#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_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	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_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	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_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	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_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	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_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
UBE2U	148581	broad.mit.edu	37	1	64707415	64707418	+	Splice_Site	DEL	AAGT	AAGT	-	rs371128509		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr1:64707415_64707418delAAGT	ENST00000371076.3	+	8	920_921	c.676_677delAAGT	c.(676-678)aag>g	p.K226fs	UBE2U_ENST00000464349.1_3'UTR	NM_152489.1	NP_689702.1	Q5VVX9	UBE2U_HUMAN	ubiquitin-conjugating enzyme E2U (putative)	226					protein ubiquitination (GO:0016567)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			large_intestine(3)|lung(2)|skin(1)	6						ATGGAATTTAAAGTAAGAAATATG	0.304																																						uc001dbn.1																			0					0						c.e8+1		ubiquitin-conjugating enzyme E2U (putative)																																				SO:0001630	splice_region_variant	148581						ATP binding|protein binding|ubiquitin-protein ligase activity	g.chr1:64707415_64707418delAAGT	BC029895	CCDS627.1	1p31.3	2008-02-05			ENSG00000177414	ENSG00000177414		"""Ubiquitin-conjugating enzymes E2"""	28559	protein-coding gene	gene with protein product						12477932	Standard	NM_152489		Approved	MGC35130	uc001dbn.1	Q5VVX9	OTTHUMG00000009023	ENST00000371076.3:c.677+1AAGT>-	1.37:g.64707415_64707418delAAGT							p.K226_splice	NM_152489	NP_689702	Q5VVX9	UBE2U_HUMAN			8	921	+								Q8N1D4	Splice_Site	DEL	ENST00000371076.3	37	c.677_splice	CCDS627.1																																																																																				0.304	UBE2U-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025005.1	NM_152489	Frame_Shift_Del
BCL10	8915	broad.mit.edu	37	1	85736511	85736511	+	Frame_Shift_Del	DEL	T	T	-			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr1:85736511delT	ENST00000370580.1	-	2	873	c.136delA	c.(136-138)atafs	p.I46fs		NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	46	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				adaptive immune response (GO:0002250)|B cell apoptotic process (GO:0001783)|cell death (GO:0008219)|cellular defense response (GO:0006968)|cellular response to mechanical stimulus (GO:0071260)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interleukin-6 biosynthetic process (GO:0042226)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of mature B cell apoptotic process (GO:0002906)|neural tube closure (GO:0001843)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|regulation of T cell receptor signaling pathway (GO:0050856)|response to food (GO:0032094)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell apoptotic process (GO:0070231)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor signaling pathway (GO:0002224)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|NF-kappaB binding (GO:0051059)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.I46fs*4(1)		haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	19				all cancers(265;0.0114)|Epithelial(280;0.0311)		CTACTGAGTATTTTTTTTGCA	0.343			T	IGH@	MALT																																NSCLC(34;993 1034 12176 32621 50182)	uc001dkz.2				Dom	yes		1	1p22	8915	T	B-cell CLL/lymphoma 10			L	IGH@		MALT 		1	Insertion - Frameshift(1)		ovary(1)	lung(2)	2						c.(136-138)ATAfs		B-cell CLL/lymphoma 10							83.0	90.0	87.0					1																	85736511		2203	4300	6503	SO:0001589	frameshift_variant	8915				apoptosis|cellular response to mechanical stimulus|innate immune response|interleukin-6 biosynthetic process|lymphotoxin A biosynthetic process|negative regulation of mature B cell apoptosis|neural tube closure|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 biosynthetic process|positive regulation of mast cell cytokine production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of transcription, DNA-dependent|protein homooligomerization|response to molecule of bacterial origin|T cell receptor signaling pathway	CBM complex|cytosol|lysosome|membrane raft|nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protease binding|protein C-terminus binding|protein kinase B binding|protein self-association|transcription coactivator activity|ubiquitin binding|ubiquitin protein ligase binding	g.chr1:85736511delT	AJ006288	CCDS704.1	1p22	2008-07-18			ENSG00000142867	ENSG00000142867			989	protein-coding gene	gene with protein product	"""CARD-like apoptotic protein"", ""CARD-containing apoptotic signaling protein"", ""CARD containing molecule enhancing NF-kB"", ""caspase-recruiting domain-containing protein"", ""CARD-containing proapoptotic protein"""	603517				9989495	Standard	NM_003921		Approved	CARMEN, CIPER, mE10, c-E10, CLAP	uc021opd.1	O95999	OTTHUMG00000009965	ENST00000370580.1:c.136delA	1.37:g.85736511delT	ENSP00000359612:p.Ile46fs						p.I46fs	NM_003921	NP_003912	O95999	BCL10_HUMAN		all cancers(265;0.0114)|Epithelial(280;0.0311)	3	841	-			46	I->A: Abolishes cell death-inducing capability.		CARD.		Q5VUF1	Frame_Shift_Del	DEL	ENST00000370580.1	37	c.136delA	CCDS704.1																																																																																				0.343	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921	
AMPD1	270	broad.mit.edu	37	1	115221096	115221096	+	Missense_Mutation	SNP	C	C	T	rs142123340	byFrequency	TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr1:115221096C>T	ENST00000520113.2	-	8	1064	c.1049G>A	c.(1048-1050)cGt>cAt	p.R350H	AMPD1_ENST00000369538.3_Missense_Mutation_p.R346H|AMPD1_ENST00000353928.6_Missense_Mutation_p.R317H			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	350					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	CTTAATAAAACGCAGCAGATG	0.368													C|||	2	0.000399361	0.0	0.0	5008	,	,		21609	0.0		0.001	False		,,,				2504	0.001					uc001efe.1																			0				ovary(2)|large_intestine(1)|skin(1)	4						c.(949-951)CGT>CAT		adenosine monophosphate deaminase 1 (isoform M)	Adenosine monophosphate(DB00131)	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	115.0	113.0	114.0		1049,1037	4.2	1.0	1	dbSNP_134	114	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	AMPD1	NM_000036.2,NM_001172626.1	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	350/781,346/777	115221096	1,13005	2203	4300	6503	SO:0001583	missense	270				purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding	g.chr1:115221096C>T	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"""AMPD isoform M"", ""skeletal muscle AMPD"""	102770	"""adenosine monophosphate deaminase 1 (isoform M)"""			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.1049G>A	1.37:g.115221096C>T	ENSP00000430075:p.Arg350His					AMPD1_uc001eff.1_Missense_Mutation_p.R313H	p.R317H	NM_000036	NP_000027	P23109	AMPD1_HUMAN		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	8	1034	-	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)	317					A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	37	c.950G>A	CCDS876.2	.	.	.	.	.	.	.	.	.	.	C	19.10	3.762270	0.69763	0.0	1.16E-4	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.83506	-1.73;-1.73;-1.73	5.1	4.17	0.49024	Adenosine/AMP deaminase (1);	0.047756	0.85682	D	0.000000	T	0.82157	0.4976	M	0.92459	3.31	0.80722	D	1	B;B	0.15930	0.011;0.015	B;B	0.15052	0.005;0.012	D	0.84714	0.0736	10	0.72032	D	0.01	-12.5081	13.3069	0.60357	0.0:0.9232:0.0:0.0768	.	346;317	Q5TF02;P23109	.;AMPD1_HUMAN	H	350;346;317	ENSP00000430075:R350H;ENSP00000358551:R346H;ENSP00000316520:R317H	ENSP00000316520:R317H	R	-	2	0	AMPD1	115022619	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.045000	0.57368	2.539000	0.85634	0.561000	0.74099	CGT		0.368	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4		
ASH1L	55870	broad.mit.edu	37	1	155449241	155449241	+	Silent	SNP	G	G	C			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr1:155449241G>C	ENST00000368346.3	-	3	4059	c.3420C>G	c.(3418-3420)tcC>tcG	p.S1140S	ASH1L_ENST00000392403.3_Silent_p.S1140S			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1140					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TGCCCTGTCTGGAGTGTAAAT	0.478																																						uc009wqq.2																			0				skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11						c.(3418-3420)TCC>TCG		absent, small, or homeotic 1-like							88.0	82.0	84.0					1																	155449241		2203	4300	6503	SO:0001819	synonymous_variant	55870				cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding	g.chr1:155449241G>C	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.3420C>G	1.37:g.155449241G>C						ASH1L_uc001fkt.2_Silent_p.S1140S|ASH1L_uc009wqr.1_Silent_p.S1140S	p.S1140S	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)		3	3900	-	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		1140					Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	37	c.3420C>G																																																																																					0.478	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
SEC16B	89866	broad.mit.edu	37	1	177937026	177937026	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr1:177937026C>T	ENST00000308284.6	-	2	180	c.91G>A	c.(91-93)Gga>Aga	p.G31R	SEC16B_ENST00000464631.2_Missense_Mutation_p.G31R|RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	31					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						CGATGATGTCCATCTCTCCGA	0.602																																						uc001gli.1																			0				ovary(3)|central_nervous_system(1)	4						c.(91-93)GGA>AGA		leucine zipper transcription regulator 2							80.0	81.0	81.0					1																	177937026		2017	4193	6210	SO:0001583	missense	89866				protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane		g.chr1:177937026C>T	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.91G>A	1.37:g.177937026C>T	ENSP00000308339:p.Gly31Arg					SEC16B_uc001glk.1_5'UTR|SEC16B_uc009wwz.1_5'UTR|SEC16B_uc001glj.1_Missense_Mutation_p.G31R|SEC16B_uc001gll.3_Missense_Mutation_p.G31R	p.G31R	NM_033127	NP_149118	Q96JE7	SC16B_HUMAN			2	181	-			31					A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	c.91G>A	CCDS44281.1	.	.	.	.	.	.	.	.	.	.	C	9.251	1.040712	0.19669	.	.	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000464631	T;T	0.51071	2.31;0.72	5.58	3.62	0.41486	.	0.247966	0.28476	N	0.015210	T	0.28499	0.0705	L	0.39397	1.21	0.29202	N	0.875135	P;B;B	0.39424	0.673;0.414;0.414	B;B;B	0.31751	0.135;0.092;0.092	T	0.21280	-1.0250	10	0.07030	T	0.85	-2.7467	8.1515	0.31143	0.0:0.8063:0.0:0.1937	.	31;31;31	E9PK14;B1AM08;Q96JE7	.;.;SC16B_HUMAN	R	31	ENSP00000308339:G31R;ENSP00000431727:G31R	ENSP00000308339:G31R	G	-	1	0	AL359075.1	176203649	0.006000	0.16342	0.201000	0.23476	0.130000	0.20726	1.820000	0.39032	0.635000	0.30488	0.557000	0.71058	GGA		0.602	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
USH2A	7399	broad.mit.edu	37	1	216595556	216595556	+	Silent	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr1:216595556C>T	ENST00000307340.3	-	2	509	c.123G>A	c.(121-123)gaG>gaA	p.E41E	USH2A_ENST00000366943.2_Silent_p.E41E|USH2A_ENST00000366942.3_Silent_p.E41E	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	41					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CTCCCACGTTCTCCAGCCTTG	0.473										HNSCC(13;0.011)																												uc001hku.1																			0				ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26						c.(121-123)GAG>GAA		usherin isoform B							85.0	89.0	88.0					1																	216595556		2203	4300	6503	SO:0001819	synonymous_variant	7399				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding	g.chr1:216595556C>T	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.123G>A	1.37:g.216595556C>T		HNSCC(13;0.011)				USH2A_uc001hkv.2_Silent_p.E41E	p.E41E	NM_206933	NP_996816	O75445	USH2A_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)	2	510	-			41			Extracellular (Potential).		Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	c.123G>A	CCDS31025.1																																																																																				0.473	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
IBA57	200205	broad.mit.edu	37	1	228362953	228362953	+	Missense_Mutation	SNP	C	C	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr1:228362953C>A	ENST00000366711.3	+	3	812	c.810C>A	c.(808-810)caC>caA	p.H270Q	IBA57_ENST00000546123.1_Missense_Mutation_p.H77Q|IBA57_ENST00000484749.1_3'UTR	NM_001010867.2	NP_001010867.1	Q5T440	CAF17_HUMAN	IBA57, iron-sulfur cluster assembly homolog (S. cerevisiae)	270					glycine catabolic process (GO:0006546)|heme biosynthetic process (GO:0006783)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|prostate(1)	11						CCCGCACCCACCACATGGGCG	0.652																																						uc001hsl.3																			0					0						c.(808-810)CAC>CAA		hypothetical protein LOC200205 precursor							66.0	61.0	63.0					1																	228362953		2202	4298	6500	SO:0001583	missense	200205				glycine catabolic process|heme biosynthetic process	mitochondrion	aminomethyltransferase activity	g.chr1:228362953C>A	AK022796	CCDS31046.1	1q42.13	2011-03-11	2011-03-11	2011-03-11	ENSG00000181873	ENSG00000181873			27302	protein-coding gene	gene with protein product	"""iron-sulfur cluster assembly factor for biotin synthase- and aconitase-like mitochondrial proteins, with a mass of 57kDa"""	615316	"""chromosome 1 open reading frame 69"""	C1orf69			Standard	NM_001010867		Approved	FLJ12734	uc001hsl.4	Q5T440	OTTHUMG00000039769	ENST00000366711.3:c.810C>A	1.37:g.228362953C>A	ENSP00000355672:p.His270Gln					C1orf69_uc010pvw.1_Missense_Mutation_p.H77Q	p.H270Q	NM_001010867	NP_001010867	Q5T440	CAF17_HUMAN			3	899	+		Prostate(94;0.0405)	270						Missense_Mutation	SNP	ENST00000366711.3	37	c.810C>A	CCDS31046.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.270216	0.59540	.	.	ENSG00000181873	ENST00000366711;ENST00000546123	T;T	0.44083	0.93;0.93	5.08	3.13	0.36017	YgfZ/GcvT conserved site (1);Glycine cleavage T-protein, C-terminal barrel (1);	0.100063	0.64402	D	0.000002	T	0.44117	0.1278	L	0.49699	1.58	0.58432	D	0.999999	P	0.44429	0.835	P	0.49477	0.612	T	0.14420	-1.0473	10	0.24483	T	0.36	-30.6588	12.8179	0.57675	0.1272:0.7493:0.1235:0.0	.	270	Q5T440	CAF17_HUMAN	Q	270;77	ENSP00000355672:H270Q;ENSP00000437347:H77Q	ENSP00000355672:H270Q	H	+	3	2	IBA57	226429576	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.372000	0.52387	2.640000	0.89533	0.655000	0.94253	CAC		0.652	IBA57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095980.1	NM_001010867	
OBSCN	84033	broad.mit.edu	37	1	228564891	228564891	+	Silent	SNP	G	G	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr1:228564891G>A	ENST00000422127.1	+	101	23222	c.23178G>A	c.(23176-23178)ccG>ccA	p.P7726P	OBSCN_ENST00000366707.4_Silent_p.P5360P|OBSCN_ENST00000570156.2_Silent_p.P8683P	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7726	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGCGCCACCCGCACCTGGCCC	0.697																																						uc009xez.1																			0				stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28						c.(23176-23178)CCG>CCA		obscurin, cytoskeletal calmodulin and							11.0	15.0	13.0					1																	228564891		2048	4202	6250	SO:0001819	synonymous_variant	84033				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding	g.chr1:228564891G>A	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.23178G>A	1.37:g.228564891G>A						OBSCN_uc001hsr.1_Silent_p.P2355P	p.P7726P	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN			101	23222	+		Prostate(94;0.0405)	7726			Protein kinase 2.		Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	c.23178G>A	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.603967	0.46423	.	.	ENSG00000154358	ENST00000441106	.	.	.	4.82	-9.64	0.00541	.	.	.	.	.	T	0.50274	0.1606	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61103	-0.7130	4	.	.	.	.	11.1923	0.48691	0.5056:0.3813:0.1131:0.0	.	.	.	.	T	2343	.	.	A	+	1	0	OBSCN	226631514	0.000000	0.05858	0.806000	0.32338	0.670000	0.39368	-5.641000	0.00107	-1.696000	0.01421	0.313000	0.20887	GCA		0.697	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ZP4	57829	broad.mit.edu	37	1	238048807	238048807	+	Silent	SNP	C	C	G			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr1:238048807C>G	ENST00000366570.4	-	8	1202	c.1044G>C	c.(1042-1044)gtG>gtC	p.V348V	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	348	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			TGGAGACCTCCACGTAAATGG	0.522																																					NSCLC(166;160 2029 11600 18754 19936)	uc001hym.2																			0				ovary(2)|skin(1)	3						c.(1042-1044)GTG>GTC		zona pellucida glycoprotein 4 preproprotein							68.0	67.0	67.0					1																	238048807		2203	4300	6503	SO:0001819	synonymous_variant	57829				acrosomal vesicle exocytosis|negative regulation of binding of sperm to zona pellucida|positive regulation of acrosome reaction|positive regulation of humoral immune response|positive regulation of protein kinase activity|positive regulation of T cell proliferation|protein kinase A signaling cascade|protein kinase C signaling cascade	integral to membrane|intracellular|plasma membrane|proteinaceous extracellular matrix	acrosin binding|receptor activity	g.chr1:238048807C>G	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"""Zona pellucida glycoproteins"""	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.1044G>C	1.37:g.238048807C>G						LOC100130331_uc010pyc.1_Intron	p.V348V	NM_021186	NP_067009	Q12836	ZP4_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		8	1044	-	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	348			ZP.|Extracellular (Potential).		B2RAE1	Silent	SNP	ENST00000366570.4	37	c.1044G>C	CCDS1615.1																																																																																				0.522	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1		
KIAA1462	57608	broad.mit.edu	37	10	30336587	30336587	+	Missense_Mutation	SNP	G	G	A	rs201422216	byFrequency	TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr10:30336587G>A	ENST00000375377.1	-	2	256	c.155C>T	c.(154-156)gCg>gTg	p.A52V		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	52					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						TGCGAGGGCCGCAGGGCCATC	0.677													G|||	2	0.000399361	0.0015	0.0	5008	,	,		17098	0.0		0.0	False		,,,				2504	0.0					uc001iux.2																			0				ovary(4)	4						c.(154-156)GCG>GTG		hypothetical protein LOC57608		G	VAL/ALA	0,4064		0,0,2032	48.0	54.0	52.0		155	3.0	0.0	10		52	2,8346		0,2,4172	no	missense	KIAA1462	NM_020848.2	64	0,2,6204	AA,AG,GG		0.024,0.0,0.0161	possibly-damaging	52/1360	30336587	2,12410	2032	4174	6206	SO:0001583	missense	57608							g.chr10:30336587G>A	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.155C>T	10.37:g.30336587G>A	ENSP00000364526:p.Ala52Val					KIAA1462_uc001iuy.2_Missense_Mutation_p.A52V|KIAA1462_uc001iuz.2_5'UTR|KIAA1462_uc009xle.1_Missense_Mutation_p.A52V	p.A52V	NM_020848	NP_065899	Q9P266	K1462_HUMAN			1	214	-			52					Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	37	c.155C>T	CCDS41500.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	15.89	2.965407	0.53507	0.0	2.4E-4	ENSG00000165757	ENST00000375377	T	0.13901	2.55	4.95	2.95	0.34219	.	0.659654	0.14204	N	0.334538	T	0.11495	0.0280	L	0.57536	1.79	0.09310	N	1	P	0.51057	0.941	B	0.39027	0.288	T	0.13845	-1.0494	10	0.14252	T	0.57	-8.0174	7.7148	0.28698	0.0914:0.1645:0.7442:0.0	.	52	Q9P266	K1462_HUMAN	V	52	ENSP00000364526:A52V	ENSP00000364526:A52V	A	-	2	0	KIAA1462	30376593	0.003000	0.15002	0.002000	0.10522	0.014000	0.08584	1.504000	0.35726	1.223000	0.43536	0.467000	0.42956	GCG		0.677	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
