#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_ACHILLES_Lineage_Results_Top_Genes	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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_ORegAnno_bin	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_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	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
SERPINH1	871	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	75277978	75277978	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr11:75277978C>T	ENST00000524558.1	+	2	2019	c.584C>T	c.(583-585)aCg>aTg	p.T195M	SERPINH1_ENST00000358171.3_Missense_Mutation_p.T195M|SERPINH1_ENST00000533603.1_Missense_Mutation_p.T195M|SERPINH1_ENST00000525876.1_5'Flank|SERPINH1_ENST00000530284.1_Missense_Mutation_p.T195M			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	195					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					GTGGAGCGCACGGACGGCGCC	0.662																																																0													34.0	33.0	33.0					11																	75277978		2200	4291	6491	SO:0001583	missense	871			X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.584C>T	11.37:g.75277978C>T	ENSP00000434412:p.Thr195Met		B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Missense_Mutation	SNP	ENST00000524558.1	37	CCDS8239.1	.	.	.	.	.	.	.	.	.	.	C	12.84	2.057063	0.36277	.	.	ENSG00000149257	ENST00000533603;ENST00000358171;ENST00000526397;ENST00000421448;ENST00000530284;ENST00000532356;ENST00000524558;ENST00000525611;ENST00000528760	D;D;D;D;D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33;-2.33;-2.33;-2.33;-2.33	4.66	4.66	0.58398	Serpin domain (3);	0.104475	0.64402	D	0.000005	T	0.77585	0.4152	L	0.29908	0.895	0.80722	D	1	P;P	0.40660	0.726;0.476	B;B	0.31495	0.131;0.057	T	0.78041	-0.2359	10	0.30078	T	0.28	.	15.0624	0.71964	0.0:1.0:0.0:0.0	.	195;195	E9PPV6;P50454	.;SERPH_HUMAN	M	195;195;195;174;195;195;195;195;195	ENSP00000434657:T195M;ENSP00000350894:T195M;ENSP00000434964:T195M;ENSP00000436305:T195M;ENSP00000436040:T195M;ENSP00000434412:T195M;ENSP00000435452:T195M;ENSP00000437108:T195M	ENSP00000350894:T195M	T	+	2	0	SERPINH1	74955626	1.000000	0.71417	0.920000	0.36463	0.871000	0.50021	5.954000	0.70298	2.140000	0.66376	0.563000	0.77884	ACG		0.662	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353		29	97	29	97
IPO4	79711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	24651580	24651580	+	Silent	SNP	G	G	A			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr14:24651580G>A	ENST00000354464.6	-	25	2678	c.2502C>T	c.(2500-2502)caC>caT	p.H834H	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	834					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CCTCTCCAGCGTGCTCCAGCA	0.622																																																0													22.0	26.0	25.0					14																	24651580		2095	4220	6315	SO:0001819	synonymous_variant	79711			AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.2502C>T	14.37:g.24651580G>A			B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Silent	SNP	ENST00000354464.6	37	CCDS9616.1																																																																																				0.622	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		17	32	17	32
BCL11B	64919	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	99641424	99641424	+	Silent	SNP	C	C	T			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr14:99641424C>T	ENST00000357195.3	-	4	1758	c.1749G>A	c.(1747-1749)gcG>gcA	p.A583A	BCL11B_ENST00000443726.2_Silent_p.A389A|BCL11B_ENST00000345514.2_Silent_p.A512A	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	583	Gly-rich.				alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		GCGCCTTggccgcgccgcccc	0.731			T	TLX3	T-ALL																																		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	0													12.0	14.0	13.0					14																	99641424		2078	4016	6094	SO:0001819	synonymous_variant	64919			AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"""Zinc fingers, C2H2-type"""	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.1749G>A	14.37:g.99641424C>T			Q9H162	Silent	SNP	ENST00000357195.3	37	CCDS9950.1																																																																																				0.731	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		28	29	28	29
PML	5371	hgsc.bcm.edu;broad.mit.edu	37	15	74290533	74290533	+	Silent	SNP	C	C	T			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr15:74290533C>T	ENST00000268058.3	+	2	414	c.318C>T	c.(316-318)aaC>aaT	p.N106N	PML_ENST00000359928.4_Silent_p.N106N|PML_ENST00000569477.1_Silent_p.N106N|PML_ENST00000435786.2_Silent_p.N106N|PML_ENST00000395135.3_Silent_p.N106N|PML_ENST00000395132.2_Silent_p.N106N|PML_ENST00000354026.6_Silent_p.N106N|PML_ENST00000268059.6_Silent_p.N106N|PML_ENST00000563500.1_Silent_p.N106N|PML_ENST00000567543.1_Silent_p.N106N|PML_ENST00000564428.1_Silent_p.N106N|PML_ENST00000565898.1_Silent_p.N106N|PML_ENST00000436891.3_Silent_p.N106N|PML_ENST00000569965.1_Silent_p.N106N	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	106					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						CCCTGGATAACGTCTTTTTCG	0.642			T	"""RARA, PAX5"""	"""APL, ALL"""																																		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	0													50.0	45.0	47.0					15																	74290533		2198	4297	6495	SO:0001819	synonymous_variant	5371			AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.318C>T	15.37:g.74290533C>T			E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Silent	SNP	ENST00000268058.3	37	CCDS10255.1																																																																																				0.642	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675		5	84	5	84
IDH2	3418	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	90631839	90631839	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr15:90631839T>C	ENST00000330062.3	-	4	627	c.514A>G	c.(514-516)Agg>Ggg	p.R172G	IDH2_ENST00000559482.1_Intron|IDH2_ENST00000540499.2_Missense_Mutation_p.R120G|IDH2_ENST00000539790.1_Missense_Mutation_p.R42G	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	172					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R172W(12)|p.R172G(2)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			TGGGCGTGCCTGCCAATGGTG	0.627			M		GBM																																		Dom	yes		15	15q26.1	3418	"""socitrate dehydrogenase 2 (NADP+), mitochondrial """		M	14	Substitution - Missense(14)	central_nervous_system(9)|biliary_tract(5)											86.0	81.0	83.0					15																	90631839		2200	4298	6498	SO:0001583	missense	3418				CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.514A>G	15.37:g.90631839T>C	ENSP00000331897:p.Arg172Gly		B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	ENST00000330062.3	37	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	T	13.35	2.210612	0.39102	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	D;D;D	0.86956	-2.19;-2.19;-2.19	5.93	0.717	0.18196	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.95655	0.8587	H	0.98487	4.245	0.51767	D	0.999936	D	0.89917	1.0	D	0.97110	1.0	D	0.95508	0.8583	10	0.87932	D	0	.	13.7144	0.62687	0.0:0.0:0.4915:0.5085	.	172	P48735	IDHP_HUMAN	G	172;42;120	ENSP00000331897:R172G;ENSP00000438457:R42G;ENSP00000446147:R120G	ENSP00000331897:R172G	R	-	1	2	IDH2	88432843	1.000000	0.71417	0.032000	0.17829	0.002000	0.02628	1.525000	0.35953	-0.113000	0.11958	-0.466000	0.05196	AGG		0.627	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1			41	58	41	58
