsc.bcm.edu	37	4	38097556	38097556	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:38097556delA	ENST00000261439.4	+	14	2598	c.2243delA	c.(2242-2244)gaafs	p.E748fs	TBC1D1_ENST00000508802.1_Frame_Shift_Del_p.E842fs	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	748					membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						CCAGCCTCTGAAAATGATTTG	0.433																																					p.E842fs		Atlas-INDEL	.											.	TBC1D1	94	.	0			c.2524delG						.						91.0	94.0	93.0					4																	38097556		2203	4300	6503	SO:0001589	frameshift_variant	23216	exon16			.	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.2243delA	chr4.hg19:g.38097556delA	ENSP00000261439:p.Glu748fs	88.0	0.0		102.0	10.0	NM_001253912	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Frame_Shift_Del	DEL	ENST00000261439.4	hg19	CCDS33972.1																																																																																			.	.		0.433	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
SAMD4A	23034	hgsc.bcm.edu	37	14	55231225	55231225	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:55231225delT	ENST00000554335.1	+	8	2226	c.1563delT	c.(1561-1563)tatfs	p.Y521fs	SAMD4A_ENST00000357634.3_Frame_Shift_Del_p.Y520fs|SAMD4A_ENST00000251091.5_Frame_Shift_Del_p.Y433fs|SAMD4A_ENST00000555192.1_Frame_Shift_Del_p.Y112fs|SAMD4A_ENST00000392067.3_Frame_Shift_Del_p.Y521fs			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	521					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						TAAGTTCCTATTTACAGCTCA	0.343																																					p.Y521fs		Atlas-INDEL	.											.	SAMD4A	68	.	0			c.1562delA						.						151.0	159.0	156.0					14																	55231225		2203	4300	6503	SO:0001589	frameshift_variant	23034	exon7			.	AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"""Sterile alpha motif (SAM) domain containing"""	23023	protein-coding gene	gene with protein product	"""smaug homolog (Drosophila)"""	610747	"""sterile alpha motif domain containing 4"""	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1563delT	chr14.hg19:g.55231225delT	ENSP00000452535:p.Tyr521fs	81.0	0.0		121.0	10.0	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Frame_Shift_Del	DEL	ENST00000554335.1	hg19	CCDS32084.2																																																																																			.	.		0.343	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589	
SUPT5H	6829	hgsc.bcm.edu	37	19	39955533	39955533	+	Frame_Shift_Del	DEL	G	G	-	rs2304217	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:39955533delG	ENST00000599117.1	+	12	1087	c.720delG	c.(718-720)gagfs	p.E240fs	SUPT5H_ENST00000402194.2_Frame_Shift_Del_p.E236fs|SUPT5H_ENST00000359191.6_Frame_Shift_Del_p.E236fs|SUPT5H_ENST00000432763.2_Frame_Shift_Del_p.E240fs|SUPT5H_ENST00000598725.1_Frame_Shift_Del_p.E240fs			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	240	Interaction with SUPT4H1.				7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AGGCCATTGAGGGGGTGGGCA	0.577																																					p.E240fs		Atlas-INDEL	.											.	SUPT5H	119	.	0			c.719delA						.						97.0	83.0	88.0					19																	39955533		2203	4300	6503	SO:0001589	frameshift_variant	6829	exon10			.	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"""suppressor of Ty (S.cerevisiae) 5 homolog"""			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.720delG	chr19.hg19:g.39955533delG	ENSP00000470252:p.Glu240fs	141.0	0.0		194.0	12.0	NM_003169	O43279|Q59G52|Q99639	Frame_Shift_Del	DEL	ENST00000599117.1	hg19	CCDS12536.1																																																																																			.	.		0.577	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169	
UNC80	285175	hgsc.bcm.edu	37	2	210837002	210837002	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:210837002delA	ENST00000439458.1	+	54	8216	c.8136delA	c.(8134-8136)ttafs	p.L2712fs	UNC80_ENST00000539183.1_Frame_Shift_Del_p.L158fs|UNC80_ENST00000272845.6_Frame_Shift_Del_p.L2707fs	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	2712					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						GGATGCTTTTAAATCTGCTCA	0.373																																					p.L2712X		Atlas-INDEL	.											.	UNC80	280	.	0			c.8135delT						.						157.0	133.0	140.0					2																	210837002		692	1591	2283	SO:0001589	frameshift_variant	285175	exon54			.	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.8136delA	chr2.hg19:g.210837002delA	ENSP00000391088:p.Leu2712fs	279.0	0.0		315.0	19.0	NM_032504	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Frame_Shift_Del	DEL	ENST00000439458.1	hg19	CCDS46504.1																																																																																			.	.		0.373	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
IQCC	55721	hgsc.bcm.edu	37	1	32671421	32671421	+	Intron	DEL	C	C	-	rs186875513		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:32671421delC	ENST00000291358.6	+	1	63				RP4-622L5.7_ENST00000421616.1_RNA|IQCC_ENST00000537469.1_Frame_Shift_Del_p.P47fs|RP4-622L5.7_ENST00000373604.4_RNA	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C											endometrium(4)|large_intestine(1)|lung(3)|ovary(4)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CACGTTCAGTCCCCTAACTGC	0.642																																					p.S46fs		Atlas-INDEL	.											.	IQCC	46	.	0			c.138delT						.						25.0	22.0	23.0					1																	32671421		692	1591	2283	SO:0001627	intron_variant	55721	exon1			.	AL049795	CCDS355.1, CCDS53293.1	1p36.11-p34.2	2008-02-05			ENSG00000160051	ENSG00000160051			25545	protein-coding gene	gene with protein product							Standard	NM_018134		Approved	FLJ10547	uc001bum.2	Q4KMZ1	OTTHUMG00000005739	ENST00000291358.6:c.42+97C>-	chr1.hg19:g.32671421delC		164.0	0.0		221.0	15.0	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Frame_Shift_Del	DEL	ENST00000291358.6	hg19	CCDS355.1																																																																																			.	.		0.642	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134	
MFAP3	4238	hgsc.bcm.edu	37	5	153432802	153432802	+	Frame_Shift_Del	DEL	C	C	-	rs142736423		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:153432802delC	ENST00000436816.1	+	3	837	c.618delC	c.(616-618)atcfs	p.I206fs	MFAP3_ENST00000322602.5_Frame_Shift_Del_p.I206fs|MFAP3_ENST00000439768.2_Frame_Shift_Del_p.I60fs	NM_001242336.1|NM_005927.4	NP_001229265.1|NP_005918.1	P55082	MFAP3_HUMAN	microfibrillar-associated protein 3	206					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)	7	Renal(175;0.00488)	Lung NSC(249;0.00145)|all_lung(500;0.00226)|all_neural(177;0.122)|Breast(839;0.14)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;9.69e-06)|GBM - Glioblastoma multiforme(465;0.0201)		CAAAACGTATCCCCATCATTA	0.448																																					p.I206fs		Atlas-INDEL	.											.	MFAP3	20	.	0			c.617delT						.						81.0	82.0	82.0					5																	153432802		2203	4300	6503	SO:0001589	frameshift_variant	4238	exon3			.		CCDS4324.1, CCDS47319.1	5q32-q33.2	2013-01-11			ENSG00000037749	ENSG00000037749		"""Immunoglobulin superfamily / I-set domain containing"""	7034	protein-coding gene	gene with protein product		600491				7782085	Standard	NM_005927		Approved		uc010jib.2	P55082	OTTHUMG00000130149	ENST00000436816.1:c.618delC	chr5.hg19:g.153432802delC	ENSP00000409933:p.Ile206fs	119.0	0.0		136.0	10.0	NM_005927	B2RDK0|B4DKA1|Q9NXA7	Frame_Shift_Del	DEL	ENST00000436816.1	hg19	CCDS4324.1																																																																																			.	.		0.448	MFAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252457.2	NM_005927	
SLMAP	7871	hgsc.bcm.edu	37	3	57902753	57902753	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:57902753delA	ENST00000428312.1	+	20	2302	c.2208delA	c.(2206-2208)ttafs	p.L736fs	SLMAP_ENST00000295952.3_Frame_Shift_Del_p.L719fs|SLMAP_ENST00000495364.1_Frame_Shift_Del_p.L270fs|SLMAP_ENST00000442599.2_Frame_Shift_Del_p.L204fs|SLMAP_ENST00000449503.2_Frame_Shift_Del_p.L698fs|SLMAP_ENST00000295951.3_Frame_Shift_Del_p.L719fs|SLMAP_ENST00000494088.1_Frame_Shift_Del_p.L229fs|SLMAP_ENST00000416870.1_Frame_Shift_Del_p.L229fs			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	736					muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|smooth endoplasmic reticulum (GO:0005790)				endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(2)	18				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		CAGCTGATTTAAAAACTCTTC	0.408																																					p.L719X		Atlas-INDEL	.											.	SLMAP	46	.	0			c.2156delT						.						92.0	89.0	90.0					3																	57902753		2203	4300	6503	SO:0001589	frameshift_variant	7871	exon19			.	AF100750	CCDS33774.1	3p21.2-p14.3	2008-07-18			ENSG00000163681	ENSG00000163681			16643	protein-coding gene	gene with protein product	"""Sarcolemmal-associated protein"""	602701				9405447, 11042152	Standard	NM_007159		Approved	SLAP, KIAA1601	uc003djd.1	Q14BN4	OTTHUMG00000133764	ENST00000428312.1:c.2208delA	chr3.hg19:g.57902753delA	ENSP00000398661:p.Leu736fs	219.0	0.0		246.0	15.0	NM_007159	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Frame_Shift_Del	DEL	ENST00000428312.1	hg19																																																																																				.	.		0.408	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159	
ZNF273	10793	hgsc.bcm.edu	37	7	64388426	64388426	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:64388426delA	ENST00000476120.1	+	4	791	c.720delA	c.(718-720)ggafs	p.G240fs	ZNF273_ENST00000319636.5_Frame_Shift_Del_p.G175fs|ZNF273_ENST00000527278.1_3'UTR	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	240					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				AGACATGTGGAAAAGCCTTTA	0.343																																					p.G240fs	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)	Atlas-INDEL	.											.	ZNF273	45	.	0			c.719delG						.						66.0	72.0	70.0					7																	64388426		2203	4297	6500	SO:0001589	frameshift_variant	10793	exon4			.	X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039		"""Zinc fingers, C2H2-type"", ""-"""	13067	protein-coding gene	gene with protein product		604756				7865130	Standard	NR_003099		Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.720delA	chr7.hg19:g.64388426delA	ENSP00000418719:p.Gly240fs	73.0	0.0		183.0	11.0	NM_021148	B3KQZ5|Q6P3V4	Frame_Shift_Del	DEL	ENST00000476120.1	hg19	CCDS5528.2																																																																																			.	.		0.343	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1		
NEK10	152110	hgsc.bcm.edu	37	3	27332187	27332187	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:27332187delG	ENST00000429845.2	-	20	2026	c.1664delC	c.(1663-1665)ccafs	p.P555fs	NEK10_ENST00000341435.5_Frame_Shift_Del_p.P555fs|NEK10_ENST00000357467.2_Intron			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	555	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						TCCAAATGCTGGGTTATGTAA	0.328																																					p.P555fs		Atlas-INDEL	.											.	NEK10	271	.	0			c.1665delA						.						116.0	102.0	106.0					3																	27332187		1568	3582	5150	SO:0001589	frameshift_variant	152110	exon20			.	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.1664delC	chr3.hg19:g.27332187delG	ENSP00000395849:p.Pro555fs	89.0	0.0		141.0	11.0	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Frame_Shift_Del	DEL	ENST00000429845.2	hg19																																																																																				.	.		0.328	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534	
C2orf57	165100	hgsc.bcm.edu	37	2	232457732	232457732	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:232457732delC	ENST00000313965.2	+	1	158	c.70delC	c.(70-72)cccfs	p.P24fs		NM_152614.2	NP_689827.2	Q53QW1	CB057_HUMAN	chromosome 2 open reading frame 57	24										endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	19		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)		AGCAGGAGAGCCCCAAGGTCA	0.617																																					p.E23fs		Atlas-INDEL	.											C2orf57,NS,carcinoma,0,1	C2orf57	35	.	0			c.69delG						.						87.0	82.0	84.0					2																	232457732		2203	4300	6503	SO:0001589	frameshift_variant	165100	exon1			.	BC034405	CCDS2487.1	2q37.1	2008-02-05			ENSG00000177673	ENSG00000177673			28563	protein-coding gene	gene with protein product						12477932	Standard	NM_152614		Approved	MGC35154	uc002vrz.3	Q53QW1	OTTHUMG00000133226	ENST00000313965.2:c.70delC	chr2.hg19:g.232457732delC	ENSP00000315557:p.Pro24fs	117.0	0.0		159.0	10.0	NM_152614	Q8N4F2	Frame_Shift_Del	DEL	ENST00000313965.2	hg19	CCDS2487.1																																																																																			.	.		0.617	C2orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256962.1	NM_152614	
ITSN2	50618	hgsc.bcm.edu	37	2	24516590	24516590	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:24516590delT	ENST00000355123.4	-	15	2133	c.1690delA	c.(1690-1692)agafs	p.R564fs	ITSN2_ENST00000361999.3_Frame_Shift_Del_p.R564fs|ITSN2_ENST00000406921.3_Frame_Shift_Del_p.R564fs	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	564					endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTTTAATTCTTTCATTTAAT	0.294																																					p.R564fs		Atlas-INDEL	.											.	ITSN2	224	.	0			c.1691delG						.						112.0	113.0	113.0					2																	24516590		2202	4291	6493	SO:0001589	frameshift_variant	50618	exon15			.	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.1690delA	chr2.hg19:g.24516590delT	ENSP00000347244:p.Arg564fs	161.0	0.0		196.0	14.0	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Frame_Shift_Del	DEL	ENST00000355123.4	hg19	CCDS1710.2																																																																																			.	.		0.294	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
TNXB	7148	hgsc.bcm.edu	37	6	32062950	32062950	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:32062950delC	ENST00000479795.1	-	4	2401	c.2261delG	c.(2260-2262)ggcfs	p.G754fs	TNXB_ENST00000375247.2_Frame_Shift_Del_p.G754fs|TNXB_ENST00000375244.3_Frame_Shift_Del_p.G754fs			P22105	TENX_HUMAN	tenascin XB	1345					actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CATCCTCATGCCCTCAATGGT	0.567																																					p.G754fs		Atlas-INDEL	.											.	TNXB	553	.	0			c.2262delC						.						140.0	132.0	134.0					6																	32062950		692	1591	2283	SO:0001589	frameshift_variant	7148	exon4			.	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000479795.1:c.2261delG	chr6.hg19:g.32062950delC	ENSP00000418248:p.Gly754fs	118.0	0.0		157.0	10.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Frame_Shift_Del	DEL	ENST00000479795.1	hg19																																																																																				.	.		0.567	TNXB-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000357059.1	NM_019105	
RCCD1	91433	hgsc.bcm.edu	37	15	91500927	91500927	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:91500927delG	ENST00000394258.2	+	4	853	c.651delG	c.(649-651)gcgfs	p.A217fs	RCCD1_ENST00000556774.1_Intron|RCCD1_ENST00000555155.1_Frame_Shift_Del_p.A217fs|RCCD1_ENST00000556618.1_Frame_Shift_Del_p.A217fs|AC068831.6_ENST00000553321.1_RNA	NM_001017919.1|NM_033544.2	NP_001017919.1|NP_291022.2	A6NED2	RCCD1_HUMAN	RCC1 domain containing 1	217						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(2)	4	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)			AGGTGGCCGCGGGGGGCTGGC	0.597																																					p.A217fs		Atlas-INDEL	.											.	RCCD1	9	.	0			c.650delC						.						109.0	107.0	108.0					15																	91500927		2198	4298	6496	SO:0001589	frameshift_variant	91433	exon4			.		CCDS32333.1	15q26.1	2005-10-21	2005-10-21			ENSG00000166965			30457	protein-coding gene	gene with protein product						12477932	Standard	XM_006720763		Approved	MGC14386	uc002bqk.3	A6NED2		ENST00000394258.2:c.651delG	chr15.hg19:g.91500927delG	ENSP00000377801:p.Ala217fs	153.0	0.0		226.0	16.0	NM_001017919	B2RTP9|Q29RX6	Frame_Shift_Del	DEL	ENST00000394258.2	hg19	CCDS32333.1																																																																																			.	.		0.597	RCCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414748.1	NM_033544	
MDN1	23195	hgsc.bcm.edu	37	6	90382309	90382309	+	Frame_Shift_Del	DEL	T	T	-	rs201481158		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:90382309delT	ENST00000369393.3	-	81	13702	c.13587delA	c.(13585-13587)aaafs	p.K4529fs	MDN1_ENST00000468568.1_5'Flank|MDN1_ENST00000428876.1_Frame_Shift_Del_p.K4529fs|RP1-122O8.7_ENST00000438877.1_RNA			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	95.0	0.0		164.0	11.0	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		
PPP2R5D	5528	hgsc.bcm.edu	37	6	42975751	42975751	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:42975751delT	ENST00000485511.1	+	7	984	c.805delT	c.(805-807)tttfs	p.F269fs	PPP2R5D_ENST00000461010.1_Frame_Shift_Del_p.F163fs|PPP2R5D_ENST00000472118.1_Frame_Shift_Del_p.F261fs|PPP2R5D_ENST00000394110.3_Frame_Shift_Del_p.F237fs	NM_001270476.1|NM_006245.3	NP_001257405.1|NP_006236.1	Q14738	2A5D_HUMAN	protein phosphatase 2, regulatory subunit B', delta	269					carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of catalytic activity (GO:0050790)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	25			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CTATGGCAAGTTTTTGGGGCT	0.527																																					p.K268fs	Melanoma(63;587 1613 29742 31770)	Atlas-INDEL	.											.	PPP2R5D	47	.	0			c.804delG						.						111.0	107.0	109.0					6																	42975751		2203	4300	6503	SO:0001589	frameshift_variant	5528	exon7			.	L76702	CCDS4878.1, CCDS43464.1, CCDS55002.1	6p21.1	2010-06-18	2010-04-14		ENSG00000112640	ENSG00000112640		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9312	protein-coding gene	gene with protein product		601646	"""protein phosphatase 2, regulatory subunit B (B56), delta isoform"", ""protein phosphatase 2, regulatory subunit B', delta isoform"""			7592815	Standard	NM_006245		Approved	B56D	uc003oth.4	Q14738	OTTHUMG00000014716	ENST00000485511.1:c.805delT	chr6.hg19:g.42975751delT	ENSP00000417963:p.Phe269fs	140.0	0.0		190.0	12.0	NM_006245	A8K3I9|B5BUA6|O00494|O00696|Q15171|Q5TC39	Frame_Shift_Del	DEL	ENST00000485511.1	hg19	CCDS4878.1																																																																																			.	.		0.527	PPP2R5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040573.3	NM_006245	
ANKRD32	84250	hgsc.bcm.edu	37	5	93989080	93989080	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:93989080delA	ENST00000265140.5	+	8	1405	c.986delA	c.(985-987)gaafs	p.E329fs		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	329						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		GTTGAACATGAAAAAATAAAA	0.308																																					p.E329fs		Atlas-INDEL	.											.	ANKRD32	117	.	0			c.985delG						.						149.0	132.0	137.0					5																	93989080		692	1591	2283	SO:0001589	frameshift_variant	84250	exon8			.	AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"""Ankyrin repeat domain containing"""	25408	protein-coding gene	gene with protein product			"""BRCT domain containing 1"""	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.986delA	chr5.hg19:g.93989080delA	ENSP00000265140:p.Glu329fs	133.0	0.0		213.0	16.0	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Frame_Shift_Del	DEL	ENST00000265140.5	hg19	CCDS4071.2																																																																																			.	.		0.308	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290	
KIAA0355	9710	hgsc.bcm.edu	37	19	34832365	34832365	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:34832365delG	ENST00000299505.6	+	10	2399	c.1526delG	c.(1525-1527)aggfs	p.R509fs		NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	509										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)					CAGCTGCAAAGGGAGATCTGT	0.393																																					p.R509fs		Atlas-INDEL	.											.	KIAA0355	105	.	0			c.1525delA						.						73.0	75.0	74.0					19																	34832365		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.1526delG	chr19.hg19:g.34832365delG	ENSP00000299505:p.Arg509fs	160.0	0.0		200.0	12.0	NM_014686	Q2M3W4	Frame_Shift_Del	DEL	ENST00000299505.6	hg19	CCDS12436.1																																																																																			.	.		0.393	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686	
PKN2	5586	hgsc.bcm.edu	37	1	89206728	89206728	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:89206728delT	ENST00000370521.3	+	2	465	c.106delT	c.(106-108)tttfs	p.F36fs	PKN2_ENST00000370505.3_Intron|PKN2_ENST00000316005.7_Frame_Shift_Del_p.F36fs|PKN2_ENST00000370513.5_Frame_Shift_Del_p.F36fs	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	36					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)		AAAATTAGACTTTTCAGATAC	0.363																																					p.D35fs		Atlas-INDEL	.											.	PKN2	109	.	0			c.105delC						.						88.0	82.0	84.0					1																	89206728		1825	4091	5916	SO:0001589	frameshift_variant	5586	exon2			.	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.106delT	chr1.hg19:g.89206728delT	ENSP00000359552:p.Phe36fs	108.0	0.0		135.0	11.0	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Frame_Shift_Del	DEL	ENST00000370521.3	hg19	CCDS714.1																																																																																			.	.		0.363	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256	
BRPF3	27154	hgsc.bcm.edu	37	6	36179276	36179276	+	Frame_Shift_Del	DEL	G	G	-	rs79041393		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:36179276delG	ENST00000357641.6	+	7	2674	c.2421delG	c.(2419-2421)cagfs	p.Q807fs	BRPF3_ENST00000534400.1_Frame_Shift_Del_p.Q807fs|BRPF3_ENST00000339717.7_Intron|BRPF3_ENST00000543502.1_Intron|BRPF3_ENST00000534694.1_Intron|BRPF3_ENST00000443324.2_Intron	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	807					blood coagulation (GO:0007596)|histone H3 acetylation (GO:0043966)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	cytosol (GO:0005829)|extracellular region (GO:0005576)|MOZ/MORF histone acetyltransferase complex (GO:0070776)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	40						CAGGGCCCCAGGGGGATGCAG	0.607																																					p.Q807fs		Atlas-INDEL	.											.	BRPF3	93	.	0			c.2420delA						.						15.0	14.0	14.0					6																	36179276		2187	4287	6474	SO:0001589	frameshift_variant	27154	exon7			.	AB033112	CCDS34437.1	6p21.31	2008-02-05			ENSG00000096070	ENSG00000096070			14256	protein-coding gene	gene with protein product						10574462	Standard	NM_015695		Approved	KIAA1286	uc003olv.4	Q9ULD4	OTTHUMG00000014589	ENST00000357641.6:c.2421delG	chr6.hg19:g.36179276delG	ENSP00000350267:p.Gln807fs	141.0	0.0		140.0	10.0	NM_015695	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Frame_Shift_Del	DEL	ENST00000357641.6	hg19	CCDS34437.1																																																																																			.	.		0.607	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695	
ANKRD42	338699	hgsc.bcm.edu	37	11	82938845	82938845	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:82938845delA	ENST00000393392.2	+	7	922	c.760delA	c.(760-762)aaafs	p.K254fs	ANKRD42_ENST00000533342.1_Frame_Shift_Del_p.K282fs|ANKRD42_ENST00000260047.6_Frame_Shift_Del_p.K281fs|ANKRD42_ENST00000531895.1_Frame_Shift_Del_p.K282fs	NM_182603.2	NP_872409.2	Q8N9B4	ANR42_HUMAN	ankyrin repeat domain 42	254					positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18						GATGCTTAAGAAATTAGTGGA	0.358																																					p.K253fs		Atlas-INDEL	.											ANKRD42,NS,carcinoma,0,1	ANKRD42	38	.	0			c.759delG						.						142.0	132.0	135.0					11																	82938845		2203	4300	6503	SO:0001589	frameshift_variant	338699	exon7			.	AK095193	CCDS8265.1, CCDS73355.1, CCDS73356.1	11q14.1	2014-06-12			ENSG00000137494	ENSG00000137494		"""Ankyrin repeat domain containing"""	26752	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 79"""						Standard	XM_005273971		Approved	FLJ37874, SARP, PPP1R79	uc001ozz.1	Q8N9B4	OTTHUMG00000167075	ENST00000393392.2:c.760delA	chr11.hg19:g.82938845delA	ENSP00000377051:p.Lys254fs	64.0	0.0		153.0	11.0	NM_182603	Q49A49	Frame_Shift_Del	DEL	ENST00000393392.2	hg19	CCDS8265.1																																																																																			.	.		0.358	ANKRD42-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000392934.1	NM_182603	
ARMC8	25852	hgsc.bcm.edu	37	3	137982594	137982594	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:137982594delA	ENST00000469044.1	+	13	1419	c.1148delA	c.(1147-1149)gaafs	p.E383fs	NME9_ENST00000536478.1_Intron|ARMC8_ENST00000491704.1_Frame_Shift_Del_p.E341fs|NME9_ENST00000341790.5_Intron|NME9_ENST00000317876.4_Intron|NME9_ENST00000484930.1_Intron|ARMC8_ENST00000485396.1_Frame_Shift_Del_p.E310fs|ARMC8_ENST00000461822.1_Frame_Shift_Del_p.E316fs|ARMC8_ENST00000393058.3_Frame_Shift_Del_p.E373fs|ARMC8_ENST00000538260.1_Frame_Shift_Del_p.E352fs|ARMC8_ENST00000481646.1_Frame_Shift_Del_p.E369fs|NME9_ENST00000383180.2_Intron	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	383										endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						ATTGAGACTGAAAATATGATG	0.393																																					p.E369fs		Atlas-INDEL	.											.	ARMC8	79	.	0			c.1105delG						.						187.0	183.0	184.0					3																	137982594		1917	4132	6049	SO:0001589	frameshift_variant	25852	exon14			.		CCDS3098.1, CCDS54646.1, CCDS58853.1, CCDS58854.1, CCDS75020.1	3q22	2013-02-14			ENSG00000114098	ENSG00000114098		"""Armadillo repeat containing"""	24999	protein-coding gene	gene with protein product	"""GID complex subunit 5, VID28 homolog (S. cerevisiae)"""					11042152	Standard	NM_014154		Approved	HSPC056, DKFZP434A043, GID5, VID28	uc003esa.2	Q8IUR7	OTTHUMG00000159821	ENST00000469044.1:c.1148delA	chr3.hg19:g.137982594delA	ENSP00000419413:p.Glu383fs	155.0	0.0		211.0	13.0	NM_015396	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Frame_Shift_Del	DEL	ENST00000469044.1	hg19																																																																																				.	.		0.393	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396	
TRAPPC3L	100128327	hgsc.bcm.edu	37	6	116818120	116818120	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:116818120delT	ENST00000368602.3	-	5	638	c.543delA	c.(541-543)aaafs	p.K181fs	RP11-259P20.1_ENST00000420595.2_RNA|TRAPPC3L_ENST00000356128.4_Frame_Shift_Del_p.K97fs	NM_001139444.2	NP_001132916.1	Q5T215	TPC3L_HUMAN	trafficking protein particle complex 3-like	181					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)											CTAGTCTTCATTTTTTCCCTC	0.368																																					p.X182E		Atlas-INDEL	.											.,2	BET3L	18	.	0			c.544delT						.						292.0	249.0	262.0					6																	116818120		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.543delA	chr6.hg19:g.116818120delT	ENSP00000357591:p.Lys181fs	104.0	0.0		135.0	12.0	NM_001139444	Q5T213|Q5T214	Frame_Shift_Del	DEL	ENST00000368602.3	hg19	CCDS47468.1																																																																																			.	.		0.368	TRAPPC3L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000101701.1	XM_166322	
LAMA4	3910	hgsc.bcm.edu	37	6	112450166	112450166	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:112450166delT	ENST00000230538.7	-	31	4642	c.4245delA	c.(4243-4245)aaafs	p.K1415fs	LAMA4_ENST00000389463.4_Frame_Shift_Del_p.K1408fs|LAMA4_ENST00000424408.2_Frame_Shift_Del_p.K1408fs|LAMA4_ENST00000522006.1_Frame_Shift_Del_p.K1408fs	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1415					blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		AATTTTTTCCTTTTTTATGGA	0.373																																					p.G1416fs		Atlas-INDEL	.											.	LAMA4	227	.	0			c.4246delG						.						113.0	111.0	111.0					6																	112450166		2203	4300	6503	SO:0001589	frameshift_variant	3910	exon31			.		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.4245delA	chr6.hg19:g.112450166delT	ENSP00000230538:p.Lys1415fs	129.0	0.0		158.0	11.0	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Frame_Shift_Del	DEL	ENST00000230538.7	hg19	CCDS43491.1																																																																																			.	.		0.373	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
NOP16	51491	hgsc.bcm.edu	37	5	175812233	175812233	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:175812233delC	ENST00000389158.5	-	4	817	c.382delG	c.(382-384)gagfs	p.E128fs	NOP16_ENST00000507413.1_Intron|NOP16_ENST00000509257.1_Frame_Shift_Del_p.E128fs|NOP16_ENST00000510123.1_Frame_Shift_Del_p.E128fs			Q9Y3C1	NOP16_HUMAN	NOP16 nucleolar protein	128						intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|lung(4)|ovary(1)	8						TTATAGTCCTCCCCGTGGTTC	0.567																																					p.E128fs		Atlas-INDEL	.											.	NOP16	26	.	0			c.383delA						.						103.0	104.0	104.0					5																	175812233		1905	4116	6021	SO:0001589	frameshift_variant	51491	exon4			.		CCDS43403.1, CCDS58991.1	5q35.2	2012-12-10	2012-12-10		ENSG00000048162	ENSG00000048162			26934	protein-coding gene	gene with protein product	"""hypothetical protein HSPC111"", ""HBV pre-S2 trans-regulated protein 3"""	612861	"""nucleolar protein 16 homolog (yeast)"", ""NOP16 nucleolar protein homolog (yeast)"""			10810093, 11042152	Standard	NM_001291308		Approved	HSPC111, HSPC185, LOC51491	uc003mee.4	Q9Y3C1	OTTHUMG00000163186	ENST00000389158.5:c.382delG	chr5.hg19:g.175812233delC	ENSP00000373810:p.Glu128fs	101.0	0.0		136.0	11.0	NM_016391	B4DV13|D6RGD3|Q05D05|Q6IAI6|Q8IXL5	Frame_Shift_Del	DEL	ENST00000389158.5	hg19	CCDS43403.1																																																																																			.	.		0.567	NOP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371963.1	NM_016391	
B3GAT2	135152	hgsc.bcm.edu	37	6	71566736	71566736	+	3'UTR	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:71566736delA	ENST00000230053.6	-	0	6210				SMAP1_ENST00000370452.3_Intron|SMAP1_ENST00000370455.3_Intron|SMAP1_ENST00000316999.5_Intron	NM_080742.2	NP_542780.1	Q9NPZ5	B3GA2_HUMAN	beta-1,3-glucuronyltransferase 2						carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						TACTCCTGGTAATGAATTTTG	0.323																																					.		Atlas-INDEL	.											.	SMAP1	77	.	0			c.961+2A>-						.						88.0	86.0	87.0					6																	71566736		2203	4300	6503	SO:0001624	3_prime_UTR_variant	60682	exon9			.	AB075843	CCDS4974.1	6q12	2014-07-08	2014-07-08		ENSG00000112309	ENSG00000112309	2.4.1.135	"""Beta-1,3-glucuronyltransferases"""	922	protein-coding gene	gene with protein product	"""glucuronosyltransferase S"", ""galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2"""	607497				12383500	Standard	NM_080742		Approved	GlcAT-S	uc003pfv.3	Q9NPZ5	OTTHUMG00000014997	ENST00000230053.6:c.*4630T>-	chr6.hg19:g.71566736delA		128.0	0.0		135.0	10.0	NM_001044305	Q5JS09|Q8TF38|Q96NK4	Splice_Site	DEL	ENST00000230053.6	hg19	CCDS4974.1																																																																																			.	.		0.323	B3GAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041150.2	NM_080742	
C11orf73	51501	hgsc.bcm.edu	37	11	86056631	86056631	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:86056631delA	ENST00000278483.3	+	5	771	c.545delA	c.(544-546)gaafs	p.E182fs	C11orf73_ENST00000533986.1_3'UTR|C11orf73_ENST00000530208.1_3'UTR	NM_016401.3	NP_057485.2	Q53FT3	HIKES_HUMAN	chromosome 11 open reading frame 73	182					cellular response to heat (GO:0034605)|Golgi organization (GO:0007030)|lung development (GO:0030324)|protein import into nucleus (GO:0006606)|protein transport (GO:0015031)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	Hsp70 protein binding (GO:0030544)|protein transporter activity (GO:0008565)			kidney(1)|large_intestine(1)|urinary_tract(1)	3		Acute lymphoblastic leukemia(157;1.17e-07)|all_hematologic(158;0.000556)				TCTAGGTATGAAAACTTTCAA	0.269																																					p.E182fs		Atlas-INDEL	.											.	C11orf73	9	.	0			c.544delG						.						44.0	49.0	47.0					11																	86056631		2194	4269	6463	SO:0001589	frameshift_variant	51501	exon5			.	BC015991	CCDS8275.1	11q14.2	2013-03-12			ENSG00000149196	ENSG00000149196			26938	protein-coding gene	gene with protein product		614908				11042152, 22541429	Standard	NM_016401		Approved	HSPC138, HSPC179, Hikeshi, OPI10	uc001pbu.3	Q53FT3	OTTHUMG00000167212	ENST00000278483.3:c.545delA	chr11.hg19:g.86056631delA	ENSP00000278483:p.Glu182fs	58.0	0.0		125.0	10.0	NM_016401	Q8WVE8|Q9NVQ2|Q9NZZ1|Q9P022|Q9P0N1	Frame_Shift_Del	DEL	ENST00000278483.3	hg19	CCDS8275.1																																																																																			.	.		0.269	C11orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393747.1	NM_016401	
SNTB2	6645	hgsc.bcm.edu	37	16	69333538	69333538	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:69333538delA	ENST00000336278.4	+	6	1429	c.1391delA	c.(1390-1392)gaafs	p.E464fs	RP11-343C2.11_ENST00000570054.2_5'Flank	NM_006750.3	NP_006741.1	Q13425	SNTB2_HUMAN	syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)	464						cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|microtubule (GO:0005874)|protein complex (GO:0043234)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	13		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)		ATTCACTATGAAAATGGGTTC	0.428																																					p.E464fs	NSCLC(58;1458 1722 3262 39967)|Melanoma(111;1698 2173 25379 28738)	Atlas-INDEL	.											.	SNTB2	22	.	0			c.1390delG						.						110.0	99.0	103.0					16																	69333538		2198	4300	6498	SO:0001589	frameshift_variant	6645	exon6			.	U40572	CCDS10873.1	16q22.1	2008-05-14	2002-08-29		ENSG00000168807	ENSG00000168807			11169	protein-coding gene	gene with protein product		600027	"""syntrophin, beta 2 (dystrophin-associated protein A1, 59kD, basic component 2)"""	SNT2B2, SNTL, D16S2531E		8576247, 8183929	Standard	NM_006750		Approved	EST25263, SNT3	uc002ewu.3	Q13425	OTTHUMG00000137567	ENST00000336278.4:c.1391delA	chr16.hg19:g.69333538delA	ENSP00000338191:p.Glu464fs	108.0	0.0		148.0	14.0	NM_006750	Q9BY09	Frame_Shift_Del	DEL	ENST00000336278.4	hg19	CCDS10873.1																																																																																			.	.		0.428	SNTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268945.1		
CCDC85C	317762	hgsc.bcm.edu	37	14	99983523	99983523	+	Intron	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:99983523delG	ENST00000380243.4	-	4	1042				CCDC85C_ENST00000557769.1_Intron|CCDC85C_ENST00000555822.1_Intron|CCNK_ENST00000555049.1_Intron	NM_001144995.1	NP_001138467.1	A6NKD9	CC85C_HUMAN	coiled-coil domain containing 85C						cerebral cortex development (GO:0021987)	apical junction complex (GO:0043296)|tight junction (GO:0005923)				endometrium(1)|skin(1)	2						GCCGGGCCCTGGGGAAGGCAA	0.672																																					.		Atlas-INDEL	.											.	CCDC85C	3	.	0			c.976-2C>-						.						9.0	14.0	12.0					14																	99983523		689	1586	2275	SO:0001627	intron_variant	317762	exon5			.		CCDS45161.1	14q32.31	2009-02-18				ENSG00000205476			35459	protein-coding gene	gene with protein product							Standard	NM_001144995		Approved		uc010avr.3	A6NKD9		ENST00000380243.4:c.976-3C>-	chr14.hg19:g.99983523delG		120.0	0.0		140.0	12.0	NM_001144995		Splice_Site	DEL	ENST00000380243.4	hg19	CCDS45161.1																																																																																			.	.		0.672	CCDC85C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413802.1	NM_001144995	
SCN1A	6323	hgsc.bcm.edu	37	2	166903448	166903448	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:166903448delA	ENST00000303395.4	-	9	1208	c.1209delT	c.(1207-1209)tttfs	p.F403fs	AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000375405.3_Frame_Shift_Del_p.F403fs|SCN1A_ENST00000409050.1_Frame_Shift_Del_p.F403fs|SCN1A_ENST00000423058.2_Frame_Shift_Del_p.F403fs|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595268.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	403			F -> L (in EIEE6; dbSNP:rs121917966). {ECO:0000269|PubMed:16713920, ECO:0000269|PubMed:17347258}.		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)	TGACCAATACAAAAAATATCA	0.393																																					p.V404fs		Atlas-Indel,Pindel	.											.	SCN1A	641	.	0			c.1210delG						.						100.0	97.0	98.0					2																	166903448		2203	4300	6503	SO:0001589	frameshift_variant	6323	exon9			.	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.1209delT	chr2.hg19:g.166903448delA	ENSP00000303540:p.Phe403fs	131.0	0.0		183.0	13.0	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Frame_Shift_Del	DEL	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.		0.393	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
ARID2	196528	hgsc.bcm.edu	37	12	46243493	46243493	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:46243493delC	ENST00000334344.6	+	14	2018	c.1846delC	c.(1846-1848)ccafs	p.P616fs	ARID2_ENST00000422737.1_Frame_Shift_Del_p.P467fs|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000444670.1_Frame_Shift_Del_p.P226fs	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	616					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|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)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TCAGCAGCAACCAGTTTCTAC	0.413			"""N, S, F"""		hepatocellular carcinoma																																p.Q615fs		Atlas-INDEL	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.1845delA						.						326.0	304.0	311.0					12																	46243493		2203	4300	6503	SO:0001589	frameshift_variant	196528	exon14			.		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.1846delC	chr12.hg19:g.46243493delC	ENSP00000335044:p.Pro616fs	175.0	0.0		180.0	11.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Del	DEL	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.		0.413	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875	
ARSJ	79642	hgsc.bcm.edu	37	4	114899693	114899693	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:114899693delT	ENST00000315366.7	-	1	1164	c.298delA	c.(298-300)acafs	p.T100fs	ARSJ_ENST00000541197.1_Frame_Shift_Del_p.T100fs|ARSJ_ENST00000503013.2_5'UTR	NM_024590.3	NP_078866.3	Q5FYB0	ARSJ_HUMAN	arylsulfatase family, member J	100					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 region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	21		Ovarian(17;0.0035)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00194)		AGAGTAGGTGTTTTAATCTCA	0.473																																					p.T100fs		Atlas-INDEL	.											.	ARSJ	55	.	0			c.299delC						.						98.0	97.0	97.0					4																	114899693		1926	4127	6053	SO:0001589	frameshift_variant	79642	exon1			.		CCDS43264.1	4q26	2013-02-14	2006-03-07		ENSG00000180801	ENSG00000180801		"""Arylsulfatase family"""	26286	protein-coding gene	gene with protein product		610010	"""arylsulfatase J"""			12975309, 16174644	Standard	NM_024590		Approved	FLJ23548	uc003ibq.1	Q5FYB0	OTTHUMG00000161067	ENST00000315366.7:c.298delA	chr4.hg19:g.114899693delT	ENSP00000320219:p.Thr100fs	175.0	0.0		154.0	10.0	NM_024590	A2RUG0|B7ZM45|Q1HA39|Q5FWE4|Q6UWT9	Frame_Shift_Del	DEL	ENST00000315366.7	hg19	CCDS43264.1																																																																																			.	.		0.473	ARSJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363650.1	NM_024590	
ZNF148	7707	hgsc.bcm.edu	37	3	125007010	125007010	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:125007010delT	ENST00000360647.4	-	5	881	c.396delA	c.(394-396)aaafs	p.K132fs	ZNF148_ENST00000485866.1_Frame_Shift_Del_p.K132fs|ZNF148_ENST00000497929.1_5'UTR|ZNF148_ENST00000492394.1_Frame_Shift_Del_p.K132fs|ZNF148_ENST00000544464.1_Intron|ZNF148_ENST00000468369.1_Intron|ZNF148_ENST00000484491.1_Frame_Shift_Del_p.K132fs	NM_021964.2	NP_068799.2	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	132					cellular defense response (GO:0006968)|gamete generation (GO:0007276)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein complex assembly (GO:0006461)|substantia nigra development (GO:0021762)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)	28						CTCTGATTTGTTTTTTGTCTC	0.343																																					p.Q133fs		Atlas-INDEL	.											ZNF148,NS,carcinoma,+1,1	ZNF148	84	.	0			c.397delC						.						202.0	174.0	183.0					3																	125007010		2203	4300	6503	SO:0001589	frameshift_variant	7707	exon5			.	U09851	CCDS3031.1	3q21.2	2013-01-08	2006-06-13		ENSG00000163848	ENSG00000163848		"""Zinc fingers, C2H2-type"""	12933	protein-coding gene	gene with protein product		601897	"""zinc finger protein 148 (pHZ-52)"""			7557990, 9925940	Standard	NM_021964		Approved	BERF-1, ZBP-89, BFCOL1, HT-BETA, ZFP148, pHZ-52	uc003ehx.4	Q9UQR1	OTTHUMG00000159448	ENST00000360647.4:c.396delA	chr3.hg19:g.125007010delT	ENSP00000353863:p.Lys132fs	105.0	0.0		126.0	10.0	NM_021964	D3DN27|O00389|O43591|Q58EY5|Q6PJ98	Frame_Shift_Del	DEL	ENST00000360647.4	hg19	CCDS3031.1																																																																																			.	.		0.343	ZNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355452.4	NM_021964	
GAMT	2593	hgsc.bcm.edu	37	19	1398959	1398959	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:1398959delC	ENST00000252288.2	-	5	592	c.526delG	c.(526-528)gagfs	p.E176fs	GAMT_ENST00000447102.3_Frame_Shift_Del_p.E176fs|AC005329.7_ENST00000501448.1_RNA	NM_000156.5	NP_000147.1	Q14353	GAMT_HUMAN	guanidinoacetate N-methyltransferase	176	RMT2. {ECO:0000255|PROSITE- ProRule:PRU00892}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine biosynthetic process (GO:0006601)|creatine metabolic process (GO:0006600)|muscle contraction (GO:0006936)|organ morphogenesis (GO:0009887)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	guanidinoacetate N-methyltransferase activity (GO:0030731)|methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(3)|kidney(1)|upper_aerodigestive_tract(1)	6		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Lung NSC(49;0.000195)|Breast(49;0.000231)|all_lung(49;0.000247)|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)	Creatine(DB00148)|Guanidine(DB00536)	TTCATCAGCTCCCCCCAGGAG	0.602																																					p.E176fs	Colon(167;1531 1939 13427 28842 31956)	Atlas-INDEL	.											.	GAMT	39	.	0			c.527delA						.						82.0	66.0	71.0					19																	1398959		2203	4300	6503	SO:0001589	frameshift_variant	2593	exon5			.	Z49878	CCDS12064.1, CCDS45897.1	19p13.3	2008-02-05							4136	protein-coding gene	gene with protein product		601240				9570966, 8547310	Standard	NM_000156		Approved	PIG2, TP53I2	uc002lsk.4	Q14353		ENST00000252288.2:c.526delG	chr19.hg19:g.1398959delC	ENSP00000252288:p.Glu176fs	197.0	0.0		285.0	20.0	NM_138924	A8K0A0|Q53Y34|Q8WVJ1	Frame_Shift_Del	DEL	ENST00000252288.2	hg19	CCDS12064.1																																																																																			.	.		0.602	GAMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449739.1	NM_138924	
DICER1	23405	hgsc.bcm.edu	37	14	95562262	95562262	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:95562262delC	ENST00000526495.1	-	25	5286	c.4995delG	c.(4993-4995)gggfs	p.G1665fs	DICER1_ENST00000343455.3_Frame_Shift_Del_p.G1665fs|DICER1_ENST00000541352.1_Frame_Shift_Del_p.G1665fs|DICER1_ENST00000556045.1_Frame_Shift_Del_p.G563fs|DICER1_ENST00000527414.1_Frame_Shift_Del_p.G1665fs|DICER1_ENST00000393063.1_Frame_Shift_Del_p.G1665fs			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	1665					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		AATTTTCAAACCCCGATATAA	0.368			"""Mis F, N"""		"""sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"""	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.F1666fs		Atlas-INDEL	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"""dicer 1, ribonuclease type III """		"""E, M, O"""	.	DICER1	181	.	0			c.4996delT						.						106.0	108.0	107.0					14																	95562262		2203	4300	6503	SO:0001589	frameshift_variant	23405	exon23	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	.	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"""dicer 1, double-stranded RNA-specific endoribonuclease"""	606241	"""Dicer1, Dcr-1 homolog (Drosophila)"", ""multinodular goitre 1"""	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.4995delG	chr14.hg19:g.95562262delC	ENSP00000437256:p.Gly1665fs	139.0	0.0		166.0	11.0	NM_001271282	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Frame_Shift_Del	DEL	ENST00000526495.1	hg19	CCDS9931.1																																																																																			.	.		0.368	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1		
RAB1A	5861	hgsc.bcm.edu	37	2	65316146	65316146	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:65316146delT	ENST00000409784.3	-	5	537	c.347delA	c.(346-348)aatfs	p.N116fs	RAB1A_ENST00000409892.1_Frame_Shift_Del_p.N52fs|RAB1A_ENST00000409751.1_Frame_Shift_Del_p.N84fs|RAB1A_ENST00000494188.1_Intron|RAB1A_ENST00000260638.8_Intron|RAB1A_ENST00000356214.7_Frame_Shift_Del_p.N84fs|RAB1A_ENST00000398529.3_Intron	NM_004161.4	NP_004152.1	P62820	RAB1A_HUMAN	RAB1A, member RAS oncogene family	116					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cargo loading into COPII-coated vesicle (GO:0090110)|cell migration (GO:0016477)|defense response to bacterium (GO:0042742)|endocytosis (GO:0006897)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|growth hormone secretion (GO:0030252)|GTP catabolic process (GO:0006184)|interleukin-8 secretion (GO:0072606)|melanosome transport (GO:0032402)|mitotic cell cycle (GO:0000278)|positive regulation of glycoprotein metabolic process (GO:1903020)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle transport along microtubule (GO:0047496)|vesicle-mediated transport (GO:0016192)|virion assembly (GO:0019068)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|melanosome (GO:0042470)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|kidney(1)|lung(3)|prostate(1)	6						TTTGTTGACATTTTCACTGGC	0.333																																					p.N116fs		Atlas-INDEL	.											.	RAB1A	15	.	0			c.348delT						.						74.0	65.0	68.0					2																	65316146		1880	4104	5984	SO:0001589	frameshift_variant	5861	exon5			.	M28209	CCDS46305.1, CCDS46306.1	2p14	2008-02-05		2002-03-17	ENSG00000138069	ENSG00000138069		"""RAB, member RAS oncogene"""	9758	protein-coding gene	gene with protein product	"""Rab GTPase YPT1 homolog (yeast)"""	179508		RAB1		2501306	Standard	NM_004161		Approved	YPT1	uc002sdm.3	P62820	OTTHUMG00000152725	ENST00000409784.3:c.347delA	chr2.hg19:g.65316146delT	ENSP00000387286:p.Asn116fs	122.0	0.0		153.0	10.0	NM_004161	P11476|Q6FIE7|Q96N61|Q9Y3T2	Frame_Shift_Del	DEL	ENST00000409784.3	hg19	CCDS46306.1																																																																																			.	.		0.333	RAB1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327572.1	NM_004161	
CLDN2	9075	hgsc.bcm.edu	37	X	106171549	106171549	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:106171549delA	ENST00000541806.1	+	2	610	c.91delA	c.(91-93)aaafs	p.K31fs	CLDN2_ENST00000540876.1_Frame_Shift_Del_p.K31fs|CLDN2_ENST00000336803.1_Frame_Shift_Del_p.K31fs	NM_001171092.1	NP_001164563.1	P57739	CLD2_HUMAN	claudin 2	31					calcium-independent cell-cell adhesion (GO:0016338)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						CCCCAGCTGGAAAACAAGTTC	0.567																																					p.W30X		Atlas-INDEL	.											.	CLDN2	22	.	0			c.90delG						.						91.0	78.0	82.0					X																	106171549		2203	4300	6503	SO:0001589	frameshift_variant	9075	exon2			.	AK075405	CCDS14524.1	Xq22.3-q23	2008-05-14			ENSG00000165376	ENSG00000165376		"""Claudins"""	2041	protein-coding gene	gene with protein product		300520				9892664	Standard	NM_020384		Approved		uc022ccc.1	P57739	OTTHUMG00000022154	ENST00000541806.1:c.91delA	chrX.hg19:g.106171549delA	ENSP00000441283:p.Lys31fs	93.0	0.0		116.0	10.0	NM_001171092	B2R6B9	Frame_Shift_Del	DEL	ENST00000541806.1	hg19	CCDS14524.1																																																																																			.	.		0.567	CLDN2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057815.1		
GLRX2	51022	hgsc.bcm.edu	37	1	193066820	193066820	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:193066820delT	ENST00000367439.3	-	3	302	c.254delA	c.(253-255)aagfs	p.K85fs	GLRX2_ENST00000367440.3_Frame_Shift_Del_p.K86fs|GLRX2_ENST00000472197.1_5'UTR	NM_197962.2	NP_932066.1	Q9NS18	GLRX2_HUMAN	glutaredoxin 2	85	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|DNA protection (GO:0042262)|glutathione metabolic process (GO:0006749)|protein folding (GO:0006457)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|response to hydrogen peroxide (GO:0042542)|response to organic substance (GO:0010033)|response to redox state (GO:0051775)|response to temperature stimulus (GO:0009266)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	2 iron, 2 sulfur cluster binding (GO:0051537)|arsenate reductase (glutaredoxin) activity (GO:0008794)|electron carrier activity (GO:0009055)|glutathione disulfide oxidoreductase activity (GO:0015038)|metal ion binding (GO:0046872)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|large_intestine(1)|lung(3)	5					Glutathione(DB00143)	ATGGAAAAGCTTTTTTGCCAT	0.333																																					p.K86fs		Atlas-INDEL	.											.	GLRX2	9	.	0			c.258delG						.						120.0	112.0	115.0					1																	193066820		2203	4300	6503	SO:0001589	frameshift_variant	51022	exon3			.	AF132495	CCDS1380.1, CCDS1381.1	1q31.2	2012-09-20			ENSG00000023572	ENSG00000023572			16065	protein-coding gene	gene with protein product	"""bA101E13.1 (GRX2 glutaredoxin (thioltransferase) 2)"""	606820				11297543	Standard	NM_016066		Approved	GRX2, bA101E13.1	uc001gsz.2	Q9NS18	OTTHUMG00000035677	ENST00000367439.3:c.254delA	chr1.hg19:g.193066820delT	ENSP00000356409:p.Lys85fs	113.0	0.0		187.0	12.0	NM_016066	Q3LR69|Q7L1N7|Q96JC0|Q9Y3D4	Frame_Shift_Del	DEL	ENST00000367439.3	hg19	CCDS1381.1																																																																																			.	.		0.333	GLRX2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086699.1	NM_016066	
PIAS2	9063	hgsc.bcm.edu	37	18	44444168	44444168	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:44444168delA	ENST00000585916.1	-	3	542	c.543delT	c.(541-543)tttfs	p.F181fs	PIAS2_ENST00000545673.1_5'UTR|PIAS2_ENST00000324794.7_Frame_Shift_Del_p.F181fs	NM_004671.3	NP_004662.2	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT, 2	181	PINIT. {ECO:0000255|PROSITE- ProRule:PRU00799}.				androgen receptor signaling pathway (GO:0030521)|negative regulation of androgen receptor signaling pathway (GO:0060766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|regulation of osteoblast differentiation (GO:0045667)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	22						GTGTCAAAGCAAAAATAAAAA	0.313																																					p.A182fs		Atlas-INDEL	.											.	PIAS2	85	.	0			c.544delG						.						53.0	58.0	56.0					18																	44444168		2202	4300	6502	SO:0001589	frameshift_variant	9063	exon3			.	AF077953	CCDS32824.1, CCDS32825.1	18q12.1-q12.3	2011-10-11				ENSG00000078043		"""Zinc fingers, MIZ-type"""	17311	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 4"""	603567				9724754, 9256341	Standard	NM_004671		Approved	PIASX-BETA, miz, PIASX-ALPHA, ZMIZ4	uc002lck.3	O75928		ENST00000585916.1:c.543delT	chr18.hg19:g.44444168delA	ENSP00000465676:p.Phe181fs	102.0	0.0		146.0	10.0	NM_173206	O75927|Q96BT5|Q96KE3	Frame_Shift_Del	DEL	ENST00000585916.1	hg19	CCDS32824.1																																																																																			.	.		0.313	PIAS2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445656.2	NM_004671	
TPRN	286262	hgsc.bcm.edu	37	9	140087119	140087119	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:140087119delT	ENST00000409012.4	-	2	1836	c.1750delA	c.(1750-1752)agcfs	p.S584fs	TPRN_ENST00000541945.1_5'UTR|TPRN_ENST00000321773.2_Frame_Shift_Del_p.S523fs	NM_001128228.2	NP_001121700.2	Q4KMQ1	TPRN_HUMAN	taperin	584					sensory perception of sound (GO:0007605)	stereocilium (GO:0032420)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	8						GTCTGCAGGCTTTTGTCGTTG	0.587																																					p.S584fs		Atlas-INDEL	.											.	TPRN	28	.	0			c.1751delG						.						98.0	91.0	94.0					9																	140087119		2203	4300	6503	SO:0001589	frameshift_variant	286262	exon2			.	AK074735	CCDS56594.1	9q34.3	2011-01-06	2010-03-24	2010-03-24	ENSG00000176058	ENSG00000176058			26894	protein-coding gene	gene with protein product		613354	"""chromosome 9 open reading frame 75"", ""deafness, autosomal recessive 79"""	C9orf75, DFNB79		20170898, 20170899	Standard	NM_001128228		Approved	FLJ90254	uc004clu.3	Q4KMQ1	OTTHUMG00000020984	ENST00000409012.4:c.1750delA	chr9.hg19:g.140087119delT	ENSP00000387100:p.Ser584fs	122.0	0.0		164.0	12.0	NM_001128228	B7ZKU5|Q5VSG5|Q5VSG6|Q6IPP2|Q8NCH2	Frame_Shift_Del	DEL	ENST00000409012.4	hg19	CCDS56594.1																																																																																			.	.		0.587	TPRN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055323.3	NM_173691	
NR1H3	10062	hgsc.bcm.edu	37	11	47283563	47283563	+	Frame_Shift_Del	DEL	A	A	-	rs191811598		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:47283563delA	ENST00000467728.1	+	6	2220	c.982delA	c.(982-984)aaafs	p.K328fs	NR1H3_ENST00000405576.1_Frame_Shift_Del_p.K223fs|NR1H3_ENST00000527949.1_Frame_Shift_Del_p.K177fs|NR1H3_ENST00000529540.1_3'UTR|NR1H3_ENST00000405853.3_Frame_Shift_Del_p.K268fs|NR1H3_ENST00000481889.2_Frame_Shift_Del_p.K347fs|NR1H3_ENST00000407404.1_Frame_Shift_Del_p.K268fs|NR1H3_ENST00000395397.3_Frame_Shift_Del_p.K283fs|NR1H3_ENST00000441012.2_Frame_Shift_Del_p.K328fs			Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	328	Ligand-binding. {ECO:0000255}.				apoptotic cell clearance (GO:0043277)|cellular lipid metabolic process (GO:0044255)|cellular response to lipopolysaccharide (GO:0071222)|cholesterol homeostasis (GO:0042632)|gene expression (GO:0010467)|lipid homeostasis (GO:0055088)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage activation (GO:0043031)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of pinocytosis (GO:0048550)|negative regulation of proteolysis (GO:0045861)|negative regulation of secretion of lysosomal enzymes (GO:0090341)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|response to progesterone (GO:0032570)|sterol homeostasis (GO:0055092)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid hormone receptor activity (GO:0003707)|sterol response element binding (GO:0032810)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(5)	20						AGACTTTGCCAAAGCAGGTGA	0.468																																					p.A333fs		Atlas-INDEL	.											.	NR1H3	52	.	0			c.999delC						.						110.0	106.0	107.0					11																	47283563		2201	4298	6499	SO:0001589	frameshift_variant	10062	exon7			.	U22662	CCDS7929.1, CCDS44584.1, CCDS44585.1, CCDS73285.1	11p11.2	2013-01-16			ENSG00000025434	ENSG00000025434		"""Nuclear hormone receptors"""	7966	protein-coding gene	gene with protein product	"""liver X receptor-alpha"""	602423				8621574, 7744246	Standard	NM_005693		Approved	LXR-a, RLD-1	uc009ylm.3	Q13133	OTTHUMG00000150628	ENST00000467728.1:c.982delA	chr11.hg19:g.47283563delA	ENSP00000420656:p.Lys328fs	95.0	0.0		162.0	10.0	NM_001251934	A8K3J9|D3DQR1|Q8IW13|Q96H87	Frame_Shift_Del	DEL	ENST00000467728.1	hg19	CCDS7929.1																																																																																			.	.		0.468	NR1H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319214.3		
TEX13B	56156	hgsc.bcm.edu	37	X	107224619	107224619	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:107224619delG	ENST00000302917.1	-	3	722	c.630delC	c.(628-630)cccfs	p.P210fs		NM_031273.2	NP_112563.1	Q9BXU2	TX13B_HUMAN	testis expressed 13B	210								p.P210P(1)		breast(1)|endometrium(5)|large_intestine(4)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28						AGACCTCTGCGGGGGCAGGCC	0.612																																					p.A211fs		Atlas-INDEL	.											.	TEX13B	40	.	1	Substitution - coding silent(1)	lung(1)	c.631delG						.						99.0	110.0	106.0					X																	107224619		2200	4299	6499	SO:0001589	frameshift_variant	56156	exon3			.	AF285598	CCDS14534.1	Xq23	2008-02-05	2007-03-13		ENSG00000170925	ENSG00000170925			11736	protein-coding gene	gene with protein product		300313	"""testis expressed sequence 13B"""			11279525	Standard	NM_031273		Approved	TSGA5, TGC3B	uc004enn.1	Q9BXU2	OTTHUMG00000022174	ENST00000302917.1:c.630delC	chrX.hg19:g.107224619delG	ENSP00000303777:p.Pro210fs	134.0	0.0		170.0	11.0	NM_031273	Q5JYF6	Frame_Shift_Del	DEL	ENST00000302917.1	hg19	CCDS14534.1																																																																																			.	.		0.612	TEX13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057857.1		
NUMB	8650	hgsc.bcm.edu	37	14	73753987	73753987	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:73753987delA	ENST00000355058.3	-	9	764	c.486delT	c.(484-486)tttfs	p.F162fs	NUMB_ENST00000555238.1_Frame_Shift_Del_p.F162fs|NUMB_ENST00000555738.2_Frame_Shift_Del_p.F151fs|NUMB_ENST00000560335.1_Frame_Shift_Del_p.F162fs|NUMB_ENST00000554546.1_Frame_Shift_Del_p.F151fs|NUMB_ENST00000554521.2_Frame_Shift_Del_p.F151fs|NUMB_ENST00000559312.1_Frame_Shift_Del_p.F162fs|NUMB_ENST00000356296.4_Frame_Shift_Del_p.F162fs|NUMB_ENST00000535282.1_Frame_Shift_Del_p.F151fs|NUMB_ENST00000555394.1_Frame_Shift_Del_p.F162fs|NUMB_ENST00000359560.3_Frame_Shift_Del_p.F151fs|NUMB_ENST00000557597.1_Frame_Shift_Del_p.F151fs|NUMB_ENST00000544991.3_Frame_Shift_Del_p.F162fs|NUMB_ENST00000454166.4_Frame_Shift_Del_p.F162fs|NUMB_ENST00000556772.1_Frame_Shift_Del_p.F18fs			P49757	NUMB_HUMAN	numb homolog (Drosophila)	162	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|lateral ventricle development (GO:0021670)|lung epithelial cell differentiation (GO:0060487)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein localization to plasma membrane (GO:1903077)|neuroblast division in subventricular zone (GO:0021849)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration (GO:0030335)|positive regulation of neurogenesis (GO:0050769)|positive regulation of polarized epithelial cell differentiation (GO:0030862)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		AACAGGCTGCAAAAGCACAGC	0.423																																					p.A163fs		Atlas-INDEL	.											.	NUMB	56	.	0			c.487delG						.						83.0	71.0	75.0					14																	73753987		2203	4300	6503	SO:0001589	frameshift_variant	8650	exon9			.	L40393	CCDS9814.1, CCDS32115.1, CCDS32116.1, CCDS55927.1	14q24.3	2011-11-25	2001-11-28			ENSG00000133961			8060	protein-coding gene	gene with protein product		603728	"""numb (Drosophila) homolog"", ""chromosome 14 open reading frame 41"""	C14orf41			Standard	NM_003744		Approved		uc001xny.1	P49757		ENST00000355058.3:c.486delT	chr14.hg19:g.73753987delA	ENSP00000347169:p.Phe162fs	147.0	0.0		164.0	10.0	NM_001005744	B1P2N5|B1P2N6|B1P2N7|B1P2N8|B1P2N9|B4E2B1|Q6NUQ7|Q86SY1|Q8WW73|Q9UBG1|Q9UEQ4|Q9UKE8|Q9UKE9|Q9UKF0|Q9UQJ4	Frame_Shift_Del	DEL	ENST00000355058.3	hg19	CCDS32116.1																																																																																			.	.		0.423	NUMB-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414416.1		
TBC1D32	221322	hgsc.bcm.edu	37	6	121624805	121624805	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:121624805delA	ENST00000398212.2	-	9	1087	c.1038delT	c.(1036-1038)tttfs	p.F346fs	TBC1D32_ENST00000275159.6_Frame_Shift_Del_p.F346fs	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	346					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										CAACTAATGCAAAAAAGTAGA	0.313																																					p.A347fs		Atlas-INDEL	.											.	C6orf170	146	.	0			c.1039delG						.						94.0	85.0	88.0					6																	121624805		1806	4073	5879	SO:0001589	frameshift_variant	221322	exon9			.	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.1038delT	chr6.hg19:g.121624805delA	ENSP00000381270:p.Phe346fs	112.0	0.0		131.0	10.0	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Frame_Shift_Del	DEL	ENST00000398212.2	hg19	CCDS43501.1																																																																																			.	.		0.313	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