SLC25A22	79751	broad.mit.edu	37	11	800341	800341	+	5'Flank	SNP	G	G	A	rs551604416		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr11:800341G>A	ENST00000531214.1	-	0	0				PIDD_ENST00000347755.5_Missense_Mutation_p.R718W|PIDD_ENST00000411829.2_Intron	NM_001191060.1	NP_001177989.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22						L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		ACCTGGCCCCGCACAGCCTGA	0.627													G|||	1	0.000199681	0.0	0.0014	5008	,	,		15463	0.0		0.0	False		,,,				2504	0.0				Colon(93;848 1468 3270 23355 49636)	uc001lro.1																			0					0						c.(2152-2154)CGG>TGG		leucine rich repeat and death domain containing							49.0	50.0	50.0					11																	800341		2202	4299	6501	SO:0001631	upstream_gene_variant	55367				apoptosis|signal transduction	cytoplasm|nucleus	death receptor binding	g.chr11:800341G>A	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"""Solute carriers"""	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310		11.37:g.800341G>A	Exception_encountered					SLC25A22_uc009yci.2_5'Flank|SLC25A22_uc001lrj.2_5'Flank|LRDD_uc009yck.1_Intron|LRDD_uc001lrk.1_Intron|LRDD_uc001lrl.1_Missense_Mutation_p.R561W|LRDD_uc001lrm.1_Missense_Mutation_p.R405W|LRDD_uc001lrn.1_Missense_Mutation_p.R561W|LRDD_uc001lrp.1_Intron	p.R718W	NM_145886	NP_665893	Q9HB75	PIDD_HUMAN		all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	13	2294	-		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)	718					A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Missense_Mutation	SNP	ENST00000531214.1	37	c.2152C>T	CCDS7715.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.008998	0.75046	.	.	ENSG00000177595	ENST00000347755	T	0.46063	0.88	4.24	2.02	0.26589	.	0.134868	0.48286	D	0.000184	T	0.46946	0.1419	L	0.27053	0.805	0.37841	D	0.929046	D;D	0.89917	1.0;1.0	D;D	0.78314	0.971;0.991	T	0.52298	-0.8594	10	0.62326	D	0.03	.	10.4014	0.44231	0.0:0.0:0.2955:0.7045	.	718;561	Q9HB75;Q9HB75-3	PIDD_HUMAN;.	W	718	ENSP00000337797:R718W	ENSP00000337797:R718W	R	-	1	2	PIDD	790341	0.994000	0.37717	0.998000	0.56505	0.923000	0.55619	2.052000	0.41316	0.862000	0.35528	0.462000	0.41574	CGG		0.627	SLC25A22-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384124.1		
OR51T1	401665	broad.mit.edu	37	11	4904033	4904033	+	Missense_Mutation	SNP	C	C	T	rs201004265		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr11:4904033C>T	ENST00000322049.1	+	1	904	c.904C>T	c.(904-906)Cgc>Tgc	p.R302C	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron|OR51T1_ENST00000380378.1_Missense_Mutation_p.R329C			Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T, member 1	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAAGACAATCCGCCAGGCTAT	0.488																																						uc010qyp.1																			0				ovary(2)|large_intestine(1)	3						c.(985-987)CGC>TGC		olfactory receptor, family 51, subfamily T,		C	CYS/ARG	0,4402		0,0,2201	96.0	91.0	92.0		985	4.0	1.0	11		92	1,8595	1.2+/-3.3	0,1,4297	no	missense	OR51T1	NM_001004759.1	180	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	329/355	4904033	1,12997	2201	4298	6499	SO:0001583	missense	401665				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:4904033C>T	BK004283	CCDS31363.1	11p15.4	2012-08-09			ENSG00000176900	ENSG00000176900		"""GPCR / Class A : Olfactory receptors"""	15205	protein-coding gene	gene with protein product							Standard	NM_001004759		Approved		uc010qyp.2	Q8NGJ9	OTTHUMG00000066507	ENST00000322049.1:c.904C>T	11.37:g.4904033C>T	ENSP00000322679:p.Arg302Cys						p.R329C	NM_001004759	NP_001004759	Q8NGJ9	O51T1_HUMAN		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)	1	985	+		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)	302			Cytoplasmic (Potential).		Q6IFH9	Missense_Mutation	SNP	ENST00000322049.1	37	c.985C>T		.	.	.	.	.	.	.	.	.	.	C	19.46	3.831063	0.71258	0.0	1.16E-4	ENSG00000176900	ENST00000380378;ENST00000322049	T;T	0.58358	0.34;0.34	4.97	4.04	0.47022	.	0.322556	0.22730	N	0.056338	T	0.41003	0.1140	N	0.08118	0	0.49582	D	0.999802	D	0.76494	0.999	P	0.53689	0.732	T	0.40515	-0.9559	10	0.72032	D	0.01	.	8.397	0.32564	0.1545:0.761:0.0:0.0846	.	302	Q8NGJ9	O51T1_HUMAN	C	329;302	ENSP00000369738:R329C;ENSP00000322679:R302C	ENSP00000322679:R302C	R	+	1	0	OR51T1	4860609	0.002000	0.14202	0.953000	0.39169	0.993000	0.82548	0.691000	0.25467	2.595000	0.87683	0.491000	0.48974	CGC		0.488	OR51T1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000142180.1	NM_001004759	
OR52H1	390067	broad.mit.edu	37	11	5565836	5565836	+	Missense_Mutation	SNP	C	C	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr11:5565836C>A	ENST00000322653.4	-	1	943	c.918G>T	c.(916-918)caG>caT	p.Q306H	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	306						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)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TATCTCTGATCTGCTTGGTCT	0.403																																						uc010qzh.1																			0				ovary(1)|breast(1)	2						c.(916-918)CAG>CAT		olfactory receptor, family 52, subfamily H,							149.0	144.0	146.0					11																	5565836		2201	4297	6498	SO:0001583	missense	390067				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:5565836C>A	AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"""GPCR / Class A : Olfactory receptors"""	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.918G>T	11.37:g.5565836C>A	ENSP00000326259:p.Gln306His					HBG2_uc001mak.1_Intron	p.Q306H	NM_001005289	NP_001005289	Q8NGJ2	O52H1_HUMAN		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	1	918	-		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)	306			Cytoplasmic (Potential).		B9EH26|Q6IF79	Missense_Mutation	SNP	ENST00000322653.4	37	c.918G>T	CCDS31386.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687591	0.29962	.	.	ENSG00000181616	ENST00000322653	T	0.38887	1.11	5.22	4.1	0.47936	.	0.114616	0.39544	N	0.001323	T	0.46833	0.1413	M	0.89353	3.025	0.34454	D	0.701043	B	0.20671	0.047	B	0.20577	0.03	T	0.62196	-0.6905	10	0.72032	D	0.01	.	7.0831	0.25241	0.0:0.7637:0.0:0.2363	.	306	Q8NGJ2	O52H1_HUMAN	H	306	ENSP00000326259:Q306H	ENSP00000326259:Q306H	Q	-	3	2	OR52H1	5522412	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.510000	0.35790	2.430000	0.82344	0.650000	0.86243	CAG		0.403	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289	
TRIM22	10346	broad.mit.edu	37	11	5730417	5730417	+	Missense_Mutation	SNP	G	G	A	rs371728648		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr11:5730417G>A	ENST00000379965.3	+	8	1313	c.1036G>A	c.(1036-1038)Ggc>Agc	p.G346S	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	346	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			kidney(3)|large_intestine(8)|lung(9)|prostate(1)|stomach(2)	23		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		TGGTGTCTTCGGCTGCCAATA	0.408																																					GBM(104;491 2336 5222)	uc001mbr.2																			0					0						c.(1036-1038)GGC>AGC		tripartite motif-containing 22		G	SER/GLY,SER/GLY	0,3682		0,0,1841	127.0	120.0	122.0		1024,1036	3.0	0.0	11		122	1,8189		0,1,4094	no	missense,missense	TRIM22	NM_001199573.1,NM_006074.4	56,56	0,1,5935	AA,AG,GG		0.0122,0.0,0.0084	probably-damaging,probably-damaging	342/495,346/499	5730417	1,11871	1841	4095	5936	SO:0001583	missense	10346				immune response|interspecies interaction between organisms|protein trimerization|response to virus	Cajal body|Golgi apparatus|nuclear speck	ligase activity|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding	g.chr11:5730417G>A	X82200	CCDS41612.1	11p15	2013-01-09	2011-01-25		ENSG00000132274	ENSG00000132274		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16379	protein-coding gene	gene with protein product		606559	"""tripartite motif-containing 22"""			11331580, 11096452	Standard	NM_006074		Approved	STAF50, GPSTAF50, RNF94	uc001mbr.3	Q8IYM9	OTTHUMG00000066904	ENST00000379965.3:c.1036G>A	11.37:g.5730417G>A	ENSP00000369299:p.Gly346Ser					TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Intron|TRIM22_uc009yes.2_Missense_Mutation_p.G342S|TRIM22_uc010qzm.1_Missense_Mutation_p.G174S|TRIM22_uc009yeu.2_Missense_Mutation_p.G157S|OR56B1_uc001mbs.1_Intron|OR56B1_uc009yev.1_Intron	p.G346S	NM_006074	NP_006065	Q8IYM9	TRI22_HUMAN		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)	8	1313	+		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)	346			B30.2/SPRY.		Q05CQ0|Q15521	Missense_Mutation	SNP	ENST00000379965.3	37	c.1036G>A	CCDS41612.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.768312	0.90020	0.0	1.22E-4	ENSG00000132274	ENST00000379965;ENST00000545338;ENST00000455293	T	0.71817	-0.6	3.94	3.02	0.34903	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	.	.	.	.	D	0.84777	0.5547	M	0.89214	3.015	0.09310	N	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.73739	-0.3888	9	0.87932	D	0	.	9.9672	0.41732	0.1066:0.0:0.8934:0.0	.	268;342;346	F8WAP8;Q8IYM9-2;Q8IYM9	.;.;TRI22_HUMAN	S	346;157;268	ENSP00000369299:G346S	ENSP00000369299:G346S	G	+	1	0	TRIM22	5686993	1.000000	0.71417	0.019000	0.16419	0.921000	0.55340	4.140000	0.58031	0.960000	0.38005	0.460000	0.39030	GGC		0.408	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
MPEG1	219972	broad.mit.edu	37	11	58978683	58978683	+	Silent	SNP	C	C	T	rs545638736		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr11:58978683C>T	ENST00000361050.3	-	1	1741	c.1656G>A	c.(1654-1656)ccG>ccA	p.P552P		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	552			P -> L (in dbSNP:rs7926933). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				TTTTCAGAGACGGTGCCCCTA	0.567													C|||	1	0.000199681	0.0	0.0	5008	,	,		15840	0.0		0.0	False		,,,				2504	0.001					uc001nnu.3																			0				ovary(1)|skin(1)	2						c.(1654-1656)CCG>CCA		macrophage expressed gene 1 precursor							42.0	46.0	44.0					11																	58978683		1865	4095	5960	SO:0001819	synonymous_variant	219972					integral to membrane		g.chr11:58978683C>T	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"""macrophage expressed gene 1"""	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.1656G>A	11.37:g.58978683C>T							p.P552P	NM_001039396	NP_001034485	Q2M385	MPEG1_HUMAN			1	1812	-		all_epithelial(135;0.125)	552			Extracellular (Potential).		Q2M1T6|Q8TEF8	Silent	SNP	ENST00000361050.3	37	c.1656G>A	CCDS41650.1																																																																																				0.567	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396	
KRTAP5-9	3846	broad.mit.edu	37	11	71260048	71260048	+	Silent	SNP	T	T	C			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr11:71260048T>C	ENST00000528743.2	+	1	583	c.345T>C	c.(343-345)tgT>tgC	p.C115C		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	115	8 X 4 AA repeats of C-C-X-P.				epidermis development (GO:0008544)	keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						GTAAGCCCTGTTGCTCCTCCT	0.622																																						uc001oqs.1																			0					0						c.(343-345)TGT>TGC		keratin associated protein 5-9							111.0	125.0	120.0					11																	71260048		2191	4293	6484	SO:0001819	synonymous_variant	3846				epidermis development	keratin filament		g.chr11:71260048T>C	AB126078	CCDS53677.1	11q13.4	2008-02-05				ENSG00000254997		"""Keratin associated proteins"""	23604	protein-coding gene	gene with protein product		148021		KRN1		15144888	Standard	NM_005553		Approved	KRTAP5.9, KRTAP5-1	uc001oqs.1	P26371		ENST00000528743.2:c.345T>C	11.37:g.71260048T>C							p.C115C	NM_005553	NP_005544	P26371	KRA59_HUMAN			1	583	+			115			8 X 4 AA repeats of C-C-X-P.		Q14564|Q3MIP8	Silent	SNP	ENST00000528743.2	37	c.345T>C	CCDS53677.1																																																																																				0.622	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2		
NCAM1	4684	broad.mit.edu	37	11	113103495	113103496	+	Frame_Shift_Ins	INS	-	-	CATTGGGC	rs367640227		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr11:113103495_113103496insCATTGGGC	ENST00000533760.1	+	11	1696_1697	c.1097_1098insCATTGGGC	c.(1096-1101)cgcattfs	p.-367fs	NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000401611.2_Frame_Shift_Ins_p.-494fs|NCAM1_ENST00000316851.7_Frame_Shift_Ins_p.-485fs	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		GCAGTGAACCGCATTGGGCAGG	0.51																																						uc009yyq.1																			0				ovary(1)	1						c.(1204-1206)CGCfs		neural cell adhesion molecule 1 isoform 3																																				SO:0001589	frameshift_variant	4684				axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane		g.chr11:113103495_113103496insCATTGGGC		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.1098_1105dupCATTGGGC	11.37:g.113103496_113103503dupCATTGGGC	ENSP00000473281:p.Ile367fs						p.R402fs	NM_001076682	NP_001070150	P13591	NCAM1_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)	13	1899_1900	+		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)	494			Ig-like C2-type 5.|Extracellular (Potential).		A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Ins	INS	ENST00000533760.1	37	c.1205_1206insCATTGGGC																																																																																					0.510	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615	
SIK3	23387	broad.mit.edu	37	11	116732043	116732043	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr11:116732043C>T	ENST00000292055.4	-	18	2089	c.2054G>A	c.(2053-2055)aGg>aAg	p.R685K	SIK3_ENST00000375300.1_Missense_Mutation_p.R743K|SIK3_ENST00000542607.1_Missense_Mutation_p.R685K|SIK3_ENST00000446921.2_Missense_Mutation_p.R743K|SIK3_ENST00000434315.2_Missense_Mutation_p.R584K|SIK3_ENST00000488337.1_Intron|SIK3_ENST00000375288.1_Intron	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	685	Gln-rich.				protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						ACTGGGCTGCCTGAAGAGATG	0.493											OREG0003492	type=REGULATORY REGION|Gene=BC035583|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																										uc001ppy.2																			0				ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12						c.(2053-2055)AGG>AAG		serine/threonine-protein kinase QSK							85.0	91.0	89.0					11																	116732043		2201	4296	6497	SO:0001583	missense	23387					cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity	g.chr11:116732043C>T	AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.2054G>A	11.37:g.116732043C>T	ENSP00000292055:p.Arg685Lys		OREG0003492	type=REGULATORY REGION|Gene=BC035583|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	1475	SIK3_uc001ppz.2_Missense_Mutation_p.R584K|SIK3_uc001pqa.2_Missense_Mutation_p.R685K|SIK3_uc001ppw.2_Missense_Mutation_p.R102K|SIK3_uc001ppx.2_Intron|SIK3_uc001pqb.2_5'UTR	p.R685K	NM_025164	NP_079440	Q9Y2K2	SIK3_HUMAN			18	2090	-			685			Gln-rich.		A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	37	c.2054G>A	CCDS8379.1	.	.	.	.	.	.	.	.	.	.	c	33	5.253198	0.95336	.	.	ENSG00000160584	ENST00000375300;ENST00000292055;ENST00000542607;ENST00000434315	T;T;T;T	0.24538	1.85;1.85;1.85;1.85	5.83	4.92	0.64577	Protein kinase-like domain (1);	0.000000	0.45361	U	0.000377	T	0.40222	0.1108	L	0.32530	0.975	0.80722	D	1	D;D;D	0.71674	0.998;0.995;0.995	D;D;D	0.75484	0.986;0.98;0.98	T	0.30765	-0.9967	10	0.72032	D	0.01	.	14.4599	0.67442	0.0:0.9286:0.0:0.0714	.	685;584;685	A1A5A8;A1A5A9;Q9Y2K2	.;.;SIK3_HUMAN	K	743;685;685;584	ENSP00000364449:R743K;ENSP00000292055:R685K;ENSP00000438108:R685K;ENSP00000415873:R584K	ENSP00000292055:R685K	R	-	2	0	SIK3	116237253	1.000000	0.71417	0.982000	0.44146	0.998000	0.95712	4.679000	0.61649	1.461000	0.47929	0.655000	0.94253	AGG		0.493	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164	
TMPRSS4	56649	broad.mit.edu	37	11	117985628	117985628	+	Missense_Mutation	SNP	C	C	T	rs201401144		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr11:117985628C>T	ENST00000437212.3	+	10	1209	c.995C>T	c.(994-996)aCg>aTg	p.T332M	TMPRSS4_ENST00000534111.1_Missense_Mutation_p.T330M|TMPRSS4_ENST00000518413.2_3'UTR|TMPRSS4_ENST00000522824.1_Missense_Mutation_p.T327M|TMPRSS4_ENST00000522307.1_Missense_Mutation_p.T185M|TMPRSS4_ENST00000523251.1_Missense_Mutation_p.T292M			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	332	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		TGGGGCTTTACGAAGCAGAAT	0.572																																						uc010rxo.1																			0				large_intestine(1)|central_nervous_system(1)	2						c.(994-996)ACG>ATG		transmembrane protease, serine 4 isoform 1		C	MET/THR,MET/THR,MET/THR,MET/THR	0,4400		0,0,2200	42.0	34.0	37.0		980,989,875,995	3.4	0.8	11		37	3,8589	2.2+/-6.3	0,3,4293	yes	missense,missense,missense,missense	TMPRSS4	NM_001083947.1,NM_001173551.1,NM_001173552.1,NM_019894.3	81,81,81,81	0,3,6493	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging	327/433,330/436,292/398,332/438	117985628	3,12989	2200	4296	6496	SO:0001583	missense	56649				proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity	g.chr11:117985628C>T	AF179224	CCDS31684.1, CCDS44743.1, CCDS53716.1, CCDS53717.1	11q23.3	2010-04-13			ENSG00000137648	ENSG00000137648		"""Serine peptidases / Transmembrane"""	11878	protein-coding gene	gene with protein product	"""transmembrane serine protease 3"", ""membrane-type serine protease 2"", ""type II membrane serine protease"""	606565				10825129	Standard	NM_001083947		Approved	TMPRSS3, MT-SP2	uc021qrd.1	Q9NRS4	OTTHUMG00000164122	ENST00000437212.3:c.995C>T	11.37:g.117985628C>T	ENSP00000416037:p.Thr332Met					TMPRSS4_uc010rxp.1_Missense_Mutation_p.T327M|TMPRSS4_uc010rxq.1_Missense_Mutation_p.T185M|TMPRSS4_uc010rxr.1_Missense_Mutation_p.T307M|TMPRSS4_uc010rxs.1_Missense_Mutation_p.T292M|TMPRSS4_uc009yzu.2_RNA|TMPRSS4_uc010rxt.1_Missense_Mutation_p.T307M	p.T332M	NM_019894	NP_063947	Q9NRS4	TMPS4_HUMAN		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)	10	1286	+	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)	332			Extracellular (Potential).|Peptidase S1.		A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Missense_Mutation	SNP	ENST00000437212.3	37	c.995C>T	CCDS31684.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.623322	0.28889	0.0	3.49E-4	ENSG00000137648	ENST00000534111;ENST00000522307;ENST00000523251;ENST00000437212;ENST00000522824	T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07	5.58	3.38	0.38709	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.095533	0.45606	D	0.000342	T	0.76126	0.3944	M	0.80746	2.51	0.44295	D	0.997165	D;D;D;D;D	0.76494	0.999;0.995;0.999;0.961;0.992	D;P;P;P;P	0.63488	0.915;0.543;0.773;0.716;0.454	T	0.78630	-0.2129	10	0.51188	T	0.08	.	12.3401	0.55089	0.0:0.8367:0.0:0.1633	.	307;292;185;332;330	B7Z900;E7ERX8;E7ESG9;Q9NRS4;Q9NRS4-3	.;.;.;TMPS4_HUMAN;.	M	330;185;292;332;327	ENSP00000435184:T330M;ENSP00000428814:T185M;ENSP00000429209:T292M;ENSP00000416037:T332M;ENSP00000430547:T327M	ENSP00000416037:T332M	T	+	2	0	TMPRSS4	117490838	0.634000	0.27190	0.750000	0.31169	0.027000	0.11550	2.358000	0.44134	1.360000	0.45960	0.561000	0.74099	ACG		0.572	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894	
