#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_Annotation_Transcript	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_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_Description	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_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_AccessionNumbers	i_HGNC_CCDS IDs	i_HGNC_CCDSIDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_DateModified	i_HGNC_DateNameChanged	i_HGNC_DateSymbolChanged	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_EnsemblGeneID	i_HGNC_EnsemblIDsuppliedbyEnsembl	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_Genefamilydescription	i_HGNC_HGNC ID	i_HGNC_HGNCID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_LocusGroup	i_HGNC_LocusType	i_HGNC_Name Synonyms	i_HGNC_NameSynonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_OMIMIDsuppliedbyNCBI	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_PreviousNames	i_HGNC_PreviousSymbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_PubmedIDs	i_HGNC_Record Type	i_HGNC_RecordType	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_RefSeqsuppliedbyNCBI	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UCSCIDsuppliedbyUCSC	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_UniProtIDsuppliedbyUniProt	i_HGNC_VEGA IDs	i_HGNC_VEGAIDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Region	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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_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_folddegenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_hg18_pos1coor	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_init_n_lod	i_init_t_lod	i_n_alt_count	i_n_alt_count_full	i_n_ref_count	i_n_ref_count_full	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_lod_fstar	i_t_lod_fstar_full	i_t_ref_count_full	i_tumor_f_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	tumor_f
SCN11A	11280	broad.mit.edu	37	3	38913708	38913708	+	Silent	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr3:38913708C>T	ENST00000302328.3	-	20	3669	c.3471G>A	c.(3469-3471)gcG>gcA	p.A1157A	SCN11A_ENST00000450244.1_Silent_p.A1157A|SCN11A_ENST00000444237.2_Silent_p.A1157A|SCN11A_ENST00000456224.3_Silent_p.A1119A	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1157					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ACTGGGACAGCGCACGAAGAG	0.478																																						ENST00000450244.1											0			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119						c.(3469-3471)gcG>gcA	sodium channel, voltage-gated, type XI, alpha subunit						163.0	158.0	160.0					3																	38913708		2203	4300	6503	SO:0001819	synonymous_variant	11280			response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity	g.chr3:38913708C>T	AF126739	AF126739	CCDS33737.1	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356	ENSG00000168356	ENSG00000168356		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10583	10583	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			604385	604385	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A		10444332, 16382098	10444332, 16382098	Standard	Standard	NM_014139	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	uc021wvy.1	Q9UI33	Q9UI33	OTTHUMG00000048246	OTTHUMG00000048246	ENST00000302328.3:c.3471G>A	3.37:g.38913708C>T			SCN11A_ENST00000444237.2_Silent_p.A1157A|SCN11A_ENST00000456224.3_Silent_p.A1119A|SCN11A_ENST00000302328.3_Silent_p.A1157A	p.A1157A			Q9UI33	SCNBA_HUMAN		Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	20	3669	-			1157		A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	37	c.3471G>A	CCDS33737.1																																																																																									0.478	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4		192.599797	-62	-62	144	144	NM_014139		60	192.599797	192.599797	60	0.500000	0	0	0	1	0	60	60	0.5
C2orf16	84226	broad.mit.edu	37	2	27804422	27804422	+	Missense_Mutation	SNP	C	C	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr2:27804422C>A	ENST00000408964.2	+	1	5034	c.4983C>A	c.(4981-4983)agC>agA	p.S1661R	ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000379717.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000355467.4_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000413371.2_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1661	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CAGAGAGAAGCCATCGCAGTT	0.582																																						ENST00000408964.2											0			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47						c.(4981-4983)agC>agA	chromosome 2 open reading frame 16						159.0	161.0	161.0					2																	27804422		1904	4127	6031	SO:0001583	missense	84226						g.chr2:27804422C>A	AL136898	AL136898	CCDS42666.1	CCDS42666.1	2p23.3	2013-09-20			2013-09-20			ENSG00000221843	ENSG00000221843	ENSG00000221843	ENSG00000221843				25275	25275	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""	"""P-S-E-R-S-H-H-S repeats containing"""										Standard	Standard	NM_032266	NM_032266		Approved	DKFZp434G118	uc002rkz.4	uc002rkz.4	Q68DN1	Q68DN1	OTTHUMG00000159099	OTTHUMG00000159099	ENST00000408964.2:c.4983C>A	2.37:g.27804422C>A	ENSP00000386190:p.Ser1661Arg			p.S1661R	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN			1	5034	+	Acute lymphoblastic leukemia(172;0.155)		1661	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	c.4983C>A	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	C	7.587	0.669947	0.14776	.	.	ENSG00000221843	ENST00000408964	T	0.05513	3.43	3.1	-1.3	0.09259	3.1	-1.3	0.09259	.	.	.	.	.	T	0.05640	0.0148	L	0.47716	1.5	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38112	-0.9676	9	0.48119	T	0.1	.	3.7016	0.08384	0.3288:0.4636:0.0:0.2076	.	1661	Q68DN1	CB016_HUMAN	R	1661	ENSP00000386190:S1661R	ENSP00000386190:S1661R	S	+	3	2	2	C2orf16	27657926	27657926	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.378000	0.00492	-0.487000	0.06735	-2.225000	0.00294	AGC		0.582	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1		16.434163	-2	-2	292	292	NM_032266		15	34.391393	34.391393	111	0.119048	1	0	4.14922e-12	1	4.40068e-12	15	111	0.119048
TAF15	8148	broad.mit.edu	37	17	34173974	34173974	+	Silent	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr17:34173974C>T	ENST00000592237.1	+	19	1747	c.1218C>T	c.(1216-1218)gtC>gtT	p.V406V	TAF15_ENST00000588240.1_3'UTR|TAF15_ENST00000311979.3_3'UTR			Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	0					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		GTTCCTTTGTCTCTGACATGA	0.393			T	"""TEC, CHN1, ZNF384"""	"""extraskeletal myxoid chondrosarcomas, ALL"""																																	ENST00000592237.1		Dom	yes		17	17q11.1-q11.2	8148	"""TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"""		"""L, M"""	0			lung(1)|ovary(1)|skin(2)|stomach(1)	5						c.(1216-1218)gtC>gtT	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa						115.0	108.0	111.0					17																	34173974		2203	4300	6503	SO:0001819	synonymous_variant	8148			positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding	g.chr17:34173974C>T	U51334	U51334	CCDS32623.1, CCDS59279.1	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		ENSG00000270647		"""RNA binding motif (RRM) containing"""	"""RNA binding motif (RRM) containing"""	11547	11547	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			601574	601574	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"""	TAF2N	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"""	TAF2N		8954779, 9795213	8954779, 9795213	Standard	Standard	NM_003487	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	uc002hkd.4	Q92804	Q92804			ENST00000592237.1:c.1218C>T	17.37:g.34173974C>T			TAF15_ENST00000311979.3_3'UTR|TAF15_ENST00000588240.1_3'UTR	p.V406V			Q92804	RBP56_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)	19	1747	+		Ovarian(249;0.17)	0	Arg/Gly-rich.	D3DPM5|Q15775|Q5T077	Silent	SNP	ENST00000592237.1	37	c.1218C>T																																																																																										0.393	TAF15-006	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000449142.1		89.199687	-11	-11	89	89	NM_139215		28	89.203609	89.203609	27	0.509091	0	0	0	1	0	28	27	0.509091