RBFOX1	54715	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	7568267	7568267	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr16:7568267C>T	ENST00000550418.1	+	5	1134	c.146C>T	c.(145-147)gCg>gTg	p.A49V	RBFOX1_ENST00000547338.1_Missense_Mutation_p.A49V|RBFOX1_ENST00000355637.4_Missense_Mutation_p.A69V|RBFOX1_ENST00000422070.4_Missense_Mutation_p.A92V|RBFOX1_ENST00000340209.4_Missense_Mutation_p.A54V|RBFOX1_ENST00000436368.2_Missense_Mutation_p.A69V|RBFOX1_ENST00000311745.5_Missense_Mutation_p.A69V|RBFOX1_ENST00000553186.1_Missense_Mutation_p.A49V|RBFOX1_ENST00000547372.1_Missense_Mutation_p.A92V|RBFOX1_ENST00000535565.2_Missense_Mutation_p.A85V|RBFOX1_ENST00000552089.1_Missense_Mutation_p.A85V	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	49					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						CCCCACCCCGCGCCAGAGTAC	0.657																																					Ovarian(157;934 2567 15163 39509)											0													116.0	113.0	114.0					16																	7568267		2197	4300	6497	SO:0001583	missense	54715			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.146C>T	16.37:g.7568267C>T	ENSP00000450031:p.Ala49Val		Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Missense_Mutation	SNP	ENST00000550418.1	37	CCDS55983.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.044648	0.75732	.	.	ENSG00000078328	ENST00000547605;ENST00000550418;ENST00000553186;ENST00000547372;ENST00000422070;ENST00000535565;ENST00000552089;ENST00000551752;ENST00000547338;ENST00000436368;ENST00000311745;ENST00000355637;ENST00000352951;ENST00000340209	T;T;T;T;T;T;T;T;T;T;T	0.35048	1.84;1.38;1.7;1.66;1.67;1.77;1.38;1.44;1.61;1.58;1.33	4.85	4.85	0.62838	.	0.296529	0.32244	N	0.006367	T	0.28532	0.0706	N	0.08118	0	0.44359	D	0.997252	P;D;P;P;B;D;B;B;D	0.62365	0.533;0.991;0.936;0.759;0.278;0.985;0.24;0.351;0.969	B;P;B;B;B;B;B;B;P	0.47891	0.091;0.481;0.173;0.245;0.157;0.352;0.065;0.109;0.56	T	0.23797	-1.0178	10	0.46703	T	0.11	-2.3794	17.9952	0.89181	0.0:1.0:0.0:0.0	.	69;85;92;69;69;69;49;49;92	F8WAC5;F5H0M1;B7Z1U7;Q9NWB1-2;Q9NWB1-4;Q9NWB1-5;Q9NWB1-3;Q9NWB1;F8VZG9	.;.;.;.;.;.;.;RFOX1_HUMAN;.	V	49;49;49;92;92;85;85;49;49;69;69;69;69;54	ENSP00000450402:A49V;ENSP00000450031:A49V;ENSP00000447753:A49V;ENSP00000446842:A92V;ENSP00000391269:A92V;ENSP00000447281:A49V;ENSP00000447717:A49V;ENSP00000402745:A69V;ENSP00000309117:A69V;ENSP00000347855:A69V;ENSP00000344196:A54V	ENSP00000309117:A69V	A	+	2	0	RBFOX1	7508268	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.970000	0.76099	2.222000	0.72286	0.557000	0.71058	GCG		0.657	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891		118	174	118	174
MYO15A	51168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	18053797	18053797	+	Missense_Mutation	SNP	G	G	A	rs530783345		TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr17:18053797G>A	ENST00000205890.5	+	36	7605	c.7267G>A	c.(7267-7269)Ggt>Agt	p.G2423S	MYO15A_ENST00000418233.3_5'Flank	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2423	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)					AGGCCAGCCCGGTGGAGGCAG	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		17268	0.001		0.0	False		,,,				2504	0.0															0													63.0	79.0	74.0					17																	18053797		2126	4246	6372	SO:0001583	missense	51168			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.7267G>A	17.37:g.18053797G>A	ENSP00000205890:p.Gly2423Ser		B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	G	9.784	1.175990	0.21704	.	.	ENSG00000091536	ENST00000205890	D	0.90324	-2.65	4.67	-0.308	0.12773	.	.	.	.	.	D	0.86393	0.5922	L	0.53249	1.67	0.09310	N	1	B	0.19445	0.036	B	0.12837	0.008	T	0.73569	-0.3941	9	0.33940	T	0.23	.	10.9018	0.47056	0.2928:0.0:0.7072:0.0	.	2423	Q9UKN7	MYO15_HUMAN	S	2423	ENSP00000205890:G2423S	ENSP00000205890:G2423S	G	+	1	0	MYO15A	17994522	0.084000	0.21492	0.185000	0.23176	0.113000	0.19764	1.122000	0.31295	0.078000	0.16900	-1.810000	0.00614	GGT		0.617	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		36	77	36	77
KCNH4	23415	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	40322247	40322247	+	Missense_Mutation	SNP	C	C	T	rs369685674		TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr17:40322247C>T	ENST00000264661.3	-	8	1600	c.1268G>A	c.(1267-1269)cGc>cAc	p.R423H	KCNH4_ENST00000607371.1_Missense_Mutation_p.R423H	NM_012285.2	NP_036417.1	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 4	423					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|urinary_tract(1)	32		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GTAGGCGCTGCGCCGTGATGG	0.622																																					NSCLC(117;707 1703 2300 21308 31858)											0								C	HIS/ARG	0,4406		0,0,2203	59.0	47.0	51.0		1268	4.0	1.0	17		51	1,8599	1.2+/-3.3	0,1,4299	no	missense	KCNH4	NM_012285.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	423/1018	40322247	1,13005	2203	4300	6503	SO:0001583	missense	23415			AB022698	CCDS11420.1	17q21	2012-07-05				ENSG00000089558		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6253	protein-coding gene	gene with protein product		604528				10455180, 16382104	Standard	NM_012285		Approved	Kv12.3, elk1	uc002hzb.2	Q9UQ05		ENST00000264661.3:c.1268G>A	17.37:g.40322247C>T	ENSP00000264661:p.Arg423His			Missense_Mutation	SNP	ENST00000264661.3	37	CCDS11420.1	.	.	.	.	.	.	.	.	.	.	C	13.74	2.327853	0.41197	0.0	1.16E-4	ENSG00000089558	ENST00000264661	D	0.98455	-4.94	3.96	3.96	0.45880	Ion transport (1);	0.000000	0.37304	N	0.002150	D	0.96134	0.8740	L	0.41492	1.28	0.49798	D	0.999825	B	0.34399	0.452	B	0.34779	0.189	D	0.96197	0.9142	10	0.46703	T	0.11	.	16.5324	0.84365	0.0:1.0:0.0:0.0	.	423	Q9UQ05	KCNH4_HUMAN	H	423	ENSP00000264661:R423H	ENSP00000264661:R423H	R	-	2	0	KCNH4	37575773	1.000000	0.71417	1.000000	0.80357	0.230000	0.25150	4.830000	0.62745	2.195000	0.70347	0.313000	0.20887	CGC		0.622	KCNH4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449791.2	NM_012285		22	39	22	39
SP6	80320	hgsc.bcm.edu;broad.mit.edu	37	17	45925200	45925200	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr17:45925200G>A	ENST00000536300.1	-	2	927	c.596C>T	c.(595-597)tCt>tTt	p.S199F	SP6_ENST00000342234.2_Missense_Mutation_p.S199F	NM_001258248.1	NP_001245177.1	Q3SY56	SP6_HUMAN	Sp6 transcription factor	199					positive regulation of cell proliferation (GO:0008284)|regulation of odontogenesis (GO:0042481)|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)|lung(5)|prostate(1)|skin(1)	8						CAGCCCTTGAGACTCCGGGGC	0.716																																																0													5.0	6.0	6.0					17																	45925200		1847	3797	5644	SO:0001583	missense	80320				CCDS11520.1	17q21.32	2013-01-08			ENSG00000189120	ENSG00000189120		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	14530	protein-coding gene	gene with protein product	"""epiprofin"""	608613				11087666, 14551215	Standard	NM_001258248		Approved	KLF14, Epfn	uc002img.2	Q3SY56	OTTHUMG00000132067	ENST00000536300.1:c.596C>T	17.37:g.45925200G>A	ENSP00000438209:p.Ser199Phe		B3KXS4	Missense_Mutation	SNP	ENST00000536300.1	37	CCDS11520.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.968108	0.53614	.	.	ENSG00000189120	ENST00000342234;ENST00000536300	T;T	0.08720	3.06;3.06	4.5	4.5	0.54988	.	0.364590	0.20211	N	0.096909	T	0.08447	0.0210	L	0.34521	1.04	0.42739	D	0.993737	B	0.22604	0.072	B	0.20384	0.029	T	0.26608	-1.0098	10	0.27785	T	0.31	.	16.1357	0.81487	0.0:0.0:1.0:0.0	.	199	Q3SY56	SP6_HUMAN	F	199	ENSP00000340799:S199F;ENSP00000438209:S199F	ENSP00000340799:S199F	S	-	2	0	SP6	43280199	0.349000	0.24870	0.999000	0.59377	0.965000	0.64279	3.193000	0.50997	2.324000	0.78689	0.462000	0.41574	TCT		0.716	SP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441395.1	NM_199262		11	15	11	15