UNC45A	55898	hgsc.bcm.edu	37	15	91488144	91488144	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:91488144delG	ENST00000418476.2	+	9	1090	c.1050delG	c.(1048-1050)gtgfs	p.V350fs	UNC45A_ENST00000394275.2_Frame_Shift_Del_p.V335fs	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	350					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			TTTTGGAAGTGGGGGGCTCTC	0.507																																					p.V350fs		Atlas-INDEL	.											.	UNC45A	57	.	0			c.1049delT						.																																			SO:0001589	frameshift_variant	55898	exon9			.		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"""smooth muscle cell associated protein-1"""	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.1050delG	chr15.hg19:g.91488144delG	ENSP00000407487:p.Val350fs	142.0	0.0		178.0	11.0	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Frame_Shift_Del	DEL	ENST00000418476.2	hg19	CCDS10367.1																																																																																			.	.		0.507	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671	
AP4M1	9179	hgsc.bcm.edu	37	7	99701731	99701731	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:99701731delT	ENST00000359593.4	+	7	718	c.560delT	c.(559-561)gttfs	p.V187fs	AP4M1_ENST00000421755.1_Frame_Shift_Del_p.V187fs|AP4M1_ENST00000422582.1_Frame_Shift_Del_p.V59fs|MCM7_ENST00000343023.6_5'Flank|MCM7_ENST00000303887.5_5'Flank|AP4M1_ENST00000429084.1_Frame_Shift_Del_p.V194fs	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	187	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|Golgi trans cisterna (GO:0000138)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AAGAATGAAGTTTTTTTGGAT	0.438																																					p.V187fs	Pancreas(174;1182 2812 29595 49511)	Atlas-INDEL	.											.	AP4M1	39	.	0			c.559delG						.						123.0	109.0	113.0					7																	99701731		2203	4300	6503	SO:0001589	frameshift_variant	9179	exon7			.	Y08387	CCDS5685.1	7q22.1	2012-06-29			ENSG00000221838	ENSG00000221838			574	protein-coding gene	gene with protein product	"""mu-adaptin-related protein-2"", ""mu subunit of AP-4"", ""AP-4 adapter complex mu subunit"", ""adaptor-related protein complex AP-4 mu4 subunit"""	602296				9013859, 10066790, 21620353	Standard	NM_004722		Approved	MU-ARP2, MU-4, SPG50	uc003utb.4	O00189	OTTHUMG00000154722	ENST00000359593.4:c.560delT	chr7.hg19:g.99701731delT	ENSP00000352603:p.Val187fs	81.0	0.0		171.0	11.0	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Frame_Shift_Del	DEL	ENST00000359593.4	hg19	CCDS5685.1																																																																																			.	.		0.438	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722	
ANKRD12	23253	hgsc.bcm.edu	37	18	9275668	9275668	+	Intron	DEL	A	A	-	rs560966362		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:9275668delA	ENST00000262126.4	+	11	6147				ANKRD12_ENST00000400020.3_Intron|snoU13_ENST00000459594.1_RNA|ANKRD12_ENST00000383440.2_Intron	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12							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						ACTCTCAGGTAAAATGTTTGT	0.353																																					.		Atlas-INDEL	.											.	ANKRD12	167	.	0			c.5838+2A>-						.						123.0	113.0	116.0					18																	9275668		2203	4300	6503	SO:0001627	intron_variant	23253	exon10			.	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.5907+3A>-	chr18.hg19:g.9275668delA		168.0	0.0		160.0	10.0	NM_001083625	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Splice_Site	DEL	ENST00000262126.4	hg19	CCDS11843.1																																																																																			.	.		0.353	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
AK7	122481	hgsc.bcm.edu	37	14	96916175	96916175	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:96916175delA	ENST00000267584.4	+	9	951	c.907delA	c.(907-909)aaafs	p.K303fs		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	303					axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GAAAATCCAGAAAATACCCAG	0.323																																					p.Q302fs		Atlas-INDEL	.											.	AK7	69	.	0			c.906delG						.						52.0	55.0	54.0					14																	96916175		2203	4300	6503	SO:0001589	frameshift_variant	122481	exon9			.	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"""Adenylate kinases"""	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.907delA	chr14.hg19:g.96916175delA	ENSP00000267584:p.Lys303fs	92.0	0.0		157.0	13.0	NM_152327	Q8IYP6	Frame_Shift_Del	DEL	ENST00000267584.4	hg19	CCDS9945.1																																																																																			.	.		0.323	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1		
NT5DC3	51559	hgsc.bcm.edu	37	12	104208851	104208851	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:104208851delA	ENST00000392876.3	-	2	297	c.257delT	c.(256-258)ttcfs	p.F86fs		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	86						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						ATTGTTTGAGAAAATGGCATC	0.333																																					p.F86fs		Atlas-INDEL	.											.	NT5DC3	113	.	0			c.258delC						.						85.0	79.0	81.0					12																	104208851		2203	4300	6503	SO:0001589	frameshift_variant	51559	exon2			.	AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.257delT	chr12.hg19:g.104208851delA	ENSP00000376615:p.Phe86fs	136.0	0.0		148.0	12.0	NM_001031701	Q9NUM7|Q9P2T2|Q9P2T3	Frame_Shift_Del	DEL	ENST00000392876.3	hg19	CCDS41824.1																																																																																			.	.		0.333	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575	
ADAMTS1	9510	hgsc.bcm.edu	37	21	28210011	28210011	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:28210011delT	ENST00000284984.3	-	9	3245	c.2791delA	c.(2791-2793)agafs	p.R931fs		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	931	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		TTCAAGCTTCTTTTTTTGTAA	0.493																																					p.R931fs		Atlas-INDEL	.											.	ADAMTS1	131	.	0			c.2792delG						.						116.0	122.0	120.0					21																	28210011		2203	4300	6503	SO:0001589	frameshift_variant	9510	exon9			.	AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	217	protein-coding gene	gene with protein product		605174	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"""			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.2791delA	chr21.hg19:g.28210011delT	ENSP00000284984:p.Arg931fs	257.0	0.0		204.0	14.0	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Frame_Shift_Del	DEL	ENST00000284984.3	hg19	CCDS33524.1																																																																																			.	.		0.493	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2		
TTN	7273	hgsc.bcm.edu	37	2	179528765	179528765	+	Intron	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:179528765delT	ENST00000591111.1	-	154	34489				TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Frame_Shift_Del_p.K12114fs|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin						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)			GACTTCAGGCTTTTTAGGAGG	0.388																																					p.K12114fs		Atlas-INDEL	.											.	TTN	18412	.	0			c.36342delG						.						130.0	126.0	127.0					2																	179528765		876	1991	2867	SO:0001627	intron_variant	7273	exon169			.	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.34265-5244A>-	chr2.hg19:g.179528765delT		186.0	0.0		215.0	13.0	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																																																																																				.	.		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RAD51AP2	729475	hgsc.bcm.edu	37	2	17698475	17698475	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:17698475delA	ENST00000399080.2	-	1	1231	c.1208delT	c.(1207-1209)ttgfs	p.L403fs		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	403										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					ATTTCTTCTCAAAATATGTCT	0.318																																					p.L403fs		Atlas-INDEL	.											.	RAD51AP2	134	.	0			c.1209delG						.						51.0	50.0	50.0					2																	17698475		1803	4073	5876	SO:0001589	frameshift_variant	729475	exon1			.	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.1208delT	chr2.hg19:g.17698475delA	ENSP00000382030:p.Leu403fs	131.0	0.0		180.0	14.0	NM_001099218		Frame_Shift_Del	DEL	ENST00000399080.2	hg19	CCDS42656.1																																																																																			.	.		0.318	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218	
SERPINF1	5176	hgsc.bcm.edu	37	17	1680585	1680585	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:1680585delG	ENST00000254722.4	+	8	1265	c.1102delG	c.(1102-1104)gggfs	p.G368fs		NM_002615.5	NP_002606.3	P36955	PEDF_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	368					aging (GO:0007568)|cell proliferation (GO:0008283)|kidney development (GO:0001822)|multicellular organismal development (GO:0007275)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of inflammatory response (GO:0050728)|positive regulation of neurogenesis (GO:0050769)|regulation of proteolysis (GO:0030162)|response to glucocorticoid (GO:0051384)|response to retinoic acid (GO:0032526)|short-term memory (GO:0007614)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	16						GAACGAGGATGGGGCGGGAAC	0.567																																					p.D367fs		Atlas-INDEL	.											.	SERPINF1	31	.	0			c.1101delT						.						125.0	125.0	125.0					17																	1680585		2203	4300	6503	SO:0001589	frameshift_variant	5176	exon8			.	M76979	CCDS11012.1	17p13.3	2014-02-18	2005-08-18		ENSG00000132386	ENSG00000132386		"""Serine (or cysteine) peptidase inhibitors"""	8824	protein-coding gene	gene with protein product	"""pigment epithelium-derived factor"", ""proliferation-inducing protein 35"""	172860	"""serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1"""	PEDF		8434014, 24172014	Standard	NM_002615		Approved	EPC-1, PIG35	uc002ftl.3	P36955	OTTHUMG00000090571	ENST00000254722.4:c.1102delG	chr17.hg19:g.1680585delG	ENSP00000254722:p.Gly368fs	239.0	0.0		163.0	10.0	NM_002615	F1T092|Q13236|Q2TU83|Q96CT1|Q96R01|Q9BWA4	Frame_Shift_Del	DEL	ENST00000254722.4	hg19	CCDS11012.1																																																																																			.	.		0.567	SERPINF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207109.4	NM_002615	
SMEK2	57223	hgsc.bcm.edu	37	2	55791450	55791450	+	Splice_Site	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:55791450delT	ENST00000345102.5	-	15	2560	c.2259delA	c.(2257-2259)aaa>aa	p.K753fs	SNORA12_ENST00000390873.1_RNA|SMEK2_ENST00000407823.3_Splice_Site_p.K721fs|SMEK2_ENST00000272313.5_Splice_Site_p.K668fs	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	753					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TTTTAATACCTTTTTTAGTCT	0.333																																					p.A754fs		Atlas-INDEL	.											.	SMEK2	86	.	0			c.2260delG						.						89.0	87.0	88.0					2																	55791450		2202	4298	6500	SO:0001630	splice_region_variant	57223	exon15			.	AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.2260+1A>-	chr2.hg19:g.55791450delT		128.0	0.0		178.0	11.0	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Frame_Shift_Del	DEL	ENST00000345102.5	hg19	CCDS46289.1																																																																																			.	.		0.333	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463	Frame_Shift_Del
TMPRSS11D	9407	hgsc.bcm.edu	37	4	68725283	68725283	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:68725283delA	ENST00000283916.6	-	2	220	c.122delT	c.(121-123)ttafs	p.L41fs	UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11D_ENST00000545541.1_Intron|TMPRSS11D_ENST00000509584.1_Intron	NM_004262.2	NP_004253.1	O60235	TM11D_HUMAN	transmembrane protease, serine 11D	41					proteolysis (GO:0006508)|respiratory gaseous exchange (GO:0007585)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						ACCAAAAGCTAAAAAGTAAAC	0.353																																					p.L41fs		Atlas-INDEL	.											.	TMPRSS11D	68	.	0			c.123delA						.						86.0	85.0	85.0					4																	68725283		2203	4300	6503	SO:0001589	frameshift_variant	9407	exon2			.	AB002134	CCDS3518.1	4q13.2	2010-04-13			ENSG00000153802	ENSG00000153802		"""Serine peptidases / Transmembrane"""	24059	protein-coding gene	gene with protein product	"""airway trypsin like protease"""	605369				9565616, 9070615	Standard	XM_005265710		Approved		uc003hdq.3	O60235	OTTHUMG00000129300	ENST00000283916.6:c.122delT	chr4.hg19:g.68725283delA	ENSP00000283916:p.Leu41fs	112.0	0.0		144.0	10.0	NM_004262	Q08AF6	Frame_Shift_Del	DEL	ENST00000283916.6	hg19	CCDS3518.1																																																																																			.	.		0.353	TMPRSS11D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251430.3	NM_004262	
NEK4	6787	hgsc.bcm.edu	37	3	52745814	52745814	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:52745814delA	ENST00000233027.5	-	16	2707	c.2505delT	c.(2503-2505)tttfs	p.F835fs	NEK4_ENST00000535191.1_Frame_Shift_Del_p.F746fs	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	835					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		TGTTTTCTTCAAAAAATTTCA	0.358																																					p.E836fs		Atlas-INDEL	.											.	NEK4	51	.	0			c.2506delG						.						140.0	163.0	155.0					3																	52745814		2202	4300	6502	SO:0001589	frameshift_variant	6787	exon16			.	L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"""serine/threonine protein kinase-2"""	601959	"""serine/threonine kinase 2"", ""NIMA (never in mitosis gene a)-related kinase 4"""	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.2505delT	chr3.hg19:g.52745814delA	ENSP00000233027:p.Phe835fs	176.0	0.0		163.0	12.0	NM_003157	A5YM70|B2R633|B7Z200|Q6P576	Frame_Shift_Del	DEL	ENST00000233027.5	hg19	CCDS2863.1																																																																																			.	.		0.358	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157	
BLZF1	8548	hgsc.bcm.edu	37	1	169351458	169351458	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:169351458delA	ENST00000367808.3	+	6	1379	c.956delA	c.(955-957)caafs	p.Q319fs	BLZF1_ENST00000329281.2_Frame_Shift_Del_p.Q319fs			Q9H2G9	GO45_HUMAN	basic leucine zipper nuclear factor 1	319					cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|Golgi to plasma membrane protein transport (GO:0043001)|mitotic cell cycle (GO:0000278)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	14	all_hematologic(923;0.208)					ATTAACAATCAAAAAAAGATT	0.383																																					p.Q319fs		Atlas-INDEL	.											.,1	BLZF1	57	.	0			c.955delC						.						85.0	84.0	84.0					1																	169351458		2203	4300	6503	SO:0001589	frameshift_variant	8548	exon6			.	U79751	CCDS1278.1	1q24	2008-08-01	2008-08-01		ENSG00000117475	ENSG00000117475			1065	protein-coding gene	gene with protein product		608692				9129147	Standard	NM_003666		Approved	JEM-1	uc001gfy.3	Q9H2G9	OTTHUMG00000035453	ENST00000367808.3:c.956delA	chr1.hg19:g.169351458delA	ENSP00000356782:p.Gln319fs	65.0	0.0		170.0	12.0	NM_003666	O15298|Q5T531|Q5T533|Q9GZX4	Frame_Shift_Del	DEL	ENST00000367808.3	hg19	CCDS1278.1																																																																																			.	.		0.383	BLZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086109.1	NM_003666	
KDM2B	84678	hgsc.bcm.edu	37	12	121880092	121880092	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:121880092delG	ENST00000377071.4	-	19	3224	c.3152delC	c.(3151-3153)ccgfs	p.P1052fs	KDM2B_ENST00000542973.1_Frame_Shift_Del_p.P420fs|KDM2B_ENST00000377069.4_Frame_Shift_Del_p.P983fs|KDM2B_ENST00000536437.1_Intron	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1052	Pro-rich.				embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						CGAGTCAGGCGGGGGGCTGAT	0.672																																					p.P1051fs		Atlas-INDEL	.											.	KDM2B	218	.	0			c.3153delG						.						14.0	16.0	16.0					12																	121880092		1912	4085	5997	SO:0001589	frameshift_variant	84678	exon19			.	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.3152delC	chr12.hg19:g.121880092delG	ENSP00000366271:p.Pro1052fs	157.0	0.0		205.0	21.0	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Frame_Shift_Del	DEL	ENST00000377071.4	hg19	CCDS41850.1																																																																																			.	.		0.672	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
ZKSCAN7	55888	hgsc.bcm.edu	37	3	44606986	44606986	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:44606986delC	ENST00000273320.3	+	3	860	c.431delC	c.(430-432)gccfs	p.A144fs	RP11-944L7.4_ENST00000457331.1_RNA|ZKSCAN7_ENST00000426540.1_Frame_Shift_Del_p.A144fs|RP11-944L7.5_ENST00000419137.1_5'Flank|ZKSCAN7_ENST00000341840.3_Frame_Shift_Del_p.A144fs|ZKSCAN7_ENST00000431636.1_Frame_Shift_Del_p.A144fs	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	144					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)										TAGGTTTCAGCCCCAGCACAG	0.498																																					p.A144fs		Atlas-INDEL	.											.	.	.	.	0			c.430delG						.						142.0	140.0	141.0					3																	44606986		2203	4300	6503	SO:0001589	frameshift_variant	55888	exon3			.	L32164, AY280798	CCDS2714.1, CCDS2715.1, CCDS74924.1	3p21.32	2013-01-09	2013-01-09	2013-01-09	ENSG00000196345	ENSG00000196345		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12955	protein-coding gene	gene with protein product			"""zinc finger protein 64"", ""zinc finger protein 448"", ""zinc finger protein 167"""	ZNF64, ZNF448, ZNF167		7814019, 1505991	Standard	XM_005265323		Approved	FLJ12738, ZSCAN39	uc003cnj.3	Q9P0L1	OTTHUMG00000133094	ENST00000273320.3:c.431delC	chr3.hg19:g.44606986delC	ENSP00000273320:p.Ala144fs	123.0	0.0		164.0	11.0	NM_018651	A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Frame_Shift_Del	DEL	ENST00000273320.3	hg19	CCDS2715.1																																																																																			.	.		0.498	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651	
KANSL1L	151050	hgsc.bcm.edu	37	2	210887743	210887743	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:210887743delT	ENST00000281772.9	-	15	3157	c.2894delA	c.(2893-2895)aagfs	p.K965fs	KANSL1L_ENST00000418791.1_Frame_Shift_Del_p.K923fs	NM_152519.2	NP_689732.2	A0AUZ9	KAL1L_HUMAN	KAT8 regulatory NSL complex subunit 1-like	965						histone acetyltransferase complex (GO:0000123)											ATCTGACTGCTTTTTTGGATG	0.383																																					p.K965fs		Atlas-INDEL	.											.	.	.	.	0			c.2895delG						.						116.0	105.0	109.0					2																	210887743		2203	4300	6503	SO:0001589	frameshift_variant	151050	exon15			.	AK074441	CCDS33370.1	2q34	2012-02-20	2012-02-20	2012-02-20	ENSG00000144445	ENSG00000144445			26310	protein-coding gene	gene with protein product	"""KIAA1267-like"""	613833	"""chromosome 2 open reading frame 67"""	C2orf67		12477932	Standard	NM_152519		Approved	FLJ23861, FLJ32349, MSL1v2, KIAA1267L	uc002vds.3	A0AUZ9	OTTHUMG00000154697	ENST00000281772.9:c.2894delA	chr2.hg19:g.210887743delT	ENSP00000281772:p.Lys965fs	178.0	0.0		241.0	15.0	NM_152519	B7ZLN1|I6L9A8|Q53TV8|Q53TW3|Q6IS05|Q8TCI1|Q96MI0|Q9UFC3	Frame_Shift_Del	DEL	ENST00000281772.9	hg19	CCDS33370.1																																																																																			.	.		0.383	KANSL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336633.3	NM_152519	
TUBA8	51807	hgsc.bcm.edu	37	22	18609172	18609172	+	Frame_Shift_Del	DEL	G	G	-	rs377420893		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:18609172delG	ENST00000330423.3	+	4	500	c.427delG	c.(427-429)gggfs	p.G144fs	TUBA8_ENST00000316027.6_Frame_Shift_Del_p.G78fs	NM_018943.2	NP_061816.1	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	144					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	14						CAGTTTTGGTGGGGGCACTGG	0.532																																					p.G142fs		Atlas-INDEL	.											.	TUBA8	36	.	0			c.426delT						.						95.0	100.0	98.0					22																	18609172		2203	4300	6503	SO:0001589	frameshift_variant	51807	exon4			.	AJ245922	CCDS13751.1, CCDS54495.1	22q11	2005-06-11			ENSG00000183785	ENSG00000183785		"""Tubulins"""	12410	protein-coding gene	gene with protein product		605742		TUBAL2		10772959, 10591208	Standard	NM_001193414		Approved		uc002znv.2	Q9NY65	OTTHUMG00000150097	ENST00000330423.3:c.427delG	chr22.hg19:g.18609172delG	ENSP00000333326:p.Gly144fs	134.0	0.0		169.0	11.0	NM_018943	B2RCX2|B3KPW9|B4DWG3|Q2M3N4	Frame_Shift_Del	DEL	ENST00000330423.3	hg19	CCDS13751.1																																																																																			.	.		0.532	TUBA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316232.3	NM_018943	
ITGB6	3694	hgsc.bcm.edu	37	2	160958277	160958277	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:160958277delT	ENST00000283249.2	-	15	2574	c.2337delA	c.(2335-2337)aaafs	p.K779fs	ITGB6_ENST00000428609.2_Frame_Shift_Del_p.K737fs|ITGB6_ENST00000409872.1_Frame_Shift_Del_p.K779fs|ITGB6_ENST00000409967.2_Frame_Shift_Del_p.K672fs	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	779					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						CTACCTTTTGTTTTTCCCTGT	0.308																																					p.Q780fs		Atlas-INDEL	.											.	ITGB6	68	.	0			c.2338delC						.						170.0	166.0	167.0					2																	160958277		2202	4300	6502	SO:0001589	frameshift_variant	3694	exon15			.		CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"""Integrins"""	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.2337delA	chr2.hg19:g.160958277delT	ENSP00000283249:p.Lys779fs	135.0	0.0		162.0	11.0	NM_000888	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Frame_Shift_Del	DEL	ENST00000283249.2	hg19	CCDS2212.1																																																																																			.	.		0.308	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888	
FHAD1	114827	hgsc.bcm.edu	37	1	15615974	15615974	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:15615974delC	ENST00000375998.4	+	3	380	c.380delC	c.(379-381)gccfs	p.A127fs	FHAD1_ENST00000358897.4_Frame_Shift_Del_p.A127fs|FHAD1_ENST00000375999.3_Frame_Shift_Del_p.A127fs|FHAD1_ENST00000417793.1_Frame_Shift_Del_p.A127fs			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	127	Pro-rich.									skin(1)|stomach(1)	2						CCAAACCAGGCCCCCCCACCA	0.647																																					p.A127fs		Atlas-INDEL	.											.,1	FHAD1	78	.	0			c.379delG						.						136.0	182.0	168.0					1																	15615974		692	1591	2283	SO:0001589	frameshift_variant	114827	exon4			.	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.380delC	chr1.hg19:g.15615974delC	ENSP00000365166:p.Ala127fs	162.0	0.0		158.0	11.0	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Frame_Shift_Del	DEL	ENST00000375998.4	hg19																																																																																				.	.		0.647	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
CCDC13	152206	hgsc.bcm.edu	37	3	42754657	42754657	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:42754657delT	ENST00000310232.6	-	14	1953	c.1870delA	c.(1870-1872)acafs	p.T624fs		NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	624										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						CCCCTACCTGTTTTGGTCCTG	0.617																																					p.T624fs		Atlas-INDEL	.											.	CCDC13	71	.	0			c.1871delC						.						97.0	89.0	92.0					3																	42754657		2203	4300	6503	SO:0001589	frameshift_variant	152206	exon14			.	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.1870delA	chr3.hg19:g.42754657delT	ENSP00000309836:p.Thr624fs	124.0	0.0		170.0	11.0	NM_144719		Frame_Shift_Del	DEL	ENST00000310232.6	hg19	CCDS2705.1																																																																																			.	.		0.617	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
FARP2	9855	hgsc.bcm.edu	37	2	242373660	242373660	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:242373660delT	ENST00000264042.3	+	10	1125	c.955delT	c.(955-957)tttfs	p.F320fs	FARP2_ENST00000545004.1_Frame_Shift_Del_p.F320fs|FARP2_ENST00000373287.4_Frame_Shift_Del_p.F320fs	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	320	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		GTATCACACCTTTTTTAGACT	0.453																																					p.T318fs		Atlas-INDEL	.											.	FARP2	92	.	0			c.954delC						.						140.0	144.0	142.0					2																	242373660		2203	4300	6503	SO:0001589	frameshift_variant	9855	exon10			.	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.955delT	chr2.hg19:g.242373660delT	ENSP00000264042:p.Phe320fs	119.0	0.0		170.0	12.0	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Frame_Shift_Del	DEL	ENST00000264042.3	hg19	CCDS33424.1																																																																																			.	.		0.453	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
IFI44L	10964	hgsc.bcm.edu	37	1	79101136	79101136	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:79101136delC	ENST00000370751.5	+	5	1017	c.838delC	c.(838-840)cccfs	p.P280fs	IFI44L_ENST00000342282.3_Frame_Shift_Del_p.P22fs|IFI44L_ENST00000476521.1_3'UTR	NM_006820.2	NP_006811.2	Q53G44	IF44L_HUMAN	interferon-induced protein 44-like	280					defense response to virus (GO:0051607)|immune response (GO:0006955)	cytoplasm (GO:0005737)				endometrium(4)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	22						GGATGACATTCCCCACATCTT	0.368																																					p.I279fs		Atlas-INDEL	.											.	IFI44L	93	.	0			c.837delT						.						145.0	143.0	144.0					1																	79101136		2203	4300	6503	SO:0001589	frameshift_variant	10964	exon5			.	AB000115	CCDS687.2	1p22.3	2008-07-18	2004-11-12	2004-11-12	ENSG00000137959	ENSG00000137959			17817	protein-coding gene	gene with protein product		613975	"""chromosome 1 open reading frame 29"""	C1orf29			Standard	NM_006820		Approved	GS3686	uc010oro.2	Q53G44	OTTHUMG00000009724	ENST00000370751.5:c.838delC	chr1.hg19:g.79101136delC	ENSP00000359787:p.Pro280fs	103.0	0.0		132.0	10.0	NM_006820	Q86TE1|Q96B64|Q99984	Frame_Shift_Del	DEL	ENST00000370751.5	hg19	CCDS687.2																																																																																			.	.		0.368	IFI44L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026834.3	NM_006820	
MAGI3	260425	hgsc.bcm.edu	37	1	114162410	114162410	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:114162410delA	ENST00000307546.9	+	8	1204	c.1129delA	c.(1129-1131)aaafs	p.K378fs	MAGI3_ENST00000369617.4_Frame_Shift_Del_p.K403fs|MAGI3_ENST00000369611.4_Frame_Shift_Del_p.K378fs|MAGI3_ENST00000369615.1_Frame_Shift_Del_p.K378fs	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	403	Poly-Pro.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGCCAAAAGGAAAAAGCAGTT	0.338																																					p.R376fs		Atlas-INDEL	.											.	MAGI3	181	.	0			c.1128delG						.						99.0	107.0	104.0					1																	114162410		2203	4300	6503	SO:0001589	frameshift_variant	260425	exon8			.	AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.1129delA	chr1.hg19:g.114162410delA	ENSP00000304604:p.Lys378fs	184.0	0.0		213.0	14.0	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Frame_Shift_Del	DEL	ENST00000307546.9	hg19	CCDS44196.1																																																																																			.	.		0.338	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900	
RAD51D	5892	hgsc.bcm.edu	37	17	33434027	33434027	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:33434027delT	ENST00000345365.6	-	5	715	c.460delA	c.(460-462)accfs	p.T154fs	RAD51D_ENST00000460118.2_Frame_Shift_Del_p.T35fs|RAD51D_ENST00000590380.1_5'UTR|RAD51L3-RFFL_ENST00000593039.1_Intron|RAD51D_ENST00000335858.7_Intron|RAD51D_ENST00000394589.4_Frame_Shift_Del_p.T154fs|RAD51D_ENST00000360276.3_Intron|RAD51D_ENST00000590016.1_Frame_Shift_Del_p.T174fs	NM_002878.3	NP_002869.3	O75771	RA51D_HUMAN	RAD51 paralog D	154					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|reciprocal meiotic recombination (GO:0007131)|strand invasion (GO:0042148)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|gamma-tubulin binding (GO:0043015)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						TCATCCTGGGTTTTAGCCTGA	0.507								Direct reversal of damage																													p.T174fs		Atlas-INDEL	.											.	RAD51D	53	.	0			c.521delC						.						103.0	89.0	94.0					17																	33434027		2203	4300	6503	SO:0001589	frameshift_variant	5892	exon5			.	AF034956	CCDS11287.1, CCDS11288.1, CCDS45646.1	17q11	2014-09-17	2013-07-02	2011-07-01	ENSG00000185379	ENSG00000185379			9823	protein-coding gene	gene with protein product	"""recombination repair protein"", ""DNA repair protein RAD51 homolog 4"""	602954	"""RAD51 (S. cerevisiae)-like 3"", ""RAD51-like 3 (S. cerevisiae)"", ""RAD51 homolog D (S. cerevisiae)"""	RAD51L3		9570954	Standard	NM_001142571		Approved	R51H3, Trad, HsTRAD	uc010ctj.2	O75771	OTTHUMG00000132930	ENST00000345365.6:c.460delA	chr17.hg19:g.33434027delT	ENSP00000338790:p.Thr154fs	103.0	0.0		122.0	10.0	NM_001142571	B4DJU7|E1P637|O43537|O60355|O75196|O75847|O75848|O76073|O76085|O94908|Q9UFU5	Frame_Shift_Del	DEL	ENST00000345365.6	hg19	CCDS11287.1																																																																																			.	.		0.507	RAD51D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256446.1	NM_002878	
SULF1	23213	hgsc.bcm.edu	37	8	70550813	70550813	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:70550813delT	ENST00000260128.4	+	20	3078	c.2361delT	c.(2359-2361)aatfs	p.N787fs	SULF1_ENST00000458141.2_Frame_Shift_Del_p.N787fs|SULF1_ENST00000419716.3_Frame_Shift_Del_p.N787fs|SULF1_ENST00000402687.4_Frame_Shift_Del_p.N787fs|SULF1_ENST00000521946.1_3'UTR	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	787					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			AGACGCATAATTTTCTTTTCT	0.353																																					p.N787fs		Atlas-INDEL	.											.	SULF1	153	.	0			c.2360delA						.						152.0	142.0	145.0					8																	70550813		2203	4300	6503	SO:0001589	frameshift_variant	23213	exon20			.	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.2361delT	chr8.hg19:g.70550813delT	ENSP00000260128:p.Asn787fs	120.0	0.0		177.0	11.0	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Frame_Shift_Del	DEL	ENST00000260128.4	hg19	CCDS6204.1																																																																																			.	.		0.353	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170	
TTC13	79573	hgsc.bcm.edu	37	1	231044702	231044702	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:231044702delT	ENST00000366661.4	-	21	2381	c.2374delA	c.(2374-2376)attfs	p.I792fs	TTC13_ENST00000414259.1_Frame_Shift_Del_p.I739fs|TTC13_ENST00000366662.4_Frame_Shift_Del_p.I738fs	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13	792										central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		CCTTTGGGAATTTTTCCTGCT	0.393																																					p.I792fs		Atlas-INDEL	.											.	TTC13	74	.	0			c.2375delT						.						161.0	170.0	167.0					1																	231044702		2203	4300	6503	SO:0001589	frameshift_variant	79573	exon21			.		CCDS1588.1, CCDS44332.1, CCDS44332.2	1q42.2	2013-01-10			ENSG00000143643	ENSG00000143643		"""Tetratricopeptide (TTC) repeat domain containing"""	26204	protein-coding gene	gene with protein product							Standard	NM_024525		Approved	FLJ22584	uc001huf.4	Q8NBP0	OTTHUMG00000037788	ENST00000366661.4:c.2374delA	chr1.hg19:g.231044702delT	ENSP00000355621:p.Ile792fs	145.0	0.0		214.0	13.0	NM_024525	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Frame_Shift_Del	DEL	ENST00000366661.4	hg19	CCDS1588.1																																																																																			.	.		0.393	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525	
MACROD2	140733	hgsc.bcm.edu	37	20	13976431	13976431	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:13976431delA	ENST00000310348.4	+	1	22	c.22delA	c.(22-24)aaafs	p.K9fs	MACROD2_ENST00000217246.4_Frame_Shift_Del_p.K9fs|SEL1L2_ENST00000486903.1_5'Flank			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	9	Poly-Lys.				brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				CAACAAGAAGAAAAAGGTGTG	0.637																																					p.K7fs		Atlas-INDEL	.											.	MACROD2	34	.	0			c.21delG						.						45.0	38.0	40.0					20																	13976431		2203	4300	6503	SO:0001589	frameshift_variant	140733	exon1			.	BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"""chromosome 20 open reading frame 133"""	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.22delA	chr20.hg19:g.13976431delA	ENSP00000309809:p.Lys9fs	130.0	0.0		160.0	10.0	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Frame_Shift_Del	DEL	ENST00000310348.4	hg19	CCDS13120.2																																																																																			.	.		0.637	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676	
DFNB59	494513	hgsc.bcm.edu	37	2	179325894	179325894	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:179325894delA	ENST00000409117.3	+	7	1308	c.952delA	c.(952-954)aaafs	p.K318fs	DFNB59_ENST00000375129.4_Frame_Shift_Del_p.K318fs	NM_001042702.3	NP_001036167.1	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	318					sensory perception of sound (GO:0007605)	neuronal cell body (GO:0043025)				breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			GGGGAACTTCAAAAGGGAGAC	0.418																																					p.F317fs		Atlas-INDEL	.											.	DFNB59	37	.	0			c.951delC						.						176.0	164.0	168.0					2																	179325894		1869	4117	5986	SO:0001589	frameshift_variant	494513	exon7			.	BC020859, BQ887979	CCDS42787.1	2q31.2	2011-07-01			ENSG00000204311	ENSG00000204311			29502	protein-coding gene	gene with protein product		610219				16804542	Standard	NM_001042702		Approved	pejvakin	uc002umi.4	Q0ZLH3	OTTHUMG00000154425	ENST00000409117.3:c.952delA	chr2.hg19:g.179325894delA	ENSP00000386647:p.Lys318fs	114.0	0.0		152.0	10.0	NM_001042702	A0PK14|B9EJE2	Frame_Shift_Del	DEL	ENST00000409117.3	hg19	CCDS42787.1																																																																																			.	.		0.418	DFNB59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335160.1		
AGRN	375790	hgsc.bcm.edu	37	1	987127	987127	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:987127delG	ENST00000379370.2	+	33	5633	c.5583delG	c.(5581-5583)gcgfs	p.A1861fs		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1865					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		AGAAGTCAGCGGGGGACGTGG	0.657																																					p.A1861fs		Atlas-INDEL	.											.	AGRN	110	.	0			c.5582delC						.						132.0	103.0	113.0					1																	987127		2203	4300	6503	SO:0001589	frameshift_variant	375790	exon33			.	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.5583delG	chr1.hg19:g.987127delG	ENSP00000368678:p.Ala1861fs	232.0	0.0		152.0	12.0	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Frame_Shift_Del	DEL	ENST00000379370.2	hg19	CCDS30551.1																																																																																			.	.		0.657	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
SPPL3	121665	hgsc.bcm.edu	37	12	121222293	121222293	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:121222293delA	ENST00000353487.2	-	4	797	c.294delT	c.(292-294)tttfs	p.F98fs		NM_139015.4	NP_620584.2	Q8TCT6	SPPL3_HUMAN	signal peptide peptidase like 3	99						Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|rough endoplasmic reticulum (GO:0005791)	aspartic endopeptidase activity, intramembrane cleaving (GO:0042500)|protein homodimerization activity (GO:0042803)					all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TACATATTGTAAAAACTACTT	0.323																																					p.T99fs		Atlas-INDEL	.											.	.	.	.	0			c.295delA						.						69.0	68.0	68.0					12																	121222293		2203	4300	6503	SO:0001589	frameshift_variant	121665	exon4			.		CCDS9208.1	12q24.31	2012-02-21			ENSG00000157837	ENSG00000157837			30424	protein-coding gene	gene with protein product	"""intramembrane protease 2"", ""presenilin-like protein 4"""	608240				12139484	Standard	NM_139015		Approved	IMP2, PSL4, MGC90402, MGC126674, MGC126676, DKFZP586C1324	uc001tzd.3	Q8TCT6	OTTHUMG00000169232	ENST00000353487.2:c.294delT	chr12.hg19:g.121222293delA	ENSP00000288680:p.Phe98fs	106.0	0.0		165.0	12.0	NM_139015	Q3MJ04|Q8TAU4|Q96DD9	Frame_Shift_Del	DEL	ENST00000353487.2	hg19	CCDS9208.1																																																																																			.	.		0.323	SPPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402980.2	NM_139015	
OSBPL8	114882	hgsc.bcm.edu	37	12	76749732	76749732	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:76749732delT	ENST00000261183.3	-	24	3086	c.2607delA	c.(2605-2607)aaafs	p.K869fs	OSBPL8_ENST00000393250.4_Frame_Shift_Del_p.K827fs|OSBPL8_ENST00000393249.2_Frame_Shift_Del_p.K827fs	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	869					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						TGAAGTAGTCTTTTTGTTGCA	0.323																																					p.D870fs		Atlas-INDEL	.											.	OSBPL8	86	.	0			c.2608delG						.						89.0	91.0	90.0					12																	76749732		2203	4300	6503	SO:0001589	frameshift_variant	114882	exon24			.	AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16396	protein-coding gene	gene with protein product		606736				1735225, 17991739	Standard	NM_020841		Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.2607delA	chr12.hg19:g.76749732delT	ENSP00000261183:p.Lys869fs	119.0	0.0		147.0	12.0	NM_020841	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	Frame_Shift_Del	DEL	ENST00000261183.3	hg19	CCDS31862.1																																																																																			.	.		0.323	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406357.1	NM_020841	
SEPT2	4735	hgsc.bcm.edu	37	2	242275390	242275390	+	Splice_Site	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:242275390delA	ENST00000391973.2	+	5	746	c.218delA	c.(217-219)gaa>ga	p.E73fs	SEPT2_ENST00000391971.2_Splice_Site_p.E73fs|SEPT2_ENST00000360051.3_Splice_Site_p.E73fs|SEPT2_ENST00000402092.2_Splice_Site_p.E73fs|SEPT2_ENST00000407971.1_Splice_Site_p.E33fs|SEPT2_ENST00000401990.1_Splice_Site_p.E83fs	NM_006155.1	NP_006146.1	Q15019	SEPT2_HUMAN	septin 2	73	Septin-type G.				cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|neuron projection development (GO:0031175)|regulation of L-glutamate transport (GO:0002036)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|synapse (GO:0045202)	enzyme regulator activity (GO:0030234)|GTP binding (GO:0005525)			central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)		TCTTTTCTAGAAAAAATTGAA	0.433																																					.		Atlas-INDEL	.											.	SEPT2	33	.	0			c.218-1A>-						.						66.0	69.0	68.0					2																	242275390		2203	4300	6503	SO:0001630	splice_region_variant	4735	exon5			.	D28540	CCDS2548.1, CCDS63195.1, CCDS74682.1	2q37.3	2013-01-21	2005-01-11	2005-01-12	ENSG00000168385	ENSG00000168385		"""Septins"""	7729	protein-coding gene	gene with protein product		601506	"""neural precursor cell expressed, developmentally down-regulated 5"""	DIFF6, NEDD5		8697812	Standard	XM_005247011		Approved	KIAA0158, hNedd5, Pnutl3	uc002wbd.3	Q15019	OTTHUMG00000133394	ENST00000391973.2:c.218-1A>-	chr2.hg19:g.242275390delA		86.0	0.0		153.0	14.0	NM_006155	B4DGE8|Q14132|Q53QU3|Q8IUK9|Q96CB0	Splice_Site	DEL	ENST00000391973.2	hg19	CCDS2548.1																																																																																			.	.		0.433	SEPT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323177.3	NM_006155	Frame_Shift_Del
CXorf40A	91966	hgsc.bcm.edu	37	X	148627384	148627384	+	Frame_Shift_Del	DEL	A	A	-	rs145921071		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:148627384delA	ENST00000441248.1	+	3	1795	c.208delA	c.(208-210)accfs	p.T70fs	CXorf40A_ENST00000423540.2_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000393985.3_Frame_Shift_Del_p.T70fs|RP5-937E21.8_ENST00000431993.1_RNA|CXorf40A_ENST00000450602.2_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000514208.1_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000359293.5_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000423421.1_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000434353.2_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000422892.2_Frame_Shift_Del_p.T70fs|CXorf40A_ENST00000428236.1_Frame_Shift_Del_p.T8fs			Q8TE69	CX04A_HUMAN	chromosome X open reading frame 40A	70				T -> A (in Ref. 2; AAL71889, 3; BAF84588/ BAH13262 and 5; AAH65539/AAI04931/ AAI04933/AAI43661/AAI43662/AAI43663). {ECO:0000305}.						breast(1)|endometrium(3)|large_intestine(1)|lung(2)	7	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					TCAGATTCAGACCTTGCTCAG	0.567																																					p.Q69fs		Atlas-INDEL	.											.	CXorf40A	15	.	0			c.207delG						.						38.0	5.0	16.0					X																	148627384		2088	3933	6021	SO:0001589	frameshift_variant	91966	exon4			.	AF011889	CCDS14687.1, CCDS55522.1	Xq28	2010-03-16	2005-09-13	2005-09-13	ENSG00000197620	ENSG00000197620			28089	protein-coding gene	gene with protein product	"""endothelial-overexpressed lipopolysaccharide-associated factor 1"""		"""chromosome X open reading frame 40"""	CXorf40		8717057, 9147653, 16383041	Standard	XM_005278212		Approved	EOLA1	uc004fdg.3	Q8TE69	OTTHUMG00000022622	ENST00000441248.1:c.208delA	chrX.hg19:g.148627384delA	ENSP00000423099:p.Thr70fs	163.0	0.0		201.0	16.0	NM_178124	A8K784|B7Z6H6|B7ZL96|D6RA72|E7ENU3|Q2M3E9	Frame_Shift_Del	DEL	ENST00000441248.1	hg19	CCDS14687.1																																																																																			.	.		0.567	CXorf40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058699.3	NM_178124	
TMEM108	66000	hgsc.bcm.edu	37	3	133099911	133099911	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:133099911delG	ENST00000321871.6	+	4	1566	c.1356delG	c.(1354-1356)gagfs	p.E452fs	TMEM108_ENST00000508711.1_Intron|TMEM108_ENST00000515826.1_Frame_Shift_Del_p.E452fs|TMEM108_ENST00000393130.3_Frame_Shift_Del_p.E452fs	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	452						integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						ATGTGGCCGAGGGGGACAAAC	0.612																																					p.E452fs		Atlas-INDEL	.											.	TMEM108	67	.	0			c.1355delA						.						115.0	97.0	103.0					3																	133099911		2203	4300	6503	SO:0001589	frameshift_variant	66000	exon4			.	AL136578	CCDS33858.1, CCDS75012.1	3q22.1	2014-04-07			ENSG00000144868	ENSG00000144868			28451	protein-coding gene	gene with protein product	"""cancer/testis antigen 124"""					11214970	Standard	XM_005247726		Approved	MGC3040, CT124	uc003epi.3	Q6UXF1	OTTHUMG00000159685	ENST00000321871.6:c.1356delG	chr3.hg19:g.133099911delG	ENSP00000324651:p.Glu452fs	210.0	0.0		226.0	14.0	NM_023943	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Frame_Shift_Del	DEL	ENST00000321871.6	hg19	CCDS33858.1																																																																																			.	.		0.612	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943	
ADRM1	11047	hgsc.bcm.edu	37	20	60882434	60882434	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:60882434delG	ENST00000253003.2	+	6	595	c.549delG	c.(547-549)ctgfs	p.L183fs	LAMA5_ENST00000492698.1_5'Flank|RP11-157P1.4_ENST00000414042.1_RNA	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	183	Gly-rich.				positive regulation of endopeptidase activity (GO:0010950)|proteasome assembly (GO:0043248)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|protease binding (GO:0002020)|proteasome binding (GO:0070628)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|urinary_tract(1)	5	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;2.51e-06)			CAGGTGGGCTGGGGGCCCTGA	0.667																																					p.L183fs		Atlas-INDEL	.											.	ADRM1	28	.	0			c.548delT						.						29.0	30.0	30.0					20																	60882434		2197	4297	6494	SO:0001589	frameshift_variant	11047	exon6			.	D64154	CCDS13496.1, CCDS74747.1	20q13.33	2008-05-22			ENSG00000130706	ENSG00000130706			15759	protein-coding gene	gene with protein product		610650				8033103	Standard	NM_007002		Approved	GP110, Rpn13, ARM1	uc002yco.3	Q16186	OTTHUMG00000032904	ENST00000253003.2:c.549delG	chr20.hg19:g.60882434delG	ENSP00000253003:p.Leu183fs	115.0	0.0		159.0	10.0	NM_175573	A0PKB1|Q96FJ7|Q9H1P2	Frame_Shift_Del	DEL	ENST00000253003.2	hg19	CCDS13496.1																																																																																			.	.		0.667	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1		
GARNL3	84253	hgsc.bcm.edu	37	9	130116628	130116628	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:130116628delG	ENST00000373387.4	+	19	2050	c.1698delG	c.(1696-1698)gagfs	p.E566fs	GARNL3_ENST00000435213.2_Frame_Shift_Del_p.E544fs|GARNL3_ENST00000314904.5_Frame_Shift_Del_p.E566fs	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	566	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						AGGGCCTTGAGGGGAAGCAGG	0.438																																					p.E566fs		Atlas-INDEL	.											.	GARNL3	83	.	0			c.1697delA						.						75.0	77.0	77.0					9																	130116628		2203	4300	6503	SO:0001589	frameshift_variant	84253	exon19			.	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 3"""			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.1698delG	chr9.hg19:g.130116628delG	ENSP00000362485:p.Glu566fs	126.0	0.0		155.0	10.0	NM_032293	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Frame_Shift_Del	DEL	ENST00000373387.4	hg19	CCDS6869.2																																																																																			.	.		0.438	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293	
ZNF385C	201181	hgsc.bcm.edu	37	17	40189831	40189831	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:40189831delG	ENST00000436535.3	-	2	323	c.323delC	c.(322-324)ccgfs	p.P108fs	CTD-2132N18.4_ENST00000602842.1_RNA|CTD-2132N18.2_ENST00000587304.1_RNA			Q66K41	Z385C_HUMAN	zinc finger protein 385C	27						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	3		all_cancers(22;0.00127)|Breast(137;0.00104)|all_epithelial(22;0.0126)				GAAGTCCAGCGGGGGCTGCAG	0.701																																					p.P29fs		Atlas-INDEL	.											.	ZNF385C	7	.	0			c.87delG						.																																			SO:0001589	frameshift_variant	201181	exon2			.	BC067901	CCDS74065.1	17q21.2	2012-10-05			ENSG00000187595	ENSG00000187595			33722	protein-coding gene	gene with protein product							Standard	NM_001242704		Approved		uc021txr.1	Q66K41	OTTHUMG00000132073	ENST00000436535.3:c.323delC	chr17.hg19:g.40189831delG	ENSP00000411514:p.Pro108fs	151.0	0.0		154.0	10.0	NM_001242704	Q4G0J1	Frame_Shift_Del	DEL	ENST00000436535.3	hg19																																																																																				.	.		0.701	ZNF385C-001	NOVEL	not_organism_supported|mRNA_end_NF|cds_end_NF|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000347740.3	NM_001013624	
PDHX	8050	hgsc.bcm.edu	37	11	34953022	34953022	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:34953022delA	ENST00000227868.4	+	2	316	c.232delA	c.(232-234)aaafs	p.K79fs	PDHX_ENST00000430469.2_Frame_Shift_Del_p.K79fs|PDHX_ENST00000448838.3_Frame_Shift_Del_p.K64fs			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	79	Lipoyl-binding. {ECO:0000255|PROSITE- ProRule:PRU01066}.				cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			GAAATGGCTGAAAAAGGAAGG	0.363																																					p.L77fs		Atlas-INDEL	.											.	PDHX	40	.	0			c.231delG						.						113.0	107.0	109.0					11																	34953022		2202	4298	6500	SO:0001589	frameshift_variant	8050	exon2			.	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491	ENST00000227868.4:c.232delA	chr11.hg19:g.34953022delA	ENSP00000227868:p.Lys79fs	184.0	0.0		211.0	14.0	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Frame_Shift_Del	DEL	ENST00000227868.4	hg19	CCDS7896.1																																																																																			.	.		0.363	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
SVIL	6840	hgsc.bcm.edu	37	10	29822101	29822101	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:29822101delG	ENST00000355867.4	-	8	1947	c.1195delC	c.(1195-1197)cagfs	p.Q399fs	SVIL_ENST00000375398.2_Frame_Shift_Del_p.Q399fs|SVIL_ENST00000375400.3_Intron	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	399					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)				GGGACATTCTGGGTGGCTGAT	0.537																																					p.Q399fs		Atlas-INDEL	.											.	SVIL	226	.	0			c.1196delA						.						81.0	67.0	72.0					10																	29822101		2203	4300	6503	SO:0001589	frameshift_variant	6840	exon8			.	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.1195delC	chr10.hg19:g.29822101delG	ENSP00000348128:p.Gln399fs	168.0	0.0		197.0	13.0	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Frame_Shift_Del	DEL	ENST00000355867.4	hg19	CCDS7164.1																																																																																			.	.		0.537	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
KCNQ2	3785	hgsc.bcm.edu	37	20	62059777	62059777	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:62059777delG	ENST00000359125.2	-	10	1334	c.1160delC	c.(1159-1161)ccgfs	p.P387fs	KCNQ2_ENST00000370224.1_Frame_Shift_Del_p.P377fs|KCNQ2_ENST00000357249.2_Frame_Shift_Del_p.P387fs|KCNQ2_ENST00000360480.3_Frame_Shift_Del_p.P377fs|KCNQ2_ENST00000359689.1_Frame_Shift_Del_p.P387fs|KCNQ2_ENST00000344462.4_Frame_Shift_Del_p.P387fs|KCNQ2_ENST00000354587.3_Frame_Shift_Del_p.P377fs	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	387					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	CTGGTTCAGCGGGGGGATAAG	0.627																																					p.P387fs		Atlas-INDEL	.											KCNQ2,rectum,carcinoma,0,1	KCNQ2	201	.	0			c.1161delG						.						31.0	30.0	30.0					20																	62059777		2200	4297	6497	SO:0001589	frameshift_variant	3785	exon10			.	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.1160delC	chr20.hg19:g.62059777delG	ENSP00000352035:p.Pro387fs	143.0	0.0		195.0	13.0	NM_172106	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Frame_Shift_Del	DEL	ENST00000359125.2	hg19	CCDS13520.1																																																																																			.	.		0.627	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109	
PPAT	5471	hgsc.bcm.edu	37	4	57272752	57272752	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:57272752delT	ENST00000264220.2	-	3	448	c.311delA	c.(310-312)aatfs	p.N104fs	PPAT_ENST00000507648.1_5'UTR	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	104	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	GGGCTGACAATTTTCTAGTTC	0.383																																					p.N104fs		Atlas-INDEL	.											.	PPAT	41	.	0			c.312delT						.						149.0	123.0	132.0					4																	57272752		2203	4300	6503	SO:0001589	frameshift_variant	5471	exon3			.		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.311delA	chr4.hg19:g.57272752delT	ENSP00000264220:p.Asn104fs	136.0	0.0		164.0	12.0	NM_002703		Frame_Shift_Del	DEL	ENST00000264220.2	hg19	CCDS3505.1																																																																																			.	.		0.383	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703	
FHOD3	80206	hgsc.bcm.edu	37	18	34335198	34335198	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:34335198delA	ENST00000359247.4	+	21	3773	c.3773delA	c.(3772-3774)gaafs	p.E1258fs	FHOD3_ENST00000591635.1_Frame_Shift_Del_p.E471fs|FHOD3_ENST00000445677.1_Frame_Shift_Del_p.E1237fs|FHOD3_ENST00000590592.1_Frame_Shift_Del_p.E1450fs|FHOD3_ENST00000257209.4_Frame_Shift_Del_p.E1275fs|FHOD3_ENST00000592128.1_Frame_Shift_Del_p.E254fs	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1258	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				ACAACCAGGGAAAGGGTTTTG	0.443																																					p.E1275fs		Atlas-INDEL	.											.	FHOD3	210	.	0			c.3823delG						.						102.0	83.0	89.0					18																	34335198		2203	4300	6503	SO:0001589	frameshift_variant	80206	exon22			.	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.3773delA	chr18.hg19:g.34335198delA	ENSP00000352186:p.Glu1258fs	133.0	0.0		154.0	10.0	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Frame_Shift_Del	DEL	ENST00000359247.4	hg19																																																																																				.	.		0.443	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114	
USP47	55031	hgsc.bcm.edu	37	11	11977603	11977603	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:11977603delA	ENST00000399455.2	+	29	4129	c.4009delA	c.(4009-4011)aaafs	p.K1338fs	USP47_ENST00000539466.1_Frame_Shift_Del_p.K120fs|USP47_ENST00000339865.5_Frame_Shift_Del_p.K1250fs|USP47_ENST00000527733.1_Frame_Shift_Del_p.K1318fs|USP47_ENST00000305481.6_3'UTR	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	1338					base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		TGAACTGATGAAAAAAGAAAG	0.358																																					p.M1248fs		Atlas-INDEL	.											.	USP47	91	.	0			c.3744delG						.						106.0	105.0	106.0					11																	11977603		1831	4077	5908	SO:0001589	frameshift_variant	55031	exon27			.	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"""Ubiquitin-specific peptidases"""	20076	protein-coding gene	gene with protein product		614460	"""Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)"", ""ubiquitin specific protease 47"""			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.4009delA	chr11.hg19:g.11977603delA	ENSP00000382382:p.Lys1338fs	137.0	0.0		150.0	11.0	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Frame_Shift_Del	DEL	ENST00000399455.2	hg19																																																																																				.	.		0.358	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944	
RARS	5917	hgsc.bcm.edu	37	5	167937675	167937675	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:167937675delA	ENST00000231572.3	+	12	1490	c.1436delA	c.(1435-1437)gaafs	p.E479fs	RARS_ENST00000538719.1_Frame_Shift_Del_p.E273fs	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	479					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		AAGTTGAAGGAAAAAGAAAGA	0.363																																					p.E479fs		Atlas-INDEL	.											.	RARS	58	.	0			c.1435delG						.						66.0	66.0	66.0					5																	167937675		2203	4300	6503	SO:0001589	frameshift_variant	5917	exon12			.	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1436delA	chr5.hg19:g.167937675delA	ENSP00000231572:p.Glu479fs	144.0	0.0		149.0	10.0	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Frame_Shift_Del	DEL	ENST00000231572.3	hg19	CCDS4367.1																																																																																			.	.		0.363	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	
EPHA7	2045	hgsc.bcm.edu	37	6	94120235	94120235	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:94120235delT	ENST00000369303.4	-	3	1000	c.816delA	c.(814-816)aaafs	p.K272fs	EPHA7_ENST00000369297.1_Frame_Shift_Del_p.K272fs	NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	272	Cys-rich.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		AAGTGTCTCCTTTTTGCTGGT	0.393																																					p.G273fs		Atlas-INDEL	.											.	EPHA7	251	.	0			c.817delG						.						120.0	125.0	123.0					6																	94120235		2203	4300	6503	SO:0001589	frameshift_variant	2045	exon3			.	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3390	protein-coding gene	gene with protein product		602190	"""EphA7"""			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.816delA	chr6.hg19:g.94120235delT	ENSP00000358309:p.Lys272fs	142.0	0.0		166.0	13.0	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Frame_Shift_Del	DEL	ENST00000369303.4	hg19	CCDS5031.1																																																																																			.	.		0.393	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1		
SEC14L1	6397	hgsc.bcm.edu	37	17	75192380	75192380	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:75192380delC	ENST00000413679.2	+	8	1109	c.806delC	c.(805-807)accfs	p.T269fs	SEC14L1_ENST00000443798.4_Frame_Shift_Del_p.T269fs|SEC14L1_ENST00000436233.4_Frame_Shift_Del_p.T269fs|SEC14L1_ENST00000585618.1_Frame_Shift_Del_p.T269fs|SEC14L1_ENST00000431431.2_Frame_Shift_Del_p.T235fs|SEC14L1_ENST00000430767.4_Frame_Shift_Del_p.T269fs|SEC14L1_ENST00000392476.2_Frame_Shift_Del_p.T269fs|SEC14L1_ENST00000591437.1_Frame_Shift_Del_p.T235fs	NM_001143998.1|NM_001143999.1|NM_003003.3	NP_001137470|NP_001137471|NP_002994	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)	269					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						CTCCAGGAGACCCACAAGGGC	0.522																																					p.T269fs		Atlas-INDEL	.											.	SEC14L1	81	.	0			c.805delA						.						56.0	52.0	53.0					17																	75192380		2203	4300	6503	SO:0001589	frameshift_variant	6397	exon10			.	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.806delC	chr17.hg19:g.75192380delC	ENSP00000394716:p.Thr269fs	101.0	0.0		179.0	11.0	NM_001204408	A8K4E8|B4DDI5|D5G3K1|Q99780	Frame_Shift_Del	DEL	ENST00000413679.2	hg19	CCDS11752.1																																																																																			.	.		0.522	SEC14L1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000436240.1	NM_003003	
YTHDC2	64848	hgsc.bcm.edu	37	5	112926912	112926912	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:112926912delT	ENST00000161863.4	+	27	4213	c.4000delT	c.(4000-4002)tttfs	p.F1334fs		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1334	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.				ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		TTACTTGGTATTTTCTGTTCA	0.393																																					p.V1333fs		Atlas-INDEL	.											.	YTHDC2	118	.	0			c.3999delA						.						145.0	147.0	146.0					5																	112926912		2202	4300	6502	SO:0001589	frameshift_variant	64848	exon27			.	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.4000delT	chr5.hg19:g.112926912delT	ENSP00000161863:p.Phe1334fs	127.0	0.0		162.0	11.0	NM_022828	B2RP66	Frame_Shift_Del	DEL	ENST00000161863.4	hg19	CCDS4113.1																																																																																			.	.		0.393	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
SLC12A2	6558	hgsc.bcm.edu	37	5	127514330	127514330	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:127514330delA	ENST00000262461.2	+	22	3238	c.3049delA	c.(3049-3051)aaafs	p.K1018fs	SLC12A2_ENST00000343225.4_Frame_Shift_Del_p.K1002fs|SLC12A2_ENST00000507791.1_3'UTR	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	1018					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	ACAGTTTCAGAAAAAACAAGG	0.313																																					p.Q1016fs		Atlas-INDEL	.											SLC12A2,NS,carcinoma,0,1	SLC12A2	119	.	0			c.3048delG						.						82.0	86.0	84.0					5																	127514330		2203	4300	6503	SO:0001589	frameshift_variant	6558	exon22			.		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"""Solute carriers"""	10911	protein-coding gene	gene with protein product	"""bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1"", ""basolateral Na-K-Cl symporter"", ""protein phosphatase 1, regulatory subunit 141"""	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.3049delA	chr5.hg19:g.127514330delA	ENSP00000262461:p.Lys1018fs	158.0	0.0		212.0	13.0	NM_001046	Q8N713|Q8WWH7	Frame_Shift_Del	DEL	ENST00000262461.2	hg19	CCDS4144.1																																																																																			.	.		0.313	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046	
HCFC2	29915	hgsc.bcm.edu	37	12	104490206	104490206	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:104490206delT	ENST00000229330.4	+	12	1839	c.1735delT	c.(1735-1737)tttfs	p.F579fs	HCFC2_ENST00000550335.1_3'UTR	NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	579					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						AGCAACGCCGTTTTCTGTAAG	0.343																																					p.P578fs	Esophageal Squamous(184;1814 2036 4771 6974 15702)	Atlas-INDEL	.											.	HCFC2	94	.	0			c.1734delG						.						121.0	120.0	120.0					12																	104490206		2203	4300	6503	SO:0001589	frameshift_variant	29915	exon12			.	AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.1735delT	chr12.hg19:g.104490206delT	ENSP00000229330:p.Phe579fs	173.0	0.0		155.0	10.0	NM_013320	B2R8Q5|C0H5X3	Frame_Shift_Del	DEL	ENST00000229330.4	hg19	CCDS9097.1																																																																																			.	.		0.343	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320	