LMO3	55885	broad.mit.edu	37	12	16753678	16753678	+	Silent	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr12:16753678C>T	ENST00000320122.6	-	2	639	c.117G>A	c.(115-117)aaG>aaA	p.K39K	LMO3_ENST00000354662.1_Silent_p.K39K|LMO3_ENST00000441439.2_Silent_p.K39K|LMO3_ENST00000537304.1_Silent_p.K39K|LMO3_ENST00000447609.1_Silent_p.K39K|LMO3_ENST00000540445.1_Silent_p.K39K|LMO3_ENST00000541846.1_Silent_p.K39K|LMO3_ENST00000261169.6_Silent_p.K50K|LMO3_ENST00000537568.1_5'UTR|LMO3_ENST00000540848.1_Silent_p.K39K|LMO3_ENST00000535535.1_Silent_p.K39K|LMO3_ENST00000541295.1_Silent_p.K57K|LMO3_ENST00000534946.1_Silent_p.K39K	NM_001243611.1	NP_001230540.1	Q8TAP4	LMO3_HUMAN	LIM domain only 3 (rhombotin-like 2)	39	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|skin(1)	5		Hepatocellular(102;0.244)				AGCAGGCACACTTCAGGCAGT	0.498																																						ENST00000320122.6											0			endometrium(2)|large_intestine(2)|skin(1)	5						c.(115-117)aaG>aaA	LIM domain only 3 (rhombotin-like 2)						154.0	133.0	140.0					12																	16753678		2203	4300	6503	SO:0001819	synonymous_variant	55885			regulation of transcription, DNA-dependent|transcription, DNA-dependent		zinc ion binding	g.chr12:16753678C>T	BC026311	BC026311	CCDS8678.1, CCDS58210.1, CCDS58211.1, CCDS58212.1	CCDS8678.1, CCDS58210.1, CCDS58211.1, CCDS58212.1	12p13	2004-05-19			2004-05-19			ENSG00000048540	ENSG00000048540	ENSG00000048540	ENSG00000048540				6643	6643	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			180386	180386		RBTNL2		RBTNL2		11489251	11489251	Standard	Standard	NM_018640	NM_018640		Approved	Rhom-3, DAT1	uc010shy.2	uc010shy.2	Q8TAP4	Q8TAP4	OTTHUMG00000168837	OTTHUMG00000168837	ENST00000320122.6:c.117G>A	12.37:g.16753678C>T			LMO3_ENST00000534946.1_Silent_p.K39K|LMO3_ENST00000354662.1_Silent_p.K39K|LMO3_ENST00000540445.1_Silent_p.K39K|LMO3_ENST00000261169.6_Silent_p.K50K|LMO3_ENST00000541295.1_Silent_p.K57K|LMO3_ENST00000441439.2_Silent_p.K39K|LMO3_ENST00000537568.1_5'UTR|LMO3_ENST00000540848.1_Silent_p.K39K|LMO3_ENST00000535535.1_Silent_p.K39K|LMO3_ENST00000537304.1_Silent_p.K39K|LMO3_ENST00000447609.1_Silent_p.K39K|LMO3_ENST00000541846.1_Silent_p.K39K	p.K39K	NM_001243611.1	NP_001230540.1	Q8TAP4	LMO3_HUMAN			2	639	-		Hepatocellular(102;0.244)	39	LIM zinc-binding 1.	B4DG90|B4DH35|Q58A66|Q58A67|Q8N974|Q9UDD5	Silent	SNP	ENST00000320122.6	37	c.117G>A	CCDS8678.1																																																																																									0.498	LMO3-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401279.1		97.719904	-11	-11	75	75	NM_018640		31	97.772668	97.772668	35	0.469697	0	0	0	1	0	31	35	0.469697
DENND3	22898	broad.mit.edu	37	8	142161751	142161751	+	Missense_Mutation	SNP	G	G	A	rs571831372		TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr8:142161751G>A	ENST00000262585.2	+	7	927	c.649G>A	c.(649-651)Gtc>Atc	p.V217I	DENND3_ENST00000519811.1_Missense_Mutation_p.V297I|DENND3_ENST00000424248.1_Missense_Mutation_p.V217I	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	217	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			ACAGCGGATCGTCTTCTTCTC	0.542													G|||	1	0.000199681	0.0	0.0	5008	,	,		16882	0.0		0.001	False		,,,				2504	0.0					ENST00000519811.1											0			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55						c.(889-891)Gtc>Atc	DENN/MADD domain containing 3						150.0	121.0	131.0					8																	142161751		2203	4300	6503	SO:0001583	missense	22898						g.chr8:142161751G>A	AB020677	AB020677	CCDS34947.1	CCDS34947.1	8q24.3	2013-01-10			2013-01-10				ENSG00000105339		ENSG00000105339		"""DENN/MADD domain containing"", ""WD repeat domain containing"""	"""DENN/MADD domain containing"", ""WD repeat domain containing"""	29134	29134	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product										10048485	10048485	Standard	Standard	NM_014957	NM_014957		Approved	KIAA0870	uc003yvy.3	uc003yvy.3	A2RUS2	A2RUS2			ENST00000262585.2:c.649G>A	8.37:g.142161751G>A	ENSP00000262585:p.Val217Ile		DENND3_ENST00000262585.2_Missense_Mutation_p.V217I|DENND3_ENST00000424248.1_Missense_Mutation_p.V217I	p.V297I			A2RUS2	DEND3_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.105)		7	959	+	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		217		B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	37	c.889G>A	CCDS34947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.52|19.52	3.842905|3.842905	0.71488|0.71488	.|.	.|.	ENSG00000105339|ENSG00000105339	ENST00000518668|ENST00000262585;ENST00000424248;ENST00000519811;ENST00000520986	.|T;T;T;T	.|0.07800	.|3.16;3.16;3.16;3.16	5.38|5.38	5.38|5.38	0.77491|0.77491	5.38|5.38	5.38|5.38	0.77491|0.77491	.|DENN (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.21801|0.21801	0.0525|0.0525	L|L	0.41573|0.41573	1.285|1.285	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.998;0.992	T|T	0.01679|0.01679	-1.1297|-1.1297	5|10	.|0.25106	.|T	.|0.35	-16.2549|-16.2549	19.1045|19.1045	0.93287|0.93287	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|297;217	.|E9PF32;A2RUS2	.|.;DEND3_HUMAN	H|I	273|217;217;297;219	.|ENSP00000262585:V217I;ENSP00000410594:V217I;ENSP00000428714:V297I;ENSP00000429780:V219I	.|ENSP00000262585:V217I	R|V	+|+	2|1	0|0	0|0	DENND3|DENND3	142230933|142230933	142230933|142230933	1.000000|1.000000	0.71417|0.71417	0.752000|0.752000	0.31206|0.31206	0.181000|0.181000	0.23173|0.23173	9.107000|9.107000	0.94261|0.94261	2.506000|2.506000	0.84524|0.84524	0.563000|0.563000	0.77884|0.77884	CGT|GTC		0.542	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding			32.080874	-27	-27	101	101	NM_014957		20	48.763545	48.763545	118	0.144928	0	0	0	1	0	20	118	0.144928
KLHL15	80311	broad.mit.edu	37	X	24007013	24007013	+	Silent	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chrX:24007013C>T	ENST00000328046.8	-	4	1095	c.840G>A	c.(838-840)ccG>ccA	p.P280P		NM_030624.2	NP_085127.2	Q96M94	KLH15_HUMAN	kelch-like family member 15	280					protein ubiquitination (GO:0016567)					autonomic_ganglia(1)|breast(1)|endometrium(8)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	22						CTGTAGTTTGCGGTTTTGCAG	0.433																																						ENST00000328046.8											0			autonomic_ganglia(1)|breast(1)|endometrium(8)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	22						c.(838-840)ccG>ccA	kelch-like family member 15						108.0	101.0	103.0					X																	24007013		2203	4300	6503	SO:0001819	synonymous_variant	80311						g.chrX:24007013C>T	AB051464	AB051464	CCDS35217.1	CCDS35217.1	Xp22.1-p21	2013-01-30	2013-01-30		2013-01-30	2013-01-30		ENSG00000174010	ENSG00000174010	ENSG00000174010	ENSG00000174010		"""Kelch-like"", ""BTB/POZ domain containing"""	"""Kelch-like"", ""BTB/POZ domain containing"""	29347	29347	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product					"""kelch-like 15 (Drosophila)"""		"""kelch-like 15 (Drosophila)"""			11214970, 14702039	11214970, 14702039	Standard	Standard	NM_030624	NM_030624		Approved	KIAA1677	uc004dba.4	uc004dba.4	Q96M94	Q96M94	OTTHUMG00000021261	OTTHUMG00000021261	ENST00000328046.8:c.840G>A	X.37:g.24007013C>T				p.P280P	NM_030624.2	NP_085127.2	Q96M94	KLH15_HUMAN			4	1095	-			280		Q32MN3|Q8NDA3|Q96BM6|Q9C0I6	Silent	SNP	ENST00000328046.8	37	c.840G>A	CCDS35217.1																																																																																									0.433	KLHL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056078.1		-28.031389	-9	-9	182	182	XM_040383		4	7.665853	7.665853	141	0.027586	0	0	0	1	0	4	141	0.027586
GNAQ	2776	broad.mit.edu	37	9	80409488	80409488	+	Missense_Mutation	SNP	T	T	G	rs121913492		TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr9:80409488T>G	ENST00000286548.4	-	5	848	c.626A>C	c.(625-627)cAa>cCa	p.Q209P	GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7P	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	209			Q -> L (found in blue naevi and uveal melanoma samples; somatic mutation; constitutive activation).		action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.Q209L(87)|p.Q209P(64)|p.Q209Y(1)|p.Q209R(1)		NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						CTCTGACCTTTGGCCCCCTAC	0.348			Mis		uveal melanoma																																	ENST00000286548.4		Dom	yes		9	9q21	2776	"""guanine nucleotide binding protein (G protein), q polypeptide"""		E	153	Substitution - Missense(153)	eye(99)|skin(43)|meninges(10)|NS(1)	NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						c.(625-627)cAa>cCa	guanine nucleotide binding protein (G protein), q polypeptide						108.0	105.0	106.0					9																	80409488		2203	4300	6503	SO:0001583	missense	2776			activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity	g.chr9:80409488T>G			CCDS6658.1	CCDS6658.1	9q21	2010-03-17			2010-03-17			ENSG00000156052	ENSG00000156052	ENSG00000156052	ENSG00000156052				4390	4390	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			600998	600998						8825633	8825633	Standard	Standard	NM_002072	NM_002072		Approved	G-ALPHA-q, GAQ	uc004akw.3	uc004akw.3	P50148	P50148	OTTHUMG00000020059	OTTHUMG00000020059	ENST00000286548.4:c.626A>C	9.37:g.80409488T>G	ENSP00000286548:p.Gln209Pro		GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7P	p.Q209P	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN			5	848	-			209		O15108|Q13462|Q6NT27|Q92471|Q9BZB9	Missense_Mutation	SNP	ENST00000286548.4	37	c.626A>C	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614273	0.87359	.	.	ENSG00000156052	ENST00000286548;ENST00000397476	D;D	0.91237	-2.81;-2.81	5.69	5.69	0.88448	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.97164	0.9073	H	0.97291	3.975	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.98607	1.0661	10	0.87932	D	0	.	15.9502	0.79827	0.0:0.0:0.0:1.0	.	209	P50148	GNAQ_HUMAN	P	209;7	ENSP00000286548:Q209P;ENSP00000443197:Q7P	ENSP00000286548:Q209P	Q	-	2	0	0	GNAQ	79599308	79599308	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	8.040000	0.89188	2.167000	0.68274	0.460000	0.39030	CAA		0.348	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1		137.879886	-22	-22	90	90	NM_002072		41	137.982794	137.982794	35	0.539474	0	0	0	1	0	41	35	0.539474