CTIF	9811	hgsc.bcm.edu;broad.mit.edu	37	18	46284511	46284511	+	Missense_Mutation	SNP	G	G	A	rs373686942		TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr18:46284511G>A	ENST00000256413.3	+	8	1101	c.806G>A	c.(805-807)cGc>cAc	p.R269H	CTIF_ENST00000382998.4_Missense_Mutation_p.R269H	NM_014772.2	NP_055587.1	O43310	CTIF_HUMAN	CBP80/20-dependent translation initiation factor	269	Interaction with NCBP1/CBP80.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	31						GGCGCACACCGCAATGCCAAA	0.642																																																0								G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	92.0	86.0	88.0		806,806	5.2	1.0	18		88	0,8600		0,0,4300	no	missense,missense	CTIF	NM_001142397.1,NM_014772.2	29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	269/601,269/599	46284511	1,13005	2203	4300	6503	SO:0001583	missense	9811			AB007887	CCDS11935.1, CCDS45864.1	18q21.1	2011-01-20	2011-01-20	2011-01-20	ENSG00000134030	ENSG00000134030			23925	protein-coding gene	gene with protein product		613178	"""KIAA0427"""	KIAA0427		9455477, 19648179	Standard	NM_014772		Approved		uc002ldd.3	O43310	OTTHUMG00000132656	ENST00000256413.3:c.806G>A	18.37:g.46284511G>A	ENSP00000256413:p.Arg269His		B3KTR8|Q8IVD5	Missense_Mutation	SNP	ENST00000256413.3	37	CCDS11935.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.315040	0.81358	2.27E-4	0.0	ENSG00000134030	ENST00000256413;ENST00000382998;ENST00000420275	T;T	0.53423	0.62;0.62	5.19	5.19	0.71726	.	0.526840	0.20022	N	0.100884	T	0.47581	0.1453	L	0.40543	1.245	0.41689	D	0.989338	P;P	0.52170	0.951;0.832	P;B	0.46076	0.503;0.306	T	0.53892	-0.8374	10	0.87932	D	0	-14.0903	16.9045	0.86123	0.0:0.0:1.0:0.0	.	269;269	O43310-2;O43310	.;CTIF_HUMAN	H	269;269;221	ENSP00000256413:R269H;ENSP00000372459:R269H	ENSP00000256413:R269H	R	+	2	0	CTIF	44538509	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.058000	0.64300	2.416000	0.81992	0.561000	0.74099	CGC		0.642	CTIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255907.1	NM_014772		5	86	5	86
MYO5B	4645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	47566657	47566657	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr18:47566657G>A	ENST00000285039.7	-	3	465	c.166C>T	c.(166-168)Cgc>Tgc	p.R56C		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	56					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		AGCTGGTTGCGTTGTACATCA	0.423																																																0													285.0	276.0	279.0					18																	47566657		1969	4164	6133	SO:0001583	missense	4645			AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.166C>T	18.37:g.47566657G>A	ENSP00000285039:p.Arg56Cys		B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	37	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	g	11.47	1.648194	0.29336	.	.	ENSG00000167306	ENST00000285039;ENST00000356732	D	0.95342	-3.68	5.95	0.703	0.18116	.	0.983709	0.08333	N	0.962025	D	0.87414	0.6171	N	0.11560	0.145	0.09310	N	1	P;B	0.45715	0.865;0.002	P;B	0.46339	0.513;0.0	T	0.80261	-0.1456	10	0.54805	T	0.06	.	1.3274	0.02128	0.2283:0.1346:0.1268:0.5103	.	55;56	Q7Z7A5;Q9ULV0	.;MYO5B_HUMAN	C	56;55	ENSP00000285039:R56C	ENSP00000285039:R56C	R	-	1	0	MYO5B	45820655	0.000000	0.05858	0.046000	0.18839	0.074000	0.17049	-0.017000	0.12590	0.165000	0.19558	-1.480000	0.00990	CGC		0.423	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			128	257	128	257
SOCS6	9306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	67993430	67993430	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr18:67993430G>A	ENST00000397942.3	+	2	1842	c.1526G>A	c.(1525-1527)cGt>cAt	p.R509H	SOCS6_ENST00000582322.1_Missense_Mutation_p.R509H	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	509	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				TTTGTTATACGTCAGTATACC	0.468																																					Melanoma(84;1024 1361 24382 36583 42651)											0													87.0	75.0	79.0					18																	67993430		2203	4300	6503	SO:0001583	missense	9306			AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	16833	protein-coding gene	gene with protein product		605118	"""suppressor of cytokine signaling 4"""	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.1526G>A	18.37:g.67993430G>A	ENSP00000381034:p.Arg509His		Q8WUM3	Missense_Mutation	SNP	ENST00000397942.3	37	CCDS11998.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.093985	0.56075	.	.	ENSG00000170677	ENST00000397942	T	0.64618	-0.11	5.7	4.84	0.62591	SOCS protein, C-terminal (4);	0.182929	0.47093	N	0.000259	T	0.65238	0.2672	M	0.79614	2.46	0.80722	D	1	B	0.23316	0.083	B	0.26770	0.073	T	0.64571	-0.6376	10	0.46703	T	0.11	-11.9494	14.7201	0.69300	0.0695:0.0:0.9305:0.0	.	509	O14544	SOCS6_HUMAN	H	509	ENSP00000381034:R509H	ENSP00000381034:R509H	R	+	2	0	SOCS6	66144410	1.000000	0.71417	0.961000	0.40146	0.446000	0.32137	9.680000	0.98651	1.412000	0.46977	-0.258000	0.10820	CGT		0.468	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2			35	51	35	51
TRMT1	55621	hgsc.bcm.edu;broad.mit.edu	37	19	13220750	13220750	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr19:13220750G>A	ENST00000592062.1	-	10	1655	c.1085C>T	c.(1084-1086)gCg>gTg	p.A362V	TRMT1_ENST00000357720.4_Missense_Mutation_p.A362V|TRMT1_ENST00000221504.8_Intron|TRMT1_ENST00000437766.1_Missense_Mutation_p.A362V			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	362	Trm1 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00958}.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)		GACTCCTGACGCTTTGCCGAG	0.652																																																0													60.0	68.0	65.0					19																	13220750		2203	4300	6503	SO:0001583	missense	55621			AF196479	CCDS12293.1, CCDS45997.1	19p13.13	2012-06-12	2012-06-12						25980	protein-coding gene	gene with protein product		611669				10982862	Standard	NM_001142554		Approved	FLJ20244, TRM1	uc002mwl.3	Q9NXH9		ENST00000592062.1:c.1085C>T	19.37:g.13220750G>A	ENSP00000466967:p.Ala362Val		O76103|Q548Y5|Q8WVA6	Missense_Mutation	SNP	ENST00000592062.1	37	CCDS12293.1	.	.	.	.	.	.	.	.	.	.	G	11.23	1.576005	0.28092	.	.	ENSG00000104907	ENST00000357720;ENST00000437766	.	.	.	4.49	4.49	0.54785	.	0.257891	0.38720	N	0.001585	T	0.20210	0.0486	N	0.11651	0.15	0.28063	N	0.932876	B	0.13145	0.007	B	0.09377	0.004	T	0.10847	-1.0612	9	0.02654	T	1	-17.3051	12.5341	0.56133	0.0:0.0:1.0:0.0	.	362	Q9NXH9	TRM1_HUMAN	V	362	.	ENSP00000350352:A362V	A	-	2	0	TRMT1	13081750	0.006000	0.16342	0.609000	0.28983	0.093000	0.18481	0.073000	0.14640	2.339000	0.79563	0.462000	0.41574	GCG		0.652	TRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452780.2	NM_017722		10	187	10	187
NOTCH3	4854	hgsc.bcm.edu;broad.mit.edu	37	19	15271838	15271838	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr19:15271838G>A	ENST00000263388.2	-	33	6676	c.6601C>T	c.(6601-6603)Ccc>Tcc	p.P2201S		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	2201					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			GGGGAGACGGGGGTCCCTGGG	0.741																																																0													3.0	5.0	4.0					19																	15271838		1902	3896	5798	SO:0001583	missense	4854			U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.6601C>T	19.37:g.15271838G>A	ENSP00000263388:p.Pro2201Ser		Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	G	1.797	-0.478125	0.04414	.	.	ENSG00000074181	ENST00000263388	T	0.81078	-1.45	3.57	2.52	0.30459	.	.	.	.	.	T	0.59810	0.2221	N	0.08118	0	0.20638	N	0.99988	B	0.19331	0.035	B	0.14023	0.01	T	0.41233	-0.9520	9	0.13108	T	0.6	.	10.0185	0.42029	0.1043:0.0:0.8957:0.0	.	2201	Q9UM47	NOTC3_HUMAN	S	2201	ENSP00000263388:P2201S	ENSP00000263388:P2201S	P	-	1	0	NOTCH3	15132838	1.000000	0.71417	0.049000	0.19019	0.043000	0.13939	0.947000	0.29082	0.846000	0.35142	-0.218000	0.12543	CCC		0.741	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		8	6	8	6
