#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	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
GAB3	139716	broad.mit.edu	37	X	153927719	153927719	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chrX:153927719G>A	ENST00000369575.3	-	6	1223	c.1192C>T	c.(1192-1194)Ccc>Tcc	p.P398S	GAB3_ENST00000496390.1_5'UTR|GAB3_ENST00000424127.2_Missense_Mutation_p.P399S	NM_001081573.1|NM_080612.2	NP_001075042.1|NP_542179.1	Q8WWW8	GAB3_HUMAN	GRB2-associated binding protein 3	398					macrophage differentiation (GO:0030225)					NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)	25	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CCAGCCTGGGGGCTCATGGGC	0.552																																						ENST00000369575.3																			0				NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)	25						c.(1192-1194)Ccc>Tcc		GRB2-associated binding protein 3							79.0	73.0	75.0					X																	153927719		2203	4300	6503	SO:0001583	missense	139716							g.chrX:153927719G>A	AY057989	CCDS14760.1, CCDS48198.1, CCDS65357.1	Xq28	2013-01-10			ENSG00000160219	ENSG00000160219		"""Pleckstrin homology (PH) domain containing"""	17515	protein-coding gene	gene with protein product	"""DOS/Gab family member 3"", ""Gab3 scaffolding protein"""	300482				11739737	Standard	XM_005274648		Approved		uc004fmk.1	Q8WWW8	OTTHUMG00000024245	ENST00000369575.3:c.1192C>T	X.37:g.153927719G>A	ENSP00000358588:p.Pro398Ser					GAB3_ENST00000496390.1_5'UTR|GAB3_ENST00000424127.2_Missense_Mutation_p.P399S	p.P398S	NM_001081573.1|NM_080612.2	NP_001075042.1|NP_542179.1	Q8WWW8	GAB3_HUMAN			6	1223	-	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)		398					A6NHF8|E9PB44	Missense_Mutation	SNP	ENST00000369575.3	37	c.1192C>T	CCDS14760.1	.	.	.	.	.	.	.	.	.	.	G	19.90	3.912474	0.72983	.	.	ENSG00000160219	ENST00000369575;ENST00000369568;ENST00000424127	T;T;T	0.38722	1.12;1.12;1.12	5.85	5.85	0.93711	.	0.288312	0.38381	N	0.001716	T	0.65933	0.2739	M	0.74881	2.28	0.52099	D	0.999949	D;D;D	0.89917	1.0;0.984;1.0	D;P;D	0.85130	0.997;0.779;0.997	T	0.69087	-0.5238	10	0.87932	D	0	-6.9968	16.3807	0.83460	0.0:0.0:1.0:0.0	.	399;399;398	A6NHF8;E9PB44;Q8WWW8	.;.;GAB3_HUMAN	S	398;399;399	ENSP00000358588:P398S;ENSP00000358581:P399S;ENSP00000399588:P399S	ENSP00000358581:P399S	P	-	1	0	GAB3	153580913	1.000000	0.71417	0.990000	0.47175	0.566000	0.35808	6.526000	0.73799	2.474000	0.83562	0.529000	0.55759	CCC		0.552	GAB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061192.2	NM_001081573		5	68	0	0	0	0.184627	0	5	68				
NPIPA5	100288332	broad.mit.edu	37	16	15457701	15457701	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr16:15457701G>A	ENST00000360151.4	-	8	867	c.868C>T	c.(868-870)Ctc>Ttc	p.L290F		NM_001277325.1	NP_001264254.1	E9PKD4	NPIA5_HUMAN	nuclear pore complex interacting protein family, member A5	290	Pro-rich.							p.L290F(2)									AGGGGAGTGAGCAGACACTCG	0.562																																						ENST00000360151.4																			2	Substitution - Missense(2)	p.L290F(2)	kidney(2)								c.(868-870)Ctc>Ttc		nuclear pore complex interacting protein family, member A5																																				SO:0001583	missense	100288332							g.chr16:15457701G>A		CCDS59264.1	16p13.11	2013-06-11			ENSG00000183793	ENSG00000183793			41980	protein-coding gene	gene with protein product							Standard	NM_001277325		Approved			E9PKD4	OTTHUMG00000166305	ENST00000360151.4:c.868C>T	16.37:g.15457701G>A	ENSP00000433597:p.Leu290Phe						p.L290F	NM_001277325.1	NP_001264254.1					8	867	-								Q0P618	Missense_Mutation	SNP	ENST00000360151.4	37	c.868C>T	CCDS59264.1	.	.	.	.	.	.	.	.	.	.	.	4.044	0.005714	0.07866	.	.	ENSG00000183793	ENST00000360151	T	0.56275	0.47	.	.	.	.	.	.	.	.	T	0.52338	0.1728	M	0.62723	1.935	0.09310	N	1	.	.	.	.	.	.	T	0.44742	-0.9308	4	0.36615	T	0.2	.	.	.	.	.	.	.	.	F	290	ENSP00000433597:L290F	ENSP00000433597:L290F	L	-	1	0	RP11-82O18.1	15365202	.	.	.	.	.	.	.	.	.	.	.	.	CTC		0.562	NPIPA5-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389069.1			4	84	0	0	0	0.184627	0	4	84				