TECTA	7007	broad.mit.edu	37	11	121037459	121037459	+	Silent	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr11:121037459C>T	ENST00000392793.1	+	18	5827	c.5556C>T	c.(5554-5556)aaC>aaT	p.N1852N	TECTA_ENST00000264037.2_Silent_p.N1852N			O75443	TECTA_HUMAN	tectorin alpha	1852	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		AGATCAACAACACCAAAGGGA	0.498																																						uc010rzo.1																			0				breast(6)|ovary(2)|skin(2)	10						c.(5554-5556)AAC>AAT		tectorin alpha precursor							100.0	96.0	97.0					11																	121037459		2203	4299	6502	SO:0001819	synonymous_variant	7007				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix		g.chr11:121037459C>T	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.5556C>T	11.37:g.121037459C>T							p.N1852N	NM_005422	NP_005413	O75443	TECTA_HUMAN		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)	17	5556	+	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)	1852			ZP.			Silent	SNP	ENST00000392793.1	37	c.5556C>T	CCDS8434.1																																																																																				0.498	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
CLEC12A	160364	broad.mit.edu	37	12	10132026	10132026	+	Missense_Mutation	SNP	G	G	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr12:10132026G>T	ENST00000304361.4	+	3	464	c.282G>T	c.(280-282)atG>atT	p.M94I	CLEC12A_ENST00000434319.2_Missense_Mutation_p.M94I|CLEC12A_ENST00000355690.4_Missense_Mutation_p.M104I|CLEC12A_ENST00000350667.4_Missense_Mutation_p.M61I	NM_138337.5|NM_201623.3	NP_612210.4|NP_963917.2	Q5QGZ9	CL12A_HUMAN	C-type lectin domain family 12, member A	94						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.M104I(1)|p.M94I(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	16						TACAACTGATGAGTAACATGA	0.363																																					Melanoma(197;1487 2125 16611 22221 34855)	uc001qwr.3																			2	Substitution - Missense(2)		lung(2)	skin(1)	1						c.(280-282)ATG>ATT		myeloid inhibitory C-type lectin-like receptor							78.0	71.0	73.0					12																	10132026		2203	4300	6503	SO:0001583	missense	160364					integral to membrane|plasma membrane	receptor activity|sugar binding	g.chr12:10132026G>T	AY498550	CCDS8608.1, CCDS8609.1, CCDS55803.1, CCDS73442.1	12p13.31	2010-08-17			ENSG00000172322	ENSG00000172322		"""C-type lectin domain containing"""	31713	protein-coding gene	gene with protein product		612088					Standard	NM_201623		Approved	CLL-1, MICL	uc001qwq.3	Q5QGZ9		ENST00000304361.4:c.282G>T	12.37:g.10132026G>T	ENSP00000302804:p.Met94Ile					CLEC12A_uc001qwq.2_Missense_Mutation_p.M104I|CLEC12A_uc001qws.3_Missense_Mutation_p.M61I|CLEC12A_uc001qwt.2_Missense_Mutation_p.M23I	p.M94I	NM_138337	NP_612210	Q5QGZ9	CL12A_HUMAN			3	470	+			94			Extracellular (Potential).		B2RA16|Q6P4H1|Q6RH77|Q6RH78|Q8TDQ6	Missense_Mutation	SNP	ENST00000304361.4	37	c.282G>T	CCDS8608.1	.	.	.	.	.	.	.	.	.	.	G	7.104	0.574580	0.13623	.	.	ENSG00000172322	ENST00000355690;ENST00000396507;ENST00000304361;ENST00000434319;ENST00000350667	T;T;T;T;T	0.06068	4.62;3.35;4.63;4.07;4.48	4.72	0.775	0.18527	C-type lectin-like (1);	.	.	.	.	T	0.03871	0.0109	N	0.17674	0.51	0.09310	N	1	B;B;B	0.17667	0.023;0.013;0.023	B;B;B	0.15052	0.012;0.005;0.012	T	0.42899	-0.9424	9	0.37606	T	0.19	.	3.8031	0.08765	0.3015:0.1838:0.5147:0.0	.	61;94;104	Q5QGZ9-4;Q5QGZ9;Q5QGZ9-1	.;CL12A_HUMAN;.	I	104;94;94;94;61	ENSP00000347916:M104I;ENSP00000379764:M94I;ENSP00000302804:M94I;ENSP00000405244:M94I;ENSP00000345448:M61I	ENSP00000302804:M94I	M	+	3	0	CLEC12A	10023293	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	-0.015000	0.12634	0.277000	0.22141	0.650000	0.86243	ATG		0.363	CLEC12A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399545.1	NM_138337	
ITGB7	3695	broad.mit.edu	37	12	53590523	53590523	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr12:53590523C>T	ENST00000267082.5	-	6	887	c.656G>A	c.(655-657)cGg>cAg	p.R219Q	ITGB7_ENST00000422257.3_Missense_Mutation_p.R219Q|ITGB7_ENST00000550743.2_Missense_Mutation_p.R219Q|ITGB7_ENST00000338737.4_Missense_Mutation_p.R219Q	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	219	VWFA.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCGCTCCAGCCGGGTGGGGCA	0.617																																						uc009zmv.2																			0				ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|breast(1)	8						c.(655-657)CGG>CAG		integrin, beta 7 precursor																																				SO:0001583	missense	3695				cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|regulation of immune response	integrin complex	identical protein binding|metal ion binding|receptor activity	g.chr12:53590523C>T		CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"""Integrins"""	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.656G>A	12.37:g.53590523C>T	ENSP00000267082:p.Arg219Gln					ITGB7_uc001scc.2_Missense_Mutation_p.R219Q|ITGB7_uc010snz.1_RNA|ITGB7_uc010soa.1_3'UTR	p.R219Q	NM_000889	NP_000880	P26010	ITB7_HUMAN			5	727	-			219			VWFA.|Extracellular (Potential).		Q9UCP7|Q9UCS7	Missense_Mutation	SNP	ENST00000267082.5	37	c.656G>A	CCDS8849.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.154793	0.78114	.	.	ENSG00000139626	ENST00000422257;ENST00000267082;ENST00000338737;ENST00000542497	D;D;D;D	0.97575	-4.44;-4.44;-4.44;-4.44	5.05	5.05	0.67936	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.276459	0.19620	N	0.109932	D	0.94155	0.8125	L	0.28556	0.865	0.20489	N	0.999897	D	0.53745	0.962	P	0.46419	0.516	D	0.87693	0.2555	10	0.17369	T	0.5	.	13.2847	0.60237	0.1592:0.8408:0.0:0.0	.	219	P26010	ITB7_HUMAN	Q	219	ENSP00000408741:R219Q;ENSP00000267082:R219Q;ENSP00000345501:R219Q;ENSP00000437375:R219Q	ENSP00000267082:R219Q	R	-	2	0	ITGB7	51876790	0.014000	0.17966	0.991000	0.47740	0.878000	0.50629	1.249000	0.32839	2.523000	0.85059	0.555000	0.69702	CGG		0.617	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2		
ACACB	32	broad.mit.edu	37	12	109609642	109609642	+	Missense_Mutation	SNP	G	G	A	rs189283811	byFrequency	TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr12:109609642G>A	ENST00000338432.7	+	5	1077	c.958G>A	c.(958-960)Gtc>Atc	p.V320I	ACACB_ENST00000377854.5_Missense_Mutation_p.V320I|ACACB_ENST00000377848.3_Missense_Mutation_p.V320I			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	320	Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	TTACGTCCCCGTCCCAGGAGG	0.502													G|||	2	0.000399361	0.0008	0.0	5008	,	,		19631	0.001		0.0	False		,,,				2504	0.0					uc001tob.2																			0				ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8						c.(958-960)GTC>ATC		acetyl-Coenzyme A carboxylase beta	Biotin(DB00121)						161.0	131.0	141.0					12																	109609642		2203	4300	6503	SO:0001583	missense	32				acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding	g.chr12:109609642G>A	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.958G>A	12.37:g.109609642G>A	ENSP00000341044:p.Val320Ile					ACACB_uc001toc.2_Missense_Mutation_p.V320I	p.V320I	NM_001093	NP_001084	O00763	ACACB_HUMAN			5	1077	+			320			Biotin carboxylation.		A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	c.958G>A	CCDS31898.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	35	5.455612	0.96223	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854	D;D;D	0.91945	-2.94;-2.94;-2.94	5.47	5.47	0.80525	Pre-ATP-grasp fold (1);PreATP-grasp-like fold (1);Biotin carboxylation domain (1);Carbamoyl-phosphate synthase, large subunit, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94679	0.8284	L	0.41961	1.31	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95116	0.8242	10	0.87932	D	0	.	19.3317	0.94293	0.0:0.0:1.0:0.0	.	320	O00763	ACACB_HUMAN	I	320	ENSP00000341044:V320I;ENSP00000367079:V320I;ENSP00000367085:V320I	ENSP00000341044:V320I	V	+	1	0	ACACB	108094025	1.000000	0.71417	0.955000	0.39395	0.922000	0.55478	9.797000	0.99108	2.582000	0.87167	0.561000	0.74099	GTC		0.502	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
XPO4	64328	broad.mit.edu	37	13	21362729	21362729	+	Frame_Shift_Del	DEL	G	G	-			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr13:21362729delG	ENST00000255305.6	-	20	3014	c.2943delC	c.(2941-2943)tacfs	p.Y981fs	XPO4_ENST00000400602.2_Frame_Shift_Del_p.Y981fs			Q9C0E2	XPO4_HUMAN	exportin 4	981					positive regulation of protein export from nucleus (GO:0046827)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(10)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	41		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		TGATTAATTTGTAGTACTGAT	0.299																																						uc001unq.3																			0				large_intestine(1)|ovary(1)|kidney(1)	3						c.(2941-2943)TACfs		exportin 4							55.0	57.0	56.0					13																	21362729		1798	4065	5863	SO:0001589	frameshift_variant	64328				protein transport	cytoplasm|nucleus	protein binding	g.chr13:21362729delG	AB051508	CCDS41872.1	13q11	2011-04-13			ENSG00000132953	ENSG00000132953		"""Exportins"""	17796	protein-coding gene	gene with protein product		611449				11214970, 10944119	Standard	NM_022459		Approved	FLJ13046, KIAA1721	uc001unq.4	Q9C0E2	OTTHUMG00000016528	ENST00000255305.6:c.2943delC	13.37:g.21362729delG	ENSP00000255305:p.Tyr981fs						p.Y981fs	NM_022459	NP_071904	Q9C0E2	XPO4_HUMAN		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)	20	2979	-		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)	981					Q5VUZ5|Q8N3V6|Q9H934	Frame_Shift_Del	DEL	ENST00000255305.6	37	c.2943delC	CCDS41872.1																																																																																				0.299	XPO4-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044096.1	NM_022459	
KCTD12	115207	broad.mit.edu	37	13	77459429	77459429	+	Silent	SNP	G	G	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr13:77459429G>A	ENST00000377474.2	-	1	1096	c.855C>T	c.(853-855)tcC>tcT	p.S285S	KCTD12_ENST00000317765.2_Silent_p.S285S|AC000403.1_ENST00000579275.1_RNA	NM_138444.3	NP_612453.1	Q96CX2	KCD12_HUMAN	potassium channel tetramerization domain containing 12	285					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(1)|ovary(1)	4		Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.0499)		AGCCCGACTCGGACAGCTTGT	0.637											OREG0022449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc010aeu.1																			0				ovary(1)	1						c.(853-855)TCC>TCT		potassium channel tetramerisation domain							47.0	40.0	42.0					13																	77459429		2203	4300	6503	SO:0001819	synonymous_variant	115207					cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity	g.chr13:77459429G>A	AF359381	CCDS9455.1	13q21	2013-06-20	2013-06-20	2003-11-26	ENSG00000178695	ENSG00000178695			14678	protein-coding gene	gene with protein product	"""predominantly fetal expressed T1 domain"""	610521	"""chromosome 13 open reading frame 2"", ""potassium channel tetramerisation domain containing 12"""	C13orf2		15357420	Standard	NM_138444		Approved	KIAA1778, PFET1	uc010aeu.1	Q96CX2	OTTHUMG00000017096	ENST00000377474.2:c.855C>T	13.37:g.77459429G>A			OREG0022449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1175	KCTD12_uc001vka.1_Silent_p.S285S	p.S285S	NM_138444	NP_612453	Q96CX2	KCD12_HUMAN		GBM - Glioblastoma multiforme(99;0.0499)	1	1112	-		Breast(118;0.212)	285						Silent	SNP	ENST00000377474.2	37	c.855C>T	CCDS9455.1																																																																																				0.637	KCTD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045309.2	NM_138444	
KCNH5	27133	broad.mit.edu	37	14	63447809	63447809	+	Silent	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr14:63447809C>T	ENST00000322893.7	-	6	991	c.723G>A	c.(721-723)aaG>aaA	p.K241K	KCNH5_ENST00000420622.2_Silent_p.K241K|KCNH5_ENST00000394968.1_Silent_p.K183K|KCNH5_ENST00000394964.2_Silent_p.K183K	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	241					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.K241K(2)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		TGTTGTTCTGCTTTGTTTTGA	0.398																																						uc001xfx.2																			2	Substitution - coding silent(2)		skin(2)	ovary(4)|skin(4)|central_nervous_system(1)	9						c.(721-723)AAG>AAA		potassium voltage-gated channel, subfamily H,							78.0	80.0	79.0					14																	63447809		2203	4300	6503	SO:0001819	synonymous_variant	27133				regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity	g.chr14:63447809C>T	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.723G>A	14.37:g.63447809C>T						KCNH5_uc001xfy.2_Silent_p.K241K|KCNH5_uc001xfz.1_Silent_p.K183K|KCNH5_uc001xga.2_Silent_p.K183K	p.K241K	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)	6	774	-			241			Extracellular (Potential).		C9JP98	Silent	SNP	ENST00000322893.7	37	c.723G>A	CCDS9756.1																																																																																				0.398	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
UNC79	57578	broad.mit.edu	37	14	94052956	94052956	+	Missense_Mutation	SNP	A	A	G			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr14:94052956A>G	ENST00000393151.2	+	21	2818	c.2818A>G	c.(2818-2820)Acc>Gcc	p.T940A	UNC79_ENST00000553484.1_Missense_Mutation_p.T940A|UNC79_ENST00000256339.4_Missense_Mutation_p.T763A|UNC79_ENST00000555664.1_Missense_Mutation_p.T940A			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	940					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						AAAGAATGATACCGAAAGAAA	0.338																																						uc001ybv.1																			0				ovary(10)|skin(4)|large_intestine(3)	17						c.(2287-2289)ACC>GCC		hypothetical protein LOC57578							53.0	52.0	52.0					14																	94052956		2202	4299	6501	SO:0001583	missense	57578					integral to membrane		g.chr14:94052956A>G	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.2818A>G	14.37:g.94052956A>G	ENSP00000376858:p.Thr940Ala					KIAA1409_uc001ybs.1_Missense_Mutation_p.T763A	p.T763A	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN		Epithelial(152;0.188)	18	2370	+		all_cancers(154;0.0354)|all_epithelial(191;0.216)	940					B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37	c.2287A>G		.	.	.	.	.	.	.	.	.	.	A	13.24	2.177975	0.38413	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.17370	2.29;2.29;2.28;2.29	5.94	4.8	0.61643	.	0.057135	0.64402	D	0.000001	T	0.11110	0.0271	N	0.24115	0.695	0.34203	D	0.67342	P	0.37207	0.587	B	0.32724	0.151	T	0.21586	-1.0241	10	0.33940	T	0.23	-8.1266	11.9423	0.52907	0.9325:0.0:0.0675:0.0	.	940	C9JQL1	.	A	763;940;940;940;940	ENSP00000256339:T763A;ENSP00000450868:T940A;ENSP00000451360:T940A;ENSP00000376858:T940A	ENSP00000256339:T763A	T	+	1	0	KIAA1409	93122709	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	3.898000	0.56281	1.079000	0.41038	0.528000	0.53228	ACC		0.338	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
SERPINA9	327657	broad.mit.edu	37	14	94933658	94933658	+	Silent	SNP	G	G	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr14:94933658G>A	ENST00000380365.3	-	3	768	c.690C>T	c.(688-690)ggC>ggT	p.G230G	SERPINA9_ENST00000298845.7_Silent_p.G148G|SERPINA9_ENST00000539349.1_5'Flank|SERPINA9_ENST00000546329.1_Silent_p.G212G|RP11-349I1.2_ENST00000536735.1_RNA|SERPINA9_ENST00000448305.2_Silent_p.G150G|SERPINA9_ENST00000424550.2_Silent_p.G99G|SERPINA9_ENST00000337425.5_Silent_p.G248G			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	230					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		TGACCTGCTCGCCCACCAGGA	0.473																																						uc001ydf.2																			0				lung(1)|central_nervous_system(1)	2						c.(742-744)GGC>GGT		serine (or cysteine) proteinase inhibitor, clade							69.0	67.0	68.0					14																	94933658		1970	4165	6135	SO:0001819	synonymous_variant	327657				regulation of proteolysis	cytoplasm|extracellular region|membrane	serine-type endopeptidase inhibitor activity	g.chr14:94933658G>A	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.690C>T	14.37:g.94933658G>A						SERPINA9_uc001yde.2_Silent_p.G148G|SERPINA9_uc010avc.2_Silent_p.G99G|SERPINA9_uc001ydg.2_Silent_p.G212G|SERPINA9_uc001ydh.1_Silent_p.G248G|SERPINA9_uc001ydi.1_Silent_p.G212G	p.G248G	NM_175739	NP_783866	Q86WD7	SPA9_HUMAN		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)	3	905	-		all_cancers(154;0.0691)|all_epithelial(191;0.233)	230					B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Silent	SNP	ENST00000380365.3	37	c.744C>T																																																																																					0.473	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
TMCO5A	145942	broad.mit.edu	37	15	38239874	38239874	+	Missense_Mutation	SNP	G	G	C	rs193920912		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr15:38239874G>C	ENST00000319669.4	+	10	747	c.645G>C	c.(643-645)aaG>aaC	p.K215N	TMCO5A_ENST00000559502.1_Missense_Mutation_p.K215N|TMCO5A_ENST00000540944.1_Missense_Mutation_p.K215N	NM_152453.2	NP_689666.2	Q8N6Q1	TMC5A_HUMAN	transmembrane and coiled-coil domains 5A	215						integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	15						CTACCCAAAAGACAGCAAGAT	0.348																																						uc001zjw.2																			0				central_nervous_system(1)	1						c.(643-645)AAG>AAC		transmembrane and coiled-coil domains 5A							68.0	71.0	70.0					15																	38239874		2200	4296	6496	SO:0001583	missense	145942					integral to membrane		g.chr15:38239874G>C	BC029221	CCDS10046.1	15q14	2008-06-10	2008-06-10	2008-06-10	ENSG00000166069	ENSG00000166069			28558	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 5"""	TMCO5		12477932	Standard	NM_152453		Approved	MGC35118	uc001zjw.3	Q8N6Q1	OTTHUMG00000129787	ENST00000319669.4:c.645G>C	15.37:g.38239874G>C	ENSP00000327234:p.Lys215Asn					TMCO5A_uc001zjv.1_Missense_Mutation_p.K215N	p.K215N	NM_152453	NP_689666	Q8N6Q1	TMC5A_HUMAN			10	748	+			215					Q8NA63	Missense_Mutation	SNP	ENST00000319669.4	37	c.645G>C	CCDS10046.1	.	.	.	.	.	.	.	.	.	.	G	7.702	0.693239	0.15039	.	.	ENSG00000166069	ENST00000540944;ENST00000319669	.	.	.	4.61	-0.402	0.12404	.	0.722949	0.12342	N	0.477383	T	0.25568	0.0622	L	0.34521	1.04	0.09310	N	1	B;B	0.23540	0.033;0.087	B;B	0.22601	0.018;0.04	T	0.23297	-1.0192	9	0.54805	T	0.06	-5.8825	1.7784	0.03026	0.135:0.3791:0.2936:0.1923	.	215;215	Q8N6Q1;Q8N6Q1-2	TMC5A_HUMAN;.	N	215	.	ENSP00000327234:K215N	K	+	3	2	TMCO5A	36027166	0.067000	0.21026	0.010000	0.14722	0.007000	0.05969	0.236000	0.17967	0.122000	0.18314	0.563000	0.77884	AAG		0.348	TMCO5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252012.1	NM_152453	