NWD1	284434	hgsc.bcm.edu;broad.mit.edu	37	19	16860910	16860910	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr19:16860910C>T	ENST00000552788.1	+	4	1457	c.1457C>T	c.(1456-1458)cCg>cTg	p.P486L	NWD1_ENST00000549814.1_Missense_Mutation_p.P486L|NWD1_ENST00000523826.1_Missense_Mutation_p.P280L|NWD1_ENST00000339803.6_Missense_Mutation_p.P351L|NWD1_ENST00000379808.3_Missense_Mutation_p.P486L|NWD1_ENST00000524140.2_Missense_Mutation_p.P486L			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	486	NACHT.						ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CTCCTGGACCCGGAGGCCTAC	0.647																																																0													56.0	59.0	58.0					19																	16860910		2203	4300	6503	SO:0001583	missense	284434			BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.1457C>T	19.37:g.16860910C>T	ENSP00000447224:p.Pro486Leu		C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		.	.	.	.	.	.	.	.	.	.	c	5.657	0.305851	0.10733	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38;-1.38;-1.38	4.45	0.913	0.19354	.	0.582761	0.16378	N	0.217010	T	0.70448	0.3225	L	0.40543	1.245	0.09310	N	1	D;D;B	0.59767	0.958;0.986;0.233	P;B;B	0.47102	0.537;0.423;0.035	T	0.59910	-0.7365	10	0.27785	T	0.31	-9.903	3.9953	0.09556	0.1673:0.5762:0.1624:0.0941	.	486;486;351	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	L	351;486;486;486;280;486;351	ENSP00000428579:P486L;ENSP00000447548:P486L;ENSP00000369136:P486L;ENSP00000428955:P280L;ENSP00000447224:P486L;ENSP00000340159:P351L	ENSP00000340159:P351L	P	+	2	0	NWD1	16721910	0.000000	0.05858	0.177000	0.23020	0.110000	0.19582	0.195000	0.17155	0.379000	0.24794	0.643000	0.83706	CCG		0.647	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		8	135	8	135
UPF1	5976	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	18968249	18968249	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr19:18968249C>T	ENST00000599848.1	+	15	2331	c.2122C>T	c.(2122-2124)Cgc>Tgc	p.R708C	UPF1_ENST00000262803.5_Missense_Mutation_p.R697C			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	708					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						CCGGCCCATCCGCCTGCAGGT	0.642																																																0													36.0	37.0	37.0					19																	18968249		2203	4300	6503	SO:0001583	missense	5976			AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"""UP Frameshift 1"", ""smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	601430	"""regulator of nonsense transcripts 1"""	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.2122C>T	19.37:g.18968249C>T	ENSP00000470142:p.Arg708Cys		O00239|O43343|Q86Z25|Q92842	Missense_Mutation	SNP	ENST00000599848.1	37		.	.	.	.	.	.	.	.	.	.	C	29.1	4.977382	0.92982	.	.	ENSG00000005007	ENST00000262803	D	0.92348	-3.02	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	D	0.96272	0.8784	M	0.85859	2.78	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.951	D	0.97064	0.9773	10	0.87932	D	0	-41.6506	16.1478	0.81583	0.0:1.0:0.0:0.0	.	708;697	Q92900;Q92900-2	RENT1_HUMAN;.	C	697	ENSP00000262803:R697C	ENSP00000262803:R697C	R	+	1	0	UPF1	18829249	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.430000	0.80321	2.159000	0.67721	0.561000	0.74099	CGC		0.642	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911		43	58	43	58
NLRP7	199713	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	55451739	55451739	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr19:55451739C>T	ENST00000590030.1	-	3	488	c.448G>A	c.(448-450)Gtc>Atc	p.V150I	NLRP7_ENST00000588756.1_Missense_Mutation_p.V150I|NLRP7_ENST00000448121.2_Missense_Mutation_p.V150I|NLRP7_ENST00000340844.2_Missense_Mutation_p.V150I|NLRP7_ENST00000328092.5_Missense_Mutation_p.V150I|NLRP7_ENST00000446217.1_Missense_Mutation_p.V178I|NLRP7_ENST00000592784.1_Missense_Mutation_p.V150I			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	150							ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		CTCAGAGTGACGTCGTCATGG	0.498																																																0													243.0	259.0	253.0					19																	55451739		2203	4300	6503	SO:0001583	missense	199713			AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.448G>A	19.37:g.55451739C>T	ENSP00000465520:p.Val150Ile		E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.962287	0.00461	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.73363	-0.67;-0.67;-0.74;-0.71	1.86	-0.351	0.12602	.	0.639881	0.11944	N	0.514369	T	0.43299	0.1241	N	0.08118	0	0.09310	N	1	B;B;B;B	0.26258	0.089;0.089;0.089;0.145	B;B;B;B	0.20384	0.013;0.013;0.013;0.029	T	0.28490	-1.0042	10	0.08381	T	0.77	.	2.8472	0.05547	0.0:0.4357:0.2467:0.3176	.	178;150;150;150	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	I	150;150;150;178	ENSP00000329568:V150I;ENSP00000409137:V150I;ENSP00000339491:V150I;ENSP00000414273:V178I	ENSP00000329568:V150I	V	-	1	0	NLRP7	60143551	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	-0.224000	0.09164	-0.024000	0.13941	0.557000	0.71058	GTC		0.498	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		153	74	153	74
OR6K2	81448	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	158669721	158669721	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr1:158669721G>A	ENST00000359610.2	-	1	765	c.722C>T	c.(721-723)aCg>aTg	p.T241M		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					AGAGACACACGTGGAAAATGC	0.463																																																0													115.0	104.0	108.0					1																	158669721		2203	4300	6503	SO:0001583	missense	81448			BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"""GPCR / Class A : Olfactory receptors"""	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.722C>T	1.37:g.158669721G>A	ENSP00000352626:p.Thr241Met		B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	37	CCDS30902.1	.	.	.	.	.	.	.	.	.	.	G	16.05	3.013641	0.54468	.	.	ENSG00000196171	ENST00000359610	T	0.42513	0.97	4.94	4.94	0.65067	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42821	D	0.000645	T	0.76564	0.4005	H	0.99026	4.405	0.48901	D	0.999721	D	0.89917	1.0	D	0.97110	1.0	D	0.86504	0.1805	10	0.87932	D	0	-6.5034	17.103	0.86654	0.0:0.0:1.0:0.0	.	241	Q8NGY2	OR6K2_HUMAN	M	241	ENSP00000352626:T241M	ENSP00000352626:T241M	T	-	2	0	OR6K2	156936345	1.000000	0.71417	0.952000	0.39060	0.118000	0.20060	7.234000	0.78134	2.538000	0.85594	0.655000	0.94253	ACG		0.463	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		40	47	40	47
NOS1AP	9722	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	162313698	162313698	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr1:162313698C>T	ENST00000361897.5	+	6	929	c.527C>T	c.(526-528)aCg>aTg	p.T176M	MIR556_ENST00000384996.1_RNA|NOS1AP_ENST00000530878.1_Missense_Mutation_p.T171M	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	176	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				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)			CTGCAGCACACGCAGCAGAAT	0.582																																																0													115.0	104.0	108.0					1																	162313698		2203	4300	6503	SO:0001583	missense	9722			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.527C>T	1.37:g.162313698C>T	ENSP00000355133:p.Thr176Met		B7ZLF5|O43564|Q3T551|Q5VU95	Missense_Mutation	SNP	ENST00000361897.5	37	CCDS1237.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.923256	0.92319	.	.	ENSG00000198929	ENST00000530878;ENST00000361897	T;T	0.78003	-1.14;-1.14	5.79	5.79	0.91817	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	0.088249	0.85682	D	0.000000	T	0.66446	0.2790	L	0.50333	1.59	.	.	.	D;P;D	0.56287	0.972;0.946;0.975	B;B;B	0.39805	0.31;0.31;0.31	T	0.73151	-0.4073	9	0.52906	T	0.07	.	18.6038	0.91259	0.0:1.0:0.0:0.0	.	171;171;176	E9PSG0;B7ZLF5;O75052	.;.;CAPON_HUMAN	M	171;176	ENSP00000431586:T171M;ENSP00000355133:T176M	ENSP00000355133:T176M	T	+	2	0	NOS1AP	160580322	0.989000	0.36119	0.970000	0.41538	0.989000	0.77384	2.867000	0.48428	2.733000	0.93635	0.655000	0.94253	ACG		0.582	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697		49	78	49	78