TAC1	6863	broad.mit.edu	37	7	97363056	97363056	+	Missense_Mutation	SNP	G	G	C			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr7:97363056G>C	ENST00000319273.5	+	3	442	c.145G>C	c.(145-147)Gag>Cag	p.E49Q	TAC1_ENST00000346867.4_Missense_Mutation_p.E49Q|TAC1_ENST00000350485.4_Missense_Mutation_p.E49Q	NM_003182.2	NP_003173.1	P20366	TKN1_HUMAN	tachykinin, precursor 1	49					associative learning (GO:0008306)|cell-cell signaling (GO:0007267)|detection of abiotic stimulus (GO:0009582)|inflammatory response (GO:0006954)|insemination (GO:0007320)|long-term memory (GO:0007616)|negative regulation of heart rate (GO:0010459)|neuropeptide signaling pathway (GO:0007218)|positive regulation of action potential (GO:0045760)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of corticosterone secretion (GO:2000854)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of ossification (GO:0045778)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of saliva secretion (GO:0046878)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of blood pressure (GO:0008217)|response to hormone (GO:0009725)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)|tachykinin receptor signaling pathway (GO:0007217)	axon (GO:0030424)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				large_intestine(4)|lung(6)|urinary_tract(1)	11	all_cancers(62;3.95e-09)|all_epithelial(64;1.1e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0358)|all_lung(186;0.0384)					GGAGCCCTTTGAGCATCTTCT	0.597																																						ENST00000319273.5																			0				large_intestine(4)|lung(6)|urinary_tract(1)	11						c.(145-147)Gag>Cag		tachykinin, precursor 1	Bacitracin(DB00626)						91.0	84.0	86.0					7																	97363056		2203	4300	6503	SO:0001583	missense	6863				detection of abiotic stimulus|elevation of cytosolic calcium ion concentration|insemination|neuropeptide signaling pathway|synaptic transmission|tachykinin receptor signaling pathway	extracellular space		g.chr7:97363056G>C	M68907	CCDS5649.1, CCDS5650.1, CCDS5651.1	7q21-q22	2013-02-26	2008-01-17		ENSG00000006128	ENSG00000006128		"""Endogenous ligands"""	11517	protein-coding gene	gene with protein product	"""substance K"", ""substance P"", ""neurokinin 1"", ""neurokinin 2"", ""neuromedin L"", ""neurokinin alpha"", ""neuropeptide K"", ""neuropeptide gamma"", ""preprotachykinin"""	162320	"""tachykinin, precursor 1 (substance K, substance P, neurokinin 1, neurokinin 2, neuromedin L, neurokinin alpha, neuropeptide K, neuropeptide gamma)"""	TAC2, NKNA		1708336	Standard	NM_003182		Approved	NPK	uc003uop.4	P20366	OTTHUMG00000154069	ENST00000319273.5:c.145G>C	7.37:g.97363056G>C	ENSP00000321106:p.Glu49Gln					TAC1_ENST00000346867.4_Missense_Mutation_p.E49Q|TAC1_ENST00000350485.4_Missense_Mutation_p.E49Q	p.E49Q	NM_003182.2	NP_003173.1	P20366	TKN1_HUMAN			3	442	+	all_cancers(62;3.95e-09)|all_epithelial(64;1.1e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0358)|all_lung(186;0.0384)		49					O60600|O60601|Q00072|Q53GH4|Q549V0|Q549V1|Q549V2|Q6FHM1	Missense_Mutation	SNP	ENST00000319273.5	37	c.145G>C	CCDS5649.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.705728	0.89018	.	.	ENSG00000006128	ENST00000319273;ENST00000350485;ENST00000346867	.	.	.	5.47	5.47	0.80525	.	0.095249	0.64402	D	0.000001	T	0.74344	0.3704	L	0.47716	1.5	0.44268	D	0.997123	D;D;D;D	0.71674	0.989;0.998;0.996;0.997	D;D;D;D	0.80764	0.979;0.994;0.986;0.99	T	0.75368	-0.3342	9	0.66056	D	0.02	-18.2334	17.1936	0.86887	0.0:0.0:1.0:0.0	.	49;49;49;49	P20366-4;P20366-3;P20366-2;P20366	.;.;.;TKN1_HUMAN	Q	49	.	ENSP00000321106:E49Q	E	+	1	0	TAC1	97200992	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.213000	0.72194	2.736000	0.93811	0.561000	0.74099	GAG		0.597	TAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333696.1	NM_003182		12	70	0	0	0	0.411799	0	12	70				