ZMPSTE24	10269	hgsc.bcm.edu	37	1	40751681	40751681	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:40751681delA	ENST00000372759.3	+	8	1204	c.1039delA	c.(1039-1041)aaafs	p.K347fs		NM_005857.4	NP_005848.2	O75844	FACE1_HUMAN	zinc metallopeptidase STE24	347					CAAX-box protein processing (GO:0071586)|nuclear envelope organization (GO:0006998)|prenylated protein catabolic process (GO:0030327)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metalloexopeptidase activity (GO:0008235)			endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	16	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;6.3e-18)			ACATACAGTCAAAAATATCAT	0.368																																					p.V346fs		Atlas-INDEL	.											ZMPSTE24,NS,carcinoma,0,1	ZMPSTE24	50	.	0			c.1038delC						.						105.0	104.0	104.0					1																	40751681		2203	4300	6503	SO:0001589	frameshift_variant	10269	exon8			.	Y13834	CCDS449.1	1p34	2014-09-17	2012-12-10		ENSG00000084073	ENSG00000084073	3.4.24.84		12877	protein-coding gene	gene with protein product	"""Hutchinson-Gilford progeria syndrome"", ""CAAX prenyl protease 1 homolog"""	606480	"""zinc metalloproteinase (STE24 homolog, yeast)"", ""zinc metallopeptidase (STE24 homolog, yeast)"", ""zinc metallopeptidase STE24 homolog (S. cerevisiae)"""			10373325, 9700155, 16671095	Standard	NM_005857		Approved	FACE-1, Ste24p, STE24, HGPS, PRO1	uc001cfg.4	O75844	OTTHUMG00000005762	ENST00000372759.3:c.1039delA	chr1.hg19:g.40751681delA	ENSP00000361845:p.Lys347fs	210.0	0.0		260.0	16.0	NM_005857	B3KQI7|D3DPU7|Q8NDZ8|Q9UBQ2	Frame_Shift_Del	DEL	ENST00000372759.3	hg19	CCDS449.1																																																																																			.	.		0.368	ZMPSTE24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015766.1		
WIPF1	7456	hgsc.bcm.edu	37	2	175436765	175436765	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:175436765delG	ENST00000392547.2	-	5	867	c.768delC	c.(766-768)cccfs	p.P256fs	WIPF1_ENST00000409891.1_Frame_Shift_Del_p.P256fs|AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000409415.3_Frame_Shift_Del_p.P256fs|WIPF1_ENST00000467149.1_5'Flank|WIPF1_ENST00000392546.2_Frame_Shift_Del_p.P256fs|WIPF1_ENST00000272746.5_Frame_Shift_Del_p.P256fs|AC018890.6_ENST00000412835.1_RNA|WIPF1_ENST00000359761.3_Frame_Shift_Del_p.P256fs	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	256					actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)			NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						AGGCCCTGCTGGGGGTAGGCG	0.647																																					p.S257fs		Atlas-INDEL	.											.	WIPF1	88	.	0			c.769delA						.						16.0	18.0	17.0					2																	175436765		2199	4296	6495	SO:0001589	frameshift_variant	7456	exon5			.	AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935			12736	protein-coding gene	gene with protein product		602357	"""Wiskott-Aldrich syndrome protein interacting protein"""	WASPIP		9405671	Standard	NM_001077269		Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.768delC	chr2.hg19:g.175436765delG	ENSP00000376330:p.Pro256fs	135.0	0.0		194.0	12.0	NM_003387	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	Frame_Shift_Del	DEL	ENST00000392547.2	hg19	CCDS2260.1																																																																																			.	.		0.647	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255453.1	NM_003387	
MAGEE1	57692	hgsc.bcm.edu	37	X	75650522	75650522	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:75650522delA	ENST00000361470.2	+	1	2477	c.2199delA	c.(2197-2199)tcafs	p.S733fs		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	733						dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						GCTATTCCTCAAAATATGCCC	0.493																																					p.S733X		Atlas-INDEL	.											.	MAGEE1	236	.	0			c.2198delC						.						73.0	59.0	64.0					X																	75650522		2203	4300	6503	SO:0001589	frameshift_variant	57692	exon1			.	AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.2199delA	chrX.hg19:g.75650522delA	ENSP00000354912:p.Ser733fs	124.0	0.0		164.0	10.0	NM_020932	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Frame_Shift_Del	DEL	ENST00000361470.2	hg19	CCDS14433.1																																																																																			.	.		0.493	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932	
ITGA9	3680	hgsc.bcm.edu	37	3	37845344	37845344	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:37845344delC	ENST00000264741.5	+	27	3176	c.2920delC	c.(2920-2922)cccfs	p.P974fs	AC093415.2_ENST00000438136.1_RNA|AC093415.2_ENST00000420870.1_RNA|AC093415.2_ENST00000450990.1_RNA|AC093415.2_ENST00000445429.1_RNA	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	974					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		CAATCTGGAGCCCCGTGGCTA	0.512																																					p.E973fs		Atlas-INDEL	.											.	ITGA9	98	.	0			c.2919delG						.						180.0	141.0	154.0					3																	37845344		2203	4300	6503	SO:0001589	frameshift_variant	3680	exon27			.	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.2920delC	chr3.hg19:g.37845344delC	ENSP00000264741:p.Pro974fs	187.0	0.0		233.0	17.0	NM_002207	Q14638	Frame_Shift_Del	DEL	ENST00000264741.5	hg19	CCDS2669.1																																																																																			.	.		0.512	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
TM9SF2	9375	hgsc.bcm.edu	37	13	100191778	100191778	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:100191778delA	ENST00000376387.4	+	7	985	c.795delA	c.(793-795)atafs	p.I265fs		NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	265					transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					CTGGGGAGATAAAAATTGCCT	0.373																																					p.I265fs		Atlas-INDEL	.											.	TM9SF2	52	.	0			c.794delT						.						122.0	131.0	128.0					13																	100191778		2203	4300	6503	SO:0001589	frameshift_variant	9375	exon7			.	U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.795delA	chr13.hg19:g.100191778delA	ENSP00000365567:p.Ile265fs	152.0	0.0		131.0	12.0	NM_004800	A8K399|Q2TAY5	Frame_Shift_Del	DEL	ENST00000376387.4	hg19	CCDS9493.1																																																																																			.	.		0.373	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3		
XYLT2	64132	hgsc.bcm.edu	37	17	48435819	48435819	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:48435819delC	ENST00000017003.2	+	10	2242	c.2193delC	c.(2191-2193)ctcfs	p.L732fs	XYLT2_ENST00000507602.1_Intron	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	732					chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(2)|urinary_tract(1)	12	Breast(11;7.18e-19)					CTGTTCGACTCCTTCAGTTCT	0.572																																					p.L731fs		Atlas-INDEL	.											.	XYLT2	51	.	0			c.2192delT						.						47.0	47.0	47.0					17																	48435819		2203	4300	6503	SO:0001589	frameshift_variant	64132	exon10			.	AJ277442	CCDS11563.1	17q21.33	2013-02-25			ENSG00000015532	ENSG00000015532	2.4.2.26		15517	protein-coding gene	gene with protein product	"""protein xylosyltransferase 2"""	608125				11099377	Standard	NM_022167		Approved	XT-II, PXYLT2	uc002iqo.3	Q9H1B5	OTTHUMG00000162057	ENST00000017003.2:c.2193delC	chr17.hg19:g.48435819delC	ENSP00000017003:p.Leu732fs	139.0	0.0		151.0	10.0	NM_022167	Q6UY41|Q86V00	Frame_Shift_Del	DEL	ENST00000017003.2	hg19	CCDS11563.1																																																																																			.	.		0.572	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167	
TMEM171	134285	hgsc.bcm.edu	37	5	72424240	72424240	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:72424240delC	ENST00000454765.2	+	3	1137	c.664delC	c.(664-666)cccfs	p.P226fs	TMEM171_ENST00000287773.5_Frame_Shift_Del_p.P226fs			Q8WVE6	TM171_HUMAN	transmembrane protein 171	226						integral component of membrane (GO:0016021)				endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|stomach(1)	15		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;1.87e-54)|Lung(70;0.115)		AATATTTCCACCCCCTCCACC	0.403																																					p.P221fs	NSCLC(112;638 2280 27369 30736)	Atlas-INDEL	.											.	TMEM171	41	.	0			c.663delA						.		,	11,4255		5,1,2127	209.0	211.0	210.0		,	-7.0	0.6	5		210	38,8214		18,2,4106	no	frameshift,frameshift	TMEM171	NM_173490.6,NM_001161342.1	,	23,3,6233	A1A1,A1R,RR		0.4605,0.2579,0.3914	,	,	72424240	49,12469	2203	4300	6503	SO:0001589	frameshift_variant	134285	exon3			.	BC018083	CCDS4017.1, CCDS54869.1	5q13.2	2008-02-05			ENSG00000157111	ENSG00000157111			27031	protein-coding gene	gene with protein product						12477932	Standard	NM_173490		Approved	PRP2	uc003kcm.2	Q8WVE6	OTTHUMG00000131269	ENST00000454765.2:c.664delC	chr5.hg19:g.72424240delC	ENSP00000415030:p.Pro226fs	196.0	0.0		220.0	15.0	NM_001161342	Q8N0S1|Q8TDT7	Frame_Shift_Del	DEL	ENST00000454765.2	hg19	CCDS4017.1																																																																																			.	.		0.403	TMEM171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254037.2	NM_173490	
GLS2	27165	hgsc.bcm.edu	37	12	56867277	56867277	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:56867277delC	ENST00000311966.4	-	13	1604	c.1326delG	c.(1324-1326)gggfs	p.G442fs	GLS2_ENST00000476991.1_5'Flank	NM_013267.2	NP_037399.2	Q9UI32	GLSL_HUMAN	glutaminase 2 (liver, mitochondrial)	442					cellular amino acid biosynthetic process (GO:0008652)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate secretion (GO:0014047)|glutamine metabolic process (GO:0006541)|neurotransmitter secretion (GO:0007269)|reactive oxygen species metabolic process (GO:0072593)|regulation of apoptotic process (GO:0042981)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13					L-Glutamine(DB00130)	TATGGCTGTTCCCCAGCTTGT	0.483																																					p.N443fs		Atlas-INDEL	.											.	GLS2	42	.	0			c.1327delA						.						81.0	77.0	78.0					12																	56867277		2203	4300	6503	SO:0001589	frameshift_variant	27165	exon13			.		CCDS8921.1, CCDS73482.1	12q13	2013-01-10			ENSG00000135423	ENSG00000135423		"""Ankyrin repeat domain containing"""	29570	protein-coding gene	gene with protein product		606365				11130979, 10620514	Standard	NM_013267		Approved	GA, GLS, LGA, hLGA	uc001slj.3	Q9UI32	OTTHUMG00000140379	ENST00000311966.4:c.1326delG	chr12.hg19:g.56867277delC	ENSP00000310447:p.Gly442fs	70.0	0.0		115.0	10.0	NM_013267	B7Z8Q9|Q8IX91|Q9NYY2|Q9UI31	Frame_Shift_Del	DEL	ENST00000311966.4	hg19	CCDS8921.1																																																																																			.	.		0.483	GLS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277113.1	NM_013267	
KIAA1841	84542	hgsc.bcm.edu	37	2	61304238	61304238	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:61304238delA	ENST00000402291.1	+	6	856	c.615delA	c.(613-615)atafs	p.I205fs	KIAA1841_ENST00000356719.2_Frame_Shift_Del_p.I205fs|KIAA1841_ENST00000453873.1_Frame_Shift_Del_p.I205fs|KIAA1841_ENST00000295031.5_Frame_Shift_Del_p.I205fs|KIAA1841_ENST00000482513.1_3'UTR	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	205										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			ACTGGTTGATAAAATACATTA	0.358																																					p.I205fs		Atlas-INDEL	.											.	KIAA1841	95	.	0			c.614delT						.						90.0	94.0	93.0					2																	61304238		2203	4300	6503	SO:0001589	frameshift_variant	84542	exon6			.	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.615delA	chr2.hg19:g.61304238delA	ENSP00000385579:p.Ile205fs	145.0	0.0		183.0	11.0	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Frame_Shift_Del	DEL	ENST00000402291.1	hg19	CCDS46296.1																																																																																			.	.		0.358	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	NM_032506	
CDC42EP4	23580	hgsc.bcm.edu	37	17	71281984	71281984	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:71281984delC	ENST00000335793.3	-	2	1050	c.656delG	c.(655-657)ggtfs	p.G219fs	CDC42EP4_ENST00000439510.2_Frame_Shift_Del_p.G149fs|CDC42EP4_ENST00000581014.1_Intron			Q9H3Q1	BORG4_HUMAN	CDC42 effector protein (Rho GTPase binding) 4	219					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	GTP-Rho binding (GO:0017049)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(7)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(166;0.0352)|Lung(188;0.0711)			GAGGACGTCACCCAGCATGGA	0.632																																					p.G219fs		Atlas-INDEL	.											.	CDC42EP4	19	.	0			c.657delT						.						81.0	72.0	75.0					17																	71281984		2203	4300	6503	SO:0001589	frameshift_variant	23580	exon2			.	AB042237	CCDS11695.1	17q24-q25	2008-07-18				ENSG00000179604			17147	protein-coding gene	gene with protein product	"""Cdc42 effector protein 4"", ""binder of Rho GTPases 4"""	605468				11035016, 10490598	Standard	NM_012121		Approved	CEP4, KAIA1777, BORG4, MGC3740, MGC17125	uc002jjo.3	Q9H3Q1		ENST00000335793.3:c.656delG	chr17.hg19:g.71281984delC	ENSP00000338258:p.Gly219fs	177.0	0.0		173.0	11.0	NM_012121	B3KUS7|O95828|Q96FT3	Frame_Shift_Del	DEL	ENST00000335793.3	hg19	CCDS11695.1																																																																																			.	.		0.632	CDC42EP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441898.1	NM_012121	
MGA	23269	hgsc.bcm.edu	37	15	42057143	42057143	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:42057143delG	ENST00000570161.1	+	22	7804	c.7804delG	c.(7804-7806)gggfs	p.G2602fs	MGA_ENST00000545763.1_Frame_Shift_Del_p.G2393fs|MGA_ENST00000219905.7_Frame_Shift_Del_p.G2602fs|MGA_ENST00000389936.4_Frame_Shift_Del_p.G2563fs|MGA_ENST00000566586.1_Frame_Shift_Del_p.G2393fs			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GACTCCGCAAGGGCAATTGCT	0.443																																					p.Q2601fs		Atlas-INDEL	.											.	MGA	264	.	0			c.7803delA						.						126.0	129.0	128.0					15																	42057143		2024	4188	6212	SO:0001589	frameshift_variant	23269	exon23			.	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7804delG	chr15.hg19:g.42057143delG	ENSP00000457035:p.Gly2602fs	146.0	0.0		194.0	12.0	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.443	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
NOS3	4846	hgsc.bcm.edu	37	7	150693569	150693569	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:150693569delC	ENST00000484524.1	+	3	348	c.348delC	c.(346-348)ggcfs	p.G116fs	NOS3_ENST00000461406.1_Intron|NOS3_ENST00000297494.3_Frame_Shift_Del_p.G116fs|NOS3_ENST00000467517.1_Frame_Shift_Del_p.G116fs	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		cctcccccggccccccggccc	0.652																																					p.G116fs		Atlas-INDEL	.											.	NOS3	131	.	0			c.347delG						.						11.0	13.0	12.0					7																	150693569		2159	4269	6428	SO:0001589	frameshift_variant	4846	exon3			.		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"""endothelial nitric oxide synthase"""	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.348delC	chr7.hg19:g.150693569delC	ENSP00000420215:p.Gly116fs	148.0	0.0		257.0	17.0	NM_001160111	Q495E5	Frame_Shift_Del	DEL	ENST00000484524.1	hg19	CCDS55182.1																																																																																			.	.		0.652	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603	
AGFG1	3267	hgsc.bcm.edu	37	2	228389615	228389615	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:228389615delT	ENST00000310078.8	+	5	938	c.678delT	c.(676-678)catfs	p.H226fs	AGFG1_ENST00000373671.3_Frame_Shift_Del_p.H226fs|AGFG1_ENST00000409171.1_Frame_Shift_Del_p.H226fs|AGFG1_ENST00000486932.1_3'UTR|AGFG1_ENST00000409315.1_Frame_Shift_Del_p.H226fs|AGFG1_ENST00000409979.2_Frame_Shift_Del_p.H226fs	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	226					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						ACTTTGCACATTTCAACAGTC	0.408																																					p.H226fs		Atlas-INDEL	.											.	AGFG1	80	.	0			c.677delA						.						143.0	129.0	134.0					2																	228389615		2203	4300	6503	SO:0001589	frameshift_variant	3267	exon5			.		CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"""ADP-ribosylation factor GTPase activating proteins"""	5175	protein-coding gene	gene with protein product		600862	"""HIV-1 Rev binding protein"""	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.678delT	chr2.hg19:g.228389615delT	ENSP00000312059:p.His226fs	175.0	0.0		214.0	13.0	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Frame_Shift_Del	DEL	ENST00000310078.8	hg19	CCDS2467.1																																																																																			.	.		0.408	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504	
ZNF354C	30832	hgsc.bcm.edu	37	5	178507066	178507066	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:178507066delT	ENST00000315475.6	+	5	1939	c.1633delT	c.(1633-1635)tttfs	p.F546fs		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	546			F -> L (in dbSNP:rs1445846).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		GTATCAGAGATTTTTTAAAGG	0.373																																					p.R544fs		Atlas-INDEL	.											.	ZNF354C	77	.	0			c.1632delA						.						59.0	65.0	63.0					5																	178507066		2201	4297	6498	SO:0001589	frameshift_variant	30832	exon5			.		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.1633delT	chr5.hg19:g.178507066delT	ENSP00000324064:p.Phe546fs	139.0	0.0		183.0	12.0	NM_014594	Q6P4P9|Q8NFX1	Frame_Shift_Del	DEL	ENST00000315475.6	hg19	CCDS4443.1																																																																																			.	.		0.373	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
ABCB9	23457	hgsc.bcm.edu	37	12	123416813	123416813	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:123416813delC	ENST00000542678.1	-	11	4804	c.1966delG	c.(1966-1968)gctfs	p.A656fs	ABCB9_ENST00000346530.5_Frame_Shift_Del_p.A613fs|ABCB9_ENST00000442028.2_Frame_Shift_Del_p.A656fs|ABCB9_ENST00000280560.8_Frame_Shift_Del_p.A656fs|ABCB9_ENST00000344275.7_Frame_Shift_Del_p.A656fs|ABCB9_ENST00000540285.1_Frame_Shift_Del_p.A593fs|ABCB9_ENST00000442833.2_Frame_Shift_Del_p.A656fs|ABCB9_ENST00000392439.3_Frame_Shift_Del_p.A656fs			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9	656	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		CGCACCAGAGCCCGGGCCATG	0.617																																					p.A656fs	Ovarian(49;786 1333 9175 38236)	Atlas-INDEL	.											.	ABCB9	50	.	0			c.1967delC						.						25.0	24.0	24.0					12																	123416813		2105	4156	6261	SO:0001589	frameshift_variant	23457	exon11			.	U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"""ATP binding cassette transporters / subfamily B"""	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78		ENST00000542678.1:c.1966delG	chr12.hg19:g.123416813delC	ENSP00000440288:p.Ala656fs	120.0	0.0		141.0	10.0	NM_019625	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Frame_Shift_Del	DEL	ENST00000542678.1	hg19	CCDS9241.1																																																																																			.	.		0.617	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624	
SFXN2	118980	hgsc.bcm.edu	37	10	104486829	104486829	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:104486829delG	ENST00000369893.5	+	3	414	c.247delG	c.(247-249)gggfs	p.G83fs	SFXN2_ENST00000602785.1_3'UTR	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	83					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		CCCCGACACTGGGGAGAAGAT	0.602																																					p.T82fs		Atlas-INDEL	.											.	SFXN2	40	.	0			c.246delT						.						84.0	74.0	77.0					10																	104486829		2203	4300	6503	SO:0001589	frameshift_variant	118980	exon3			.	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"""Sideroflexins"""	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.247delG	chr10.hg19:g.104486829delG	ENSP00000358909:p.Gly83fs	210.0	0.0		161.0	11.0	NM_178858	Q5JSM6	Frame_Shift_Del	DEL	ENST00000369893.5	hg19	CCDS7539.1																																																																																			.	.		0.602	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359	
RNF144A	9781	hgsc.bcm.edu	37	2	7137130	7137130	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:7137130delG	ENST00000320892.6	+	3	515	c.73delG	c.(73-75)gggfs	p.G25fs	RNF144A_ENST00000467276.1_Intron	NM_014746.3	NP_055561.2	P50876	R144A_HUMAN	ring finger protein 144A	25					protein ubiquitination (GO:0016567)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)	25	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)		GCTCTGTCTTGGGGAGTACCC	0.507																																					p.L24fs		Atlas-INDEL	.											.	RNF144A	38	.	0			c.72delT						.						135.0	119.0	124.0					2																	7137130		2203	4300	6503	SO:0001589	frameshift_variant	9781	exon3			.	D79983	CCDS1657.1	2p25.2	2008-02-05	2007-08-20	2007-08-20	ENSG00000151692	ENSG00000151692		"""RING-type (C3HC4) zinc fingers"""	20457	protein-coding gene	gene with protein product			"""ring finger protein 144"""	RNF144		8724849, 10431818	Standard	NM_014746		Approved	UBCE7IP4, KIAA0161	uc002qys.3	P50876	OTTHUMG00000090353	ENST00000320892.6:c.73delG	chr2.hg19:g.7137130delG	ENSP00000321330:p.Gly25fs	143.0	0.0		187.0	12.0	NM_014746	D6W4Y6|Q585H5	Frame_Shift_Del	DEL	ENST00000320892.6	hg19	CCDS1657.1																																																																																			.	.		0.507	RNF144A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206725.2	NM_014746	
MUT	4594	hgsc.bcm.edu	37	6	49416619	49416619	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:49416619delT	ENST00000274813.3	-	7	1481	c.1354delA	c.(1354-1356)atgfs	p.M452fs		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	452					cellular lipid metabolic process (GO:0044255)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|homocysteine metabolic process (GO:0050667)|post-embryonic development (GO:0009791)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)|methylmalonyl-CoA mutase activity (GO:0004494)|modified amino acid binding (GO:0072341)			endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	30	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATTCCACCCATTTCTTCAATT	0.318																																					p.M452fs		Atlas-INDEL	.											.	MUT	70	.	0			c.1355delT						.						121.0	122.0	122.0					6																	49416619		2203	4300	6503	SO:0001589	frameshift_variant	4594	exon7			.		CCDS4924.1	6p21	2012-10-02	2010-04-30		ENSG00000146085	ENSG00000146085	5.4.99.2		7526	protein-coding gene	gene with protein product		609058	"""methylmalonyl Coenzyme A mutase"""			2907507, 9503014	Standard	NM_000255		Approved		uc003ozg.4	P22033	OTTHUMG00000014814	ENST00000274813.3:c.1354delA	chr6.hg19:g.49416619delT	ENSP00000274813:p.Met452fs	116.0	0.0		162.0	11.0	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Frame_Shift_Del	DEL	ENST00000274813.3	hg19	CCDS4924.1																																																																																			.	.		0.318	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1		
VPS4B	9525	hgsc.bcm.edu	37	18	61067829	61067829	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:61067829delA	ENST00000238497.5	-	6	795	c.592delT	c.(592-594)tcafs	p.S198fs	VPS4B_ENST00000591383.1_5'UTR	NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN	vacuolar protein sorting 4 homolog B (S. cerevisiae)	198					ATP catabolic process (GO:0006200)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|intracellular cholesterol transport (GO:0032367)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|response to lipid (GO:0033993)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|nucleus (GO:0005634)|vacuolar membrane (GO:0005774)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						GAAGATATTGAAAAAAATGTT	0.373																																					p.S198X		Atlas-INDEL	.											.	VPS4B	33	.	0			c.593delC						.						115.0	115.0	115.0					18																	61067829		2203	4300	6503	SO:0001589	frameshift_variant	9525	exon6			.	AF038960	CCDS11983.1	18q21.33	2010-04-21	2006-04-04	2002-06-14	ENSG00000119541	ENSG00000119541		"""ATPases / AAA-type"""	10895	protein-coding gene	gene with protein product		609983	"""suppressor of K+ transport defect 1"", ""vacuolar protein sorting 4B (yeast)"""	SKD1		11563910	Standard	XM_006722582		Approved	VPS4-2, SKD1B	uc002lix.3	O75351	OTTHUMG00000132790	ENST00000238497.5:c.592delT	chr18.hg19:g.61067829delA	ENSP00000238497:p.Ser198fs	151.0	0.0		150.0	10.0	NM_004869	Q69HW4|Q9GZS7	Frame_Shift_Del	DEL	ENST00000238497.5	hg19	CCDS11983.1																																																																																			.	.		0.373	VPS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256198.2	NM_004869	
MFSD9	84804	hgsc.bcm.edu	37	2	103334977	103334978	+	Frame_Shift_Ins	INS	-	-	G	rs145424077	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:103334977_103334978insG	ENST00000258436.5	-	6	1369_1370	c.1326_1327insC	c.(1324-1329)cccagcfs	p.S443fs	MFSD9_ENST00000496253.1_5'Flank	NM_032718.3	NP_116107.3	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing 9	443					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(3)|large_intestine(7)|liver(1)|lung(6)|ovary(2)|skin(1)	20						GCGCCCAGGCTGGGGGGGCCGC	0.554																																					p.S443fs		Atlas-Indel,Pindel	.											.	MFSD9	56	.	0			c.1327_1328insC						.																																			SO:0001589	frameshift_variant	84804	exon6			.		CCDS2063.1	2q12.1	2007-01-12			ENSG00000135953	ENSG00000135953			28158	protein-coding gene	gene with protein product							Standard	NM_032718		Approved	MGC11332	uc002tcb.2	Q8NBP5	OTTHUMG00000130781	ENST00000258436.5:c.1327dupC	chr2.hg19:g.103334984_103334984dupG	ENSP00000258436:p.Ser443fs	106.0	0.0		133.0	23.0	NM_032718	Q4ZG89|Q53TU0|Q96GQ4|Q9BRI8	Frame_Shift_Ins	INS	ENST00000258436.5	hg19	CCDS2063.1																																																																																			.	.		0.554	MFSD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253295.2	NM_032718	
RAD9A	5883	hgsc.bcm.edu	37	11	67164988	67164988	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:67164988delC	ENST00000307980.2	+	11	1227	c.1134delC	c.(1132-1134)ggcfs	p.G378fs	PPP1CA_ENST00000532446.1_5'Flank|RNU6-1238P_ENST00000517215.1_RNA|RAD9A_ENST00000535644.1_3'UTR	NM_001243224.1|NM_004584.2	NP_001230153.1|NP_004575.1	Q99638	RAD9A_HUMAN	RAD9 homolog A (S. pombe)	378	Sufficient for interaction with ABL1.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|intra-S DNA damage checkpoint (GO:0031573)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|enzyme binding (GO:0019899)|exodeoxyribonuclease III activity (GO:0008853)|histone deacetylase binding (GO:0042826)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			lung(7)|upper_aerodigestive_tract(1)	8			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)			CCCCCCAGGGCCCCAGCCCTG	0.607								Other conserved DNA damage response genes																													p.G378fs		Atlas-INDEL	.											.	RAD9A	15	.	0			c.1133delG						.						61.0	50.0	54.0					11																	67164988		2200	4295	6495	SO:0001589	frameshift_variant	5883	exon11			.	U53174	CCDS8159.1	11q13.1-q13.2	2008-02-05	2003-07-21	2003-07-23	ENSG00000172613	ENSG00000172613			9827	protein-coding gene	gene with protein product		603761	"""RAD9 (S. pombe) homolog"""	RAD9		8943031	Standard	NM_004584		Approved		uc001okr.3	Q99638	OTTHUMG00000167670	ENST00000307980.2:c.1134delC	chr11.hg19:g.67164988delC	ENSP00000311360:p.Gly378fs	146.0	0.0		257.0	16.0	NM_004584	B2RCZ8|Q6FI29|Q96C41	Frame_Shift_Del	DEL	ENST00000307980.2	hg19	CCDS8159.1																																																																																			.	.		0.607	RAD9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395481.2	NM_004584	
COBL	23242	hgsc.bcm.edu	37	7	51287562	51287562	+	Frame_Shift_Del	DEL	G	G	-	rs368613191		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:51287562delG	ENST00000265136.7	-	2	286	c.121delC	c.(121-123)cacfs	p.H41fs	COBL_ENST00000395540.2_Frame_Shift_Del_p.H41fs|COBL_ENST00000441453.1_Frame_Shift_Del_p.H41fs|COBL_ENST00000395542.2_Frame_Shift_Del_p.H41fs	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	41					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					GCCCCATCGTGGGGGGGCTTC	0.602																																					p.H41fs	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-INDEL	.											.,1	COBL	167	.	0			c.122delA						.						40.0	42.0	42.0					7																	51287562		2203	4300	6503	SO:0001589	frameshift_variant	23242	exon2			.	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"""cordon-bleu homolog (mouse)"""				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.121delC	chr7.hg19:g.51287562delG	ENSP00000265136:p.His41fs	146.0	0.0		169.0	16.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Frame_Shift_Del	DEL	ENST00000265136.7	hg19	CCDS34637.1																																																																																			.	.		0.602	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
GPR114	221188	hgsc.bcm.edu	37	16	57597883	57597883	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:57597883delT	ENST00000340339.4	+	5	944	c.421delT	c.(421-423)tttfs	p.F142fs	GPR114_ENST00000349457.3_Frame_Shift_Del_p.F142fs|GPR114_ENST00000394361.4_3'UTR	NM_153837.1	NP_722579.1	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114	142					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)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(5)|ovary(2)|stomach(1)|urinary_tract(1)	23						CAACACCCACTTTTTCAAGGT	0.637																																					p.H140fs		Atlas-INDEL	.											.	GPR114	52	.	0			c.420delC						.						74.0	76.0	76.0					16																	57597883		2198	4300	6498	SO:0001589	frameshift_variant	221188	exon5			.	AY140956	CCDS10785.1	16q13	2014-08-08			ENSG00000159618	ENSG00000159618		"""-"", ""GPCR / Class B : Orphans"""	19010	protein-coding gene	gene with protein product						12435584	Standard	NM_153837		Approved	PGR27	uc002ely.3	Q8IZF4	OTTHUMG00000133461	ENST00000340339.4:c.421delT	chr16.hg19:g.57597883delT	ENSP00000342981:p.Phe142fs	130.0	0.0		173.0	13.0	NM_153837	B3KXZ5|Q6ZMH7|Q6ZML4|Q86SL8|Q8IZ14	Frame_Shift_Del	DEL	ENST00000340339.4	hg19	CCDS10785.1																																																																																			.	.		0.637	GPR114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257336.3	NM_153837	
NUP210L	91181	hgsc.bcm.edu	37	1	154031143	154031143	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:154031143delA	ENST00000368559.3	-	21	2948	c.2877delT	c.(2875-2877)tttfs	p.F959fs	NUP210L_ENST00000368553.1_5'Flank|NUP210L_ENST00000271854.3_Frame_Shift_Del_p.F959fs	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	959					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			CCTCCAAGGTAAAAAATCCAG	0.423																																					p.T960fs		Atlas-INDEL	.											.	NUP210L	181	.	0			c.2878delA						.						86.0	77.0	80.0					1																	154031143		1835	4094	5929	SO:0001589	frameshift_variant	91181	exon21			.	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.2877delT	chr1.hg19:g.154031143delA	ENSP00000357547:p.Phe959fs	82.0	0.0		149.0	10.0	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Frame_Shift_Del	DEL	ENST00000368559.3	hg19	CCDS41399.1																																																																																			.	.		0.423	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308	
BRWD3	254065	hgsc.bcm.edu	37	X	79938011	79938011	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:79938011delT	ENST00000373275.4	-	38	4566	c.4350delA	c.(4348-4350)aaafs	p.K1450fs	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1450					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						TTCTTAGACGTTTTCTGTACC	0.368																																					p.R1451fs		Atlas-INDEL	.											.	BRWD3	251	.	0			c.4351delC						.						304.0	238.0	261.0					X																	79938011		2203	4300	6503	SO:0001589	frameshift_variant	254065	exon38			.		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"""WD repeat domain containing"""	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.4350delA	chrX.hg19:g.79938011delT	ENSP00000362372:p.Lys1450fs	163.0	0.0		149.0	10.0	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Frame_Shift_Del	DEL	ENST00000373275.4	hg19	CCDS14447.1																																																																																			.	.		0.368	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252	
ATF3	467	hgsc.bcm.edu	37	1	212788594	212788594	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:212788594delA	ENST00000341491.4	+	2	496	c.231delA	c.(229-231)acafs	p.T77fs	RN7SL512P_ENST00000578962.1_RNA|ATF3_ENST00000492118.1_Intron|ATF3_ENST00000366985.1_Frame_Shift_Del_p.T20fs|ATF3_ENST00000336937.4_Frame_Shift_Del_p.T48fs|ATF3_ENST00000366983.1_Frame_Shift_Del_p.T77fs|ATF3_ENST00000366987.2_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	78.0	0.0		164.0	11.0	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	
TUBGCP4	27229	hgsc.bcm.edu	37	15	43675520	43675520	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:43675520delG	ENST00000260383.7	+	7	795	c.541delG	c.(541-543)gggfs	p.G181fs	TUBGCP4_ENST00000399460.3_Frame_Shift_Del_p.G45fs|TUBGCP4_ENST00000564079.1_Frame_Shift_Del_p.G181fs			Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4	181					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|spindle pole (GO:0000922)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(4)|prostate(2)|upper_aerodigestive_tract(2)	21		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		CGTTTGTCATGGGGTCATGTA	0.453																																					p.H180fs		Atlas-INDEL	.											.	TUBGCP4	48	.	0			c.540delT						.						83.0	79.0	81.0					15																	43675520		1884	4131	6015	SO:0001589	frameshift_variant	27229	exon7			.	AJ249677	CCDS42030.1, CCDS66745.1	15q15.3	2014-08-12			ENSG00000137822	ENSG00000137822			16691	protein-coding gene	gene with protein product		609610				10562286	Standard	NM_001286414		Approved	76P, FLJ14797	uc001zrn.3	Q9UGJ1	OTTHUMG00000176647	ENST00000260383.7:c.541delG	chr15.hg19:g.43675520delG	ENSP00000260383:p.Gly181fs	159.0	0.0		150.0	10.0	NM_014444	B3KNK6|Q969X3|Q9NVF0	Frame_Shift_Del	DEL	ENST00000260383.7	hg19																																																																																				.	.		0.453	TUBGCP4-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000432970.1	NM_014444	
ABCC8	6833	hgsc.bcm.edu	37	11	17449417	17449417	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:17449417delG	ENST00000389817.3	-	15	2181	c.2113delC	c.(2113-2115)cgafs	p.R705fs	ABCC8_ENST00000302539.4_Frame_Shift_Del_p.R705fs|ABCC8_ENST00000528202.1_5'Flank			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	705	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|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 ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	GCCATACCTCGGGGGATACGA	0.537																																					p.R705fs		Atlas-INDEL	.											.	ABCC8	170	.	0			c.2114delG						.						138.0	112.0	121.0					11																	17449417		2200	4293	6493	SO:0001589	frameshift_variant	6833	exon15			.	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"""ATP binding cassette transporters / subfamily C"""	59	protein-coding gene	gene with protein product	"""sulfonylurea receptor (hyperinsulinemia)"""	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.2113delC	chr11.hg19:g.17449417delG	ENSP00000374467:p.Arg705fs	176.0	0.0		210.0	13.0	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Frame_Shift_Del	DEL	ENST00000389817.3	hg19	CCDS31437.1																																																																																			.	.		0.537	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352	
PHF21A	51317	hgsc.bcm.edu	37	11	45957241	45957241	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:45957241delT	ENST00000418153.2	-	17	1930	c.1731delA	c.(1729-1731)aaafs	p.K577fs	PHF21A_ENST00000323180.6_Frame_Shift_Del_p.K531fs|PHF21A_ENST00000257821.4_Frame_Shift_Del_p.K578fs|PHF21A_ENST00000527753.1_5'Flank			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	577	Required for transcriptional repression.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						CTCGTTCTTGTTTTAAATCTG	0.328																																					p.Q578fs		Atlas-INDEL	.											.	PHF21A	107	.	0			c.1732delC						.						344.0	287.0	307.0					11																	45957241		2202	4298	6500	SO:0001589	frameshift_variant	51317	exon17			.	AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"""Zinc fingers, PHD-type"""	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.1731delA	chr11.hg19:g.45957241delT	ENSP00000398824:p.Lys577fs	161.0	0.0		145.0	10.0	NM_001101802	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Frame_Shift_Del	DEL	ENST00000418153.2	hg19	CCDS44578.1																																																																																			.	.		0.328	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621	
ZNF805	390980	hgsc.bcm.edu	37	19	57766049	57766049	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:57766049delC	ENST00000414468.2	+	4	1862	c.1862delC	c.(1861-1863)accfs	p.T621fs	ZNF805_ENST00000535550.1_Frame_Shift_Del_p.T488fs|ZNF805_ENST00000354309.4_Frame_Shift_Del_p.T488fs	NM_001023563.3	NP_001018857.2	Q5CZA5	ZN805_HUMAN	zinc finger protein 805	621					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(3)|kidney(3)|lung(1)|stomach(1)	9						CAAAGAGAAACCCCACAAGTG	0.393																																					p.T621fs		Atlas-INDEL	.											.	ZNF805	30	.	0			c.1861delA						.						37.0	33.0	34.0					19																	57766049		692	1591	2283	SO:0001589	frameshift_variant	390980	exon4			.	AF024708	CCDS46207.1, CCDS46208.1	19q13.43	2013-01-08			ENSG00000204524	ENSG00000204524		"""Zinc fingers, C2H2-type"", ""-"""	23272	protein-coding gene	gene with protein product							Standard	NM_001023563		Approved		uc010ygt.2	Q5CZA5		ENST00000414468.2:c.1862delC	chr19.hg19:g.57766049delC	ENSP00000412999:p.Thr621fs	129.0	0.0		205.0	13.0	NM_001023563	B4DNM5	Frame_Shift_Del	DEL	ENST00000414468.2	hg19	CCDS46207.1																																																																																			.	.		0.393	ZNF805-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465722.1	NM_001023563	
DST	667	hgsc.bcm.edu	37	6	56336022	56336022	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:56336022delT	ENST00000361203.3	-	90	21250	c.21243delA	c.(21241-21243)aaafs	p.K7081fs	DST_ENST00000370754.5_Frame_Shift_Del_p.K7370fs|DST_ENST00000446842.2_Frame_Shift_Del_p.K6866fs|DST_ENST00000312431.6_3'UTR|DST_ENST00000370769.4_Frame_Shift_Del_p.K7192fs|DST_ENST00000370788.2_Frame_Shift_Del_p.K4995fs|DST_ENST00000421834.2_Frame_Shift_Del_p.K5077fs|DST_ENST00000244364.6_Frame_Shift_Del_p.K4778fs			Q03001	DYST_HUMAN	dystonin	7190					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ATCGCATGTATTTTTTGCGCC	0.358																																					p.Y4779fs		Atlas-INDEL	.											.	DST	1427	.	0			c.14335delT						.						59.0	54.0	55.0					6																	56336022		1870	4146	6016	SO:0001589	frameshift_variant	667	exon76			.	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.21243delA	chr6.hg19:g.56336022delT	ENSP00000354508:p.Lys7081fs	142.0	0.0		158.0	11.0	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Frame_Shift_Del	DEL	ENST00000361203.3	hg19																																																																																				.	.		0.358	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
KLRK1	22914	hgsc.bcm.edu	37	12	10539504	10539504	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:10539504delT	ENST00000240618.6	-	3	286	c.146delA	c.(145-147)aatfs	p.N49fs	KLRK1_ENST00000540818.1_Frame_Shift_Del_p.N49fs|KLRC4-KLRK1_ENST00000539300.1_3'UTR|RP11-277P12.20_ENST00000500682.1_RNA	NM_001199805.1|NM_007360.3	NP_001186734.1|NP_031386.2	P26718	NKG2D_HUMAN	killer cell lectin-like receptor subfamily K, member 1	49					cell differentiation (GO:0030154)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|skin(1)	9						GGACTTACCATTTTCTCTACA	0.323																																					p.N49fs		Atlas-INDEL	.											.	.	.	.	0			c.147delT						.						193.0	172.0	179.0					12																	10539504		2203	4298	6501	SO:0001589	frameshift_variant	0	exon8			.	AJ001687	CCDS8623.1	12p13.2-p12.3	2010-02-17	2003-02-19		ENSG00000213809	ENSG00000213809		"""Killer cell lectin-like receptors"", ""CD molecules"""	18788	protein-coding gene	gene with protein product		611817	"""DNA segment on chromosome 12 (unique) 2489 expressed sequence"""	D12S2489E		9683661, 2007850	Standard	NM_007360		Approved	NKG2D, KLR, NKG2-D, CD314	uc009zhj.3	P26718	OTTHUMG00000168574	ENST00000240618.6:c.146delA	chr12.hg19:g.10539504delT	ENSP00000240618:p.Asn49fs	121.0	0.0		183.0	11.0	NM_001199805	A8K7K5|A8K7P4|Q9NR41	Frame_Shift_Del	DEL	ENST00000240618.6	hg19	CCDS8623.1																																																																																			.	.		0.323	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360	
NBPF15	284565	hgsc.bcm.edu	37	1	148744584	148744584	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:148744584delC	ENST00000417839.1	+	6	921	c.731delC	c.(730-732)tccfs	p.S245fs		NM_001102663.1	NP_001096133	Q5SXJ2	NBPFG_HUMAN		245	NBPF 1. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4	all_hematologic(923;0.032)					ATTGGCTCATCCTCTCATGTT	0.443																																					p.S244fs		Atlas-INDEL	.											.	NBPF16	7	.	0			c.730delT						.						6.0	3.0	5.0					1																	148744584		630	176	806	SO:0001589	frameshift_variant	728936	exon6			.																												ENST00000417839.1:c.731delC	chr1.hg19:g.148744584delC	ENSP00000395369:p.Ser245fs	74.0	0.0		160.0	11.0	NM_001102663	A8MPT6	Frame_Shift_Del	DEL	ENST00000417839.1	hg19	CCDS41384.1																																																																																			.	.		0.443	NBPF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097693.1		
ANGPT1	284	hgsc.bcm.edu	37	8	108348381	108348381	+	5'UTR	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:108348381delT	ENST00000520734.1	-	0	257				ANGPT1_ENST00000520052.1_5'UTR			Q15389	ANGP1_HUMAN	angiopoietin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell-substrate adhesion (GO:0031589)|glomerulus vasculature development (GO:0072012)|hemopoiesis (GO:0030097)|heparin biosynthetic process (GO:0030210)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of vascular permeability (GO:0043116)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|protein localization to cell surface (GO:0034394)|regulation of satellite cell proliferation (GO:0014842)|sprouting angiogenesis (GO:0002040)|Tie signaling pathway (GO:0048014)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(13)|ovary(4)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	43	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			TCCTCACCTGTTTTTTTCATG	0.368																																					p.N191fs		Atlas-INDEL	.											.	ANGPT1	111	.	0			c.573delC						.						135.0	123.0	127.0					8																	108348381		2203	4300	6503	SO:0001623	5_prime_UTR_variant	284	exon3			.	D13628	CCDS6306.1, CCDS56551.1	8q23.1	2013-02-06			ENSG00000154188	ENSG00000154188		"""Fibrinogen C domain containing"""	484	protein-coding gene	gene with protein product		601667				9545648	Standard	NM_001146		Approved	KIAA0003, Ang1	uc003ymn.3	Q15389	OTTHUMG00000164812	ENST00000520734.1:c.-29A>-	chr8.hg19:g.108348381delT		107.0	0.0		175.0	12.0	NM_001199859	Q5HYA0	Frame_Shift_Del	DEL	ENST00000520734.1	hg19																																																																																				.	.		0.368	ANGPT1-002	PUTATIVE	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000380428.2	NM_001146, NM_139290	
SYT3	84258	hgsc.bcm.edu	37	19	51133356	51133356	+	Frame_Shift_Del	DEL	C	C	-	rs10407511	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:51133356delC	ENST00000338916.4	-	3	1380	c.747delG	c.(745-747)cggfs	p.R249fs	SYT3_ENST00000600079.1_Frame_Shift_Del_p.R249fs|SYT3_ENST00000544769.1_Frame_Shift_Del_p.R249fs|SYT3_ENST00000593901.1_Frame_Shift_Del_p.R249fs	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	249					calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		GGGCAGGTGGCCGCTCCTCAC	0.657																																					p.P250fs		Atlas-INDEL	.											.	SYT3	85	.	0			c.748delC						.						32.0	32.0	32.0					19																	51133356		2203	4300	6503	SO:0001589	frameshift_variant	84258	exon3			.	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"""Synaptotagmins"""	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.747delG	chr19.hg19:g.51133356delC	ENSP00000340914:p.Arg249fs	106.0	0.0		145.0	10.0	NM_032298	Q8N5Z1|Q8N640	Frame_Shift_Del	DEL	ENST00000338916.4	hg19	CCDS12798.1																																																																																			.	.		0.657	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298	
PNMA5	114824	hgsc.bcm.edu	37	X	152159005	152159005	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:152159005delG	ENST00000439251.1	-	2	1576	c.1138delC	c.(1138-1140)cagfs	p.Q380fs	PNMA5_ENST00000361887.5_Frame_Shift_Del_p.Q380fs|PNMA5_ENST00000535214.1_Frame_Shift_Del_p.Q380fs|PNMA5_ENST00000452693.1_Frame_Shift_Del_p.Q380fs	NM_001103150.1	NP_001096620.1	Q96PV4	PNMA5_HUMAN	paraneoplastic Ma antigen family member 5	380					positive regulation of apoptotic process (GO:0043065)					breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					TGTATGGTCTGGGGGCTGCTG	0.607																																					p.Q380fs		Atlas-INDEL	.											.	PNMA5	63	.	0			c.1139delA						.						88.0	78.0	81.0					X																	152159005		2203	4300	6503	SO:0001589	frameshift_variant	114824	exon2			.	AB067521	CCDS14718.1	Xq28	2012-02-09	2012-02-09		ENSG00000198883	ENSG00000198883		"""Paraneoplastic Ma antigens"""	18743	protein-coding gene	gene with protein product	"""paraneoplastic antigen family 5"""	300916	"""paraneoplastic antigen like 5"""			16214224	Standard	NM_052926		Approved	KIAA1934	uc004fgy.4	Q96PV4	OTTHUMG00000024184	ENST00000439251.1:c.1138delC	chrX.hg19:g.152159005delG	ENSP00000388850:p.Gln380fs	93.0	0.0		144.0	10.0	NM_001103150	B4DI72|B7Z9Y9|Q495L5|Q8NET3	Frame_Shift_Del	DEL	ENST00000439251.1	hg19	CCDS14718.1																																																																																			.	.		0.607	PNMA5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060925.1	NM_052926	
DCANP1	140947	hgsc.bcm.edu	37	5	134785335	134785335	+	5'Flank	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:134785335delG	ENST00000503143.2	-	0	0				TIFAB_ENST00000537858.1_Frame_Shift_Del_p.L99fs|CTB-138E5.1_ENST00000510230.1_RNA	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN								nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACGGTGCTCAGGGGGACCTGC	0.592																																					p.L99fs		Atlas-INDEL	.											.	TIFAB	23	.	0			c.296delT						.						100.0	104.0	103.0					5																	134785335		2114	4228	6342	SO:0001631	upstream_gene_variant	497189	exon2			.																													chr5.hg19:g.134785335delG	Exception_encountered	129.0	0.0		168.0	11.0	NM_001099221		Frame_Shift_Del	DEL	ENST00000503143.2	hg19	CCDS4186.1																																																																																			.	.		0.592	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1		
CAT	847	hgsc.bcm.edu	37	11	34470817	34470817	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:34470817delC	ENST00000241052.4	+	2	234	c.145delC	c.(145-147)cccfs	p.P49fs		NM_001752.3	NP_001743.1	P04040	CATA_HUMAN	catalase	49					aerobic respiration (GO:0009060)|cellular response to growth factor stimulus (GO:0071363)|cholesterol metabolic process (GO:0008203)|hemoglobin metabolic process (GO:0020027)|hydrogen peroxide catabolic process (GO:0042744)|menopause (GO:0042697)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleobase-containing small molecule metabolic process (GO:0055086)|osteoblast differentiation (GO:0001649)|positive regulation of cell division (GO:0051781)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to reactive oxygen species (GO:0000302)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|ureteric bud development (GO:0001657)|UV protection (GO:0009650)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	aminoacylase activity (GO:0004046)|antioxidant activity (GO:0016209)|catalase activity (GO:0004096)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|oxidoreductase activity, acting on peroxide as acceptor (GO:0016684)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(3)	26		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)	GCCCCGTGGGCCCCTTCTTGT	0.468																																					p.G48fs		Atlas-INDEL	.											.	CAT	42	.	0			c.144delG						.						95.0	96.0	95.0					11																	34470817		2202	4298	6500	SO:0001589	frameshift_variant	847	exon2			.	AY028632	CCDS7891.1	11p13	2012-10-02			ENSG00000121691	ENSG00000121691	1.11.1.6		1516	protein-coding gene	gene with protein product		115500					Standard	NM_001752		Approved		uc001mvm.3	P04040	OTTHUMG00000044353	ENST00000241052.4:c.145delC	chr11.hg19:g.34470817delC	ENSP00000241052:p.Pro49fs	106.0	0.0		164.0	10.0	NM_001752	A8K6C0|B2RCZ9|D3DR07|Q2M1U4|Q4VXX5|Q9BWT9|Q9UC85	Frame_Shift_Del	DEL	ENST00000241052.4	hg19	CCDS7891.1																																																																																			.	.		0.468	CAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103197.2	NM_001752	
PPAP2B	8613	hgsc.bcm.edu	37	1	56990119	56990119	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:56990119delA	ENST00000371250.3	-	3	956	c.405delT	c.(403-405)tttfs	p.F135fs		NM_003713.4	NP_003704.3	O14495	LPP3_HUMAN	phosphatidic acid phosphatase type 2B	135					Bergmann glial cell differentiation (GO:0060020)|blood vessel development (GO:0001568)|canonical Wnt signaling pathway involved in positive regulation of cell-cell adhesion (GO:0044329)|canonical Wnt signaling pathway involved in positive regulation of endothelial cell migration (GO:0044328)|canonical Wnt signaling pathway involved in positive regulation of wound healing (GO:0044330)|dephosphorylation (GO:0016311)|gastrulation with mouth forming second (GO:0001702)|germ cell migration (GO:0008354)|homotypic cell-cell adhesion (GO:0034109)|lipid metabolic process (GO:0006629)|negative regulation of protein phosphorylation (GO:0001933)|phospholipid metabolic process (GO:0006644)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of sphingolipid mediated signaling pathway (GO:1902068)|regulation of Wnt signaling pathway (GO:0030111)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)|sphingosine-1-phosphate phosphatase activity (GO:0042392)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						TGGCACAGCCAAAGAGGAAGC	0.532																																					p.G136fs		Atlas-INDEL	.											.	PPAP2B	30	.	0			c.406delG						.						91.0	96.0	94.0					1																	56990119		2203	4300	6503	SO:0001589	frameshift_variant	8613	exon3			.	AB000889	CCDS604.1	1p32.2	2009-05-27			ENSG00000162407	ENSG00000162407	3.1.3.4		9229	protein-coding gene	gene with protein product		607125				9305923	Standard	NM_003713		Approved	PAP-2b, LPP3	uc001cyj.2	O14495	OTTHUMG00000008160	ENST00000371250.3:c.405delT	chr1.hg19:g.56990119delA	ENSP00000360296:p.Phe135fs	109.0	0.0		151.0	10.0	NM_003713	B2R651|D3DQ52|Q5U0F7|Q96GW0|Q99782	Frame_Shift_Del	DEL	ENST00000371250.3	hg19	CCDS604.1																																																																																			.	.		0.532	PPAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022334.2	NM_003713	
PLCB3	5331	hgsc.bcm.edu	37	11	64031017	64031017	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:64031017delG	ENST00000540288.1	+	20	2506	c.2403delG	c.(2401-2403)gagfs	p.E801fs	PLCB3_ENST00000279230.6_Frame_Shift_Del_p.E801fs|PLCB3_ENST00000325234.5_Frame_Shift_Del_p.E734fs	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	801	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						CCTTTGAGGAGGGGGGTAAAT	0.657																																					p.E801fs		Atlas-INDEL	.											.	PLCB3	103	.	0			c.2402delA						.																																			SO:0001589	frameshift_variant	5331	exon20			.	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.2403delG	chr11.hg19:g.64031017delG	ENSP00000443631:p.Glu801fs	79.0	0.0		169.0	11.0	NM_000932	A5PKZ6|G5E960|Q8N1A4	Frame_Shift_Del	DEL	ENST00000540288.1	hg19	CCDS8064.1																																																																																			.	.		0.657	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
SCAF1	58506	hgsc.bcm.edu	37	19	50156035	50156035	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:50156035delC	ENST00000360565.3	+	7	2513	c.2389delC	c.(2389-2391)cccfs	p.P798fs		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	798	Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		GAAGGCCCGGCCCCCCAAGGA	0.667																																					p.R796fs		Atlas-INDEL	.											.	SCAF1	78	.	0			c.2388delG						.						37.0	47.0	44.0					19																	50156035		2199	4300	6499	SO:0001589	frameshift_variant	58506	exon7			.	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.2389delC	chr19.hg19:g.50156035delC	ENSP00000353769:p.Pro798fs	113.0	0.0		159.0	13.0	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Frame_Shift_Del	DEL	ENST00000360565.3	hg19	CCDS33074.1																																																																																			.	.		0.667	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
SYT11	23208	hgsc.bcm.edu	37	1	155851197	155851197	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:155851197delG	ENST00000368324.4	+	4	1447	c.1194delG	c.(1192-1194)ctgfs	p.L398fs	SYT11_ENST00000539162.1_Frame_Shift_Del_p.L91fs	NM_152280.4	NP_689493.3	Q9BT88	SYT11_HUMAN	synaptotagmin XI	398					negative regulation of neurotransmitter secretion (GO:0046929)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(1)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;0.000162)			GGCTGATCCTGGGGGCACACA	0.587																																					p.L398fs		Atlas-INDEL	.											.	SYT11	55	.	0			c.1193delT						.						133.0	138.0	136.0					1																	155851197		2203	4300	6503	SO:0001589	frameshift_variant	23208	exon4			.	D38522	CCDS1122.1	1q22	2013-01-21			ENSG00000132718	ENSG00000132718		"""Synaptotagmins"""	19239	protein-coding gene	gene with protein product		608741				11543631	Standard	NM_152280		Approved	KIAA0080, MGC10881, MGC17226, DKFZp781D015	uc001fmg.3	Q9BT88	OTTHUMG00000014105	ENST00000368324.4:c.1194delG	chr1.hg19:g.155851197delG	ENSP00000357307:p.Leu398fs	132.0	0.0		258.0	17.0	NM_152280	Q14998|Q5W0D4|Q68CT5|Q8IXU3|Q96SU2	Frame_Shift_Del	DEL	ENST00000368324.4	hg19	CCDS1122.1																																																																																			.	.		0.587	SYT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039597.1	NM_152280	
HRG	3273	hgsc.bcm.edu	37	3	186392941	186392941	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:186392941delA	ENST00000232003.4	+	6	783	c.703delA	c.(703-705)aaafs	p.K235fs		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	235	Cystatin 2.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		GGAAAGCCCGAAAAACCTTGT	0.443																																					p.P234fs		Atlas-INDEL	.											HRG,rectum,carcinoma,+1,1	HRG	81	.	0			c.702delG						.						229.0	233.0	232.0					3																	186392941		2203	4300	6503	SO:0001589	frameshift_variant	3273	exon6			.		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"""histidine-proline rich glycoprotein"", ""thrombophilia due to elevated HRG"""	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.703delA	chr3.hg19:g.186392941delA	ENSP00000232003:p.Lys235fs	164.0	0.0		249.0	17.0	NM_000412	B9EK35|D3DNU7	Frame_Shift_Del	DEL	ENST00000232003.4	hg19	CCDS3280.1																																																																																			.	.		0.443	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412	
TBC1D23	55773	hgsc.bcm.edu	37	3	100002490	100002490	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:100002490delT	ENST00000394144.4	+	4	318	c.311delT	c.(310-312)cttfs	p.L105fs	TBC1D23_ENST00000344949.5_Frame_Shift_Del_p.L105fs|TBC1D23_ENST00000486274.1_3'UTR|TBC1D23_ENST00000475134.1_Intron	NM_001199198.2	NP_001186127.1	Q9NUY8	TBC23_HUMAN	TBC1 domain family, member 23	105	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of interleukin-6 production (GO:0032755)|regulation of inflammatory response (GO:0050727)|regulation of tumor necrosis factor production (GO:0032680)		Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(10)|ovary(1)|prostate(2)|skin(2)	25						GCAGAATTACTTTTGGATATT	0.368																																					p.L104fs		Atlas-INDEL	.											.	TBC1D23	133	.	0			c.310delC						.						104.0	100.0	101.0					3																	100002490		2203	4300	6503	SO:0001589	frameshift_variant	55773	exon4			.	AK001908	CCDS2936.1, CCDS56265.1	3q12.2	2013-07-10			ENSG00000036054	ENSG00000036054			25622	protein-coding gene	gene with protein product						22312129	Standard	NM_001199198		Approved	FLJ11046	uc003dtt.4	Q9NUY8	OTTHUMG00000159067	ENST00000394144.4:c.311delT	chr3.hg19:g.100002490delT	ENSP00000377700:p.Leu105fs	122.0	0.0		139.0	11.0	NM_018309	B9A6M5|Q8TCN8|Q8WUB7|Q96D90|Q9NV75	Frame_Shift_Del	DEL	ENST00000394144.4	hg19	CCDS56265.1																																																																																			.	.		0.368	TBC1D23-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353150.1	NM_018309	
MYO3A	53904	hgsc.bcm.edu	37	10	26359089	26359089	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:26359089delT	ENST00000265944.5	+	13	1386	c.1220delT	c.(1219-1221)attfs	p.I407fs	MYO3A_ENST00000543632.1_Frame_Shift_Del_p.I407fs	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	407	Myosin motor.				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						CCTCCTCACATTTTTGCAATG	0.318																																					p.I407fs		Atlas-INDEL	.											.	MYO3A	371	.	0			c.1219delA						.						69.0	70.0	70.0					10																	26359089		2202	4300	6502	SO:0001589	frameshift_variant	53904	exon13			.	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.1220delT	chr10.hg19:g.26359089delT	ENSP00000265944:p.Ile407fs	149.0	0.0		174.0	11.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Frame_Shift_Del	DEL	ENST00000265944.5	hg19	CCDS7148.1																																																																																			.	.		0.318	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
TMEM139	135932	hgsc.bcm.edu	37	7	142983605	142983605	+	Frame_Shift_Del	DEL	C	C	-	rs200902226		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:142983605delC	ENST00000359333.3	+	3	847	c.334delC	c.(334-336)cccfs	p.P113fs	TMEM139_ENST00000409102.1_Frame_Shift_Del_p.P113fs|AC073342.12_ENST00000446192.1_RNA|AC073342.12_ENST00000427392.1_RNA|TMEM139_ENST00000409541.1_Frame_Shift_Del_p.P113fs|TMEM139_ENST00000410004.1_Frame_Shift_Del_p.P113fs|CASP2_ENST00000310447.5_5'Flank|CASP2_ENST00000392925.2_5'Flank|TMEM139_ENST00000409244.1_Frame_Shift_Del_p.P113fs|TMEM139_ENST00000471161.1_3'UTR	NM_001242775.2|NM_001282876.1|NM_001282877.1	NP_001229704.1|NP_001269805.1|NP_001269806.1	Q8IV31	TM139_HUMAN	transmembrane protein 139	113						integral component of membrane (GO:0016021)				endometrium(1)|lung(4)|ovary(1)|prostate(1)	7	Melanoma(164;0.059)					GGACCAACCACCCCCCTACAG	0.577																																					p.P111fs		Atlas-INDEL	.											.	TMEM139	18	.	0			c.333delA						.		,,,,,	0,4264		0,0,2132	74.0	78.0	77.0		,,,,,	-0.1	1.0	7	dbSNP_126	77	1,8253		0,1,4126	no	frameshift,utr-5,utr-5,frameshift,frameshift,frameshift	TMEM139	NM_153345.2,NM_001242777.1,NM_001242776.1,NM_001242775.1,NM_001242774.1,NM_001242773.1	,,,,,	0,1,6258	A1A1,A1R,RR		0.0121,0.0,0.0080	,,,,,	,,,,,	142983605	1,12517	2203	4300	6503	SO:0001589	frameshift_variant	135932	exon4			.	AK075067	CCDS5878.1	7q34	2006-03-17			ENSG00000178826	ENSG00000178826			22058	protein-coding gene	gene with protein product							Standard	NM_153345		Approved	FLJ90586	uc003wck.4	Q8IV31	OTTHUMG00000152652	ENST00000359333.3:c.334delC	chr7.hg19:g.142983605delC	ENSP00000352284:p.Pro113fs	101.0	0.0		163.0	11.0	NM_001242773	B2RCL5|D3DXD4|Q6ZME2|Q8NC22|Q96AU8	Frame_Shift_Del	DEL	ENST00000359333.3	hg19	CCDS5878.1																																																																																			.	.		0.577	TMEM139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327145.1	NM_153345	