SRRM2	23524	broad.mit.edu	37	16	2812739	2812739	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr16:2812739C>T	ENST00000301740.8	+	11	2759	c.2210C>T	c.(2209-2211)tCt>tTt	p.S737F		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	737	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						TCCAGAACATCTCAAAGAAGA	0.448																																						uc002crk.2																			0				ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						c.(2209-2211)TCT>TTT		splicing coactivator subunit SRm300							84.0	88.0	86.0					16																	2812739		2198	4300	6498	SO:0001583	missense	23524					Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding	g.chr16:2812739C>T	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.2210C>T	16.37:g.2812739C>T	ENSP00000301740:p.Ser737Phe					SRRM2_uc002crj.1_Missense_Mutation_p.S641F|SRRM2_uc002crl.1_Missense_Mutation_p.S737F|SRRM2_uc010bsu.1_Missense_Mutation_p.S641F	p.S737F	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN			11	2759	+			737			Arg-rich.|Ser-rich.		A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	c.2210C>T	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	9.094	1.002356	0.19121	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000426305	T	0.30182	1.54	5.8	5.8	0.92144	.	0.000000	0.53938	D	0.000045	T	0.42653	0.1212	N	0.24115	0.695	0.40261	D	0.978174	D	0.65815	0.995	D	0.67231	0.95	T	0.37478	-0.9704	10	0.66056	D	0.02	-12.4175	17.5501	0.87873	0.0:1.0:0.0:0.0	.	737	Q9UQ35	SRRM2_HUMAN	F	737;737;702	ENSP00000301740:S737F	ENSP00000301740:S737F	S	+	2	0	SRRM2	2752740	0.649000	0.27322	1.000000	0.80357	0.753000	0.42808	3.584000	0.53936	2.746000	0.94184	0.563000	0.77884	TCT		0.448	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
VPS53	55275	broad.mit.edu	37	17	440383	440383	+	Nonsense_Mutation	SNP	G	G	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr17:440383G>A	ENST00000571805.1	-	18	2036	c.1900C>T	c.(1900-1902)Cag>Tag	p.Q634*	RP5-1029F21.4_ENST00000570974.1_RNA|VPS53_ENST00000576149.1_5'UTR|VPS53_ENST00000446250.2_Nonsense_Mutation_p.Q436*|VPS53_ENST00000437048.2_Nonsense_Mutation_p.Q634*|VPS53_ENST00000291074.5_Nonsense_Mutation_p.Q605*|VPS53_ENST00000574029.1_Intron|VPS53_ENST00000401468.3_Nonsense_Mutation_p.Q357*			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	634					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		TAGGGGCTCTGGTCACCAACG	0.547																																						uc002frn.2																			0					0						c.(1900-1902)CAG>TAG		vacuolar protein sorting 53 isoform 2							152.0	103.0	120.0					17																	440383		2203	4300	6503	SO:0001587	stop_gained	55275				protein transport	endosome membrane|Golgi apparatus		g.chr17:440383G>A		CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"""vacuolar protein sorting 53 (yeast)"""			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.1900C>T	17.37:g.440383G>A	ENSP00000459312:p.Gln634*					VPS53_uc002frk.2_Nonsense_Mutation_p.Q153*|VPS53_uc010cjo.1_Nonsense_Mutation_p.Q634*|VPS53_uc002frl.2_RNA|VPS53_uc002frm.2_Nonsense_Mutation_p.Q605*|VPS53_uc002fro.2_Nonsense_Mutation_p.Q436*|VPS53_uc010cjp.1_Nonsense_Mutation_p.Q357*	p.Q634*	NM_018289	NP_060759	Q5VIR6	VPS53_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)	18	2047	-			634					A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Nonsense_Mutation	SNP	ENST00000571805.1	37	c.1900C>T		.	.	.	.	.	.	.	.	.	.	G	46	12.626409	0.99683	.	.	ENSG00000141252	ENST00000437048;ENST00000446250;ENST00000291074;ENST00000401468	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-15.1476	19.1891	0.93656	0.0:0.0:1.0:0.0	.	.	.	.	X	634;436;605;357	.	ENSP00000291074:Q605X	Q	-	1	0	VPS53	387133	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	9.476000	0.97823	2.786000	0.95864	0.585000	0.79938	CAG		0.547	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289	
GSDMB	55876	broad.mit.edu	37	17	38062400	38062400	+	Silent	SNP	G	G	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr17:38062400G>A	ENST00000394179.1	-	7	967	c.837C>T	c.(835-837)ctC>ctT	p.L279L	GSDMB_ENST00000360317.3_Silent_p.L284L|GSDMB_ENST00000418519.1_Silent_p.L284L|GSDMB_ENST00000394175.2_Silent_p.L262L|GSDMB_ENST00000520542.1_Silent_p.L275L|GSDMB_ENST00000309481.7_Silent_p.L271L			Q8TAX9	GSDMB_HUMAN	gasdermin B	279						cytoplasm (GO:0005737)				breast(2)|endometrium(3)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|stomach(2)	21						CCTCCTTGCCGAGGCACTTAG	0.522																																						uc010cwj.2																			0				breast(1)|pancreas(1)	2						c.(850-852)CTC>CTT		gasdermin B isoform 1							172.0	139.0	151.0					17																	38062400		2203	4300	6503	SO:0001819	synonymous_variant	55876					cytoplasm		g.chr17:38062400G>A	AF119884	CCDS11354.1, CCDS42313.1, CCDS54119.1, CCDS54120.1	17q21.2	2008-07-31	2008-07-31	2008-07-31	ENSG00000073605	ENSG00000073605			23690	protein-coding gene	gene with protein product		611221	"""gasdermin-like"""	GSDML		12883658, 15010812, 17350798	Standard	NM_001042471		Approved	PRO2521	uc010cwj.3	Q8TAX9	OTTHUMG00000133248	ENST00000394179.1:c.837C>T	17.37:g.38062400G>A						GSDMB_uc010cwi.2_Silent_p.L31L|GSDMB_uc010cwk.2_RNA|GSDMB_uc010cwl.2_RNA|GSDMB_uc010cwm.2_RNA|GSDMB_uc002htg.2_Silent_p.L262L|GSDMB_uc002hth.2_Silent_p.L271L|GSDMB_uc010wem.1_Silent_p.L275L	p.L284L	NM_001042471	NP_001035936	Q8TAX9	GSDMB_HUMAN			7	857	-			279					B4DKK7|Q7Z377|Q8WY76|Q9NX71|Q9P163	Silent	SNP	ENST00000394179.1	37	c.852C>T		.	.	.	.	.	.	.	.	.	.	G	2.627	-0.287337	0.05605	.	.	ENSG00000073605	ENST00000420491	.	.	.	3.74	0.492	0.16872	.	.	.	.	.	T	0.21186	0.0510	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.21965	-1.0230	4	.	.	.	.	2.1528	0.03804	0.1127:0.1979:0.4855:0.2039	.	.	.	.	L	216	.	.	S	-	2	0	GSDMB	35315926	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.583000	0.05807	0.165000	0.19558	0.609000	0.83330	TCG		0.522	GSDMB-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_018530	
ITGA3	3675	broad.mit.edu	37	17	48156217	48156217	+	Missense_Mutation	SNP	G	G	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr17:48156217G>A	ENST00000320031.8	+	19	2657	c.2327G>A	c.(2326-2328)gGg>gAg	p.G776E	ITGA3_ENST00000007722.7_Missense_Mutation_p.G776E	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	776					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						AGCTTCTTTGGGGGGACAGTG	0.582																																						uc010dbl.2																			0				ovary(2)|pancreas(1)	3						c.(2326-2328)GGG>GAG		integrin alpha 3 isoform a precursor							102.0	107.0	105.0					17																	48156217		2203	4300	6503	SO:0001583	missense	3675				blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|leukocyte migration	cell surface|integrin complex	protein binding|receptor activity	g.chr17:48156217G>A	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"""CD molecules"", ""Integrins"""	6139	protein-coding gene	gene with protein product		605025	"""antigen identified by monoclonal antibody J143"""	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.2327G>A	17.37:g.48156217G>A	ENSP00000315190:p.Gly776Glu					ITGA3_uc010dbm.2_Missense_Mutation_p.G776E	p.G776E	NM_002204	NP_002195	P26006	ITA3_HUMAN			19	2791	+			776			Extracellular (Potential).		A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Missense_Mutation	SNP	ENST00000320031.8	37	c.2327G>A	CCDS11558.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.5|29.5	5.013303|5.013303	0.93346|0.93346	.|.	.|.	ENSG00000005884|ENSG00000005884	ENST00000007722;ENST00000538917;ENST00000320031|ENST00000506827	T;T|.	0.50001|.	0.76;0.76|.	4.53|4.53	4.53|4.53	0.55603|0.55603	Integrin alpha-2 (1);|.	0.212708|.	0.49916|.	D|.	0.000122|.	T|.	0.73892|.	0.3645|.	M|M	0.70595|0.70595	2.14|2.14	0.80722|0.80722	D|D	1|1	D;D|.	0.57257|.	0.979;0.962|.	P;P|.	0.57846|.	0.642;0.828|.	T|.	0.74200|.	-0.3742|.	10|.	0.38643|.	T|.	0.18|.	.|.	16.5234|16.5234	0.84322|0.84322	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	776;776|.	P26006-1;P26006|.	.;ITA3_HUMAN|.	E|X	776;762;776|154	ENSP00000007722:G776E;ENSP00000315190:G776E|.	ENSP00000007722:G776E|.	G|W	+|+	2|3	0|0	ITGA3|ITGA3	45511216|45511216	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	6.479000|6.479000	0.73600|0.73600	2.528000|2.528000	0.85240|0.85240	0.491000|0.491000	0.48974|0.48974	GGG|TGG		0.582	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501	
ANKRD40	91369	broad.mit.edu	37	17	48776813	48776813	+	Missense_Mutation	SNP	G	G	A	rs148279576		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr17:48776813G>A	ENST00000285243.6	-	3	994	c.725C>T	c.(724-726)gCg>gTg	p.A242V	Y_RNA_ENST00000364470.1_RNA	NM_052855.3	NP_443087.1	Q6AI12	ANR40_HUMAN	ankyrin repeat domain 40	242	Pro-rich.									breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)|urinary_tract(1)	11			BRCA - Breast invasive adenocarcinoma(22;2.03e-09)			GAATGCTGGCGCTGGTCCTGC	0.522																																						uc002iso.2																			0					0						c.(724-726)GCG>GTG		ankyrin repeat domain 40		G	VAL/ALA	0,4406		0,0,2203	107.0	114.0	112.0		725	3.2	0.3	17	dbSNP_134	112	1,8599	1.2+/-3.3	0,1,4299	no	missense	ANKRD40	NM_052855.3	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	242/369	48776813	1,13005	2203	4300	6503	SO:0001583	missense	91369							g.chr17:48776813G>A	BC012978	CCDS11572.1	17q21.33	2013-01-10			ENSG00000154945	ENSG00000154945		"""Ankyrin repeat domain containing"""	28233	protein-coding gene	gene with protein product						12477932	Standard	NM_052855		Approved	MGC15396	uc002iso.3	Q6AI12	OTTHUMG00000162255	ENST00000285243.6:c.725C>T	17.37:g.48776813G>A	ENSP00000285243:p.Ala242Val						p.A242V	NM_052855	NP_443087	Q6AI12	ANR40_HUMAN	BRCA - Breast invasive adenocarcinoma(22;2.03e-09)		3	980	-			242			Pro-rich.		Q96E32	Missense_Mutation	SNP	ENST00000285243.6	37	c.725C>T	CCDS11572.1	.	.	.	.	.	.	.	.	.	.	G	2.222	-0.378139	0.05000	0.0	1.16E-4	ENSG00000154945	ENST00000285243	T	0.20332	2.08	5.17	3.17	0.36434	.	0.530450	0.21334	N	0.076246	T	0.06096	0.0158	N	0.01352	-0.895	0.21184	N	0.999763	B	0.02656	0.0	B	0.01281	0.0	T	0.39396	-0.9616	10	0.09590	T	0.72	-1.1816	8.8098	0.34961	0.3545:0.0:0.6455:0.0	.	242	Q6AI12	ANR40_HUMAN	V	242	ENSP00000285243:A242V	ENSP00000285243:A242V	A	-	2	0	ANKRD40	46131812	0.004000	0.15560	0.281000	0.24762	0.853000	0.48598	1.501000	0.35693	0.686000	0.31488	-0.145000	0.13849	GCG		0.522	ANKRD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368201.2	NM_052855	
COIL	8161	broad.mit.edu	37	17	55027963	55027963	+	Missense_Mutation	SNP	G	G	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr17:55027963G>T	ENST00000240316.4	-	2	674	c.640C>A	c.(640-642)Cag>Aag	p.Q214K		NM_004645.2	NP_004636.1	P38432	COIL_HUMAN	coilin	214						Cajal body (GO:0015030)|cytoplasm (GO:0005737)|female germ cell nucleus (GO:0001674)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	disulfide oxidoreductase activity (GO:0015036)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	15	Breast(9;6.15e-08)					CTACATCTCTGATTGGCCCAG	0.403																																						uc002iuu.2																			0				ovary(1)	1						c.(640-642)CAG>AAG		coilin							135.0	129.0	131.0					17																	55027963		2203	4300	6503	SO:0001583	missense	8161					Cajal body|nucleolus	protein C-terminus binding	g.chr17:55027963G>T	U06632	CCDS11592.1	17q22	2012-10-02			ENSG00000121058	ENSG00000121058			2184	protein-coding gene	gene with protein product		600272				7971277	Standard	NM_004645		Approved	CLN80, p80-coilin	uc002iuu.3	P38432	OTTHUMG00000178126	ENST00000240316.4:c.640C>A	17.37:g.55027963G>T	ENSP00000240316:p.Gln214Lys						p.Q214K	NM_004645	NP_004636	P38432	COIL_HUMAN			2	671	-	Breast(9;6.15e-08)		214					B2R931	Missense_Mutation	SNP	ENST00000240316.4	37	c.640C>A	CCDS11592.1	.	.	.	.	.	.	.	.	.	.	G	9.286	1.049350	0.19827	.	.	ENSG00000121058	ENST00000240316	T	0.75704	-0.96	5.82	3.66	0.41972	.	1.094130	0.06723	N	0.775322	T	0.59649	0.2209	L	0.29908	0.895	0.09310	N	1	B	0.17667	0.023	B	0.15484	0.013	T	0.47209	-0.9135	10	0.12103	T	0.63	-0.0035	5.4141	0.16363	0.08:0.1083:0.6081:0.2036	.	214	P38432	COIL_HUMAN	K	214	ENSP00000240316:Q214K	ENSP00000240316:Q214K	Q	-	1	0	COIL	52382962	0.005000	0.15991	0.019000	0.16419	0.076000	0.17211	0.782000	0.26788	1.470000	0.48102	0.557000	0.71058	CAG		0.403	COIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440618.1		
ABCA9	10350	broad.mit.edu	37	17	66981088	66981088	+	Silent	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr17:66981088C>T	ENST00000340001.4	-	34	4528	c.4317G>A	c.(4315-4317)ccG>ccA	p.P1439P	ABCA9_ENST00000370732.2_Intron|ABCA9_ENST00000482072.1_5'Flank|ABCA9_ENST00000453985.2_Silent_p.P1401P	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	1439	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.P1439P(1)		NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					GCACCACTGACGGGTTCCCCA	0.587																																						uc002jhu.2																			1	Substitution - coding silent(1)		prostate(1)	ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6						c.(4315-4317)CCG>CCA		ATP-binding cassette, sub-family A, member 9							126.0	113.0	117.0					17																	66981088		2203	4300	6503	SO:0001819	synonymous_variant	10350				transport	integral to membrane	ATP binding|ATPase activity	g.chr17:66981088C>T	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"""ATP binding cassette transporters / subfamily A"""	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.4317G>A	17.37:g.66981088C>T						ABCA9_uc010dez.2_Silent_p.P1401P	p.P1439P	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN			34	4460	-	Breast(10;1.47e-12)		1439			ABC transporter 2.		Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Silent	SNP	ENST00000340001.4	37	c.4317G>A	CCDS11681.1																																																																																				0.587	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386	
SETBP1	26040	broad.mit.edu	37	18	42529847	42529847	+	Splice_Site	SNP	C	C	G			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr18:42529847C>G	ENST00000282030.5	+	4	838	c.542C>G	c.(541-543)gCt>gGt	p.A181G		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	181						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		CACCCTTAGGCTTACGAGAGG	0.468									Schinzel-Giedion syndrome																													uc010dni.2																			0				upper_aerodigestive_tract(2)|large_intestine(1)	3						c.(541-543)GCT>GGT		SET binding protein 1 isoform a							45.0	42.0	43.0					18																	42529847		2203	4300	6503	SO:0001630	splice_region_variant	26040	Schinzel-Giedion_syndrome	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome		nucleus	DNA binding	g.chr18:42529847C>G	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.541-1C>G	18.37:g.42529847C>G							p.A181G	NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN		Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)	4	838	+			181					A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	c.542C>G	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	C	13.80	2.343822	0.41498	.	.	ENSG00000152217	ENST00000282030	T	0.69806	-0.43	5.79	4.82	0.62117	.	0.185646	0.47852	D	0.000218	T	0.47801	0.1465	N	0.22421	0.69	0.32845	D	0.505939	B	0.34015	0.435	B	0.35510	0.204	T	0.57820	-0.7745	10	0.49607	T	0.09	.	3.8293	0.08867	0.0:0.6719:0.0:0.3281	.	181	Q9Y6X0	SETBP_HUMAN	G	181	ENSP00000282030:A181G	ENSP00000282030:A181G	A	+	2	0	SETBP1	40783845	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.404000	0.52623	2.751000	0.94390	0.650000	0.86243	GCT		0.468	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	Missense_Mutation
SLC14A1	6563	broad.mit.edu	37	18	43310353	43310353	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr18:43310353C>T	ENST00000321925.4	+	3	300	c.68C>T	c.(67-69)tCg>tTg	p.S23L	SLC14A1_ENST00000589700.1_Missense_Mutation_p.S23L|SLC14A1_ENST00000415427.3_Missense_Mutation_p.S79L|SLC14A1_ENST00000586142.1_Missense_Mutation_p.S23L|SLC14A1_ENST00000402943.2_Intron|SLC14A1_ENST00000591943.1_3'UTR|SLC14A1_ENST00000535474.1_Intron|SLC14A1_ENST00000436407.3_Missense_Mutation_p.S79L|SLC14A1_ENST00000502059.2_Intron|RP11-116O18.3_ENST00000589510.1_RNA|RP11-116O18.3_ENST00000586213.1_RNA	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	23					transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						AACCAGGTTTCGCCATGTCAA	0.507																																						uc010xcn.1																			0				central_nervous_system(1)|pancreas(1)	2						c.(67-69)TCG>TTG		solute carrier family 14 (urea transporter),							129.0	109.0	116.0					18																	43310353		2203	4300	6503	SO:0001583	missense	6563					integral to plasma membrane	urea transmembrane transporter activity	g.chr18:43310353C>T	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"""Blood group antigens"", ""Solute carriers"""	10918	protein-coding gene	gene with protein product		613868	"""Kidd blood group"", ""solute carrier family 14 (urea transporter), member 1"""	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.68C>T	18.37:g.43310353C>T	ENSP00000318546:p.Ser23Leu					SLC14A1_uc010dnk.2_Missense_Mutation_p.S79L|SLC14A1_uc002lbf.3_Missense_Mutation_p.S23L|SLC14A1_uc002lbg.3_RNA|SLC14A1_uc010xco.1_Intron|SLC14A1_uc002lbh.3_Intron|SLC14A1_uc002lbi.3_Intron|SLC14A1_uc002lbj.3_Missense_Mutation_p.S79L|SLC14A1_uc002lbk.3_Missense_Mutation_p.S23L	p.S23L	NM_001146036	NP_001139508	Q13336	UT1_HUMAN			4	387	+			23					A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Missense_Mutation	SNP	ENST00000321925.4	37	c.68C>T	CCDS11925.1	.	.	.	.	.	.	.	.	.	.	C	10.17	1.276200	0.23307	.	.	ENSG00000141469	ENST00000321925;ENST00000415427;ENST00000436407	T;T;T	0.55052	0.73;0.54;0.54	5.84	1.79	0.24919	.	1.289600	0.05356	N	0.532809	T	0.38134	0.1029	L	0.31664	0.95	0.09310	N	1	B;B	0.12630	0.006;0.0	B;B	0.09377	0.004;0.001	T	0.19257	-1.0311	10	0.25106	T	0.35	-15.6914	4.5148	0.11930	0.1517:0.5877:0.0:0.2606	.	79;23	Q13336-2;Q13336	.;UT1_HUMAN	L	23;79;79	ENSP00000318546:S23L;ENSP00000412309:S79L;ENSP00000390637:S79L	ENSP00000318546:S23L	S	+	2	0	SLC14A1	41564351	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	0.712000	0.25779	0.337000	0.23665	0.655000	0.94253	TCG		0.507	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865	
SF3A2	8175	broad.mit.edu	37	19	2248259	2248260	+	Frame_Shift_Ins	INS	-	-	G			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr19:2248259_2248260insG	ENST00000221494.5	+	9	1527_1528	c.1109_1110insG	c.(1108-1113)gcggggfs	p.AG370fs	AMH_ENST00000221496.4_5'Flank|MIR4321_ENST00000592276.1_RNA	NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	370	Pro-rich.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCCCATCAGCGGGGGTTCACC	0.748																																						uc002lvg.2																			0					0						c.(1108-1110)GCGfs		splicing factor 3a, subunit 2																																				SO:0001589	frameshift_variant	8175				nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nucleoplasm|small nuclear ribonucleoprotein complex	nucleic acid binding|zinc ion binding	g.chr19:2248259_2248260insG	L21990	CCDS12084.1	19p13.3	2012-10-02	2002-08-29		ENSG00000104897	ENSG00000104897			10766	protein-coding gene	gene with protein product		600796	"""splicing factor 3a, subunit 2, 66kD"""			8211113, 8541848	Standard	NM_007165		Approved	SF3a66, SAP62, PRPF11, Prp11	uc002lvg.3	Q15428	OTTHUMG00000180414	ENST00000221494.5:c.1114dupG	19.37:g.2248264_2248264dupG	ENSP00000221494:p.Ala370fs					AMH_uc002lvh.2_5'Flank|hsa-mir-4321|MI0015852_5'Flank	p.A370fs	NM_007165	NP_009096	Q15428	SF3A2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	9	1231_1232	+		Hepatocellular(1079;0.137)	370			Pro-rich.		B2RBU1|D6W605|O75245	Frame_Shift_Ins	INS	ENST00000221494.5	37	c.1109_1110insG	CCDS12084.1																																																																																				0.748	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451268.3		