CHST2	9435	broad.mit.edu	37	3	142840289	142840289	+	Missense_Mutation	SNP	T	T	G			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr3:142840289T>G	ENST00000309575.3	+	2	2015	c.631T>G	c.(631-633)Tcc>Gcc	p.S211A		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	211					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						GGACGCCGTTTCCCTGCAGGG	0.602																																						ENST00000309575.3																			0				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						c.(631-633)Tcc>Gcc		carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2							62.0	76.0	71.0					3																	142840289		2195	4295	6490	SO:0001583	missense	9435				inflammatory response|multicellular organismal development|N-acetylglucosamine metabolic process|sulfur compound metabolic process	integral to membrane|intrinsic to Golgi membrane|trans-Golgi network	N-acetylglucosamine 6-O-sulfotransferase activity	g.chr3:142840289T>G	BC042160	CCDS3129.1	3q24	2007-03-14			ENSG00000175040	ENSG00000175040		"""Sulfotransferases, membrane-bound"""	1970	protein-coding gene	gene with protein product		603798				10049591	Standard	NM_004267		Approved	C6ST	uc003evm.3	Q9Y4C5	OTTHUMG00000159351	ENST00000309575.3:c.631T>G	3.37:g.142840289T>G	ENSP00000307911:p.Ser211Ala						p.S211A	NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN			2	2015	+			211					D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	37	c.631T>G	CCDS3129.1	.	.	.	.	.	.	.	.	.	.	T	16.27	3.075949	0.55646	.	.	ENSG00000175040	ENST00000309575	T	0.81247	-1.47	4.45	4.45	0.53987	Sulfotransferase domain (1);	0.000000	0.64402	U	0.000001	T	0.77864	0.4194	L	0.46885	1.475	0.45025	D	0.998048	B	0.29301	0.241	B	0.40602	0.334	T	0.71192	-0.4665	10	0.12103	T	0.63	-19.7688	13.8553	0.63522	0.0:0.0:0.0:1.0	.	211	Q9Y4C5	CHST2_HUMAN	A	211	ENSP00000307911:S211A	ENSP00000307911:S211A	S	+	1	0	CHST2	144322979	0.994000	0.37717	0.966000	0.40874	0.987000	0.75469	3.347000	0.52200	1.859000	0.53934	0.334000	0.21626	TCC		0.602	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267		14	123	0	0	0	0.457914	0	14	123				
OR6C75	390323	broad.mit.edu	37	12	55759683	55759683	+	Silent	SNP	A	A	G			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr12:55759683A>G	ENST00000343399.3	+	1	789	c.789A>G	c.(787-789)agA>agG	p.R263R		NM_001005497.1	NP_001005497.1	A6NL08	O6C75_HUMAN	olfactory receptor, family 6, subfamily C, member 75	263						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)	25						CTTCTGCCAGAGAAAGGGTGA	0.423																																						ENST00000343399.3																			0				endometrium(2)|large_intestine(5)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)	25						c.(787-789)agA>agG		olfactory receptor, family 6, subfamily C, member 75							91.0	80.0	84.0					12																	55759683		2203	4300	6503	SO:0001819	synonymous_variant	390323				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr12:55759683A>G		CCDS31820.1	12q13.2	2013-09-23			ENSG00000187857	ENSG00000187857		"""GPCR / Class A : Olfactory receptors"""	31304	protein-coding gene	gene with protein product							Standard	NM_001005497		Approved		uc010spk.2	A6NL08	OTTHUMG00000169886	ENST00000343399.3:c.789A>G	12.37:g.55759683A>G							p.R263R	NM_001005497.1	NP_001005497.1	A6NL08	O6C75_HUMAN			1	789	+			263						Silent	SNP	ENST00000343399.3	37	c.789A>G	CCDS31820.1																																																																																				0.423	OR6C75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406418.1			10	91	0	0	0	0.411799	0	10	91				
LOC645752	645752	broad.mit.edu	37	15	78217315	78217315	+	lincRNA	SNP	T	T	C	rs2004373	byFrequency	TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr15:78217315T>C	ENST00000565869.1	+	0	706				RP11-114H24.2_ENST00000567226.1_RNA																							AGTGGTTGTCTCAGGGCTACT	0.527													t|||	722	0.144169	0.1036	0.1744	5008	,	,		17278	0.1091		0.2406	False		,,,				2504	0.1145					ENST00000567226.1																			0																																																			645752							g.chr15:78217315T>C																													15.37:g.78217315T>C														0	187	-									RNA	SNP	ENST00000565869.1	37																																																																																						0.527	RP11-114H24.7-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000421587.1			3	69	0	0	0	0.115264	0	3	69				