SUCO	51430	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	172558108	172558108	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr1:172558108A>G	ENST00000263688.3	+	18	2086	c.1867A>G	c.(1867-1869)Att>Gtt	p.I623V	SUCO_ENST00000367723.4_Missense_Mutation_p.I774V|SUCO_ENST00000610051.1_Intron|SUCO_ENST00000608151.1_Missense_Mutation_p.I775V	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	623					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											ACTGACCACAATTTGTTGTAT	0.413																																																0													91.0	93.0	92.0					1																	172558108		2203	4300	6503	SO:0001583	missense	51430			AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"""SUN-like protein 1"", ""osteopotentia"""		"""chromosome 1 open reading frame 9"""	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.1867A>G	1.37:g.172558108A>G	ENSP00000263688:p.Ile623Val		B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	37	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	A	9.781	1.175438	0.21704	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.45	2.8	0.32819	.	0.458628	0.24566	N	0.037431	T	0.11367	0.0277	L	0.29908	0.895	0.28099	N	0.931489	B;B;B	0.15473	0.003;0.013;0.004	B;B;B	0.12156	0.003;0.007;0.004	T	0.22487	-1.0215	9	0.23302	T	0.38	-8.7741	8.2097	0.31476	0.7678:0.0:0.2322:0.0	.	623;775;623	B4DZJ3;Q5H945;Q9UBS9	.;.;OSPT_HUMAN	V	775;623	.	ENSP00000263688:I623V	I	+	1	0	C1orf9	170824731	0.009000	0.17119	1.000000	0.80357	0.986000	0.74619	0.834000	0.27518	0.905000	0.36596	-0.371000	0.07208	ATT		0.413	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		18	28	18	28
KDM5B	10765	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	202705465	202705465	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr1:202705465C>T	ENST00000367265.3	-	21	4304	c.3140G>A	c.(3139-3141)cGa>cAa	p.R1047Q	KDM5B_ENST00000367264.2_Missense_Mutation_p.R1083Q	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1047					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						GGGGATAGATCGGCCTCGTGT	0.428																																																0													108.0	100.0	103.0					1																	202705465		2203	4300	6503	SO:0001583	missense	10765			AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.3140G>A	1.37:g.202705465C>T	ENSP00000356234:p.Arg1047Gln		O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.042343	0.75732	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	T;T;T	0.46063	0.88;0.88;0.88	5.66	5.66	0.87406	Lysine-specific demethylase-like domain (1);	0.114404	0.64402	D	0.000008	T	0.49762	0.1576	L	0.45228	1.405	0.52501	D	0.99995	P;P	0.46706	0.512;0.883	B;P	0.49451	0.05;0.611	T	0.45527	-0.9255	10	0.59425	D	0.04	-11.108	20.1253	0.97977	0.0:1.0:0.0:0.0	.	1083;1047	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	Q	1047;889;1083;889	ENSP00000356234:R1047Q;ENSP00000356233:R1083Q;ENSP00000235790:R889Q	ENSP00000235790:R889Q	R	-	2	0	KDM5B	200972088	1.000000	0.71417	0.864000	0.33941	0.996000	0.88848	4.823000	0.62694	2.832000	0.97577	0.655000	0.94253	CGA		0.428	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618		11	69	11	69
MAPKAPK2	9261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	206904037	206904037	+	Silent	SNP	A	A	C			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr1:206904037A>C	ENST00000367103.3	+	6	889	c.696A>C	c.(694-696)ccA>ccC	p.P232P	MAPKAPK2_ENST00000294981.4_Silent_p.P232P	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	232	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|arachidonic acid metabolic process (GO:0019369)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|G2 DNA damage checkpoint (GO:0031572)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|leukotriene metabolic process (GO:0006691)|macropinocytosis (GO:0044351)|MAPK cascade (GO:0000165)|mRNA metabolic process (GO:0016071)|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)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of interleukin-6 production (GO:0032675)|regulation of tumor necrosis factor production (GO:0032680)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|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)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	19	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			TTGCAGCTCCAGAAGTGCTGG	0.552																																																0													118.0	111.0	114.0					1																	206904037		2203	4300	6503	SO:0001819	synonymous_variant	9261			U12779	CCDS1466.1, CCDS31001.1	1q32	2008-02-05			ENSG00000162889	ENSG00000162889			6887	protein-coding gene	gene with protein product		602006				8179591, 8280084	Standard	NM_004759		Approved		uc001hem.2	P49137	OTTHUMG00000036342	ENST00000367103.3:c.696A>C	1.37:g.206904037A>C			Q5SY30|Q5SY41|Q8IYD6	Silent	SNP	ENST00000367103.3	37	CCDS31001.1																																																																																				0.552	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759		30	58	30	58
TRPM2	7226	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	21	45774548	45774548	+	Silent	SNP	G	G	A			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr21:45774548G>A	ENST00000397928.1	+	2	628	c.183G>A	c.(181-183)tcG>tcA	p.S61S	TRPM2_ENST00000300481.9_Silent_p.S61S|TRPM2_ENST00000397932.2_Silent_p.S61S|TRPM2_ENST00000300482.5_Silent_p.S61S	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	61					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GCCTCAGTTCGTGGATTCCTG	0.458																																																0													299.0	268.0	278.0					21																	45774548		2203	4300	6503	SO:0001819	synonymous_variant	7226			AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.183G>A	21.37:g.45774548G>A			D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	ENST00000397928.1	37	CCDS13710.1																																																																																				0.458	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		12	108	12	108
GIGYF2	26058	hgsc.bcm.edu;broad.mit.edu	37	2	233714984	233714984	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr2:233714984G>A	ENST00000409547.1	+	30	4008	c.3697G>A	c.(3697-3699)Ggg>Agg	p.G1233R	GIGYF2_ENST00000373563.4_Missense_Mutation_p.G1233R|GIGYF2_ENST00000409451.3_Missense_Mutation_p.G1254R|GIGYF2_ENST00000409480.1_Missense_Mutation_p.G1255R|GIGYF2_ENST00000373566.3_Missense_Mutation_p.G1255R|GIGYF2_ENST00000409196.3_Missense_Mutation_p.G1227R	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	1233	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		CTCTGTGTGGGGGATGAACCA	0.433																																																0													142.0	130.0	134.0					2																	233714984		2203	4300	6503	SO:0001583	missense	26058			U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.3697G>A	2.37:g.233714984G>A	ENSP00000386537:p.Gly1233Arg		A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.857903	0.91433	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451	T;T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53;-0.53	5.49	5.49	0.81192	.	0.159639	0.56097	D	0.000031	T	0.73001	0.3531	L	0.34521	1.04	0.80722	D	1	P;P;P	0.52577	0.954;0.954;0.954	P;P;P	0.55785	0.784;0.784;0.784	T	0.69877	-0.5026	10	0.32370	T	0.25	-23.8564	17.9206	0.88965	0.0:0.0:1.0:0.0	.	1254;1233;1227	A6H8W4;Q6Y7W6;E9PBB0	.;PERQ2_HUMAN;.	R	1255;1233;1255;1233;1227;1254	ENSP00000362667:G1255R;ENSP00000362664:G1233R;ENSP00000386765:G1255R;ENSP00000386537:G1233R;ENSP00000387070:G1227R;ENSP00000387170:G1254R	ENSP00000362664:G1233R	G	+	1	0	GIGYF2	233423228	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.380000	0.90149	2.734000	0.93682	0.655000	0.94253	GGG		0.433	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		6	106	6	106