LRRC8E	80131	broad.mit.edu	37	19	7965735	7965735	+	Silent	SNP	G	G	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr19:7965735G>T	ENST00000306708.6	+	3	2429	c.2328G>T	c.(2326-2328)ctG>ctT	p.L776L	MAP2K7_ENST00000397981.3_5'Flank|RN7SL115P_ENST00000392196.5_RNA|AC010336.1_ENST00000539278.1_5'UTR	NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	776					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						CGGGGCTCCTGGTGGAAGACA	0.597																																						uc002mir.2																			0				lung(1)|pancreas(1)	2						c.(2326-2328)CTG>CTT		leucine rich repeat containing 8 family, member							32.0	38.0	36.0					19																	7965735		2202	4294	6496	SO:0001819	synonymous_variant	80131					integral to membrane		g.chr19:7965735G>T		CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.2328G>T	19.37:g.7965735G>T							p.L776L	NM_025061	NP_079337	Q6NSJ5	LRC8E_HUMAN			3	2429	+			776					B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Silent	SNP	ENST00000306708.6	37	c.2328G>T	CCDS12189.1																																																																																				0.597	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061	
MUC16	94025	broad.mit.edu	37	19	9072143	9072143	+	Silent	SNP	T	T	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr19:9072143T>A	ENST00000397910.4	-	3	15506	c.15303A>T	c.(15301-15303)tcA>tcT	p.S5101S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5103	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTATCTTATCTGAGGTGCTGC	0.423																																						uc002mkp.2																			0				lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						c.(15301-15303)TCA>TCT		mucin 16							162.0	147.0	151.0					19																	9072143		1901	4134	6035	SO:0001819	synonymous_variant	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:9072143T>A	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15303A>T	19.37:g.9072143T>A							p.S5101S	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN			3	15507	-			5103			Thr-rich.|Extracellular (Potential).		Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	c.15303A>T	CCDS54212.1																																																																																				0.423	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DTNB	1838	broad.mit.edu	37	2	25674485	25674485	+	Nonsense_Mutation	SNP	G	G	A	rs373229134		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr2:25674485G>A	ENST00000406818.3	-	12	1438	c.1189C>T	c.(1189-1191)Cga>Tga	p.R397*	DTNB_ENST00000405222.1_Nonsense_Mutation_p.R367*|DTNB_ENST00000407038.3_Nonsense_Mutation_p.R367*|DTNB_ENST00000496972.2_Nonsense_Mutation_p.R340*|DTNB_ENST00000407661.3_Nonsense_Mutation_p.R397*|DTNB_ENST00000545439.1_Nonsense_Mutation_p.R193*|DTNB_ENST00000407186.1_Nonsense_Mutation_p.R367*|DTNB_ENST00000404103.3_Nonsense_Mutation_p.R397*|DTNB_ENST00000288642.8_Nonsense_Mutation_p.R397*	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	397						cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCATCCAGTCGGCTAGGACTG	0.468																																						uc002rgh.2																			0				large_intestine(2)|ovary(2)	4						c.(1189-1191)CGA>TGA		dystrobrevin, beta isoform 1		G	stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG	0,3782		0,0,1891	58.0	53.0	54.0		1189,1189,1099,1189,1099	1.4	1.0	2		54	2,8260		0,2,4129	no	stop-gained,stop-gained,stop-gained,stop-gained,stop-gained	DTNB	NM_021907.3,NM_033147.2,NM_033148.2,NM_183360.1,NM_183361.1	,,,,	0,2,6020	AA,AG,GG		0.0242,0.0,0.0166	,,,,	397/628,397/598,367/568,397/610,367/561	25674485	2,12042	1891	4131	6022	SO:0001587	stop_gained	1838					cytoplasm	calcium ion binding|zinc ion binding	g.chr2:25674485G>A	AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101			3058	protein-coding gene	gene with protein product		602415				9419360	Standard	NM_021907		Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.1189C>T	2.37:g.25674485G>A	ENSP00000384084:p.Arg397*					DTNB_uc002rgg.2_Nonsense_Mutation_p.R26*|DTNB_uc010yko.1_Nonsense_Mutation_p.R340*|DTNB_uc010ykp.1_Nonsense_Mutation_p.R193*|DTNB_uc002rgo.2_Nonsense_Mutation_p.R188*|DTNB_uc002rgi.2_Nonsense_Mutation_p.R397*|DTNB_uc002rgj.2_Nonsense_Mutation_p.R397*|DTNB_uc002rgk.2_Nonsense_Mutation_p.R367*|DTNB_uc002rgl.2_Nonsense_Mutation_p.R367*|DTNB_uc002rgq.2_Nonsense_Mutation_p.R397*|DTNB_uc002rgm.2_Nonsense_Mutation_p.R367*|DTNB_uc002rgn.2_Nonsense_Mutation_p.R193*|DTNB_uc002rgr.1_Nonsense_Mutation_p.R386*|DTNB_uc010ykq.1_Nonsense_Mutation_p.R250*	p.R397*	NM_021907	NP_068707	O60941	DTNB_HUMAN			12	1439	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)		397					B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Nonsense_Mutation	SNP	ENST00000406818.3	37	c.1189C>T	CCDS46237.1	.	.	.	.	.	.	.	.	.	.	G	40	7.987716	0.98596	0.0	2.42E-4	ENSG00000138101	ENST00000496972;ENST00000406818;ENST00000404103;ENST00000407661;ENST00000407038;ENST00000405222;ENST00000407186;ENST00000288642;ENST00000545439;ENST00000535791	.	.	.	5.51	1.42	0.22433	.	0.129068	0.53938	D	0.000056	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-6.9078	13.4217	0.61001	0.0:0.0:0.4591:0.5409	.	.	.	.	X	340;397;397;397;367;367;367;397;193;250	.	ENSP00000288642:R397X	R	-	1	2	DTNB	25527989	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	1.731000	0.38135	-0.022000	0.13986	-0.181000	0.13052	CGA		0.468	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147	
DUSP11	8446	broad.mit.edu	37	2	74007043	74007043	+	Missense_Mutation	SNP	C	C	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr2:74007043C>A	ENST00000272444.3	-	1	241	c.200G>T	c.(199-201)cGc>cTc	p.R67L	DUSP11_ENST00000443070.1_Missense_Mutation_p.R67L|DUSP11_ENST00000377706.4_Missense_Mutation_p.R20L|DUSP11_ENST00000480948.1_5'Flank	NM_003584.2	NP_003575.2	O75319	DUS11_HUMAN	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	20					peptidyl-tyrosine dephosphorylation (GO:0035335)|polynucleotide 5' dephosphorylation (GO:0098507)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide phosphatase activity, acting on free nucleotides (GO:0098519)|phosphatase activity (GO:0016791)|poly(A) RNA binding (GO:0044822)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|skin(1)	12						GGCTGAGGAGCGTCCTGAAAA	0.617											OREG0014714	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc002sjp.2																			0				skin(1)	1						c.(199-201)CGC>CTC		dual specificity phosphatase 11							119.0	101.0	107.0					2																	74007043		2203	4300	6503	SO:0001583	missense	8446				RNA processing	nucleus	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity|RNA binding	g.chr2:74007043C>A	AF023917	CCDS1928.2	2p13.1	2011-06-09			ENSG00000144048	ENSG00000144048		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	3066	protein-coding gene	gene with protein product		603092				9685386	Standard	NM_003584		Approved	PIR1	uc002sjp.3	O75319	OTTHUMG00000129816	ENST00000272444.3:c.200G>T	2.37:g.74007043C>A	ENSP00000272444:p.Arg67Leu		OREG0014714	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1149	DUSP11_uc002sjq.3_Missense_Mutation_p.R67L	p.R67L	NM_003584	NP_003575	O75319	DUS11_HUMAN			1	242	-			20					B2RCT8|Q6AI47|Q9BWE3	Missense_Mutation	SNP	ENST00000272444.3	37	c.200G>T	CCDS1928.2	.	.	.	.	.	.	.	.	.	.	C	13.65	2.300360	0.40694	.	.	ENSG00000144048	ENST00000272444;ENST00000443070;ENST00000377706;ENST00000452812	T;T	0.34275	1.37;1.9	4.6	-0.619	0.11572	.	0.995923	0.08138	N	0.992099	T	0.22551	0.0544	L	0.40543	1.245	0.09310	N	1	B;B	0.29646	0.253;0.145	B;B	0.23716	0.048;0.033	T	0.24584	-1.0156	10	0.14656	T	0.56	0.0062	4.5577	0.12145	0.0:0.4779:0.1614:0.3607	.	67;20	C9JYA6;O75319	.;DUS11_HUMAN	L	67;67;20;18	ENSP00000413444:R67L;ENSP00000366935:R20L	ENSP00000272444:R67L	R	-	2	0	DUSP11	73860551	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.180000	0.16860	-0.109000	0.12044	0.655000	0.94253	CGC		0.617	DUSP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252047.3		
MAP4K4	9448	broad.mit.edu	37	2	102483026	102483026	+	Missense_Mutation	SNP	C	C	T	rs369479508		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr2:102483026C>T	ENST00000347699.4	+	18	2107	c.2107C>T	c.(2107-2109)Cgc>Tgc	p.R703C	MAP4K4_ENST00000456652.1_Missense_Mutation_p.R502C|MAP4K4_ENST00000302217.5_Missense_Mutation_p.R503C|MAP4K4_ENST00000413150.2_Missense_Mutation_p.R618C|MAP4K4_ENST00000350878.4_Missense_Mutation_p.R676C|MAP4K4_ENST00000350198.4_Missense_Mutation_p.R619C|MAP4K4_ENST00000324219.4_Missense_Mutation_p.R781C|MAP4K4_ENST00000425019.1_Missense_Mutation_p.R672C	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	703					intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CTCCGGGGAACGCTTCAGAGT	0.532																																						uc002tbg.2																			0				stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4						c.(2107-2109)CGC>TGC		mitogen-activated protein kinase kinase kinase		C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	1,3895		0,1,1947	64.0	72.0	69.0		2107,2086,1852,2017,2017	5.8	1.0	2		69	0,8288		0,0,4144	no	missense,missense,missense,missense,missense	MAP4K4	NM_001242559.1,NM_001242560.1,NM_004834.4,NM_145686.3,NM_145687.3	180,180,180,180,180	0,1,6091	TT,TC,CC		0.0,0.0257,0.0082	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	703/1240,696/1236,618/1166,673/1274,673/1213	102483026	1,12183	1948	4144	6092	SO:0001583	missense	9448				intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity	g.chr2:102483026C>T	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6866	protein-coding gene	gene with protein product	"""HPK/GCK-like kinase"", ""hepatocyte progenitor kinase-like/germinal center kinase-like kinase"""	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.2107C>T	2.37:g.102483026C>T	ENSP00000314363:p.Arg703Cys					MAP4K4_uc002tbc.2_Missense_Mutation_p.R781C|MAP4K4_uc002tbd.2_Missense_Mutation_p.R673C|MAP4K4_uc002tbe.2_Missense_Mutation_p.R619C|MAP4K4_uc002tbf.2_Missense_Mutation_p.R673C|MAP4K4_uc010yvy.1_Missense_Mutation_p.R696C|MAP4K4_uc002tbh.2_Missense_Mutation_p.R618C|MAP4K4_uc002tbi.2_Missense_Mutation_p.R503C|MAP4K4_uc010yvz.1_Missense_Mutation_p.R676C|MAP4K4_uc002tbk.2_Missense_Mutation_p.R158C|MAP4K4_uc002tbl.2_Translation_Start_Site	p.R703C	NM_145687	NP_663720	O95819	M4K4_HUMAN			18	2162	+			703					O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	37	c.2107C>T	CCDS56130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.19|18.19	3.569407|3.569407	0.65765|0.65765	2.57E-4|2.57E-4	0.0|0.0	ENSG00000071054|ENSG00000071054	ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699;ENST00000417294;ENST00000350878|ENST00000421882	T;T;T;T;T;T;T;T;T|.	0.16597|.	2.33;2.33;2.33;2.33;2.33;2.33;2.33;2.33;2.33|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76292|0.76292	0.3967|0.3967	M|M	0.78456|0.78456	2.415|2.415	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D;D;D|.	0.89917|.	0.999;0.997;0.994;0.997;0.998;1.0;1.0;0.998;1.0;1.0|.	P;P;P;P;P;D;D;P;D;D|.	0.85130|.	0.549;0.548;0.451;0.548;0.736;0.997;0.991;0.736;0.977;0.992|.	T|T	0.76337|0.76337	-0.2996|-0.2996	10|5	0.72032|.	D|.	0.01|.	.|.	15.6438|15.6438	0.77033|0.77033	0.1378:0.8622:0.0:0.0|0.1378:0.8622:0.0:0.0	.|.	676;696;502;503;618;703;672;619;672;781|.	B7Z388;B7Z3V5;E7EX83;C9J840;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948|.	.;.;.;.;.;M4K4_HUMAN;.;.;.;.|.	C|M	672;781;619;503;618;502;703;634;676|519	ENSP00000392830:R672C;ENSP00000313644:R781C;ENSP00000281111:R619C;ENSP00000303600:R503C;ENSP00000389752:R618C;ENSP00000387370:R502C;ENSP00000314363:R703C;ENSP00000409720:R634C;ENSP00000343658:R676C|.	ENSP00000303600:R503C|.	R|T	+|+	1|2	0|0	MAP4K4|MAP4K4	101849458|101849458	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.611000|1.611000	0.36879|0.36879	2.735000|2.735000	0.93741|0.93741	0.655000|0.655000	0.94253|0.94253	CGC|ACG		0.532	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	
WASH2P	375260	broad.mit.edu	37	2	114355998	114355998	+	RNA	SNP	C	C	G	rs17857355	byFrequency	TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr2:114355998C>G	ENST00000538033.2	+	0	2178							Q6VEQ5	WASH2_HUMAN	WAS protein family homolog 2 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)										CCAAGGTGGGCACTTGATGTC	0.612																																						uc002tkh.2																			0					0						c.(616-618)CAC>GAC		WAS protein family homolog 1																																						375260							g.chr2:114355998C>G			2q13	2010-07-08	2008-01-16	2008-01-16	ENSG00000146556	ENSG00000146556		"""WAS protein homologs"""	33145	pseudogene	pseudogene			"""family with sequence similarity 39, member B"""	FAM39B		18159949	Standard	NR_024077		Approved	MGC52000	uc002tkh.3	Q6VEQ5	OTTHUMG00000047822		2.37:g.114355998C>G						WASH2P_uc002tka.2_RNA|WASH2P_uc002tkb.2_RNA|WASH2P_uc002tkd.2_RNA	p.H206D	NM_182905	NP_878908					5	674	+									Missense_Mutation	SNP	ENST00000538033.2	37	c.616C>G																																																																																					0.612	WASH2P-002	KNOWN	mRNA_end_NF|basic	retained_intron	pseudogene	OTTHUMT00000467782.1	NM_198943	
ZAK	51776	broad.mit.edu	37	2	174131422	174131422	+	Missense_Mutation	SNP	G	G	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr2:174131422G>A	ENST00000375213.3	+	20	2425	c.2347G>A	c.(2347-2349)Gcc>Acc	p.A783T	MLK7-AS1_ENST00000422703.1_RNA|MLTK_ENST00000409176.2_Missense_Mutation_p.A783T|MLK7-AS1_ENST00000423106.2_RNA	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		783					activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)	p.A783S(1)									GCCATCTCCCGCCAAAACCAA	0.473																																						uc002uhz.2																			1	Substitution - Missense(1)		lung(1)	lung(3)|stomach(1)|ovary(1)|skin(1)	6						c.(2347-2349)GCC>ACC		MLK-related kinase isoform 1							18.0	22.0	20.0					2																	174131422		1866	4107	5973	SO:0001583	missense	51776				activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation	cytoplasm|nucleus	ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding	g.chr2:174131422G>A																												ENST00000375213.3:c.2347G>A	2.37:g.174131422G>A	ENSP00000364361:p.Ala783Thr					uc002uib.2_Intron	p.A783T	NM_016653	NP_057737	Q9NYL2	MLTK_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.176)		20	2547	+			783					B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Missense_Mutation	SNP	ENST00000375213.3	37	c.2347G>A	CCDS42777.1	.	.	.	.	.	.	.	.	.	.	G	10.63	1.403132	0.25291	.	.	ENSG00000091436	ENST00000409176;ENST00000375213	T;T	0.74526	-0.85;-0.85	6.08	4.28	0.50868	.	0.312255	0.36972	N	0.002317	T	0.59959	0.2232	N	0.24115	0.695	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.54689	-0.8256	10	0.49607	T	0.09	.	10.341	0.43877	0.2013:0.0:0.7987:0.0	.	783	Q9NYL2	MLTK_HUMAN	T	783	ENSP00000387259:A783T;ENSP00000364361:A783T	ENSP00000364361:A783T	A	+	1	0	AC013461.1	173839668	0.802000	0.28943	0.737000	0.30932	0.006000	0.05464	1.140000	0.31516	0.896000	0.36366	-0.229000	0.12294	GCC		0.473	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1		
MYO1B	4430	broad.mit.edu	37	2	192261188	192261188	+	Missense_Mutation	SNP	G	G	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr2:192261188G>A	ENST00000392318.3	+	21	2507	c.2260G>A	c.(2260-2262)Gcc>Acc	p.A754T	MYO1B_ENST00000339514.4_Missense_Mutation_p.A754T|MYO1B_ENST00000439065.2_Missense_Mutation_p.A28T|MYO1B_ENST00000304164.4_Missense_Mutation_p.A754T|MYO1B_ENST00000392316.1_Missense_Mutation_p.A754T	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	754	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			AAAGAGTTCCGCCTTAGTAAT	0.373																																						uc010fsg.2																			0				central_nervous_system(5)|large_intestine(2)|ovary(1)	8						c.(2260-2262)GCC>ACC		myosin IB isoform 1							148.0	145.0	146.0					2																	192261188		2203	4300	6503	SO:0001583	missense	4430					myosin complex	actin binding|ATP binding|calmodulin binding|motor activity	g.chr2:192261188G>A	L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"""Myosins / Myosin superfamily : Class I"""	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.2260G>A	2.37:g.192261188G>A	ENSP00000376132:p.Ala754Thr					MYO1B_uc002usq.2_Missense_Mutation_p.A754T|MYO1B_uc002usr.2_Missense_Mutation_p.A754T|MYO1B_uc002usu.2_Missense_Mutation_p.A28T	p.A754T	NM_001130158	NP_001123630	O43795	MYO1B_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)		21	2515	+			754			IQ 3.		O43794|Q7Z6L5	Missense_Mutation	SNP	ENST00000392318.3	37	c.2260G>A	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.636307	0.47049	.	.	ENSG00000128641	ENST00000339514;ENST00000392318;ENST00000304164;ENST00000392316;ENST00000439065	T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9	5.67	3.86	0.44501	.	0.110502	0.64402	N	0.000005	T	0.36166	0.0957	L	0.51422	1.61	0.46927	D	0.999255	B;B;B	0.27765	0.004;0.188;0.023	B;B;B	0.27500	0.006;0.08;0.026	T	0.10314	-1.0635	10	0.35671	T	0.21	.	10.8241	0.46622	0.1474:0.0:0.8526:0.0	.	28;754;754	E7EPB4;O43795;O43795-2	.;MYO1B_HUMAN;.	T	754;754;754;754;28	ENSP00000341903:A754T;ENSP00000376132:A754T;ENSP00000306382:A754T;ENSP00000376130:A754T;ENSP00000391442:A28T	ENSP00000306382:A754T	A	+	1	0	MYO1B	191969433	0.727000	0.28069	0.646000	0.29493	0.996000	0.88848	1.065000	0.30592	0.737000	0.32582	0.655000	0.94253	GCC		0.373	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223	
CRKL	1399	broad.mit.edu	37	22	21272527	21272527	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr22:21272527C>T	ENST00000354336.3	+	1	814	c.305C>T	c.(304-306)gCg>gTg	p.A102V		NM_005207.3	NP_005198.1	P46109	CRKL_HUMAN	v-crk avian sarcoma virus CT10 oncogene homolog-like	102	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of MAPKK activity (GO:0000186)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|heart development (GO:0007507)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|parathyroid gland development (GO:0060017)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|thymus development (GO:0048538)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	poly(A) RNA binding (GO:0044822)|SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)	14	all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176)			ATCGAGCCTGCGCCCAGGTAC	0.607																																					Pancreas(85;3 1441 23889 42519 42763)	uc002ztf.2																			0					0						c.(304-306)GCG>GTG		v-crk sarcoma virus CT10 oncogene homolog							29.0	29.0	29.0					22																	21272527		2203	4300	6503	SO:0001583	missense	1399				JNK cascade|Ras protein signal transduction	cytosol	protein tyrosine kinase activity|SH3/SH2 adaptor activity|signal transducer activity	g.chr22:21272527C>T		CCDS13785.1	22q11.21	2013-07-09	2013-07-09		ENSG00000099942	ENSG00000099942		"""SH2 domain containing"""	2363	protein-coding gene	gene with protein product		602007				8361759, 8798523	Standard	NM_005207		Approved		uc002ztf.2	P46109	OTTHUMG00000150807	ENST00000354336.3:c.305C>T	22.37:g.21272527C>T	ENSP00000346300:p.Ala102Val					CRKL_uc002ztg.1_RNA	p.A102V	NM_005207	NP_005198	P46109	CRKL_HUMAN	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176)		1	814	+	all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	102			SH2.		A8KA44|D3DX35	Missense_Mutation	SNP	ENST00000354336.3	37	c.305C>T	CCDS13785.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.222308	0.39300	.	.	ENSG00000099942	ENST00000354336	T	0.21031	2.03	5.37	5.37	0.77165	Src homology-3 domain (1);SH2 motif (2);	0.047237	0.85682	N	0.000000	T	0.09468	0.0233	N	0.01140	-0.99	0.80722	D	1	D	0.63046	0.992	P	0.45474	0.482	T	0.39840	-0.9594	10	0.11485	T	0.65	.	16.9579	0.86264	0.0:1.0:0.0:0.0	.	102	P46109	CRKL_HUMAN	V	102	ENSP00000346300:A102V	ENSP00000346300:A102V	A	+	2	0	CRKL	19602527	1.000000	0.71417	1.000000	0.80357	0.685000	0.39939	3.779000	0.55379	2.674000	0.91012	0.650000	0.86243	GCG		0.607	CRKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320158.1	NM_005207	