RASGEF1B	153020	broad.mit.edu	37	4	82355860	82355860	+	Missense_Mutation	SNP	A	A	C			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr4:82355860A>C	ENST00000264400.2	-	11	1284	c.1133T>G	c.(1132-1134)aTc>aGc	p.I378S	RASGEF1B_ENST00000335927.7_Missense_Mutation_p.I336S|RASGEF1B_ENST00000509081.1_Missense_Mutation_p.I377S	NM_152545.1	NP_689758.1	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B	378	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			endometrium(2)|kidney(5)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	26						AATATCTTTGATTAAGAGACT	0.363																																						ENST00000509081.1																			0				endometrium(2)|kidney(5)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	26						c.(1129-1131)aTc>aGc		RasGEF domain family, member 1B							63.0	59.0	61.0					4																	82355860		2203	4300	6503	SO:0001583	missense	153020				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity	g.chr4:82355860A>C	AK056257	CCDS34022.1, CCDS75151.1, CCDS75152.1	4q21.21	2013-09-24				ENSG00000138670			24881	protein-coding gene	gene with protein product		614532				12488504	Standard	XM_005262776		Approved	GPIG4, FLJ31695	uc003hmi.1	Q0VAM2		ENST00000264400.2:c.1133T>G	4.37:g.82355860A>C	ENSP00000264400:p.Ile378Ser					RASGEF1B_ENST00000264400.2_Missense_Mutation_p.I378S|RASGEF1B_ENST00000335927.7_Missense_Mutation_p.I336S	p.I377S			Q0VAM2	RGF1B_HUMAN			11	1351	-			378			Ras-GEF.		Q0VAM1|Q4W5L7|Q4W5M3|Q96MY8	Missense_Mutation	SNP	ENST00000264400.2	37	c.1130T>G	CCDS34022.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.128842	0.77549	.	.	ENSG00000138670	ENST00000509081;ENST00000264400;ENST00000335927;ENST00000504863	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	4.62	4.62	0.57501	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine-nucleotide exchange factor, conserved site (1);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.53498	0.1800	M	0.73598	2.24	0.80722	D	1	D;D;D	0.58970	0.98;0.98;0.984	P;P;D	0.66497	0.907;0.865;0.944	T	0.59490	-0.7445	10	0.87932	D	0	.	13.8491	0.63485	1.0:0.0:0.0:0.0	.	336;377;378	Q0VAM2-2;Q0VAM2-3;Q0VAM2	.;.;RGF1B_HUMAN	S	377;378;336;223	ENSP00000425393:I377S;ENSP00000264400:I378S;ENSP00000338437:I336S;ENSP00000426929:I223S	ENSP00000264400:I378S	I	-	2	0	RASGEF1B	82574884	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.685000	0.91246	1.954000	0.56735	0.477000	0.44152	ATC		0.363	RASGEF1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362830.1	NM_152545		3	25	0	0	0	0.115264	0	3	25				
OR8K1	390157	broad.mit.edu	37	11	56113847	56113847	+	Missense_Mutation	SNP	G	G	T			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr11:56113847G>T	ENST00000279783.2	+	1	427	c.333G>T	c.(331-333)gaG>gaT	p.E111D		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	111						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					CATTCTTTGAGATTTTCATCA	0.408										HNSCC(65;0.19)																												ENST00000279783.2																			0				large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						c.(331-333)gaG>gaT		olfactory receptor, family 8, subfamily K, member 1							181.0	182.0	182.0					11																	56113847		2201	4296	6497	SO:0001583	missense	390157				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:56113847G>T	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"""GPCR / Class A : Olfactory receptors"""	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.333G>T	11.37:g.56113847G>T	ENSP00000279783:p.Glu111Asp	HNSCC(65;0.19)					p.E111D	NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN			1	427	+	Esophageal squamous(21;0.00448)		111					B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	37	c.333G>T	CCDS31528.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.094672	0.36952	.	.	ENSG00000150261	ENST00000279783	T	0.00551	6.65	5.0	1.76	0.24704	GPCR, rhodopsin-like superfamily (1);	0.561532	0.15800	N	0.244009	T	0.00241	0.0007	N	0.01048	-1.04	0.09310	N	1	B	0.24186	0.099	B	0.12837	0.008	T	0.43048	-0.9415	10	0.45353	T	0.12	-6.9851	8.1077	0.30896	0.0:0.2251:0.269:0.506	.	111	Q8NGG5	OR8K1_HUMAN	D	111	ENSP00000279783:E111D	ENSP00000279783:E111D	E	+	3	2	OR8K1	55870423	0.000000	0.05858	0.671000	0.29857	0.967000	0.64934	-0.374000	0.07484	0.450000	0.26774	0.549000	0.68633	GAG		0.408	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		32	279	1	0	1.36615e-20	0.769981	1.90285e-20	32	279				