TAMM41	132001	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	11887995	11887995	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr3:11887995C>T	ENST00000444133.2	-	1	258	c.116G>A	c.(115-117)gGg>gAg	p.G39E	TAMM41_ENST00000455809.1_Missense_Mutation_p.G39E|TAMM41_ENST00000273037.5_Missense_Mutation_p.G39E			Q96BW9	TAM41_HUMAN	TAM41, mitochondrial translocator assembly and maintenance protein, homolog (S. cerevisiae)	39					cardiolipin biosynthetic process (GO:0032049)|CDP-diacylglycerol biosynthetic process (GO:0016024)	extrinsic component of mitochondrial inner membrane (GO:0031314)	phosphatidate cytidylyltransferase activity (GO:0004605)										TGAACTCGGCCCTGCCTGGCG	0.622																																																0													64.0	64.0	64.0					3																	11887995		2203	4300	6503	SO:0001583	missense	132001				CCDS2607.1, CCDS68345.1	3p25.2	2013-10-18	2011-08-09	2011-08-09	ENSG00000144559	ENSG00000144559			25187	protein-coding gene	gene with protein product		614948	"""chromosome 3 open reading frame 31"""	C3orf31		19237595	Standard	XM_005264873		Approved	MGC16471, DKFZp434E0519	uc003bwh.3	Q96BW9	OTTHUMG00000129741	ENST00000444133.2:c.116G>A	3.37:g.11887995C>T	ENSP00000388598:p.Gly39Glu		B4DIY7|C9J2U4	Missense_Mutation	SNP	ENST00000444133.2	37		.	.	.	.	.	.	.	.	.	.	C	21.4	4.142886	0.77888	.	.	ENSG00000144559	ENST00000455809;ENST00000273037;ENST00000444133	T;T;T	0.32272	1.46;1.46;1.46	4.71	4.71	0.59529	.	0.118505	0.56097	D	0.000025	T	0.54062	0.1835	M	0.82323	2.585	0.58432	D	0.999999	D;P;P	0.63880	0.993;0.893;0.72	P;P;P	0.61940	0.896;0.658;0.725	T	0.58284	-0.7663	10	0.51188	T	0.08	-34.6949	13.039	0.58889	0.0:1.0:0.0:0.0	.	39;39;39	B4DIY7;C9J2U4;Q96BW9	.;.;TAM41_HUMAN	E	39	ENSP00000398596:G39E;ENSP00000273037:G39E;ENSP00000388598:G39E	ENSP00000273037:G39E	G	-	2	0	TAMM41	11862995	1.000000	0.71417	1.000000	0.80357	0.553000	0.35397	5.902000	0.69869	2.445000	0.82738	0.467000	0.42956	GGG		0.622	TAMM41-008	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000339258.2	NM_138807		52	90	52	90
GPR128	84873	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	100373800	100373800	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr3:100373800G>A	ENST00000273352.3	+	12	1769	c.1501G>A	c.(1501-1503)Ggt>Agt	p.G501S	GPR128_ENST00000475887.1_Missense_Mutation_p.G206S|GPR128_ENST00000481506.1_3'UTR	NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	501					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)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						GACAAGTGATGGTGACATCAA	0.408																																					Pancreas(87;185 1975 7223 18722)											0													175.0	154.0	161.0					3																	100373800		2203	4300	6503	SO:0001583	missense	84873			AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"""-"", ""GPCR / Class B : Orphans"""	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.1501G>A	3.37:g.100373800G>A	ENSP00000273352:p.Gly501Ser		Q14D94|Q86SQ2	Missense_Mutation	SNP	ENST00000273352.3	37	CCDS2938.1	.	.	.	.	.	.	.	.	.	.	G	1.201	-0.632562	0.03584	.	.	ENSG00000144820	ENST00000273352;ENST00000475887	T;T	0.41400	1.0;1.0	5.48	-2.66	0.06077	GPCR, family 2-like (1);	1.248000	0.05273	N	0.517933	T	0.11665	0.0284	N	0.00683	-1.26	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.08055	0.003;0.003	T	0.26643	-1.0097	10	0.07325	T	0.83	.	6.6253	0.22826	0.4057:0.143:0.4513:0.0	.	206;501	E9PHI0;Q96K78	.;GP128_HUMAN	S	501;206	ENSP00000273352:G501S;ENSP00000419788:G206S	ENSP00000273352:G501S	G	+	1	0	GPR128	101856490	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.947000	0.03901	-0.485000	0.06754	-0.150000	0.13652	GGT		0.408	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1			60	80	60	80
ACPP	55	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	132086622	132086622	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr3:132086622C>T	ENST00000351273.7	+	11	1263	c.1213C>T	c.(1213-1215)Cgc>Tgc	p.R405C		NM_001134194.1	NP_001127666.1	P15309	PPAP_HUMAN	acid phosphatase, prostate	0					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						TATCCACATTCGCCGTGGACT	0.463																																																0													399.0	339.0	357.0					3																	132086622		1568	3582	5150	SO:0001583	missense	55				CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000351273.7:c.1213C>T	3.37:g.132086622C>T	ENSP00000323036:p.Arg405Cys		D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Missense_Mutation	SNP	ENST00000351273.7	37	CCDS46916.1	.	.	.	.	.	.	.	.	.	.	C	11.03	1.520350	0.27211	.	.	ENSG00000014257	ENST00000351273	T	0.07688	3.17	4.96	4.96	0.65561	.	0.424638	0.22602	N	0.057947	T	0.23492	0.0568	.	.	.	0.24888	N	0.992185	D	0.89917	1.0	D	0.63703	0.917	T	0.01520	-1.1334	9	0.49607	T	0.09	.	14.4466	0.67356	0.0:1.0:0.0:0.0	.	405	P15309-2	.	C	405	ENSP00000323036:R405C	ENSP00000323036:R405C	R	+	1	0	ACPP	133569312	0.859000	0.29813	0.504000	0.27639	0.176000	0.22953	1.943000	0.40253	2.699000	0.92147	0.655000	0.94253	CGC		0.463	ACPP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356701.1	NM_001099		90	242	90	242
IQCJ-SCHIP1	100505385	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	159482639	159482639	+	Silent	SNP	C	C	A			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr3:159482639C>A	ENST00000460298.1	+	2	631	c.390C>A	c.(388-390)ccC>ccA	p.P130P	IQCJ-SCHIP1_ENST00000412423.2_Silent_p.P157P|IQCJ-SCHIP1_ENST00000527095.1_Intron|IQCJ-SCHIP1_ENST00000485419.1_Silent_p.P233P|IQCJ-SCHIP1_ENST00000476809.1_Silent_p.P206P|IQCJ-SCHIP1-AS1_ENST00000460574.1_RNA|IQCJ-SCHIP1_ENST00000337808.6_Silent_p.P157P					IQCJ-SCHIP1 readthrough											central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(7)	12						AGCACGACCCCCAGGACCTCA	0.756																																																0													5.0	4.0	5.0					3																	159482639		1831	3629	5460	SO:0001819	synonymous_variant	100505385				CCDS56289.1, CCDS56291.1	3q25.33	2011-03-24			ENSG00000250588	ENSG00000250588			38842	other	readthrough							Standard	NM_001197113		Approved		uc003fcq.2		OTTHUMG00000162426	ENST00000460298.1:c.390C>A	3.37:g.159482639C>A				Silent	SNP	ENST00000460298.1	37																																																																																					0.756	IQCJ-SCHIP1-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000352558.2	NM_001197113		8	11	8	11
DDX4	54514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	55075828	55075828	+	Missense_Mutation	SNP	C	C	T	rs137993034		TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr5:55075828C>T	ENST00000505374.1	+	8	523	c.431C>T	c.(430-432)cCa>cTa	p.P144L	DDX4_ENST00000514278.2_Missense_Mutation_p.P124L|RNA5SP183_ENST00000362452.1_RNA|DDX4_ENST00000353507.5_Intron|DDX4_ENST00000511853.1_Intron|DDX4_ENST00000354991.5_Intron	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	144	Gly-rich.				male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				GCTTCAGGGCCATACAGAAGA	0.413																																																0								C	,LEU/PRO,,LEU/PRO	0,4406		0,0,2203	146.0	135.0	139.0		,371,,431	5.4	0.8	5	dbSNP_134	139	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense,intron,missense	DDX4	NM_001142549.1,NM_001166533.1,NM_001166534.1,NM_024415.2	,98,,98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,benign,,benign	,124/705,,144/725	55075828	1,13005	2203	4300	6503	SO:0001583	missense	54514			AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"""DEAD-boxes"""	18700	protein-coding gene	gene with protein product		605281	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"""			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.431C>T	5.37:g.55075828C>T	ENSP00000424838:p.Pro144Leu		A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Missense_Mutation	SNP	ENST00000505374.1	37	CCDS3969.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.731966	0.69189	0.0	1.16E-4	ENSG00000152670	ENST00000514278;ENST00000505374;ENST00000506511;ENST00000515709;ENST00000514679;ENST00000511491	T;T;T;T;T;T	0.51817	2.07;2.01;3.55;0.84;0.75;0.69	5.37	5.37	0.77165	.	0.696652	0.13921	N	0.353568	T	0.36220	0.0959	L	0.36672	1.1	0.26798	N	0.969265	B;B	0.18741	0.01;0.03	B;B	0.21151	0.033;0.022	T	0.15235	-1.0444	10	0.16420	T	0.52	-7.1262	9.9516	0.41642	0.0:0.9106:0.0:0.0894	.	124;144	D6RDK4;Q9NQI0	.;DDX4_HUMAN	L	124;144;124;118;144;144	ENSP00000425359:P124L;ENSP00000424838:P144L;ENSP00000427167:P124L;ENSP00000424779:P118L;ENSP00000424112:P144L;ENSP00000427522:P144L	ENSP00000424838:P144L	P	+	2	0	DDX4	55111585	0.003000	0.15002	0.787000	0.31911	0.990000	0.78478	1.682000	0.37628	2.798000	0.96311	0.650000	0.86243	CCA		0.413	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415		11	40	11	40