HNRNPL	3191	hgsc.bcm.edu	37	19	39329068	39329068	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:39329068delG	ENST00000221419.5	-	10	1892	c.1526delC	c.(1525-1527)ccgfs	p.P509fs	HNRNPL_ENST00000600873.1_Frame_Shift_Del_p.P376fs|AC104534.3_ENST00000594769.1_Frame_Shift_Del_p.R126fs	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	509	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			CACCTCCAGCGGGGCGTTGAA	0.597																																					p.P509fs		Atlas-INDEL	.											.	HNRNPL	67	.	0			c.1527delG						.						67.0	58.0	61.0					19																	39329068		2203	4300	6503	SO:0001589	frameshift_variant	3191	exon10			.	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"""RNA binding motif (RRM) containing"""	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.1526delC	chr19.hg19:g.39329068delG	ENSP00000221419:p.Pro509fs	139.0	0.0		150.0	10.0	NM_001533	A6ND69|A6NIT8|Q9H3P3	Frame_Shift_Del	DEL	ENST00000221419.5	hg19	CCDS33015.1																																																																																			.	.		0.597	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1		
CD82	3732	hgsc.bcm.edu	37	11	44639810	44639810	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:44639810delG	ENST00000227155.4	+	8	785	c.537delG	c.(535-537)aagfs	p.K179fs	CD82_ENST00000530931.1_3'UTR|CD82_ENST00000342935.3_Frame_Shift_Del_p.K154fs	NM_002231.3	NP_002222.1	P27701	CD82_HUMAN	CD82 molecule	179						extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				large_intestine(1)|ovary(1)	2						GCGAAGTCAAGGGGGAAGAGG	0.597																																					p.K179fs		Atlas-INDEL	.											.	CD82	27	.	0			c.536delA						.						68.0	60.0	63.0					11																	44639810		2203	4299	6502	SO:0001589	frameshift_variant	3732	exon8			.	U20770	CCDS7909.1, CCDS31469.1	11p11.2	2013-02-14	2006-03-28	2005-03-03		ENSG00000085117		"""CD molecules"", ""Tetraspanins"""	6210	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 6"", ""R2 leukocyte antigen"""	600623	"""kangai 1 (suppression of tumorigenicity 6, prostate; CD82 antigen (R2 leukocyte antigen, antigen detected by monoclonal and antibody IA4))"", ""CD82 antigen"""	ST6, KAI1			Standard	XM_006718222		Approved	R2, IA4, TSPAN27	uc001myc.3	P27701		ENST00000227155.4:c.537delG	chr11.hg19:g.44639810delG	ENSP00000227155:p.Lys179fs	129.0	0.0		163.0	10.0	NM_002231	D3DQN6|E9PC70|Q7Z2D4|Q7Z5N2	Frame_Shift_Del	DEL	ENST00000227155.4	hg19	CCDS7909.1																																																																																			.	.		0.597	CD82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389886.1		
SP100	6672	hgsc.bcm.edu	37	2	231339124	231339124	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:231339124delA	ENST00000264052.5	+	17	1917	c.1562delA	c.(1561-1563)gaafs	p.E521fs	SP100_ENST00000409112.1_Frame_Shift_Del_p.E521fs|SP100_ENST00000340126.4_Frame_Shift_Del_p.E521fs	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	521					cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cellular component movement (GO:0051271)|negative regulation of DNA binding (GO:0043392)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of Fas signaling pathway (GO:1902044)|response to cytokine (GO:0034097)|response to interferon-gamma (GO:0034341)|response to retinoic acid (GO:0032526)|response to type I interferon (GO:0034340)|retinoic acid receptor signaling pathway (GO:0048384)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(4)|upper_aerodigestive_tract(1)	25		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		ATGGATGTTGAAAACAATTCT	0.284																																					p.E521fs		Atlas-INDEL	.											.	SP100	167	.	0			c.1561delG						.						62.0	66.0	65.0					2																	231339124		2203	4299	6502	SO:0001589	frameshift_variant	6672	exon17			.	AF056322	CCDS2477.1, CCDS42832.1, CCDS56170.1, CCDS56171.1, CCDS56172.1, CCDS56173.1	2q37.1	2013-01-28	2005-11-30		ENSG00000067066	ENSG00000067066		"""Zinc fingers, PHD-type"""	11206	protein-coding gene	gene with protein product		604585	"""nuclear antigen Sp100"""			2258622, 8695863	Standard	NM_001080391		Approved		uc002vqu.1	P23497	OTTHUMG00000133203	ENST00000264052.5:c.1562delA	chr2.hg19:g.231339124delA	ENSP00000264052:p.Glu521fs	166.0	0.0		229.0	18.0	NM_001206701	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Frame_Shift_Del	DEL	ENST00000264052.5	hg19	CCDS2477.1																																																																																			.	.		0.284	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113	
ARHGEF35	445328	hgsc.bcm.edu	37	7	143884040	143884040	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:143884040delT	ENST00000378115.2	-	2	1566	c.1437delA	c.(1435-1437)aaafs	p.K479fs	ARHGEF35_ENST00000543357.1_Frame_Shift_Del_p.K479fs	NM_001003702.2	NP_001003702.2	A5YM69	ARG35_HUMAN	Rho guanine nucleotide exchange factor (GEF) 35	479										kidney(1)|large_intestine(1)|lung(3)|stomach(1)	6						CTGATAGAAGTTTTTCCTTGT	0.408																																					p.L480fs		Atlas-INDEL	.											.	ARHGEF35	11	.	0			c.1438delC						.						19.0	19.0	19.0					7																	143884040		2128	4129	6257	SO:0001589	frameshift_variant	445328	exon2			.	AK125680	CCDS34770.1	7q35	2012-07-24	2010-04-13	2010-04-13	ENSG00000213214	ENSG00000213214		"""Rho guanine nucleotide exchange factors"""	33846	protein-coding gene	gene with protein product			"""Rho guanine nucleotide exchange factor (GEF) 5-like"""	ARHGEF5L			Standard	NM_001003702		Approved	FLJ43692, CTAGE4	uc003wdz.2	A5YM69	OTTHUMG00000158010	ENST00000378115.2:c.1437delA	chr7.hg19:g.143884040delT	ENSP00000367355:p.Lys479fs	103.0	0.0		201.0	14.0	NM_001003702	Q6ZUI2	Frame_Shift_Del	DEL	ENST00000378115.2	hg19	CCDS34770.1																																																																																			.	.		0.408	ARHGEF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349997.1	NM_001003702	
AGTPBP1	23287	hgsc.bcm.edu	37	9	88204546	88204546	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:88204546delA	ENST00000357081.3	-	20	2763	c.2619delT	c.(2617-2619)tttfs	p.F873fs	AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000432218.1_Intron|AGTPBP1_ENST00000376109.3_Frame_Shift_Del_p.F885fs|AGTPBP1_ENST00000376083.3_Frame_Shift_Del_p.F833fs			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	873					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						CATCTTTCCGAAAATAGATTT	0.343																																					p.R834fs		Atlas-INDEL	.											AGTPBP1,NS,carcinoma,0,1	AGTPBP1	128	.	0			c.2500delC						.						98.0	94.0	95.0					9																	88204546		2203	4299	6502	SO:0001589	frameshift_variant	23287	exon20			.	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 1"", ""tubulinyl-Tyr carboxypeptidase"", ""carboxypeptidase-tubulin"", ""tyrosine carboxypeptidase"", ""soluble carboxypeptidase"""	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.2619delT	chr9.hg19:g.88204546delA	ENSP00000349592:p.Phe873fs	93.0	0.0		142.0	10.0	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Frame_Shift_Del	DEL	ENST00000357081.3	hg19																																																																																				.	.		0.343	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239	
PHGDH	26227	hgsc.bcm.edu	37	1	120266001	120266001	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:120266001delC	ENST00000369409.4	+	3	429	c.293delC	c.(292-294)accfs	p.T98fs	PHGDH_ENST00000369407.3_Frame_Shift_Del_p.T64fs	NM_006623.3	NP_006614.2	O43175	SERA_HUMAN	phosphoglycerate dehydrogenase	98					brain development (GO:0007420)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|G1 to G0 transition (GO:0070314)|gamma-aminobutyric acid metabolic process (GO:0009448)|glial cell development (GO:0021782)|glutamine metabolic process (GO:0006541)|glycine metabolic process (GO:0006544)|L-serine biosynthetic process (GO:0006564)|neural tube development (GO:0021915)|neuron projection development (GO:0031175)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|taurine metabolic process (GO:0019530)|threonine metabolic process (GO:0006566)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|phosphoglycerate dehydrogenase activity (GO:0004617)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	18	all_cancers(5;1.18e-09)|all_epithelial(5;2.16e-10)|Melanoma(3;1.93e-05)|all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0347)		Lung(183;0.0111)|LUSC - Lung squamous cell carcinoma(189;0.0593)		ATCTTTAGCACCCCCAATGGG	0.527																																					p.T98fs		Atlas-INDEL	.											.	PHGDH	51	.	0			c.292delA						.						165.0	150.0	155.0					1																	120266001		2203	4300	6503	SO:0001589	frameshift_variant	26227	exon3			.	BC011262	CCDS904.1	1p12	2008-02-05			ENSG00000092621	ENSG00000092621	1.1.1.95		8923	protein-coding gene	gene with protein product		606879					Standard	NM_006623		Approved	SERA, PGDH, PDG	uc001ehz.3	O43175	OTTHUMG00000012100	ENST00000369409.4:c.293delC	chr1.hg19:g.120266001delC	ENSP00000358417:p.Thr98fs	209.0	0.0		239.0	16.0	NM_006623	B2RD08|Q5SZU3|Q9BQ01	Frame_Shift_Del	DEL	ENST00000369409.4	hg19	CCDS904.1																																																																																			.	.		0.527	PHGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033464.1	NM_006623	
FILIP1	27145	hgsc.bcm.edu	37	6	76124421	76124421	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:76124421delC	ENST00000237172.7	-	2	598	c.268delG	c.(268-270)gagfs	p.E90fs	FILIP1_ENST00000393004.2_Frame_Shift_Del_p.E90fs	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	90				ELSKEDLIQLLSIMEGE -> AQYAIYIVSRLILLHFL (in Ref. 2; BAA86589). {ECO:0000305}.						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						ACCTGCAACTCCCCTTCCATT	0.383																																					p.E90fs		Atlas-INDEL	.											.	FILIP1	173	.	0			c.269delA						.						175.0	168.0	171.0					6																	76124421		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.268delG	chr6.hg19:g.76124421delC	ENSP00000237172:p.Glu90fs	112.0	0.0		143.0	10.0	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Frame_Shift_Del	DEL	ENST00000237172.7	hg19	CCDS4984.1																																																																																			.	.		0.383	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179	
PCSK9	255738	hgsc.bcm.edu	37	1	55523861	55523861	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:55523861delC	ENST00000302118.5	+	8	1623	c.1333delC	c.(1333-1335)cccfs	p.P446fs	PCSK9_ENST00000543384.1_Intron|PCSK9_ENST00000490692.1_3'UTR	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	446					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						GGCCGCCCTGCCCCCCAGCAC	0.622																																					p.L444fs	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-INDEL	.											.	PCSK9	76	.	0			c.1332delG						.						33.0	34.0	34.0					1																	55523861		2203	4300	6503	SO:0001589	frameshift_variant	255738	exon8			.	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.1333delC	chr1.hg19:g.55523861delC	ENSP00000303208:p.Pro446fs	168.0	0.0		171.0	12.0	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Frame_Shift_Del	DEL	ENST00000302118.5	hg19	CCDS603.1																																																																																			.	.		0.622	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
NRG3	10718	hgsc.bcm.edu	37	10	84711320	84711320	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:84711320delA	ENST00000404547.1	+	5	1150	c.1150delA	c.(1150-1152)aaafs	p.K384fs	NRG3_ENST00000404576.2_Frame_Shift_Del_p.K188fs|NRG3_ENST00000545131.1_Frame_Shift_Del_p.K34fs|NRG3_ENST00000372142.2_Frame_Shift_Del_p.K163fs|NRG3_ENST00000537893.1_Frame_Shift_Del_p.K34fs|NRG3_ENST00000556918.1_Frame_Shift_Del_p.K214fs|NRG3_ENST00000372141.2_Frame_Shift_Del_p.K384fs			P56975	NRG3_HUMAN	neuregulin 3	384					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		ATTCTACTTCAAAAGCAAGTA	0.398																																					p.F383fs		Atlas-INDEL	.											.	NRG3	301	.	0			c.1149delC						.						195.0	179.0	184.0					10																	84711320		2203	4300	6503	SO:0001589	frameshift_variant	10718	exon5			.	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.1150delA	chr10.hg19:g.84711320delA	ENSP00000384796:p.Lys384fs	232.0	0.0		212.0	13.0	NM_001010848	A4D7U1|Q0PEH2|Q5VYH3	Frame_Shift_Del	DEL	ENST00000404547.1	hg19	CCDS31233.1																																																																																			.	.		0.398	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086	
TRABD	80305	hgsc.bcm.edu	37	22	50632890	50632890	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:50632890delG	ENST00000303434.4	+	4	353	c.234delG	c.(232-234)gtgfs	p.V78fs	TRABD_ENST00000395827.1_Frame_Shift_Del_p.V78fs|RP3-402G11.25_ENST00000607943.1_RNA|TRABD_ENST00000380909.4_Frame_Shift_Del_p.V78fs|TRABD_ENST00000395829.1_Frame_Shift_Del_p.V78fs	NM_025204.2	NP_079480.2	Q9H4I3	TRABD_HUMAN	TraB domain containing	78										breast(1)|central_nervous_system(1)|large_intestine(1)|liver(2)|lung(1)|upper_aerodigestive_tract(1)	7		all_cancers(38;1.07e-07)|all_epithelial(38;9.6e-07)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		LUAD - Lung adenocarcinoma(64;0.105)		TGTACGTGGTGGGGACAGCCC	0.652																																					p.V78fs		Atlas-INDEL	.											.	TRABD	21	.	0			c.233delT						.						51.0	49.0	50.0					22																	50632890		2199	4295	6494	SO:0001589	frameshift_variant	80305	exon4			.	AL449244	CCDS14086.1	22q13.33	2006-07-06			ENSG00000170638	ENSG00000170638			28805	protein-coding gene	gene with protein product						12477932	Standard	NM_025204		Approved	PP2447	uc003bjs.1	Q9H4I3	OTTHUMG00000044644	ENST00000303434.4:c.234delG	chr22.hg19:g.50632890delG	ENSP00000305664:p.Val78fs	184.0	0.0		161.0	10.0	NM_025204	Q19CC5|Q96ED8|Q9H7N1|Q9UGX6|Q9UGX7	Frame_Shift_Del	DEL	ENST00000303434.4	hg19	CCDS14086.1																																																																																			.	.		0.652	TRABD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316987.1	NM_025204	
MGA	23269	hgsc.bcm.edu	37	15	41961559	41961559	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:41961559delT	ENST00000570161.1	+	1	467	c.467delT	c.(466-468)gttfs	p.V156fs	MGA_ENST00000545763.1_Frame_Shift_Del_p.V156fs|MGA_ENST00000219905.7_Frame_Shift_Del_p.V156fs|MGA_ENST00000389936.4_Frame_Shift_Del_p.V156fs|MGA_ENST00000566586.1_Frame_Shift_Del_p.V156fs|MGA_ENST00000568630.1_Intron			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TTGGGGAGGGTTTTCATTCAT	0.423																																					p.V156fs		Atlas-INDEL	.											.	MGA	264	.	0			c.466delG						.						279.0	277.0	278.0					15																	41961559		1897	4101	5998	SO:0001589	frameshift_variant	23269	exon2			.	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.467delT	chr15.hg19:g.41961559delT	ENSP00000457035:p.Val156fs	171.0	0.0		203.0	15.0	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.		0.423	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
C2CD5	9847	hgsc.bcm.edu	37	12	22666279	22666279	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:22666279delC	ENST00000333957.4	-	9	1242	c.987delG	c.(985-987)gggfs	p.G329fs	C2CD5_ENST00000536386.1_Frame_Shift_Del_p.G320fs|C2CD5_ENST00000544930.1_Frame_Shift_Del_p.G122fs|C2CD5_ENST00000446597.1_Frame_Shift_Del_p.G329fs|C2CD5_ENST00000396028.2_Frame_Shift_Del_p.G320fs|C2CD5_ENST00000542676.1_Frame_Shift_Del_p.G329fs|C2CD5_ENST00000545552.1_Frame_Shift_Del_p.G320fs	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	329					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										CTTTAAAGGGCCCCCCTTCTT	0.363																																					p.P330fs		Atlas-INDEL	.											.	.	.	.	0			c.988delC						.						144.0	133.0	137.0					12																	22666279		2203	4300	6503	SO:0001589	frameshift_variant	9847	exon9			.	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"""138 kDa C2 domain-containing phosphoprotein"""		"""KIAA0528"""	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.987delG	chr12.hg19:g.22666279delC	ENSP00000334229:p.Gly329fs	115.0	0.0		142.0	10.0	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Frame_Shift_Del	DEL	ENST00000333957.4	hg19	CCDS31758.1																																																																																			.	.		0.363	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802	
RYR1	6261	hgsc.bcm.edu	37	19	39025415	39025415	+	Frame_Shift_Del	DEL	G	G	-	rs193922839		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:39025415delG	ENST00000359596.3	+	79	11315	c.11315delG	c.(11314-11316)cggfs	p.R3772fs	RYR1_ENST00000355481.4_Frame_Shift_Del_p.R3767fs|RYR1_ENST00000360985.3_Frame_Shift_Del_p.R3772fs|AC067969.2_ENST00000595853.1_RNA			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3772			R -> Q (in CCD; autosomal recessive form). {ECO:0000269|PubMed:18253926}.|R -> W (in MHS1). {ECO:0000269|PubMed:19191329}.		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTGCACACCCGGGGGGCGGCC	0.587																																					p.R3772fs		Atlas-INDEL	.											.,1	RYR1	708	.	0			c.11314delC	GRCh37	CM073325	RYR1	M		.						41.0	40.0	40.0					19																	39025415		2203	4300	6503	SO:0001589	frameshift_variant	6261	exon79			.	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.11315delG	chr19.hg19:g.39025415delG	ENSP00000352608:p.Arg3772fs	132.0	0.0		194.0	12.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Frame_Shift_Del	DEL	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.587	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
PPIL1	51645	hgsc.bcm.edu	37	6	36823778	36823778	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:36823778delC	ENST00000373699.5	-	4	563	c.312delG	c.(310-312)gggfs	p.G104fs	PPIL1_ENST00000483552.1_5'UTR	NM_016059.4	NP_057143.1	Q9Y3C6	PPIL1_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 1	104	Cyclosporin A binding.|PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			lung(1)|ovary(1)	2						TGGTATCTGGCCCCGCATTGG	0.547																																					p.P105fs		Atlas-INDEL	.											PPIL1,caecum,carcinoma,0,1	PPIL1	6	.	0			c.313delC						.						50.0	48.0	49.0					6																	36823778		2203	4300	6503	SO:0001589	frameshift_variant	51645	exon4			.	AF090992	CCDS4826.1	6p21.1	2008-08-29			ENSG00000137168	ENSG00000137168			9260	protein-coding gene	gene with protein product		601301				10072585, 8978786	Standard	NM_016059		Approved	CYPL1	uc003omu.2	Q9Y3C6	OTTHUMG00000014612	ENST00000373699.5:c.312delG	chr6.hg19:g.36823778delC	ENSP00000362803:p.Gly104fs	132.0	0.0		161.0	11.0	NM_016059	O15001|Q5TDC9	Frame_Shift_Del	DEL	ENST00000373699.5	hg19	CCDS4826.1																																																																																			.	.		0.547	PPIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040382.1		
CYTH4	27128	hgsc.bcm.edu	37	22	37707049	37707049	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:37707049delA	ENST00000248901.6	+	10	1016	c.829delA	c.(829-831)aaafs	p.K277fs		NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4	277	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(2)|stomach(1)	15						GAAGACGTGGAAACGGCGCTG	0.637																																					p.W276X		Atlas-INDEL	.											.	CYTH4	51	.	0			c.828delG						.						169.0	137.0	148.0					22																	37707049		2203	4300	6503	SO:0001589	frameshift_variant	27128	exon10			.	AF075458	CCDS13946.1	22q12.3-q13.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000100055	ENSG00000100055		"""Pleckstrin homology (PH) domain containing"""	9505	protein-coding gene	gene with protein product		606514	"""pleckstrin homology, Sec7 and coiled/coil domains 4"", ""pleckstrin homology, Sec7 and coiled-coil domains 4"""	PSCD4		10591208	Standard	NM_013385		Approved	CYT4, cytohesin-4	uc003arf.3	Q9UIA0	OTTHUMG00000150562	ENST00000248901.6:c.829delA	chr22.hg19:g.37707049delA	ENSP00000248901:p.Lys277fs	140.0	0.0		178.0	13.0	NM_013385	Q5R3F9|Q9UGT6	Frame_Shift_Del	DEL	ENST00000248901.6	hg19	CCDS13946.1																																																																																			.	.		0.637	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318917.1		
POLQ	10721	hgsc.bcm.edu	37	3	121238748	121238748	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:121238748delG	ENST00000264233.5	-	9	1566	c.1438delC	c.(1438-1440)cgtfs	p.R480fs	POLQ_ENST00000488282.1_5'Flank	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	480	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CTGCCAGCACGGCCAACCATC	0.428								DNA polymerases (catalytic subunits)																													p.R480fs	Pancreas(152;907 1925 26081 31236 36904)	Atlas-INDEL	.											.	POLQ	273	.	0			c.1439delG						.						156.0	165.0	162.0					3																	121238748		2203	4300	6503	SO:0001589	frameshift_variant	10721	exon9			.	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.1438delC	chr3.hg19:g.121238748delG	ENSP00000264233:p.Arg480fs	116.0	0.0		169.0	11.0	NM_199420	O95160|Q6VMB5	Frame_Shift_Del	DEL	ENST00000264233.5	hg19	CCDS33833.1																																																																																			.	.		0.428	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
LINGO2	158038	hgsc.bcm.edu	37	9	27950495	27950495	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:27950495delT	ENST00000379992.2	-	6	624	c.175delA	c.(175-177)accfs	p.T59fs	LINGO2_ENST00000308675.3_Frame_Shift_Del_p.T59fs	NM_152570.2	NP_689783.1	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	59						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	44	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		AAGATTTTGGTTTCGATGGGA	0.478																																					p.T59fs		Atlas-INDEL	.											.	LINGO2	244	.	0			c.176delC						.						180.0	183.0	182.0					9																	27950495		2203	4300	6503	SO:0001589	frameshift_variant	158038	exon7			.	AL353746	CCDS6524.1	9p21.2	2013-01-11	2007-02-01	2007-02-01	ENSG00000174482	ENSG00000174482		"""Immunoglobulin superfamily / I-set domain containing"""	21207	protein-coding gene	gene with protein product		609793	"""leucine rich repeat neuronal 6C"""	LRRN6C		14686891	Standard	NM_152570		Approved	LERN3	uc003zqu.2	Q7L985	OTTHUMG00000019721	ENST00000379992.2:c.175delA	chr9.hg19:g.27950495delT	ENSP00000369328:p.Thr59fs	352.0	0.0		232.0	15.0	NM_152570	A8K4K7|B2RPM5|Q6ZMD0	Frame_Shift_Del	DEL	ENST00000379992.2	hg19	CCDS6524.1																																																																																			.	.		0.478	LINGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051978.2	NM_152570	
EXOC7	23265	hgsc.bcm.edu	37	17	74099763	74099763	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:74099763delG	ENST00000335146.7	-	1	64	c.11delC	c.(10-12)ccafs	p.P4fs	EXOC7_ENST00000467929.2_5'Flank|EXOC7_ENST00000405575.4_Frame_Shift_Del_p.P4fs|EXOC7_ENST00000332065.5_Frame_Shift_Del_p.P4fs|EXOC7_ENST00000607838.1_Frame_Shift_Del_p.P4fs|EXOC7_ENST00000589210.1_Frame_Shift_Del_p.P4fs|EXOC7_ENST00000406660.3_Frame_Shift_Del_p.P4fs|EXOC7_ENST00000411744.2_Frame_Shift_Del_p.P4fs			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	4					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			TGCCTCCTGTGGGGGAATCAT	0.682																																					p.P4fs		Atlas-INDEL	.											.	EXOC7	47	.	0			c.12delA						.						30.0	31.0	31.0					17																	74099763		2203	4300	6503	SO:0001589	frameshift_variant	23265	exon1			.	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.11delC	chr17.hg19:g.74099763delG	ENSP00000334100:p.Pro4fs	104.0	0.0		170.0	12.0	NM_001145298	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Frame_Shift_Del	DEL	ENST00000335146.7	hg19	CCDS45782.1																																																																																			.	.		0.682	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219	
ASTE1	28990	hgsc.bcm.edu	37	3	130743653	130743653	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:130743653delA	ENST00000264992.3	-	3	939	c.498delT	c.(496-498)tttfs	p.F166fs	NEK11_ENST00000507910.1_5'Flank|NEK11_ENST00000356918.4_5'Flank|ASTE1_ENST00000514044.1_Frame_Shift_Del_p.F166fs|NEK11_ENST00000510769.1_5'Flank|NEK11_ENST00000429253.2_5'Flank|NEK11_ENST00000383366.4_5'Flank|NEK11_ENST00000412440.2_5'Flank|NEK11_ENST00000510688.1_5'Flank|NEK11_ENST00000511262.1_5'Flank	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	166					DNA repair (GO:0006281)		nuclease activity (GO:0004518)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						TTTTCAGGTCAAAAATGCAAA	0.403																																					p.D167fs		Atlas-INDEL	.											.	ASTE1	67	.	0			c.499delG						.						64.0	63.0	63.0					3																	130743653		2203	4300	6503	SO:0001589	frameshift_variant	28990	exon3			.	AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.498delT	chr3.hg19:g.130743653delA	ENSP00000264992:p.Phe166fs	121.0	0.0		172.0	11.0	NM_014065	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Frame_Shift_Del	DEL	ENST00000264992.3	hg19	CCDS3068.1																																																																																			.	.		0.403	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065	
OTOF	9381	hgsc.bcm.edu	37	2	26724640	26724640	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:26724640delC	ENST00000272371.2	-	8	873	c.747delG	c.(745-747)gggfs	p.G249fs	OTOF_ENST00000403946.3_Frame_Shift_Del_p.G249fs	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	249	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCATGGGCCGCCCAGCACTTG	0.537																																					p.R250fs	GBM(102;732 1451 20652 24062 31372)	Atlas-INDEL	.											.	OTOF	524	.	0			c.748delC						.						90.0	80.0	83.0					2																	26724640		2203	4300	6503	SO:0001589	frameshift_variant	9381	exon8			.	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.747delG	chr2.hg19:g.26724640delC	ENSP00000272371:p.Gly249fs	144.0	0.0		195.0	12.0	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Frame_Shift_Del	DEL	ENST00000272371.2	hg19	CCDS1725.1																																																																																			.	.		0.537	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
RRH	10692	hgsc.bcm.edu	37	4	110754368	110754368	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:110754368delA	ENST00000317735.4	+	2	214	c.180delA	c.(178-180)acafs	p.T60fs		NM_006583.2	NP_006574.1	O14718	OPSX_HUMAN	retinal pigment epithelium-derived rhodopsin homolog	60					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	12		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00109)		GGACACCCACAAATGCAATTA	0.393																																					p.T60fs		Atlas-INDEL	.											.	RRH	24	.	0			c.179delC						.						99.0	95.0	97.0					4																	110754368		2203	4300	6503	SO:0001589	frameshift_variant	10692	exon2			.	AF012270	CCDS3687.1	4q25	2012-08-08			ENSG00000180245	ENSG00000180245		"""GPCR / Class A : Opsin receptors"""	10450	protein-coding gene	gene with protein product	"""peropsin"""	605224				9275222	Standard	NM_006583		Approved	peropsin	uc003hzv.3	O14718	OTTHUMG00000132045	ENST00000317735.4:c.180delA	chr4.hg19:g.110754368delA	ENSP00000314992:p.Thr60fs	190.0	0.0		154.0	10.0	NM_006583	A1A4V2|Q7RTS4	Frame_Shift_Del	DEL	ENST00000317735.4	hg19	CCDS3687.1																																																																																			.	.		0.393	RRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255066.1	NM_006583	
ANKRD17	26057	hgsc.bcm.edu	37	4	73985933	73985933	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:73985933delA	ENST00000358602.4	-	21	4087	c.3971delT	c.(3970-3972)ttafs	p.L1324fs	ANKRD17_ENST00000509867.2_Frame_Shift_Del_p.L1211fs|ANKRD17_ENST00000330838.6_Frame_Shift_Del_p.L1073fs|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	1324					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)			TGCTATGGTTAAAGCTGTATC	0.448																																					p.L1324fs		Atlas-INDEL	.											.	ANKRD17	214	.	0			c.3972delA						.						169.0	153.0	159.0					4																	73985933		2203	4300	6503	SO:0001589	frameshift_variant	26057	exon21			.	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.3971delT	chr4.hg19:g.73985933delA	ENSP00000351416:p.Leu1324fs	145.0	0.0		162.0	10.0	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Frame_Shift_Del	DEL	ENST00000358602.4	hg19	CCDS34004.1																																																																																			.	.		0.448	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
FASTKD3	79072	hgsc.bcm.edu	37	5	7867769	7867769	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:7867769delT	ENST00000264669.5	-	2	564	c.428delA	c.(427-429)aagfs	p.K143fs	MTRR_ENST00000502509.1_Intron|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000264668.2_5'Flank|MTRR_ENST00000341013.6_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	143					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						ATCACCATCCTTTTTTTCCAC	0.418																																					p.K143fs		Atlas-INDEL	.											.,2	FASTKD3	88	.	0			c.429delG						.						67.0	62.0	64.0					5																	7867769		2203	4300	6503	SO:0001589	frameshift_variant	79072	exon2			.	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.428delA	chr5.hg19:g.7867769delT	ENSP00000264669:p.Lys143fs	198.0	0.0		226.0	14.0	NM_024091	Q9BVD3	Frame_Shift_Del	DEL	ENST00000264669.5	hg19	CCDS3873.1																																																																																			.	.		0.418	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091	
HCN1	348980	hgsc.bcm.edu	37	5	45262631	45262631	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:45262631delG	ENST00000303230.4	-	8	2122	c.2065delC	c.(2065-2067)cagfs	p.Q689fs		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	689					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						GCTGATGGCTGGGGGGTCTGT	0.637																																					p.Q689fs		Atlas-INDEL	.											.	HCN1	298	.	0			c.2066delA						.						82.0	82.0	82.0					5																	45262631		2203	4300	6503	SO:0001589	frameshift_variant	348980	exon8			.	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.2065delC	chr5.hg19:g.45262631delG	ENSP00000307342:p.Gln689fs	158.0	0.0		182.0	11.0	NM_021072		Frame_Shift_Del	DEL	ENST00000303230.4	hg19	CCDS3952.1																																																																																			.	.		0.637	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072	
YJEFN3	374887	hgsc.bcm.edu	37	19	19645920	19645920	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:19645920delG	ENST00000514277.4	+	4	434	c.396delG	c.(394-396)gtgfs	p.V132fs	CTC-260F20.3_ENST00000555938.1_Frame_Shift_Del_p.V131fs|YJEFN3_ENST00000436027.5_Frame_Shift_Del_p.V82fs|YJEFN3_ENST00000608404.1_Frame_Shift_Del_p.V131fs	NM_198537.3	NP_940939.2	A6XGL0	YJEN3_HUMAN	YjeF N-terminal domain containing 3	132	YjeF N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00719}.									NS(1)|breast(1)|lung(3)	5						ACGGGGCAGTGGGGCTGGTCT	0.627																																					p.V132fs		Atlas-INDEL	.											.	YJEFN3	10	.	0			c.395delT						.						72.0	91.0	85.0					19																	19645920		2111	4223	6334	SO:0001589	frameshift_variant	374887	exon4			.		CCDS42530.1, CCDS54236.1	19p13.11	2014-09-11			ENSG00000250067	ENSG00000250067			24785	protein-coding gene	gene with protein product						17533573	Standard	NM_198537		Approved	hYjeF_N3-19p13.11, FLJ44968	uc002nmt.2	A6XGL0	OTTHUMG00000162251	ENST00000514277.4:c.396delG	chr19.hg19:g.19645920delG	ENSP00000426964:p.Val132fs	102.0	0.0		146.0	13.0	NM_198537	A6XGK9|Q4G1C0	Frame_Shift_Del	DEL	ENST00000514277.4	hg19	CCDS42530.1																																																																																			.	.		0.627	YJEFN3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368157.5	NM_198537	
NR4A2	4929	hgsc.bcm.edu	37	2	157184439	157184439	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:157184439delG	ENST00000339562.4	-	5	1444	c.1082delC	c.(1081-1083)ccgfs	p.P361fs	NR4A2_ENST00000409108.2_Frame_Shift_Del_p.P361fs|NR4A2_ENST00000409572.1_Frame_Shift_Del_p.P361fs|NR4A2_ENST00000539077.1_Frame_Shift_Del_p.P372fs|NR4A2_ENST00000429376.1_Frame_Shift_Del_p.P298fs|NR4A2_ENST00000426264.1_Frame_Shift_Del_p.P298fs	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	361	Pro-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)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						CAGACTCACCGGGGGCGAAGG	0.597																																					p.P361fs		Atlas-INDEL	.											.	NR4A2	82	.	0			c.1083delG						.						25.0	26.0	26.0					2																	157184439		2203	4298	6501	SO:0001589	frameshift_variant	4929	exon5			.	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.1082delC	chr2.hg19:g.157184439delG	ENSP00000344479:p.Pro361fs	138.0	0.0		200.0	12.0	NM_006186	Q16311|Q53RZ2|Q6NXU0	Frame_Shift_Del	DEL	ENST00000339562.4	hg19	CCDS2201.1																																																																																			.	.		0.597	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2		
SP2	6668	hgsc.bcm.edu	37	17	45994350	45994350	+	Frame_Shift_Del	DEL	C	C	-	rs142857959		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:45994350delC	ENST00000376741.4	+	3	1050	c.913delC	c.(913-915)cccfs	p.P306fs	AC003665.1_ENST00000585280.1_RNA|AC003665.1_ENST00000451140.2_RNA|AC003665.1_ENST00000433001.1_RNA|AC003665.1_ENST00000411573.2_RNA	NM_003110.5	NP_003101.3	Q02086	SP2_HUMAN	Sp2 transcription factor	306					cardiovascular system development (GO:0072358)|embryonic organ development (GO:0048568)|fibroblast proliferation (GO:0048144)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	13						CCAGGTGGTGCCCCCCAAGGC	0.652																																					p.V304fs		Atlas-INDEL	.											.	SP2	38	.	0			c.912delG						.						43.0	47.0	46.0					17																	45994350		2203	4300	6503	SO:0001589	frameshift_variant	6668	exon3			.		CCDS11521.2	17q21.3-q22	2013-01-08			ENSG00000167182	ENSG00000167182		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11207	protein-coding gene	gene with protein product		601801				1341900, 9730617	Standard	NM_003110		Approved	KIAA0048	uc002imk.3	Q02086	OTTHUMG00000150196	ENST00000376741.4:c.913delC	chr17.hg19:g.45994350delC	ENSP00000365931:p.Pro306fs	124.0	0.0		166.0	10.0	NM_003110	A6NK74	Frame_Shift_Del	DEL	ENST00000376741.4	hg19	CCDS11521.2																																																																																			.	.		0.652	SP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316777.1	NM_003110	
ATP1B4	23439	hgsc.bcm.edu	37	X	119509268	119509268	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:119509268delC	ENST00000218008.3	+	5	661	c.604delC	c.(604-606)cccfs	p.P203fs	ATP1B4_ENST00000361319.3_Frame_Shift_Del_p.P199fs|ATP1B4_ENST00000539306.1_Frame_Shift_Del_p.P160fs	NM_001142447.2	NP_001135919.1	Q9UN42	AT1B4_HUMAN	ATPase, Na+/K+ transporting, beta 4 polypeptide	203					monovalent inorganic cation transport (GO:0015672)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|nuclear inner membrane (GO:0005637)|sodium:potassium-exchanging ATPase complex (GO:0005890)	monovalent inorganic cation transmembrane transporter activity (GO:0015077)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	33						TGTAGATTGTCCCCCGGGGCA	0.483																																					p.C201fs		Atlas-INDEL	.											.	ATP1B4	61	.	0			c.603delT						.						121.0	111.0	114.0					X																	119509268		2203	4300	6503	SO:0001589	frameshift_variant	23439	exon5			.	AF158383	CCDS14598.1, CCDS48158.1	Xq24	2012-10-22	2010-04-20		ENSG00000101892	ENSG00000101892		"""ATPases / P-type"""	808	protein-coding gene	gene with protein product	"""Na,K-ATPase beta m-subunit"""		"""ATPase, (Na+)/K+ transporting, beta 4 polypeptide"""			10456317, 17592128	Standard	NM_012069		Approved		uc004esr.3	Q9UN42	OTTHUMG00000022299	ENST00000218008.3:c.604delC	chrX.hg19:g.119509268delC	ENSP00000218008:p.Pro203fs	138.0	0.0		170.0	13.0	NM_001142447	Q17RR0|Q9UN41	Frame_Shift_Del	DEL	ENST00000218008.3	hg19	CCDS48158.1																																																																																			.	.		0.483	ATP1B4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058095.1	NM_001142447	
PCNX	22990	hgsc.bcm.edu	37	14	71522272	71522272	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:71522272delA	ENST00000304743.2	+	25	5075	c.4629delA	c.(4627-4629)agafs	p.R1543fs	PCNX_ENST00000439984.3_Frame_Shift_Del_p.R1432fs|PCNX_ENST00000238570.5_Frame_Shift_Del_p.R1543fs	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1543						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		AGCTTGATAGAAATCCAGGTA	0.308																																					p.R1543fs		Atlas-INDEL	.											.	PCNX	198	.	0			c.4628delG						.						109.0	117.0	114.0					14																	71522272		2203	4300	6503	SO:0001589	frameshift_variant	22990	exon25			.	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.4629delA	chr14.hg19:g.71522272delA	ENSP00000304192:p.Arg1543fs	171.0	0.0		192.0	12.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Frame_Shift_Del	DEL	ENST00000304743.2	hg19	CCDS9806.1																																																																																			.	.		0.308	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
COG2	22796	hgsc.bcm.edu	37	1	230800279	230800279	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:230800279delA	ENST00000366669.4	+	5	546	c.431delA	c.(430-432)gaafs	p.E144fs	COG2_ENST00000535166.1_Frame_Shift_Del_p.E28fs|COG2_ENST00000534989.1_Frame_Shift_Del_p.E85fs|COG2_ENST00000366668.3_Frame_Shift_Del_p.E144fs	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	144					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GAGAAAATTGAAAAAATCTTA	0.269																																					p.E144fs		Atlas-INDEL	.											.	COG2	61	.	0			c.430delG						.						28.0	30.0	29.0					1																	230800279		2196	4274	6470	SO:0001589	frameshift_variant	22796	exon5			.	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"""Components of oligomeric golgi complex"""	6546	protein-coding gene	gene with protein product		606974	"""low density lipoprotein receptor defect C complementing"""	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.431delA	chr1.hg19:g.230800279delA	ENSP00000355629:p.Glu144fs	77.0	0.0		153.0	12.0	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	
RBFOX1	54715	hgsc.bcm.edu	37	16	7680656	7680656	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:7680656delC	ENST00000550418.1	+	11	1716	c.728delC	c.(727-729)gccfs	p.A243fs	RBFOX1_ENST00000552089.1_Frame_Shift_Del_p.A260fs|RBFOX1_ENST00000311745.5_Frame_Shift_Del_p.A263fs|RBFOX1_ENST00000422070.4_Frame_Shift_Del_p.A286fs|RBFOX1_ENST00000436368.2_Frame_Shift_Del_p.A263fs|RBFOX1_ENST00000547338.1_Frame_Shift_Del_p.A243fs|RBFOX1_ENST00000535565.2_Frame_Shift_Del_p.A200fs|RBFOX1_ENST00000355637.4_Frame_Shift_Del_p.A263fs|RBFOX1_ENST00000553186.1_Intron|RBFOX1_ENST00000340209.4_Frame_Shift_Del_p.A248fs|RBFOX1_ENST00000547372.1_Frame_Shift_Del_p.A286fs	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	243					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						ATGTACAGTGCCCCCAGTTCA	0.483																																					p.A263fs	Ovarian(157;934 2567 15163 39509)	Atlas-INDEL	.											RBFOX1_ENST00000550418,colon,carcinoma,0,3	RBFOX1	341	.	0			c.787delG						.						195.0	157.0	170.0					16																	7680656		2197	4300	6497	SO:0001589	frameshift_variant	54715	exon8			.	AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"""RNA binding motif (RRM) containing"""	18222	protein-coding gene	gene with protein product	"""ataxin 2-binding protein 1"", ""hexaribonucleotide binding protein 1"""	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.728delC	chr16.hg19:g.7680656delC	ENSP00000450031:p.Ala243fs	154.0	0.0		213.0	15.0	NM_145891	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Frame_Shift_Del	DEL	ENST00000550418.1	hg19	CCDS55983.1																																																																																			.	.		0.483	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891	
ZNF17	7565	hgsc.bcm.edu	37	19	57932806	57932806	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:57932806delA	ENST00000601808.1	+	3	2159	c.1946delA	c.(1945-1947)caafs	p.Q649fs	ZNF17_ENST00000307658.7_Frame_Shift_Del_p.Q651fs|AC004076.7_ENST00000597410.1_Intron	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	649					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)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		GTCTTTAACCAAAATTCTCAT	0.388																																					p.Q649fs	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-INDEL	.											.	ZNF17	49	.	0			c.1945delC						.						50.0	53.0	52.0					19																	57932806		2119	4282	6401	SO:0001589	frameshift_variant	7565	exon3			.	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"""Zinc fingers, C2H2-type"", ""-"""	12958	protein-coding gene	gene with protein product			"""zinc finger protein 17 (HPF3, KOX 10)"""			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.1946delA	chr19.hg19:g.57932806delA	ENSP00000471905:p.Gln649fs	120.0	0.0		177.0	11.0	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Frame_Shift_Del	DEL	ENST00000601808.1	hg19	CCDS42636.1																																																																																			.	.		0.388	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959	
KCNU1	157855	hgsc.bcm.edu	37	8	36793121	36793121	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:36793121delA	ENST00000399881.3	+	27	3170	c.3133delA	c.(3133-3135)aaafs	p.K1045fs		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	1045					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TGCTTGTTATAAAAGGAATGA	0.418																																					p.Y1044X		Atlas-INDEL	.											.	KCNU1	359	.	0			c.3132delT						.						122.0	117.0	119.0					8																	36793121		1893	4115	6008	SO:0001589	frameshift_variant	157855	exon27			.	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.3133delA	chr8.hg19:g.36793121delA	ENSP00000382770:p.Lys1045fs	132.0	0.0		180.0	15.0	NM_001031836		Frame_Shift_Del	DEL	ENST00000399881.3	hg19	CCDS55220.1																																																																																			.	.		0.418	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	
PAXIP1-AS2	100132707	hgsc.bcm.edu	37	7	154720408	154720408	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:154720408delC	ENST00000397551.2	+	1	182	c.50delC	c.(49-51)gccfs	p.A17fs																								ggtaccagggccccagctact	0.557																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.																																			SO:0001589	frameshift_variant	0	.			.																												ENST00000397551.2:c.50delC	chr7.hg19:g.154720408delC	ENSP00000380684:p.Ala17fs	157.0	0.0		213.0	13.0	.		RNA	DEL	ENST00000397551.2	hg19																																																																																				.	.		0.557	PAXIP1-AS2-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322233.1		
MTRR	4552	hgsc.bcm.edu	37	5	7900115	7900115	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:7900115delA	ENST00000264668.2	+	15	2152	c.2122delA	c.(2122-2124)aaafs	p.K708fs	MTRR_ENST00000440940.2_Frame_Shift_Del_p.K681fs	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	708					cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	AGAAGCAATGAAAACCCTGGC	0.353																																					p.M707fs		Atlas-INDEL	.											.	MTRR	74	.	0			c.2121delG						.						89.0	93.0	92.0					5																	7900115		2203	4300	6503	SO:0001589	frameshift_variant	4552	exon15			.	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.2122delA	chr5.hg19:g.7900115delA	ENSP00000264668:p.Lys708fs	150.0	0.0		132.0	10.0	NM_024010	O60471|Q32MA9|Q7Z4M8	Frame_Shift_Del	DEL	ENST00000264668.2	hg19	CCDS3874.1																																																																																			.	.		0.353	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
C15orf48	84419	hgsc.bcm.edu	37	15	45725320	45725320	+	3'UTR	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:45725320delT	ENST00000344300.3	+	0	548				C15orf48_ENST00000396650.2_3'UTR|RP11-519G16.5_ENST00000559553.1_RNA|MIR147B_ENST00000390185.1_RNA	NM_032413.3	NP_115789.1	Q9C002	NMES1_HUMAN	chromosome 15 open reading frame 48							mitochondrion (GO:0005739)|nucleus (GO:0005634)				large_intestine(1)|lung(2)|ovary(1)	4		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.67e-16)|GBM - Glioblastoma multiforme(94;1.71e-06)		TTCTGCTACATTTTTAGGGTT	0.383																																					.		Atlas-INDEL	.											.	.	.	.	0			.						.						74.0	74.0	74.0					15																	45725320		1563	3580	5143	SO:0001624	3_prime_UTR_variant	100126311	.			.		CCDS10124.1	15q21.1	2014-05-29			ENSG00000166920	ENSG00000166920			29898	protein-coding gene	gene with protein product	"""normal mucosa of esophagus specific 1"""	608409				12209954	Standard	NM_032413		Approved	NMES1	uc001zvh.4	Q9C002	OTTHUMG00000131424	ENST00000344300.3:c.*106T>-	chr15.hg19:g.45725320delT		186.0	0.0		203.0	13.0	.		RNA	DEL	ENST00000344300.3	hg19	CCDS10124.1																																																																																			.	.		0.383	C15orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254217.2	NM_032413	
EZH2	2146	hgsc.bcm.edu	37	7	148515025	148515025	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:148515025delC	ENST00000460911.1	-	10	1257	c.1169delG	c.(1168-1170)ggafs	p.G390fs	EZH2_ENST00000350995.2_Frame_Shift_Del_p.G351fs|EZH2_ENST00000476773.1_Frame_Shift_Del_p.G381fs|EZH2_ENST00000478654.1_Frame_Shift_Del_p.G381fs|EZH2_ENST00000541220.1_Frame_Shift_Del_p.G381fs|EZH2_ENST00000320356.2_Frame_Shift_Del_p.G395fs|EZH2_ENST00000483967.1_Frame_Shift_Del_p.G381fs			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	390	Interaction with CDYL.				cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			ATTGTTCTCTCCCCCCGTTTC	0.458			Mis		DLBCL																																p.G395fs		Atlas-INDEL	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	.	EZH2	823	.	0			c.1185delA						.						240.0	186.0	204.0					7																	148515025		2203	4300	6503	SO:0001589	frameshift_variant	2146	exon10			.		CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"""Chromatin-modifying enzymes / K-methyltransferases"""	3527	protein-coding gene	gene with protein product		601573	"""enhancer of zeste (Drosophila) homolog 2"", ""enhancer of zeste homolog 2 (Drosophila)"""			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.1169delG	chr7.hg19:g.148515025delC	ENSP00000419711:p.Gly390fs	190.0	0.0		336.0	23.0	NM_004456	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Frame_Shift_Del	DEL	ENST00000460911.1	hg19	CCDS56516.1																																																																																			.	.		0.458	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456	
TNFRSF14	8764	hgsc.bcm.edu	37	1	2492097	2492097	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:2492097delC	ENST00000355716.4	+	5	794	c.495delC	c.(493-495)tgcfs	p.C165fs	TNFRSF14_ENST00000409119.1_Frame_Shift_Del_p.C165fs	NM_003820.2	NP_003811.2	Q92956	TNR14_HUMAN	tumor necrosis factor receptor superfamily, member 14	165					cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell migration (GO:2000406)|T cell costimulation (GO:0031295)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)			kidney(1)	1	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;1.11e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000326)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.199)		GTCAGAACTGCCCCCCGGGGA	0.667			"""Mis, N, F"""		follicular lymphoma																																p.C165fs		Atlas-INDEL	.		Rec	yes		1	1p36.32	8764	"""tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"""		L	.	TNFRSF14	89	.	0			c.494delG						.						51.0	51.0	51.0					1																	2492097		2202	4300	6502	SO:0001589	frameshift_variant	8764	exon5			.	U70321	CCDS44046.1	1p36.32	2012-02-27	2011-08-11		ENSG00000157873	ENSG00000157873		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11912	protein-coding gene	gene with protein product	"""herpesvirus entry mediator"""	602746	"""tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"""			8898196, 9162061	Standard	XM_006711018		Approved	HVEM, ATAR, TR2, LIGHTR, HVEA, CD270	uc001ajt.1	Q92956	OTTHUMG00000000792	ENST00000355716.4:c.495delC	chr1.hg19:g.2492097delC	ENSP00000347948:p.Cys165fs	146.0	0.0		154.0	11.0	NM_003820	B3KW30|B9DI89|Q6IB95|Q8N634|Q8WXR1|Q96J31|Q9UM65	Frame_Shift_Del	DEL	ENST00000355716.4	hg19	CCDS44046.1																																																																																			.	.		0.667	TNFRSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002088.1		
L3MBTL1	26013	hgsc.bcm.edu	37	20	42162009	42162009	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:42162009delC	ENST00000427442.2	+	13	1557	c.1398delC	c.(1396-1398)cacfs	p.H466fs	L3MBTL1_ENST00000418998.1_Frame_Shift_Del_p.H466fs|L3MBTL1_ENST00000444063.1_Frame_Shift_Del_p.H398fs|L3MBTL1_ENST00000373135.3_Frame_Shift_Del_p.H398fs|L3MBTL1_ENST00000373134.1_Frame_Shift_Del_p.H398fs			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	398					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						CCTACATCCACCCAGTGGGCT	0.582																																					p.H466fs		Atlas-INDEL	.											.	L3MBTL1	105	.	0			c.1397delA						.						76.0	73.0	74.0					20																	42162009		2203	4300	6503	SO:0001589	frameshift_variant	26013	exon13			.	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"""Zinc fingers, C2HC-type containing"", ""Sterile alpha motif (SAM) domain containing"""	15905	protein-coding gene	gene with protein product	"""lethal (3) malignant brain tumor l(3)"""	608802	"""l(3)mbt (Drosophila)-like"", ""l(3)mbt-like (Drosophila)"""	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.1398delC	chr20.hg19:g.42162009delC	ENSP00000402107:p.His466fs	97.0	0.0		148.0	10.0	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Frame_Shift_Del	DEL	ENST00000427442.2	hg19	CCDS46602.2																																																																																			.	.		0.582	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107	
PA2G4	5036	hgsc.bcm.edu	37	12	56498590	56498590	+	Frame_Shift_Del	DEL	G	G	-	rs144476801		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:56498590delG	ENST00000303305.6	+	1	488	c.69delG	c.(67-69)atgfs	p.M23fs	PA2G4_ENST00000552766.1_Frame_Shift_Del_p.M23fs|RP11-603J24.9_ENST00000548861.1_Intron|RP11-603J24.17_ENST00000548595.1_RNA	NM_006191.2	NP_006182.2	Q9UQ80	PA2G4_HUMAN	proliferation-associated 2G4, 38kDa	23	Necessary for nucleolar localization.				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)			AGTATAAGATGGGGGGCGACA	0.607																																					p.M23fs		Atlas-INDEL	.											.	PA2G4	24	.	0			c.68delT						.						108.0	99.0	102.0					12																	56498590		2203	4300	6503	SO:0001589	frameshift_variant	5036	exon1			.	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.69delG	chr12.hg19:g.56498590delG	ENSP00000302886:p.Met23fs	166.0	0.0		164.0	11.0	NM_006191	O43846|Q9UM59	Frame_Shift_Del	DEL	ENST00000303305.6	hg19	CCDS8902.1																																																																																			.	.		0.607	PA2G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407767.1	NM_006191	
HELZ2	85441	hgsc.bcm.edu	37	20	62193204	62193204	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:62193204delG	ENST00000467148.1	-	11	6732	c.6663delC	c.(6661-6663)cccfs	p.P2221fs	HELZ2_ENST00000427522.2_Frame_Shift_Del_p.P1652fs	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2221	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										ACTTGTTGGAGGGGCCGCAGT	0.667																																					p.S2222fs		Atlas-INDEL	.											.	.	.	.	0			c.6664delT						.						8.0	10.0	9.0					20																	62193204		2149	4237	6386	SO:0001589	frameshift_variant	85441	exon12			.	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.6663delC	chr20.hg19:g.62193204delG	ENSP00000417401:p.Pro2221fs	109.0	0.0		139.0	11.0	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Frame_Shift_Del	DEL	ENST00000467148.1	hg19	CCDS33508.1																																																																																			.	.		0.667	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
DDX20	11218	hgsc.bcm.edu	37	1	112309341	112309341	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:112309341delT	ENST00000369702.4	+	11	2915	c.2295delT	c.(2293-2295)agtfs	p.S765fs	DDX20_ENST00000475700.1_Frame_Shift_Del_p.S373fs	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	765					ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TACGTCTGAGTTTTTCTGATA	0.453																																					p.S765fs		Atlas-INDEL	.											.	DDX20	50	.	0			c.2294delG						.						107.0	105.0	106.0					1																	112309341		2203	4300	6503	SO:0001589	frameshift_variant	11218	exon11			.	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.2295delT	chr1.hg19:g.112309341delT	ENSP00000358716:p.Ser765fs	140.0	0.0		198.0	12.0	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Frame_Shift_Del	DEL	ENST00000369702.4	hg19	CCDS842.1																																																																																			.	.		0.453	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
ZCCHC24	219654	hgsc.bcm.edu	37	10	81154153	81154153	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:81154153delT	ENST00000372336.3	-	3	677	c.491delA	c.(490-492)aagfs	p.K164fs	ZCCHC24_ENST00000372333.3_Frame_Shift_Del_p.K104fs|RP11-342M3.5_ENST00000438554.2_RNA	NM_153367.3	NP_699198.2	Q8N2G6	ZCH24_HUMAN	zinc finger, CCHC domain containing 24	164							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)	9						GAAGCAGCGCTTTTTGCCCTG	0.577																																					p.K164fs		Atlas-INDEL	.											.	ZCCHC24	22	.	0			c.492delG						.						138.0	111.0	120.0					10																	81154153		2203	4300	6503	SO:0001589	frameshift_variant	219654	exon3			.	AK075279	CCDS7359.1	10q22.3	2014-02-20	2008-06-23	2008-06-23	ENSG00000165424	ENSG00000165424		"""Zinc fingers, CCHC domain containing"""	26911	protein-coding gene	gene with protein product	"""zinc finger, 3CxxC-type 8"""		"""chromosome 10 open reading frame 56"""	C10orf56		12477932	Standard	NM_153367		Approved	FLJ90798, Z3CXXC8	uc010qlr.2	Q8N2G6	OTTHUMG00000018561	ENST00000372336.3:c.491delA	chr10.hg19:g.81154153delT	ENSP00000361411:p.Lys164fs	196.0	0.0		166.0	11.0	NM_153367	Q5U5T9|Q8TAG0	Frame_Shift_Del	DEL	ENST00000372336.3	hg19	CCDS7359.1																																																																																			.	.		0.577	ZCCHC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048947.1	NM_153367	
HEBP1	50865	hgsc.bcm.edu	37	12	13142225	13142225	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:13142225delC	ENST00000014930.4	-	2	361	c.203delG	c.(202-204)ggcfs	p.G68fs	HEBP1_ENST00000536942.1_Frame_Shift_Del_p.G68fs	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1	68					circadian rhythm (GO:0007623)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	heme binding (GO:0020037)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	7		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		GTCATTGGTGCCCCCCGCATA	0.552																																					p.G68fs		Atlas-INDEL	.											.	HEBP1	16	.	0			c.204delC						.						239.0	174.0	196.0					12																	13142225		2203	4300	6503	SO:0001589	frameshift_variant	50865	exon2			.	AF117615	CCDS31749.1	12p13.2	2014-01-30			ENSG00000013583	ENSG00000013583		"""Endogenous ligands"""	17176	protein-coding gene	gene with protein product		605826				10640688	Standard	NM_015987		Approved	HEBP, HBP	uc001rbd.3	Q9NRV9	OTTHUMG00000168771	ENST00000014930.4:c.203delG	chr12.hg19:g.13142225delC	ENSP00000014930:p.Gly68fs	199.0	0.0		275.0	17.0	NM_015987	A8K1G2|Q9Y5Z5	Frame_Shift_Del	DEL	ENST00000014930.4	hg19	CCDS31749.1																																																																																			.	.		0.552	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401001.1		
TEK	7010	hgsc.bcm.edu	37	9	27157926	27157926	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:27157926delC	ENST00000380036.4	+	2	592	c.150delC	c.(148-150)cgcfs	p.R50fs	TEK_ENST00000519097.1_Intron|TEK_ENST00000406359.4_Frame_Shift_Del_p.R50fs	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	50	Ig-like C2-type 1.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	CTGGGTGGCGCCCCCATGAGC	0.502																																					p.R50fs		Atlas-INDEL	.											TEK_ENST00000380036,caecum,carcinoma,0,1	TEK	250	.	0			c.149delG						.						145.0	128.0	134.0					9																	27157926		2203	4300	6503	SO:0001589	frameshift_variant	7010	exon2			.	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.150delC	chr9.hg19:g.27157926delC	ENSP00000369375:p.Arg50fs	184.0	0.0		133.0	10.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Frame_Shift_Del	DEL	ENST00000380036.4	hg19	CCDS6519.1																																																																																			.	.		0.502	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
AKT1	207	hgsc.bcm.edu	37	14	105240253	105240253	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:105240253delC	ENST00000554581.1	-	7	2178	c.698delG	c.(697-699)ggcfs	p.G233fs	AKT1_ENST00000544168.1_Frame_Shift_Del_p.G171fs|AKT1_ENST00000554585.1_5'Flank|AKT1_ENST00000554192.1_5'Flank|AKT1_ENST00000349310.3_Frame_Shift_Del_p.G233fs|AKT1_ENST00000555458.1_5'Flank|AKT1_ENST00000402615.2_Frame_Shift_Del_p.G233fs|AKT1_ENST00000554848.1_Frame_Shift_Del_p.G233fs|AKT1_ENST00000407796.2_Frame_Shift_Del_p.G233fs|AKT1_ENST00000555528.1_Frame_Shift_Del_p.G233fs			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	233	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation-induced cell death of T cells (GO:0006924)|aging (GO:0007568)|anagen (GO:0042640)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell projection organization (GO:0030030)|cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to mechanical stimulus (GO:0071260)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|execution phase of apoptosis (GO:0097194)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycogen cell differentiation involved in embryonic placenta development (GO:0060709)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|labyrinthine layer blood vessel development (GO:0060716)|mammary gland epithelial cell differentiation (GO:0060644)|maternal placenta development (GO:0001893)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of proteolysis (GO:0045861)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|osteoblast differentiation (GO:0001649)|peptidyl-serine phosphorylation (GO:0018105)|peripheral nervous system myelin maintenance (GO:0032287)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell growth (GO:0030307)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle checkpoint (GO:1901976)|regulation of cell migration (GO:0030334)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of neuron projection development (GO:0010975)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of translation (GO:0006417)|response to fluid shear stress (GO:0034405)|response to food (GO:0032094)|response to heat (GO:0009408)|response to UV-A (GO:0070141)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|striated muscle cell differentiation (GO:0051146)|T cell costimulation (GO:0031295)|translation (GO:0006412)	cell-cell junction (GO:0005911)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|nitric-oxide synthase regulator activity (GO:0030235)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(3)|breast(97)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(7)|lung(10)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|thyroid(10)|urinary_tract(15)	176		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)	CCCTACCTCGCCCCCGTTGGC	0.677		1	Mis		"""breast, colorectal, ovarian, NSCLC"""																																p.G233fs		Atlas-INDEL	.		Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1	379	.	0			c.699delC						.						32.0	29.0	30.0					14																	105240253		2202	4299	6501	SO:0001589	frameshift_variant	207	exon9			.	M63167	CCDS9994.1	14q32.33	2014-09-17			ENSG00000142208	ENSG00000142208	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	391	protein-coding gene	gene with protein product		164730					Standard	XM_005267401		Approved	RAC, PKB, PRKBA, AKT	uc001ypn.3	P31749	OTTHUMG00000170795	ENST00000554581.1:c.698delG	chr14.hg19:g.105240253delC	ENSP00000451828:p.Gly233fs	168.0	0.0		173.0	11.0	NM_001014432	B2RAM5|B7Z5R1|Q9BWB6	Frame_Shift_Del	DEL	ENST00000554581.1	hg19	CCDS9994.1																																																																																			.	.		0.677	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163	