CDH5	1003	broad.mit.edu	37	16	66420782	66420782	+	Missense_Mutation	SNP	G	G	T			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr16:66420782G>T	ENST00000341529.3	+	3	429	c.281G>T	c.(280-282)cGg>cTg	p.R94L	CDH5_ENST00000563425.2_Missense_Mutation_p.R94L	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	94	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel maturation (GO:0001955)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|negative regulation of cell proliferation (GO:0008285)|regulation of establishment of cell polarity (GO:2000114)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(18)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)	Lenalidomide(DB00480)	AAGGTCTTCCGGGTCGATGCA	0.517																																						ENST00000341529.3																			0				central_nervous_system(1)|endometrium(3)|kidney(18)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54						c.(280-282)cGg>cTg		cadherin 5, type 2 (vascular endothelium)							88.0	76.0	80.0					16																	66420782		2202	4300	6502	SO:0001583	missense	1003				adherens junction organization|cell junction assembly|homophilic cell adhesion|regulation of establishment of cell polarity	integral to membrane|membrane fraction	beta-catenin binding|calcium ion binding|ion channel binding|receptor binding	g.chr16:66420782G>T	X79981	CCDS10804.1	16q22.1	2010-01-26	2008-07-25		ENSG00000179776	ENSG00000179776		"""CD molecules"", ""Cadherins / Major cadherins"""	1764	protein-coding gene	gene with protein product	"""VE-cadherin"""	601120	"""cadherin 5, type 2, VE-cadherin (vascular epithelium)"""			2059658	Standard	NM_001795		Approved	7B4, CD144	uc002eom.4	P33151	OTTHUMG00000137495	ENST00000341529.3:c.281G>T	16.37:g.66420782G>T	ENSP00000344115:p.Arg94Leu					CDH5_ENST00000563425.2_Missense_Mutation_p.R94L	p.R94L	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.107)	3	429	+		Ovarian(137;0.0955)	94			Cadherin 1.		Q4VAI5|Q4VAI6	Missense_Mutation	SNP	ENST00000341529.3	37	c.281G>T	CCDS10804.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.089|8.089	0.774103|0.774103	0.16051|0.16051	.|.	.|.	ENSG00000179776|ENSG00000179776	ENST00000539262|ENST00000341529;ENST00000379531	.|T	.|0.55413	.|0.52	5.89|5.89	-8.52|-8.52	0.00920|0.00920	.|Cadherin (5);Cadherin-like (1);	.|.	.|.	.|.	.|.	T|T	0.41073|0.41073	0.1143|0.1143	L|L	0.35341|0.35341	1.055|1.055	0.09310|0.09310	N|N	1|1	.|B	.|0.10296	.|0.003	.|B	.|0.16722	.|0.016	T|T	0.17653|0.17653	-1.0362|-1.0362	6|9	0.87932|0.33940	D|T	0|0.23	.|.	19.9506|19.9506	0.97198|0.97198	0.8475:0.0:0.1525:0.0|0.8475:0.0:0.1525:0.0	.|.	.|94	.|P33151	.|CADH5_HUMAN	W|L	16|94	.|ENSP00000344115:R94L	ENSP00000437691:G16W|ENSP00000344115:R94L	G|R	+|+	1|2	0|0	CDH5|CDH5	64978283|64978283	0.000000|0.000000	0.05858|0.05858	0.004000|0.004000	0.12327|0.12327	0.140000|0.140000	0.21249|0.21249	-0.292000|-0.292000	0.08332|0.08332	-1.811000|-1.811000	0.01229|0.01229	-0.150000|-0.150000	0.13652|0.13652	GGG|CGG		0.517	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795		3	40	1	0	0.115264	0.115264	0.124869	3	40				
OR2T6	254879	broad.mit.edu	37	1	248551308	248551308	+	Silent	SNP	T	T	C			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr1:248551308T>C	ENST00000355728.2	+	1	399	c.399T>C	c.(397-399)ccT>ccC	p.P133P		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	133						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGCGCTATCCTGTCCTCATCA	0.567																																						ENST00000355728.2																			0				endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						c.(397-399)ccT>ccC		olfactory receptor, family 2, subfamily T, member 6							86.0	83.0	84.0					1																	248551308		2203	4300	6503	SO:0001819	synonymous_variant	254879				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248551308T>C	AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"""GPCR / Class A : Olfactory receptors"""	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.399T>C	1.37:g.248551308T>C							p.P133P	NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		1	399	+	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		133					A6NE36	Silent	SNP	ENST00000355728.2	37	c.399T>C	CCDS31114.1																																																																																				0.567	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471		5	70	0	0	0	0.184627	0	5	70				