NPY	4852	hgsc.bcm.edu;broad.mit.edu	37	7	24324984	24324984	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr7:24324984C>T	ENST00000407573.1	+	3	415	c.125C>T	c.(124-126)gCg>gTg	p.A42V	NPY_ENST00000242152.2_Missense_Mutation_p.A42V|NPY_ENST00000405982.1_Missense_Mutation_p.A42V			P01303	NPY_HUMAN	neuropeptide Y	42					adult feeding behavior (GO:0008343)|behavior (GO:0007610)|blood circulation (GO:0008015)|calcium ion transport (GO:0006816)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of appetite (GO:0032100)|regulation of blood pressure (GO:0008217)|synaptic transmission (GO:0007268)	cell (GO:0005623)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)	p.A42V(1)		breast(1)|kidney(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	9						GACGCACCAGCGGAGGACATG	0.682																																																1	Substitution - Missense(1)	large_intestine(1)											82.0	62.0	69.0					7																	24324984		2203	4300	6503	SO:0001583	missense	4852			K01911	CCDS5387.1	7p15.3	2013-02-26			ENSG00000122585	ENSG00000122585		"""Endogenous ligands"""	7955	protein-coding gene	gene with protein product	"""prepro-neuropeptide Y"""	162640					Standard	NM_000905		Approved	PYY4	uc003sww.2	P01303	OTTHUMG00000022973	ENST00000407573.1:c.125C>T	7.37:g.24324984C>T	ENSP00000384364:p.Ala42Val			Missense_Mutation	SNP	ENST00000407573.1	37	CCDS5387.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.480203	0.84747	.	.	ENSG00000122585	ENST00000242152;ENST00000407573;ENST00000405982	T;T;T	0.42131	0.98;0.98;0.98	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.39733	0.1089	.	.	.	0.80722	D	1	P	0.47841	0.901	B	0.37888	0.26	T	0.29549	-1.0008	9	0.45353	T	0.12	-11.1598	20.1986	0.98248	0.0:1.0:0.0:0.0	.	42	P01303	NPY_HUMAN	V	42	ENSP00000242152:A42V;ENSP00000384364:A42V;ENSP00000385282:A42V	ENSP00000242152:A42V	A	+	2	0	NPY	24291509	1.000000	0.71417	0.923000	0.36655	0.679000	0.39708	7.783000	0.85696	2.781000	0.95711	0.650000	0.86243	GCG		0.682	NPY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326748.1	NM_000905		7	96	7	96
HDHD3	81932	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	116136465	116136465	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr9:116136465C>T	ENST00000238379.5	-	2	1067	c.170G>A	c.(169-171)aGc>aAc	p.S57N	HDHD3_ENST00000485934.1_5'UTR|HDHD3_ENST00000374180.3_Missense_Mutation_p.S57N	NM_031219.2	NP_112496.1	Q9BSH5	HDHD3_HUMAN	haloacid dehalogenase-like hydrolase domain containing 3	57						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			large_intestine(2)|liver(1)	3						GAAGCTGTGGCTCTGAGCCCT	0.657																																																0													53.0	44.0	47.0					9																	116136465		2203	4300	6503	SO:0001583	missense	81932			AK097067	CCDS6793.1	9q33.1	2006-04-12	2004-08-09	2004-08-12	ENSG00000119431	ENSG00000119431			28171	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 158"""	C9orf158		12477932	Standard	NM_031219		Approved	MGC12904	uc004bhi.1	Q9BSH5	OTTHUMG00000020524	ENST00000238379.5:c.170G>A	9.37:g.116136465C>T	ENSP00000238379:p.Ser57Asn		B2RD47	Missense_Mutation	SNP	ENST00000238379.5	37	CCDS6793.1	.	.	.	.	.	.	.	.	.	.	C	8.965	0.971415	0.18736	.	.	ENSG00000119431	ENST00000238379;ENST00000374180	T;T	0.42513	0.97;0.97	5.95	1.61	0.23674	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);	0.184945	0.64402	N	0.000019	T	0.29423	0.0733	L	0.39566	1.225	0.58432	D	0.999999	B	0.17268	0.021	B	0.15870	0.014	T	0.08659	-1.0711	10	0.12430	T	0.62	-10.1386	11.3884	0.49800	0.0:0.7174:0.0:0.2826	.	57	Q9BSH5	HDHD3_HUMAN	N	57	ENSP00000238379:S57N;ENSP00000363295:S57N	ENSP00000238379:S57N	S	-	2	0	HDHD3	115176286	1.000000	0.71417	1.000000	0.80357	0.284000	0.27059	1.397000	0.34543	0.436000	0.26393	-0.136000	0.14681	AGC		0.657	HDHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053731.1	NM_031219		26	38	26	38
PASD1	139135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	150793999	150793999	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chrX:150793999T>C	ENST00000370357.4	+	8	871	c.626T>C	c.(625-627)cTc>cCc	p.L209P		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	209						nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					GTGGGAGAGCTCAGGTGAGAG	0.333																																																0													173.0	171.0	172.0					X																	150793999		2203	4300	6503	SO:0001583	missense	139135			AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"""cancer/testis antigen 63"""					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.626T>C	X.37:g.150793999T>C	ENSP00000359382:p.Leu209Pro		Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	37	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	T	9.241	1.038367	0.19669	.	.	ENSG00000166049	ENST00000370357	T	0.70045	-0.45	4.52	-9.05	0.00730	.	.	.	.	.	T	0.43964	0.1271	N	0.24115	0.695	0.23076	N	0.998339	P	0.49253	0.921	B	0.43701	0.428	T	0.52124	-0.8617	9	0.72032	D	0.01	-18.4634	2.5024	0.04637	0.4675:0.202:0.2301:0.1004	.	209	Q8IV76	PASD1_HUMAN	P	209	ENSP00000359382:L209P	ENSP00000359382:L209P	L	+	2	0	PASD1	150544655	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.057000	0.00625	-2.498000	0.00512	-1.444000	0.01066	CTC		0.333	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		85	267	85	267
BAG4	9530	broad.mit.edu;ucsc.edu	37	8	38065246	38065246	+	Missense_Mutation	SNP	C	C	G	rs150045830	byFrequency	TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr8:38065246C>G	ENST00000287322.4	+	3	866	c.595C>G	c.(595-597)Cct>Gct	p.P199A	BAG4_ENST00000521282.1_3'UTR|BAG4_ENST00000432471.2_Missense_Mutation_p.P163A	NM_004874.3	NP_004865.1	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	199					cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to tumor necrosis factor (GO:0071356)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA modification (GO:0090367)|negative regulation of phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:2001145)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein localization to plasma membrane (GO:0072659)|ruffle assembly (GO:0097178)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|urinary_tract(1)	11	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)				TGAAGCACCCCCTCTTAGGGG	0.488													C|||	7	0.00139776	0.0	0.0029	5008	,	,		18519	0.0		0.004	False		,,,				2504	0.001															0								C	ALA/PRO,ALA/PRO	3,4403	8.1+/-20.4	0,3,2200	72.0	74.0	73.0		487,595	1.4	0.6	8	dbSNP_134	73	43,8557	27.9+/-77.7	0,43,4257	yes	missense,missense	BAG4	NM_001204878.1,NM_004874.3	27,27	0,46,6457	GG,GC,CC		0.5,0.0681,0.3537	probably-damaging,probably-damaging	163/422,199/458	38065246	46,12960	2203	4300	6503	SO:0001583	missense	9530			AF095194	CCDS6104.1, CCDS56533.1	8p11.23	2008-08-07			ENSG00000156735	ENSG00000156735			940	protein-coding gene	gene with protein product	"""silencer of death domains"""	603884				9873016, 9915703	Standard	NM_004874		Approved	SODD	uc003xky.2	O95429	OTTHUMG00000164064	ENST00000287322.4:c.595C>G	8.37:g.38065246C>G	ENSP00000287322:p.Pro199Ala		B4E217|O95818	Missense_Mutation	SNP	ENST00000287322.4	37	CCDS6104.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	13.33	2.203580	0.38905	6.81E-4	0.005	ENSG00000156735	ENST00000432471;ENST00000287322;ENST00000521311	T;T	0.80304	-1.33;-1.36	5.3	1.37	0.22104	.	0.539837	0.19103	N	0.122658	T	0.65037	0.2653	M	0.63428	1.95	0.22468	N	0.999078	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.003	T	0.56709	-0.7934	10	0.35671	T	0.21	-6.892	3.8699	0.09031	0.1348:0.5888:0.1304:0.1459	.	163;199	B4E217;O95429	.;BAG4_HUMAN	A	163;199;46	ENSP00000393298:P163A;ENSP00000287322:P199A	ENSP00000287322:P199A	P	+	1	0	BAG4	38184403	0.004000	0.15560	0.563000	0.28383	0.910000	0.53928	-0.195000	0.09546	0.194000	0.20326	-0.182000	0.12963	CCT		0.488	BAG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377038.2	NM_004874		27	38	27	38