GTDC1	79712	broad.mit.edu	37	2	144966218	144966218	+	Missense_Mutation	SNP	G	G	A	rs115723847		TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr2:144966218G>A	ENST00000392869.2	-	3	283	c.131C>T	c.(130-132)aCa>aTa	p.T44I	GTDC1_ENST00000542155.1_Missense_Mutation_p.T44I|GTDC1_ENST00000392867.3_Missense_Mutation_p.T44I|GTDC1_ENST00000344850.4_Missense_Mutation_p.T44I|GTDC1_ENST00000241391.5_Missense_Mutation_p.T44I|GTDC1_ENST00000409298.1_Missense_Mutation_p.T44I|GTDC1_ENST00000463875.2_Intron|GTDC1_ENST00000409214.1_Missense_Mutation_p.T44I|GTDC1_ENST00000467352.1_5'Flank	NM_001284234.1	NP_001271163.1	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1	44					biosynthetic process (GO:0009058)		transferase activity, transferring glycosyl groups (GO:0016757)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.0914)		TAAAGCAGATGTCCGGGCTCT	0.428													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16013	0.0		0.0	False		,,,				2504	0.0					ENST00000392869.2											0			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25						c.(130-132)aCa>aTa	glycosyltransferase-like domain containing 1						86.0	86.0	86.0					2																	144966218		2203	4300	6503	SO:0001583	missense	79712			biosynthetic process		transferase activity, transferring glycosyl groups	g.chr2:144966218G>A	AY281366	AY281366	CCDS2185.1, CCDS33300.1, CCDS63029.1, CCDS74582.1, CCDS74583.1	CCDS2185.1, CCDS33300.1, CCDS63029.1, CCDS74582.1, CCDS74583.1	2q22.3	2013-02-22			2013-02-22			ENSG00000121964	ENSG00000121964	ENSG00000121964	ENSG00000121964		"""Glycosyltransferase group 1 domain containing"""	"""Glycosyltransferase group 1 domain containing"""	20887	20887	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""mannosyltransferase-like"""	"""mannosyltransferase-like"""	610165	610165						15068588, 21821951	15068588, 21821951	Standard	Standard	NM_024659	NM_024659		Approved	FLJ11753, Hmat-Xa	uc010fnn.3	uc010fnn.3	Q4AE62	Q4AE62	OTTHUMG00000131835	OTTHUMG00000131835	ENST00000392869.2:c.131C>T	2.37:g.144966218G>A	ENSP00000376608:p.Thr44Ile		GTDC1_ENST00000409214.1_Missense_Mutation_p.T44I|GTDC1_ENST00000392867.3_Missense_Mutation_p.T44I|GTDC1_ENST00000542155.1_Missense_Mutation_p.T44I|GTDC1_ENST00000241391.5_Missense_Mutation_p.T44I|GTDC1_ENST00000409298.1_Missense_Mutation_p.T44I|GTDC1_ENST00000344850.4_Missense_Mutation_p.T44I|GTDC1_ENST00000463875.2_Intron	p.T44I	NM_001284234.1	NP_001271163.1	Q4AE62	GTDC1_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.0914)	3	283	-					A8K5P2|D3DP81|Q53SM7|Q53TC5|Q6P7E7|Q6PJB6|Q6WKW6|Q9HAE5	Missense_Mutation	SNP	ENST00000392869.2	37	c.131C>T	CCDS33300.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	25.7	4.666378	0.88251	.	.	ENSG00000121964	ENST00000392869;ENST00000409214;ENST00000392867;ENST00000409298;ENST00000542155;ENST00000241391;ENST00000344850;ENST00000437114;ENST00000417450	T;T;T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97	6.08	6.08	0.98989	6.08	6.08	0.98989	Glycosyltransferase family 1, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.67813	0.2933	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.89917	0.958;1.0;1.0;1.0	P;D;D;D	0.91635	0.693;0.993;0.999;0.991	T	0.65660	-0.6114	10	0.52906	T	0.07	0.0079	20.6634	0.99662	0.0:0.0:1.0:0.0	.	44;44;44;44	Q4AE62-2;B8ZZ45;Q4AE62;Q4AE62-3	.;.;GTDC1_HUMAN;.	I	44	ENSP00000376608:T44I;ENSP00000386581:T44I;ENSP00000376606:T44I;ENSP00000386691:T44I;ENSP00000438323:T44I;ENSP00000241391:T44I;ENSP00000339750:T44I;ENSP00000403869:T44I;ENSP00000400661:T44I	ENSP00000241391:T44I	T	-	2	0	0	GTDC1	144682688	144682688	1.000000	0.71417	0.982000	0.44146	0.852000	0.48524	9.320000	0.96346	2.894000	0.99253	0.655000	0.94253	ACA		0.428	GTDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254779.2		16.671035	0	0	64	64	NM_024659		8	21.288097	21.288097	38	0.173913	0	0	0	1	0	8	38	0.173913
NCF2	4688	broad.mit.edu	37	1	183529380	183529380	+	Missense_Mutation	SNP	T	T	G			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr1:183529380T>G	ENST00000367535.3	-	14	1570	c.1319A>C	c.(1318-1320)aAg>aCg	p.K440T	NCF2_ENST00000418089.1_Missense_Mutation_p.K359T|NCF2_ENST00000367536.1_Missense_Mutation_p.K440T|NCF2_ENST00000469280.1_Intron|NCF2_ENST00000413720.1_Missense_Mutation_p.K395T	NM_000433.3	NP_000424.2	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	440					aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cellular response to hormone stimulus (GO:0032870)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron apoptotic process (GO:0043525)|respiratory burst (GO:0045730)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hyperoxia (GO:0055093)|response to laminar fluid shear stress (GO:0034616)|response to lipopolysaccharide (GO:0032496)|response to progesterone (GO:0032570)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|NADPH oxidase complex (GO:0043020)|nucleolus (GO:0005730)|phagolysosome (GO:0032010)	electron carrier activity (GO:0009055)|protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30					Dextromethorphan(DB00514)	TTCACTTTCCTTGGGTTCATC	0.438																																						ENST00000413720.1											0			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30						c.(1183-1185)aAg>aCg	neutrophil cytosolic factor 2						217.0	201.0	207.0					1																	183529380		2203	4300	6503	SO:0001583	missense	4688			cellular defense response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex|nucleolus	electron carrier activity|protein C-terminus binding	g.chr1:183529380T>G	BC001606	BC001606	CCDS1356.1, CCDS53446.1, CCDS53447.1	CCDS1356.1, CCDS53446.1, CCDS53447.1	1q25	2014-09-17	2008-07-31		2014-09-17	2008-07-31		ENSG00000116701	ENSG00000116701	ENSG00000116701	ENSG00000116701		"""Tetratricopeptide (TTC) repeat domain containing"""	"""Tetratricopeptide (TTC) repeat domain containing"""	7661	7661	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""NADPH oxidase activator 2"", ""chronic granulomatous disease, autosomal 2"""	"""NADPH oxidase activator 2"", ""chronic granulomatous disease, autosomal 2"""	608515	608515	"""neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)"""		"""neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)"""					Standard	Standard	NM_000433	NM_000433		Approved	p67phox, NOXA2	uc001gqk.4	uc001gqk.4	P19878	P19878	OTTHUMG00000035329	OTTHUMG00000035329	ENST00000367535.3:c.1319A>C	1.37:g.183529380T>G	ENSP00000356505:p.Lys440Thr		NCF2_ENST00000469280.1_Intron|NCF2_ENST00000367535.3_Missense_Mutation_p.K440T|NCF2_ENST00000418089.1_Missense_Mutation_p.K359T|NCF2_ENST00000367536.1_Missense_Mutation_p.K440T	p.K395T	NM_001190794.1	NP_001177723.1	P19878	NCF2_HUMAN			13	1458	-			440	OPR.	B2R6Q1|B4DKQ7|B4DQA7|E9PHJ2|E9PHX3|Q2PP06|Q8NFC7|Q9BV51	Missense_Mutation	SNP	ENST00000367535.3	37	c.1184A>C	CCDS1356.1	.	.	.	.	.	.	.	.	.	.	T	12.39	1.922659	0.33908	.	.	ENSG00000116701	ENST00000367536;ENST00000392014;ENST00000413720;ENST00000418089;ENST00000367535	T;T;T;T	0.70749	-0.51;-0.16;-0.05;-0.51	5.18	2.71	0.32032	5.18	2.71	0.32032	Src homology-3 domain (1);	0.788960	0.11865	N	0.522014	T	0.58481	0.2125	L	0.47716	1.5	0.09310	N	1	B;B;B	0.24823	0.001;0.112;0.036	B;B;B	0.26416	0.001;0.069;0.021	T	0.43376	-0.9395	10	0.14656	T	0.56	-16.6308	5.4961	0.16804	0.3006:0.0:0.1559:0.5435	.	359;395;440	E9PHJ2;E9PHX3;P19878	.;.;NCF2_HUMAN	T	440;512;395;359;440	ENSP00000356506:K440T;ENSP00000399294:K395T;ENSP00000407217:K359T;ENSP00000356505:K440T	ENSP00000356505:K440T	K	-	2	0	0	NCF2	181796003	181796003	0.001000	0.12720	0.002000	0.10522	0.919000	0.55068	0.822000	0.27352	0.241000	0.21283	0.533000	0.62120	AAG		0.438	NCF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085483.1		101.571981	-20	-20	166	166	NM_000433		34	102.83067	102.830670	57	0.373626	0	0	0	1	0	34	57	0.373626