CMTR2	55783	broad.mit.edu	37	16	71318686	71318686	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr16:71318686G>A	ENST00000338099.5	-	3	1474	c.1138C>T	c.(1138-1140)Cgt>Tgt	p.R380C	CMTR2_ENST00000434935.2_Missense_Mutation_p.R380C			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	380					7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										TCAAATAGACGAATGTTTTCA	0.328																																						ENST00000338099.5																			0				breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						c.(1138-1140)Cgt>Tgt									36.0	39.0	38.0					16																	71318686		2194	4296	6490	SO:0001583	missense	55783					integral to membrane	methyltransferase activity|nucleic acid binding	g.chr16:71318686G>A	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"""adrift homolog (Drosophila)"""		"""FtsJ methyltransferase domain containing 1"""	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.1138C>T	16.37:g.71318686G>A	ENSP00000337512:p.Arg380Cys					FTSJD1_ENST00000434935.2_Missense_Mutation_p.R380C	p.R380C			Q8IYT2	FTSJ1_HUMAN			3	1474	-			380					B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	c.1138C>T	CCDS10898.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.867348	0.51588	.	.	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.16196	2.36;2.36	5.95	4.99	0.66335	.	0.426470	0.26003	N	0.026928	T	0.18635	0.0447	L	0.56769	1.78	0.49051	D	0.99974	B	0.26445	0.149	B	0.17433	0.018	T	0.01940	-1.1243	10	0.49607	T	0.09	-1.7208	12.3497	0.55141	0.1403:0.0:0.8597:0.0	.	380	Q8IYT2	FTSJ1_HUMAN	C	380	ENSP00000337512:R380C;ENSP00000411148:R380C	ENSP00000337512:R380C	R	-	1	0	FTSJD1	69876187	0.999000	0.42202	1.000000	0.80357	0.921000	0.55340	1.613000	0.36900	1.530000	0.49136	0.491000	0.48974	CGT		0.328	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348		6	43	0	0	0	0.217242	0	6	43				
LINC00969	440993	broad.mit.edu	37	3	195395402	195395402	+	lincRNA	SNP	C	C	A	rs199554501	byFrequency	TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr3:195395402C>A	ENST00000445430.1	+	0	809									long intergenic non-protein coding RNA 969																		TACGGGCGCACCTACTTGAGC	0.597																																						ENST00000445430.1																			0																																																			440993							g.chr3:195395402C>A	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195395402C>A														0	809	+									RNA	SNP	ENST00000445430.1	37																																																																																						0.597	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			5	42	1	0	0.00621372	0.335167	0.0071275	5	42				
EEF1A1	1915	broad.mit.edu	37	6	74228192	74228192	+	Missense_Mutation	SNP	C	C	A			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr6:74228192C>A	ENST00000316292.9	-	5	1905	c.914G>T	c.(913-915)gGg>gTg	p.G305V	EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000309268.6_Missense_Mutation_p.G305V|EEF1A1_ENST00000331523.2_Missense_Mutation_p.G305V	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	305					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						CACATTGTCCCCAGGAAGAGC	0.483											OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																										ENST00000316292.9																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						c.(913-915)gGg>gTg		eukaryotic translation elongation factor 1 alpha 1							36.0	35.0	35.0					6																	74228192		2002	4169	6171	SO:0001583	missense	1915					cytosol|eukaryotic translation elongation factor 1 complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity	g.chr6:74228192C>A	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"""leukocyte receptor cluster (LRC) member 7"""	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.914G>T	6.37:g.74228192C>A	ENSP00000339063:p.Gly305Val		OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	1151	EEF1A1_ENST00000309268.6_Missense_Mutation_p.G305V|EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000331523.2_Missense_Mutation_p.G305V	p.G305V	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN			5	1905	-			305					P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	37	c.914G>T	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.148587	0.78001	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.71817	-0.6;-0.6;-0.6	4.71	4.71	0.59529	Translation elongation factor EFTu/EF1A, domain 2 (2);Translation elongation/initiation factor/Ribosomal, beta-barrel (2);	0.000000	0.85682	U	0.000000	D	0.91492	0.7314	H	0.99964	5.085	0.80722	D	1	P;P;P;P	0.51057	0.941;0.941;0.941;0.941	P;P;P;D	0.63488	0.888;0.888;0.888;0.915	D	0.95600	0.8662	10	0.87932	D	0	.	