REV1	51455	broad.mit.edu;hgsc.bcm.edu	37	2	100055074	100055076	+	In_Frame_Del	DEL	ACA	ACA	-			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr2:100055074_100055076delACA	ENST00000258428.3	-	6	1428_1430	c.1200_1202delTGT	c.(1198-1203)gttgta>gta	p.400_401VV>V	REV1_ENST00000393445.3_In_Frame_Del_p.400_401VV>V|REV1_ENST00000465835.1_5'UTR	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	400					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGTGTCAGTTACAACAAGTGCAG	0.335								Direct reversal of damage																																								0									,	0,4264		0,0,2132					,	4.7	1.0			64	3,8251		1,1,4125	no	coding,coding	REV1	NM_016316.2,NM_001037872.1	,	1,1,6257	A1A1,A1R,RR		0.0363,0.0,0.024	,	,		3,12515				SO:0001651	inframe_deletion	51455			AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"""DNA polymerases"""	14060	protein-coding gene	gene with protein product		606134	"""REV1 (yeast homolog)- like"", ""REV1-like (yeast)"", ""REV1 homolog (S. cerevisiae)"""	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.1200_1202delTGT	2.37:g.100055077_100055079delACA	ENSP00000258428:p.Val401del		O95941|Q53SI7|Q9C0J4|Q9NUP2	In_Frame_Del	DEL	ENST00000258428.3	37	CCDS2045.1																																																																																				0.335	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		26	48	26	48
RBPJ	3516	broad.mit.edu;hgsc.bcm.edu	37	4	26426014	26426017	+	Frame_Shift_Del	DEL	CAGA	CAGA	-			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr4:26426014_26426017delCAGA	ENST00000361572.6	+	6	780_783	c.586_589delCAGA	c.(586-591)cagacafs	p.QT196fs	RBPJ_ENST00000355476.3_Frame_Shift_Del_p.QT182fs|RBPJ_ENST00000342320.4_Frame_Shift_Del_p.QT182fs|RBPJ_ENST00000507561.1_Frame_Shift_Del_p.QT161fs|RBPJ_ENST00000504907.1_Frame_Shift_Del_p.QT182fs|RBPJ_ENST00000345843.3_Frame_Shift_Del_p.QT181fs|RBPJ_ENST00000342295.1_Frame_Shift_Del_p.QT196fs|RBPJ_ENST00000348160.4_Frame_Shift_Del_p.QT183fs			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	196					angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				ACTACGATCCCAGACAGTTAGTAC	0.422																																																0																																										SO:0001589	frameshift_variant	3516			L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214			5724	protein-coding gene	gene with protein product	"""suppressor of hairless homolog (Drosophila)"""	147183	"""recombining binding protein suppressor of hairless (Drosophila)"""	IGKJRB1, RBPSUH		8406481, 9290259	Standard	NM_005349		Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000361572.6:c.586_589delCAGA	4.37:g.26426014_26426017delCAGA	ENSP00000354528:p.Gln196fs		B4DY22|Q5XKH9|Q6P1N3	Frame_Shift_Del	DEL	ENST00000361572.6	37	CCDS3437.1																																																																																				0.422	RBPJ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215046.2	NM_015874		41	31	41	31
TCF7L2	6934	broad.mit.edu;hgsc.bcm.edu	37	10	114911515	114911517	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr10:114911515_114911517delAAG	ENST00000355995.4	+	10	1540_1542	c.1033_1035delAAG	c.(1033-1035)aagdel	p.K347del	TCF7L2_ENST00000542695.1_In_Frame_Del_p.K63del|TCF7L2_ENST00000355717.4_In_Frame_Del_p.K371del|TCF7L2_ENST00000536810.1_In_Frame_Del_p.K347del|TCF7L2_ENST00000369389.1_In_Frame_Del_p.K58del|TCF7L2_ENST00000543371.1_In_Frame_Del_p.K347del|TCF7L2_ENST00000538897.1_In_Frame_Del_p.K347del|TCF7L2_ENST00000369397.4_In_Frame_Del_p.K324del|TCF7L2_ENST00000352065.5_In_Frame_Del_p.K324del|TCF7L2_ENST00000369386.1_5'UTR|TCF7L2_ENST00000534894.1_In_Frame_Del_p.K347del|TCF7L2_ENST00000545257.1_In_Frame_Del_p.K347del			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	347	Mediates interaction with MAD2L2.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|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 type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		GGAAGAAGAAAAGAAGAAGCCCC	0.443			T	VTI1A	colorectal																																		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	0																																										SO:0001651	inframe_deletion	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1033_1035delAAG	10.37:g.114911521_114911523delAAG	ENSP00000348274:p.Lys347del		B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	In_Frame_Del	DEL	ENST00000355995.4	37																																																																																					0.443	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		19	55	19	55
FKBP3	2287	broad.mit.edu;hgsc.bcm.edu	37	14	45590142	45590144	+	In_Frame_Del	DEL	TTC	TTC	-			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr14:45590142_45590144delTTC	ENST00000216330.3	-	6	878_880	c.468_470delGAA	c.(466-471)aagaaa>aaa	p.156_157KK>K	FKBP3_ENST00000396062.3_In_Frame_Del_p.156_157KK>K			Q00688	FKBP3_HUMAN	FK506 binding protein 3, 25kDa	156	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			NS(1)|biliary_tract(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	12						CTTGGCATTTTTCTTCTTCTTTG	0.32																																																0																																										SO:0001651	inframe_deletion	2287			M96256	CCDS9683.1	14q21.2	2008-08-11	2002-08-29		ENSG00000100442	ENSG00000100442			3719	protein-coding gene	gene with protein product		186947	"""FK506-binding protein 3 (25kD)"""			1374240, 1532945	Standard	NM_002013		Approved	FKBP-25, PPIase	uc010tqf.2	Q00688	OTTHUMG00000140267	ENST00000216330.3:c.468_470delGAA	14.37:g.45590148_45590150delTTC	ENSP00000216330:p.Lys157del		B2R4Q9|Q14317	In_Frame_Del	DEL	ENST00000216330.3	37	CCDS9683.1																																																																																				0.320	FKBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276796.1	NM_002013		23	56	23	56
CIC	23152	broad.mit.edu;hgsc.bcm.edu	37	19	42799067	42799069	+	In_Frame_Del	DEL	GAT	GAT	-			TCGA-HT-A5R9-01A-11D-A289-08	TCGA-HT-A5R9-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10708a85-0155-45b3-9652-24c348b68882	a6d0ae7b-eb25-48c6-a048-ecf0d30b9059	g.chr19:42799067_42799069delGAT	ENST00000575354.2	+	20	4591_4593	c.4551_4553delGAT	c.(4549-4554)aagatc>aac	p.1517_1518KI>N	CIC_ENST00000572681.2_In_Frame_Del_p.2423_2424KI>N|CIC_ENST00000160740.3_In_Frame_Del_p.1515_1516KI>N	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1517					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				TGCGCCAGAAGATCATGCAGGCT	0.65			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0																																										SO:0001651	inframe_deletion	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4551_4553delGAT	19.37:g.42799067_42799069delGAT	ENSP00000458663:p.Lys1517_Ile1518delinsAsn		Q7LGI1|Q9UEG5|Q9Y6T1	In_Frame_Del	DEL	ENST00000575354.2	37	CCDS12601.1																																																																																				0.650	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			44	36	44	36