MTMR3	8897	broad.mit.edu	37	22	30413988	30413988	+	Missense_Mutation	SNP	A	A	G			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr22:30413988A>G	ENST00000401950.2	+	16	2089	c.1747A>G	c.(1747-1749)Acc>Gcc	p.T583A	MTMR3_ENST00000333027.3_Missense_Mutation_p.T583A|MTMR3_ENST00000351488.3_Missense_Mutation_p.T583A|CTA-85E5.10_ENST00000453743.2_RNA|MTMR3_ENST00000406629.1_Missense_Mutation_p.T583A|MTMR3_ENST00000323630.5_Missense_Mutation_p.T447A|CTA-85E5.10_ENST00000429350.1_RNA	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	583					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			CCCATCCCCAACCACCCCTGT	0.632																																						uc003agv.3																			0				breast(3)|ovary(1)|skin(1)	5						c.(1747-1749)ACC>GCC		myotubularin-related protein 3 isoform c							168.0	123.0	138.0					22																	30413988		2203	4300	6503	SO:0001583	missense	8897				phosphatidylinositol dephosphorylation	cytoplasm|membrane|membrane fraction|nucleus	metal ion binding|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity	g.chr22:30413988A>G	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.1747A>G	22.37:g.30413988A>G	ENSP00000384651:p.Thr583Ala					MTMR3_uc003agu.3_Missense_Mutation_p.T583A|MTMR3_uc003agw.3_Missense_Mutation_p.T583A	p.T583A	NM_021090	NP_066576	Q13615	MTMR3_HUMAN	OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)		16	2075	+			583					A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Missense_Mutation	SNP	ENST00000401950.2	37	c.1747A>G	CCDS13870.1	.	.	.	.	.	.	.	.	.	.	A	11.96	1.793730	0.31685	.	.	ENSG00000100330	ENST00000401950;ENST00000333027;ENST00000323630;ENST00000351488;ENST00000406629	D;D;D;D;D	0.92595	-2.87;-2.85;-3.07;-2.9;-2.85	5.93	3.79	0.43588	.	0.287412	0.40064	N	0.001197	D	0.85483	0.5707	L	0.28344	0.845	0.36601	D	0.874672	B;B;B	0.17852	0.024;0.001;0.024	B;B;B	0.16289	0.015;0.001;0.015	T	0.80070	-0.1536	10	0.40728	T	0.16	.	10.6642	0.45719	0.2651:0.0:0.0:0.7349	.	583;583;583	Q13615-3;Q13615;Q13615-2	.;MTMR3_HUMAN;.	A	583;583;447;583;583	ENSP00000384651:T583A;ENSP00000331649:T583A;ENSP00000318070:T447A;ENSP00000307271:T583A;ENSP00000384077:T583A	ENSP00000318070:T447A	T	+	1	0	MTMR3	28743988	1.000000	0.71417	0.667000	0.29798	0.970000	0.65996	3.937000	0.56575	0.472000	0.27344	-0.649000	0.03915	ACC		0.632	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090	
SLC5A4	6527	broad.mit.edu	37	22	32626981	32626981	+	Missense_Mutation	SNP	G	G	A	rs150200210	byFrequency	TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr22:32626981G>A	ENST00000266086.4	-	10	1114	c.1103C>T	c.(1102-1104)aCg>aTg	p.T368M	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	368					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CAGCACCATCGTGGGGTATGC	0.537																																						uc003ami.2																			0					0						c.(1102-1104)ACG>ATG		solute carrier family 5 (low affinity glucose		G	MET/THR	0,4406		0,0,2203	113.0	85.0	95.0		1103	-0.0	0.0	22	dbSNP_134	95	1,8599		0,1,4299	yes	missense	SLC5A4	NM_014227.2	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	368/660	32626981	1,13005	2203	4300	6503	SO:0001583	missense	6527				carbohydrate transport|sodium ion transport	integral to membrane	symporter activity	g.chr22:32626981G>A	U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"""Solute carriers"""	11039	protein-coding gene	gene with protein product			"""solute carrier family 5 (low affinity glucose cotransporter), member 4"""			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.1103C>T	22.37:g.32626981G>A	ENSP00000266086:p.Thr368Met						p.T368M	NM_014227	NP_055042	Q9NY91	SC5A4_HUMAN			10	1105	-			368			Extracellular (Potential).		O15279	Missense_Mutation	SNP	ENST00000266086.4	37	c.1103C>T	CCDS13903.1	.	.	.	.	.	.	.	.	.	.	.	6.813	0.519064	0.13005	0.0	1.16E-4	ENSG00000100191	ENST00000266086	D	0.88818	-2.43	4.86	-0.0133	0.13985	.	0.486097	0.25011	N	0.033833	T	0.82135	0.4971	L	0.55481	1.735	0.09310	N	1	B	0.12013	0.005	B	0.20184	0.028	T	0.71507	-0.4572	10	0.59425	D	0.04	.	2.9873	0.05972	0.4833:0.0:0.2191:0.2976	.	368	Q9NY91	SC5A4_HUMAN	M	368	ENSP00000266086:T368M	ENSP00000266086:T368M	T	-	2	0	SLC5A4	30956981	0.034000	0.19679	0.018000	0.16275	0.158000	0.22134	0.342000	0.19926	0.219000	0.20840	0.650000	0.86243	ACG		0.537	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227	
MKL1	57591	broad.mit.edu	37	22	40814904	40814904	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr22:40814904C>T	ENST00000355630.3	-	12	2128	c.1538G>A	c.(1537-1539)gGg>gAg	p.G513E	MKL1_ENST00000396617.3_Missense_Mutation_p.G513E|MKL1_ENST00000402042.1_Missense_Mutation_p.G463E|MKL1_ENST00000407029.1_Missense_Mutation_p.G513E	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	513					negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						CGCCCGCCCCCCAGGGCTCAG	0.672			T	RBM15	acute megakaryocytic leukemia																																	uc003ayv.1				Dom	yes		22	22q13	57591	T	megakaryoblastic leukemia (translocation) 1			L	RBM15		acute megakaryocytic leukemia		0				ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						c.(1537-1539)GGG>GAG		megakaryoblastic leukemia 1 protein							25.0	31.0	29.0					22																	40814904		2198	4294	6492	SO:0001583	missense	57591				positive regulation of transcription from RNA polymerase II promoter|smooth muscle cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	actin monomer binding|leucine zipper domain binding|nucleic acid binding|transcription coactivator activity	g.chr22:40814904C>T	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"""megakaryocytic acute leukemia"", ""myocardin-related transcription factor A"", ""basic, SAP and coiled-coil domain"""	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.1538G>A	22.37:g.40814904C>T	ENSP00000347847:p.Gly513Glu					MKL1_uc003ayw.1_Missense_Mutation_p.G513E|MKL1_uc010gye.1_Missense_Mutation_p.G513E|MKL1_uc010gyf.1_Missense_Mutation_p.G463E	p.G513E	NM_020831	NP_065882	Q969V6	MKL1_HUMAN			9	1745	-			513					Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	37	c.1538G>A	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	C	9.521	1.108320	0.20714	.	.	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029	T;T;T;T	0.44482	0.94;0.92;0.94;0.94	4.78	3.76	0.43208	.	0.588613	0.17030	N	0.189776	T	0.29556	0.0737	L	0.58101	1.795	0.09310	N	1	B;B;B	0.11235	0.003;0.004;0.001	B;B;B	0.12837	0.008;0.005;0.003	T	0.39522	-0.9610	10	0.02654	T	1	-20.307	3.7351	0.08507	0.1785:0.5814:0.1506:0.0895	.	463;513;513	B0QY83;E7ER32;Q969V6	.;.;MKL1_HUMAN	E	513;513;463;513	ENSP00000347847:G513E;ENSP00000379861:G513E;ENSP00000385584:G463E;ENSP00000385835:G513E	ENSP00000347847:G513E	G	-	2	0	MKL1	39144850	0.013000	0.17824	0.540000	0.28089	0.983000	0.72400	1.350000	0.34010	1.236000	0.43740	0.591000	0.81541	GGG		0.672	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831	
TEF	7008	broad.mit.edu	37	22	41790269	41790269	+	Silent	SNP	C	C	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr22:41790269C>A	ENST00000266304.4	+	3	761	c.645C>A	c.(643-645)ccC>ccA	p.P215P	TEF_ENST00000406644.3_Silent_p.P185P	NM_003216.3	NP_003207.1	Q10587	TEF_HUMAN	thyrotrophic embryonic factor	215	Pro-rich (proline/acidic region (PAR)).				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)	6						ACCTGAAGCCCCAGCCTATGA	0.547																																						uc003azy.2																			0				ovary(1)	1						c.(643-645)CCC>CCA		thyrotrophic embryonic factor isoform 1							51.0	48.0	49.0					22																	41790269		2203	4300	6503	SO:0001819	synonymous_variant	7008				rhythmic process	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr22:41790269C>A		CCDS14014.1, CCDS46716.1	22q13.2	2013-01-10			ENSG00000167074	ENSG00000167074		"""basic leucine zipper proteins"""	11722	protein-coding gene	gene with protein product		188595				7835883, 15665112	Standard	NM_001145398		Approved	KIAA1655	uc003azy.4	Q10587	OTTHUMG00000150968	ENST00000266304.4:c.645C>A	22.37:g.41790269C>A						TEF_uc003azx.2_Silent_p.P185P|TEF_uc011apa.1_Silent_p.P220P	p.P215P	NM_003216	NP_003207	Q10587	TEF_HUMAN			3	731	+			215			Pro-rich (proline/acidic region (PAR)).		B0QYS8|B2RC22|Q15729|Q7Z3J7|Q8IU94|Q96TG4	Silent	SNP	ENST00000266304.4	37	c.645C>A	CCDS14014.1	.	.	.	.	.	.	.	.	.	.	C	9.691	1.151825	0.21371	.	.	ENSG00000167074	ENST00000413942	.	.	.	6.08	-0.258	0.12975	.	0.000000	0.85682	D	0.000000	T	0.48960	0.1529	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48703	-0.9012	6	0.87932	D	0	-29.3794	1.3657	0.02200	0.1757:0.263:0.3401:0.2212	.	.	.	.	H	181	.	ENSP00000411170:P181H	P	+	2	0	TEF	40120215	0.135000	0.22499	1.000000	0.80357	0.994000	0.84299	-0.463000	0.06696	0.425000	0.26087	-0.175000	0.13238	CCC		0.547	TEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320692.1	NM_003216	
ZNF385D	79750	broad.mit.edu	37	3	21792472	21792472	+	De_novo_Start_OutOfFrame	SNP	G	G	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr3:21792472G>A	ENST00000281523.2	-	0	455				ZNF385D_ENST00000494118.1_Intron	NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D							nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						AGGCTGGCACGTAGAGCAGAG	0.557																																						uc003cce.2																			0				large_intestine(2)|skin(2)|ovary(1)	5						c.(-65--61)TACGT>TATGT		zinc finger protein 385D							52.0	46.0	48.0					3																	21792472		692	1591	2283			79750					nucleus	nucleic acid binding|zinc ion binding	g.chr3:21792472G>A	BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"""zinc finger protein 659"""	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.-64C>T	3.37:g.21792472G>A						ZNF385D_uc010hfb.1_Intron		NM_024697	NP_078973	Q9H6B1	Z385D_HUMAN			1	345	-									Translation_Start_Site	SNP	ENST00000281523.2	37	c.-63C>T	CCDS2636.1																																																																																				0.557	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697	
SUCLG2	8801	broad.mit.edu	37	3	67570993	67570993	+	Silent	SNP	G	G	C	rs533065054	byFrequency	TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr3:67570993G>C	ENST00000307227.5	-	5	510	c.483C>G	c.(481-483)tcC>tcG	p.S161S	SUCLG2_ENST00000493112.1_Silent_p.S161S|SUCLG2_ENST00000492795.1_Silent_p.S161S	NM_003848.3	NP_003839.2	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming, beta subunit	161	ATP-grasp.				cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP binding (GO:0005524)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	10		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)	GGCCATTGCAGGACCGGTCCA	0.502																																						uc003dna.3																			0				central_nervous_system(1)|skin(1)	2						c.(481-483)TCC>TCG		succinate-CoA ligase, GDP-forming beta subunit	Succinic acid(DB00139)						75.0	77.0	76.0					3																	67570993		1843	4091	5934	SO:0001819	synonymous_variant	8801				succinyl-CoA metabolic process|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|GTP binding|succinate-CoA ligase (GDP-forming) activity	g.chr3:67570993G>C	AF058954	CCDS43104.1, CCDS54605.1	3p14.3	2004-05-17			ENSG00000172340	ENSG00000172340	6.2.1.4		11450	protein-coding gene	gene with protein product		603922				9765291	Standard	NM_001177599		Approved		uc003dna.4	Q96I99	OTTHUMG00000158740	ENST00000307227.5:c.483C>G	3.37:g.67570993G>C						SUCLG2_uc010hob.2_Silent_p.S42S	p.S161S	NM_003848	NP_003839	Q96I99	SUCB2_HUMAN		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	5	511	-		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)	161			ATP-grasp.		C9JVT2|O95195|Q6NUH7|Q86VX8|Q8WUQ1	Silent	SNP	ENST00000307227.5	37	c.483C>G	CCDS43104.1	.	.	.	.	.	.	.	.	.	.	G	10.05	1.243188	0.22796	.	.	ENSG00000172340	ENST00000460567	.	.	.	5.7	3.85	0.44370	.	.	.	.	.	T	0.54498	0.1862	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48703	-0.9012	4	.	.	.	.	5.4577	0.16600	0.2136:0.0:0.6338:0.1525	.	.	.	.	V	53	.	.	L	-	1	2	SUCLG2	67653683	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	0.697000	0.25556	0.705000	0.31890	0.650000	0.86243	CTG		0.502	SUCLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351993.1	NM_003848	
IFT122	55764	broad.mit.edu	37	3	129214370	129214370	+	Missense_Mutation	SNP	G	G	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr3:129214370G>A	ENST00000348417.2	+	18	2205	c.2128G>A	c.(2128-2130)Gcc>Acc	p.A710T	IFT122_ENST00000296266.3_Missense_Mutation_p.A761T|IFT122_ENST00000431818.2_Missense_Mutation_p.A560T|IFT122_ENST00000507564.1_Missense_Mutation_p.A702T|IFT122_ENST00000440957.2_Missense_Mutation_p.A501T|IFT122_ENST00000513932.1_3'UTR|IFT122_ENST00000504021.1_Missense_Mutation_p.A586T|IFT122_ENST00000347300.2_Missense_Mutation_p.A651T|IFT122_ENST00000349441.2_Missense_Mutation_p.A599T	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	710					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						CCATGAGGCCGCCAAACTGTA	0.512																																						uc003emm.2																			0				ovary(1)|skin(1)	2						c.(2128-2130)GCC>ACC		WD repeat domain 10 isoform 2							108.0	94.0	99.0					3																	129214370		2203	4300	6503	SO:0001583	missense	55764				camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium		g.chr3:129214370G>A	AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	13556	protein-coding gene	gene with protein product		606045	"""WD repeat domain 10"", ""intraflagellar transport 122 homolog (Chlamydomonas)"""	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.2128G>A	3.37:g.129214370G>A	ENSP00000324005:p.Ala710Thr					IFT122_uc003eml.2_Missense_Mutation_p.A761T|IFT122_uc003emn.2_Missense_Mutation_p.A651T|IFT122_uc003emo.2_Missense_Mutation_p.A599T|IFT122_uc003emp.2_Missense_Mutation_p.A560T|IFT122_uc010htc.2_Missense_Mutation_p.A702T|IFT122_uc011bky.1_Missense_Mutation_p.A501T|IFT122_uc003emq.2_Missense_Mutation_p.A550T|IFT122_uc003emr.2_Missense_Mutation_p.A462T|IFT122_uc011bla.1_Missense_Mutation_p.A483T|IFT122_uc010hte.2_Intron|IFT122_uc003ems.2_Missense_Mutation_p.A91T|IFT122_uc011bkx.1_Missense_Mutation_p.A550T|IFT122_uc010htd.1_Missense_Mutation_p.A189T	p.A710T	NM_052989	NP_443715	Q9HBG6	IF122_HUMAN			18	2334	+			710					B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	37	c.2128G>A	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	G	35	5.463880	0.96257	.	.	ENSG00000163913	ENST00000347300;ENST00000296266;ENST00000507564;ENST00000454840;ENST00000431818;ENST00000504021;ENST00000349441;ENST00000348417;ENST00000446384;ENST00000440957;ENST00000509522;ENST00000507221	D;D;D;D;T;D;D;D;T	0.82344	-1.6;-1.6;-1.6;-1.6;0.62;-1.6;-1.6;-1.6;0.67	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	D	0.93281	0.7859	M	0.91768	3.24	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.83275	0.996;0.986;0.995;0.979;0.985;0.979;0.991;0.99;0.996	D	0.94406	0.7627	10	0.87932	D	0	-22.0944	19.2895	0.94093	0.0:0.0:1.0:0.0	.	501;702;97;586;550;599;651;710;761	E9PDG2;E7EQF4;B3KT43;B4DEY9;B4DPW7;Q9BTY4;Q9HBG6-3;Q9HBG6;G3XAB1	.;.;.;.;.;.;.;IF122_HUMAN;.	T	651;761;702;651;560;586;599;710;550;501;207;72	ENSP00000323973:A651T;ENSP00000296266:A761T;ENSP00000425536:A702T;ENSP00000410946:A560T;ENSP00000422179:A586T;ENSP00000324165:A599T;ENSP00000324005:A710T;ENSP00000401569:A501T;ENSP00000424727:A207T	ENSP00000296266:A761T	A	+	1	0	IFT122	130697060	1.000000	0.71417	0.991000	0.47740	0.984000	0.73092	9.452000	0.97615	2.607000	0.88179	0.655000	0.94253	GCC		0.512	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262	
GRK7	131890	broad.mit.edu	37	3	141497201	141497201	+	Silent	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr3:141497201C>T	ENST00000264952.2	+	1	212	c.75C>T	c.(73-75)tgC>tgT	p.C25C		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	25					protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						CCTCGGACTGCGACAGCAAAG	0.701																																						uc011bnd.1																			0				lung(2)|stomach(1)|ovary(1)|skin(1)	5						c.(73-75)TGC>TGT		G-protein-coupled receptor kinase 7 precursor							31.0	38.0	36.0					3																	141497201		2202	4297	6499	SO:0001819	synonymous_variant	131890				visual perception	membrane	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity	g.chr3:141497201C>T		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.75C>T	3.37:g.141497201C>T							p.C25C	NM_139209	NP_631948	Q8WTQ7	GRK7_HUMAN			1	159	+			25						Silent	SNP	ENST00000264952.2	37	c.75C>T	CCDS3120.1																																																																																				0.701	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209	
TM4SF1	4071	broad.mit.edu	37	3	149093335	149093335	+	Missense_Mutation	SNP	C	C	G			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr3:149093335C>G	ENST00000305366.3	-	3	625	c.308G>C	c.(307-309)gGa>gCa	p.G103A	TM4SF1-AS1_ENST00000484046.1_RNA|TM4SF1-AS1_ENST00000496491.1_RNA|TM4SF1_ENST00000472441.1_Missense_Mutation_p.G14A	NM_014220.2	NP_055035.1	P30408	T4S1_HUMAN	transmembrane 4 L six family member 1	103						integral component of plasma membrane (GO:0005887)				endometrium(3)|large_intestine(1)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			GTAGCCAGATCCTGCAATTCC	0.507																																						uc003exb.1																			0					0						c.(307-309)GGA>GCA		transmembrane 4 superfamily member 1							86.0	72.0	77.0					3																	149093335		2203	4300	6503	SO:0001583	missense	4071					integral to plasma membrane		g.chr3:149093335C>G	M90657	CCDS3143.1	3q21-q25	2005-03-21	2005-03-21		ENSG00000169908	ENSG00000169908			11853	protein-coding gene	gene with protein product		191155	"""transmembrane 4 superfamily member 1"""	M3S1		1565644	Standard	NM_014220		Approved	L6	uc003exb.1	P30408	OTTHUMG00000159597	ENST00000305366.3:c.308G>C	3.37:g.149093335C>G	ENSP00000304277:p.Gly103Ala					TM4SF1_uc003exc.1_Missense_Mutation_p.G14A	p.G103A	NM_014220	NP_055035	P30408	T4S1_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)		3	542	-			103			Helical; (Probable).		Q6IB51	Missense_Mutation	SNP	ENST00000305366.3	37	c.308G>C	CCDS3143.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.240378	0.58995	.	.	ENSG00000169908	ENST00000305366;ENST00000472441;ENST00000383054	T;T	0.41065	1.01;1.01	5.77	4.88	0.63580	.	0.000000	0.64402	D	0.000001	T	0.56978	0.2022	M	0.91818	3.245	0.80722	D	1	P;B	0.37663	0.604;0.45	B;B	0.38954	0.286;0.214	T	0.66586	-0.5886	10	0.54805	T	0.06	-15.0578	16.6578	0.85233	0.0:0.8701:0.1299:0.0	.	14;103	C9J611;P30408	.;T4S1_HUMAN	A	103;14;103	ENSP00000304277:G103A;ENSP00000417084:G14A	ENSP00000304277:G103A	G	-	2	0	TM4SF1	150576025	0.910000	0.30920	0.946000	0.38457	0.941000	0.58515	2.667000	0.46808	1.393000	0.46605	0.655000	0.94253	GGA		0.507	TM4SF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356368.1		