18.0919	0.89478	0.0:1.0:0.0:0.0	.	305;305;305;305	P68104;Q53HR5;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;.;EF1A3_HUMAN	V	305;303;305;305;284	ENSP00000339063:G305V;ENSP00000339053:G305V;ENSP00000330054:G305V	ENSP00000339053:G305V	G	-	2	0	EEF1A1	74284913	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.736000	0.68597	2.323000	0.78572	0.556000	0.70494	GGG		0.483	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		4	59	1	0	0.00198382	0.248553	0.00234451	4	59				
VWF	7450	broad.mit.edu	37	12	6161870	6161870	+	Silent	SNP	C	C	T			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr12:6161870C>T	ENST00000261405.5	-	16	2279	c.2025G>A	c.(2023-2025)ccG>ccA	p.P675P		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	675	TIL 2.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	ATTCCTCATCCGGGTAAGAGA	0.622																																						ENST00000261405.5																			0				NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129						c.(2023-2025)ccG>ccA		von Willebrand factor	Antihemophilic Factor(DB00025)						50.0	49.0	49.0					12																	6161870		2203	4300	6503	SO:0001819	synonymous_variant	7450				blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding	g.chr12:6161870C>T		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.2025G>A	12.37:g.6161870C>T							p.P675P	NM_000552.3	NP_000543.2	P04275	VWF_HUMAN			16	2279	-			675			TIL 2.		Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	c.2025G>A	CCDS8539.1																																																																																				0.622	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		5	43	0	0	0	0.217242	0	5	43				
GPR17	2840	broad.mit.edu	37	2	128408751	128408751	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr2:128408751G>A	ENST00000272644.3	+	3	600	c.526G>A	c.(526-528)Gca>Aca	p.A176T	GPR17_ENST00000393018.3_Missense_Mutation_p.A176T|GPR17_ENST00000486700.1_3'UTR|LIMS2_ENST00000324938.5_Intron|LIMS2_ENST00000545738.2_Intron|LIMS2_ENST00000409455.1_Intron|LIMS2_ENST00000410038.1_5'Flank|LIMS2_ENST00000355119.4_Intron|GPR17_ENST00000544369.1_Missense_Mutation_p.A176T|LIMS2_ENST00000409808.2_Intron|LIMS2_ENST00000410011.1_Intron|LIMS2_ENST00000409254.1_5'Flank	NM_001161416.1|NM_001161417.1|NM_005291.2	NP_001154888.1|NP_001154889.1|NP_005282.1	Q13304	GPR17_HUMAN	G protein-coupled receptor 17	176					chemokine-mediated signaling pathway (GO:0070098)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)|urinary_tract(1)	19	Colorectal(110;0.1)	Ovarian(717;0.15)		BRCA - Breast invasive adenocarcinoma(221;0.0677)		GCCCCTCTACGCACACCTGGC	0.642																																						ENST00000544369.1																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)|urinary_tract(1)	19						c.(526-528)Gca>Aca		G protein-coupled receptor 17							108.0	96.0	100.0					2																	128408751		2203	4300	6503	SO:0001583	missense	2840					integral to plasma membrane	chemokine receptor activity|purinergic nucleotide receptor activity, G-protein coupled	g.chr2:128408751G>A		CCDS2148.1	2q21	2014-01-30			ENSG00000144230	ENSG00000144230		"""GPCR / Class A : Orphans"""	4471	protein-coding gene	gene with protein product		603071				8558062	Standard	NM_001161415		Approved		uc002tpc.3	Q13304	OTTHUMG00000131533	ENST00000272644.3:c.526G>A	2.37:g.128408751G>A	ENSP00000272644:p.Ala176Thr					GPR17_ENST00000486700.1_3'UTR|GPR17_ENST00000272644.3_Missense_Mutation_p.A176T|LIMS2_ENST00000410011.1_Intron|LIMS2_ENST00000545738.2_Intron|LIMS2_ENST00000324938.5_Intron|LIMS2_ENST00000409455.1_Intron|LIMS2_ENST00000355119.4_Intron|GPR17_ENST00000393018.3_Missense_Mutation_p.A176T|LIMS2_ENST00000409808.2_Intron	p.A176T	NM_001161415.1	NP_001154887.1	Q13304	GPR17_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.0677)	4	1137	+	Colorectal(110;0.1)	Ovarian(717;0.15)	176					A8K9L0|B2R9X0|Q8N5S7|Q9UDZ6|Q9UE21	Missense_Mutation	SNP	ENST00000272644.3	37	c.526G>A	CCDS2148.1	.	