RAPGEF2	9693	hgsc.bcm.edu	37	4	160273871	160273871	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:160273871delT	ENST00000264431.4	+	21	3836	c.3417delT	c.(3415-3417)aatfs	p.N1139fs		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	1139	Ser-rich.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|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)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		CTGTGGATAATTTTTCAGATT	0.423																																					p.N1139fs		Atlas-INDEL	.											.	RAPGEF2	171	.	0			c.3416delA						.						109.0	102.0	104.0					4																	160273871		1884	4107	5991	SO:0001589	frameshift_variant	9693	exon21			.	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"""Rap GEP"""	609530	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 1"""	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.3417delT	chr4.hg19:g.160273871delT	ENSP00000264431:p.Asn1139fs	218.0	0.0		179.0	12.0	NM_014247	D3DP27	Frame_Shift_Del	DEL	ENST00000264431.4	hg19	CCDS43277.1																																																																																			.	.		0.423	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247	
CHEK1	1111	hgsc.bcm.edu	37	11	125505404	125505404	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:125505404delA	ENST00000534070.1	+	7	949	c.694delA	c.(694-696)aaafs	p.K233fs	CHEK1_ENST00000532449.1_3'UTR|CHEK1_ENST00000438015.1_Frame_Shift_Del_p.K233fs|CHEK1_ENST00000544373.1_Frame_Shift_Del_p.K233fs|CHEK1_ENST00000524737.1_Frame_Shift_Del_p.K233fs|CHEK1_ENST00000278916.3_Frame_Shift_Del_p.K233fs|CHEK1_ENST00000427383.2_Frame_Shift_Del_p.K249fs|CHEK1_ENST00000428830.2_Frame_Shift_Del_p.K233fs	NM_001274.5	NP_001265.2	O14757	CHK1_HUMAN	checkpoint kinase 1	233	Interaction with CLSPN. {ECO:0000250}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to caffeine (GO:0071313)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to mechanical stimulus (GO:0071260)|chromatin-mediated maintenance of transcription (GO:0048096)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of mitosis (GO:0045839)|peptidyl-threonine phosphorylation (GO:0018107)|regulation of cell proliferation (GO:0042127)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of histone H3-K9 acetylation (GO:2000615)|regulation of mitotic centrosome separation (GO:0046602)|regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010767)|replicative senescence (GO:0090399)	centrosome (GO:0005813)|chromatin (GO:0000785)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	ATP binding (GO:0005524)|histone kinase activity (H3-T11 specific) (GO:0035402)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(3)|large_intestine(2)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	26	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)		CAACCCTTGGAAAAAAATCGA	0.383								Other conserved DNA damage response genes																													p.W231X		Atlas-INDEL	.											.,1	CHEK1	44	.	0			c.693delG						.						86.0	93.0	90.0					11																	125505404		2201	4299	6500	SO:0001589	frameshift_variant	1111	exon7			.	AF016582, BC017575	CCDS8459.1, CCDS58191.1	11q24.2	2011-11-11	2011-11-11		ENSG00000149554	ENSG00000149554			1925	protein-coding gene	gene with protein product		603078	"""CHK1 (checkpoint, S.pombe) homolog"", ""CHK1 checkpoint homolog (S. pombe)"""			9278511, 9382850	Standard	NM_001114121		Approved	CHK1	uc001qcg.4	O14757	OTTHUMG00000165853	ENST00000534070.1:c.694delA	chr11.hg19:g.125505404delA	ENSP00000435371:p.Lys233fs	99.0	0.0		129.0	10.0	NM_001114122	A8K934|B4DDD0|B4DSK3|B5BTY6|F5H7S4|H2BI51	Frame_Shift_Del	DEL	ENST00000534070.1	hg19	CCDS8459.1																																																																																			.	.		0.383	CHEK1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386714.1	NM_001274	
ANO1	55107	hgsc.bcm.edu	37	11	70017033	70017033	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:70017033delC	ENST00000355303.5	+	22	2543	c.2238delC	c.(2236-2238)ttcfs	p.F746fs	ANO1_ENST00000398543.2_Frame_Shift_Del_p.F600fs|ANO1_ENST00000530676.1_Frame_Shift_Del_p.F600fs|ANO1_ENST00000531349.1_Frame_Shift_Del_p.F455fs|ANO1_ENST00000538023.1_Frame_Shift_Del_p.F746fs|ANO1_ENST00000525494.1_3'UTR	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	746					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	TCGCCTCCTTCCCCCTGGCCC	0.587																																					p.F746fs		Atlas-INDEL	.											.	ANO1	156	.	0			c.2237delT						.						64.0	72.0	70.0					11																	70017033		2117	4227	6344	SO:0001589	frameshift_variant	55107	exon22			.	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	21625	protein-coding gene	gene with protein product		610108	"""oral cancer overexpressed 2"", ""transmembrane protein 16A"""	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.2238delC	chr11.hg19:g.70017033delC	ENSP00000347454:p.Phe746fs	135.0	0.0		244.0	15.0	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Frame_Shift_Del	DEL	ENST00000355303.5	hg19	CCDS44663.1																																																																																			.	.		0.587	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043	
PPM1F	9647	hgsc.bcm.edu	37	22	22277539	22277539	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:22277539delG	ENST00000263212.5	-	8	1396	c.1291delC	c.(1291-1293)cagfs	p.Q431fs	PPM1F_ENST00000407142.1_Frame_Shift_Del_p.Q263fs|PPM1F_ENST00000538191.1_Frame_Shift_Del_p.Q327fs	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	431					cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		CCTTCTGCCTGGGGGTCCCCT	0.662																																					p.Q431fs		Atlas-INDEL	.											.	PPM1F	34	.	0			c.1292delA						.						53.0	62.0	59.0					22																	22277539		2203	4300	6503	SO:0001589	frameshift_variant	9647	exon8			.	D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	19388	protein-coding gene	gene with protein product	"""partner of PIX 2"", ""Ca(2+)/calmodulin-dependent protein kinase phosphatase"""		"""protein phosphatase 1F (PP2C domain containing)"""			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.1291delC	chr22.hg19:g.22277539delG	ENSP00000263212:p.Gln431fs	128.0	0.0		182.0	11.0	NM_014634	A8K6G3|B7Z2C3|Q96PM2	Frame_Shift_Del	DEL	ENST00000263212.5	hg19	CCDS13796.1																																																																																			.	.		0.662	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634	
ATAD2B	54454	hgsc.bcm.edu	37	2	24087705	24087705	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:24087705delA	ENST00000238789.5	-	11	1621	c.1278delT	c.(1276-1278)tttfs	p.F426fs		NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	426						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)					TAAACTTTTCAAAAATTTCTG	0.318																																					p.E427fs		Atlas-INDEL	.											.	ATAD2B	110	.	0			c.1279delG						.						37.0	35.0	36.0					2																	24087705		1796	4067	5863	SO:0001589	frameshift_variant	54454	exon11			.	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.1278delT	chr2.hg19:g.24087705delA	ENSP00000238789:p.Phe426fs	107.0	0.0		163.0	13.0	NM_017552	B9ZVQ5|Q6ZNA6|Q8N9E7	Frame_Shift_Del	DEL	ENST00000238789.5	hg19	CCDS46227.1																																																																																			.	.		0.318	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552	
PTTG1	9232	hgsc.bcm.edu	37	5	159854837	159854837	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:159854837delC	ENST00000393964.1	+	4	889	c.486delC	c.(484-486)ggcfs	p.G162fs	PTTG1_ENST00000520452.1_Frame_Shift_Del_p.G162fs|PTTG1_ENST00000519287.1_3'UTR|PTTG1_ENST00000352433.5_Frame_Shift_Del_p.G162fs	NM_001282382.1	NP_001269311.1	O95997	PTTG1_HUMAN	pituitary tumor-transforming 1	162					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)		TTCAGCTGGGCCCCCCTTCAC	0.527																																					p.G162fs		Atlas-INDEL	.											.	PTTG1	15	.	0			c.485delG						.						80.0	75.0	77.0					5																	159854837		2203	4300	6503	SO:0001589	frameshift_variant	9232	exon5			.	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.486delC	chr5.hg19:g.159854837delC	ENSP00000377536:p.Gly162fs	131.0	0.0		164.0	10.0	NM_004219		Frame_Shift_Del	DEL	ENST00000393964.1	hg19	CCDS4353.1																																																																																			.	.		0.527	PTTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252677.1	NM_004219	
BFSP2	8419	hgsc.bcm.edu	37	3	133119111	133119111	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:133119111delC	ENST00000302334.2	+	1	273	c.184delC	c.(184-186)cccfs	p.P62fs		NM_003571.2	NP_003562.1	Q13515	BFSP2_HUMAN	beaded filament structural protein 2, phakinin	62	Head.				cell maturation (GO:0048469)|intermediate filament cytoskeleton organization (GO:0045104)|lens fiber cell development (GO:0070307)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|urinary_tract(1)	13						AGGAACAGCACCCAGTGGGTG	0.667																																					p.A61fs		Atlas-INDEL	.											.	BFSP2	48	.	0			c.183delA						.						46.0	51.0	49.0					3																	133119111		2203	4300	6503	SO:0001589	frameshift_variant	8419	exon1			.	U48224	CCDS33859.1	3q22.1	2013-01-16			ENSG00000170819	ENSG00000170819		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1041	protein-coding gene	gene with protein product		603212					Standard	NM_003571		Approved	CP47, CP49, LIFL-L, phakinin	uc003epn.1	Q13515	OTTHUMG00000159719	ENST00000302334.2:c.184delC	chr3.hg19:g.133119111delC	ENSP00000304987:p.Pro62fs	188.0	0.0		153.0	11.0	NM_003571	Q14D32|Q9HBW5	Frame_Shift_Del	DEL	ENST00000302334.2	hg19	CCDS33859.1																																																																																			.	.		0.667	BFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357031.1		
COL11A2	1302	hgsc.bcm.edu	37	6	33152022	33152022	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:33152022delG	ENST00000341947.2	-	8	1246	c.1019delC	c.(1018-1020)cctfs	p.P340fs	COL11A2_ENST00000361917.1_Intron|COL11A2_ENST00000374712.1_Intron|COL11A2_ENST00000374708.4_Intron|COL11A2_ENST00000374714.1_Frame_Shift_Del_p.P314fs|COL11A2_ENST00000374713.1_Frame_Shift_Del_p.P293fs|COL11A2_ENST00000357486.1_Frame_Shift_Del_p.P319fs|COL11A2_ENST00000395197.1_Intron	NM_080680.2	NP_542411.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	340	Nonhelical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						GGGCCCTTCAGGGGGGTCTGT	0.617																																					p.P340fs	Melanoma(1;90 116 3946 5341 17093)	Atlas-INDEL	.											.	COL11A2	124	.	0			c.1020delT						.						63.0	65.0	64.0					6																	33152022		2203	4300	6503	SO:0001589	frameshift_variant	1302	exon8			.	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000341947.2:c.1019delC	chr6.hg19:g.33152022delG	ENSP00000339915:p.Pro340fs	72.0	0.0		102.0	11.0	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Frame_Shift_Del	DEL	ENST00000341947.2	hg19																																																																																				.	.		0.617	COL11A2-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			
SIL1	64374	hgsc.bcm.edu	37	5	138286953	138286953	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:138286953delC	ENST00000394817.2	-	9	1075	c.936delG	c.(934-936)gggfs	p.G312fs	SIL1_ENST00000515008.1_5'UTR|SIL1_ENST00000265195.5_Frame_Shift_Del_p.G312fs|SIL1_ENST00000509534.1_Frame_Shift_Del_p.G319fs	NM_022464.4	NP_071909.1	Q9H173	SIL1_HUMAN	SIL1 nucleotide exchange factor	312					intracellular protein transport (GO:0006886)|protein folding (GO:0006457)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GGACCTGCAGCCCCCCGAGCT	0.657									Marinesco-Sjgren syndrome																												p.L313fs		Atlas-INDEL	.											.	SIL1	31	.	0			c.937delC						.						26.0	24.0	25.0					5																	138286953		2202	4297	6499	SO:0001589	frameshift_variant	64374	exon9	Familial Cancer Database	Marinesco-Sjogren syndrome	.	AK075177	CCDS4209.1	5q31	2013-08-21	2013-08-21		ENSG00000120725	ENSG00000120725			24624	protein-coding gene	gene with protein product		608005	"""Marinesco-Sjogren syndrome"", ""SIL1 homolog, endoplasmic reticulum chaperone (S. cerevisiae)"""	MSS		11101517, 12356756, 16282977	Standard	XM_006714671		Approved	BAP, ULG5	uc003ldp.3	Q9H173	OTTHUMG00000129226	ENST00000394817.2:c.936delG	chr5.hg19:g.138286953delC	ENSP00000378294:p.Gly312fs	144.0	0.0		183.0	11.0	NM_022464	D3DQC2|Q8N2L3	Frame_Shift_Del	DEL	ENST00000394817.2	hg19	CCDS4209.1																																																																																			.	.		0.657	SIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251319.1	NM_022464	
RAPH1	65059	hgsc.bcm.edu	37	2	204305064	204305064	+	Frame_Shift_Del	DEL	G	G	-	rs137885175		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:204305064delG	ENST00000319170.5	-	14	3148	c.2849delC	c.(2848-2850)cctfs	p.P950fs	ABI2_ENST00000295851.5_3'UTR|RAPH1_ENST00000457812.1_Intron|RAPH1_ENST00000374493.3_Frame_Shift_Del_p.P1002fs	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	950					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						ACTTTTGTCAggggtaggaga	0.592																																					p.P950fs		Atlas-INDEL	.											.	RAPH1	118	.	0			c.2850delT						.						62.0	62.0	62.0					2																	204305064		2203	4300	6503	SO:0001589	frameshift_variant	65059	exon14			.	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"""Pleckstrin homology (PH) domain containing"""	14436	protein-coding gene	gene with protein product	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"""	609035	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"""	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.2849delC	chr2.hg19:g.204305064delG	ENSP00000316543:p.Pro950fs	98.0	0.0		152.0	10.0	NM_213589	Q96Q37|Q9C0I2	Frame_Shift_Del	DEL	ENST00000319170.5	hg19	CCDS2359.1																																																																																			.	.		0.592	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252	
NOP56	10528	hgsc.bcm.edu	37	20	2634016	2634016	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:2634016delA	ENST00000329276.5	+	3	701	c.185delA	c.(184-186)gaafs	p.E62fs	SNORD110_ENST00000408189.1_RNA|SNORD86_ENST00000391196.1_RNA|MIR1292_ENST00000408135.1_RNA|SNORA51_ENST00000606420.1_RNA	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	62					cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						GTTGCCTTGGAAAATGCCAAC	0.547																																					p.E62fs		Atlas-INDEL	.											.	NOP56	73	.	0			c.184delG						.						208.0	179.0	189.0					20																	2634016		2203	4300	6503	SO:0001589	frameshift_variant	10528	exon3			.	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 36"""	614154	"""nucleolar protein 5A (56kD with KKE/D repeat)"", ""nucleolar protein 5A (56kDa with KKE/D repeat)"", ""NOP56 ribonucleoprotein homolog (yeast)"""	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.185delA	chr20.hg19:g.2634016delA	ENSP00000370589:p.Glu62fs	201.0	0.0		250.0	16.0	NM_006392	Q2M3T6|Q9NQ05	Frame_Shift_Del	DEL	ENST00000329276.5	hg19	CCDS13030.1																																																																																			.	.		0.547	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392	
CFHR5	81494	hgsc.bcm.edu	37	1	196953169	196953169	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:196953169delA	ENST00000256785.4	+	3	441	c.332delA	c.(331-333)caafs	p.Q111fs	CFHR5_ENST00000367414.5_Frame_Shift_Del_p.Q135fs			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	111	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, alternative pathway (GO:0006957)	extracellular region (GO:0005576)				NS(2)|breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(23)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	49						GATACTGTACAAATTATTTGC	0.383																																					p.Q111fs		Atlas-INDEL	.											CFHR5,right_upper_lobe,carcinoma,0,1	CFHR5	150	.	0			c.331delC						.						110.0	98.0	102.0					1																	196953169		2203	4300	6503	SO:0001589	frameshift_variant	81494	exon3			.	AF295327	CCDS1387.1	1q31.3	2014-09-17		2006-02-28	ENSG00000134389	ENSG00000134389		"""Complement system"""	24668	protein-coding gene	gene with protein product	"""factor H related protein 5"""	608593		CFHL5		11058592, 12041828	Standard	NM_030787		Approved	FHR5, FHR-5	uc001gts.4	Q9BXR6	OTTHUMG00000036517	ENST00000256785.4:c.332delA	chr1.hg19:g.196953169delA	ENSP00000256785:p.Gln111fs	103.0	0.0		194.0	12.0	NM_030787	Q2NKK2	Frame_Shift_Del	DEL	ENST00000256785.4	hg19	CCDS1387.1																																																																																			.	.		0.383	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787	
FAM170A	340069	hgsc.bcm.edu	37	5	118969957	118969957	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:118969957delC	ENST00000515256.1	+	3	686	c.514delC	c.(514-516)cccfs	p.P173fs				A1A519	F170A_HUMAN	family with sequence similarity 170, member A	173			P -> S (in dbSNP:rs328694).		positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	24						GGTAGGTACTCCCCCCTCTGA	0.537																																					p.T171fs		Atlas-INDEL	.											.	FAM170A	47	.	0			c.513delT						.						92.0	96.0	95.0					5																	118969957		1992	4181	6173	SO:0001589	frameshift_variant	340069	exon3			.	AF427126	CCDS43353.1, CCDS54889.1	5q23.1	2008-06-12			ENSG00000164334	ENSG00000164334			27963	protein-coding gene	gene with protein product						12477932	Standard	NM_182761		Approved		uc003ksn.3	A1A519	OTTHUMG00000162946	ENST00000515256.1:c.514delC	chr5.hg19:g.118969957delC	ENSP00000422684:p.Pro173fs	132.0	0.0		145.0	10.0	NM_182761	Q66LM8|Q7Z4V2|Q8IW94	Frame_Shift_Del	DEL	ENST00000515256.1	hg19																																																																																				.	.		0.537	FAM170A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371126.1	NM_182761	
ABCC6	368	hgsc.bcm.edu	37	16	16292011	16292011	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:16292011delT	ENST00000205557.7	-	10	1234	c.1205delA	c.(1204-1206)aagfs	p.K402fs	ABCC6_ENST00000574094.1_5'UTR	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	402	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CGCACTGGCCTTTCTGGAGCC	0.652																																					p.K402fs		Atlas-INDEL	.											.	ABCC6	110	.	0			c.1206delG						.						37.0	28.0	31.0					16																	16292011		2196	4300	6496	SO:0001589	frameshift_variant	368	exon10			.	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.1205delA	chr16.hg19:g.16292011delT	ENSP00000205557:p.Lys402fs	149.0	0.0		155.0	12.0	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Frame_Shift_Del	DEL	ENST00000205557.7	hg19	CCDS10568.1																																																																																			.	.		0.652	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
ZNF354B	117608	hgsc.bcm.edu	37	5	178311121	178311121	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:178311121delA	ENST00000322434.3	+	5	1894	c.1668delA	c.(1666-1668)ggafs	p.G556fs	RNU1-39P_ENST00000383897.1_RNA|ZNF354B_ENST00000522714.1_3'UTR	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	556					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(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATACATGTGGAAAAACTTTTA	0.368																																					p.G556fs		Atlas-Indel,Pindel	.											.	ZNF354B	67	.	0			c.1667delG						.						66.0	63.0	64.0					5																	178311121		2203	4300	6503	SO:0001589	frameshift_variant	117608	exon5			.	AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"""Zinc fingers, C2H2-type"", ""-"""	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.1668delA	chr5.hg19:g.178311121delA	ENSP00000327143:p.Gly556fs	107.0	0.0		127.0	31.0	NM_058230	A8K0V2|Q5U5Z4	Frame_Shift_Del	DEL	ENST00000322434.3	hg19	CCDS4439.1																																																																																			.	.		0.368	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72496514	72496514	+	Frame_Shift_Del	DEL	C	C	-	rs553557226		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:72496514delC	ENST00000373207.1	+	10	1564	c.1564delC	c.(1564-1566)cccfs	p.P523fs	ADAMTS14_ENST00000373208.1_Frame_Shift_Del_p.P526fs	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	523	Disintegrin.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CAAGAAGGGGCCCCCGCTGGA	0.617																																					p.G524fs		Atlas-INDEL	.											.	ADAMTS14	148	.	0			c.1572delG						.						81.0	73.0	76.0					10																	72496514		2203	4300	6503	SO:0001589	frameshift_variant	140766	exon10			.	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.1564delC	chr10.hg19:g.72496514delC	ENSP00000362303:p.Pro523fs	152.0	0.0		147.0	10.0	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Frame_Shift_Del	DEL	ENST00000373207.1	hg19	CCDS7306.1																																																																																			.	.		0.617	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
COL7A1	1294	hgsc.bcm.edu	37	3	48610625	48610625	+	Frame_Shift_Del	DEL	G	G	-	rs61729223	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:48610625delG	ENST00000328333.8	-	84	6803	c.6696delC	c.(6694-6696)cccfs	p.P2232fs	COL7A1_ENST00000454817.1_Frame_Shift_Del_p.P2200fs	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2232	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTGAAGGGCCGGGGGGTCCAG	0.607																																					p.G2233fs		Atlas-INDEL	.											.	COL7A1	320	.	0			c.6697delG						.						52.0	53.0	53.0					3																	48610625		2203	4300	6503	SO:0001589	frameshift_variant	1294	exon84			.	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.6696delC	chr3.hg19:g.48610625delG	ENSP00000332371:p.Pro2232fs	83.0	0.0		129.0	10.0	NM_000094	Q14054|Q16507	Frame_Shift_Del	DEL	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.607	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
ARID3C	138715	hgsc.bcm.edu	37	9	34625744	34625744	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:34625744delT	ENST00000378909.2	-	2	478	c.386delA	c.(385-387)aagfs	p.K129fs		NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	129	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane raft (GO:0045121)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	14	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		CTCACCCCTCTTTTGCATGAA	0.547																																					p.K129fs		Atlas-INDEL	.											.	ARID3C	33	.	0			c.387delG						.						196.0	157.0	170.0					9																	34625744		2203	4300	6503	SO:0001589	frameshift_variant	138715	exon2			.		CCDS35006.1	9p13.2	2013-02-07	2006-11-08		ENSG00000205143	ENSG00000205143		"""-"""	21209	protein-coding gene	gene with protein product			"""AT rich interactive domain 3C (BRIGHT- like)"""				Standard	NM_001017363		Approved		uc011lon.2	A6NKF2	OTTHUMG00000000445	ENST00000378909.2:c.386delA	chr9.hg19:g.34625744delT	ENSP00000368189:p.Lys129fs	144.0	0.0		163.0	10.0	NM_001017363		Frame_Shift_Del	DEL	ENST00000378909.2	hg19	CCDS35006.1																																																																																			.	.		0.547	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061	
BIRC2	329	hgsc.bcm.edu	37	11	102239232	102239232	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:102239232delA	ENST00000227758.2	+	6	2718	c.1319delA	c.(1318-1320)gaafs	p.E440fs	BIRC2_ENST00000527910.1_3'UTR|BIRC2_ENST00000530675.1_Frame_Shift_Del_p.E391fs|BIRC2_ENST00000532672.1_Frame_Shift_Del_p.E419fs	NM_001166.4|NM_001256163.1	NP_001157.1|NP_001243092.1	Q13490	BIRC2_HUMAN	baculoviral IAP repeat containing 2	440					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)		GCTGAAGATGAAAAAAGAGAA	0.388																																					p.E440fs		Atlas-INDEL	.											.	BIRC2	51	.	0			c.1318delG						.						117.0	122.0	120.0					11																	102239232		2203	4299	6502	SO:0001589	frameshift_variant	329	exon6			.	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.1319delA	chr11.hg19:g.102239232delA	ENSP00000227758:p.Glu440fs	97.0	0.0		150.0	10.0	NM_001256163	B4E026|Q16516|Q4TTG0	Frame_Shift_Del	DEL	ENST00000227758.2	hg19	CCDS8316.1																																																																																			.	.		0.388	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166	
WDR72	256764	hgsc.bcm.edu	37	15	54004983	54004983	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:54004983delA	ENST00000396328.1	-	7	936	c.697delT	c.(697-699)tctfs	p.S233fs	WDR72_ENST00000557913.1_Frame_Shift_Del_p.S232fs|WDR72_ENST00000559418.1_Frame_Shift_Del_p.S233fs|WDR72_ENST00000360509.5_Frame_Shift_Del_p.S233fs	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	233										NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		CAACATTTAGAAAATACCACC	0.289																																					p.S233fs		Atlas-INDEL	.											.	WDR72	177	.	0			c.698delC						.						53.0	56.0	55.0					15																	54004983		2191	4293	6484	SO:0001589	frameshift_variant	256764	exon7			.	BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"""WD repeat domain containing"""	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.697delT	chr15.hg19:g.54004983delA	ENSP00000379619:p.Ser233fs	203.0	0.0		229.0	14.0	NM_182758	Q7Z3I3|Q8N8X2	Frame_Shift_Del	DEL	ENST00000396328.1	hg19	CCDS10151.1																																																																																			.	.		0.289	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
FARSA	2193	hgsc.bcm.edu	37	19	13033615	13033615	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:13033615delG	ENST00000314606.4	-	13	1492	c.1474delC	c.(1474-1476)ctgfs	p.L492fs	FARSA_ENST00000423140.2_Frame_Shift_Del_p.L461fs|MIR5695_ENST00000579717.1_RNA|FARSA_ENST00000588025.1_Frame_Shift_Del_p.L532fs	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	492					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	20					L-Phenylalanine(DB00120)	AGGCGGCACAGGGGACTGTCA	0.612																																					p.L492fs		Atlas-INDEL	.											.	FARSA	46	.	0			c.1475delT						.						150.0	124.0	133.0					19																	13033615		2203	4300	6503	SO:0001589	frameshift_variant	2193	exon13			.	U07424	CCDS12287.1	19p13.2	2014-05-06	2007-02-23	2007-02-23	ENSG00000179115	ENSG00000179115	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	3592	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 1, alpha, cytoplasmic"""	602918	"""phenylalanine-tRNA synthetase-like"", ""phenylalanyl-tRNA synthetase-like, alpha subunit"""	FARSL, FARSLA		9177188	Standard	NM_004461		Approved	CML33	uc002mvs.2	Q9Y285	OTTHUMG00000180569	ENST00000314606.4:c.1474delC	chr19.hg19:g.13033615delG	ENSP00000320309:p.Leu492fs	113.0	0.0		169.0	11.0	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Frame_Shift_Del	DEL	ENST00000314606.4	hg19	CCDS12287.1																																																																																			.	.		0.612	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461	
SCN10A	6336	hgsc.bcm.edu	37	3	38793887	38793887	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:38793887delA	ENST00000449082.2	-	11	1577	c.1578delT	c.(1576-1578)tttfs	p.F526fs		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	526					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	GGTCTCCAGGAAAGACTCCAT	0.607																																					p.P527fs		Atlas-INDEL	.											.	SCN10A	359	.	0			c.1579delC						.						52.0	57.0	55.0					3																	38793887		2203	4300	6503	SO:0001589	frameshift_variant	6336	exon11			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.1578delT	chr3.hg19:g.38793887delA	ENSP00000390600:p.Phe526fs	121.0	0.0		151.0	10.0	NM_006514	A6NDQ1	Frame_Shift_Del	DEL	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.		0.607	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
SMARCA5	8467	hgsc.bcm.edu	37	4	144442631	144442631	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:144442631delT	ENST00000283131.3	+	3	764	c.302delT	c.(301-303)cttfs	p.L101fs		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	101					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					CAGACAGAACTTTTTGCACAT	0.353																																					p.L101fs		Atlas-INDEL	.											.	SMARCA5	73	.	0			c.301delC						.						60.0	64.0	63.0					4																	144442631		2203	4300	6503	SO:0001589	frameshift_variant	8467	exon3			.	AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.302delT	chr4.hg19:g.144442631delT	ENSP00000283131:p.Leu101fs	125.0	0.0		106.0	12.0	NM_003601		Frame_Shift_Del	DEL	ENST00000283131.3	hg19	CCDS3761.1																																																																																			.	.		0.353	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3		
ZNF416	55659	hgsc.bcm.edu	37	19	58084579	58084579	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:58084579delA	ENST00000196489.3	-	4	915	c.693delT	c.(691-693)tttfs	p.F231fs		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	231					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(3)|large_intestine(5)|lung(12)|prostate(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		CTCTAGGGTGAAAAAAAGTGT	0.453																																					p.H232fs		Atlas-INDEL	.											.	ZNF416	50	.	0			c.694delC						.						161.0	161.0	161.0					19																	58084579		2203	4300	6503	SO:0001589	frameshift_variant	55659	exon4			.	BC000130	CCDS12954.1	19q13.4	2013-01-08				ENSG00000083817		"""Zinc fingers, C2H2-type"", ""-"""	20645	protein-coding gene	gene with protein product							Standard	NM_017879		Approved	FLJ20557	uc002qpf.3	Q9BWM5		ENST00000196489.3:c.693delT	chr19.hg19:g.58084579delA	ENSP00000196489:p.Phe231fs	117.0	0.0		199.0	13.0	NM_017879	Q9NWW8	Frame_Shift_Del	DEL	ENST00000196489.3	hg19	CCDS12954.1																																																																																			.	.		0.453	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879	
NIM1K	167359	hgsc.bcm.edu	37	5	43245927	43245927	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:43245927delC	ENST00000512796.1	+	2	1549	c.50delC	c.(49-51)gccfs	p.A17fs	NIM1_ENST00000326035.2_Frame_Shift_Del_p.A17fs			Q8IY84	NIM1_HUMAN		17					protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)										CCCCACTATGCCCGGTGGGAT	0.607																																					p.A17fs		Atlas-INDEL	.											.	.	.	.	0			c.49delG						.						123.0	117.0	119.0					5																	43245927		2203	4300	6503	SO:0001589	frameshift_variant	0	exon2			.																												ENST00000512796.1:c.50delC	chr5.hg19:g.43245927delC	ENSP00000420849:p.Ala17fs	170.0	0.0		170.0	11.0	NM_153361	B3KVM1	Frame_Shift_Del	DEL	ENST00000512796.1	hg19	CCDS3943.1																																																																																			.	.		0.607	NIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368017.1		
MYO10	4651	hgsc.bcm.edu	37	5	16763789	16763789	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:16763789delA	ENST00000513610.1	-	13	1856	c.1402delT	c.(1402-1404)tctfs	p.S468fs		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	468	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						TGTTCTAAAGAAAAAATATGC	0.323																																					p.S468fs		Atlas-INDEL	.											.	MYO10	198	.	0			c.1403delC						.						64.0	60.0	61.0					5																	16763789		1802	4068	5870	SO:0001589	frameshift_variant	4651	exon13			.	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.1402delT	chr5.hg19:g.16763789delA	ENSP00000421280:p.Ser468fs	211.0	0.0		232.0	14.0	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Frame_Shift_Del	DEL	ENST00000513610.1	hg19	CCDS54834.1																																																																																			.	.		0.323	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
LRRC40	55631	hgsc.bcm.edu	37	1	70618181	70618181	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:70618181delA	ENST00000370952.3	-	12	1453	c.1374delT	c.(1372-1374)tttfs	p.F458fs		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	458						membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						AAAGTTTATTAAAACTGAGAT	0.303																																					p.N459fs		Atlas-INDEL	.											.	LRRC40	66	.	0			c.1375delA						.						75.0	74.0	75.0					1																	70618181		2203	4298	6501	SO:0001589	frameshift_variant	55631	exon12			.		CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.1374delT	chr1.hg19:g.70618181delA	ENSP00000359990:p.Phe458fs	189.0	0.0		237.0	16.0	NM_017768	Q9BTR7|Q9NSK1|Q9NXC1	Frame_Shift_Del	DEL	ENST00000370952.3	hg19	CCDS646.1																																																																																			.	.		0.303	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768	
SPATA22	84690	hgsc.bcm.edu	37	17	3352342	3352342	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:3352342delT	ENST00000573128.1	-	6	914	c.431delA	c.(430-432)aatfs	p.N144fs	SPATA22_ENST00000541913.1_Frame_Shift_Del_p.N128fs|SPATA22_ENST00000268981.5_Frame_Shift_Del_p.N144fs|SPATA22_ENST00000355380.4_Frame_Shift_Del_p.N101fs|SPATA22_ENST00000575375.1_Frame_Shift_Del_p.N144fs|SPATA22_ENST00000572969.1_Frame_Shift_Del_p.N144fs|SPATA22_ENST00000397168.3_Frame_Shift_Del_p.N144fs			Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	144					fertilization (GO:0009566)|gamete generation (GO:0007276)|meiotic DNA repair synthesis (GO:0000711)|regulation of meiotic cell cycle (GO:0051445)|reproductive system development (GO:0061458)|synapsis (GO:0007129)	chromosome (GO:0005694)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|skin(2)	19						TGGACAAGAATTTTTTCCATC	0.358																																					p.N144fs		Atlas-INDEL	.											.	SPATA22	49	.	0			c.432delT						.						197.0	189.0	192.0					17																	3352342		2203	4300	6503	SO:0001589	frameshift_variant	84690	exon6			.	AY035868	CCDS11027.1, CCDS54066.1, CCDS54067.1	17p13.3	2005-12-19							30705	protein-coding gene	gene with protein product						12477932	Standard	NM_001170696		Approved	NYD-SP20	uc002fvn.3	Q8NHS9		ENST00000573128.1:c.431delA	chr17.hg19:g.3352342delT	ENSP00000459580:p.Asn144fs	158.0	0.0		138.0	11.0	NM_032598	B4DXB1|D3DTI9|J3KN63|Q969H3|Q96JT4	Frame_Shift_Del	DEL	ENST00000573128.1	hg19	CCDS11027.1																																																																																			.	.		0.358	SPATA22-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438067.2	NM_032598	
MAMDC4	158056	hgsc.bcm.edu	37	9	139753286	139753286	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:139753286delG	ENST00000317446.2	+	23	2987	c.2937delG	c.(2935-2937)atgfs	p.M979fs	MAMDC4_ENST00000485732.1_3'UTR|MAMDC4_ENST00000445819.1_Frame_Shift_Del_p.M1058fs	NM_206920.2	NP_996803.2			MAM domain containing 4											breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	19	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		GGTACCACATGGGTTTTCCTG	0.706																																					p.M979fs		Atlas-INDEL	.											.	MAMDC4	117	.	0			c.2936delT						.						17.0	20.0	19.0					9																	139753286		2190	4295	6485	SO:0001589	frameshift_variant	158056	exon23			.	AL834531	CCDS7010.1	9q34.3	2013-10-21			ENSG00000177943	ENSG00000177943			24083	protein-coding gene	gene with protein product	"""apical early endosomal glycoprotein precursor"", ""endotubin"""					7829488	Standard	NM_206920		Approved	AEGP, DKFZp434M1411	uc004cjs.3	Q6UXC1	OTTHUMG00000020951	ENST00000317446.2:c.2937delG	chr9.hg19:g.139753286delG	ENSP00000319388:p.Met979fs	112.0	0.0		110.0	10.0	NM_206920		Frame_Shift_Del	DEL	ENST00000317446.2	hg19	CCDS7010.1																																																																																			.	.		0.706	MAMDC4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254642.3	NM_206920	
MYOM1	8736	hgsc.bcm.edu	37	18	3129514	3129514	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:3129514delC	ENST00000356443.4	-	18	2843	c.2510delG	c.(2509-2511)ggafs	p.G838fs	MYOM1_ENST00000582016.1_5'UTR|MYOM1_ENST00000261606.7_Intron|MYOM1_ENST00000400569.3_Frame_Shift_Del_p.G838fs	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	838					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						AGACACTCCTCCCCCTACAGT	0.547											OREG0024838	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G837fs		Atlas-INDEL	.											.	MYOM1	192	.	0			c.2511delA						.						52.0	54.0	53.0					18																	3129514		1998	4178	6176	SO:0001589	frameshift_variant	8736	exon18			.	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.2510delG	chr18.hg19:g.3129514delC	ENSP00000348821:p.Gly838fs	182.0	0.0	608	233.0	15.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Frame_Shift_Del	DEL	ENST00000356443.4	hg19	CCDS45824.1																																																																																			.	.		0.547	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
LRP4	4038	hgsc.bcm.edu	37	11	46903431	46903431	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:46903431delC	ENST00000378623.1	-	20	2878	c.2636delG	c.(2635-2637)ggtfs	p.G879fs		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	879					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GGGGCTCGCACCCCAGTCAGT	0.493																																					p.G879fs		Atlas-INDEL	.											.	LRP4	160	.	0			c.2637delT						.						69.0	63.0	65.0					11																	46903431		2201	4299	6500	SO:0001589	frameshift_variant	4038	exon20			.	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.2636delG	chr11.hg19:g.46903431delC	ENSP00000367888:p.Gly879fs	129.0	0.0		157.0	10.0	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Frame_Shift_Del	DEL	ENST00000378623.1	hg19	CCDS31478.1																																																																																			.	.		0.493	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
SNAP91	9892	hgsc.bcm.edu	37	6	84368767	84368767	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:84368767delT	ENST00000439399.2	-	6	813	c.497delA	c.(496-498)aagfs	p.K166fs	SNAP91_ENST00000195649.6_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000437520.1_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000428679.2_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000369694.2_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000521743.1_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000520213.1_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000521485.1_Frame_Shift_Del_p.K166fs|SNAP91_ENST00000520302.1_Frame_Shift_Del_p.K166fs	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	166					clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		TGGCATACTCTTTAGCAGCTT	0.353																																					p.K166fs		Atlas-INDEL	.											.	SNAP91	199	.	0			c.498delG						.						116.0	112.0	114.0					6																	84368767		1877	4099	5976	SO:0001589	frameshift_variant	9892	exon6			.	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"""synaptosomal-associated protein, 91 kDa (mouse) homolog"", ""synaptosomal-associated protein, 91kDa homolog (mouse)"""			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.497delA	chr6.hg19:g.84368767delT	ENSP00000400459:p.Lys166fs	118.0	0.0		129.0	10.0	NM_001242794	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Frame_Shift_Del	DEL	ENST00000439399.2	hg19	CCDS47455.1																																																																																			.	.		0.353	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1		
NAALAD2	10003	hgsc.bcm.edu	37	11	89911108	89911108	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:89911108delA	ENST00000534061.1	+	16	1911	c.1681delA	c.(1681-1683)aaafs	p.K562fs	NAALAD2_ENST00000375944.3_Intron|NAALAD2_ENST00000321955.4_Frame_Shift_Del_p.K529fs	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	562	NAALADase.				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)				CCCCACATTTAAAAAACAACT	0.338																																					p.F560fs		Atlas-INDEL	.											.	NAALAD2	113	.	0			c.1680delT						.						66.0	73.0	71.0					11																	89911108		2201	4295	6496	SO:0001589	frameshift_variant	10003	exon16			.	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.1681delA	chr11.hg19:g.89911108delA	ENSP00000432481:p.Lys562fs	162.0	0.0		243.0	18.0	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Frame_Shift_Del	DEL	ENST00000534061.1	hg19	CCDS8288.1																																																																																			.	.		0.338	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467	
ACAN	176	hgsc.bcm.edu	37	15	89398305	89398305	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:89398305delC	ENST00000561243.1	+	11	2489	c.2489delC	c.(2488-2490)tccfs	p.S830fs	ACAN_ENST00000559004.1_Frame_Shift_Del_p.S830fs|ACAN_ENST00000352105.7_Frame_Shift_Del_p.S830fs|ACAN_ENST00000439576.2_Frame_Shift_Del_p.S830fs			P16112	PGCA_HUMAN	aggrecan	829	12 X 6 AA approximate tandem repeats of E-[GVE]-P-[SFY]-[APT]-[TSP].|KS.				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)			AAGGAGCCATCCCCCTCAGAG	0.632																																					p.S830fs		Atlas-INDEL	.											.	ACAN	220	.	0			c.2488delT						.						32.0	37.0	35.0					15																	89398305		1967	4151	6118	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.2489delC	chr15.hg19:g.89398305delC	ENSP00000453342:p.Ser830fs	129.0	0.0		184.0	12.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Frame_Shift_Del	DEL	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.		0.632	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
CD55	1604	hgsc.bcm.edu	37	1	207510725	207510725	+	Frame_Shift_Del	DEL	C	C	-	rs150172588	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:207510725delC	ENST00000367064.3	+	8	1289	c.1031delC	c.(1030-1032)accfs	p.T344fs	CD55_ENST00000465534.1_3'UTR|CD55_ENST00000367065.5_Frame_Shift_Del_p.T344fs|CD55_ENST00000367062.4_Frame_Shift_Del_p.T344fs|CD55_ENST00000314754.8_Frame_Shift_Del_p.T344fs|CD55_ENST00000391921.4_Frame_Shift_Del_p.T280fs|CD55_ENST00000391920.4_Frame_Shift_Del_p.T344fs|CD55_ENST00000367067.4_3'UTR|CD55_ENST00000367063.2_Frame_Shift_Del_p.T344fs	NM_000574.3	NP_000565.1	P08174	DAF_HUMAN	CD55 molecule, decay accelerating factor for complement (Cromer blood group)	344	Ser/Thr-rich.				CD4-positive, alpha-beta T cell cytokine production (GO:0035743)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|maternal process involved in parturition (GO:0060137)|negative regulation of complement activation (GO:0045916)|positive regulation of CD4-positive, alpha-beta T cell activation (GO:2000516)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of complement activation (GO:0030449)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|respiratory burst (GO:0045730)|response to peptide hormone (GO:0043434)|response to virus (GO:0009615)|spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	enzyme inhibitor activity (GO:0004857)|lipid binding (GO:0008289)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16					Chloramphenicol(DB00446)	CATGAAACAACCCCAAATAAA	0.413																																					p.T344fs		Atlas-INDEL	.											.	CD55	55	.	0			c.1030delA						.						154.0	135.0	142.0					1																	207510725		2203	4300	6503	SO:0001589	frameshift_variant	1604	exon8			.	BC001288	CCDS31006.1, CCDS44307.1, CCDS73022.1	1q32	2014-09-17	2006-03-28	2006-02-23	ENSG00000196352	ENSG00000196352		"""CD molecules"", ""Blood group antigens"""	2665	protein-coding gene	gene with protein product		125240	"""decay accelerating factor for complement (CD55, Cromer blood group system)"""	DAF			Standard	XM_005273077		Approved	CR, TC, CROM	uc001hfr.4	P08174	OTTHUMG00000036255	ENST00000367064.3:c.1031delC	chr1.hg19:g.207510725delC	ENSP00000356031:p.Thr344fs	161.0	0.0		261.0	17.0	NM_001114752	B1AP14|D3DT83|D3DT84|E7ER69|P09679|P78361|Q14UF2|Q14UF3|Q14UF4|Q14UF5|Q14UF6	Frame_Shift_Del	DEL	ENST00000367064.3	hg19	CCDS31006.1																																																																																			.	.		0.413	CD55-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088208.2	NM_000574	
OR56B1	387748	hgsc.bcm.edu	37	11	5758619	5758619	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:5758619delC	ENST00000317121.3	+	1	939	c.873delC	c.(871-873)atcfs	p.I291fs	TRIM5_ENST00000380027.1_Intron	NM_001005180.2	NP_001005180.1	Q8NGI3	O56B1_HUMAN	olfactory receptor, family 56, subfamily B, member 1	291						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.086)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.184)		ACAACATCATCCCCCCTTCCC	0.403																																					p.I291fs		Atlas-INDEL	.											.	OR56B1	38	.	0			c.872delT						.						290.0	270.0	277.0					11																	5758619		2201	4297	6498	SO:0001589	frameshift_variant	387748	exon1			.	BK004386	CCDS31395.1	11p15.4	2012-08-09		2004-03-10	ENSG00000181023	ENSG00000181023		"""GPCR / Class A : Olfactory receptors"""	15245	protein-coding gene	gene with protein product				OR56B1P			Standard	NM_001005180		Approved		uc001mbt.2	Q8NGI3	OTTHUMG00000066891	ENST00000317121.3:c.873delC	chr11.hg19:g.5758619delC	ENSP00000322939:p.Ile291fs	120.0	0.0		146.0	10.0	NM_001005180	B2RNY6|B3KV42|Q6IF76	Frame_Shift_Del	DEL	ENST00000317121.3	hg19	CCDS31395.1																																																																																			.	.		0.403	OR56B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143354.1	NM_001005180	
SLC11A2	4891	hgsc.bcm.edu	37	12	51386667	51386667	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:51386667delA	ENST00000262051.7	-	12	1210	c.1123delT	c.(1123-1125)tggfs	p.W375fs	SLC11A2_ENST00000546743.1_Frame_Shift_Del_p.W296fs|SLC11A2_ENST00000545993.2_Frame_Shift_Del_p.W371fs|SLC11A2_ENST00000394904.3_Frame_Shift_Del_p.W404fs|SLC11A2_ENST00000541174.2_Frame_Shift_Del_p.W375fs|SLC11A2_ENST00000547688.1_Frame_Shift_Del_p.W404fs|SLC11A2_ENST00000547198.1_Frame_Shift_Del_p.W375fs|SLC11A2_ENST00000262052.5_Frame_Shift_Del_p.W375fs	NM_001174126.1|NM_001174127.1	NP_001167597.1|NP_001167598.1	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2	375					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cadmium ion transmembrane transport (GO:0070574)|cation transmembrane transport (GO:0098655)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to iron ion (GO:0071281)|cellular response to oxidative stress (GO:0034599)|cellular response to tumor necrosis factor (GO:0071356)|cobalt ion transport (GO:0006824)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detection of oxygen (GO:0003032)|erythrocyte development (GO:0048821)|ferrous iron import (GO:0070627)|ferrous iron transport (GO:0015684)|heme biosynthetic process (GO:0006783)|lead ion transport (GO:0015692)|learning or memory (GO:0007611)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organismal iron ion homeostasis (GO:0060586)|nickel cation transmembrane transport (GO:0035444)|nickel cation transport (GO:0015675)|response to cadmium ion (GO:0046686)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to manganese ion (GO:0010042)|transmembrane transport (GO:0055085)|vanadium ion transport (GO:0015676)|zinc ion transmembrane transport (GO:0071577)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|brush border (GO:0005903)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|paraferritin complex (GO:0070826)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	cadmium ion binding (GO:0046870)|cadmium ion transmembrane transporter activity (GO:0015086)|cobalt ion binding (GO:0050897)|cobalt ion transmembrane transporter activity (GO:0015087)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|ferrous iron transmembrane transporter activity (GO:0015093)|hydrogen ion transmembrane transporter activity (GO:0015078)|inorganic cation transmembrane transporter activity (GO:0022890)|iron ion binding (GO:0005506)|lead ion transmembrane transporter activity (GO:0015094)|manganese ion binding (GO:0030145)|manganese ion transmembrane transporter activity (GO:0005384)|nickel cation binding (GO:0016151)|nickel cation transmembrane transporter activity (GO:0015099)|solute:proton symporter activity (GO:0015295)|vanadium ion transmembrane transporter activity (GO:0015100)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|cervix(1)|endometrium(3)|kidney(16)|large_intestine(4)|lung(9)|upper_aerodigestive_tract(1)	36						CCCACTGCCCAAATGTAGAGT	0.512																																					p.W404fs		Atlas-INDEL	.											.	SLC11A2	51	.	0			c.1211delG						.						130.0	111.0	117.0					12																	51386667		2203	4300	6503	SO:0001589	frameshift_variant	4891	exon12			.	AB015355	CCDS8805.1, CCDS53791.1, CCDS53792.1, CCDS53793.1	12q13	2013-07-18	2013-07-18		ENSG00000110911	ENSG00000110911		"""Solute carriers"""	10908	protein-coding gene	gene with protein product		600523		NRAMP2		7613023	Standard	NM_000617		Approved	DCT1, DMT1	uc001rxk.2	P49281	OTTHUMG00000169493	ENST00000262051.7:c.1123delT	chr12.hg19:g.51386667delA	ENSP00000262051:p.Trp375fs	110.0	0.0		152.0	10.0	NM_001174125	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Frame_Shift_Del	DEL	ENST00000262051.7	hg19	CCDS53792.1																																																																																			.	.		0.512	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1		
KIF5B	3799	hgsc.bcm.edu	37	10	32320045	32320045	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:32320045delT	ENST00000302418.4	-	14	1994	c.1537delA	c.(1537-1539)actfs	p.T513fs		NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	513					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)		KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				TATTCCTTAGTTTTGTCTTCA	0.318			T	"""RET, ALK"""	NSCLC																																p.T513fs		Atlas-INDEL	.		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	.	KIF5B	81	.	0			c.1538delC						.						104.0	102.0	103.0					10																	32320045		2203	4300	6503	SO:0001589	frameshift_variant	3799	exon14			.	X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"""Kinesins"""	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.1537delA	chr10.hg19:g.32320045delT	ENSP00000307078:p.Thr513fs	121.0	0.0		145.0	11.0	NM_004521	A0AVB2|Q5VZ85	Frame_Shift_Del	DEL	ENST00000302418.4	hg19	CCDS7171.1																																																																																			.	.		0.318	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521	
INTS2	57508	hgsc.bcm.edu	37	17	59946495	59946495	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:59946495delA	ENST00000444766.3	-	23	3243	c.3168delT	c.(3166-3168)tttfs	p.F1056fs	INTS2_ENST00000251334.6_Frame_Shift_Del_p.F1048fs	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	1056					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						ACTGGATAGCAAATATCTGCA	0.323																																					p.A1057fs		Atlas-INDEL	.											.	INTS2	89	.	0			c.3169delG						.						92.0	84.0	87.0					17																	59946495		1838	4080	5918	SO:0001589	frameshift_variant	57508	exon23			.	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"""KIAA1287"""	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.3168delT	chr17.hg19:g.59946495delA	ENSP00000414237:p.Phe1056fs	133.0	0.0		160.0	10.0	NM_020748	Q9ULD3	Frame_Shift_Del	DEL	ENST00000444766.3	hg19	CCDS45750.1																																																																																			.	.		0.323	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748	
IL21R	50615	hgsc.bcm.edu	37	16	27441412	27441412	+	Frame_Shift_Del	DEL	C	C	-	rs559469718		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:27441412delC	ENST00000337929.3	+	2	493	c.20delC	c.(19-21)gccfs	p.A7fs	IL21R_ENST00000395755.1_Frame_Shift_Del_p.A7fs|IL21R_ENST00000395754.4_Frame_Shift_Del_p.A7fs|IL21R_ENST00000564089.1_Frame_Shift_Del_p.A7fs	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	7					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						GGCTGGGCCGCCCCCTTGCTC	0.721			T	BCL6	NHL																																p.A29fs		Atlas-INDEL	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.85delG						.						19.0	20.0	20.0					16																	27441412		2194	4295	6489	SO:0001589	frameshift_variant	50615	exon3			.	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"""Interleukins and interleukin receptors"", ""CD molecules"""	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.20delC	chr16.hg19:g.27441412delC	ENSP00000338010:p.Ala7fs	144.0	0.0		135.0	10.0	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Frame_Shift_Del	DEL	ENST00000337929.3	hg19	CCDS10630.1																																																																																			.	.		0.721	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078	
ARL2BP	23568	hgsc.bcm.edu	37	16	57282542	57282542	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:57282542delT	ENST00000219204.3	+	3	464	c.194delT	c.(193-195)attfs	p.I65fs	RP11-407G23.4_ENST00000562409.1_RNA|ARL2BP_ENST00000562023.1_Intron|RP11-407G23.3_ENST00000564376.1_RNA	NM_012106.3	NP_036238.1	Q9Y2Y0	AR2BP_HUMAN	ADP-ribosylation factor-like 2 binding protein	65					maintenance of protein location in nucleus (GO:0051457)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of catalytic activity (GO:0050790)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	centrosome (GO:0005813)|cilium (GO:0005929)|midbody (GO:0030496)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	small GTPase regulator activity (GO:0005083)|transcription coactivator activity (GO:0003713)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|urinary_tract(1)	12						TACACACCTATTTTTAATGAA	0.338																																					p.I65fs		Atlas-INDEL	.											.	ARL2BP	20	.	0			c.193delA						.						78.0	79.0	79.0					16																	57282542		2198	4300	6498	SO:0001589	frameshift_variant	23568	exon3			.	AF126062	CCDS10776.1	16q13	2014-01-30			ENSG00000102931	ENSG00000102931			17146	protein-coding gene	gene with protein product	"""binder of Arl2"""	615407	"""retinitis pigmentosa 66 (autosomal recessive)"""	RP66		10488091, 18981177, 23849777	Standard	NM_012106		Approved	BART1, BART	uc002elf.1	Q9Y2Y0	OTTHUMG00000133459	ENST00000219204.3:c.194delT	chr16.hg19:g.57282542delT	ENSP00000219204:p.Ile65fs	105.0	0.0		163.0	10.0	NM_012106	B3KQJ5|Q504R0	Frame_Shift_Del	DEL	ENST00000219204.3	hg19	CCDS10776.1																																																																																			.	.		0.338	ARL2BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257334.2	NM_012106	
SMG1	23049	hgsc.bcm.edu	37	16	18865999	18865999	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:18865999delT	ENST00000446231.2	-	30	4874	c.4462delA	c.(4462-4464)accfs	p.T1488fs	SMG1_ENST00000389467.3_Frame_Shift_Del_p.T1488fs			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1488	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|Interaction with SMG8 and SMG9.				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						AGCAATTTGGTTTTTTCAATA	0.318																																					p.T1488fs		Atlas-INDEL	.											SMG1,colon,carcinoma,0,1	SMG1	401	.	0			c.4463delC						.						64.0	58.0	60.0					16																	18865999		1808	4072	5880	SO:0001589	frameshift_variant	23049	exon30			.	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.4462delA	chr16.hg19:g.18865999delT	ENSP00000402515:p.Thr1488fs	158.0	0.0		196.0	13.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Frame_Shift_Del	DEL	ENST00000446231.2	hg19	CCDS45430.1																																																																																			.	.		0.318	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
HAUS6	54801	hgsc.bcm.edu	37	9	19094365	19094365	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:19094365delT	ENST00000380502.3	-	3	720	c.253delA	c.(253-255)agtfs	p.S85fs	HAUS6_ENST00000380496.1_5'Flank	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	85					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TCAGTGTCACTTTTTTGGTCA	0.318																																					p.S85fs		Atlas-INDEL	.											.	HAUS6	66	.	0			c.254delG						.						42.0	44.0	43.0					9																	19094365		2203	4299	6502	SO:0001589	frameshift_variant	54801	exon3			.	AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"""HAUS augmin-like complex subunits"""	25948	protein-coding gene	gene with protein product		613433	"""family with sequence similarity 29, member A"""	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.253delA	chr9.hg19:g.19094365delT	ENSP00000369871:p.Ser85fs	279.0	0.0		211.0	13.0	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Frame_Shift_Del	DEL	ENST00000380502.3	hg19	CCDS6489.1																																																																																			.	.		0.318	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
OVCH2	341277	hgsc.bcm.edu	37	11	7721868	7721868	+	RNA	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:7721868delG	ENST00000534193.2	-	0	902				OVCH2_ENST00000454689.1_RNA			Q7RTZ1	OVCH2_HUMAN	ovochymase 2 (gene/pseudogene)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(2)	15				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)		CGTGGATCCAGGGAAGCACTT	0.507																																					p.W293fs		Atlas-INDEL	.											.	OVCH2	47	.	0			c.877delT						.						100.0	94.0	96.0					11																	7721868		1982	4166	6148			341277	exon7			.	BN000120	CCDS73251.1	11p15.4	2012-10-02	2010-06-08		ENSG00000183378	ENSG00000183378			29970	protein-coding gene	gene with protein product			"""ovochymase 2"""			12838346	Standard	XM_006718221		Approved	OVTN	uc031pyw.1	Q7RTZ1	OTTHUMG00000165418		chr11.hg19:g.7721868delG		184.0	0.0		208.0	13.0	NM_198185		Frame_Shift_Del	DEL	ENST00000534193.2	hg19																																																																																				.	.		0.507	OVCH2-001	KNOWN	non_canonical_polymorphism|not_organism_supported|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000383929.7	NM_198185	
CPA4	51200	hgsc.bcm.edu	37	7	129944394	129944394	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:129944394delA	ENST00000222482.4	+	5	489	c.461delA	c.(460-462)gaafs	p.E154fs	CPA4_ENST00000493259.1_Frame_Shift_Del_p.E50fs|CPA4_ENST00000445470.2_Frame_Shift_Del_p.E121fs	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	154					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					CATTCGTTTGAAAACCGGCCG	0.522																																					p.E154fs		Atlas-INDEL	.											.	CPA4	47	.	0			c.460delG						.						159.0	142.0	148.0					7																	129944394		2203	4300	6503	SO:0001589	frameshift_variant	51200	exon5			.	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.461delA	chr7.hg19:g.129944394delA	ENSP00000222482:p.Glu154fs	169.0	0.0		188.0	12.0	NM_016352	B7Z576|Q86UY9	Frame_Shift_Del	DEL	ENST00000222482.4	hg19	CCDS5818.1																																																																																			.	.		0.522	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
TAC3	6866	hgsc.bcm.edu	37	12	57406176	57406176	+	Frame_Shift_Del	DEL	G	G	-	rs368243990		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:57406176delG	ENST00000458521.2	-	6	512	c.353delC	c.(352-354)ccgfs	p.P118fs	TAC3_ENST00000441881.1_Frame_Shift_Del_p.P100fs|TAC3_ENST00000415231.1_Frame_Shift_Del_p.P118fs	NM_013251.3	NP_037383.1	Q9UHF0	TKNK_HUMAN	tachykinin 3	118					female pregnancy (GO:0007565)|neuropeptide signaling pathway (GO:0007218)|tachykinin receptor signaling pathway (GO:0007217)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7						TTCTGCTCTCGGGGGATACTT	0.527																																					p.P118fs		Atlas-INDEL	.											.	TAC3	11	.	0			c.354delG						.						73.0	66.0	68.0					12																	57406176		2203	4300	6503	SO:0001589	frameshift_variant	6866	exon6			.	AF186112	CCDS8928.1, CCDS53803.1	12q13-q21	2013-02-26	2008-07-31		ENSG00000166863	ENSG00000166863		"""Endogenous ligands"""	11521	protein-coding gene	gene with protein product	"""preprotachykinin-B"""	162330	"""neuromedin K"", ""neurokinin beta"""	NKNB		3479225, 10866201	Standard	NM_013251		Approved	ZNEUROK1, NKB	uc001smp.3	Q9UHF0	OTTHUMG00000156958	ENST00000458521.2:c.353delC	chr12.hg19:g.57406176delG	ENSP00000404056:p.Pro118fs	104.0	0.0		146.0	10.0	NM_013251	Q6IAG2|Q71BC6|Q71BC9	Frame_Shift_Del	DEL	ENST00000458521.2	hg19	CCDS8928.1																																																																																			.	.		0.527	TAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346793.1	NM_001006667	