PEX26	55670	ucsc.edu	37	22	18566443	18566443	+	Silent	SNP	G	G	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr22:18566443G>A	ENST00000329627.7	+	4	818	c.612G>A	c.(610-612)caG>caA	p.Q204Q	PEX26_ENST00000428061.2_Silent_p.Q204Q|PEX26_ENST00000399744.3_Silent_p.Q204Q	NM_017929.5	NP_060399.1	Q7Z412	PEX26_HUMAN	peroxisomal biogenesis factor 26	204					protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)	integral component of peroxisomal membrane (GO:0005779)|peroxisome (GO:0005777)	ATPase binding (GO:0051117)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|kidney(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						CAGCGAGGCAGCAGCAGAAAC	0.577																																																	0																	84.0	79.0	81.0					22																	18566443		2203	4300	6503	SO:0001819	synonymous_variant	55670							AB089678	AB089678	CCDS13750.1, CCDS56221.1	CCDS13750.1, CCDS56221.1	22q11.21	2008-08-26	2008-08-26		2008-08-26	2008-08-26		ENSG00000215193	ENSG00000215193	ENSG00000215193	ENSG00000215193				22965	22965	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			608666	608666	"""peroxisome biogenesis factor 26"""		"""peroxisome biogenesis factor 26"""			12717447, 12851857	12717447, 12851857	Standard	Standard	NM_017929	NM_017929		Approved	FLJ20695	uc002znp.4	uc002znp.4	Q7Z412	Q7Z412	OTTHUMG00000149970	OTTHUMG00000149970	ENST00000329627.7:c.612G>A	22.37:g.18566443G>A																		F6UBB5|Q7Z413|Q7Z414|Q7Z415|Q7Z416|Q96B12|Q9NWQ0|Q9NXU0	Silent	SNP	ENST00000329627.7	37		CCDS13750.1																																																																																									0.577	PEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314644.3			-4	-4	47	47	NM_017929		4			33							4	33	
NPEPL1	79716	broad.mit.edu	37	20	57276201	57276201	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr20:57276201G>A	ENST00000356091.6	+	6	1097	c.809G>A	c.(808-810)aGc>aAc	p.S270N	NPEPL1_ENST00000525817.1_Missense_Mutation_p.S222N|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Missense_Mutation_p.S242N	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	270						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			GGAGGCCTCAGCATCAAAGGG	0.687																																						ENST00000356091.6											0			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14						c.(808-810)aGc>aAc	aminopeptidase-like 1						24.0	24.0	24.0					20																	57276201		2037	4189	6226	SO:0001583	missense	79716			proteolysis	cytoplasm	aminopeptidase activity|manganese ion binding|metalloexopeptidase activity	g.chr20:57276201G>A	AK021645	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			2008-07-02			ENSG00000215440	ENSG00000215440	ENSG00000215440	ENSG00000215440				16244	16244	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product										14702039	14702039	Standard	Standard	NM_001204872	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	uc010zzs.1	Q8NDH3	Q8NDH3	OTTHUMG00000033060	OTTHUMG00000033060	ENST00000356091.6:c.809G>A	20.37:g.57276201G>A	ENSP00000348395:p.Ser270Asn		NPEPL1_ENST00000525967.1_Missense_Mutation_p.S242N|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525817.1_Missense_Mutation_p.S222N	p.S270N	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)		6	1097	+	all_lung(29;0.0175)		270		A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	37	c.809G>A	CCDS46621.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.668192	0.88348	.	.	ENSG00000215440	ENST00000525967;ENST00000525817;ENST00000356091	T;T;T	0.48201	0.82;0.82;0.82	5.01	5.01	0.66863	5.01	5.01	0.66863	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.66025	0.2748	M	0.66939	2.045	0.80722	D	1	D;D;D;D	0.89917	0.998;0.997;1.0;0.961	D;D;D;P	0.81914	0.985;0.975;0.995;0.835	T	0.65829	-0.6073	10	0.41790	T	0.15	-41.2309	15.4714	0.75441	0.0:0.0:1.0:0.0	.	270;222;242;270	Q8NDH3;G5EA34;E9PN47;Q8NDH3-3	PEPL1_HUMAN;.;.;.	N	242;222;270	ENSP00000434810:S242N;ENSP00000437112:S222N;ENSP00000348395:S270N	ENSP00000348395:S270N	S	+	2	0	0	NPEPL1	56709608	56709608	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.375000	0.97178	2.313000	0.78055	0.585000	0.79938	AGC		0.687	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6		16.476751	0	0	10	10	NM_024663		5	16.586418	16.586418	3	0.625000	0	0	0	1	0	5	3	0.625
SF3B1	23451	broad.mit.edu	37	2	198267484	198267484	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr2:198267484G>A	ENST00000335508.6	-	14	1964	c.1873C>T	c.(1873-1875)Cgt>Tgt	p.R625C	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	625					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.R625C(5)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GTTGTGTTACGGACATACTCA	0.433			Mis		myelodysplastic syndrome																																	ENST00000335508.6		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	5	Substitution - Missense(5)	haematopoietic_and_lymphoid_tissue(5)	NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633						c.(1873-1875)Cgt>Tgt	splicing factor 3b, subunit 1, 155kDa						93.0	90.0	91.0					2																	198267484		2203	4300	6503	SO:0001583	missense	23451			nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding	g.chr2:198267484G>A	AF054284	AF054284	CCDS33356.1, CCDS46479.1	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524	ENSG00000115524	ENSG00000115524				10768	10768	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			605590	605590	"""splicing factor 3b, subunit 1, 155kD"""		"""splicing factor 3b, subunit 1, 155kD"""			9585501	9585501	Standard	Standard	XM_005246428	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	uc002uue.3	O75533	O75533	OTTHUMG00000154447	OTTHUMG00000154447	ENST00000335508.6:c.1873C>T	2.37:g.198267484G>A	ENSP00000335321:p.Arg625Cys			p.R625C	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.246)		14	1964	-					E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	c.1873C>T	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	G	19.68	3.873082	0.72180	.	.	ENSG00000115524	ENST00000335508	T	0.74421	-0.84	5.82	4.93	0.64822	5.82	4.93	0.64822	Armadillo-like helical (1);Armadillo-type fold (1);	0.053241	0.64402	D	0.000001	D	0.90331	0.6975	H	0.96333	3.805	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.93337	0.6706	10	0.87932	D	0	.	15.2676	0.73675	0.0:0.0:0.7451:0.2549	.	625	O75533	SF3B1_HUMAN	C	625	ENSP00000335321:R625C	ENSP00000335321:R625C	R	-	1	0	0	SF3B1	197975729	197975729	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.689000	0.61723	1.444000	0.47605	-0.182000	0.12963	CGT		0.433	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		65.565585	0	0	54	54			21	66.064531	66.064531	32	0.396226	0	0	0	1	0	21	32	0.396226
C7orf55	154791	broad.mit.edu	37	7	139026134	139026134	+	Missense_Mutation	SNP	G	G	A	rs75669887		TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr7:139026134G>A	ENST00000297534.6	+	1	257	c.4G>A	c.(4-6)Gcg>Acg	p.A2T	LUC7L2_ENST00000541515.3_Missense_Mutation_p.A2T|C7orf55_ENST00000481123.1_Intron|C7orf55-LUC7L2_ENST00000541170.3_Intron	NM_197964.4	NP_932068.2	Q96HJ9	CG055_HUMAN	chromosome 7 open reading frame 55	2						mitochondrion (GO:0005739)				breast(1)|lung(2)	3						CAGGACAATGGCGGCCTTAGG	0.657											OREG0018357	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		15526	0.0		0.001	False		,,,				2504	0.0					ENST00000541515.3											0			NS(2)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	16						c.(4-6)Gcg>Acg	LUC7-like 2 (S. cerevisiae)						54.0	63.0	60.0					7																	139026134		2203	4300	6503	SO:0001583	missense	51631					enzyme binding|metal ion binding	g.chr7:139026134G>A	AF161386	AF151832	CCDS5853.1	CCDS43656.1, CCDS59085.1, CCDS59510.1	7q34	2009-01-22	2009-01-22	2009-01-22	2013-05-09			ENSG00000164898	ENSG00000164898	ENSG00000269955	ENSG00000269955				26946	21608	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""formation of mitochondrial complexes 1 homolog (S. cerevisiae)"""	"""CGI-74 protein"""		613056						12477932	10810093	Standard	Standard	NM_197964	NM_001244585		Approved	HSPC268, FMC1			Q96HJ9	Q9Y383	OTTHUMG00000151719	OTTHUMG00000185163	ENST00000297534.6:c.4G>A	7.37:g.139026134G>A	ENSP00000297534:p.Ala2Thr	1645	C7orf55-LUC7L2_ENST00000541170.3_Intron|C7orf55_ENST00000297534.6_Missense_Mutation_p.A2T|C7orf55_ENST00000481123.1_Intron	p.A2T	NM_001244584.2	NP_001231513.1	Q9Y383	LC7L2_HUMAN			1	29	+	Melanoma(164;0.242)		0		B7Z4Q3|Q75M90|Q9P0B3	Missense_Mutation	SNP	ENST00000297534.6	37	c.4G>A	CCDS5853.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	24.4	4.529993	0.85706	.	.	ENSG00000164898;ENSG00000146963	ENST00000297534;ENST00000541515	T;T	0.53640	0.61;1.28	5.46	4.58	0.56647	5.46	4.58	0.56647	.	0.067803	0.56097	D	0.000025	T	0.48205	0.1487	M	0.68593	2.085	0.49130	D	0.999758	B;B	0.22746	0.02;0.074	B;B	0.20955	0.006;0.032	T	0.51593	-0.8686	10	0.72032	D	0.01	-0.0343	14.2126	0.65773	0.0713:0.0:0.9287:0.0	.	2;2	B7Z4Q3;Q96HJ9	.;CG055_HUMAN	T	2	ENSP00000297534:A2T;ENSP00000440222:A2T	ENSP00000297534:A2T	A	+	1	0	0	LUC7L2;C7orf55	138676674	138676674	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.514000	0.60482	1.546000	0.49388	0.591000	0.81541	GCG		0.657	C7orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323626.1		60.091348	-26	-26	49	49	NM_197964		20	60.382398	60.382398	28	0.416667	0	0	0	1	0	20	28	0.416667