ADAMTS3	9508	broad.mit.edu	37	4	73184402	73184402	+	Missense_Mutation	SNP	C	C	G	rs80237783		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr4:73184402C>G	ENST00000286657.4	-	10	1408	c.1372G>C	c.(1372-1374)Gat>Cat	p.D458H		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	458	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AAAGGGTCATCAAGGAGACAG	0.343																																					NSCLC(168;1941 2048 2918 13048 43078)	uc003hgk.1																			0				ovary(1)|lung(1)	2						c.(1372-1374)GAT>CAT		ADAM metallopeptidase with thrombospondin type 1							88.0	82.0	84.0					4																	73184402		2203	4300	6503	SO:0001583	missense	9508				collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding	g.chr4:73184402C>G	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"""ADAM metallopeptidases with thrombospondin type 1 motif"""	219	protein-coding gene	gene with protein product		605011	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"""			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.1372G>C	4.37:g.73184402C>G	ENSP00000286657:p.Asp458His						p.D458H	NM_014243	NP_055058	O15072	ATS3_HUMAN	Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)		10	1409	-			458			Peptidase M12B.		A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	37	c.1372G>C	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.755940	0.89843	.	.	ENSG00000156140	ENST00000286657	D	0.89050	-2.46	5.83	5.83	0.93111	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	D	0.95993	0.8695	M	0.91459	3.21	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96006	0.8997	10	0.66056	D	0.02	.	20.1338	0.98010	0.0:1.0:0.0:0.0	.	458	O15072	ATS3_HUMAN	H	458	ENSP00000286657:D458H	ENSP00000286657:D458H	D	-	1	0	ADAMTS3	73403266	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.743000	0.85020	2.770000	0.95276	0.655000	0.94253	GAT		0.343	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2		
MRPL1	65008	broad.mit.edu	37	4	78804480	78804480	+	Silent	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr4:78804480C>T	ENST00000315567.8	+	3	557	c.228C>T	c.(226-228)ccC>ccT	p.P76P	MRPL1_ENST00000506674.1_3'UTR	NM_020236.3	NP_064621.3	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1	76					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.P76P(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)	17						AAGCATATCCCTATATGGAAG	0.323																																						uc003hku.2																			1	Substitution - coding silent(1)		lung(1)		0						c.(226-228)CCC>CCT		mitochondrial ribosomal protein L1 precursor							70.0	72.0	71.0					4																	78804480		2203	4300	6503	SO:0001819	synonymous_variant	65008						RNA binding	g.chr4:78804480C>T	AB049474	CCDS3583.2	4q21.1	2012-09-13			ENSG00000169288	ENSG00000169288		"""Mitochondrial ribosomal proteins / large subunits"""	14275	protein-coding gene	gene with protein product		611821					Standard	NM_020236		Approved	BM022	uc003hku.2	Q9BYD6	OTTHUMG00000130200	ENST00000315567.8:c.228C>T	4.37:g.78804480C>T						MRPL1_uc010iji.1_5'UTR	p.P76P	NM_020236	NP_064621	Q9BYD6	RM01_HUMAN			3	426	+			76					A6NG03|Q4W5B8|Q6IAG4|Q96BW3|Q9H793|Q9NRL5	Silent	SNP	ENST00000315567.8	37	c.228C>T	CCDS3583.2																																																																																				0.323	MRPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252518.3	NM_020236	
UNC5C	8633	broad.mit.edu	37	4	96090460	96090460	+	Silent	SNP	G	G	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr4:96090460G>A	ENST00000453304.1	-	16	3069	c.2721C>T	c.(2719-2721)agC>agT	p.S907S		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	907	Death.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		CTGCCAGCATGCTCAGGTTTC	0.483																																						uc003htp.1																			0				ovary(3)|pancreas(1)	4						c.(2719-2721)AGC>AGT		unc5C precursor							164.0	154.0	157.0					4																	96090460		2203	4300	6503	SO:0001819	synonymous_variant	8633				apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity	g.chr4:96090460G>A	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"""Immunoglobulin superfamily / I-set domain containing"""	12569	protein-coding gene	gene with protein product		603610	"""unc5 (C.elegans homolog) c"""			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.2721C>T	4.37:g.96090460G>A						uc003hto.2_5'Flank	p.S907S	NM_003728	NP_003719	O95185	UNC5C_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)	16	2875	-		Hepatocellular(203;0.114)	907			Cytoplasmic (Potential).|Death.		Q8IUT0	Silent	SNP	ENST00000453304.1	37	c.2721C>T	CCDS3643.1																																																																																				0.483	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
NAF1	92345	broad.mit.edu	37	4	164054388	164054388	+	Silent	SNP	A	A	G			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr4:164054388A>G	ENST00000274054.2	-	7	1144	c.951T>C	c.(949-951)gaT>gaC	p.D317D	NAF1_ENST00000422287.2_Silent_p.D317D|NAF1_ENST00000509434.1_Intron	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	317					pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				TCTCTTTTTCATCATCACTAA	0.333																																						uc003iqj.2																			0				ovary(2)	2						c.(949-951)GAT>GAC		nuclear assembly factor 1 homolog isoform a							105.0	100.0	102.0					4																	164054388		2201	4300	6501	SO:0001819	synonymous_variant	92345				rRNA processing|snRNA pseudouridine synthesis	cytoplasm|nucleus|small nucleolar ribonucleoprotein complex	protein binding|snoRNA binding	g.chr4:164054388A>G		CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"""nuclear assembly factor 1 homolog (S. cerevisiae)"""			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.951T>C	4.37:g.164054388A>G						NAF1_uc010iqw.1_Silent_p.D317D	p.D317D	NM_138386	NP_612395	Q96HR8	NAF1_HUMAN			7	1145	-	all_hematologic(180;0.166)	Prostate(90;0.109)	317					D3DP28|E9PAZ2	Silent	SNP	ENST00000274054.2	37	c.951T>C	CCDS3803.1																																																																																				0.333	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386	
TENM3	55714	broad.mit.edu	37	4	183574978	183574978	+	Missense_Mutation	SNP	T	T	C			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr4:183574978T>C	ENST00000511685.1	+	6	1166	c.1043T>C	c.(1042-1044)tTt>tCt	p.F348S	TENM3_ENST00000406950.2_Missense_Mutation_p.F348S			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	348					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										AATGACACATTTGAGAATGGA	0.418																																						uc003ivd.1																			0					0						c.(1042-1044)TTT>TCT		odz, odd Oz/ten-m homolog 3							119.0	114.0	116.0					4																	183574978		1930	4144	6074	SO:0001583	missense	55714				signal transduction	integral to membrane		g.chr4:183574978T>C	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.1043T>C	4.37:g.183574978T>C	ENSP00000424226:p.Phe348Ser						p.F348S	NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)	5	1080	+		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)	348			Extracellular (Potential).		Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	c.1043T>C	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.419476	0.83559	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.86230	-2.09;-2.09	5.95	5.95	0.96441	.	.	.	.	.	D	0.89763	0.6809	L	0.50333	1.59	0.53005	D	0.999967	P	0.40431	0.717	P	0.52217	0.693	D	0.89576	0.3817	9	0.51188	T	0.08	.	16.4323	0.83853	0.0:0.0:0.0:1.0	.	348	Q9P273	TEN3_HUMAN	S	348	ENSP00000424226:F348S;ENSP00000385276:F348S	ENSP00000385276:F348S	F	+	2	0	ODZ3	183811972	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.833000	0.69349	2.281000	0.76405	0.528000	0.53228	TTT		0.418	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
SH3RF2	153769	broad.mit.edu	37	5	145393517	145393517	+	Missense_Mutation	SNP	C	C	T	rs563187260	byFrequency	TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr5:145393517C>T	ENST00000511217.1	+	4	1004	c.952C>T	c.(952-954)Cgc>Tgc	p.R318C	SH3RF2_ENST00000359120.4_Missense_Mutation_p.R318C			Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	318					negative regulation of phosphatase activity (GO:0010923)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)|zinc ion binding (GO:0008270)	p.R318C(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCTTCAGGGCGCCATATGGT	0.577													C|||	10	0.00199681	0.0	0.0	5008	,	,		20277	0.0		0.0	False		,,,				2504	0.0102					uc003lnt.2																			1	Substitution - Missense(1)		haematopoietic_and_lymphoid_tissue(1)	ovary(1)|skin(1)	2						c.(952-954)CGC>TGC		SH3 domain containing ring finger 2							118.0	114.0	115.0					5																	145393517		2203	4300	6503	SO:0001583	missense	153769						ligase activity|protein phosphatase 1 binding|zinc ion binding	g.chr5:145393517C>T	AL833297	CCDS4280.1	5q32	2013-01-09	2011-11-04	2011-11-04	ENSG00000156463	ENSG00000156463		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26299	protein-coding gene	gene with protein product	"""heart protein phosphatase 1-binding protein"", ""POSH-eliminating RING protein"""	613377	"""protein phosphatase 1, regulatory subunit 39"""	PPP1R39		22128169	Standard	NM_152550		Approved	FLJ23654, RNF158, Hepp1, POSHER	uc003lnt.3	Q8TEC5	OTTHUMG00000129685	ENST00000511217.1:c.952C>T	5.37:g.145393517C>T	ENSP00000424497:p.Arg318Cys					SH3RF2_uc011dbl.1_Missense_Mutation_p.R318C	p.R318C	NM_152550	NP_689763	Q8TEC5	SH3R2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		5	1190	+			318					A8K961|Q08AM9|Q6GMR9|Q8N5S8|Q96LP8	Missense_Mutation	SNP	ENST00000511217.1	37	c.952C>T	CCDS4280.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.564879	0.86439	.	.	ENSG00000156463	ENST00000359120;ENST00000511217	T;T	0.09073	3.02;3.02	5.47	5.47	0.80525	.	0.149558	0.48286	D	0.000192	T	0.12347	0.0300	N	0.19112	0.55	0.49130	D	0.999757	D	0.71674	0.998	P	0.51170	0.661	T	0.02378	-1.1168	10	0.87932	D	0	-13.6685	19.6825	0.95970	0.0:1.0:0.0:0.0	.	318	Q8TEC5	SH3R2_HUMAN	C	318	ENSP00000352028:R318C;ENSP00000424497:R318C	ENSP00000352028:R318C	R	+	1	0	SH3RF2	145373710	1.000000	0.71417	0.908000	0.35775	0.916000	0.54674	3.642000	0.54367	2.727000	0.93392	0.591000	0.81541	CGC		0.577	SH3RF2-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372804.1	NM_152550	
FRK	2444	broad.mit.edu	37	6	116265439	116265439	+	Frame_Shift_Del	DEL	C	C	-			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr6:116265439delC	ENST00000606080.1	-	6	1554	c.1108delG	c.(1108-1110)gtafs	p.V370fs	FRK_ENST00000538210.1_Frame_Shift_Del_p.V228fs	NM_002031.2	NP_002022.1	P42685	FRK_HUMAN	fyn-related Src family tyrosine kinase	370	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|skin(1)|urinary_tract(1)	27		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)	Regorafenib(DB08896)	AAATCTGCTACTTTGTAGATA	0.388																																						uc003pwi.1																			0				ovary(3)|lung(3)	6						c.(1108-1110)GTAfs		fyn-related kinase							75.0	74.0	75.0					6																	116265439		2203	4300	6503	SO:0001589	frameshift_variant	2444				negative regulation of cell proliferation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding	g.chr6:116265439delC	U00803	CCDS5103.1	6q21-q22.3	2014-06-25	2014-06-25		ENSG00000111816	ENSG00000111816	2.7.10.1	"""SH2 domain containing"""	3955	protein-coding gene	gene with protein product		606573	"""PTK5 protein tyrosine kinase 5"", ""fyn-related kinase"""	PTK5		7510261	Standard	NM_002031		Approved	RAK, GTK	uc003pwi.1	P42685	OTTHUMG00000015424	ENST00000606080.1:c.1108delG	6.37:g.116265439delC	ENSP00000476145:p.Val370fs						p.V370fs	NM_002031	NP_002022	P42685	FRK_HUMAN		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)	6	1555	-		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)	370			Protein kinase.		B4DY49|Q13128|Q9NTR5	Frame_Shift_Del	DEL	ENST00000606080.1	37	c.1108delG	CCDS5103.1																																																																																				0.388	FRK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041924.2	NM_002031	
NKAIN2	154215	broad.mit.edu	37	6	124979424	124979424	+	Silent	SNP	T	T	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr6:124979424T>A	ENST00000368417.1	+	4	426	c.366T>A	c.(364-366)ccT>ccA	p.P122P	NKAIN2_ENST00000368416.1_Silent_p.P122P|NKAIN2_ENST00000545433.1_Silent_p.P107P|NKAIN2_ENST00000546092.1_Intron	NM_001040214.1	NP_001035304.1	Q5VXU1	NKAI2_HUMAN	Na+/K+ transporting ATPase interacting 2	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|large_intestine(3)|lung(12)|skin(2)	19				GBM - Glioblastoma multiforme(226;0.104)		CAGTGACACCTGCCCCAGACT	0.502																																						uc003pzo.2																			0					0						c.(364-366)CCT>CCA		T-cell lymphoma breakpoint-associated target 1							160.0	133.0	142.0					6																	124979424		2203	4300	6503	SO:0001819	synonymous_variant	154215					integral to membrane|plasma membrane		g.chr6:124979424T>A	AB070452	CCDS34526.1	6q21	2008-02-05	2007-10-04	2007-10-04	ENSG00000188580	ENSG00000188580		"""Na+/K+ transporting ATPase interacting"""	16443	protein-coding gene	gene with protein product		609758	"""T-cell lymphoma breakpoint associated target 1"""	TCBA1		17606467	Standard	XM_005266833		Approved	FAM77B	uc003pzo.3	Q5VXU1	OTTHUMG00000015500	ENST00000368417.1:c.366T>A	6.37:g.124979424T>A						NKAIN2_uc003pzn.1_Silent_p.P122P|NKAIN2_uc003pzp.2_Silent_p.P121P|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Silent_p.P32P	p.P122P	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN		GBM - Glioblastoma multiforme(226;0.104)	4	643	+			122					Q8IYR4|Q8TF67	Silent	SNP	ENST00000368417.1	37	c.366T>A	CCDS34526.1																																																																																				0.502	NKAIN2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042057.1	NM_001040214	
NOX3	50508	broad.mit.edu	37	6	155743923	155743923	+	Missense_Mutation	SNP	C	C	T	rs200781503		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr6:155743923C>T	ENST00000159060.2	-	10	1315	c.1213G>A	c.(1213-1215)Gtt>Att	p.V405I		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	405					detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		CCCGCGGCAACGCACACACAC	0.537																																						uc003qqm.2																			0				ovary(1)	1						c.(1213-1215)GTT>ATT		NADPH oxidase 3							137.0	134.0	135.0					6																	155743923		2203	4300	6503	SO:0001583	missense	50508						electron carrier activity|flavin adenine dinucleotide binding|iron ion binding	g.chr6:155743923C>T	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.1213G>A	6.37:g.155743923C>T	ENSP00000159060:p.Val405Ile						p.V405I	NM_015718	NP_056533	Q9HBY0	NOX3_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)	10	1316	-		Breast(66;0.0183)	405			Helical; (Potential).		Q9HBJ9	Missense_Mutation	SNP	ENST00000159060.2	37	c.1213G>A	CCDS5250.1	.	.	.	.	.	.	.	.	.	.	c	5.479	0.273409	0.10403	.	.	ENSG00000074771	ENST00000159060	T	0.60672	0.17	5.81	-4.5	0.03493	Ferric reductase, NAD binding (1);	0.609935	0.16441	N	0.214295	T	0.16041	0.0386	N	0.12920	0.275	0.22581	N	0.998963	B	0.10296	0.003	B	0.08055	0.003	T	0.13818	-1.0495	10	0.29301	T	0.29	-1.7004	14.2651	0.66113	0.0:0.5284:0.0:0.4716	.	405	Q9HBY0	NOX3_HUMAN	I	405	ENSP00000159060:V405I	ENSP00000159060:V405I	V	-	1	0	NOX3	155785615	0.997000	0.39634	0.033000	0.17914	0.007000	0.05969	0.414000	0.21164	-1.169000	0.02772	-1.507000	0.00952	GTT		0.537	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1		
PLG	5340	broad.mit.edu	37	6	161134138	161134138	+	Silent	SNP	C	C	T	rs558599800		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr6:161134138C>T	ENST00000308192.9	+	5	591	c.528C>T	c.(526-528)tgC>tgT	p.C176C	PLG_ENST00000462918.1_3'UTR	NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	176	Kringle 1. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	ATGACTACTGCGACATTCTTG	0.473																																						uc003qtm.3																			0				skin(3)|ovary(1)	4						c.(526-528)TGC>TGT		plasminogen	Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)						144.0	139.0	141.0					6																	161134138		2203	4300	6503	SO:0001819	synonymous_variant	5340				extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity	g.chr6:161134138C>T	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.528C>T	6.37:g.161134138C>T							p.C176C	NM_000301	NP_000292	P00747	PLMN_HUMAN		OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	5	591	+			176			Kringle 1.		Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	c.528C>T	CCDS5279.1																																																																																				0.473	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
TBX20	57057	broad.mit.edu	37	7	35242129	35242129	+	Silent	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr7:35242129C>T	ENST00000408931.3	-	8	1783	c.1257G>A	c.(1255-1257)ccG>ccA	p.P419P		NM_001077653.2|NM_001166220.1	NP_001071121.1|NP_001159692.1	Q9UMR3	TBX20_HUMAN	T-box 20	419					aortic valve morphogenesis (GO:0003180)|atrial septum morphogenesis (GO:0060413)|blood circulation (GO:0008015)|cardiac chamber formation (GO:0003207)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|dorsal/ventral pattern formation (GO:0009953)|embryonic heart tube elongation (GO:0036306)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion formation (GO:0003272)|endocardial cushion morphogenesis (GO:0003203)|endoderm formation (GO:0001706)|foramen ovale closure (GO:0035922)|heart looping (GO:0001947)|lateral mesoderm formation (GO:0048370)|muscle contraction (GO:0006936)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|outflow tract septum morphogenesis (GO:0003148)|patterning of blood vessels (GO:0001569)|pericardium morphogenesis (GO:0003344)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary valve formation (GO:0003193)|pulmonary vein morphogenesis (GO:0060577)|tricuspid valve development (GO:0003175)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P419P(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(9)|prostate(1)|skin(1)|stomach(1)	18						GATGGTATCGCGGCATGTGGA	0.522																																						uc011kas.1																			1	Substitution - coding silent(1)		lung(1)	central_nervous_system(1)	1						c.(1255-1257)CCG>CCA		T-box transcription factor TBX20							32.0	33.0	32.0					7																	35242129		1933	4132	6065	SO:0001819	synonymous_variant	57057					nucleus	DNA binding	g.chr7:35242129C>T	AJ237589	CCDS43568.1	7p14.3	2014-09-17			ENSG00000164532	ENSG00000164532		"""T-boxes"""	11598	protein-coding gene	gene with protein product		606061				10936053	Standard	NM_001077653		Approved		uc011kas.2	Q9UMR3	OTTHUMG00000099411	ENST00000408931.3:c.1257G>A	7.37:g.35242129C>T							p.P419P	NM_001077653	NP_001071121	Q9UMR3	TBX20_HUMAN			8	1268	-			419					A4D1Y6|Q000T4|Q0IJ70|Q0VAS1|Q9Y2N5	Silent	SNP	ENST00000408931.3	37	c.1257G>A	CCDS43568.1																																																																																				0.522	TBX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216870.2	NM_020417	