SLC4A4	8671	hgsc.bcm.edu	37	4	72363374	72363374	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:72363374delA	ENST00000264485.5	+	16	2248	c.2131delA	c.(2131-2133)aaafs	p.K712fs	SLC4A4_ENST00000425175.1_Frame_Shift_Del_p.K712fs|SLC4A4_ENST00000340595.3_Frame_Shift_Del_p.K668fs|SLC4A4_ENST00000351898.6_Frame_Shift_Del_p.K712fs	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	712					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)	CATGGCTCTGAAAAAATTCAA	0.363																																					p.L710fs		Atlas-INDEL	.											SLC4A4_ENST00000425175,caecum,carcinoma,0,2	SLC4A4	269	.	0			c.2130delG						.						113.0	117.0	115.0					4																	72363374		2203	4300	6503	SO:0001589	frameshift_variant	8671	exon16			.	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.2131delA	chr4.hg19:g.72363374delA	ENSP00000264485:p.Lys712fs	101.0	0.0		132.0	11.0	NM_001134742	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Frame_Shift_Del	DEL	ENST00000264485.5	hg19	CCDS43236.1																																																																																			.	.		0.363	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759	
DMPK	1760	hgsc.bcm.edu	37	19	46283130	46283130	+	Intron	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:46283130delG	ENST00000291270.4	-	2	286				DMPK_ENST00000343373.4_Frame_Shift_Del_p.P63fs|DMPK_ENST00000458663.2_Intron|AC011530.4_ENST00000593999.1_Intron|DMPK_ENST00000595361.1_5'Flank|DMPK_ENST00000354227.5_Intron|DMPK_ENST00000447742.2_Intron|DMPK_ENST00000600757.1_Frame_Shift_Del_p.P63fs	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase						cellular calcium ion homeostasis (GO:0006874)|muscle cell apoptotic process (GO:0010657)|nuclear envelope organization (GO:0006998)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction (GO:0014853)|regulation of heart contraction (GO:0008016)|regulation of myotube differentiation (GO:0010830)|regulation of skeletal muscle contraction by calcium ion signaling (GO:0014722)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of mitochondrial outer membrane (GO:0031307)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|myosin phosphatase regulator activity (GO:0017020)|protein serine/threonine kinase activity (GO:0004674)			endometrium(5)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)|urinary_tract(2)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		GGGCTCCGCTGGGGGGGTGGT	0.617																																					p.P63fs	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-INDEL	.											.	DMPK	74	.	0			c.189delA						.						37.0	40.0	39.0					19																	46283130		2203	4300	6503	SO:0001627	intron_variant	1760	exon1			.	L19268	CCDS12674.1, CCDS46117.1, CCDS46118.1, CCDS46119.1, CCDS74400.1	19q13.3	2014-02-05					2.7.11.1		2933	protein-coding gene	gene with protein product	"""dystrophia myotonica 1"", ""DM protein kinase"", ""myotonin protein kinase A"", ""myotonic dystrophy associated protein kinase"", ""thymopoietin homolog"""	605377	"""dystrophia myotonica 1 (includes dystrophia myotonia protein kinase)"""	DM1, DM		1546325, 1546326	Standard	NM_001288765		Approved	DMK, DM1PK, MDPK, MT-PK	uc002pdf.1	Q09013		ENST00000291270.4:c.161-3C>-	chr19.hg19:g.46283130delG		70.0	0.0		107.0	10.0	NM_001081563	E5KR08|Q16205|Q6P5Z6	Frame_Shift_Del	DEL	ENST00000291270.4	hg19	CCDS12674.1																																																																																			.	.		0.617	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409	
TMEM69	51249	hgsc.bcm.edu	37	1	46158890	46158890	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:46158890delT	ENST00000372025.4	+	3	1214	c.57delT	c.(55-57)tctfs	p.S19fs	TMEM69_ENST00000496366.1_3'UTR|RP11-767N6.7_ENST00000430643.1_RNA	NM_016486.3	NP_057570.2	Q5SWH9	TMM69_HUMAN	transmembrane protein 69	19						integral component of membrane (GO:0016021)				kidney(3)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(166;0.155)					TGAAGTACTCTTTCCCAGTGG	0.358																																					p.S19fs		Atlas-INDEL	.											.	TMEM69	20	.	0			c.56delC						.						145.0	141.0	142.0					1																	46158890		1831	4082	5913	SO:0001589	frameshift_variant	51249	exon3			.	BC040289, BC013608	CCDS41325.1	1p34.1	2008-02-05	2005-08-17	2005-08-17	ENSG00000159596	ENSG00000159596			28035	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 154"""	C1orf154			Standard	NM_016486		Approved	FLJ21029	uc001cor.1	Q5SWH9	OTTHUMG00000040993	ENST00000372025.4:c.57delT	chr1.hg19:g.46158890delT	ENSP00000361095:p.Ser19fs	136.0	0.0		165.0	10.0	NM_016486	Q3SWW5|Q7Z2G0|Q9P0P9	Frame_Shift_Del	DEL	ENST00000372025.4	hg19	CCDS41325.1																																																																																			.	.		0.358	TMEM69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098390.1	NM_016486	
CPEB4	80315	hgsc.bcm.edu	37	5	173317577	173317577	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:173317577delC	ENST00000265085.5	+	1	2295	c.841delC	c.(841-843)cccfs	p.P282fs	CPEB4_ENST00000520867.1_Frame_Shift_Del_p.P282fs|CPEB4_ENST00000519835.1_Frame_Shift_Del_p.P282fs|CPEB4_ENST00000522336.1_5'Flank|CPEB4_ENST00000334035.5_Frame_Shift_Del_p.P282fs|CPEB4_ENST00000517880.1_5'Flank	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	282					cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TCTTAACAAACCCCCCTCTCC	0.577																																					p.K280fs		Atlas-INDEL	.											.	CPEB4	54	.	0			c.840delA						.						185.0	198.0	194.0					5																	173317577		2203	4300	6503	SO:0001589	frameshift_variant	80315	exon1			.	BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"""RNA binding motif (RRM) containing"""	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.841delC	chr5.hg19:g.173317577delC	ENSP00000265085:p.Pro282fs	92.0	0.0		140.0	11.0	NM_030627	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Frame_Shift_Del	DEL	ENST00000265085.5	hg19	CCDS4390.1																																																																																			.	.		0.577	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627	
CGNL1	84952	hgsc.bcm.edu	37	15	57743740	57743740	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:57743740delA	ENST00000281282.5	+	5	1924	c.1846delA	c.(1846-1848)aaafs	p.K616fs		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	616						myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		ATTGGAACAGAAAAGCAAGTT	0.328																																					p.Q615fs		Atlas-INDEL	.											.	CGNL1	125	.	0			c.1845delG						.						88.0	94.0	92.0					15																	57743740		2192	4292	6484	SO:0001589	frameshift_variant	84952	exon6			.	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.1846delA	chr15.hg19:g.57743740delA	ENSP00000281282:p.Lys616fs	154.0	0.0		179.0	11.0	NM_001252335	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Frame_Shift_Del	DEL	ENST00000281282.5	hg19	CCDS10161.1																																																																																			.	.		0.328	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866	
NXPE4	54827	hgsc.bcm.edu	37	11	114450944	114450944	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:114450944delT	ENST00000375478.3	-	5	1189	c.1009delA	c.(1009-1011)atgfs	p.M337fs	NXPE4_ENST00000424261.2_Frame_Shift_Del_p.M53fs	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	337						extracellular vesicular exosome (GO:0070062)											CATTCCTTCATTTTGACTGTA	0.448																																					p.M337fs		Atlas-INDEL	.											.	.	.	.	0			c.1010delT						.						193.0	182.0	186.0					11																	114450944		1879	4127	6006	SO:0001589	frameshift_variant	54827	exon5			.	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 33"", ""family with sequence similarity 55, member D"""	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.1009delA	chr11.hg19:g.114450944delT	ENSP00000364627:p.Met337fs	254.0	0.0		293.0	18.0	NM_001077639	Q6QDB4|Q9NXP5	Frame_Shift_Del	DEL	ENST00000375478.3	hg19	CCDS41718.1																																																																																			.	.		0.448	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678	
RUFY2	55680	hgsc.bcm.edu	37	10	70139221	70139221	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:70139221delT	ENST00000602465.1	-	12	1265	c.1165delA	c.(1165-1167)accfs	p.T389fs	RUFY2_ENST00000472394.2_5'Flank|RUFY2_ENST00000454950.2_Frame_Shift_Del_p.T331fs|RUFY2_ENST00000265865.3_5'Flank|RUFY2_ENST00000399200.2_Frame_Shift_Del_p.T355fs|RUFY2_ENST00000388768.2_Frame_Shift_Del_p.T424fs			Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain containing 2	438						nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)	20						ATTTTATTGGTTTTTTCTTCT	0.333																																					p.T424fs		Atlas-INDEL	.											.	RUFY2	58	.	0			c.1271delC						.						117.0	118.0	118.0					10																	70139221		1826	4078	5904	SO:0001589	frameshift_variant	55680	exon12			.	AF461266	CCDS41534.1, CCDS44414.1, CCDS60544.1	10q22.2	2007-01-29			ENSG00000204130	ENSG00000204130		"""Zinc fingers, FYVE domain containing"""	19761	protein-coding gene	gene with protein product		610328				11877430	Standard	NM_001042417		Approved	RABIP4R, FLJ10063, KIAA1537, ZFYVE13	uc001job.3	Q8WXA3	OTTHUMG00000018353	ENST00000602465.1:c.1165delA	chr10.hg19:g.70139221delT	ENSP00000473462:p.Thr389fs	125.0	0.0		151.0	11.0	NM_017987	B3KXB2|B4DFR0|Q5TC48|Q8IW33|Q96P51|Q9P1Z1	Frame_Shift_Del	DEL	ENST00000602465.1	hg19																																																																																				.	.		0.333	RUFY2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467567.1	NM_017987	
ABCG5	64240	hgsc.bcm.edu	37	2	44047175	44047175	+	Frame_Shift_Del	DEL	G	G	-	rs199984328	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:44047175delG	ENST00000260645.1	-	11	1667	c.1528delC	c.(1528-1530)cacfs	p.H510fs	ABCG5_ENST00000543989.1_Frame_Shift_Del_p.H115fs|ABCG5_ENST00000405322.1_Frame_Shift_Del_p.H339fs	NM_022436.2	NP_071881.1	Q9H222	ABCG5_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 5	510	ABC transmembrane type-2.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	CCAATTAAGTGGGGGGCCAAG	0.463																																					p.H510fs		Atlas-INDEL	.											.	ABCG5	72	.	0			c.1529delA	GRCh37	CM074664	ABCG5	M		.						73.0	74.0	74.0					2																	44047175		2203	4300	6503	SO:0001589	frameshift_variant	64240	exon11			.	T93792	CCDS1814.1	2p21	2012-03-14	2008-07-31		ENSG00000138075	ENSG00000138075		"""ATP binding cassette transporters / subfamily G"""	13886	protein-coding gene	gene with protein product	"""sterolin 1"""	605459				11099417, 11452359	Standard	NM_022436		Approved	STSL	uc002rtn.3	Q9H222	OTTHUMG00000128758	ENST00000260645.1:c.1528delC	chr2.hg19:g.44047175delG	ENSP00000260645:p.His510fs	148.0	0.0		150.0	10.0	NM_022436	Q2T9G2|Q96QZ2|Q96QZ3	Frame_Shift_Del	DEL	ENST00000260645.1	hg19	CCDS1814.1																																																																																			.	.		0.463	ABCG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250675.1	NM_022436	
CDKAL1	54901	hgsc.bcm.edu	37	6	21108646	21108646	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:21108646delA	ENST00000378610.1	+	11	1261	c.1251delA	c.(1249-1251)acafs	p.T417fs	CDKAL1_ENST00000378624.4_Intron|CDKAL1_ENST00000274695.4_Frame_Shift_Del_p.T417fs			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	417					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			AGCAAAGGACAAAAGATCTTT	0.294																																					p.T417fs		Atlas-INDEL	.											.	CDKAL1	55	.	0			c.1250delC						.						56.0	56.0	56.0					6																	21108646		2203	4291	6494	SO:0001589	frameshift_variant	54901	exon13			.	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.1251delA	chr6.hg19:g.21108646delA	ENSP00000367873:p.Thr417fs	106.0	0.0		139.0	11.0	NM_017774	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Frame_Shift_Del	DEL	ENST00000378610.1	hg19	CCDS4546.1																																																																																			.	.		0.294	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774	
GPC5	2262	hgsc.bcm.edu	37	13	92797194	92797194	+	Frame_Shift_Del	DEL	G	G	-	rs368333375		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:92797194delG	ENST00000377067.3	+	7	1885	c.1513delG	c.(1513-1515)gggfs	p.G506fs		NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	506					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				AGATGGTTGCGGGGGATCAGG	0.438																																					p.C504fs		Atlas-INDEL	.											GPC5,NS,carcinoma,0,1	GPC5	140	.	0			c.1512delC						.						164.0	140.0	148.0					13																	92797194		2203	4300	6503	SO:0001589	frameshift_variant	2262	exon7			.	AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"""Proteoglycans / Cell Surface : Glypicans"""	4453	protein-coding gene	gene with protein product	"""glypican proteoglycan 5"""	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.1513delG	chr13.hg19:g.92797194delG	ENSP00000366267:p.Gly506fs	169.0	0.0		160.0	10.0	NM_004466	B2R726|O60436|Q9BX27	Frame_Shift_Del	DEL	ENST00000377067.3	hg19	CCDS9468.1																																																																																			.	.		0.438	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466	
YLPM1	56252	hgsc.bcm.edu	37	14	75264632	75264632	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:75264632delA	ENST00000325680.7	+	5	2756	c.2632delA	c.(2632-2634)aaafs	p.K878fs	YLPM1_ENST00000238571.3_Frame_Shift_Del_p.K683fs|YLPM1_ENST00000552421.1_Intron	NM_019589.2	NP_062535.2	P49750	YLPM1_HUMAN	YLP motif containing 1	683	Arg-rich.				regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		GAAGAATTTTAAAATGCAATC	0.438																																					p.F877fs		Atlas-INDEL	.											.	YLPM1	298	.	0			c.2631delT						.						63.0	61.0	62.0					14																	75264632		1891	4114	6005	SO:0001589	frameshift_variant	56252	exon5			.	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 169"""		"""chromosome 14 open reading frame 170"""	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000325680.7:c.2632delA	chr14.hg19:g.75264632delA	ENSP00000324463:p.Lys878fs	146.0	0.0		194.0	12.0	NM_019589	P49752|Q96I64|Q9P1V7	Frame_Shift_Del	DEL	ENST00000325680.7	hg19	CCDS45135.1																																																																																			.	.		0.438	YLPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404451.1	NM_019589	
DCAF16	54876	hgsc.bcm.edu	37	4	17805674	17805674	+	Frame_Shift_Del	DEL	C	C	-	rs372001633		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:17805674delC	ENST00000382247.1	-	3	1151	c.91delG	c.(91-93)gaafs	p.E32fs	DCAF16_ENST00000536863.1_Frame_Shift_Del_p.E32fs|DCAF16_ENST00000507768.1_5'Flank	NM_017741.3	NP_060211.3	Q9NXF7	DCA16_HUMAN	DDB1 and CUL4 associated factor 16	32					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)				cervix(1)|endometrium(1)|lung(2)|ovary(1)	5						TCCCACTCTTCCCCAGAACTC	0.428																																					p.E31fs		Atlas-INDEL	.											.	DCAF16	19	.	0			c.92delA						.						67.0	71.0	70.0					4																	17805674		2203	4300	6503	SO:0001589	frameshift_variant	54876	exon3			.	AK000287	CCDS3423.1	4p15.32	2009-07-17	2009-07-17	2009-07-17	ENSG00000163257	ENSG00000163257		"""DDB1 and CUL4 associated factors"""	25987	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 30"""	C4orf30		12477932	Standard	XM_005248169		Approved	FLJ20280	uc003gpn.3	Q9NXF7	OTTHUMG00000128536	ENST00000382247.1:c.91delG	chr4.hg19:g.17805674delC	ENSP00000371682:p.Glu32fs	105.0	0.0		146.0	10.0	NM_017741	B3KPB7	Frame_Shift_Del	DEL	ENST00000382247.1	hg19	CCDS3423.1																																																																																			.	.		0.428	DCAF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250371.1	NM_017741	
AGPAT9	84803	hgsc.bcm.edu	37	4	84465717	84465717	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:84465717delC	ENST00000395226.2	+	3	388	c.170delC	c.(169-171)accfs	p.T57fs	AGPAT9_ENST00000264409.4_Frame_Shift_Del_p.T57fs	NM_001256421.1	NP_001243350.1	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9	57					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|regulation of TOR signaling (GO:0032006)|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)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(3)	13		Hepatocellular(203;0.114)				GAAAAAGGAACCCCAAAGGAG	0.348																																					p.T57fs		Atlas-INDEL	.											.	AGPAT9	41	.	0			c.169delA						.						195.0	211.0	205.0					4																	84465717		2203	4300	6503	SO:0001589	frameshift_variant	84803	exon2			.	AK055749	CCDS3606.1	4q21.23	2014-02-13	2008-01-29		ENSG00000138678	ENSG00000138678	2.3.1.15	"""1-acylglycerol-3-phosphate O-acyltransferases"""	28157	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, theta"""	610958	"""1-acylglycerol-3-phosphate O-acyltransferase 9 (lysophosphatidic acid acyltransferase, theta)"""			12975309	Standard	NM_001256421		Approved	MGC11324, LPAAT-theta, MAG1, HMFN0839	uc003how.4	Q53EU6	OTTHUMG00000130431	ENST00000395226.2:c.170delC	chr4.hg19:g.84465717delC	ENSP00000378651:p.Thr57fs	117.0	0.0		166.0	11.0	NM_032717	Q68CJ4|Q6GPI6|Q96NA3	Frame_Shift_Del	DEL	ENST00000395226.2	hg19	CCDS3606.1																																																																																			.	.		0.348	AGPAT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252821.3	NM_032717	
STAT6	6778	hgsc.bcm.edu	37	12	57499025	57499025	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:57499025delC	ENST00000300134.3	-	9	1235	c.910delG	c.(910-912)gccfs	p.A304fs	STAT6_ENST00000538913.2_Frame_Shift_Del_p.A194fs|STAT6_ENST00000537215.2_Frame_Shift_Del_p.A194fs|STAT6_ENST00000454075.3_Frame_Shift_Del_p.A304fs|STAT6_ENST00000543873.2_Frame_Shift_Del_p.A304fs|STAT6_ENST00000556155.1_Frame_Shift_Del_p.A304fs	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	304					cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.A304T(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						TTGGCTGGGGCCCCCAGGAAC	0.632																																					p.A304fs		Atlas-INDEL	.											.	STAT6	69	.	1	Substitution - Missense(1)	large_intestine(1)	c.911delC						.						39.0	43.0	42.0					12																	57499025		2203	4300	6503	SO:0001589	frameshift_variant	6778	exon9			.	BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"""SH2 domain containing"""	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.910delG	chr12.hg19:g.57499025delC	ENSP00000300134:p.Ala304fs	98.0	0.0		133.0	10.0	NM_003153	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Frame_Shift_Del	DEL	ENST00000300134.3	hg19	CCDS8931.1																																																																																			.	.		0.632	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153	
UTP15	84135	hgsc.bcm.edu	37	5	72864105	72864105	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:72864105delT	ENST00000296792.4	+	3	391	c.136delT	c.(136-138)tttfs	p.F46fs	UTP15_ENST00000508491.1_Intron|ANKRA2_ENST00000296785.3_5'Flank|UTP15_ENST00000543251.1_5'UTR	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	46					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		AAAAGTAGACTTTTCTCCTCA	0.308																																					p.D45fs		Atlas-INDEL	.											.	UTP15	30	.	0			c.135delC						.						75.0	80.0	79.0					5																	72864105		2203	4299	6502	SO:0001589	frameshift_variant	84135	exon3			.	AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"""WD repeat domain containing"""	25758	protein-coding gene	gene with protein product			"""UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"""			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.136delT	chr5.hg19:g.72864105delT	ENSP00000296792:p.Phe46fs	171.0	0.0		249.0	17.0	NM_032175	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Frame_Shift_Del	DEL	ENST00000296792.4	hg19	CCDS34186.1																																																																																			.	.		0.308	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175	
SETD1A	9739	hgsc.bcm.edu	37	16	30990582	30990582	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:30990582delC	ENST00000262519.8	+	14	4161	c.3475delC	c.(3475-3477)cccfs	p.P1161fs		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	1161	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						CCCCCTCCTGCCCCCACCCAA	0.701																																					p.L1158fs		Atlas-INDEL	.											.	SETD1A	143	.	0			c.3474delG						.						15.0	19.0	17.0					16																	30990582		2155	4223	6378	SO:0001589	frameshift_variant	9739	exon14			.	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.3475delC	chr16.hg19:g.30990582delC	ENSP00000262519:p.Pro1161fs	212.0	0.0		246.0	18.0	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Frame_Shift_Del	DEL	ENST00000262519.8	hg19	CCDS32435.1																																																																																			.	.		0.701	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712	
TESK1	7016	hgsc.bcm.edu	37	9	35607647	35607647	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:35607647delG	ENST00000336395.5	+	6	939	c.689delG	c.(688-690)cggfs	p.R230fs	CD72_ENST00000490239.1_5'Flank|MIR4667_ENST00000578933.1_RNA|TESK1_ENST00000498522.1_3'UTR	NM_006285.2	NP_006276.2	Q15569	TESK1_HUMAN	testis-specific kinase 1	230	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell junction assembly (GO:0034329)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	27			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GAGGTGTTACGGGGTGAGCTG	0.582																																					p.R230fs		Atlas-INDEL	.											.	TESK1	46	.	0			c.688delC						.						99.0	94.0	96.0					9																	35607647		2203	4300	6503	SO:0001589	frameshift_variant	7016	exon6			.	D50863	CCDS6580.1	9p13	2010-04-27			ENSG00000107140	ENSG00000107140	2.7.12.1		11731	protein-coding gene	gene with protein product	"""testis-specific kinase-1"", ""testis specific kinase-1"""	601782				8537404	Standard	NM_006285		Approved		uc003zxa.3	Q15569	OTTHUMG00000019863	ENST00000336395.5:c.689delG	chr9.hg19:g.35607647delG	ENSP00000338127:p.Arg230fs	125.0	0.0		119.0	11.0	NM_006285	Q8IXZ8	Frame_Shift_Del	DEL	ENST00000336395.5	hg19	CCDS6580.1																																																																																			.	.		0.582	TESK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052314.1	NM_006285	
GRIA3	2892	hgsc.bcm.edu	37	X	122528855	122528855	+	Frame_Shift_Del	DEL	G	G	-	rs191962905		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:122528855delG	ENST00000371251.1	+	6	839	c.787delG	c.(787-789)gggfs	p.G264fs	GRIA3_ENST00000371256.5_Frame_Shift_Del_p.G264fs|GRIA3_ENST00000541091.1_Frame_Shift_Del_p.G248fs|GRIA3_ENST00000264357.5_Frame_Shift_Del_p.G264fs|GRIA3_ENST00000542149.1_Frame_Shift_Del_p.G264fs			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	264					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	AGTCATGCATGGGGGAGCCAA	0.428																																					p.H262fs		Atlas-INDEL	.											.	GRIA3	386	.	0			c.786delT						.						113.0	102.0	106.0					X																	122528855		2203	4300	6503	SO:0001589	frameshift_variant	2892	exon6			.	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4573	protein-coding gene	gene with protein product		305915	"""glutamate receptor, ionotrophic, AMPA 3"""	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.787delG	chrX.hg19:g.122528855delG	ENSP00000360297:p.Gly264fs	155.0	0.0		200.0	12.0	NM_000828	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Frame_Shift_Del	DEL	ENST00000371251.1	hg19	CCDS14604.1																																																																																			.	.		0.428	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828	
TSPAN18	90139	hgsc.bcm.edu	37	11	44931375	44931375	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:44931375delG	ENST00000520358.2	+	5	598	c.183delG	c.(181-183)atgfs	p.M61fs	TSPAN18_ENST00000340160.3_Frame_Shift_Del_p.M61fs			Q96SJ8	TSN18_HUMAN	tetraspanin 18	61						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(6)|lung(3)	10						TCCTGGCCATGGGGGGCCTGC	0.647																																					p.M61fs		Atlas-INDEL	.											.	TSPAN18	38	.	0			c.182delT						.						48.0	52.0	51.0					11																	44931375		2203	4299	6502	SO:0001589	frameshift_variant	90139	exon4			.	AY358087	CCDS7910.1	11p11.2	2013-02-14				ENSG00000157570		"""Tetraspanins"""	20660	protein-coding gene	gene with protein product						11756464	Standard	NM_130783		Approved	TSPAN	uc001mye.4	Q96SJ8		ENST00000520358.2:c.183delG	chr11.hg19:g.44931375delG	ENSP00000429993:p.Met61fs	110.0	0.0		149.0	11.0	NM_130783	Q6UY44|Q8NBI9	Frame_Shift_Del	DEL	ENST00000520358.2	hg19	CCDS7910.1																																																																																			.	.		0.647	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376197.3	NM_130783	
ABCB7	22	hgsc.bcm.edu	37	X	74282215	74282215	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:74282215delG	ENST00000373394.3	-	14	1890	c.1883delC	c.(1882-1884)ccafs	p.P628fs	ABCB7_ENST00000339447.4_Frame_Shift_Del_p.P588fs|ABCB7_ENST00000253577.3_Frame_Shift_Del_p.P629fs|ABCB7_ENST00000534570.1_5'Flank			O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 7	628	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)			breast(1)|endometrium(5)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)	20						GAGTATGACTGGGGGGTCCTT	0.348																																					p.P629fs		Atlas-Indel,Pindel	.											.	ABCB7	69	.	0			c.1887delA						.						101.0	90.0	94.0					X																	74282215		2203	4300	6503	SO:0001589	frameshift_variant	22	exon14			.	AF038950	CCDS14428.1, CCDS65290.1, CCDS65291.1, CCDS75994.1	Xq13.3	2012-03-14			ENSG00000131269	ENSG00000131269		"""ATP binding cassette transporters / subfamily B"""	48	protein-coding gene	gene with protein product		300135		ABC7		9143506	Standard	NM_004299		Approved	EST140535, Atm1p, ASAT	uc004ebz.4	O75027	OTTHUMG00000021862	ENST00000373394.3:c.1883delC	chrX.hg19:g.74282215delG	ENSP00000362492:p.Pro628fs	126.0	0.0		166.0	13.0	NM_004299	G3XAC4|O75345|Q5VWY7|Q5VWY8|Q9BRE1|Q9UND1|Q9UP01	Frame_Shift_Del	DEL	ENST00000373394.3	hg19																																																																																				.	.		0.348	ABCB7-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000057274.1	NM_004299	
AQR	9716	hgsc.bcm.edu	37	15	35182501	35182501	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:35182501delT	ENST00000156471.5	-	24	2821	c.2596delA	c.(2596-2598)atcfs	p.I866fs		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	866					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)		AATGCCATGATTTTCTCAAAC	0.428																																					p.I866fs		Atlas-INDEL	.											.	AQR	139	.	0			c.2597delT						.						164.0	155.0	158.0					15																	35182501		1902	4136	6038	SO:0001589	frameshift_variant	9716	exon24			.	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.2596delA	chr15.hg19:g.35182501delT	ENSP00000156471:p.Ile866fs	145.0	0.0		152.0	10.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Frame_Shift_Del	DEL	ENST00000156471.5	hg19	CCDS42013.1																																																																																			.	.		0.428	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691	
ZNF493	284443	hgsc.bcm.edu	37	19	21588652	21588652	+	Intron	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:21588652delC	ENST00000355504.4	+	1	135				ZNF493_ENST00000594390.1_Frame_Shift_Del_p.P84fs|ZNF493_ENST00000596302.1_Frame_Shift_Del_p.P85fs|ZNF493_ENST00000392288.2_Frame_Shift_Del_p.P84fs|CTD-2561J22.3_ENST00000600810.1_Frame_Shift_Del_p.P65fs|ZNF493_ENST00000339914.6_Frame_Shift_Del_p.P85fs	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						GGTAGTCAAACCCCCAGGTAG	0.418																																					p.K83fs		Atlas-INDEL	.											.	ZNF493	178	.	0			c.249delA						.						78.0	81.0	80.0					19																	21588652		2203	4300	6503	SO:0001627	intron_variant	284443	exon3			.	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"""Zinc fingers, C2H2-type"", ""-"""	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.-132+8583C>-	chr19.hg19:g.21588652delC		74.0	0.0		103.0	11.0	NM_145326	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Frame_Shift_Del	DEL	ENST00000355504.4	hg19	CCDS12412.1																																																																																			.	.		0.418	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910	
PKN1	5585	hgsc.bcm.edu	37	19	14561143	14561143	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:14561143delG	ENST00000242783.6	+	5	789	c.624delG	c.(622-624)ctgfs	p.L208fs	PKN1_ENST00000342216.4_Frame_Shift_Del_p.L214fs	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	208					activation of JUN kinase activity (GO:0007257)|epithelial cell migration (GO:0010631)|histone H3-T11 phosphorylation (GO:0035407)|hyperosmotic response (GO:0006972)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|GTP-Rho binding (GO:0017049)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|histone kinase activity (H3-T11 specific) (GO:0035402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)	31						GTCCTGACCTGGGGGCTGTGG	0.647																																					p.L214fs	NSCLC(185;2539 2965 10733 52867)	Atlas-INDEL	.											.	PKN1	99	.	0			c.641delT						.						17.0	20.0	19.0					19																	14561143		2134	4222	6356	SO:0001589	frameshift_variant	5585	exon5			.	S75546	CCDS42513.1, CCDS42514.1	19p13.12	2008-05-14	2004-07-01	2004-07-01	ENSG00000123143	ENSG00000123143			9405	protein-coding gene	gene with protein product		601032	"""protein kinase C-like 1"""	PRKCL1		9570957	Standard	NM_002741		Approved	DBK, PRK1, PKN, MGC46204, PAK1	uc002myq.3	Q16512	OTTHUMG00000039611	ENST00000242783.6:c.624delG	chr19.hg19:g.14561143delG	ENSP00000242783:p.Leu208fs	219.0	0.0		227.0	16.0	NM_213560	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Frame_Shift_Del	DEL	ENST00000242783.6	hg19	CCDS42513.1																																																																																			.	.		0.647	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	NM_002741, NM_213560	
GPKOW	27238	hgsc.bcm.edu	37	X	48970804	48970804	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:48970804delG	ENST00000156109.5	-	10	1361	c.1283delC	c.(1282-1284)ccafs	p.P428fs		NM_015698.4	NP_056513.2	Q92917	GPKOW_HUMAN	G patch domain and KOW motifs	428	KOW 2.					nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)	21						TCCAGTCTGTGGGCCCAGCAC	0.592																																					p.P428fs		Atlas-INDEL	.											.	GPKOW	38	.	0			c.1284delA						.						142.0	92.0	109.0					X																	48970804		2203	4300	6503	SO:0001589	frameshift_variant	27238	exon10			.	U66359	CCDS35251.1	Xp11.23	2013-01-28			ENSG00000068394	ENSG00000068394		"""G patch domain containing"""	30677	protein-coding gene	gene with protein product	"""G patch domain containing 5"""					21880142, 22365833	Standard	NM_015698		Approved	T54, GPATC5, GPATCH5, Spp2	uc004dmr.3	Q92917	OTTHUMG00000021511	ENST00000156109.5:c.1283delC	chrX.hg19:g.48970804delG	ENSP00000156109:p.Pro428fs	103.0	0.0		156.0	10.0	NM_015698	Q59EK5|Q9BQA8	Frame_Shift_Del	DEL	ENST00000156109.5	hg19	CCDS35251.1																																																																																			.	.		0.592	GPKOW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056535.2	NM_015698	
RMND5A	64795	hgsc.bcm.edu	37	2	86992185	86992185	+	Frame_Shift_Del	DEL	A	A	-	rs201043371		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:86992185delA	ENST00000283632.4	+	5	1052	c.557delA	c.(556-558)caafs	p.Q186fs		NM_022780.3	NP_073617.1	Q9H871	RMD5A_HUMAN	required for meiotic nuclear division 5 homolog A (S. cerevisiae)	186	CTLH. {ECO:0000255|PROSITE- ProRule:PRU00058}.									kidney(1)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	17						CTTATAGCTCAAAACAGCTCC	0.358																																					p.Q186fs		Atlas-INDEL	.											.	RMND5A	33	.	0			c.556delC						.						135.0	130.0	132.0					2																	86992185		2203	4300	6503	SO:0001589	frameshift_variant	64795	exon5			.	BC012165	CCDS1991.1	2p11.2	2012-07-20			ENSG00000153561	ENSG00000153561			25850	protein-coding gene	gene with protein product	"""GID complex subunit 2 homolog A"""					12477932	Standard	NM_022780		Approved	FLJ13910, RMD5, GID2, GID2A	uc002srs.4	Q9H871	OTTHUMG00000130262	ENST00000283632.4:c.557delA	chr2.hg19:g.86992185delA	ENSP00000283632:p.Gln186fs	173.0	0.0		214.0	13.0	NM_022780	D6W5M6|Q6NTF0|Q9H6W5|Q9H9H2	Frame_Shift_Del	DEL	ENST00000283632.4	hg19	CCDS1991.1																																																																																			.	.		0.358	RMND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252591.2	NM_022780	
SETX	23064	hgsc.bcm.edu	37	9	135173586	135173586	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:135173586delT	ENST00000224140.5	-	13	5844	c.5662delA	c.(5662-5664)aggfs	p.R1888fs	SETX_ENST00000393220.1_Frame_Shift_Del_p.R1888fs|SETX_ENST00000372169.2_Frame_Shift_Del_p.R1888fs	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1888					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TTCAACTTCCTTTGTGTAGTT	0.413																																					p.R1888fs		Atlas-INDEL	.											.	SETX	234	.	0			c.5663delG						.						135.0	125.0	128.0					9																	135173586		2203	4300	6503	SO:0001589	frameshift_variant	23064	exon13			.	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.5662delA	chr9.hg19:g.135173586delT	ENSP00000224140:p.Arg1888fs	155.0	0.0		174.0	11.0	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Frame_Shift_Del	DEL	ENST00000224140.5	hg19	CCDS6947.1																																																																																			.	.		0.413	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
PLXNC1	10154	hgsc.bcm.edu	37	12	94642030	94642030	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:94642030delA	ENST00000258526.4	+	14	2869	c.2620delA	c.(2620-2622)aaafs	p.K875fs		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	875					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						CAACATTTCCAAAAAAGACAT	0.338																																					p.S873fs		Atlas-INDEL	.											.	PLXNC1	135	.	0			c.2619delC						.						35.0	37.0	37.0					12																	94642030		2203	4300	6503	SO:0001589	frameshift_variant	10154	exon14			.	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.2620delA	chr12.hg19:g.94642030delA	ENSP00000258526:p.Lys875fs	131.0	0.0		148.0	10.0	NM_005761	Q59H25	Frame_Shift_Del	DEL	ENST00000258526.4	hg19	CCDS9049.1																																																																																			.	.		0.338	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
VIPR2	7434	hgsc.bcm.edu	37	7	158902515	158902515	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:158902515delA	ENST00000262178.2	-	3	432	c.247delT	c.(247-249)tacfs	p.Y83fs	VIPR2_ENST00000402066.1_Frame_Shift_Del_p.Y224fs	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	83					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|negative regulation of smooth muscle cell proliferation (GO:0048662)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		GCTTTGCTGTAAAAATTGCTG	0.547																																					p.Y83fs	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-INDEL	.											.	VIPR2	53	.	0			c.248delA						.						110.0	97.0	101.0					7																	158902515		2203	4300	6503	SO:0001589	frameshift_variant	7434	exon3			.	CA449700, X95097	CCDS5950.1	7q36.3	2012-08-10			ENSG00000106018	ENSG00000106018		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12695	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 2"""	601970				7811244	Standard	NM_003382		Approved	VPAC2, VPAC2R	uc003woh.3	P41587	OTTHUMG00000151446	ENST00000262178.2:c.247delT	chr7.hg19:g.158902515delA	ENSP00000262178:p.Tyr83fs	75.0	0.0		145.0	11.0	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Frame_Shift_Del	DEL	ENST00000262178.2	hg19	CCDS5950.1																																																																																			.	.		0.547	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382	
WDR17	116966	hgsc.bcm.edu	37	4	177052791	177052791	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:177052791delT	ENST00000280190.4	+	8	1228	c.1072delT	c.(1072-1074)tttfs	p.F358fs	WDR17_ENST00000393643.2_Frame_Shift_Del_p.F334fs|WDR17_ENST00000507824.2_Frame_Shift_Del_p.F341fs|WDR17_ENST00000508596.1_Frame_Shift_Del_p.F334fs			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	358										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)		GAATCAAGCATTTTCTCTTCC	0.403																																					p.A357fs		Atlas-INDEL	.											.	WDR17	198	.	0			c.1071delA						.						289.0	279.0	282.0					4																	177052791		2203	4300	6503	SO:0001589	frameshift_variant	116966	exon8			.	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.1072delT	chr4.hg19:g.177052791delT	ENSP00000280190:p.Phe358fs	223.0	0.0		173.0	12.0	NM_170710	E7EQX0|Q0QD35	Frame_Shift_Del	DEL	ENST00000280190.4	hg19	CCDS3825.1																																																																																			.	.		0.403	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		
PLEKHG4	25894	hgsc.bcm.edu	37	16	67316441	67316441	+	Frame_Shift_Del	DEL	G	G	-	rs143955884	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:67316441delG	ENST00000360461.5	+	9	3824	c.1289delG	c.(1288-1290)cggfs	p.R430fs	PLEKHG4_ENST00000427155.2_Frame_Shift_Del_p.R430fs|PLEKHG4_ENST00000379344.3_Frame_Shift_Del_p.R430fs|PLEKHG4_ENST00000450733.1_Frame_Shift_Del_p.R349fs	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	430							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		CTATATGACCGGGTGGATGGA	0.582																																					p.R430fs		Atlas-INDEL	.											PLEKHG4,NS,carcinoma,0,1	PLEKHG4	94	.	0			c.1288delC						.						102.0	87.0	92.0					16																	67316441		2198	4300	6498	SO:0001589	frameshift_variant	25894	exon10			.	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24501	protein-coding gene	gene with protein product	"""puratrophin-1"""	609526	"""spinocerebellar ataxia 4"""	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.1289delG	chr16.hg19:g.67316441delG	ENSP00000353646:p.Arg430fs	110.0	0.0		156.0	10.0	NM_001129729	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Frame_Shift_Del	DEL	ENST00000360461.5	hg19	CCDS32466.1																																																																																			.	.		0.582	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432	
FCER1A	2205	hgsc.bcm.edu	37	1	159275825	159275825	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:159275825delC	ENST00000368115.1	+	5	478	c.379delC	c.(379-381)cccfs	p.P127fs	FCER1A_ENST00000368114.1_Frame_Shift_Del_p.P94fs	NM_002001.3	NP_001992.1	P12319	FCERA_HUMAN	Fc fragment of IgE, high affinity I, receptor for; alpha polypeptide	127	Ig-like 2.				activation of JUN kinase activity (GO:0007257)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|leukotriene biosynthetic process (GO:0019370)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of type I hypersensitivity (GO:0001812)|serotonin secretion (GO:0001820)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	IgE receptor activity (GO:0019767)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(19)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_hematologic(112;0.0429)				Benzylpenicilloyl Polylysine(DB00895)|Omalizumab(DB00043)	GGAGGGCCAGCCCCTCTTCCT	0.453																																					p.Q126fs		Atlas-INDEL	.											.	FCER1A	74	.	0			c.378delG						.						92.0	86.0	88.0					1																	159275825		2203	4300	6503	SO:0001589	frameshift_variant	2205	exon5			.	BC015195	CCDS1184.1	1q23	2013-01-11			ENSG00000179639	ENSG00000179639		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3609	protein-coding gene	gene with protein product		147140		FCE1A		8245459	Standard	NM_002001		Approved		uc001ftq.3	P12319	OTTHUMG00000037176	ENST00000368115.1:c.379delC	chr1.hg19:g.159275825delC	ENSP00000357097:p.Pro127fs	123.0	0.0		199.0	12.0	NM_002001		Frame_Shift_Del	DEL	ENST00000368115.1	hg19	CCDS1184.1																																																																																			.	.		0.453	FCER1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090328.2	NM_002001	
RIPK1	8737	hgsc.bcm.edu	37	6	3077159	3077159	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:3077159delT	ENST00000259808.4	+	2	400	c.102delT	c.(100-102)tgtfs	p.C34fs	RIPK1_ENST00000479389.1_Intron|RIPK1_ENST00000380409.2_Frame_Shift_Del_p.C34fs|RIPK1_ENST00000541791.1_Frame_Shift_Del_p.C34fs			Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine kinase 1	34	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|amyloid fibril formation (GO:1990000)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to tumor necrosis factor (GO:0071356)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of ATP:ADP antiporter activity (GO:0070926)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to tumor necrosis factor (GO:0034612)|ripoptosome assembly (GO:0097343)|ripoptosome assembly involved in necroptotic process (GO:1901026)|T cell apoptotic process (GO:0070231)|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)	cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|death domain binding (GO:0070513)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				TGTCTCTGTGTTTCCACAGAA	0.507																																					p.C34fs		Atlas-INDEL	.											.	RIPK1	56	.	0			c.101delG						.						81.0	74.0	76.0					6																	3077159		2203	4300	6503	SO:0001589	frameshift_variant	8737	exon1			.	U25994	CCDS4482.1	6p25.2	2008-02-05			ENSG00000137275	ENSG00000137275			10019	protein-coding gene	gene with protein product		603453				7538908, 8612133	Standard	XM_005249458		Approved	RIP	uc003mux.3	Q13546	OTTHUMG00000014134	ENST00000259808.4:c.102delT	chr6.hg19:g.3077159delT	ENSP00000259808:p.Cys34fs	129.0	0.0		181.0	11.0	NM_003804	A0AV89|B2RAG1|B4E3F9|Q13180|Q59H33	Frame_Shift_Del	DEL	ENST00000259808.4	hg19	CCDS4482.1																																																																																			.	.		0.507	RIPK1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039659.2	NM_003804	
DHTKD1	55526	hgsc.bcm.edu	37	10	12154919	12154919	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:12154919delG	ENST00000263035.4	+	13	2237	c.2175delG	c.(2173-2175)gagfs	p.E725fs		NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	725					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			GTGCGGAAGAGGGGGTGGACG	0.493																																					p.E725fs		Atlas-INDEL	.											.	DHTKD1	104	.	0			c.2174delA						.						162.0	142.0	149.0					10																	12154919		2203	4300	6503	SO:0001589	frameshift_variant	55526	exon13			.	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.2175delG	chr10.hg19:g.12154919delG	ENSP00000263035:p.Glu725fs	111.0	0.0		154.0	12.0	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Frame_Shift_Del	DEL	ENST00000263035.4	hg19	CCDS7087.1																																																																																			.	.		0.493	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706	
CFH	3075	hgsc.bcm.edu	37	1	196706674	196706674	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:196706674delA	ENST00000367429.4	+	17	2906	c.2666delA	c.(2665-2667)gaafs	p.E889fs		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	889	Sushi 15. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						TCTTCACAAGAAAGTTATGCA	0.358																																					p.E889fs		Atlas-INDEL	.											.	CFH	251	.	0			c.2665delG						.						77.0	73.0	74.0					1																	196706674		2203	4300	6503	SO:0001589	frameshift_variant	3075	exon17			.	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2666delA	chr1.hg19:g.196706674delA	ENSP00000356399:p.Glu889fs	104.0	0.0		171.0	11.0	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Frame_Shift_Del	DEL	ENST00000367429.4	hg19	CCDS1385.1																																																																																			.	.		0.358	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186	
LBR	3930	hgsc.bcm.edu	37	1	225607149	225607149	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:225607149delT	ENST00000338179.2	-	5	581	c.456delA	c.(454-456)aaafs	p.K152fs	LBR_ENST00000487054.1_5'Flank|LBR_ENST00000272163.4_Frame_Shift_Del_p.K152fs	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	152					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		ACAAACTGAATTTTTCCTAAA	0.303																																					p.F153fs		Atlas-INDEL	.											.	LBR	54	.	0			c.457delT						.						53.0	51.0	52.0					1																	225607149		2203	4300	6503	SO:0001589	frameshift_variant	3930	exon5			.	L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"""Tudor domain containing"""	6518	protein-coding gene	gene with protein product	"""tudor domain containing 18"""	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.456delA	chr1.hg19:g.225607149delT	ENSP00000339883:p.Lys152fs	80.0	0.0		159.0	10.0	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Frame_Shift_Del	DEL	ENST00000338179.2	hg19	CCDS1545.1																																																																																			.	.		0.303	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296	
C10orf55	414236	hgsc.bcm.edu	37	10	75673438	75673438	+	Intron	DEL	G	G	-	rs549461157	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:75673438delG	ENST00000409178.1	-	3	268				PLAU_ENST00000446342.1_Frame_Shift_Del_p.R184fs|PLAU_ENST00000372762.4_Frame_Shift_Del_p.R165fs|C10orf55_ENST00000412307.2_Intron|PLAU_ENST00000494287.1_3'UTR|PLAU_ENST00000372764.3_Frame_Shift_Del_p.R201fs	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55											endometrium(1)	1	Prostate(51;0.0112)					AGGAGGCACCGGGGGGGCTCT	0.587																																					p.R201fs		Atlas-INDEL	.											.,1	PLAU	47	.	0			c.601delC						.		,,	17,4245		5,7,2119					,,	2.0	0.9			66	27,8227		11,5,4111	no	frameshift,frameshift,intron	PLAU,C10orf55	NM_002658.3,NM_001145031.1,NM_001001791.2	,,	16,12,6230	A1A1,A1R,RR		0.3271,0.3989,0.3516	,,	,,		44,12472				SO:0001627	intron_variant	5328	exon7			.		CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.73-605C>-	chr10.hg19:g.75673438delG		189.0	0.0		264.0	16.0	NM_002658	Q3KRG4|Q8NAK4	Frame_Shift_Del	DEL	ENST00000409178.1	hg19	CCDS53541.1																																																																																			.	.		0.587	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791	
DMXL1	1657	hgsc.bcm.edu	37	5	118483090	118483090	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:118483090delT	ENST00000311085.8	+	17	2916	c.2836delT	c.(2836-2838)tttfs	p.F946fs	DMXL1_ENST00000539542.1_Frame_Shift_Del_p.F946fs	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	946										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GTTGACTCTGTTTTCAGAAAT	0.368																																					p.L945fs		Atlas-INDEL	.											.	DMXL1	268	.	0			c.2835delG						.						61.0	64.0	63.0					5																	118483090		2202	4300	6502	SO:0001589	frameshift_variant	1657	exon17			.	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.2836delT	chr5.hg19:g.118483090delT	ENSP00000309690:p.Phe946fs	167.0	0.0		216.0	14.0	NM_005509		Frame_Shift_Del	DEL	ENST00000311085.8	hg19	CCDS4125.1																																																																																			.	.		0.368	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
TMEM108	66000	hgsc.bcm.edu	37	3	133098904	133098904	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:133098904delC	ENST00000321871.6	+	4	559	c.349delC	c.(349-351)cccfs	p.P117fs	TMEM108_ENST00000508711.1_Intron|TMEM108_ENST00000515826.1_Frame_Shift_Del_p.P117fs|TMEM108_ENST00000393130.3_Frame_Shift_Del_p.P117fs	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	117	Pro-rich.					integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						GTCCACAGGGCCCGCTCCAGC	0.672																																					p.G116fs		Atlas-INDEL	.											.	TMEM108	67	.	0			c.348delG						.						47.0	41.0	43.0					3																	133098904		2201	4298	6499	SO:0001589	frameshift_variant	66000	exon4			.	AL136578	CCDS33858.1, CCDS75012.1	3q22.1	2014-04-07			ENSG00000144868	ENSG00000144868			28451	protein-coding gene	gene with protein product	"""cancer/testis antigen 124"""					11214970	Standard	XM_005247726		Approved	MGC3040, CT124	uc003epi.3	Q6UXF1	OTTHUMG00000159685	ENST00000321871.6:c.349delC	chr3.hg19:g.133098904delC	ENSP00000324651:p.Pro117fs	153.0	0.0		181.0	11.0	NM_023943	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Frame_Shift_Del	DEL	ENST00000321871.6	hg19	CCDS33858.1																																																																																			.	.		0.672	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943	
DNAJC2	27000	hgsc.bcm.edu	37	7	102953447	102953447	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:102953447delT	ENST00000379263.3	-	16	1988	c.1738delA	c.(1738-1740)atafs	p.I580fs	PMPCB_ENST00000249269.4_3'UTR|PMPCB_ENST00000420236.2_Intron|DNAJC2_ENST00000249270.7_Frame_Shift_Del_p.I527fs	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	580	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)			endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						GCTTCTGCTATTTTTTCCCAT	0.398																																					p.I580fs		Atlas-INDEL	.											.	DNAJC2	46	.	0			c.1739delT						.						267.0	247.0	253.0					7																	102953447		1852	4090	5942	SO:0001589	frameshift_variant	27000	exon16			.	X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"""Heat shock proteins / DNAJ (HSP40)"""	13192	protein-coding gene	gene with protein product		605502	"""zuotin related factor 1"""	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.1738delA	chr7.hg19:g.102953447delT	ENSP00000368565:p.Ile580fs	152.0	0.0		176.0	12.0	NM_014377	A4VCI0|Q9BVX1	Frame_Shift_Del	DEL	ENST00000379263.3	hg19	CCDS43628.1																																																																																			.	.		0.398	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1		
HDC	3067	hgsc.bcm.edu	37	15	50549687	50549687	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:50549687delT	ENST00000267845.3	-	4	778	c.376delA	c.(376-378)atgfs	p.M126fs	HDC_ENST00000543581.1_Frame_Shift_Del_p.M126fs	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		AGTCCCAGCATTTTTGCCAAC	0.577																																					p.M126fs	GBM(95;1627 1936 6910 9570)	Atlas-INDEL	.											HDC,NS,carcinoma,0,1	HDC	86	.	0			c.377delT						.						139.0	117.0	124.0					15																	50549687		2196	4295	6491	SO:0001589	frameshift_variant	3067	exon4			.		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.376delA	chr15.hg19:g.50549687delT	ENSP00000267845:p.Met126fs	108.0	0.0		164.0	16.0	NM_002112		Frame_Shift_Del	DEL	ENST00000267845.3	hg19	CCDS10134.1																																																																																			.	.		0.577	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1		
HTR6	3362	hgsc.bcm.edu	37	1	19992674	19992674	+	Frame_Shift_Del	DEL	C	C	-	rs201579153		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:19992674delC	ENST00000289753.1	+	1	895	c.428delC	c.(427-429)gccfs	p.A143fs		NM_000871.1	NP_000862.1	P50406	5HT6R_HUMAN	5-hydroxytryptamine (serotonin) receptor 6, G protein-coupled	143					brain development (GO:0007420)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|long-term synaptic potentiation (GO:0060291)|negative regulation of acetylcholine secretion, neurotransmission (GO:0014058)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|synaptic transmission (GO:0007268)	cilium (GO:0005929)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)|serotonin receptor activity (GO:0004993)			endometrium(1)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;5.81e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00117)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Mianserin(DB06148)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Quetiapine(DB01224)|Sertindole(DB06144)|Ziprasidone(DB00246)	CCCCTGCGTGCCCTGGCCCTA	0.701																																					p.A143fs	Esophageal Squamous(168;1879 2619 6848 21062)	Atlas-INDEL	.											.	HTR6	38	.	0			c.427delG						.						47.0	42.0	43.0					1																	19992674		2203	4300	6503	SO:0001589	frameshift_variant	3362	exon1			.	L41147	CCDS197.1	1p36-p35	2012-08-08	2012-02-03		ENSG00000158748	ENSG00000158748		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5301	protein-coding gene	gene with protein product		601109	"""5-hydroxytryptamine (serotonin) receptor 6"""			8522988	Standard	NM_000871		Approved	5-HT6, 5-HT6R	uc001bcl.3	P50406	OTTHUMG00000002713	ENST00000289753.1:c.428delC	chr1.hg19:g.19992674delC	ENSP00000289753:p.Ala143fs	185.0	0.0		192.0	13.0	NM_000871	Q13640|Q5TGZ1	Frame_Shift_Del	DEL	ENST00000289753.1	hg19	CCDS197.1																																																																																			.	.		0.701	HTR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007704.1	NM_000871	
ACTR8	93973	hgsc.bcm.edu	37	3	53902877	53902877	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:53902877delG	ENST00000335754.3	-	13	1844	c.1744delC	c.(1744-1746)cggfs	p.R582fs	ACTR8_ENST00000488802.1_5'UTR|ACTR8_ENST00000231909.7_Frame_Shift_Del_p.R287fs|ACTR8_ENST00000482349.1_Frame_Shift_Del_p.R471fs	NM_022899.4	NP_075050.3	Q9H981	ARP8_HUMAN	ARP8 actin-related protein 8 homolog (yeast)	582					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	ATP binding (GO:0005524)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		GCAATCAGCCGGGGGTCCATG	0.478																																					p.R582fs		Atlas-INDEL	.											.	ACTR8	56	.	0			c.1745delG						.						70.0	65.0	67.0					3																	53902877		2203	4300	6503	SO:0001589	frameshift_variant	93973	exon13			.		CCDS2875.1	3p21.31	2011-07-06	2001-11-28		ENSG00000113812	ENSG00000113812		"""INO80 complex subunits"""	14672	protein-coding gene	gene with protein product	"""INO80 complex subunit N"""		"""ARP8 (actin-related protein 8, yeast) homolog"""			18163988, 16230350	Standard	NM_022899		Approved	INO80N	uc003dhd.3	Q9H981	OTTHUMG00000158279	ENST00000335754.3:c.1744delC	chr3.hg19:g.53902877delG	ENSP00000336842:p.Arg582fs	123.0	0.0		163.0	10.0	NM_022899	B3KSW7|Q8N566|Q9H663	Frame_Shift_Del	DEL	ENST00000335754.3	hg19	CCDS2875.1																																																																																			.	.		0.478	ACTR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350562.2	NM_022899	
ANKRD20A2	441430	hgsc.bcm.edu	37	9	42380200	42380200	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:42380200delA	ENST00000377601.2	+	6	899	c.787delA	c.(787-789)aaafs	p.K263fs	ANKRD20A2_ENST00000477139.2_3'UTR|RNU6-1269P_ENST00000391139.1_RNA	NM_001012421.1	NP_001012421.1	Q5SQ80	A20A2_HUMAN	ankyrin repeat domain 20 family, member A2	263										large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	4						TAAAAAGGAGAAATCAGGTAA	0.264																																					p.E262fs		Atlas-INDEL	.											.	.	.	.	0			c.786delG						.						14.0	8.0	13.0					9																	42380200		979	225	1204	SO:0001589	frameshift_variant	441425	exon6			.		CCDS35028.1	9p12	2013-01-10			ENSG00000183148	ENSG00000183148		"""Ankyrin repeat domain containing"""	31979	protein-coding gene	gene with protein product							Standard	XM_005272519		Approved			Q5SQ80	OTTHUMG00000058641	ENST00000377601.2:c.787delA	chr9.hg19:g.42380200delA	ENSP00000366826:p.Lys263fs	129.0	0.0		156.0	10.0	NM_001012419		Frame_Shift_Del	DEL	ENST00000377601.2	hg19	CCDS35028.1																																																																																			.	.		0.264	ANKRD20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129794.1	NM_001012421	
PRRC2C	23215	hgsc.bcm.edu	37	1	171527040	171527040	+	Frame_Shift_Del	DEL	C	C	-	rs553054787		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:171527040delC	ENST00000338920.4	+	19	6020	c.5783delC	c.(5782-5784)gccfs	p.A1928fs	PRRC2C_ENST00000426496.2_Frame_Shift_Del_p.A1928fs|PRRC2C_ENST00000367742.3_Frame_Shift_Del_p.A1930fs|PRRC2C_ENST00000392078.3_Frame_Shift_Del_p.A1930fs	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1928	Ala-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										gccccacctgccccagcccAG	0.597																																					p.A1928fs		Atlas-INDEL	.											.	.	.	.	0			c.5782delG						.						73.0	62.0	66.0					1																	171527040		2177	4257	6434	SO:0001589	frameshift_variant	23215	exon19			.	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.5783delC	chr1.hg19:g.171527040delC	ENSP00000343629:p.Ala1928fs	186.0	0.0		279.0	19.0	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Frame_Shift_Del	DEL	ENST00000338920.4	hg19	CCDS1296.2																																																																																			.	.		0.597	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
FOXI1	2299	hgsc.bcm.edu	37	5	169533034	169533034	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:169533034delC	ENST00000306268.6	+	1	134	c.73delC	c.(73-75)cccfs	p.P26fs	FOXI1_ENST00000449804.2_Frame_Shift_Del_p.P26fs			Q12951	FOXI1_HUMAN	forkhead box I1	26	Pro-rich.				embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGGCCAGGAGCCCCCCGAGAT	0.697									Pendred syndrome																												p.E24fs		Atlas-INDEL	.											.	FOXI1	70	.	0			c.72delG						.						24.0	28.0	26.0					5																	169533034		2203	4298	6501	SO:0001589	frameshift_variant	2299	exon1	Familial Cancer Database	Goiter-Deafness syndrome	.	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"""Forkhead boxes"""	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.73delC	chr5.hg19:g.169533034delC	ENSP00000304286:p.Pro26fs	296.0	0.0		294.0	18.0	NM_012188	Q14518|Q66SR7|Q8N6L8	Frame_Shift_Del	DEL	ENST00000306268.6	hg19	CCDS4372.1																																																																																			.	.		0.697	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188	
ZNF8	7554	hgsc.bcm.edu	37	19	58806805	58806805	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:58806805delA	ENST00000196548.5	+	4	1762	c.1631delA	c.(1630-1632)caafs	p.Q544fs	ZNF8_ENST00000608843.1_Frame_Shift_Del_p.Q544fs|AC010642.1_ENST00000591325.1_3'UTR			P17098	ZNF8_HUMAN	zinc finger protein 8	544					BMP signaling pathway (GO:0030509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	19		all_cancers(17;6.46e-05)|Lung NSC(17;0.0233)|all_neural(62;0.0381)|all_epithelial(17;0.0427)|all_lung(17;0.057)|Ovarian(87;0.17)|Colorectal(82;0.227)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.00619)		TTTGACATCCAAAAAATCATG	0.507																																					p.Q544fs		Atlas-INDEL	.											.	ZNF8	60	.	0			c.1630delC						.						43.0	46.0	45.0					19																	58806805		2201	4298	6499	SO:0001589	frameshift_variant	7554	exon4			.	M29581	CCDS12974.1	19q13.43	2013-01-08	2006-05-09					"""Zinc fingers, C2H2-type"", ""-"""	13154	protein-coding gene	gene with protein product		194532	"""zinc finger protein 8 (clone HF.18)"""			2106481	Standard	NM_021089		Approved	HF.18, Zfp128	uc002qry.1	P17098		ENST00000196548.5:c.1631delA	chr19.hg19:g.58806805delA	ENSP00000196548:p.Gln544fs	90.0	0.0		117.0	10.0	NM_021089	Q6PI99	Frame_Shift_Del	DEL	ENST00000196548.5	hg19	CCDS12974.1																																																																																			.	.		0.507	ZNF8-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000459135.1	NM_021089	
ZNF813	126017	hgsc.bcm.edu	37	19	53995078	53995078	+	Frame_Shift_Del	DEL	T	T	-	rs111582892	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:53995078delT	ENST00000396403.4	+	4	1720	c.1592delT	c.(1591-1593)gttfs	p.V531fs	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	531					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(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		TGTGGCAAGGTTTTTAATCGA	0.363																																					p.V531fs		Atlas-INDEL	.											.	ZNF813	81	.	0			c.1591delG						.						50.0	54.0	52.0					19																	53995078		2198	4295	6493	SO:0001589	frameshift_variant	126017	exon4			.	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.1592delT	chr19.hg19:g.53995078delT	ENSP00000379684:p.Val531fs	108.0	0.0		164.0	11.0	NM_001004301		Frame_Shift_Del	DEL	ENST00000396403.4	hg19	CCDS46172.1																																																																																			.	.		0.363	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