PITPNM2	57605	broad.mit.edu	37	12	123481386	123481386	+	Missense_Mutation	SNP	G	G	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr12:123481386G>T	ENST00000542749.1	-	10	1607	c.1544C>A	c.(1543-1545)cCc>cAc	p.P515H	PITPNM2_ENST00000320201.4_Missense_Mutation_p.P515H|PITPNM2_ENST00000280562.5_Missense_Mutation_p.P515H|PITPNM2_ENST00000392428.1_Missense_Mutation_p.P236H			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	515					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		GGCCAGCAGGGGGAGGGCAGC	0.637																																						ENST00000280562.5											0			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39						c.(1543-1545)cCc>cAc	phosphatidylinositol transfer protein, membrane-associated 2						49.0	49.0	49.0					12																	123481386		2203	4300	6503	SO:0001583	missense	57605			metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding	g.chr12:123481386G>T	AF334585	AF334585	CCDS9242.1, CCDS73543.1	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05			2008-02-05				ENSG00000090975		ENSG00000090975				21044	21044	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			608920	608920						10022914	10022914	Standard	Standard	XM_005253582	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	uc001uej.1	Q9BZ72	Q9BZ72			ENST00000542749.1:c.1544C>A	12.37:g.123481386G>T	ENSP00000437611:p.Pro515His		PITPNM2_ENST00000320201.4_Missense_Mutation_p.P515H|PITPNM2_ENST00000392428.1_Missense_Mutation_p.P236H|PITPNM2_ENST00000542749.1_Missense_Mutation_p.P515H	p.P515H			Q9BZ72	PITM2_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)	11	1749	-	all_neural(191;0.101)|Medulloblastoma(191;0.163)		515		Q9P271	Missense_Mutation	SNP	ENST00000542749.1	37	c.1544C>A	CCDS9242.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.002812	0.74932	.	.	ENSG00000090975	ENST00000280562;ENST00000320201;ENST00000392428;ENST00000542749	T;T;T;T	0.19669	2.13;2.13;2.13;2.13	4.81	3.92	0.45320	4.81	3.92	0.45320	.	0.000000	0.85682	D	0.000000	T	0.48589	0.1508	M	0.82193	2.58	0.53688	D	0.999975	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.55153	-0.8185	10	0.87932	D	0	-17.2931	13.0406	0.58897	0.0784:0.0:0.9216:0.0	.	515;515	Q9BZ72-2;Q9BZ72	.;PITM2_HUMAN	H	515;515;236;515	ENSP00000280562:P515H;ENSP00000322218:P515H;ENSP00000376223:P236H;ENSP00000437611:P515H	ENSP00000280562:P515H	P	-	2	0	0	PITPNM2	122047339	122047339	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	7.976000	0.88070	1.033000	0.39918	0.460000	0.39030	CCC		0.637	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1		54.440222	-7	-7	74	74	NM_020845		18	54.446323	54.446323	19	0.486486	1	0	8.34094e-07	1	8.58626e-07	18	19	0.486486
KRT32	3882	broad.mit.edu	37	17	39620401	39620401	+	Nonsense_Mutation	SNP	G	G	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr17:39620401G>A	ENST00000225899.3	-	5	1028	c.925C>T	c.(925-927)Cag>Tag	p.Q309*		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	309	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				ATGTCTGACTGGTAGTTCTGA	0.577																																						ENST00000225899.3											0			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						c.(925-927)Cag>Tag	keratin 32						177.0	133.0	148.0					17																	39620401		2203	4300	6503	SO:0001587	stop_gained	3882			epidermis development	intermediate filament	protein binding|structural molecule activity	g.chr17:39620401G>A	X90761	X90761	CCDS11393.1	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	6449	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""hard keratin type I"""	"""hard keratin type I"""	602760	602760	"""keratin, hair, acidic, 2"""	KRTHA2	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	7556444, 8823373, 16831889	Standard	Standard	NM_002278	NM_002278		Approved	Ha-2	uc002hwr.3	uc002hwr.3	Q14532	Q14532	OTTHUMG00000133430	OTTHUMG00000133430	ENST00000225899.3:c.925C>T	17.37:g.39620401G>A	ENSP00000225899:p.Gln309*			p.Q309*	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN			5	1028	-		Breast(137;0.000812)	309	Coil 2.|Rod.		Nonsense_Mutation	SNP	ENST00000225899.3	37	c.925C>T	CCDS11393.1	.	.	.	.	.	.	.	.	.	.	G	36	5.782073	0.96937	.	.	ENSG00000108759	ENST00000225899	.	.	.	5.04	5.04	0.67666	5.04	5.04	0.67666	.	0.000000	0.37348	N	0.002139	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	13.4096	0.60935	0.0:0.0:0.8328:0.1672	.	.	.	.	X	309	.	ENSP00000225899:Q309X	Q	-	1	0	0	KRT32	36873927	36873927	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.284000	0.43478	2.492000	0.84095	0.655000	0.94253	CAG		0.577	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1		59.819754	7	7	56	56	NM_002278		19	59.946346	59.946346	24	0.441860	0	0	0	1	0	19	24	0.44186
RYR3	6263	broad.mit.edu	37	15	34103222	34103222	+	Nonsense_Mutation	SNP	T	T	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr15:34103222T>A	ENST00000389232.4	+	72	10311	c.10241T>A	c.(10240-10242)tTg>tAg	p.L3414*	RYR3_ENST00000415757.3_Nonsense_Mutation_p.L3409*	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3414					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CGGAACAACTTGCACTTGCAG	0.478																																						ENST00000389232.4											0			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311						c.(10240-10242)tTg>tAg	ryanodine receptor 3						46.0	45.0	46.0					15																	34103222		1984	4170	6154	SO:0001587	stop_gained	6263			cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr15:34103222T>A			CCDS45210.1, CCDS58351.1	CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10			2013-01-10				ENSG00000198838		ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	10485	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			180903	180903						8276408	8276408	Standard	Standard	NM_001036	NM_001036		Approved		uc001zhi.3	uc001zhi.3	Q15413	Q15413			ENST00000389232.4:c.10241T>A	15.37:g.34103222T>A	ENSP00000373884:p.Leu3414*		RYR3_ENST00000415757.3_Nonsense_Mutation_p.L3409*	p.L3414*	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)	72	10311	+		all_lung(180;7.18e-09)	3414		O15175|Q15412	Nonsense_Mutation	SNP	ENST00000389232.4	37	c.10241T>A	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	53	20.138827	0.99927	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	.	.	.	5.51	5.51	0.81932	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6314	0.76912	0.0:0.0:0.0:1.0	.	.	.	.	X	3414;3414;3409	.	ENSP00000354735:L3409X	L	+	2	0	0	RYR3	31890514	31890514	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.431000	0.80335	2.094000	0.63399	0.459000	0.35465	TTG		0.478	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		8.622836	8	8	16	16			3	8.732633	8.732633	5	0.375000	0	0	0	1	0	3	5	0.375
PPM1J	333926	ucsc.edu	37	1	113255025	113255025	+	Missense_Mutation	SNP	C	C	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr1:113255025C>A	ENST00000309276.6	-	4	959	c.784G>T	c.(784-786)Gca>Tca	p.A262S	RP11-426L16.10_ENST00000606505.1_5'Flank|PPM1J_ENST00000464951.1_Missense_Mutation_p.A56S|RP11-426L16.10_ENST00000471038.2_5'Flank|PPM1J_ENST00000359994.4_Missense_Mutation_p.A56S	NM_005167.5	NP_005158.5	Q5JR12	PPM1J_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1J	262	PP2C-like.				protein dephosphorylation (GO:0006470)		protein serine/threonine phosphatase activity (GO:0004722)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	14	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAACCAGTGCACAGCAGCCC	0.622																																																	0																	74.0	62.0	66.0					1																	113255025		2203	4300	6503	SO:0001583	missense	333926							AK093270	AK093270	CCDS855.2	CCDS855.2	1p13.1	2012-04-17	2010-03-05		2012-04-17	2010-03-05		ENSG00000155367	ENSG00000155367	ENSG00000155367	ENSG00000155367	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	20785	20785	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""protein phosphatase 2C zeta"""	"""protein phosphatase 2C zeta"""	609957	609957	"""protein phosphatase 1J (PP2C domain containing)"""		"""protein phosphatase 1J (PP2C domain containing)"""			12633878	12633878	Standard	Standard	NM_005167	NM_005167		Approved	FLJ35951, MGC19531, DKFZp434P1514, PP2Czeta, PPP2CZ	uc001ect.1	uc001ect.1	Q5JR12	Q5JR12	OTTHUMG00000012019	OTTHUMG00000012019	ENST00000309276.6:c.784G>T	1.37:g.113255025C>A	ENSP00000308926:p.Ala262Ser																	B3KSB7|Q6DKJ7|Q96EZ7|Q9UF84	Missense_Mutation	SNP	ENST00000309276.6	37		CCDS855.2	.	.	.	.	.	.	.	.	.	.	C	34	5.398311	0.96030	.	.	ENSG00000155367	ENST00000309276;ENST00000359994	T;T	0.29142	1.58;1.58	5.61	5.61	0.85477	5.61	5.61	0.85477	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	T	0.57844	0.2081	M	0.87971	2.92	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.982	T	0.64563	-0.6378	10	0.72032	D	0.01	-13.3802	19.2182	0.93786	0.0:1.0:0.0:0.0	.	262;56	Q5JR12;Q5JR12-2	PPM1J_HUMAN;.	S	262;56	ENSP00000308926:A262S;ENSP00000353088:A56S	ENSP00000308926:A262S	A	-	1	0	0	PPM1J	113056548	113056548	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.440000	0.80464	2.643000	0.89663	0.462000	0.41574	GCA		0.622	PPM1J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033251.1			1	1	37	37	NM_005167		4			24							4	24	