NPC1L1	29881	broad.mit.edu	37	7	44560418	44560418	+	Splice_Site	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr7:44560418C>T	ENST00000289547.4	-	14	3137	c.3082G>A	c.(3082-3084)Ggc>Agc	p.G1028S	NPC1L1_ENST00000381160.3_Splice_Site_p.G1028S|NPC1L1_ENST00000546276.1_Splice_Site_p.G982S	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	1028					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	GCTGCCAGGCCGCTGCAAGAA	0.572																																						uc003tlb.2																			0				ovary(3)|central_nervous_system(1)|skin(1)	5						c.(3082-3084)GGC>AGC		Niemann-Pick C1-like protein 1 isoform 1	Ezetimibe(DB00973)						83.0	78.0	80.0					7																	44560418		2203	4300	6503	SO:0001630	splice_region_variant	29881				cholesterol biosynthetic process|intestinal cholesterol absorption|lipoprotein metabolic process	apical plasma membrane|cytoplasmic vesicle membrane|integral to membrane	hedgehog receptor activity|protein binding	g.chr7:44560418C>T		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"""NPC1 (Niemann-Pick disease, type C1, gene)-like 1"""			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.3081-1G>A	7.37:g.44560418C>T						NPC1L1_uc003tlc.2_Missense_Mutation_p.G1028S|NPC1L1_uc011kbw.1_Missense_Mutation_p.G982S|NPC1L1_uc003tla.2_Missense_Mutation_p.G31S	p.G1028S	NM_013389	NP_037521	Q9UHC9	NPCL1_HUMAN			14	3138	-			1028			Cytoplasmic (Potential).		A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Missense_Mutation	SNP	ENST00000289547.4	37	c.3082G>A	CCDS5491.1	.	.	.	.	.	.	.	.	.	.	C	17.12	3.307651	0.60305	.	.	ENSG00000015520	ENST00000289547;ENST00000381160;ENST00000546276	D;D;D	0.97870	-3.84;-4.39;-4.58	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	D	0.98692	0.9561	M	0.85859	2.78	0.50813	D	0.999899	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;0.999;1.0	D	0.99636	1.0987	10	0.66056	D	0.02	-30.9264	15.2951	0.73898	0.0:1.0:0.0:0.0	.	982;1028;1028;1028	B7ZLE6;Q17RV5;D3DVK9;Q9UHC9	.;.;.;NPCL1_HUMAN	S	1028;1028;982	ENSP00000289547:G1028S;ENSP00000370552:G1028S;ENSP00000438033:G982S	ENSP00000289547:G1028S	G	-	1	0	NPC1L1	44526943	0.988000	0.35896	0.925000	0.36789	0.194000	0.23727	4.296000	0.59055	2.214000	0.71695	0.462000	0.41574	GGC		0.572	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389	Missense_Mutation
CACNA2D1	781	broad.mit.edu	37	7	81594957	81594957	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr7:81594957C>T	ENST00000356253.5	-	32	2818	c.2563G>A	c.(2563-2565)Gat>Aat	p.D855N	CACNA2D1_ENST00000356860.3_Missense_Mutation_p.D843N|CACNA2D1_ENST00000535308.1_Missense_Mutation_p.D55N			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	855					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.D843N(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	AACCCACCATCATCCAGAATC	0.368																																						uc003uhr.1																			1	Substitution - Missense(1)		lung(1)	ovary(5)|pancreas(1)	6						c.(2527-2529)GAT>AAT		calcium channel, voltage-dependent, alpha	Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)						153.0	136.0	142.0					7																	81594957		2203	4300	6503	SO:0001583	missense	781					voltage-gated calcium channel complex	metal ion binding	g.chr7:81594957C>T	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2563G>A	7.37:g.81594957C>T	ENSP00000348589:p.Asp855Asn					CACNA2D1_uc011kgy.1_Missense_Mutation_p.D55N	p.D843N	NM_000722	NP_000713	P54289	CA2D1_HUMAN			32	2783	-			855			Extracellular (Potential).		Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	37	c.2527G>A		.	.	.	.	.	.	.	.	.	.	C	13.72	2.321307	0.41096	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253;ENST00000535308	D;D;D	0.82344	-1.6;-1.6;-1.6	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.89245	0.6660	M	0.74647	2.275	0.45354	D	0.998349	D;D	0.89917	1.0;1.0	D;D	0.75484	0.984;0.986	D	0.85496	0.1188	10	0.05620	T	0.96	-24.6422	18.672	0.91514	0.0:1.0:0.0:0.0	.	55;843	B7Z658;P54289-2	.;.	N	843;862;855;55	ENSP00000349320:D843N;ENSP00000348589:D855N;ENSP00000443124:D55N	ENSP00000284088:D862N	D	-	1	0	CACNA2D1	81432893	1.000000	0.71417	1.000000	0.80357	0.724000	0.41520	5.561000	0.67339	2.407000	0.81776	0.591000	0.81541	GAT		0.368	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			
ZNF804B	219578	broad.mit.edu	37	7	88965893	88965893	+	Silent	SNP	A	A	G			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr7:88965893A>G	ENST00000333190.4	+	4	4206	c.3597A>G	c.(3595-3597)ccA>ccG	p.P1199P		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1199							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AGACAGTTCCAGTTCACCAGC	0.502										HNSCC(36;0.09)																												uc011khi.1																			0				ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11						c.(3595-3597)CCA>CCG		zinc finger protein 804B							162.0	131.0	142.0					7																	88965893		2203	4300	6503	SO:0001819	synonymous_variant	219578					intracellular	zinc ion binding	g.chr7:88965893A>G	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.3597A>G	7.37:g.88965893A>G		HNSCC(36;0.09)					p.P1199P	NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	STAD - Stomach adenocarcinoma(171;0.0513)		4	4135	+	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		1199					B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	37	c.3597A>G	CCDS5613.1																																																																																				0.502	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
MUC17	140453	broad.mit.edu	37	7	100680859	100680859	+	Silent	SNP	G	G	A	rs534149898		TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr7:100680859G>A	ENST00000306151.4	+	3	6226	c.6162G>A	c.(6160-6162)acG>acA	p.T2054T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2054	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCAGCACTACGCTTGTGGTCA	0.493													G|||	1	0.000199681	0.0	0.0	5008	,	,		26212	0.0		0.0	False		,,,				2504	0.001					uc003uxp.1																			0				ovary(14)|skin(8)|breast(3)|lung(2)	27						c.(6160-6162)ACG>ACA		mucin 17 precursor							172.0	164.0	166.0					7																	100680859		2203	4300	6503	SO:0001819	synonymous_variant	140453					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity	g.chr7:100680859G>A	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.6162G>A	7.37:g.100680859G>A						MUC17_uc010lho.1_RNA	p.T2054T	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN			3	6215	+	Lung NSC(181;0.136)|all_lung(186;0.182)		2054			Extracellular (Potential).|32.|59 X approximate tandem repeats.|Ser-rich.		O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	c.6162G>A	CCDS34711.1																																																																																				0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
TFEC	22797	broad.mit.edu	37	7	115590932	115590932	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr7:115590932C>T	ENST00000265440.7	-	6	691	c.511G>A	c.(511-513)Gat>Aat	p.D171N	TFEC_ENST00000457268.1_Missense_Mutation_p.D104N|TFEC_ENST00000484212.1_Missense_Mutation_p.D261N|TFEC_ENST00000320239.7_Missense_Mutation_p.D142N|TFEC_ENST00000393485.1_Missense_Mutation_p.D142N	NM_012252.3	NP_036384.1	O14948	TFEC_HUMAN	transcription factor EC	171	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cellular response to heat (GO:0034605)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|kidney(1)|large_intestine(5)|lung(13)|prostate(2)|skin(1)|urinary_tract(2)	25			STAD - Stomach adenocarcinoma(10;0.00878)			ACTCACGGATCATTAGACTTT	0.323																																						uc003vhj.1																			0				large_intestine(1)	1						c.(511-513)GAT>AAT		transcription factor EC isoform a							41.0	44.0	43.0					7																	115590932		2203	4299	6502	SO:0001583	missense	22797					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity	g.chr7:115590932C>T	D43945	CCDS5762.1, CCDS34738.1, CCDS59076.1	7q31.2	2013-05-21			ENSG00000105967	ENSG00000105967		"""Basic helix-loop-helix proteins"""	11754	protein-coding gene	gene with protein product		604732				9256061	Standard	NM_012252		Approved	TCFEC, TFECL, bHLHe34	uc003vhj.2	O14948	OTTHUMG00000023518	ENST00000265440.7:c.511G>A	7.37:g.115590932C>T	ENSP00000265440:p.Asp171Asn					TFEC_uc003vhk.1_Missense_Mutation_p.D142N|TFEC_uc003vhl.3_Missense_Mutation_p.D142N|TFEC_uc011kmw.1_Missense_Mutation_p.D261N	p.D171N	NM_012252	NP_036384	O14948	TFEC_HUMAN	STAD - Stomach adenocarcinoma(10;0.00878)		6	695	-			171			Helix-loop-helix motif.		B2R8X5|Q5H9U8|Q709A4|Q8N6J9	Missense_Mutation	SNP	ENST00000265440.7	37	c.511G>A	CCDS5762.1	.	.	.	.	.	.	.	.	.	.	C	33	5.219540	0.95139	.	.	ENSG00000105967	ENST00000265440;ENST00000457268;ENST00000320239;ENST00000393485;ENST00000484212	D;D;D;D;D	0.97870	-4.58;-4.58;-4.58;-4.58;-4.58	5.19	5.19	0.71726	Helix-loop-helix DNA-binding (5);	0.101254	0.64402	D	0.000003	D	0.98229	0.9414	L	0.58510	1.815	0.80722	D	1	D;D;D;D	0.89917	0.996;0.999;1.0;0.999	D;D;D;D	0.73708	0.96;0.969;0.981;0.962	D	0.99636	1.0987	10	0.87932	D	0	.	16.9012	0.86114	0.0:1.0:0.0:0.0	.	261;142;142;171	B7Z757;O14948-3;O14948-2;O14948	.;.;.;TFEC_HUMAN	N	171;104;142;142;261	ENSP00000265440:D171N;ENSP00000387650:D104N;ENSP00000318676:D142N;ENSP00000377125:D142N;ENSP00000417432:D261N	ENSP00000265440:D171N	D	-	1	0	TFEC	115378168	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.710000	0.84655	2.409000	0.81822	0.655000	0.94253	GAT		0.323	TFEC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059839.4	NM_012252	
CDKN2A	1029	broad.mit.edu	37	9	21971029	21971029	+	Nonsense_Mutation	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr9:21971029C>T	ENST00000304494.5	-	2	599	c.329G>A	c.(328-330)tGg>tAg	p.W110*	CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.W59*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000579755.1_Silent_p.L124L|CDKN2A_ENST00000530628.2_Silent_p.L124L|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.W110*|CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.W59*|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.W59*|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.W59*|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.W110*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.W110*|CDKN2A_ENST00000361570.3_Silent_p.L165L|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.W59*	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	110					cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(44)|p.W110*(13)|p.L165L(2)|p.H83fs*2(2)|p.D105fs*8(1)|p.0(1)|p.A68fs*3(1)|p.R107fs*33(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CAGACGGCCCCAGGCATCGCG	0.731		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																												uc003zpk.2		17																	1380	Whole gene deletion(1316)|Unknown(44)|Substitution - Nonsense(13)|Deletion - Frameshift(5)|Substitution - coding silent(2)	p.0?(1112)|p.W110*(38)|p.?(13)|p.H83fs*2(2)|p.W110fs*9(1)|p.D105fs*8(1)|p.A68fs*3(1)|p.R107fs*33(1)|p.W110fs*36(1)|p.W110C(1)	haematopoietic_and_lymphoid_tissue(283)|skin(177)|central_nervous_system(167)|lung(148)|urinary_tract(91)|bone(74)|soft_tissue(57)|oesophagus(52)|upper_aerodigestive_tract(52)|pleura(51)|pancreas(37)|ovary(36)|kidney(32)|breast(32)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(9)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3678						c.(328-330)TGG>TAG		cyclin-dependent kinase inhibitor 2A isoform 1							18.0	20.0	20.0					9																	21971029		2198	4294	6492	SO:0001587	stop_gained	1029	Uveal_Melanoma_Familial|Familial_Malignant_Melanoma_and_Tumors_of_the_Nervous_System|Hereditary_Melanoma			cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	g.chr9:21971029C>T	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"""cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"""	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.329G>A	9.37:g.21971029C>T	ENSP00000307101:p.Trp110*	HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)				MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Silent_p.L165L	p.W110*	NM_000077	NP_000068	P42771	CD2A1_HUMAN		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)	2	541	-		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)	110			ANK 4.		A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Nonsense_Mutation	SNP	ENST00000304494.5	37	c.329G>A	CCDS6510.1	.	.	.	.	.	.	.	.	.	.	C	37	6.223773	0.97390	.	.	ENSG00000147889	ENST00000304494;ENST00000446177	.	.	.	5.93	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.50632	D	0.999889	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-14.7138	7.5355	0.27708	0.2896:0.6341:0.0:0.0762	.	.	.	.	X	110	.	ENSP00000307101:W110X	W	-	2	0	CDKN2A	21961029	0.001000	0.12720	0.995000	0.50966	0.918000	0.54935	0.120000	0.15647	2.808000	0.96608	0.655000	0.94253	TGG		0.731	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077	
IKBKAP	8518	broad.mit.edu	37	9	111659518	111659518	+	Missense_Mutation	SNP	C	C	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr9:111659518C>A	ENST00000374647.5	-	23	2718	c.2411G>T	c.(2410-2412)aGt>aTt	p.S804I	IKBKAP_ENST00000537196.1_Missense_Mutation_p.S455I	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	804					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CAGGTAGACACTGCTGGTAAC	0.463																																						uc004bdm.3																			0				ovary(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	7						c.(2410-2412)AGT>ATT		inhibitor of kappa light polypeptide gene							199.0	170.0	180.0					9																	111659518		2203	4300	6503	SO:0001583	missense	8518				immune response|protein complex assembly|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding|signal transducer activity	g.chr9:111659518C>A	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.2411G>T	9.37:g.111659518C>A	ENSP00000363779:p.Ser804Ile					IKBKAP_uc004bdl.2_Missense_Mutation_p.S455I|IKBKAP_uc011lwc.1_Missense_Mutation_p.S690I|IKBKAP_uc010mtq.2_Missense_Mutation_p.S455I	p.S804I	NM_003640	NP_003631	O95163	ELP1_HUMAN			23	2931	-			804					Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	37	c.2411G>T	CCDS6773.1	.	.	.	.	.	.	.	.	.	.	C	8.702	0.909885	0.17833	.	.	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.27256	1.68;1.68	5.37	-1.59	0.08453	.	0.711491	0.15013	N	0.285435	T	0.20333	0.0489	M	0.66297	2.02	0.09310	N	1	B	0.14438	0.01	B	0.18263	0.021	T	0.24190	-1.0167	10	0.41790	T	0.15	0.3458	2.0735	0.03618	0.1106:0.1781:0.3133:0.398	.	804	O95163	ELP1_HUMAN	I	804;455	ENSP00000363779:S804I;ENSP00000439367:S455I	ENSP00000363779:S804I	S	-	2	0	IKBKAP	110699339	0.000000	0.05858	0.000000	0.03702	0.126000	0.20510	-0.222000	0.09190	-0.130000	0.11599	-0.251000	0.11542	AGT		0.463	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
EHMT1	79813	broad.mit.edu	37	9	140638536	140638536	+	Silent	SNP	C	C	A			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chr9:140638536C>A	ENST00000460843.1	+	6	1191	c.1164C>A	c.(1162-1164)gcC>gcA	p.A388A	EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000462484.1_Silent_p.A388A|EHMT1_ENST00000334856.6_Silent_p.A357A	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	388			A -> T (in dbSNP:rs11137198).		chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		CTGATCGCGCCCAGAAGGTAT	0.567																																						uc011mfc.1																			0				breast(2)|pancreas(1)	3						c.(1162-1164)GCC>GCA		euchromatic histone-lysine N-methyltransferase 1							60.0	63.0	62.0					9																	140638536		2203	4300	6503	SO:0001819	synonymous_variant	79813				DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding	g.chr9:140638536C>A	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.1164C>A	9.37:g.140638536C>A						EHMT1_uc004coa.2_Silent_p.A388A|EHMT1_uc004cob.1_Silent_p.A357A	p.A388A	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)	6	1201	+	all_cancers(76;0.164)		388					B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	37	c.1164C>A	CCDS7050.2																																																																																				0.567	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
OTUD6A	139562	broad.mit.edu	37	X	69283226	69283226	+	Silent	SNP	C	C	G			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chrX:69283226C>G	ENST00000338352.2	+	1	886	c.852C>G	c.(850-852)ctC>ctG	p.L284L		NM_207320.1	NP_997203.1	Q7L8S5	OTU6A_HUMAN	OTU deubiquitinase 6A	284					protein K11-linked deubiquitination (GO:0035871)|protein K27-linked deubiquitination (GO:1990167)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)		ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|skin(3)|urinary_tract(1)	23						GGGGCGTGCTCCCGCGTCTCC	0.637																																						uc004dxu.1																			0				lung(1)|skin(1)	2						c.(850-852)CTC>CTG		OTU domain containing 6A							13.0	10.0	11.0					X																	69283226		2135	4177	6312	SO:0001819	synonymous_variant	139562							g.chrX:69283226C>G	AK098697	CCDS14395.1	Xq13.1	2014-02-24	2014-02-24			ENSG00000189401		"""OTU domain containing"""	32312	protein-coding gene	gene with protein product		300714	"""OTU domain containing 6A"""			23827681	Standard	NM_207320		Approved	FLJ25831, HSHIN6, DUBA2	uc004dxu.1	Q7L8S5		ENST00000338352.2:c.852C>G	X.37:g.69283226C>G							p.L284L	NM_207320	NP_997203	Q7L8S5	OTU6A_HUMAN			1	886	+			284					B2RPB7	Silent	SNP	ENST00000338352.2	37	c.852C>G	CCDS14395.1																																																																																				0.637	OTUD6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358763.1	NM_207320	
GLUD2	2747	broad.mit.edu	37	X	120181603	120181603	+	Missense_Mutation	SNP	C	C	T			TCGA-32-2638-01A-01D-1495-08	TCGA-32-2638-10A-01D-1495-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	1e103221-ab46-4a5c-9b96-5e34f0d49fc2	1f0b3a10-8f1e-432c-9c39-cdcb8855a4c2	g.chrX:120181603C>T	ENST00000328078.1	+	1	142	c.65C>T	c.(64-66)gCg>gTg	p.A22V		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	22					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						CTGGGCTCCGCGGCCAACCAC	0.786																																						uc004eto.2																			0				pancreas(1)	1						c.(64-66)GCG>GTG		glutamate dehydrogenase 2 precursor	L-Glutamic Acid(DB00142)|NADH(DB00157)						10.0	12.0	11.0					X																	120181603		1543	2953	4496	SO:0001583	missense	2747				glutamate biosynthetic process|glutamate catabolic process	mitochondrial matrix	ADP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|leucine binding	g.chrX:120181603C>T	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"""glutamate dehydrogenase pseudogene 1"""	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.65C>T	X.37:g.120181603C>T	ENSP00000327589:p.Ala22Val						p.A22V	NM_012084	NP_036216	P49448	DHE4_HUMAN			1	142	+			22					B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	37	c.65C>T	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.510395	0.44660	.	.	ENSG00000182890	ENST00000328078	D	0.96619	-4.07	1.18	1.18	0.20946	.	.	.	.	.	D	0.91164	0.7217	N	0.08118	0	0.27689	N	0.946164	D	0.67145	0.996	P	0.54372	0.75	D	0.85316	0.1081	9	0.13470	T	0.59	.	5.4646	0.16635	0.0:1.0:0.0:0.0	.	22	P49448	DHE4_HUMAN	V	22	ENSP00000327589:A22V	ENSP00000327589:A22V	A	+	2	0	GLUD2	120009284	.	.	0.002000	0.10522	0.007000	0.05969	.	.	0.908000	0.36671	0.372000	0.22366	GCG		0.786	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084	