GPCPD1	56261	hgsc.bcm.edu	37	20	5560674	5560674	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:5560674delT	ENST00000379019.4	-	7	665	c.453delA	c.(451-453)aaafs	p.K151fs	GPCPD1_ENST00000481038.1_5'UTR	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	151					glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)	glycerophosphocholine phosphodiesterase activity (GO:0047389)|starch binding (GO:2001070)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)	16						ATTTTTTTAATTTTTTCTTGG	0.338																																					p.L152X		Atlas-INDEL	.											.	GPCPD1	52	.	0			c.454delT						.						53.0	55.0	54.0					20																	5560674		2203	4296	6499	SO:0001589	frameshift_variant	56261	exon7			.		CCDS13090.1	20p12.3	2011-01-25			ENSG00000125772	ENSG00000125772			26957	protein-coding gene	gene with protein product		614124				10718198, 20576599	Standard	NM_019593		Approved	KIAA1434, GDE5, GDPD6	uc002wme.4	Q9NPB8	OTTHUMG00000031806	ENST00000379019.4:c.453delA	chr20.hg19:g.5560674delT	ENSP00000368305:p.Lys151fs	104.0	0.0		202.0	13.0	NM_019593	D3DW06|Q9BQL8|Q9NUX0	Frame_Shift_Del	DEL	ENST00000379019.4	hg19	CCDS13090.1																																																																																			.	.		0.338	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077869.1	NM_019593	
CYP2B6	1555	hgsc.bcm.edu	37	19	41510031	41510031	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:41510031delA	ENST00000324071.4	+	2	304	c.297delA	c.(295-297)ggafs	p.G99fs	CYP2B6_ENST00000593831.1_Frame_Shift_Del_p.G23fs|CYP2B6_ENST00000598834.1_3'UTR|CYP2B6_ENST00000330446.5_Frame_Shift_Del_p.G59fs	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	99			G -> E (in allele CYP2B6*12; dbSNP:rs36060847). {ECO:0000269|PubMed:15190123}.		cellular ketone metabolic process (GO:0042180)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			NS(1)|breast(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(20;0.00322)		Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Antipyrine(DB01435)|Artemether(DB06697)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Brompheniramine(DB00835)|Bupropion(DB01156)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Citalopram(DB00215)|Clobazam(DB00349)|Clofibrate(DB00636)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Doxorubicin(DB00997)|Efavirenz(DB00625)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erythromycin(DB00199)|Estrone(DB00655)|Ethanol(DB00898)|Ethylmorphine(DB01466)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosphenytoin(DB01320)|Halothane(DB01159)|Ifosfamide(DB01181)|Imipramine(DB00458)|Irinotecan(DB00762)|Isoflurane(DB00753)|Itraconazole(DB01167)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lidocaine(DB00281)|Loperamide(DB00836)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Malathion(DB00772)|Memantine(DB01043)|Methadone(DB00333)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyltestosterone(DB06710)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitric Oxide(DB00435)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Paroxetine(DB00715)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Prasugrel(DB06209)|Primidone(DB00794)|Promethazine(DB01069)|Propofol(DB00818)|Quinidine(DB00908)|Raloxifene(DB00481)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Ropivacaine(DB00296)|Roxithromycin(DB00778)|Selegiline(DB01037)|Sertraline(DB01104)|Sevoflurane(DB01236)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Temazepam(DB00231)|Testosterone(DB00624)|Thiotepa(DB04572)|Ticlopidine(DB00208)|Tramadol(DB00193)|Tretinoin(DB00755)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)	CTGGCCGGGGAAAAATCGCCA	0.622																																					p.G99fs		Atlas-INDEL	.											CYP2B6,NS,malignant_melanoma,0,1	CYP2B6	79	.	0			c.296delG						.						78.0	79.0	79.0					19																	41510031		2203	4300	6503	SO:0001589	frameshift_variant	1555	exon2			.	AF182277	CCDS12570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000197408	ENSG00000197408		"""Cytochrome P450s"""	2615	protein-coding gene	gene with protein product		123930	"""cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6"", ""cytochrome P450, family 2, subfamily B"", ""cytochrome P450, subfamily IIB (phenobarbital-inducible)"""	CYP2B		7668294, 15128046	Standard	NM_000767		Approved	CPB6, CYPIIB6	uc002opr.1	P20813	OTTHUMG00000182714	ENST00000324071.4:c.297delA	chr19.hg19:g.41510031delA	ENSP00000324648:p.Gly99fs	120.0	0.0		147.0	10.0	NM_000767	B4DWP3|Q2V565|Q9UK46	Frame_Shift_Del	DEL	ENST00000324071.4	hg19	CCDS12570.1																																																																																			.	.		0.622	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767	
FOXN4	121643	hgsc.bcm.edu	37	12	109725737	109725737	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:109725737delC	ENST00000299162.5	-	5	484	c.380delG	c.(379-381)ggcfs	p.G127fs	FOXN4_ENST00000355216.1_Intron	NM_213596.2	NP_998761.2	Q96NZ1	FOXN4_HUMAN	forkhead box N4	127	Pro-rich.				amacrine cell differentiation (GO:0035881)|atrioventricular canal development (GO:0036302)|heart looping (GO:0001947)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of heart contraction (GO:0008016)|regulation of transcription, DNA-templated (GO:0006355)|retina layer formation (GO:0010842)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(5)|lung(9)|ovary(2)	16						TGAGGGCTGGCCCCCCACGGG	0.677																																					p.G127fs		Atlas-INDEL	.											.	FOXN4	74	.	0			c.381delC						.						12.0	19.0	17.0					12																	109725737		690	1590	2280	SO:0001589	frameshift_variant	121643	exon5			.	AF425596	CCDS9126.2	12q24.12	2008-02-05			ENSG00000139445	ENSG00000139445		"""Forkhead boxes"""	21399	protein-coding gene	gene with protein product		609429					Standard	NM_213596		Approved		uc001toe.4	Q96NZ1	OTTHUMG00000152868	ENST00000299162.5:c.380delG	chr12.hg19:g.109725737delC	ENSP00000299162:p.Gly127fs	139.0	0.0		182.0	11.0	NM_213596	Q6ZMR4|Q96NZ0	Frame_Shift_Del	DEL	ENST00000299162.5	hg19	CCDS9126.2																																																																																			.	.		0.677	FOXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328306.1	XM_062735	
TNPO2	30000	hgsc.bcm.edu	37	19	12825735	12825735	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:12825735delG	ENST00000592287.1	-	9	898	c.790delC	c.(790-792)cagfs	p.Q264fs	TNPO2_ENST00000425528.1_Frame_Shift_Del_p.Q264fs|TNPO2_ENST00000356861.5_Frame_Shift_Del_p.Q264fs|TNPO2_ENST00000589956.1_Intron|TNPO2_ENST00000588216.1_Frame_Shift_Del_p.Q264fs|TNPO2_ENST00000441499.1_Frame_Shift_Del_p.Q264fs|TNPO2_ENST00000450764.2_Frame_Shift_Del_p.Q264fs	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	264					intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						TCATGGTCCTGGGTCCTCTGC	0.662																																					p.Q264fs		Atlas-INDEL	.											.	TNPO2	108	.	0			c.791delA						.						115.0	121.0	119.0					19																	12825735		2121	4228	6349	SO:0001589	frameshift_variant	30000	exon9			.	AF019039	CCDS45991.1, CCDS45992.1	19p13.13	2009-01-12	2009-01-12			ENSG00000105576		"""Importins"""	19998	protein-coding gene	gene with protein product	"""importin 3"", ""karyopherin beta 2b"""	603002				9298975, 12384575	Standard	NM_013433		Approved	IPO3, KPNB2B, FLJ12155, TRN2	uc002muo.3	O14787		ENST00000592287.1:c.790delC	chr19.hg19:g.12825735delG	ENSP00000468434:p.Gln264fs	152.0	0.0		148.0	10.0	NM_013433	O14655|Q6IN77	Frame_Shift_Del	DEL	ENST00000592287.1	hg19	CCDS45991.1																																																																																			.	.		0.662	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433	
LETM1	3954	hgsc.bcm.edu	37	4	1818594	1818594	+	Frame_Shift_Del	DEL	C	C	-	rs9328763	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:1818594delC	ENST00000302787.2	-	12	2087	c.1791delG	c.(1789-1791)aagfs	p.K597fs		NM_012318.2	NP_036450.1	O95202	LETM1_HUMAN	leucine zipper-EF-hand containing transmembrane protein 1	597					cristae formation (GO:0042407)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(2)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	13			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)			CTTCCACGTACTTTTCTTCAC	0.418																																					p.Y598fs		Atlas-INDEL	.											.	LETM1	48	.	0			c.1792delT						.						137.0	122.0	127.0					4																	1818594		2203	4300	6503	SO:0001589	frameshift_variant	3954	exon12			.	AF061025	CCDS3355.1	4p16.3	2013-01-10			ENSG00000168924	ENSG00000168924		"""EF-hand domain containing"""	6556	protein-coding gene	gene with protein product	"""Mdm38 homolog (yeast)"""	604407				10486213	Standard	NM_012318		Approved		uc003gdv.3	O95202	OTTHUMG00000121149	ENST00000302787.2:c.1791delG	chr4.hg19:g.1818594delC	ENSP00000305653:p.Lys597fs	258.0	0.0		316.0	20.0	NM_012318	B4DED2|Q9UF65	Frame_Shift_Del	DEL	ENST00000302787.2	hg19	CCDS3355.1																																																																																			.	.		0.418	LETM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241634.1		
DTX3L	151636	hgsc.bcm.edu	37	3	122284754	122284754	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:122284754delA	ENST00000296161.4	+	2	425	c.236delA	c.(235-237)gaafs	p.E79fs	PARP9_ENST00000360356.2_5'Flank|PARP9_ENST00000492382.1_5'Flank|DTX3L_ENST00000383661.3_Frame_Shift_Del_p.E79fs|PARP9_ENST00000462315.1_5'Flank|PARP9_ENST00000477522.2_5'Flank|PARP9_ENST00000471785.1_5'Flank	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	79					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone monoubiquitination (GO:0010390)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0459)		CTTGTTGACGAAAAACCTGTG	0.398																																					p.E79fs		Atlas-INDEL	.											DTX3L,colon,carcinoma,0,2	DTX3L	59	.	0			c.235delG						.						116.0	109.0	111.0					3																	122284754		2203	4300	6503	SO:0001589	frameshift_variant	151636	exon2			.		CCDS3015.1	3q21.1	2014-01-28	2014-01-28		ENSG00000163840	ENSG00000163840		"""RING-type (C3HC4) zinc fingers"""	30323	protein-coding gene	gene with protein product	"""rhysin 2"""	613143	"""deltex 3-like (Drosophila)"""			12670957, 22411408	Standard	NM_138287		Approved	BBAP	uc003efk.3	Q8TDB6	OTTHUMG00000159524	ENST00000296161.4:c.236delA	chr3.hg19:g.122284754delA	ENSP00000296161:p.Glu79fs	135.0	0.0		149.0	13.0	NM_138287	B3KWH6|Q53ZZ3|Q5MJP7	Frame_Shift_Del	DEL	ENST00000296161.4	hg19	CCDS3015.1																																																																																			.	.		0.398	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287	
TAS2R13	50838	hgsc.bcm.edu	37	12	11061232	11061232	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:11061232delG	ENST00000390677.2	-	1	929	c.666delC	c.(664-666)cccfs	p.P222fs	PRR4_ENST00000536668.1_Intron	NM_023920.2	NP_076409.1	Q9NYV9	T2R13_HUMAN	taste receptor, type 2, member 13	222					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						CCTTGGTCCTGGGGTCTCTGT	0.393																																					p.R223fs		Atlas-INDEL	.											.	TAS2R13	29	.	0			c.667delA						.						98.0	99.0	99.0					12																	11061232		2203	4300	6503	SO:0001589	frameshift_variant	50838	exon1			.	AF227137	CCDS8635.1	12p13	2012-08-22			ENSG00000212128	ENSG00000212128		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14919	protein-coding gene	gene with protein product		604792				10761934, 10766242	Standard	NM_023920		Approved	T2R13, TRB3	uc001qzg.1	Q9NYV9		ENST00000390677.2:c.666delC	chr12.hg19:g.11061232delG	ENSP00000375095:p.Pro222fs	171.0	0.0		216.0	14.0	NM_023920	Q4G0I5|Q502V8|Q645X2	Frame_Shift_Del	DEL	ENST00000390677.2	hg19	CCDS8635.1																																																																																			.	.		0.393	TAS2R13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400229.1		
LAMA3	3909	hgsc.bcm.edu	37	18	21425024	21425024	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:21425024delA	ENST00000313654.9	+	30	3896	c.3655delA	c.(3655-3657)aaafs	p.K1220fs	LAMA3_ENST00000399516.3_Frame_Shift_Del_p.K1220fs	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1220	Domain IV 1 (domain IV B).				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)					AATACTTCACAAAAAATCCAT	0.413																																					p.H1218fs		Atlas-INDEL	.											.	LAMA3	397	.	0			c.3654delC						.						141.0	132.0	135.0					18																	21425024		1886	4123	6009	SO:0001589	frameshift_variant	3909	exon30			.	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.3655delA	chr18.hg19:g.21425024delA	ENSP00000324532:p.Lys1220fs	126.0	0.0		166.0	10.0	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Frame_Shift_Del	DEL	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.		0.413	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
VPS13D	55187	hgsc.bcm.edu	37	1	12439636	12439636	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:12439636delG	ENST00000358136.3	+	57	11306	c.11176delG	c.(11176-11178)gggfs	p.G3726fs	VPS13D_ENST00000356315.4_Frame_Shift_Del_p.G3701fs|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)		TGGGTTACATGGGTTGGTCGT	0.478																																					p.H3725fs		Atlas-INDEL	.											.	VPS13D	316	.	0			c.11175delT						.						115.0	97.0	103.0					1																	12439636		2203	4300	6503	SO:0001589	frameshift_variant	55187	exon57			.	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.11176delG	chr1.hg19:g.12439636delG	ENSP00000350854:p.Gly3726fs	133.0	0.0		155.0	10.0	NM_015378		Frame_Shift_Del	DEL	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.		0.478	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
SELENBP1	8991	hgsc.bcm.edu	37	1	151341939	151341939	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:151341939delG	ENST00000368868.5	-	3	244	c.153delC	c.(151-153)cccfs	p.P51fs	SELENBP1_ENST00000435071.1_5'UTR|SELENBP1_ENST00000473693.1_5'UTR|SELENBP1_ENST00000426705.2_Frame_Shift_Del_p.P93fs|SELENBP1_ENST00000447402.3_Frame_Shift_Del_p.P51fs	NM_003944.3	NP_003935.2	Q13228	SBP1_HUMAN	selenium binding protein 1	51					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)			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)			GGGGAGACTTGGGGTCAACAT	0.607																																					p.K94fs		Atlas-INDEL	.											.	SELENBP1	44	.	0			c.280delA						.						43.0	39.0	40.0					1																	151341939		2203	4300	6503	SO:0001589	frameshift_variant	8991	exon3			.	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.153delC	chr1.hg19:g.151341939delG	ENSP00000357861:p.Pro51fs	102.0	0.0		214.0	13.0	NM_001258289	A6NML9|A6PVW9|B2RDR3|B4DKP6|B4E1F3|Q49AQ8|Q96GX7	Frame_Shift_Del	DEL	ENST00000368868.5	hg19	CCDS995.1																																																																																			.	.		0.607	SELENBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034904.4		
STOML1	9399	hgsc.bcm.edu	37	15	74284520	74284520	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:74284520delA	ENST00000316900.5	-	1	169	c.45delT	c.(43-45)tttfs	p.F15fs	PML_ENST00000395135.3_5'Flank|STOML1_ENST00000316911.6_Frame_Shift_Del_p.F15fs|PML_ENST00000563500.1_5'Flank|STOML1_ENST00000564777.1_Frame_Shift_Del_p.F15fs|PML_ENST00000268058.3_5'Flank|PML_ENST00000565898.1_5'Flank|STOML1_ENST00000359750.4_Frame_Shift_Del_p.F15fs|STOML1_ENST00000561656.1_Intron|PML_ENST00000435786.2_5'Flank|PML_ENST00000436891.3_5'Flank|PML_ENST00000395132.2_5'Flank|PML_ENST00000564428.1_5'Flank|PML_ENST00000569965.1_5'Flank|PML_ENST00000354026.6_5'Flank|STOML1_ENST00000541638.1_5'UTR|PML_ENST00000268059.6_5'Flank|PML_ENST00000567543.1_5'Flank|PML_ENST00000359928.4_5'Flank|PML_ENST00000569477.1_5'Flank	NM_001256672.1|NM_001256675.1|NM_001256677.1|NM_004809.4	NP_001243601.1|NP_001243604.1|NP_001243606.1|NP_004800.2	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	15						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						GGAAGCGGTCAAAATCACCCA	0.711																																					p.D16fs		Atlas-INDEL	.											.	STOML1	22	.	0			c.46delG						.						22.0	27.0	25.0					15																	74284520		2191	4290	6481	SO:0001589	frameshift_variant	9399	exon1			.	Y16522	CCDS10254.1, CCDS58381.1, CCDS58382.1, CCDS58383.1, CCDS58384.1, CCDS58385.1	15q24-q25	2008-07-18			ENSG00000067221	ENSG00000067221			14560	protein-coding gene	gene with protein product	"""stomatin-like 1"", ""stomatin (EBP72)-like 1"""	608326				9931417	Standard	NM_004809		Approved	hUNC-24, SLP-1, STORP, FLJ36370	uc002awe.4	Q9UBI4	OTTHUMG00000137608	ENST00000316900.5:c.45delT	chr15.hg19:g.74284520delA	ENSP00000319323:p.Phe15fs	188.0	0.0		155.0	11.0	NM_004809	B3KQN0|B4DUU5|B4DXM9|E7ESC0|H3BRP3|O95675|Q4PNR4|Q6FGL8|Q8WYI7|Q9UMB9|Q9UMC0|Q9Y6H9	Frame_Shift_Del	DEL	ENST00000316900.5	hg19	CCDS10254.1																																																																																			.	.		0.711	STOML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269022.1	NM_004809	
ERICH6	131831	hgsc.bcm.edu	37	3	150421477	150421477	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:150421477delG	ENST00000295910.6	-	1	261	c.209delC	c.(208-210)cctfs	p.P70fs	RP11-103G8.2_ENST00000471093.1_RNA|RP11-103G8.2_ENST00000475393.1_RNA|FAM194A_ENST00000491361.1_Intron	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						GAACGTCTCAGGGGCCTCCAA	0.622																																					p.P70fs		Atlas-INDEL	.											.	FAM194A	91	.	0			c.210delT						.						235.0	183.0	201.0					3																	150421477		2203	4300	6503	SO:0001589	frameshift_variant	131831	exon1			.																												ENST00000295910.6:c.209delC	chr3.hg19:g.150421477delG	ENSP00000295910:p.Pro70fs	175.0	0.0		183.0	11.0	NM_152394		Frame_Shift_Del	DEL	ENST00000295910.6	hg19	CCDS3151.2																																																																																			.	.		0.622	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1		
FKBP5	2289	hgsc.bcm.edu	37	6	35587912	35587912	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:35587912delA	ENST00000539068.1	-	4	592	c.390delT	c.(388-390)tttfs	p.F130fs	FKBP5_ENST00000357266.4_Frame_Shift_Del_p.F130fs|FKBP5_ENST00000536438.1_Frame_Shift_Del_p.F130fs|FKBP5_ENST00000542713.1_Frame_Shift_Del_p.F130fs|FKBP5_ENST00000540787.1_Intron	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	130	PPIase FKBP-type 1. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						TACTTGCCTCAAAAAAGAGAG	0.443																																					p.E131fs		Atlas-INDEL	.											FKBP5_ENST00000542713,NS,carcinoma,0,2	FKBP5	64	.	0			c.391delG						.						130.0	112.0	118.0					6																	35587912		2203	4300	6503	SO:0001589	frameshift_variant	2289	exon5			.	U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060		"""Tetratricopeptide (TTC) repeat domain containing"""	3721	protein-coding gene	gene with protein product		602623	"""FK506-binding protein 5"""			9001212	Standard	NM_004117		Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000539068.1:c.390delT	chr6.hg19:g.35587912delA	ENSP00000441205:p.Phe130fs	105.0	0.0		139.0	11.0	NM_001145775	F5H7R1|Q59EB8|Q5TGM6	Frame_Shift_Del	DEL	ENST00000539068.1	hg19	CCDS4808.1																																																																																			.	.		0.443	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2		
PCED1B	91523	hgsc.bcm.edu	37	12	47471280	47471280	+	5'Flank	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:47471280delC	ENST00000546455.1	+	0	0				AMIGO2_ENST00000550413.1_Frame_Shift_Del_p.G502fs|AMIGO2_ENST00000429635.1_Frame_Shift_Del_p.G502fs|AMIGO2_ENST00000266581.4_Frame_Shift_Del_p.G502fs|AMIGO2_ENST00000321382.3_Frame_Shift_Del_p.G502fs			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B								hydrolase activity (GO:0016787)										AGTCAGATTTCCCCCTCGTGG	0.463																																					p.K503fs		Atlas-INDEL	.											.	AMIGO2	50	.	0			c.1507delA						.						70.0	67.0	68.0					12																	47471280		2203	4300	6503	SO:0001631	upstream_gene_variant	347902	exon2			.	BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"""family with sequence similarity 113, member B"""	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617		chr12.hg19:g.47471280delC	Exception_encountered	133.0	0.0		173.0	11.0	NM_181847	Q96B20	Frame_Shift_Del	DEL	ENST00000546455.1	hg19	CCDS8752.1																																																																																			.	.		0.463	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371	
STEAP1B	256227	hgsc.bcm.edu	37	7	22533027	22533027	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:22533027delA	ENST00000406890.2	-	3	550	c.456delT	c.(454-456)tttfs	p.F152fs	STEAP1B_ENST00000404369.4_Frame_Shift_Del_p.F171fs	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B	152						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(2)	4						GCAGTACAGCAAAAAACAAAC	0.388																																					p.A172fs		Atlas-INDEL	.											.	STEAP1B	22	.	0			c.514delG						.						204.0	166.0	178.0					7																	22533027		692	1591	2283	SO:0001589	frameshift_variant	256227	exon3			.		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.456delT	chr7.hg19:g.22533027delA	ENSP00000385239:p.Phe152fs	177.0	0.0		225.0	17.0	NM_001164460	B5MCI2	Frame_Shift_Del	DEL	ENST00000406890.2	hg19	CCDS55094.1																																																																																			.	.		0.388	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2		
RINL	126432	hgsc.bcm.edu	37	19	39359906	39359906	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:39359906delT	ENST00000591812.1	-	11	1705	c.1619delA	c.(1618-1620)aagfs	p.K540fs	RINL_ENST00000340740.3_Frame_Shift_Del_p.K426fs|CTC-360G5.6_ENST00000593830.1_RNA|RINL_ENST00000598904.1_Frame_Shift_Del_p.K426fs|RINL_ENST00000602238.1_5'Flank			Q6ZS11	RINL_HUMAN	Ras and Rab interactor-like	540					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|ruffle (GO:0001726)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|urinary_tract(2)	17						GGGATGATCCTTTCTGTGCAG	0.677																																					p.K540fs		Atlas-INDEL	.											.	RINL	32	.	0			c.1620delG						.						84.0	83.0	84.0					19																	39359906		2203	4300	6503	SO:0001589	frameshift_variant	126432	exon11			.	AK127808	CCDS12522.1, CCDS59386.1	19q13.2	2010-07-13			ENSG00000187994	ENSG00000187994			24795	protein-coding gene	gene with protein product							Standard	NM_001195833		Approved	FLJ45909	uc010xuo.2	Q6ZS11		ENST00000591812.1:c.1619delA	chr19.hg19:g.39359906delT	ENSP00000467107:p.Lys540fs	157.0	0.0		156.0	10.0	NM_001195833	B4DPG5	Frame_Shift_Del	DEL	ENST00000591812.1	hg19	CCDS59386.1																																																																																			.	.		0.677	RINL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460433.1	NM_198445	
CNTN3	5067	hgsc.bcm.edu	37	3	74413707	74413707	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:74413707delT	ENST00000263665.6	-	9	1151	c.1124delA	c.(1123-1125)aacfs	p.N375fs		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	375	Ig-like C2-type 4.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CACACTTAGGTTTGATATTGT	0.348																																					p.N375fs		Atlas-INDEL	.											CNTN3,NS,carcinoma,0,1	CNTN3	174	.	0			c.1125delC						.						204.0	184.0	191.0					3																	74413707		2203	4300	6503	SO:0001589	frameshift_variant	5067	exon9			.	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.1124delA	chr3.hg19:g.74413707delT	ENSP00000263665:p.Asn375fs	130.0	0.0		179.0	12.0	NM_020872	B9EK50|Q9H039	Frame_Shift_Del	DEL	ENST00000263665.6	hg19	CCDS33790.1																																																																																			.	.		0.348	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
CYLD	1540	hgsc.bcm.edu	37	16	50785567	50785567	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:50785567delT	ENST00000427738.3	+	3	762	c.557delT	c.(556-558)cttfs	p.L186fs	CYLD_ENST00000569418.1_Frame_Shift_Del_p.L186fs|CYLD_ENST00000540145.1_Frame_Shift_Del_p.L186fs|CYLD_ENST00000398568.2_Frame_Shift_Del_p.L186fs|CYLD_ENST00000311559.9_Frame_Shift_Del_p.L186fs|CYLD_ENST00000566206.1_Frame_Shift_Del_p.L186fs|CYLD_ENST00000564326.1_Frame_Shift_Del_p.L186fs|CYLD_ENST00000568704.2_Frame_Shift_Del_p.L186fs			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	186	CAP-Gly 1. {ECO:0000255|PROSITE- ProRule:PRU00045}.|Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				GGGAAACAGCTTTTTCAGTGT	0.428			"""Mis, N, F, S"""		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.L186fs		Atlas-INDEL	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	.	CYLD	150	.	0			c.556delC						.						215.0	204.0	208.0					16																	50785567		1990	4169	6159	SO:0001589	frameshift_variant	1540	exon4	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"""ubiquitin specific peptidase like 2"""	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.557delT	chr16.hg19:g.50785567delT	ENSP00000392025:p.Leu186fs	116.0	0.0		142.0	10.0	NM_001042355	O94934|Q7L3N6|Q96EH0|Q9NZX9	Frame_Shift_Del	DEL	ENST00000427738.3	hg19	CCDS45482.1																																																																																			.	.		0.428	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2		
PABPC3	5042	hgsc.bcm.edu	37	13	25670906	25670906	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr13:25670906delC	ENST00000281589.3	+	1	607	c.570delC	c.(568-570)ttcfs	p.F190fs		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	190					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		CAAAAGAGTTCCCCAATGTTT	0.423																																					p.F190fs		Atlas-INDEL	.											.	PABPC3	129	.	0			c.569delT						.						100.0	93.0	95.0					13																	25670906		2203	4300	6503	SO:0001589	frameshift_variant	5042	exon1			.	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.570delC	chr13.hg19:g.25670906delC	ENSP00000281589:p.Phe190fs	164.0	0.0		110.0	10.0	NM_030979	Q8NHV0|Q9H086	Frame_Shift_Del	DEL	ENST00000281589.3	hg19	CCDS9311.1																																																																																			.	.		0.423	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
TTC3	7267	hgsc.bcm.edu	37	21	38494152	38494152	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:38494152delG	ENST00000399017.2	+	12	3683	c.936delG	c.(934-936)ctgfs	p.L312fs	TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Frame_Shift_Del_p.L312fs|TTC3_ENST00000540756.1_Frame_Shift_Del_p.L2fs|TTC3_ENST00000355666.1_Frame_Shift_Del_p.L312fs	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	312					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)				TTTCTATGCTGGGGGAATATG	0.353																																					p.L312fs	Ovarian(38;194 1649 35661)	Atlas-INDEL	.											.	TTC3	182	.	0			c.935delT						.						59.0	60.0	60.0					21																	38494152		2203	4300	6503	SO:0001589	frameshift_variant	7267	exon12			.	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.936delG	chr21.hg19:g.38494152delG	ENSP00000381981:p.Leu312fs	204.0	0.0		187.0	12.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Frame_Shift_Del	DEL	ENST00000399017.2	hg19	CCDS13651.1																																																																																			.	.		0.353	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
DRAP1	10589	hgsc.bcm.edu	37	11	65688853	65688853	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:65688853delC	ENST00000312515.2	+	7	810	c.565delC	c.(565-567)cccfs	p.P190fs	C11orf68_ENST00000438576.2_5'Flank|DRAP1_ENST00000532933.1_Frame_Shift_Del_p.P170fs|DRAP1_ENST00000376991.2_Frame_Shift_Del_p.P197fs|C11orf68_ENST00000449692.3_5'Flank|DRAP1_ENST00000527119.1_Frame_Shift_Del_p.P146fs	NM_006442.3	NP_006433.2	Q14919	NC2A_HUMAN	DR1-associated protein 1 (negative cofactor 2 alpha)	190	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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 corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	5				READ - Rectum adenocarcinoma(159;0.166)		GCCCCCAGCGCCCCCGGGCCC	0.627																																					p.A188fs		Atlas-INDEL	.											.	DRAP1	18	.	0			c.564delG						.						72.0	81.0	78.0					11																	65688853		2201	4296	6497	SO:0001589	frameshift_variant	10589	exon7			.	U41843	CCDS8123.1	11q13	2010-09-29			ENSG00000175550	ENSG00000175550			3019	protein-coding gene	gene with protein product	"""negative cofactor 2 alpha"", ""DR1-associated corepressor"""	602289				8608938	Standard	NM_006442		Approved	NC2-alpha	uc001ogj.2	Q14919	OTTHUMG00000166723	ENST00000312515.2:c.565delC	chr11.hg19:g.65688853delC	ENSP00000307850:p.Pro190fs	218.0	0.0		378.0	23.0	NM_006442	Q13448	Frame_Shift_Del	DEL	ENST00000312515.2	hg19	CCDS8123.1																																																																																			.	.		0.627	DRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391197.2	NM_006442	
LIG3	3980	hgsc.bcm.edu	37	17	33323630	33323630	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:33323630delT	ENST00000378526.4	+	11	1914	c.1781delT	c.(1780-1782)gttfs	p.V594fs	LIG3_ENST00000262327.5_Frame_Shift_Del_p.V594fs	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	594					base-excision repair (GO:0006284)|base-excision repair, DNA ligation (GO:0006288)|DNA biosynthetic process (GO:0071897)|DNA repair (GO:0006281)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitochondrial DNA repair (GO:0043504)|negative regulation of DNA recombination (GO:0045910)|nucleotide-excision repair (GO:0006289)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(8)|lung(9)|ovary(3)|pancreas(2)|prostate(1)|skin(3)|stomach(1)	31		Ovarian(249;0.17)			Bleomycin(DB00290)	TGCCTGTTTGTTTTTGATTGT	0.403								Other BER factors																													p.V594fs		Atlas-INDEL	.											.	LIG3	164	.	0			c.1780delG						.						232.0	197.0	209.0					17																	33323630		2203	4300	6503	SO:0001589	frameshift_variant	3980	exon11			.		CCDS11284.2, CCDS11285.2	17q11.2-q12	2008-10-29			ENSG00000005156	ENSG00000005156			6600	protein-coding gene	gene with protein product		600940	"""ligase II, DNA, ATP-dependent"""	LIG2		7760816	Standard	NM_002311		Approved		uc002hik.2	P49916	OTTHUMG00000128519	ENST00000378526.4:c.1781delT	chr17.hg19:g.33323630delT	ENSP00000367787:p.Val594fs	127.0	0.0		167.0	11.0	NM_013975	Q16714|Q6NVK3	Frame_Shift_Del	DEL	ENST00000378526.4	hg19	CCDS11284.2																																																																																			.	.		0.403	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975	
FAM161A	84140	hgsc.bcm.edu	37	2	62067256	62067256	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:62067256delG	ENST00000405894.3	-	3	984	c.883delC	c.(883-885)cttfs	p.L295fs	FAM161A_ENST00000404929.1_Frame_Shift_Del_p.L295fs	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	295					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TCATGGTAAAGGGGGAGAAAG	0.393																																					p.L295fs		Atlas-INDEL	.											.	FAM161A	200	.	0			c.884delT						.						169.0	153.0	158.0					2																	62067256		1850	4091	5941	SO:0001589	frameshift_variant	84140	exon3			.		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.883delC	chr2.hg19:g.62067256delG	ENSP00000385893:p.Leu295fs	155.0	0.0		156.0	11.0	NM_032180	B4DJV7|Q9H8R2	Frame_Shift_Del	DEL	ENST00000405894.3	hg19	CCDS42687.2																																																																																			.	.		0.393	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
MAP1S	55201	hgsc.bcm.edu	37	19	17836717	17836717	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:17836717delG	ENST00000324096.4	+	5	675	c.524delG	c.(523-525)tggfs	p.W175fs	MAP1S_ENST00000597681.1_Intron|MAP1S_ENST00000544059.2_Frame_Shift_Del_p.W149fs|CTD-3149D2.4_ENST00000595363.1_RNA	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	175	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						TTCGGTGACTGGGCTCAGCTG	0.687																																					p.W175fs		Atlas-INDEL	.											.	MAP1S	74	.	0			c.523delT						.						32.0	32.0	32.0					19																	17836717		2201	4297	6498	SO:0001589	frameshift_variant	55201	exon5			.	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"""chromosome 19 open reading frame 5"", ""VCY2 interacting protein 1"", ""BPY2 interacting protein 1"""	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.524delG	chr19.hg19:g.17836717delG	ENSP00000325313:p.Trp175fs	208.0	0.0		171.0	12.0	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Frame_Shift_Del	DEL	ENST00000324096.4	hg19	CCDS32954.1																																																																																			.	.		0.687	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174	
RNPS1	10921	hgsc.bcm.edu	37	16	2314622	2314622	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:2314622delT	ENST00000565678.1	-	2	568	c.23delA	c.(22-24)aagfs	p.K9fs	RNPS1_ENST00000397086.2_Frame_Shift_Del_p.K9fs|RNPS1_ENST00000301730.8_Frame_Shift_Del_p.K9fs|RNPS1_ENST00000566397.1_5'Flank|RNPS1_ENST00000566458.1_Intron|RNPS1_ENST00000568631.1_Frame_Shift_Del_p.K9fs|RNPS1_ENST00000561718.1_Intron|RNPS1_ENST00000569598.2_Frame_Shift_Del_p.K9fs|RNPS1_ENST00000567147.1_Intron|RNPS1_ENST00000320225.5_Frame_Shift_Del_p.K9fs			Q15287	RNPS1_HUMAN	RNA binding protein S1, serine-rich domain	9	Lys-rich.|Necessary for interaction with SRP54, nuclear localization and exon-skipping.|Necessary for interaction with the cleaved p110 isoform of CDC2L1.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(4)|ovary(2)|urinary_tract(1)	9						CAAGCTCTTCTTTTTCACTCC	0.413																																					p.K8fs		Atlas-INDEL	.											.	RNPS1	18	.	0			c.24delG						.						118.0	114.0	116.0					16																	2314622		2198	4300	6498	SO:0001589	frameshift_variant	10921	exon2			.	AF015608	CCDS10465.1, CCDS66907.1, CCDS73811.1	16p13.3	2013-02-12	2001-11-28		ENSG00000205937	ENSG00000205937		"""RNA binding motif (RRM) containing"""	10080	protein-coding gene	gene with protein product		606447	"""RNA-binding protein S1, serine-rich domain"""			9580558, 8543184	Standard	XM_005255048		Approved		uc002cpu.3	Q15287	OTTHUMG00000128828	ENST00000565678.1:c.23delA	chr16.hg19:g.2314622delT	ENSP00000457723:p.Lys9fs	90.0	0.0		126.0	11.0	NM_006711	A8K1P0|B4DDU8|B4DZU7|B7ZA17|O75308|Q32P25|Q8WY42|Q9NYG3	Frame_Shift_Del	DEL	ENST00000565678.1	hg19	CCDS10465.1																																																																																			.	.		0.413	RNPS1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435415.1	NM_080594	
DYNC1LI1	51143	hgsc.bcm.edu	37	3	32570036	32570036	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:32570036delT	ENST00000273130.4	-	12	1467	c.1364delA	c.(1363-1365)aagfs	p.K455fs	DYNC1LI1_ENST00000432458.2_Frame_Shift_Del_p.K339fs	NM_016141.3	NP_057225.2	Q9Y6G9	DC1L1_HUMAN	dynein, cytoplasmic 1, light intermediate chain 1	455					microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(1)|lung(3)|ovary(1)	7						AGAGCCAGTCTTTTTACTCAA	0.453																																					p.K455fs		Atlas-INDEL	.											.	DYNC1LI1	23	.	0			c.1365delG						.						66.0	68.0	68.0					3																	32570036		2203	4300	6503	SO:0001589	frameshift_variant	51143	exon12			.	AF078849	CCDS2654.1	3p23	2013-01-18	2005-11-25	2005-11-25	ENSG00000144635	ENSG00000144635		"""Cytoplasmic dyneins"""	18745	protein-coding gene	gene with protein product		615890	"""dynein, cytoplasmic, light intermediate polypeptide 1"""	DNCLI1		16260502	Standard	NM_016141		Approved		uc003cfb.4	Q9Y6G9	OTTHUMG00000130750	ENST00000273130.4:c.1364delA	chr3.hg19:g.32570036delT	ENSP00000273130:p.Lys455fs	101.0	0.0		116.0	10.0	NM_016141	A2RRG7|Q53HC8|Q53HK7	Frame_Shift_Del	DEL	ENST00000273130.4	hg19	CCDS2654.1																																																																																			.	.		0.453	DYNC1LI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253250.1	NM_016141	
PDYN	5173	hgsc.bcm.edu	37	20	1961108	1961108	+	Frame_Shift_Del	DEL	C	C	-	rs141379855		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:1961108delC	ENST00000217305.2	-	4	851	c.626delG	c.(625-627)ggcfs	p.G209fs	RP4-684O24.5_ENST00000446562.1_RNA|PDYN_ENST00000540134.1_Frame_Shift_Del_p.G209fs|PDYN_ENST00000539905.1_Frame_Shift_Del_p.G209fs	NM_001190892.1|NM_001190898.2|NM_024411.4	NP_001177821.1|NP_001177827.1|NP_077722.1	P01213	PDYN_HUMAN	prodynorphin	209					cell death (GO:0008219)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CCGCAAGAAGCCCCCATAGCG	0.597																																					p.G209fs		Atlas-INDEL	.											.	PDYN	74	.	0			c.627delC						.						104.0	115.0	111.0					20																	1961108		2203	4300	6503	SO:0001589	frameshift_variant	5173	exon4			.		CCDS13023.1	20p13	2014-09-17			ENSG00000101327	ENSG00000101327		"""Endogenous ligands"""	8820	protein-coding gene	gene with protein product	"""preproenkephalin B"", ""rimorphin"", ""beta-neoendorphin"", ""dynorphin"", ""leu-enkephalin"", ""leumorphin"", ""neoendorphin-dynorphin-enkephalin prepropeptide"""	131340	"""spinocerebellar ataxia 23"""	SCA23		21035104	Standard	NM_001190892		Approved	PENKB, ADCA	uc021vzs.1	P01213	OTTHUMG00000031683	ENST00000217305.2:c.626delG	chr20.hg19:g.1961108delC	ENSP00000217305:p.Gly209fs	189.0	0.0		219.0	16.0	NM_001190898	A8K0Q3	Frame_Shift_Del	DEL	ENST00000217305.2	hg19	CCDS13023.1																																																																																			.	.		0.597	PDYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077569.2		
ANKS1B	56899	hgsc.bcm.edu	37	12	100166806	100166806	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:100166806delT	ENST00000547776.2	-	8	1021	c.1022delA	c.(1021-1023)aagfs	p.K341fs	ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000329257.7_Frame_Shift_Del_p.K341fs	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	341						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		CGAATAATCCTTTTCTTGACA	0.353																																					p.K341fs		Atlas-INDEL	.											.	ANKS1B	180	.	0			c.1023delG						.						130.0	122.0	125.0					12																	100166806		1823	4078	5901	SO:0001589	frameshift_variant	56899	exon8			.	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.1022delA	chr12.hg19:g.100166806delT	ENSP00000449629:p.Lys341fs	212.0	0.0		234.0	15.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Frame_Shift_Del	DEL	ENST00000547776.2	hg19	CCDS55872.1																																																																																			.	.		0.353	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
STK32B	55351	hgsc.bcm.edu	37	4	5053615	5053615	+	Frame_Shift_Del	DEL	C	C	-	rs142664782		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:5053615delC	ENST00000282908.5	+	1	447	c.25delC	c.(25-27)cccfs	p.P10fs		NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						CTCCCACAAGCCCCCCGTGTT	0.657																																					p.K8fs		Atlas-INDEL	.											.	STK32B	87	.	0			c.24delG						.						61.0	57.0	58.0					4																	5053615		2198	4295	6493	SO:0001589	frameshift_variant	55351	exon1			.	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.25delC	chr4.hg19:g.5053615delC	ENSP00000282908:p.Pro10fs	145.0	0.0		166.0	14.0	NM_018401		Frame_Shift_Del	DEL	ENST00000282908.5	hg19	CCDS3380.1																																																																																			.	.		0.657	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401	
ZNF248	57209	hgsc.bcm.edu	37	10	38121237	38121237	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr10:38121237delC	ENST00000395867.3	-	6	1596	c.1046delG	c.(1045-1047)ggafs	p.G349fs	AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000494133.1_Intron|ZNF248_ENST00000374648.3_Intron|ZNF248_ENST00000357328.4_Frame_Shift_Del_p.G349fs	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	349					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(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						ATAAGACTTTCCCCCCATGTG	0.398																																					p.G349fs		Atlas-INDEL	.											.	ZNF248	61	.	0			c.1047delA						.						107.0	103.0	104.0					10																	38121237		2203	4299	6502	SO:0001589	frameshift_variant	57209	exon6			.	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"""Zinc fingers, C2H2-type"", ""-"""	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.1046delG	chr10.hg19:g.38121237delC	ENSP00000379208:p.Gly349fs	172.0	0.0		243.0	15.0	NM_021045	Q8NDV8|Q9UMP3	Frame_Shift_Del	DEL	ENST00000395867.3	hg19	CCDS7194.1																																																																																			.	.		0.398	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045	
CCDC73	493860	hgsc.bcm.edu	37	11	32663555	32663555	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr11:32663555delT	ENST00000335185.5	-	13	1056	c.1013delA	c.(1012-1014)aatfs	p.N338fs	CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	338										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					TTCATGCTCATTTTGAAGATT	0.249																																					p.T338fs		Atlas-INDEL	.											.	CCDC73	136	.	0			c.1014delT						.						77.0	69.0	71.0					11																	32663555		1785	4050	5835	SO:0001589	frameshift_variant	493860	exon13			.	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.1013delA	chr11.hg19:g.32663555delT	ENSP00000335325:p.Asn338fs	172.0	0.0		161.0	10.0	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	Frame_Shift_Del	DEL	ENST00000335185.5	hg19	CCDS41630.1																																																																																			.	.		0.249	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391	
KLK6	5653	hgsc.bcm.edu	37	19	51470427	51470427	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:51470427delT	ENST00000376851.3	-	3	634	c.195delA	c.(193-195)aaafs	p.K65fs	KLK6_ENST00000376853.4_Frame_Shift_Del_p.K65fs|KLK6_ENST00000310157.2_Frame_Shift_Del_p.K65fs|CTB-147C22.9_ENST00000594512.1_RNA|KLK6_ENST00000424910.2_Intron|KLK6_ENST00000594641.1_Frame_Shift_Del_p.K65fs|KLK6_ENST00000391808.1_5'UTR	NM_001012964.1	NP_001012982.1	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6	65	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				amyloid precursor protein metabolic process (GO:0042982)|central nervous system development (GO:0007417)|collagen catabolic process (GO:0030574)|hormone metabolic process (GO:0042445)|myelination (GO:0042552)|neuron death (GO:0070997)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|protein autoprocessing (GO:0016540)|regulation of cell differentiation (GO:0045595)|regulation of neuron projection development (GO:0010975)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|skin(4)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		AGACTCACGGTTTTTTGCAGT	0.557																																					p.P66fs		Atlas-INDEL	.											.	KLK6	35	.	0			c.196delC						.						102.0	92.0	95.0					19																	51470427		2203	4300	6503	SO:0001589	frameshift_variant	5653	exon3			.	U62801	CCDS12811.1, CCDS42599.1	19q13.3	2011-09-07	2006-10-27			ENSG00000167755		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6367	protein-coding gene	gene with protein product		602652	"""protease, serine, 18"", ""kallikrein 6 (neurosin, zyme)"""	PRSS9, PRSS18		9003450, 16800724, 16800723	Standard	NM_002774		Approved	Bssp, Klk7, neurosin	uc002pui.3	Q92876		ENST00000376851.3:c.195delA	chr19.hg19:g.51470427delT	ENSP00000366047:p.Lys65fs	104.0	0.0		190.0	13.0	NM_001012964	A6NJA1|A8MW09|Q6H301	Frame_Shift_Del	DEL	ENST00000376851.3	hg19	CCDS12811.1																																																																																			.	.		0.557	KLK6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465060.1	NM_002774	
BPIFB3	359710	hgsc.bcm.edu	37	20	31656746	31656746	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:31656746delG	ENST00000375494.3	+	10	1116	c.1116delG	c.(1114-1116)aagfs	p.K372fs		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	372					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										ATGTCCCTAAGGGGACCCCTG	0.592																																					p.K372fs		Atlas-INDEL	.											.	.	.	.	0			c.1115delA						.						101.0	79.0	86.0					20																	31656746		2203	4300	6503	SO:0001589	frameshift_variant	359710	exon10			.	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1116delG	chr20.hg19:g.31656746delG	ENSP00000364643:p.Lys372fs	150.0	0.0		155.0	11.0	NM_182658	Q5TDX7	Frame_Shift_Del	DEL	ENST00000375494.3	hg19	CCDS13212.1																																																																																			.	.		0.592	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	
PNN	5411	hgsc.bcm.edu	37	14	39648419	39648419	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:39648419delT	ENST00000216832.4	+	7	690	c.623delT	c.(622-624)cttfs	p.L209fs	PNN_ENST00000557680.1_3'UTR|PNN_ENST00000553331.1_3'UTR	NM_002687.3	NP_002678	Q9H307	PININ_HUMAN	pinin, desmosome associated protein	209	Glu-rich.|Necessary for interaction with RNPS1.				cell adhesion (GO:0007155)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)|stomach(1)	27	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0119)		GAACTGCGGCTTTTGGAACAG	0.418																																					p.L208fs		Atlas-INDEL	.											.	PNN	67	.	0			c.622delC						.						127.0	131.0	130.0					14																	39648419		2203	4300	6503	SO:0001589	frameshift_variant	5411	exon7			.	U77718	CCDS9671.1	14q21.1	2010-07-02			ENSG00000100941	ENSG00000100941			9162	protein-coding gene	gene with protein product		603154				8922384	Standard	NM_002687		Approved	memA	uc001wuw.4	Q9H307	OTTHUMG00000028821	ENST00000216832.4:c.623delT	chr14.hg19:g.39648419delT	ENSP00000216832:p.Leu209fs	106.0	0.0		145.0	11.0	NM_002687	B4DZX8|O60899|Q53EM7|Q6P5X4|Q7KYL1|Q99738|Q9UHZ9|Q9UQR9	Frame_Shift_Del	DEL	ENST00000216832.4	hg19	CCDS9671.1																																																																																			.	.		0.418	PNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276776.2	NM_002687	
SEMA5B	54437	hgsc.bcm.edu	37	3	122680077	122680077	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:122680077delG	ENST00000357599.3	-	2	420	c.34delC	c.(34-36)cacfs	p.H13fs	SEMA5B_ENST00000451055.2_Frame_Shift_Del_p.H67fs|SEMA5B_ENST00000195173.4_Frame_Shift_Del_p.H13fs|SEMA5B_ENST00000465147.1_Intron	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	13					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		ACGAGGTGGTGGGCAACAGGA	0.592																																					p.H66fs		Atlas-INDEL	.											.	SEMA5B	303	.	0			c.197delA						.						82.0	74.0	77.0					3																	122680077		2203	4300	6503	SO:0001589	frameshift_variant	54437	exon2			.	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.34delC	chr3.hg19:g.122680077delG	ENSP00000350215:p.His13fs	151.0	0.0		204.0	14.0	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Frame_Shift_Del	DEL	ENST00000357599.3	hg19	CCDS35491.1																																																																																			.	.		0.592	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
ZNF518B	85460	hgsc.bcm.edu	37	4	10445202	10445202	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:10445202delA	ENST00000326756.3	-	3	3189	c.2751delT	c.(2749-2751)tttfs	p.F917fs		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	917					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						TTGCAACCTGAAAAATTGAAG	0.413																																					p.Q918fs		Atlas-INDEL	.											.	ZNF518B	116	.	0			c.2752delC						.						102.0	102.0	102.0					4																	10445202		2203	4300	6503	SO:0001589	frameshift_variant	85460	exon3			.	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"""Zinc fingers, C2H2-type"""	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.2751delT	chr4.hg19:g.10445202delA	ENSP00000317614:p.Phe917fs	141.0	0.0		158.0	10.0	NM_053042	Q96LN8	Frame_Shift_Del	DEL	ENST00000326756.3	hg19	CCDS33960.1																																																																																			.	.		0.413	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
KHSRP	8570	hgsc.bcm.edu	37	19	6415893	6415893	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:6415893delG	ENST00000398148.3	-	16	1705	c.1613delC	c.(1612-1614)cctfs	p.P539fs	MIR3940_ENST00000579148.1_RNA	NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	539	Ala/Gly/Pro-rich.				gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of miRNA metabolic process (GO:2000628)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|transcription, DNA-templated (GO:0006351)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|liver(1)|lung(6)|skin(1)|soft_tissue(1)	17						CTGGTGAGGAGGGGGCCCCCC	0.662																																					p.P538fs	Colon(55;593 1006 2067 9135 22980)	Atlas-INDEL	.											.	KHSRP	51	.	0			c.1614delT						.						6.0	8.0	7.0					19																	6415893		1850	4037	5887	SO:0001589	frameshift_variant	8570	exon16			.	U94832	CCDS45936.1	19p13.3	2010-11-23	2008-02-04		ENSG00000088247	ENSG00000088247			6316	protein-coding gene	gene with protein product	"""FUSE binding protein 2"""	603445				9136930, 8940189	Standard	NM_003685		Approved	KSRP, FBP2, FUBP2	uc002mer.4	Q92945		ENST00000398148.3:c.1613delC	chr19.hg19:g.6415893delG	ENSP00000381216:p.Pro539fs	154.0	0.0		193.0	12.0	NM_003685	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	Frame_Shift_Del	DEL	ENST00000398148.3	hg19	CCDS45936.1																																																																																			.	.		0.662	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453305.1		
SPATA31A2	642265	hgsc.bcm.edu	37	9	39890582	39890582	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:39890582delA	ENST00000456183.2	+	4	3598	c.3569delA	c.(3568-3570)caafs	p.Q1190fs		NM_001040065.1	NP_001035154.1	Q5RGS2	S31A2_HUMAN	SPATA31 subfamily A, member 2	1190					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GCTGAGAGCCAAAAAACAGTG	0.438																																					p.Q1190fs		Atlas-INDEL	.											.,1	.	.	.	0			c.3568delC						.						1.0	1.0	1.0					9																	39890582		1	3	4	SO:0001589	frameshift_variant	647060	exon4			.			9p13.1	2012-10-15	2012-10-12	2012-10-12	ENSG00000204848				32002	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A2"""	FAM75A2		20850414	Standard			Approved	OTTHUMG00000013563	uc004abm.3	Q5RGS2	OTTHUMG00000013563	ENST00000456183.2:c.3569delA	chr9.hg19:g.39890582delA	ENSP00000406957:p.Gln1190fs	153.0	0.0		187.0	14.0	NM_001085452		Frame_Shift_Del	DEL	ENST00000456183.2	hg19	CCDS43809.1																																																																																			.	.		0.438	SPATA31A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037739.1	NM_001040065	
TTLL12	23170	hgsc.bcm.edu	37	22	43572405	43572405	+	Intron	DEL	A	A	-	rs374769998		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:43572405delA	ENST00000216129.6	-	6	904				TTLL12_ENST00000484118.1_5'Flank	NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12						cellular protein modification process (GO:0006464)					central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	13		Ovarian(80;0.221)|Glioma(61;0.222)				AGAATGGCCTAAAAGGAAACA	0.572																																					.		Atlas-INDEL	.											.	TTLL12	50	.	0			c.841-2T>-						.						49.0	45.0	46.0					22																	43572405		2200	4294	6494	SO:0001627	intron_variant	23170	exon7			.	D63487	CCDS14047.1	22q13.31	2013-02-14	2006-02-02		ENSG00000100304	ENSG00000100304		"""Tubulin tyrosine ligase-like family"""	28974	protein-coding gene	gene with protein product						15890843	Standard	NM_015140		Approved	KIAA0153	uc003bdp.3	Q14166	OTTHUMG00000150682	ENST00000216129.6:c.841-3T>-	chr22.hg19:g.43572405delA		143.0	0.0		190.0	13.0	NM_015140	Q20WK5|Q9UGU3	Splice_Site	DEL	ENST00000216129.6	hg19	CCDS14047.1																																																																																			.	.		0.572	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140	
MTFMT	123263	hgsc.bcm.edu	37	15	65295429	65295429	+	Frame_Shift_Del	DEL	T	T	-	rs368759868		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:65295429delT	ENST00000220058.4	-	9	1154	c.1141delA	c.(1141-1143)actfs	p.T381fs		NM_139242.3	NP_640335.2	Q96DP5	FMT_HUMAN	mitochondrial methionyl-tRNA formyltransferase	381						mitochondrion (GO:0005739)	methionyl-tRNA formyltransferase activity (GO:0004479)			endometrium(1)|large_intestine(3)|lung(3)|ovary(3)	10					Tetrahydrofolic acid(DB00116)	ATAGCAACAGTTTTTTTCTGC	0.343																																					p.T381fs		Atlas-INDEL	.											.	MTFMT	28	.	0			c.1142delC						.						114.0	102.0	106.0					15																	65295429		1828	4086	5914	SO:0001589	frameshift_variant	123263	exon9			.	AK055688	CCDS45280.1	15q22.31	2006-11-29		2005-08-09		ENSG00000103707			29666	protein-coding gene	gene with protein product		611766				9614118	Standard	NM_139242		Approved	FMT1	uc002aof.4	Q96DP5		ENST00000220058.4:c.1141delA	chr15.hg19:g.65295429delT	ENSP00000220058:p.Thr381fs	76.0	0.0		115.0	10.0	NM_139242	B7Z734	Frame_Shift_Del	DEL	ENST00000220058.4	hg19	CCDS45280.1																																																																																			.	.		0.343	MTFMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418155.1	NM_139242	
IQCC	55721	hgsc.bcm.edu	37	1	32673443	32673443	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:32673443delG	ENST00000291358.6	+	5	1182	c.1161delG	c.(1159-1161)ttgfs	p.L387fs	DCDC2B_ENST00000409358.1_5'Flank|RP4-622L5.7_ENST00000421616.1_RNA|IQCC_ENST00000537469.1_Frame_Shift_Del_p.L467fs|RP4-622L5.7_ENST00000373604.4_RNA	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C	387										endometrium(4)|large_intestine(1)|lung(3)|ovary(4)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				ATGGTACCTTGGGGGGGCCAG	0.552																																					p.L467fs		Atlas-INDEL	.											.,1	IQCC	46	.	0			c.1400delT						.						82.0	89.0	87.0					1																	32673443		2203	4300	6503	SO:0001589	frameshift_variant	55721	exon5			.	AL049795	CCDS355.1, CCDS53293.1	1p36.11-p34.2	2008-02-05			ENSG00000160051	ENSG00000160051			25545	protein-coding gene	gene with protein product							Standard	NM_018134		Approved	FLJ10547	uc001bum.2	Q4KMZ1	OTTHUMG00000005739	ENST00000291358.6:c.1161delG	chr1.hg19:g.32673443delG	ENSP00000291358:p.Leu387fs	135.0	0.0		187.0	13.0	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Frame_Shift_Del	DEL	ENST00000291358.6	hg19	CCDS355.1																																																																																			.	.		0.552	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134	
TSHR	7253	hgsc.bcm.edu	37	14	81610522	81610522	+	Frame_Shift_Del	DEL	G	G	-	rs368452281		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:81610522delG	ENST00000541158.2	+	11	2442	c.2120delG	c.(2119-2121)cggfs	p.R707fs	RP11-114N19.3_ENST00000557775.1_RNA|TSHR_ENST00000298171.2_Frame_Shift_Del_p.R707fs			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	707					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)			breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	CAGGCATACCGGGGGCAGAGG	0.488			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																														p.R707fs		Atlas-INDEL	.	yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	TSHR,NS,carcinoma,0,1	TSHR	462	.	0			c.2119delC						.						114.0	109.0	111.0					14																	81610522		2203	4300	6503	SO:0001589	frameshift_variant	7253	exon10			.	AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"""GPCR / Class A : Gonadotropin and TSH receptors"""	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.2120delG	chr14.hg19:g.81610522delG	ENSP00000441235:p.Arg707fs	152.0	0.0		200.0	13.0	NM_000369	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Frame_Shift_Del	DEL	ENST00000541158.2	hg19	CCDS9872.1																																																																																			.	.		0.488	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369	
TSPYL5	85453	hgsc.bcm.edu	37	8	98289664	98289664	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:98289664delG	ENST00000322128.3	-	1	512	c.409delC	c.(409-411)cgcfs	p.R137fs		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	137					cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					TTTCCAACGCGGGGGGCATTT	0.677																																					p.R137fs		Atlas-INDEL	.											.	TSPYL5	48	.	0			c.410delG						.						20.0	24.0	23.0					8																	98289664		2196	4292	6488	SO:0001589	frameshift_variant	85453	exon1			.	AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.409delC	chr8.hg19:g.98289664delG	ENSP00000322802:p.Arg137fs	178.0	0.0		187.0	13.0	NM_033512	B3KRF0|Q9C0B3	Frame_Shift_Del	DEL	ENST00000322128.3	hg19	CCDS34927.1																																																																																			.	.		0.677	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512	
PXDN	7837	hgsc.bcm.edu	37	2	1670061	1670061	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:1670061delC	ENST00000252804.4	-	10	1266	c.1216delG	c.(1216-1218)gacfs	p.D406fs	PXDN_ENST00000483018.1_5'UTR	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	406	Ig-like C2-type 2.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		TCTCCGCTGTCCCCCTGTACG	0.582																																					p.D406fs		Atlas-INDEL	.											.	PXDN	255	.	0			c.1217delA						.						65.0	70.0	68.0					2																	1670061		2147	4254	6401	SO:0001589	frameshift_variant	7837	exon10			.	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"""Immunoglobulin superfamily / I-set domain containing"""	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1216delG	chr2.hg19:g.1670061delC	ENSP00000252804:p.Asp406fs	257.0	0.0		287.0	18.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Frame_Shift_Del	DEL	ENST00000252804.4	hg19	CCDS46221.1																																																																																			.	.		0.582	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
CDH20	28316	hgsc.bcm.edu	37	18	59195338	59195338	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:59195338delC	ENST00000262717.4	+	7	1554	c.1156delC	c.(1156-1158)cccfs	p.P387fs	CDH20_ENST00000538374.1_Frame_Shift_Del_p.P387fs|CDH20_ENST00000536675.2_Frame_Shift_Del_p.P387fs			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	387	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)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				CGTGGACGAGCCCCCTGTGTT	0.517																																					p.E385fs		Atlas-INDEL	.											.	CDH20	117	.	0			c.1155delG						.						158.0	152.0	154.0					18																	59195338		2203	4300	6503	SO:0001589	frameshift_variant	28316	exon6			.	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"""Cadherins / Major cadherins"""	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1156delC	chr18.hg19:g.59195338delC	ENSP00000262717:p.Pro387fs	227.0	0.0		281.0	17.0	NM_031891	Q495S3	Frame_Shift_Del	DEL	ENST00000262717.4	hg19	CCDS11977.1																																																																																			.	.		0.517	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891	
AFF3	3899	hgsc.bcm.edu	37	2	100170975	100170975	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:100170975delG	ENST00000409236.2	-	22	3469	c.3357delC	c.(3355-3357)cccfs	p.P1119fs	AFF3_ENST00000317233.4_Frame_Shift_Del_p.P1119fs|AFF3_ENST00000356421.2_Frame_Shift_Del_p.P1144fs|AFF3_ENST00000409579.1_Frame_Shift_Del_p.P1144fs			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	1119					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						TGGGAGACATGGGGGATGGGG	0.652																																					p.M1145fs		Atlas-INDEL	.											.	AFF3	164	.	0			c.3433delA						.						28.0	29.0	28.0					2																	100170975		2203	4299	6502	SO:0001589	frameshift_variant	3899	exon23			.	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"""lymphoid nuclear protein related to AF4"""	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.3357delC	chr2.hg19:g.100170975delG	ENSP00000387207:p.Pro1119fs	70.0	0.0		103.0	10.0	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Frame_Shift_Del	DEL	ENST00000409236.2	hg19	CCDS42723.1																																																																																			.	.		0.652	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285	
FKBP15	23307	hgsc.bcm.edu	37	9	115931867	115931867	+	Frame_Shift_Del	DEL	G	G	-	rs370970009		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:115931867delG	ENST00000238256.3	-	26	3239	c.3122delC	c.(3121-3123)ccgfs	p.P1041fs		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	1041					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						AATTGAAGTCGGGGGCCCTAG	0.557																																					p.P1041fs		Atlas-INDEL	.											.	FKBP15	128	.	0			c.3123delG						.						84.0	88.0	87.0					9																	115931867		1901	4126	6027	SO:0001589	frameshift_variant	23307	exon26			.	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.3122delC	chr9.hg19:g.115931867delG	ENSP00000238256:p.Pro1041fs	146.0	0.0		202.0	13.0	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Frame_Shift_Del	DEL	ENST00000238256.3	hg19	CCDS48007.1																																																																																			.	.		0.557	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