THOC2	57187	broad.mit.edu	37	X	122769935	122769935	+	Silent	SNP	G	G	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chrX:122769935G>T	ENST00000245838.8	-	19	2044	c.2013C>A	c.(2011-2013)ggC>ggA	p.G671G	THOC2_ENST00000355725.4_Silent_p.G671G|THOC2_ENST00000491737.1_Silent_p.G556G	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	671					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						AATACCTTTTGCCCGCCTTTA	0.363																																						ENST00000245838.8											0			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						c.(2011-2013)ggC>ggA	THO complex 2						92.0	77.0	81.0					X																	122769935		1822	4075	5897	SO:0001819	synonymous_variant	57187			intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding	g.chrX:122769935G>T	AF441770	AF441770	CCDS43988.1	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676	ENSG00000125676	ENSG00000125676		"""THO complex subunits"""	"""THO complex subunits"""	19073	19073	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			300395	300395	"""chromosome X open reading frame 3"""	CXorf3	"""chromosome X open reading frame 3"""	CXorf3		11979277	11979277	Standard	Standard	NM_001081550	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	uc004etu.3	Q8NI27	Q8NI27	OTTHUMG00000022334	OTTHUMG00000022334	ENST00000245838.8:c.2013C>A	X.37:g.122769935G>T			THOC2_ENST00000355725.4_Silent_p.G671G|THOC2_ENST00000491737.1_Silent_p.G556G	p.G671G	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN			19	2044	-			671		A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Silent	SNP	ENST00000245838.8	37	c.2013C>A	CCDS43988.1																																																																																									0.363	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3		111.595349	-9	-9	78	78			36	111.607161	111.607161	38	0.486486	1	0	5.43694e-19	1	5.94665e-19	36	38	0.486486
MPP3	4356	ucsc.edu	37	17	41909266	41909266	+	Silent	SNP	C	C	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr17:41909266C>A	ENST00000398389.4	-	3	174	c.9G>T	c.(7-9)gtG>gtT	p.V3V	MPP3_ENST00000398393.1_Silent_p.V28V	NM_001932.4	NP_001923.2	Q13368	MPP3_HUMAN	membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	3					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	guanylate kinase activity (GO:0004385)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)		CCTCCGATAGCACTGGCATGC	0.587																																																	0																	33.0	38.0	37.0					17																	41909266		1958	4139	6097	SO:0001819	synonymous_variant	4356									CCDS42344.1	CCDS42344.1	17q12-q21	2008-07-18			2008-07-18			ENSG00000161647	ENSG00000161647	ENSG00000161647	ENSG00000161647				7221	7221	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""MAGUK p55 subfamily member 3"", ""discs, large (Drosophila) homolog 3"", ""membrane protein palmitoylated 3"""	"""MAGUK p55 subfamily member 3"", ""discs, large (Drosophila) homolog 3"", ""membrane protein palmitoylated 3"""	601114	601114		DLG3		DLG3		8824795	8824795	Standard	Standard	NR_003562	NR_003562		Approved		uc002iei.4	uc002iei.4	Q13368	Q13368	OTTHUMG00000133838	OTTHUMG00000133838	ENST00000398389.4:c.9G>T	17.37:g.41909266C>A																		B2R7N0|D3DX47|Q4GX05|Q6PGR3|Q86SV1	Silent	SNP	ENST00000398389.4	37		CCDS42344.1																																																																																									0.587	MPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258371.1			-5	-5	29	29	NM_001932		4			28							4	28	
OR6K3	391114	broad.mit.edu	37	1	158686997	158686997	+	Silent	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr1:158686997C>T	ENST00000368146.1	-	1	956	c.957G>A	c.(955-957)ctG>ctA	p.L319L	OR6K3_ENST00000368145.1_Silent_p.L303L			Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K, member 3	319						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41	all_hematologic(112;0.0378)					GAAGACAGAACAGTTTTTTAA	0.388																																						ENST00000368146.1											0			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41						c.(955-957)ctG>ctA	olfactory receptor, family 6, subfamily K, member 3						125.0	128.0	127.0					1																	158686997		2203	4300	6503	SO:0001819	synonymous_variant	391114			sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:158686997C>T	AB065633	AB065633	CCDS30903.1, CCDS30903.2	CCDS30903.1, CCDS30903.2	1q23.1	2012-08-09			2012-08-09			ENSG00000203757	ENSG00000203757	ENSG00000203757	ENSG00000203757		"""GPCR / Class A : Olfactory receptors"""	"""GPCR / Class A : Olfactory receptors"""	15030	15030	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product												Standard	Standard	NM_001005327	NM_001005327		Approved		uc021pbn.1	uc021pbn.1	Q8NGY3	Q8NGY3	OTTHUMG00000022770	OTTHUMG00000022770	ENST00000368146.1:c.957G>A	1.37:g.158686997C>T			OR6K3_ENST00000368145.1_Silent_p.L303L	p.L319L			Q8NGY3	OR6K3_HUMAN			1	956	-	all_hematologic(112;0.0378)		319		Q5VUV0|Q6IFR5	Silent	SNP	ENST00000368146.1	37	c.957G>A																																																																																										0.388	OR6K3-201	KNOWN	basic	protein_coding	protein_coding			102.372283	-8	-8	116	116			33	102.400542	102.400542	36	0.478261	0	0	0	1	0	33	36	0.478261
SAP130	79595	broad.mit.edu	37	2	128775359	128775359	+	Missense_Mutation	SNP	C	C	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr2:128775359C>A	ENST00000259235.3	-	3	450	c.321G>T	c.(319-321)ttG>ttT	p.L107F	SAP130_ENST00000259234.6_Missense_Mutation_p.L81F|SAP130_ENST00000357702.5_Missense_Mutation_p.L107F	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	107					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		GGTGTGTCGACAACATCTGCA	0.582																																						ENST00000357702.5											0			NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45						c.(319-321)ttG>ttT	Sin3A-associated protein, 130kDa						149.0	126.0	134.0					2																	128775359		2203	4300	6503	SO:0001583	missense	79595			histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity	g.chr2:128775359C>A	BC017453	BC017453	CCDS2153.1, CCDS54397.1	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715	ENSG00000136715	ENSG00000136715				29813	29813	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			609697	609697	"""sin3A-associated protein, 130kDa"""		"""sin3A-associated protein, 130kDa"""			11230166, 12724404	11230166, 12724404	Standard	Standard	NM_001145928	NM_001145928		Approved	FLJ12761	uc010fmd.2	uc010fmd.2	Q9H0E3	Q9H0E3	OTTHUMG00000131571	OTTHUMG00000131571	ENST00000259235.3:c.321G>T	2.37:g.128775359C>A	ENSP00000259235:p.Leu107Phe		SAP130_ENST00000259234.6_Missense_Mutation_p.L81F|SAP130_ENST00000259235.3_Missense_Mutation_p.L107F	p.L107F	NM_001145928.1	NP_001139400.1	Q9H0E3	SP130_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.0771)	3	452	-	Colorectal(110;0.1)		107		B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Missense_Mutation	SNP	ENST00000259235.3	37	c.321G>T	CCDS2153.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.238823	0.58995	.	.	ENSG00000136715	ENST00000357702;ENST00000259235;ENST00000259234;ENST00000424298;ENST00000450957	.	.	.	5.79	4.92	0.64577	5.79	4.92	0.64577	.	0.247403	0.34750	N	0.003714	T	0.59824	0.2222	L	0.32530	0.975	0.44515	D	0.99746	P;D;D	0.71674	0.487;0.997;0.998	B;D;D	0.65010	0.189;0.931;0.914	T	0.54655	-0.8261	9	0.09084	T	0.74	-9.8508	13.0129	0.58741	0.0:0.9254:0.0:0.0746	.	107;81;107	B7ZLM3;Q96DP1;Q9H0E3	.;.;SP130_HUMAN	F	107;107;81;81;81	.	ENSP00000259234:L81F	L	-	3	2	2	SAP130	128491829	128491829	1.000000	0.71417	0.994000	0.49952	0.719000	0.41307	5.228000	0.65310	1.442000	0.47568	0.585000	0.79938	TTG		0.582	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3		104.473721	-46	-46	98	98	NM_024545		36	106.19866	106.198660	64	0.360000	1	0	3.93418e-24	1	4.44182e-24	36	64	0.36
ROS1	6098	broad.mit.edu	37	6	117710788	117710788	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr6:117710788G>A	ENST00000368508.3	-	12	1682	c.1484C>T	c.(1483-1485)cCc>cTc	p.P495L	ROS1_ENST00000368507.3_Missense_Mutation_p.P504L|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	495					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		ATCAGCAAAGGGGATGCGAGG	0.423			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																	ENST00000368508.3		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	0			NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162						c.(1483-1485)cCc>cTc	c-ros oncogene 1 , receptor tyrosine kinase						90.0	81.0	84.0					6																	117710788		2203	4300	6503	SO:0001583	missense	6098			transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity	g.chr6:117710788G>A	M13599	M13599	CCDS5116.1	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936	ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	"""Fibronectin type III domain containing"""	10261	10261	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			165020	165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""		"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	1611909	Standard	Standard	NM_002944	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	uc003pxp.1	P08922	P08922	OTTHUMG00000016188	OTTHUMG00000016188	ENST00000368508.3:c.1484C>T	6.37:g.117710788G>A	ENSP00000357494:p.Pro495Leu		ROS1_ENST00000368507.3_Missense_Mutation_p.P504L|GOPC_ENST00000467125.1_Intron	p.P495L	NM_002944.2	NP_002935.2	P08922	ROS_HUMAN		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)	12	1682	-		all_cancers(87;0.00846)|all_epithelial(87;0.0242)	495		Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	c.1484C>T	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	G	9.247	1.039770	0.19669	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	D;D	0.90900	-2.75;-2.75	5.92	4.12	0.48240	5.92	4.12	0.48240	.	0.571379	0.17934	N	0.157078	T	0.74550	0.3731	N	0.24115	0.695	0.46701	D	0.999164	B	0.09022	0.002	B	0.06405	0.002	T	0.71553	-0.4558	10	0.66056	D	0.02	.	9.5245	0.39156	0.0748:0.1426:0.7826:0.0	.	495	P08922	ROS1_HUMAN	L	495;504	ENSP00000357494:P495L;ENSP00000357493:P504L	ENSP00000357493:P504L	P	-	2	0	0	ROS1	117817481	117817481	0.998000	0.40836	0.183000	0.23137	0.044000	0.14063	2.718000	0.47236	0.829000	0.34733	0.561000	0.74099	CCC		0.423	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		70.792554	-6	-6	57	57			19	72.939192	72.939192	1	0.950000	0	0	0	1	0	19	1	0.95
TRAF2	7186	broad.mit.edu	37	9	139820173	139820173	+	Silent	SNP	C	C	T	rs560077345		TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr9:139820173C>T	ENST00000247668.2	+	11	1378	c.1326C>T	c.(1324-1326)caC>caT	p.H442H	TRAF2_ENST00000536468.1_Silent_p.H442H|TRAF2_ENST00000359662.3_Silent_p.H494H	NM_021138.3	NP_066961.2	Q12933	TRAF2_HUMAN	TNF receptor-associated factor 2	442	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein complex assembly (GO:0043623)|cellular response to nitric oxide (GO:0071732)|innate immune response (GO:0045087)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron death (GO:1901215)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|programmed necrotic cell death (GO:0097300)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein complex assembly (GO:0006461)|protein heterooligomerization (GO:0051291)|protein homotrimerization (GO:0070207)|protein K63-linked ubiquitination (GO:0070534)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of immunoglobulin secretion (GO:0051023)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|membrane raft (GO:0045121)|ubiquitin ligase complex (GO:0000151)	CD40 receptor binding (GO:0005174)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein phosphatase binding (GO:0019903)|signal transducer activity (GO:0004871)|sphingolipid binding (GO:0046625)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.229)	OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06)		ACCGGGAGCACGTGATTGACG	0.602													C|||	1	0.000199681	0.0	0.0	5008	,	,		19017	0.001		0.0	False		,,,				2504	0.0					ENST00000359662.3											0			breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						c.(1480-1482)caC>caT	TNF receptor-associated factor 2						97.0	73.0	81.0					9																	139820173		2203	4300	6503	SO:0001819	synonymous_variant	7186			activation of caspase activity|activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cellular protein complex assembly|induction of apoptosis by extracellular signals|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|protein autoubiquitination|protein homotrimerization|protein K63-linked ubiquitination|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane	CD40 receptor binding|enzyme binding|protein binding|signal transducer activity|sphingolipid binding|ubiquitin-protein ligase activity|zinc ion binding	g.chr9:139820173C>T	U12597	U12597	CCDS7013.1	CCDS7013.1	9q34	2013-01-09			2013-01-09			ENSG00000127191	ENSG00000127191	ENSG00000127191	ENSG00000127191		"""RING-type (C3HC4) zinc fingers"""	"""RING-type (C3HC4) zinc fingers"""	12032	12032	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			601895	601895						7639698	7639698	Standard	Standard	NM_021138	NM_021138		Approved	TRAP3	uc004cjv.3	uc004cjv.3	Q12933	Q12933	OTTHUMG00000020952	OTTHUMG00000020952	ENST00000247668.2:c.1326C>T	9.37:g.139820173C>T			TRAF2_ENST00000247668.2_Silent_p.H442H|TRAF2_ENST00000536468.1_Silent_p.H442H	p.H494H			Q12933	TRAF2_HUMAN	STAD - Stomach adenocarcinoma(284;0.229)	OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06)	11	1527	+	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	442	MATH.	A8K107|B4DPJ7|Q7Z337|Q96NT2	Silent	SNP	ENST00000247668.2	37	c.1482C>T	CCDS7013.1																																																																																									0.602	TRAF2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055166.1		51.535277	-11	-11	64	64	NM_021138		18	52.507637	52.507637	33	0.352941	0	0	0	1	0	18	33	0.352941
KIAA1024	23251	broad.mit.edu	37	15	79760547	79760547	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr15:79760547C>T	ENST00000305428.3	+	4	2647	c.2572C>T	c.(2572-2574)Cca>Tca	p.P858S		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	858						integral component of membrane (GO:0016021)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						ATCTTTAAACCCAAATAATTT	0.388																																						ENST00000305428.3											0			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						c.(2572-2574)Cca>Tca	KIAA1024						38.0	34.0	35.0					15																	79760547		2196	4293	6489	SO:0001583	missense	23251				integral to membrane		g.chr15:79760547C>T	AB028947	AB028947	CCDS32306.1	CCDS32306.1	15q25.1	2007-12-12			2007-12-12				ENSG00000169330		ENSG00000169330				29172	29172	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product										10470851	10470851	Standard	Standard	NM_015206	NM_015206		Approved		uc002bew.1	uc002bew.1	Q9UPX6	Q9UPX6			ENST00000305428.3:c.2572C>T	15.37:g.79760547C>T	ENSP00000307461:p.Pro858Ser			p.P858S	NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN			4	2647	+			858		A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	c.2572C>T	CCDS32306.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812684	0.70912	.	.	ENSG00000169330	ENST00000305428	T	0.63744	-0.06	5.67	5.67	0.87782	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.78898	0.4356	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77088	-0.2717	9	.	.	.	.	19.7863	0.96440	0.0:1.0:0.0:0.0	.	858	Q9UPX6	K1024_HUMAN	S	858	ENSP00000307461:P858S	.	P	+	1	0	0	KIAA1024	77547602	77547602	1.000000	0.71417	1.000000	0.80357	0.209000	0.24338	7.456000	0.80751	2.665000	0.90641	0.655000	0.94253	CCA		0.388	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1		41.370463	-15	-15	36	36	NM_015206		13	41.546242	41.546242	18	0.419355	0	0	0	1	0	13	18	0.419355