ZNF354A	6940	hgsc.bcm.edu	37	5	178139937	178139937	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:178139937delA	ENST00000335815.2	-	5	1139	c.942delT	c.(940-942)tttfs	p.F314fs		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	314					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|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;0.185)		TTTGATGTATAAAAAGGCCTG	0.393																																					p.I315fs		Atlas-INDEL	.											.	ZNF354A	74	.	0			c.943delA						.						54.0	57.0	56.0					5																	178139937		2202	4300	6502	SO:0001589	frameshift_variant	6940	exon5			.	AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"""Zinc fingers, C2H2-type"", ""-"""	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.942delT	chr5.hg19:g.178139937delA	ENSP00000337122:p.Phe314fs	104.0	0.0		158.0	12.0	NM_005649	Q9UNJ8	Frame_Shift_Del	DEL	ENST00000335815.2	hg19	CCDS4438.1																																																																																			.	.		0.393	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649	
RACGAP1	29127	hgsc.bcm.edu	37	12	50399098	50399098	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:50399098delT	ENST00000427314.2	-	6	589	c.366delA	c.(364-366)aaafs	p.K122fs	RACGAP1_ENST00000454520.2_Frame_Shift_Del_p.K122fs|RACGAP1_ENST00000434422.1_Frame_Shift_Del_p.K122fs|RACGAP1_ENST00000551016.1_Frame_Shift_Del_p.K122fs|RACGAP1_ENST00000312377.5_Frame_Shift_Del_p.K122fs|RACGAP1_ENST00000547061.1_5'Flank|RACGAP1_ENST00000547905.1_Frame_Shift_Del_p.K122fs	NM_013277.3	NP_037409.2			Rac GTPase activating protein 1											cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						CCAGAGCTGATTTTTGCTCCT	0.458																																					p.S123fs		Atlas-INDEL	.											.	RACGAP1	36	.	0			c.367delT						.						136.0	118.0	124.0					12																	50399098		2203	4300	6503	SO:0001589	frameshift_variant	29127	exon6			.		CCDS8795.1	12q13	2004-05-17				ENSG00000161800			9804	protein-coding gene	gene with protein product		604980				9497316	Standard	NM_013277		Approved	MgcRacGAP	uc001rvs.2	Q9H0H5		ENST00000427314.2:c.366delA	chr12.hg19:g.50399098delT	ENSP00000404190:p.Lys122fs	143.0	0.0		144.0	10.0	NM_013277		Frame_Shift_Del	DEL	ENST00000427314.2	hg19	CCDS8795.1																																																																																			.	.		0.458	RACGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405997.1	NM_013277	
KLHDC8B	200942	hgsc.bcm.edu	37	3	49210244	49210244	+	Frame_Shift_Del	DEL	C	C	-	rs201475255	byFrequency	TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr3:49210244delC	ENST00000332780.2	+	2	251	c.42delC	c.(40-42)ttcfs	p.F14fs	KLHDC8B_ENST00000476495.2_3'UTR	NM_173546.2	NP_775817.1	Q8IXV7	KLD8B_HUMAN	kelch domain containing 8B	14						cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|stomach(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGCAAGTGTTCCCCCCCATGC	0.637																																					p.F14fs		Atlas-INDEL	.											.	KLHDC8B	28	.	0			c.41delT						.						54.0	52.0	53.0					3																	49210244		2203	4300	6503	SO:0001589	frameshift_variant	200942	exon2			.		CCDS2791.1	3p21.31	2008-02-05			ENSG00000185909	ENSG00000185909			28557	protein-coding gene	gene with protein product		613169					Standard	NM_173546		Approved	MGC35097	uc003cwh.3	Q8IXV7	OTTHUMG00000156814	ENST00000332780.2:c.42delC	chr3.hg19:g.49210244delC	ENSP00000327468:p.Phe14fs	128.0	0.0		145.0	10.0	NM_173546		Frame_Shift_Del	DEL	ENST00000332780.2	hg19	CCDS2791.1																																																																																			.	.		0.637	KLHDC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345974.1	NM_173546	
NFAT5	10725	hgsc.bcm.edu	37	16	69727260	69727260	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:69727260delT	ENST00000354436.2	+	12	3796	c.3478delT	c.(3478-3480)tttfs	p.F1161fs	NFAT5_ENST00000393742.2_Frame_Shift_Del_p.F1085fs|NFAT5_ENST00000349945.1_Frame_Shift_Del_p.F1085fs|NFAT5_ENST00000432919.1_Frame_Shift_Del_p.F1179fs|NFAT5_ENST00000566899.1_Frame_Shift_Del_p.F1085fs|NFAT5_ENST00000567239.1_Frame_Shift_Del_p.F1178fs	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	1161					cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						CCAAGAAGCATTTTTTGCAGC	0.438																																					p.A1177fs		Atlas-INDEL	.											.	NFAT5	184	.	0			c.3531delA						.						140.0	132.0	134.0					16																	69727260		2198	4300	6498	SO:0001589	frameshift_variant	10725	exon13			.	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"""Nuclear factor of activated T-cells"""	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.3478delT	chr16.hg19:g.69727260delT	ENSP00000346420:p.Phe1161fs	112.0	0.0		206.0	15.0	NM_138713	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	Frame_Shift_Del	DEL	ENST00000354436.2	hg19	CCDS10881.1																																																																																			.	.		0.438	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714	
DEFB131	644414	hgsc.bcm.edu	37	4	9446272	9446272	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:9446272delT	ENST00000334879.1	+	1	13	c.13delT	c.(13-15)tttfs	p.F6fs		NM_001040448.2|NM_001242853.1	NP_001035538.2|NP_001229782.1	P59861	DB131_HUMAN	defensin, beta 131	6					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				lung(2)	2						GAGGGTCTTGTTTTTTGTCTT	0.368																																					p.L4fs		Atlas-INDEL	.											.,1	DEFB131	12	.	0			c.12delG						.						166.0	131.0	142.0					4																	9446272		1841	4085	5926	SO:0001589	frameshift_variant	644414	exon1			.	AF529414	CCDS43213.1	4p16.1	2010-03-30			ENSG00000186146	ENSG00000186146		"""Defensins, beta"""	18108	protein-coding gene	gene with protein product						11854508, 16033865, 12600824	Standard	NM_001040448		Approved	DEFB-31	uc011bwt.2	P59861	OTTHUMG00000160187	ENST00000334879.1:c.13delT	chr4.hg19:g.9446272delT	ENSP00000335538:p.Phe6fs	208.0	0.0		213.0	14.0	NM_001040448		Frame_Shift_Del	DEL	ENST00000334879.1	hg19	CCDS43213.1																																																																																			.	.		0.368	DEFB131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359607.1	NM_001040448	
ZBTB12	221527	hgsc.bcm.edu	37	6	31868583	31868583	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:31868583delG	ENST00000375527.2	-	2	675	c.500delC	c.(499-501)ccafs	p.P171fs	C2_ENST00000452323.2_5'Flank|C2_ENST00000469372.1_Intron	NM_181842.2	NP_862825.1	Q9Y330	ZBT12_HUMAN	zinc finger and BTB domain containing 12	171	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)			endometrium(2)|kidney(1)|lung(5)|prostate(1)|skin(1)	10						AGGTGGGGGTGGGGGCTTCGG	0.617																																					p.P167fs		Atlas-INDEL	.											.	ZBTB12	25	.	0			c.501delA						.						22.0	27.0	25.0					6																	31868583		2203	4296	6499	SO:0001589	frameshift_variant	221527	exon2			.	BC043609	CCDS4727.1	6p21.31	2013-01-08	2004-04-15	2004-04-16	ENSG00000204366	ENSG00000204366		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	19066	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 46"""	C6orf46		9545376	Standard	NM_181842		Approved	G10, NG35, D6S59E	uc003nyd.1	Q9Y330	OTTHUMG00000031169	ENST00000375527.2:c.500delC	chr6.hg19:g.31868583delG	ENSP00000364677:p.Pro171fs	59.0	0.0		164.0	12.0	NM_181842	B0UY00|Q5JQ98	Frame_Shift_Del	DEL	ENST00000375527.2	hg19	CCDS4727.1																																																																																			.	.		0.617	ZBTB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076315.2	NM_181842	
MAPK14	1432	hgsc.bcm.edu	37	6	36063826	36063826	+	Frame_Shift_Del	DEL	A	A	-	rs150174370		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:36063826delA	ENST00000229794.4	+	9	1133	c.745delA	c.(745-747)aaafs	p.K249fs	MAPK14_ENST00000310795.4_Frame_Shift_Del_p.K249fs|MAPK14_ENST00000229795.3_Intron|MAPK14_ENST00000468133.1_Frame_Shift_Del_p.K172fs	NM_139012.2|NM_139014.2	NP_620581.1|NP_620583.1	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14	249	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cartilage condensation (GO:0001502)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to ionizing radiation (GO:0071479)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chemotaxis (GO:0006935)|chondrocyte differentiation (GO:0002062)|DNA damage checkpoint (GO:0000077)|fatty acid oxidation (GO:0019395)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoclast differentiation (GO:0030316)|p38MAPK cascade (GO:0038066)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myoblast fusion (GO:1901741)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to muramyl dipeptide (GO:0032495)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|signal transduction in response to DNA damage (GO:0042770)|skeletal muscle tissue development (GO:0007519)|stress-activated MAPK cascade (GO:0051403)|stress-induced premature senescence (GO:0090400)|striated muscle cell differentiation (GO:0051146)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|MAP kinase kinase activity (GO:0004708)|NFAT protein binding (GO:0051525)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|stomach(1)	16						GCTTTTGAAGAAAATCTCCTC	0.438																																					p.K248fs	Pancreas(20;8 363 26997 32430 36377 43317 49243 50560 51947)|Colon(176;951 1093 20177 30266 32328 34418 35271 44052 51610)	Atlas-INDEL	.											MAPK14_ENST00000229794,NS,carcinoma,0,1	MAPK14	75	.	0			c.744delG						.						116.0	114.0	115.0					6																	36063826		2203	4300	6503	SO:0001589	frameshift_variant	1432	exon9			.	L35263	CCDS4815.1, CCDS4816.1, CCDS4817.1	6p21.3-p21.2	2011-06-09			ENSG00000112062	ENSG00000112062		"""Mitogen-activated protein kinase cascade / Kinases"""	6876	protein-coding gene	gene with protein product	"""p38 MAP kinase"""	600289		CSPB1, CSBP1, CSBP2		7997261	Standard	NM_139012		Approved	PRKM14, p38, Mxi2, PRKM15	uc003olq.3	Q16539	OTTHUMG00000159806	ENST00000229794.4:c.745delA	chr6.hg19:g.36063826delA	ENSP00000229794:p.Lys249fs	118.0	0.0		118.0	10.0	NM_139014	A6ZJ92|A8K6P4|B0LPH0|B5TY32|O60776|Q13083|Q14084|Q8TDX0	Frame_Shift_Del	DEL	ENST00000229794.4	hg19	CCDS4816.1																																																																																			.	.		0.438	MAPK14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357450.1	NM_001315	
HIRA	7290	hgsc.bcm.edu	37	22	19346949	19346949	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:19346949delC	ENST00000263208.5	-	18	2400	c.2144delG	c.(2143-2145)ggcfs	p.G715fs	HIRA_ENST00000340170.4_Intron|HIRA_ENST00000541063.1_Frame_Shift_Del_p.G671fs|HIRA_ENST00000546308.1_Frame_Shift_Del_p.G671fs	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	715	Interaction with CCNA1.|Interaction with PAX3. {ECO:0000250}.|Interaction with histone H2B.				anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					CAGCTTCACGCCCCCCACCAC	0.597																																					p.G715fs		Atlas-INDEL	.											.	HIRA	100	.	0			c.2145delC						.						146.0	121.0	129.0					22																	19346949		2203	4300	6503	SO:0001589	frameshift_variant	7290	exon18			.	X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"""WD repeat domain containing"""	4916	protein-coding gene	gene with protein product	"""DiGeorge critical region gene 1"""	600237	"""HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)"", ""HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"""	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.2144delG	chr22.hg19:g.19346949delC	ENSP00000263208:p.Gly715fs	112.0	0.0		154.0	10.0	NM_003325	Q05BU9|Q8IXN2	Frame_Shift_Del	DEL	ENST00000263208.5	hg19	CCDS13759.1																																																																																			.	.		0.597	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325	
GNPAT	8443	hgsc.bcm.edu	37	1	231403484	231403484	+	Frame_Shift_Del	DEL	A	A	-	rs201138311		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:231403484delA	ENST00000366647.4	+	9	1283	c.1114delA	c.(1114-1116)aaafs	p.K372fs	GNPAT_ENST00000366646.3_Frame_Shift_Del_p.K311fs	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	372					cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				AGTTGCCTACAAAATGGAGCT	0.438																																					p.Y371X		Atlas-INDEL	.											.	GNPAT	73	.	0			c.1113delC						.						126.0	120.0	122.0					1																	231403484		2203	4300	6503	SO:0001589	frameshift_variant	8443	exon9			.	AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024	ENST00000366647.4:c.1114delA	chr1.hg19:g.231403484delA	ENSP00000355607:p.Lys372fs	73.0	0.0		146.0	10.0	NM_014236	B4DNM9|Q5TBH7|Q9BWC2	Frame_Shift_Del	DEL	ENST00000366647.4	hg19	CCDS1592.1																																																																																			.	.		0.438	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1		
DOCK5	80005	hgsc.bcm.edu	37	8	25136115	25136115	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr8:25136115delC	ENST00000276440.7	+	5	299	c.255delC	c.(253-255)ctcfs	p.L85fs	DOCK5_ENST00000481100.1_Frame_Shift_Del_p.L85fs	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	85					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)		CTGGCGAGCTCCCCCTGGTGC	0.552																																					p.L85fs	Pancreas(145;34 1887 3271 10937 30165)	Atlas-INDEL	.											.	DOCK5	167	.	0			c.254delT						.						137.0	112.0	121.0					8																	25136115		2203	4300	6503	SO:0001589	frameshift_variant	80005	exon5			.		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.255delC	chr8.hg19:g.25136115delC	ENSP00000276440:p.Leu85fs	215.0	0.0		198.0	12.0	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Frame_Shift_Del	DEL	ENST00000276440.7	hg19	CCDS6047.1																																																																																			.	.		0.552	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
ALS2CR12	130540	hgsc.bcm.edu	37	2	202164026	202164026	+	Intron	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:202164026delA	ENST00000286190.5	-	11	926				ALS2CR12_ENST00000439709.1_Intron|ALS2CR12_ENST00000405148.2_Intron|ALS2CR12_ENST00000392257.3_Intron			Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12						regulation of GTPase activity (GO:0043087)	outer dense fiber (GO:0001520)|sperm fibrous sheath (GO:0035686)|sperm flagellum (GO:0036126)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)	21						AAGAGCTCCTAAAAACAATTT	0.383																																					.		Atlas-INDEL	.											.	ALS2CR12	54	.	0			c.880-2T>-						.						171.0	168.0	169.0					2																	202164026		2203	4300	6503	SO:0001627	intron_variant	130540	exon13			.	AB053314	CCDS2346.1, CCDS46488.1	2q33.1	2009-10-06			ENSG00000155749	ENSG00000155749			14439	protein-coding gene	gene with protein product							Standard	XM_006712272		Approved		uc002uya.4	Q96Q35	OTTHUMG00000132824	ENST00000286190.5:c.880-3T>-	chr2.hg19:g.202164026delA		117.0	0.0		145.0	13.0	NM_001127391	G5E9S3|Q53TT6|Q8N1B6	Splice_Site	DEL	ENST00000286190.5	hg19	CCDS2346.1																																																																																			.	.		0.383	ALS2CR12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256286.1	NM_139163	
ZNF385B	151126	hgsc.bcm.edu	37	2	180634453	180634453	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:180634453delA	ENST00000410066.1	-	3	633	c.30delT	c.(28-30)tttfs	p.F10fs		NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	10	Required for induction of apoptosis.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			CCTTTTCTTCAAAGCCCCGTA	0.418																																					p.E11fs	Colon(155;204 2491 32774 51842)	Atlas-INDEL	.											.	ZNF385B	68	.	0			c.31delG						.						64.0	68.0	67.0					2																	180634453		2203	4300	6503	SO:0001589	frameshift_variant	151126	exon3			.	AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"""zinc finger protein 533"""	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.30delT	chr2.hg19:g.180634453delA	ENSP00000386845:p.Phe10fs	118.0	0.0		146.0	10.0	NM_152520	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Frame_Shift_Del	DEL	ENST00000410066.1	hg19	CCDS33339.1																																																																																			.	.		0.418	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520	
AP1G2	8906	hgsc.bcm.edu	37	14	24032654	24032654	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:24032654delC	ENST00000308724.5	-	13	2100	c.1345delG	c.(1345-1347)gccfs	p.A449fs	AP1G2_ENST00000397120.3_Frame_Shift_Del_p.A449fs|RP11-66N24.3_ENST00000555968.1_RNA|RP11-66N24.4_ENST00000553985.1_RNA|AP1G2_ENST00000556277.1_5'Flank	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	449					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		AGCTCCTGGGCCCCCCCAATC	0.612											OREG0022605	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A449fs		Atlas-INDEL	.											.,1	AP1G2	75	.	0			c.1346delC						.						65.0	53.0	57.0					14																	24032654		2203	4300	6503	SO:0001589	frameshift_variant	8906	exon14			.	AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.1345delG	chr14.hg19:g.24032654delC	ENSP00000312442:p.Ala449fs	163.0	0.0	768	249.0	15.0	NM_003917	D3DS51|O75504	Frame_Shift_Del	DEL	ENST00000308724.5	hg19	CCDS9602.1																																																																																			.	.		0.612	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917	
MYO18B	84700	hgsc.bcm.edu	37	22	26164836	26164836	+	Frame_Shift_Del	DEL	G	G	-	rs369889484		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr22:26164836delG	ENST00000407587.2	+	4	1122	c.953delG	c.(952-954)tggfs	p.W318fs	MYO18B_ENST00000335473.7_Frame_Shift_Del_p.W318fs|MYO18B_ENST00000536101.1_Frame_Shift_Del_p.W318fs			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	318						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GGGAGAAAGTGGGGAGGTTTC	0.537																																					p.W318fs		Atlas-INDEL	.											.	MYO18B	322	.	0			c.952delT						.						29.0	30.0	30.0					22																	26164836		1949	4146	6095	SO:0001589	frameshift_variant	84700	exon4			.	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.953delG	chr22.hg19:g.26164836delG	ENSP00000386096:p.Trp318fs	99.0	0.0		127.0	11.0	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Frame_Shift_Del	DEL	ENST00000407587.2	hg19																																																																																				.	.		0.537	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
DCST2	127579	hgsc.bcm.edu	37	1	155001838	155001838	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:155001838delA	ENST00000368424.3	-	8	1271	c.1213delT	c.(1213-1215)tacfs	p.Y405fs	DCST2_ENST00000295536.5_Frame_Shift_Del_p.Y405fs	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	405						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TCCAGAATGTAAAAAAACTTC	0.537																																					p.Y405fs		Atlas-INDEL	.											.	DCST2	80	.	0			c.1214delA						.						123.0	115.0	118.0					1																	155001838		2203	4300	6503	SO:0001589	frameshift_variant	127579	exon8			.	AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.1213delT	chr1.hg19:g.155001838delA	ENSP00000357409:p.Tyr405fs	93.0	0.0		209.0	13.0	NM_144622	Q2M2R2|Q8N810|Q96M03	Frame_Shift_Del	DEL	ENST00000368424.3	hg19	CCDS1082.2																																																																																			.	.		0.537	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622	
SLC35D3	340146	hgsc.bcm.edu	37	6	137243900	137243900	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:137243900delC	ENST00000331858.4	+	1	499	c.334delC	c.(334-336)cccfs	p.P112fs		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	112					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	13	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000136)|OV - Ovarian serous cystadenocarcinoma(155;0.00365)		GCGCTGCCTGCCCCTGGTCAC	0.711																																					p.L111fs		Atlas-INDEL	.											.	SLC35D3	33	.	0			c.333delG						.						12.0	13.0	13.0					6																	137243900		2178	4274	6452	SO:0001589	frameshift_variant	340146	exon1			.		CCDS34544.1	6q23.2	2013-05-22			ENSG00000182747	ENSG00000182747		"""Solute carriers"""	15621	protein-coding gene	gene with protein product		612519		FRCL1			Standard	NM_001008783		Approved		uc003qhe.3	Q5M8T2	OTTHUMG00000015651	ENST00000331858.4:c.334delC	chr6.hg19:g.137243900delC	ENSP00000333591:p.Pro112fs	252.0	0.0		218.0	19.0	NM_001008783	B4DI58|Q5QNZ6|Q6NX71	Frame_Shift_Del	DEL	ENST00000331858.4	hg19	CCDS34544.1																																																																																			.	.		0.711	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017	
SLC35D2	11046	hgsc.bcm.edu	37	9	99099002	99099002	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:99099002delA	ENST00000253270.7	-	9	811	c.749delT	c.(748-750)ttgfs	p.L250fs	SLC35D2_ENST00000375259.4_Intron	NM_007001.2	NP_008932.2	Q76EJ3	S35D2_HUMAN	solute carrier family 35 (UDP-GlcNAc/UDP-glucose transporter), member D2	250					carbohydrate derivative transport (GO:1901264)|carbohydrate metabolic process (GO:0005975)|carbohydrate transport (GO:0008643)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)			endometrium(3)|large_intestine(3)|lung(4)|skin(2)	12		Acute lymphoblastic leukemia(62;0.0167)				TTCTTACCCCAAAAAACAGGA	0.328																																					p.L250fs		Atlas-INDEL	.											.	SLC35D2	20	.	0			c.750delG						.						55.0	49.0	51.0					9																	99099002		2192	4297	6489	SO:0001589	frameshift_variant	11046	exon9			.	AB122077	CCDS6717.1, CCDS69625.1	9q22.33	2013-07-17	2013-07-17		ENSG00000130958	ENSG00000130958		"""Solute carriers"""	20799	protein-coding gene	gene with protein product		609182	"""solute carrier family 35, member D2"""			15607426	Standard	NM_007001		Approved	UGTrel8, SQV7L	uc004awc.3	Q76EJ3	OTTHUMG00000020293	ENST00000253270.7:c.749delT	chr9.hg19:g.99099002delA	ENSP00000253270:p.Leu250fs	115.0	0.0		149.0	10.0	NM_007001	O95454|Q498C1|Q75W21|Q7Z5X5	Frame_Shift_Del	DEL	ENST00000253270.7	hg19	CCDS6717.1																																																																																			.	.		0.328	SLC35D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053261.1		
TPCN1	53373	hgsc.bcm.edu	37	12	113704017	113704017	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:113704017delC	ENST00000335509.6	+	4	584	c.270delC	c.(268-270)cacfs	p.H90fs	TPCN1_ENST00000392569.4_Frame_Shift_Del_p.H22fs|TPCN1_ENST00000541517.1_Frame_Shift_Del_p.H162fs|TPCN1_ENST00000550785.1_Frame_Shift_Del_p.H162fs	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	90					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						TCTTCACCCACCCCAAGGATG	0.587																																					p.H162fs		Atlas-INDEL	.											.	TPCN1	109	.	0			c.485delA						.						202.0	177.0	186.0					12																	113704017		2203	4300	6503	SO:0001589	frameshift_variant	53373	exon5			.	AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"""Voltage-gated ion channels / Two-pore channels"""	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.270delC	chr12.hg19:g.113704017delC	ENSP00000335300:p.His90fs	179.0	0.0		149.0	10.0	NM_001143819	A7E258|Q86XS9|Q8NC20	Frame_Shift_Del	DEL	ENST00000335509.6	hg19	CCDS31908.1																																																																																			.	.		0.587	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901	
SEC31A	22872	hgsc.bcm.edu	37	4	83763594	83763594	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:83763594delC	ENST00000395310.2	-	22	2849	c.2667delG	c.(2665-2667)gggfs	p.G889fs	SEC31A_ENST00000348405.4_Frame_Shift_Del_p.G850fs|SEC31A_ENST00000500777.2_Intron|SEC31A_ENST00000509142.1_Intron|SEC31A_ENST00000432794.1_Frame_Shift_Del_p.G889fs|SEC31A_ENST00000448323.1_Frame_Shift_Del_p.G889fs|SEC31A_ENST00000264405.5_Frame_Shift_Del_p.G653fs|SEC31A_ENST00000508502.1_Frame_Shift_Del_p.G889fs|SEC31A_ENST00000513858.1_Intron|SEC31A_ENST00000326950.5_Frame_Shift_Del_p.G850fs|SEC31A_ENST00000443462.2_Frame_Shift_Del_p.G884fs|SEC31A_ENST00000355196.2_Frame_Shift_Del_p.G889fs|SEC31A_ENST00000505984.1_Frame_Shift_Del_p.G850fs|SEC31A_ENST00000505472.1_Frame_Shift_Del_p.G920fs|SEC31A_ENST00000311785.7_Intron	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	889	Interaction with PDCD6.|Pro-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				ACATTGCTGACCCCCCTGTTC	0.458																																					p.S890fs		Atlas-INDEL	.											.	SEC31A	227	.	0			c.2668delT						.						43.0	36.0	38.0					4																	83763594		2203	4300	6503	SO:0001589	frameshift_variant	22872	exon22			.	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"""WD repeat domain containing"""	17052	protein-coding gene	gene with protein product		610257	"""SEC31-like 1 (S. cerevisiae)"", ""Sec31 homolog A (S. cerevisiae)"""	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.2667delG	chr4.hg19:g.83763594delC	ENSP00000378721:p.Gly889fs	127.0	0.0		151.0	12.0	NM_001077207	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Frame_Shift_Del	DEL	ENST00000395310.2	hg19	CCDS3596.1																																																																																			.	.		0.458	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211	
IRAK1	3654	hgsc.bcm.edu	37	X	153278528	153278528	+	Frame_Shift_Del	DEL	C	C	-	rs192366956		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:153278528delC	ENST00000369980.3	-	12	2063	c.1896delG	c.(1894-1896)gggfs	p.G632fs	IRAK1_ENST00000477274.1_Intron|IRAK1_ENST00000393687.2_Frame_Shift_Del_p.G602fs|IRAK1_ENST00000429936.2_Frame_Shift_Del_p.G628fs|IRAK1_ENST00000369974.2_Frame_Shift_Del_p.G553fs|IRAK1_ENST00000393682.1_Frame_Shift_Del_p.G613fs	NM_001025242.1|NM_001569.3	NP_001020413.1|NP_001560.2	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	632					activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|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)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|interleukin-1 receptor complex (GO:0045323)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|NF-kappaB-inducing kinase activity (GO:0004704)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(15)|ovary(2)	25	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTGGGCCACTCCCCCAGCTCG	0.667																																					p.S633fs		Atlas-INDEL	.											.	IRAK1	107	.	0			c.1897delA						.						14.0	16.0	15.0					X																	153278528		2184	4254	6438	SO:0001589	frameshift_variant	3654	exon12			.	L76191	CCDS14740.1, CCDS35443.1, CCDS35444.1	Xq28	2011-07-08			ENSG00000184216	ENSG00000184216			6112	protein-coding gene	gene with protein product		300283				9374458, 8599092	Standard	XM_005274668		Approved	IRAK, pelle	uc004fjs.1	P51617	OTTHUMG00000024228	ENST00000369980.3:c.1896delG	chrX.hg19:g.153278528delC	ENSP00000358997:p.Gly632fs	85.0	0.0		123.0	10.0	NM_001569	D3DWW3|D3DWW4|Q7Z5V4|Q96C06|Q96RL2	Frame_Shift_Del	DEL	ENST00000369980.3	hg19	CCDS14740.1																																																																																			.	.		0.667	IRAK1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061143.3		
CLDN8	9073	hgsc.bcm.edu	37	21	31587622	31587622	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr21:31587622delT	ENST00000399899.1	-	1	769	c.622delA	c.(622-624)agtfs	p.S208fs	CLDN8_ENST00000286809.1_Frame_Shift_Del_p.S208fs	NM_199328.2	NP_955360.1	P56748	CLD8_HUMAN	claudin 8	208					calcium-independent cell-cell adhesion (GO:0016338)	basolateral plasma membrane (GO:0016323)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|large_intestine(6)|lung(6)	15						GTGTGATAACTTTTTTGGGTT	0.423																																					p.S208fs		Atlas-INDEL	.											.	CLDN8	40	.	0			c.623delG						.						152.0	138.0	142.0					21																	31587622		2203	4300	6503	SO:0001589	frameshift_variant	9073	exon1			.	AJ250711	CCDS13587.1	21q22.1	2008-07-31			ENSG00000156284	ENSG00000156284		"""Claudins"""	2050	protein-coding gene	gene with protein product		611231				9892664	Standard	NM_199328		Approved		uc002ynu.2	P56748	OTTHUMG00000081872	ENST00000399899.1:c.622delA	chr21.hg19:g.31587622delT	ENSP00000382783:p.Ser208fs	207.0	0.0		182.0	12.0	NM_199328	D3DSE3|Q53EX7	Frame_Shift_Del	DEL	ENST00000399899.1	hg19	CCDS13587.1																																																																																			.	.		0.423	CLDN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182260.1	NM_199328	
PCED1B	91523	hgsc.bcm.edu	37	12	47630043	47630043	+	Frame_Shift_Del	DEL	T	T	-	rs202147059		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:47630043delT	ENST00000546455.1	+	4	1928	c.1197delT	c.(1195-1197)ggtfs	p.G399fs	PCED1B_ENST00000432328.1_Frame_Shift_Del_p.G399fs|RP11-493L12.3_ENST00000547748.1_RNA			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	399	Pro-rich.						hydrolase activity (GO:0016787)										TACATAGGGGTTTTGGCAGGT	0.582																																					p.G399fs		Atlas-INDEL	.											.	.	.	.	0			c.1196delG						.																																			SO:0001589	frameshift_variant	91523	exon2			.	BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"""family with sequence similarity 113, member B"""	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617	ENST00000546455.1:c.1197delT	chr12.hg19:g.47630043delT	ENSP00000446688:p.Gly399fs	127.0	0.0		186.0	12.0	NM_138371	Q96B20	Frame_Shift_Del	DEL	ENST00000546455.1	hg19	CCDS8752.1																																																																																			.	.		0.582	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371	
NFATC1	4772	hgsc.bcm.edu	37	18	77227633	77227633	+	Intron	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr18:77227633delT	ENST00000427363.2	+	8	2092				NFATC1_ENST00000586434.1_Intron|NFATC1_ENST00000253506.5_Intron|NFATC1_ENST00000591814.1_Frame_Shift_Del_p.F716fs|NFATC1_ENST00000587635.1_3'UTR|NFATC1_ENST00000329101.4_Intron|NFATC1_ENST00000318065.5_Intron|NFATC1_ENST00000545796.1_Intron|NFATC1_ENST00000397790.2_Intron|NFATC1_ENST00000592223.1_Frame_Shift_Del_p.F703fs|NFATC1_ENST00000542384.1_Intron			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1						calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	CGTGGGGTGCTTTTTCTAAAG	0.537																																					p.C714fs	GBM(151;1210 2593 28719 45011)	Atlas-INDEL	.											.	NFATC1	105	.	0			c.2142delC						.						69.0	60.0	63.0					18																	77227633		2202	4300	6502	SO:0001627	intron_variant	4772	exon8			.	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.2092+51T>-	chr18.hg19:g.77227633delT		76.0	0.0		149.0	10.0	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Frame_Shift_Del	DEL	ENST00000427363.2	hg19																																																																																				.	.		0.537	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
GABRQ	55879	hgsc.bcm.edu	37	X	151820189	151820189	+	Frame_Shift_Del	DEL	C	C	-	rs76177030		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chrX:151820189delC	ENST00000370306.2	+	8	1122	c.1102delC	c.(1102-1104)cccfs	p.P368fs		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	368					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)	ACACAGGAGACCCCGAAGAGT	0.517																																					p.R367fs		Atlas-INDEL	.											.	GABRQ	131	.	0			c.1101delA						.						128.0	107.0	114.0					X																	151820189		2203	4300	6503	SO:0001589	frameshift_variant	55879	exon8			.	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.1102delC	chrX.hg19:g.151820189delC	ENSP00000359329:p.Pro368fs	78.0	0.0		105.0	11.0	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Frame_Shift_Del	DEL	ENST00000370306.2	hg19	CCDS14707.1																																																																																			.	.		0.517	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558	
JAZF1	221895	hgsc.bcm.edu	37	7	28220144	28220144	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:28220144delC	ENST00000283928.5	-	1	218	c.53delG	c.(52-54)ggcfs	p.G18fs	JAZF1-AS1_ENST00000436758.1_RNA|JAZF1-AS1_ENST00000455963.1_RNA	NM_175061.3	NP_778231.2	Q86VZ6	JAZF1_HUMAN	JAZF zinc finger 1	18					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|transcription corepressor activity (GO:0003714)		JAZF1/SUZ12(133)	endometrium(1)|large_intestine(1)|lung(4)	6						GAGTCCGCAGCCCCCGAATCG	0.682			T	SUZ12	endometrial stromal tumours																																p.G18fs		Atlas-INDEL	.		Dom	yes		7	7p15.2-p15.1	221895	juxtaposed with another zinc finger gene 1		M	.	JAZF1	13	.	0			c.54delC						.						41.0	41.0	41.0					7																	28220144		2203	4300	6503	SO:0001589	frameshift_variant	221895	exon1			.	BC047229	CCDS5416.1	7p15.2-p15.1	2010-04-14			ENSG00000153814	ENSG00000153814		"""Zinc fingers, C2H2-type"""	28917	protein-coding gene	gene with protein product		606246				8401585	Standard	XM_006715656		Approved	TIP27, DKFZp761K2222, ZNF802	uc003szn.3	Q86VZ6	OTTHUMG00000128545	ENST00000283928.5:c.53delG	chr7.hg19:g.28220144delC	ENSP00000283928:p.Gly18fs	113.0	0.0		187.0	12.0	NM_175061	A4D195|Q8N3L7	Frame_Shift_Del	DEL	ENST00000283928.5	hg19	CCDS5416.1																																																																																			.	.		0.682	JAZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250382.2	NM_175061	
N4BP1	9683	hgsc.bcm.edu	37	16	48596002	48596002	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr16:48596002delT	ENST00000262384.3	-	2	788	c.552delA	c.(550-552)aaafs	p.K184fs	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	184					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)				TCAAAAGTTCTTTTTTCAAGG	0.368																																					p.E185fs		Atlas-INDEL	.											.	N4BP1	121	.	0			c.553delG						.						98.0	87.0	91.0					16																	48596002		1851	4094	5945	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.552delA	chr16.hg19:g.48596002delT	ENSP00000262384:p.Lys184fs	121.0	0.0		128.0	11.0	NM_153029	A7MD49|Q2YDX1	Frame_Shift_Del	DEL	ENST00000262384.3	hg19	CCDS45479.1																																																																																			.	.		0.368	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664	
HSP90B1	7184	hgsc.bcm.edu	37	12	104340586	104340586	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:104340586delT	ENST00000299767.5	+	16	2311	c.2129delT	c.(2128-2130)gttfs	p.V710fs		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	710					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	GATAAAACAGTTTTGGATCTT	0.353																																					p.V710fs		Atlas-INDEL	.											.	HSP90B1	72	.	0			c.2128delG						.						74.0	72.0	73.0					12																	104340586		2203	4300	6503	SO:0001589	frameshift_variant	7184	exon16			.	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"""Heat shock proteins / HSPC"""	12028	protein-coding gene	gene with protein product		191175	"""tumor rejection antigen (gp96) 1"""	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.2129delT	chr12.hg19:g.104340586delT	ENSP00000299767:p.Val710fs	123.0	0.0		189.0	13.0	NM_003299	Q96A97	Frame_Shift_Del	DEL	ENST00000299767.5	hg19	CCDS9094.1																																																																																			.	.		0.353	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299	
C6orf89	221477	hgsc.bcm.edu	37	6	36870160	36870160	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:36870160delA	ENST00000480824.2	+	4	647	c.353delA	c.(352-354)gaafs	p.E118fs	C6orf89_ENST00000373685.1_Frame_Shift_Del_p.E118fs|C6orf89_ENST00000359359.2_Frame_Shift_Del_p.E12fs|C6orf89_ENST00000355190.3_Frame_Shift_Del_p.E125fs|C6orf89_ENST00000510325.2_Frame_Shift_Del_p.E12fs			Q6UWU4	CF089_HUMAN	chromosome 6 open reading frame 89	118					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	15						TACATGTCAGAAAATAAGGGA	0.438																																					p.E125fs		Atlas-INDEL	.											.	C6orf89	39	.	0			c.373delG						.						117.0	111.0	113.0					6																	36870160		2203	4300	6503	SO:0001589	frameshift_variant	221477	exon3			.	AK058086	CCDS4827.1, CCDS69100.1, CCDS75444.1	6p21.31	2013-03-14			ENSG00000198663	ENSG00000198663			21114	protein-coding gene	gene with protein product	"""bombesin receptor activated protein"""					21857995, 23460338	Standard	NM_152734		Approved	FLJ25357, BRAP	uc003omw.3	Q6UWU4	OTTHUMG00000014613	ENST00000480824.2:c.353delA	chr6.hg19:g.36870160delA	ENSP00000475947:p.Glu118fs	135.0	0.0		155.0	10.0	NM_152734	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Frame_Shift_Del	DEL	ENST00000480824.2	hg19																																																																																				.	.		0.438	C6orf89-004	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000040387.2	NM_152734	
MAP1A	4130	hgsc.bcm.edu	37	15	43816721	43816721	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr15:43816721delA	ENST00000300231.5	+	4	3500	c.3050delA	c.(3049-3051)gaafs	p.E1017fs	MAP1A_ENST00000399453.1_Frame_Shift_Del_p.E1017fs|MAP1A_ENST00000382031.1_Frame_Shift_Del_p.E1255fs			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1017					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	CCAGTGGAAGAAAAGTCTGAG	0.562																																					p.E1017fs		Atlas-INDEL	.											.	MAP1A	189	.	0			c.3049delG						.						61.0	64.0	63.0					15																	43816721		1995	4159	6154	SO:0001589	frameshift_variant	4130	exon4			.	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.3050delA	chr15.hg19:g.43816721delA	ENSP00000300231:p.Glu1017fs	108.0	0.0		123.0	10.0	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Frame_Shift_Del	DEL	ENST00000300231.5	hg19	CCDS42031.1																																																																																			.	.		0.562	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
SREK1IP1	285672	hgsc.bcm.edu	37	5	64050152	64050152	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr5:64050152delT	ENST00000513458.4	-	2	218	c.51delA	c.(49-51)aaafs	p.K17fs	SREK1IP1_ENST00000506252.1_5'UTR	NM_173829.3	NP_776190.1	Q8N9Q2	SR1IP_HUMAN	SREK1-interacting protein 1	17					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)		nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6						GGTAGCCACATTTTTTACAGC	0.353																																					p.C18fs		Atlas-INDEL	.											.	SREK1IP1	28	.	0			c.52delT						.						93.0	86.0	89.0					5																	64050152		2203	4300	6503	SO:0001589	frameshift_variant	285672	exon2			.	AK094073	CCDS34171.1	5q12.3	2010-09-20	2010-09-20	2010-09-20	ENSG00000153006	ENSG00000153006			26716	protein-coding gene	gene with protein product	"""p18 splicing regulatory protein"""		"""SFRS12-interacting protein 1"""	SFRS12IP1		15456940	Standard	NM_173829		Approved	FLJ36754, P18SRP	uc003jtk.3	Q8N9Q2	OTTHUMG00000162291	ENST00000513458.4:c.51delA	chr5.hg19:g.64050152delT	ENSP00000427401:p.Lys17fs	175.0	0.0		243.0	17.0	NM_173829	Q32NC8	Frame_Shift_Del	DEL	ENST00000513458.4	hg19	CCDS34171.1																																																																																			.	.		0.353	SREK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368457.4	NM_173829	
RUFY4	285180	hgsc.bcm.edu	37	2	218938584	218938584	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr2:218938584delA	ENST00000344321.7	+	8	1094	c.576delA	c.(574-576)agafs	p.R192fs	RUFY4_ENST00000441828.2_Frame_Shift_Del_p.K158fs|RUFY4_ENST00000374155.3_Frame_Shift_Del_p.R192fs|RUFY4_ENST00000463872.1_Intron	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	192							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGAGACCCAGAAAAAACAAAG	0.547											OREG0015195	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R192fs		Atlas-INDEL	.											.	RUFY4	59	.	0			c.575delG						.						85.0	97.0	93.0					2																	218938584		1970	4160	6130	SO:0001589	frameshift_variant	285180	exon8			.	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"""Zinc fingers, FYVE domain containing"""	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.576delA	chr2.hg19:g.218938584delA	ENSP00000345900:p.Arg192fs	131.0	0.0	2255	153.0	11.0	NM_198483	Q6ZR96	Frame_Shift_Del	DEL	ENST00000344321.7	hg19																																																																																				.	.		0.547	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483	
ENTPD5	957	hgsc.bcm.edu	37	14	74453565	74453565	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:74453565delA	ENST00000334696.6	-	5	568	c.249delT	c.(247-249)tttfs	p.F83fs	ENTPD5_ENST00000557325.1_Frame_Shift_Del_p.F83fs|ENTPD5_ENST00000554664.1_5'Flank|ENTPD5_ENST00000556242.1_3'UTR	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	83					'de novo' posttranslational protein folding (GO:0051084)|ATP metabolic process (GO:0046034)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|positive regulation of glycolytic process (GO:0045821)|protein N-linked glycosylation (GO:0006487)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	guanosine-diphosphatase activity (GO:0004382)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(234;0.00394)		TCACAGAATCAAAAACTTCCC	0.403																																					p.D84fs		Atlas-INDEL	.											.,1	ENTPD5	26	.	0			c.250delG						.						113.0	105.0	108.0					14																	74453565		2203	4300	6503	SO:0001589	frameshift_variant	957	exon5			.	AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097			3367	protein-coding gene	gene with protein product		603162	"""proto-oncogene CPH"""	CD39L4, PCPH		9271669, 9676430	Standard	NM_001249		Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000334696.6:c.249delT	chr14.hg19:g.74453565delA	ENSP00000335246:p.Phe83fs	162.0	0.0		201.0	13.0	NM_001249	A1L4C5|Q96RX0	Frame_Shift_Del	DEL	ENST00000334696.6	hg19	CCDS9825.1																																																																																			.	.		0.403	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249	
UNC79	57578	hgsc.bcm.edu	37	14	94100954	94100954	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:94100954delC	ENST00000393151.2	+	32	5804	c.5804delC	c.(5803-5805)gccfs	p.A1935fs	UNC79_ENST00000553484.1_Frame_Shift_Del_p.A1957fs|UNC79_ENST00000256339.4_Frame_Shift_Del_p.A1758fs|UNC79_ENST00000555664.1_Intron			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1935					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						CAGTCTAGCGCCCCCCATAAC	0.498																																					p.A1758fs		Atlas-INDEL	.											.	UNC79	366	.	0			c.5272delG						.						115.0	112.0	113.0					14																	94100954		2203	4300	6503	SO:0001589	frameshift_variant	57578	exon32			.	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.5804delC	chr14.hg19:g.94100954delC	ENSP00000376858:p.Ala1935fs	196.0	0.0		207.0	15.0	NM_020818	B5MDL6|Q6ZUT7	Frame_Shift_Del	DEL	ENST00000393151.2	hg19																																																																																				.	.		0.498	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
GAS2L3	283431	hgsc.bcm.edu	37	12	101017470	101017470	+	Frame_Shift_Del	DEL	A	A	-	rs201339445		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:101017470delA	ENST00000539410.1	+	9	1273	c.887delA	c.(886-888)caafs	p.Q296fs	GAS2L3_ENST00000266754.5_Frame_Shift_Del_p.Q296fs|GAS2L3_ENST00000537247.1_Frame_Shift_Del_p.Q192fs|GAS2L3_ENST00000547754.1_Frame_Shift_Del_p.Q296fs			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	296					actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						TTAGCATTTCAAAAAGGAGTT	0.388																																					p.Q296fs		Atlas-INDEL	.											.	GAS2L3	76	.	0			c.886delC						.						67.0	70.0	69.0					12																	101017470		2203	4299	6502	SO:0001589	frameshift_variant	283431	exon10			.	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.887delA	chr12.hg19:g.101017470delA	ENSP00000439672:p.Gln296fs	149.0	0.0		183.0	11.0	NM_174942	B2RCN2	Frame_Shift_Del	DEL	ENST00000539410.1	hg19	CCDS9079.1																																																																																			.	.		0.388	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942	
OCSTAMP	128506	hgsc.bcm.edu	37	20	45170221	45170221	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr20:45170221delC	ENST00000279028.2	-	3	1406	c.1393delG	c.(1393-1395)gatfs	p.D465fs		NM_080721.1	NP_542452.1	Q9BR26	OCSTP_HUMAN	osteoclast stimulatory transmembrane protein	465					cellular response to estrogen stimulus (GO:0071391)|cellular response to tumor necrosis factor (GO:0071356)|multinuclear osteoclast differentiation (GO:0072674)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of osteoclast proliferation (GO:0090290)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)	2						CAAGAAGGATCCCCTAGGGGC	0.632																																					p.D465fs		Atlas-INDEL	.											.	OCSTAMP	34	.	0			c.1394delA						.						62.0	65.0	64.0					20																	45170221		692	1591	2283	SO:0001589	frameshift_variant	128506	exon3			.	AL034424	CCDS54468.1	20q13.12	2012-03-27	2012-03-27	2012-03-27	ENSG00000149635	ENSG00000149635			16116	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 123"""	C20orf123		18064667	Standard	NM_080721		Approved	dJ257E24.3	uc010zxu.2	Q9BR26	OTTHUMG00000032652	ENST00000279028.2:c.1393delG	chr20.hg19:g.45170221delC	ENSP00000279028:p.Asp465fs	128.0	0.0		178.0	11.0	NM_080721		Frame_Shift_Del	DEL	ENST00000279028.2	hg19	CCDS54468.1																																																																																			.	.		0.632	OCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079573.2	XM_496476	
ACTR6	64431	hgsc.bcm.edu	37	12	100599500	100599500	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:100599500delT	ENST00000188312.2	+	3	998	c.233delT	c.(232-234)cttfs	p.L78fs	ACTR6_ENST00000550813.1_3'UTR|ACTR6_ENST00000551617.1_5'UTR|ACTR6_ENST00000546902.1_5'UTR|ACTR6_ENST00000552376.1_Frame_Shift_Del_p.L78fs	NM_022496.4	NP_071941.1	Q9GZN1	ARP6_HUMAN	ARP6 actin-related protein 6 homolog (yeast)	78						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	14						TGGGATTACCTTTTTGGAAAA	0.234																																					p.L78fs		Atlas-INDEL	.											.	ACTR6	29	.	0			c.232delC						.						57.0	62.0	60.0					12																	100599500		2198	4270	6468	SO:0001589	frameshift_variant	64431	exon3			.	AF212251	CCDS9074.1	12q23.1	2012-07-09			ENSG00000075089	ENSG00000075089			24025	protein-coding gene	gene with protein product						11368909	Standard	NM_022496		Approved	ARP6, FLJ13433	uc001thb.2	Q9GZN1	OTTHUMG00000170245	ENST00000188312.2:c.233delT	chr12.hg19:g.100599500delT	ENSP00000188312:p.Leu78fs	110.0	0.0		175.0	13.0	NM_022496	B3KW37|B4DLG9|Q53GH2|Q9BY39|Q9H8H6	Frame_Shift_Del	DEL	ENST00000188312.2	hg19	CCDS9074.1																																																																																			.	.		0.234	ACTR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408159.1	NM_022496	
CORO2A	7464	hgsc.bcm.edu	37	9	100889088	100889088	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:100889088delG	ENST00000343933.5	-	11	1446	c.1189delC	c.(1189-1191)cttfs	p.L397fs	CORO2A_ENST00000375077.4_Frame_Shift_Del_p.L397fs	NM_003389.3	NP_003380.3	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A	397					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	actin cytoskeleton (GO:0015629)|transcriptional repressor complex (GO:0017053)	actin filament binding (GO:0051015)			endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|skin(4)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				CCAGGCCTAAGGGACACCAGG	0.602																																					p.L397fs		Atlas-INDEL	.											.	CORO2A	54	.	0			c.1190delT						.						72.0	74.0	73.0					9																	100889088		2203	4300	6503	SO:0001589	frameshift_variant	7464	exon11			.	U57057	CCDS6735.1	9q22.3	2013-01-10	2001-11-28		ENSG00000106789	ENSG00000106789		"""Coronins"", ""WD repeat domain containing"""	2255	protein-coding gene	gene with protein product	"""coronin 2A"", ""coronin-like protein B"", ""WD protein IR10"", ""WD-repeat protein 2"""	602159	"""coronin, actin-binding protein, 2A"""			8985118	Standard	NM_052820		Approved	IR10, WDR2	uc004aym.3	Q92828	OTTHUMG00000020340	ENST00000343933.5:c.1189delC	chr9.hg19:g.100889088delG	ENSP00000343746:p.Leu397fs	80.0	0.0		120.0	10.0	NM_003389	Q5TBR5|Q92829|Q9BWS5	Frame_Shift_Del	DEL	ENST00000343933.5	hg19	CCDS6735.1																																																																																			.	.		0.602	CORO2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053357.1	NM_003389	
ZNF286A	57335	hgsc.bcm.edu	37	17	15619756	15619756	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:15619756delA	ENST00000464847.2	+	5	1271	c.718delA	c.(718-720)aaafs	p.K241fs	ZNF286A_ENST00000593105.1_Frame_Shift_Del_p.K231fs|ZNF286A_ENST00000583566.1_Frame_Shift_Del_p.K241fs|ZNF286A_ENST00000395894.2_3'UTR|ZNF286A_ENST00000472486.1_3'UTR|ZNF286A_ENST00000421016.1_Frame_Shift_Del_p.K241fs|ZNF286A_ENST00000585171.1_Intron|ZNF286A_ENST00000413242.2_Frame_Shift_Del_p.K241fs			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	241					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		TTATAAAGAGAAAAAACCTCA	0.368																																					p.E239fs		Atlas-INDEL	.											ZNF286A,NS,carcinoma,0,1	ZNF286A	58	.	0			c.717delG						.						28.0	28.0	28.0					17																	15619756		2199	4291	6490	SO:0001589	frameshift_variant	57335	exon6			.	AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"""Zinc fingers, C2H2-type"", ""-"""	13501	protein-coding gene	gene with protein product			"""zinc finger protein 286"""	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.718delA	chr17.hg19:g.15619756delA	ENSP00000464218:p.Lys241fs	177.0	0.0		228.0	14.0	NM_020652	B4DKF9|Q96JF3	Frame_Shift_Del	DEL	ENST00000464847.2	hg19	CCDS11172.1																																																																																			.	.		0.368	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652	
PDGFRA	5156	hgsc.bcm.edu	37	4	55146491	55146491	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr4:55146491delT	ENST00000257290.5	+	16	2496	c.2165delT	c.(2164-2166)attfs	p.I722fs	FIP1L1_ENST00000507166.1_Frame_Shift_Del_p.I482fs	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	722	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	AGCTATGTTATTTTATCTTTT	0.393			"""Mis, O, T"""	FIP1L1	"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											p.I722fs	Pancreas(151;208 1913 7310 23853 37092)	Atlas-INDEL	.		Dom	yes		4	4q11-q13	5156	"""platelet-derived growth factor, alpha-receptor"""		"""L, M, O"""	.	PDGFRA	1583	.	0			c.2164delA						.						114.0	111.0	112.0					4																	55146491		2203	4300	6503	SO:0001589	frameshift_variant	5156	exon16	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	.	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.2165delT	chr4.hg19:g.55146491delT	ENSP00000257290:p.Ile722fs	174.0	0.0		185.0	12.0	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Frame_Shift_Del	DEL	ENST00000257290.5	hg19	CCDS3495.1																																																																																			.	.		0.393	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
ADAP1	11033	hgsc.bcm.edu	37	7	939058	939058	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr7:939058delG	ENST00000265846.5	-	9	1084	c.865delC	c.(865-867)ctgfs	p.L289fs	ADAP1_ENST00000539900.1_Frame_Shift_Del_p.L300fs|ADAP1_ENST00000449296.2_Frame_Shift_Del_p.L217fs	NM_001284308.1|NM_001284309.1|NM_001284311.1|NM_006869.2	NP_001271237.1|NP_001271238.1|NP_001271240.1|NP_006860	O75689	ADAP1_HUMAN	ArfGAP with dual PH domains 1	289	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell surface receptor signaling pathway (GO:0007166)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF GTPase activity (GO:0032312)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	6						CTCCTTACCAGGGGGTCTTTG	0.657																																					p.L289fs		Atlas-INDEL	.											.	ADAP1	23	.	0			c.866delT						.						58.0	49.0	52.0					7																	939058		2203	4300	6503	SO:0001589	frameshift_variant	11033	exon9			.	AJ006422	CCDS5318.1, CCDS64576.1, CCDS64577.1, CCDS75558.1	7p22.3	2013-01-10	2008-09-22	2008-09-22	ENSG00000105963	ENSG00000105963		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16486	protein-coding gene	gene with protein product		608114	"""centaurin, alpha 1"""	CENTA1		10333475	Standard	NM_006869		Approved	GCS1L	uc003sjo.4	O75689	OTTHUMG00000023380	ENST00000265846.5:c.865delC	chr7.hg19:g.939058delG	ENSP00000265846:p.Leu289fs	202.0	0.0		254.0	16.0	NM_006869	A4D2Q2|B3KRZ4|B4DVA6|F6XZ68|H7C2Q4	Frame_Shift_Del	DEL	ENST00000265846.5	hg19	CCDS5318.1																																																																																			.	.		0.657	ADAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059701.2	NM_006869	
SLC6A15	55117	hgsc.bcm.edu	37	12	85279291	85279291	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:85279291delA	ENST00000266682.5	-	4	1038	c.497delT	c.(496-498)ttgfs	p.L166fs	SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000552192.1_Frame_Shift_Del_p.L59fs|SLC6A15_ENST00000450363.3_Frame_Shift_Del_p.L166fs	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	166					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						AAAATAAAACAAACTCCAGCC	0.373																																					p.L166fs		Atlas-INDEL	.											.	SLC6A15	159	.	0			c.498delG						.						97.0	95.0	96.0					12																	85279291		2203	4300	6503	SO:0001589	frameshift_variant	55117	exon4			.	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.497delT	chr12.hg19:g.85279291delA	ENSP00000266682:p.Leu166fs	145.0	0.0		155.0	10.0	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Frame_Shift_Del	DEL	ENST00000266682.5	hg19	CCDS9026.1																																																																																			.	.		0.373	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767	
PTGR1	22949	hgsc.bcm.edu	37	9	114355220	114355220	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr9:114355220delC	ENST00000407693.2	-	4	457	c.195delG	c.(193-195)gggfs	p.G65fs	PTGR1_ENST00000238248.3_5'UTR|PTGR1_ENST00000309195.5_Frame_Shift_Del_p.G65fs|PTGR1_ENST00000538962.1_Frame_Shift_Del_p.G65fs	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	134.0	0.0		208.0	15.0	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		
HCFC2	29915	hgsc.bcm.edu	37	12	104495863	104495863	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr12:104495863delA	ENST00000229330.4	+	14	2100	c.1996delA	c.(1996-1998)aaafs	p.K666fs	HCFC2_ENST00000550335.1_3'UTR	NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	666	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						TCCTTTCAGCAAAATCAGTGA	0.428																																					p.S665fs	Esophageal Squamous(184;1814 2036 4771 6974 15702)	Atlas-INDEL	.											.	HCFC2	94	.	0			c.1995delC						.						161.0	152.0	155.0					12																	104495863		2203	4300	6503	SO:0001589	frameshift_variant	29915	exon14			.	AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.1996delA	chr12.hg19:g.104495863delA	ENSP00000229330:p.Lys666fs	162.0	0.0		164.0	11.0	NM_013320	B2R8Q5|C0H5X3	Frame_Shift_Del	DEL	ENST00000229330.4	hg19	CCDS9097.1																																																																																			.	.		0.428	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320	
MUC16	94025	hgsc.bcm.edu	37	19	9066715	9066715	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:9066715delT	ENST00000397910.4	-	3	20934	c.20731delA	c.(20731-20733)accfs	p.T6911fs		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6913	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGGCCTTGGTTTTTTCTGAG	0.473																																					p.T6911fs		Atlas-INDEL	.											.	MUC16	4315	.	0			c.20732delC						.						296.0	280.0	285.0					19																	9066715		2106	4215	6321	SO:0001589	frameshift_variant	94025	exon3			.	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.20731delA	chr19.hg19:g.9066715delT	ENSP00000381008:p.Thr6911fs	164.0	0.0		196.0	13.0	NM_024690	Q6ZQW5|Q96RK2	Frame_Shift_Del	DEL	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412200	105412200	+	Frame_Shift_Del	DEL	G	G	-	rs55752740		TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr14:105412200delG	ENST00000333244.5	-	7	9707	c.9588delC	c.(9586-9588)cccfs	p.P3196fs	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3196						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GTTGGGCAGAGGGGGGCTCAA	0.632																																					p.S3197fs		Pindel	.											.	AHNAK2	719	.	0			c.9589delT						.						113.0	77.0	89.0					14																	105412200		1948	3947	5895	SO:0001589	frameshift_variant	113146	exon7			.	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.9588delC	chr14.hg19:g.105412200delG	ENSP00000353114:p.Pro3196fs	166.0	0.0		254.0	11.0	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Frame_Shift_Del	DEL	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ZNF443	10224	hgsc.bcm.edu	37	19	12541062	12541062	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr19:12541062delT	ENST00000301547.5	-	4	2121	c.1924delA	c.(1924-1926)actfs	p.T642fs	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	642					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						CCAGTGTGAGTTTTTTTCCAG	0.398																																					p.T642fs		Pindel	.											.	ZNF443	63	.	0			c.1925delC						.						105.0	108.0	107.0					19																	12541062		2203	4300	6503	SO:0001589	frameshift_variant	10224	exon4			.	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1924delA	chr19.hg19:g.12541062delT	ENSP00000301547:p.Thr642fs	219.0	0.0		277.0	14.0	NM_005815		Frame_Shift_Del	DEL	ENST00000301547.5	hg19	CCDS32918.1																																																																																			.	.		0.398	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
TRMT13	54482	hgsc.bcm.edu	37	1	100613582	100613582	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr1:100613582delA	ENST00000370141.2	+	10	956	c.950delA	c.(949-951)gaafs	p.E317fs		NM_019083.2	NP_061956.2	Q9NUP7	TRM13_HUMAN	tRNA methyltransferase 13 homolog (S. cerevisiae)	317					tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										GAAGGAAATGAAAAAAATGTC	0.403																																					p.E317fs		Pindel	.											.	.	.	.	0			c.949delG						.						85.0	87.0	86.0					1																	100613582		2203	4300	6503	SO:0001589	frameshift_variant	54482	exon10			.	BC075811	CCDS765.1	1p21.2	2012-06-07	2012-06-07	2012-06-07	ENSG00000122435	ENSG00000122435			25502	protein-coding gene	gene with protein product			"""coiled-coil domain containing 76"""	CCDC76		11799066	Standard	NM_019083		Approved	FLJ10287, FLJ11219	uc001dsv.3	Q9NUP7	OTTHUMG00000010841	ENST00000370141.2:c.950delA	chr1.hg19:g.100613582delA	ENSP00000359160:p.Glu317fs	183.0	0.0		201.0	10.0	NM_019083	Q5VVL0|Q9NW65	Frame_Shift_Del	DEL	ENST00000370141.2	hg19	CCDS765.1																																																																																			.	.		0.403	TRMT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029919.1	NM_019083	
BZRAP1	9256	hgsc.bcm.edu	37	17	56393388	56393388	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr17:56393388delA	ENST00000343736.4	-	16	2257	c.2094delT	c.(2092-2094)tttfs	p.F698fs	BZRAP1_ENST00000355701.3_Frame_Shift_Del_p.F698fs|BZRAP1_ENST00000268893.6_Frame_Shift_Del_p.F638fs			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		Pindel	.											.	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	202.0	0.0		232.0	11.0	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	
ZNF311	282890	hgsc.bcm.edu	37	6	28963809	28963809	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DD-A3A0-01A-11D-A20W-10	TCGA-DD-A3A0-11A-11D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	148ae891-9087-42b8-afa7-4365f5f6f571	e13dd465-5367-4faa-82bf-be30550c67b3	g.chr6:28963809delT	ENST00000377179.3	-	7	1482	c.970delA	c.(970-972)accfs	p.T324fs	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	324					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						CCACTGTGGGTTTTTTTATGT	0.507																																					p.T324fs		Pindel	.											.	ZNF311	59	.	0			c.971delC						.						72.0	62.0	66.0					6																	28963809		1511	2709	4220	SO:0001589	frameshift_variant	282890	exon7			.	AL833166	CCDS34357.1	6p21.33	2013-01-08			ENSG00000197935	ENSG00000197935		"""Zinc fingers, C2H2-type"", ""-"""	13847	protein-coding gene	gene with protein product							Standard	XM_006715067		Approved		uc003nlu.2	Q5JNZ3	OTTHUMG00000031292	ENST00000377179.3:c.970delA	chr6.hg19:g.28963809delT	ENSP00000366384:p.Thr324fs	165.0	0.0		204.0	10.0	NM_001010877	A2BFK5|B0S7Y4|Q92971	Frame_Shift_Del	DEL	ENST00000377179.3	hg19	CCDS34357.1																																																																																			.	.		0.507	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	XM_212581	