C2orf16	84226	broad.mit.edu	37	2	27804437	27804437	+	Silent	SNP	T	T	A	rs201236336	byFrequency	TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr2:27804437T>A	ENST00000408964.2	+	1	5049	c.4998T>A	c.(4996-4998)tcT>tcA	p.S1666S	ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000379717.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000355467.4_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000413371.2_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1666	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GCAGTTCCTCTGAGAGAAGAC	0.577																																						ENST00000408964.2											0			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47						c.(4996-4998)tcT>tcA	chromosome 2 open reading frame 16						153.0	156.0	155.0					2																	27804437		1905	4118	6023	SO:0001819	synonymous_variant	84226						g.chr2:27804437T>A	AL136898	AL136898	CCDS42666.1	CCDS42666.1	2p23.3	2013-09-20			2013-09-20			ENSG00000221843	ENSG00000221843	ENSG00000221843	ENSG00000221843				25275	25275	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""	"""P-S-E-R-S-H-H-S repeats containing"""										Standard	Standard	NM_032266	NM_032266		Approved	DKFZp434G118	uc002rkz.4	uc002rkz.4	Q68DN1	Q68DN1	OTTHUMG00000159099	OTTHUMG00000159099	ENST00000408964.2:c.4998T>A	2.37:g.27804437T>A				p.S1666S	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN			1	5049	+	Acute lymphoblastic leukemia(172;0.155)		1666	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	c.4998T>A	CCDS42666.1																																																																																									0.577	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1		37.446423	-1	-1	280	280	NM_032266		19	51.252151	51.252151	103	0.155738	0	0	0	1	0	19	103	0.155738
RNF43	54894	broad.mit.edu	37	17	56435332	56435332	+	Missense_Mutation	SNP	T	T	C			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr17:56435332T>C	ENST00000584437.1	-	8	3760	c.1805A>G	c.(1804-1806)aAc>aGc	p.N602S	RNF43_ENST00000407977.2_Missense_Mutation_p.N602S|RNF43_ENST00000583753.1_Missense_Mutation_p.N561S|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000581868.1_Missense_Mutation_p.N475S|RNF43_ENST00000500597.2_Missense_Mutation_p.N561S|RNF43_ENST00000577625.1_Missense_Mutation_p.N475S|RNF43_ENST00000577716.1_Missense_Mutation_p.N602S			Q68DV7	RNF43_HUMAN	ring finger protein 43	602	Pro-rich.				negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GGCTGCTGAGTTGGATCTGGT	0.657																																						ENST00000584437.1											0			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60						c.(1804-1806)aAc>aGc	ring finger protein 43						57.0	69.0	65.0					17																	56435332		2203	4299	6502	SO:0001583	missense	54894				endoplasmic reticulum membrane|integral to membrane|nuclear envelope	ligase activity|protein binding|zinc ion binding	g.chr17:56435332T>C			CCDS11607.1	CCDS11607.1	17q23.2	2013-01-09			2013-01-09								"""RING-type (C3HC4) zinc fingers"""	"""RING-type (C3HC4) zinc fingers"""	18505	18505	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			612482	612482								Standard	Standard	NM_017763	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	uc002iwh.4	Q68DV7	Q68DV7			ENST00000584437.1:c.1805A>G	17.37:g.56435332T>C	ENSP00000463069:p.Asn602Ser		RNF43_ENST00000577716.1_Missense_Mutation_p.N602S|RNF43_ENST00000500597.2_Missense_Mutation_p.N561S|RNF43_ENST00000577625.1_Missense_Mutation_p.N475S|RNF43_ENST00000583753.1_Missense_Mutation_p.N561S|RNF43_ENST00000581868.1_Missense_Mutation_p.N475S|RNF43_ENST00000407977.2_Missense_Mutation_p.N602S|BZRAP1-AS1_ENST00000583841.1_RNA	p.N602S			Q68DV7	RNF43_HUMAN			8	3760	-	Medulloblastoma(34;0.127)|all_neural(34;0.237)		602	Pro-rich.	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	c.1805A>G	CCDS11607.1	.	.	.	.	.	.	.	.	.	.	T	2.674	-0.276978	0.05679	.	.	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.16897	2.31;2.31	5.18	-1.62	0.08372	5.18	-1.62	0.08372	.	1.287800	0.04918	N	0.454417	T	0.06872	0.0175	N	0.14661	0.345	0.09310	N	1	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.06405	0.001;0.002;0.0	T	0.27297	-1.0078	10	0.05833	T	0.94	-9.4984	0.8	0.01074	0.1725:0.2915:0.1572:0.3788	.	561;602;602	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	S	602;561	ENSP00000385328:N602S;ENSP00000441969:N561S	ENSP00000385328:N602S	N	-	2	0	0	RNF43	53790331	53790331	0.814000	0.29104	0.003000	0.11579	0.140000	0.21249	0.357000	0.20199	0.006000	0.14734	0.172000	0.16884	AAC		0.657	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1		133.428577	-27	-27	90	90	NM_017763		43	135.021007	135.021007	72	0.373913	0	0	0	1	0	43	72	0.373913
ADRBK1	156	broad.mit.edu	37	11	67051341	67051342	+	Frame_Shift_Ins	INS	-	-	C			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr11:67051341_67051342insC	ENST00000308595.5	+	17	1702_1703	c.1412_1413insC	c.(1411-1416)atccccfs	p.IP471fs	ADRBK1_ENST00000527176.1_3'UTR|ADRBK1_ENST00000526285.1_Intron	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	471	AGC-kinase C-terminal.				activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	CCCCCGCTGATCCCCCCACGAG	0.634																																						ENST00000308595.5											0			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22						c.(1411-1416)atccccfs	adrenergic, beta, receptor kinase 1																																			SO:0001589	frameshift_variant	156			activation of phospholipase C activity|cardiac muscle contraction|desensitization of G-protein coupled receptor protein signaling pathway|muscarinic acetylcholine receptor signaling pathway|negative regulation of striated muscle contraction|negative regulation of the force of heart contraction by chemical signal|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of catecholamine secretion|tachykinin receptor signaling pathway	cytosol|soluble fraction	alpha-2A adrenergic receptor binding|ATP binding|beta-adrenergic receptor kinase activity|Edg-2 lysophosphatidic acid receptor binding|G-protein coupled receptor kinase activity|signal transducer activity	g.chr11:67051341_67051342insC	X61157	X61157	CCDS8156.1	CCDS8156.1	11q13	2013-01-10			2013-01-10			ENSG00000173020	ENSG00000173020	ENSG00000173020	ENSG00000173020		"""Pleckstrin homology (PH) domain containing"""	"""Pleckstrin homology (PH) domain containing"""	289	289	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			109635	109635						2037065	2037065	Standard	Standard	NM_001619	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	uc009yrn.1	P25098	P25098	OTTHUMG00000167104	OTTHUMG00000167104	ENST00000308595.5:c.1418dupC	11.37:g.67051347_67051347dupC	ENSP00000312262:p.Ile471fs		ADRBK1_ENST00000527176.1_3'UTR|ADRBK1_ENST00000526285.1_Intron	p.IP471fs	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		17	1702_1703	+			471	AGC-kinase C-terminal.	B0ZBE1|Q13837|Q6GTT3	Frame_Shift_Ins	INS	ENST00000308595.5	37	c.1412_1413insC	CCDS8156.1																																																																																									0.634	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	.	.	10	10	31	31	NM_001619		2			4	0.33						2	4	0.33
PRSS50	29122	broad.mit.edu	37	3	46755884	46755901	+	In_Frame_Del	DEL	CGGTACCTGCTATGCATG	CGGTACCTGCTATGCATG	-	rs201421841|rs142097717	byFrequency	TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr3:46755884_46755901delCGGTACCTGCTATGCATG	ENST00000460241.1	-	9	2231_2248	c.561_578delCATGCATAGCAGGTACCG	c.(559-579)atcatgcatagcaggtaccgg>atg	p.187_193IMHSRYR>M	PRSS50_ENST00000315170.7_In_Frame_Del_p.187_193IMHSRYR>M			Q9UI38	TSP50_HUMAN	protease, serine, 50	187	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	serine-type endopeptidase activity (GO:0004252)|threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11						CCGCTGGGCCCGGTACCTGCTATGCATGATGACCTGGA	0.61																																					Pancreas(41;915 1239 11561 17469)	ENST00000460241.1											0			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11						c.(559-579)atcatgcatagcaggtaccgg>atg	protease, serine, 50																																			SO:0001651	inframe_deletion	29122			proteolysis	endoplasmic reticulum	serine-type endopeptidase activity|threonine-type endopeptidase activity	g.chr3:46755884_46755901delCGGTACCTGCTATGCATG	AF100707	AF100707	CCDS2745.1	CCDS2745.1	3p21.31	2011-05-24			2011-05-24			ENSG00000206549	ENSG00000206549	ENSG00000206549	ENSG00000206549		"""Serine peptidases / Serine peptidases"""	"""Serine peptidases / Serine peptidases"""	17910	17910	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""cancer/testis antigen 20"", ""testes specific protease 50"""	"""cancer/testis antigen 20"", ""testes specific protease 50"""	607950	607950						10397268	10397268	Standard	Standard	NM_013270	NM_013270		Approved	TSP50, CT20	uc003cqe.1	uc003cqe.1	Q9UI38	Q9UI38	OTTHUMG00000164067	OTTHUMG00000164067	ENST00000460241.1:c.561_578delCATGCATAGCAGGTACCG	3.37:g.46755884_46755901delCGGTACCTGCTATGCATG	ENSP00000418875:p.Ile187_Arg193delinsMet		PRSS50_ENST00000315170.7_In_Frame_Del_p.187_193IMHSRYR>M	p.187_193IMHSRYR>M			Q9UI38	TSP50_HUMAN			9	2231_2248	-			187	Peptidase S1.		In_Frame_Del	DEL	ENST00000460241.1	37	c.561_578delCATGCATAGCAGGTACCG	CCDS2745.1																																																																																									0.610	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1	.	.	1	1	18	18			2			4	0.33						2	4	0.33