.	.	.	.	.	.	.	.	.	g	33	5.214551	0.95104	.	.	ENSG00000144230	ENST00000544369;ENST00000272644;ENST00000393018	T;T;T	0.40756	1.02;1.02;1.02	5.47	5.47	0.80525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.69097	0.3073	M	0.83692	2.655	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.71951	-0.4437	10	0.54805	T	0.06	.	19.3366	0.94322	0.0:0.0:1.0:0.0	.	176	Q13304	GPR17_HUMAN	T	176	ENSP00000442982:A176T;ENSP00000272644:A176T;ENSP00000376741:A176T	ENSP00000272644:A176T	A	+	1	0	GPR17	128125221	1.000000	0.71417	0.968000	0.41197	0.960000	0.62799	9.827000	0.99397	2.573000	0.86826	0.655000	0.94253	GCA		0.642	GPR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254390.1			13	124	0	0	0	0.457914	0	13	124				
GPR149	344758	broad.mit.edu	37	3	154056047	154056047	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr3:154056047G>A	ENST00000389740.2	-	4	1736	c.1637C>T	c.(1636-1638)gCc>gTc	p.A546V		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	546					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			AATGGCAAGGGCATAACCGGA	0.438																																						ENST00000389740.2																			0				autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47						c.(1636-1638)gCc>gTc		G protein-coupled receptor 149							92.0	92.0	92.0					3																	154056047		1883	4105	5988	SO:0001583	missense	344758					integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chr3:154056047G>A	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.1637C>T	3.37:g.154056047G>A	ENSP00000374390:p.Ala546Val						p.A546V	NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)		4	1736	-			546						Missense_Mutation	SNP	ENST00000389740.2	37	c.1637C>T	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.884701	0.51908	.	.	ENSG00000174948	ENST00000389740	.	.	.	5.5	2.65	0.31530	.	0.322692	0.32952	N	0.005442	T	0.51143	0.1657	L	0.53249	1.67	0.32996	D	0.52556	B	0.32573	0.376	B	0.34590	0.186	T	0.63216	-0.6687	9	0.87932	D	0	-3.8441	16.2794	0.82664	0.0:0.5031:0.4968:0.0	.	546	Q86SP6	GP149_HUMAN	V	546	.	ENSP00000374390:A546V	A	-	2	0	GPR149	155538741	0.999000	0.42202	0.332000	0.25469	0.916000	0.54674	2.132000	0.42083	0.251000	0.21505	0.655000	0.94253	GCC		0.438	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		5	170	0	0	0	0.184627	0	5	170				
ELMO3	79767	broad.mit.edu	37	16	67237658	67237658	+	Missense_Mutation	SNP	A	A	T			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr16:67237658A>T	ENST00000360833.1	+	19	2206	c.2149A>T	c.(2149-2151)Atg>Ttg	p.M717L	ELMO3_ENST00000393997.2_Missense_Mutation_p.M734L|MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000477898.1_Missense_Mutation_p.M568L			Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	681					apoptotic process (GO:0006915)|phagocytosis (GO:0006909)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				cervix(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)		GCTGCTGACCATGGAGACCAA	0.642																																						ENST00000393997.2																			0				cervix(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	18						c.(2200-2202)Atg>Ttg		engulfment and cell motility 3							36.0	43.0	41.0					16																	67237658		2124	4221	6345	SO:0001583	missense	79767				apoptosis|phagocytosis	cytoplasm|cytoskeleton	SH3 domain binding	g.chr16:67237658A>T		CCDS10833.2	16q22.1	2010-03-18	2006-01-20		ENSG00000102890	ENSG00000102890		"""Engulfment and cell motility proteins"""	17289	protein-coding gene	gene with protein product		606422	"""engulfment and cell motility 3 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_024712		Approved	FLJ13824, CED12, ELMO-3, CED-12	uc002esa.3	Q96BJ8	OTTHUMG00000133570	ENST00000360833.1:c.2149A>T	16.37:g.67237658A>T	ENSP00000354077:p.Met717Leu					ELMO3_ENST00000477898.1_Missense_Mutation_p.M568L|ELMO3_ENST00000360833.1_Missense_Mutation_p.M717L	p.M734L	NM_024712.3	NP_078988.2	Q96BJ8	ELMO3_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)	20	2257	+		Ovarian(137;0.0563)	681					B4DV86|Q9H8A5	Missense_Mutation	SNP	ENST00000360833.1	37	c.2200A>T		.	.	.	.	.	.	.	.	.	.	A	17.68	3.450150	0.63290	.	.	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.16196	2.36;2.38	5.19	5.19	0.71726	.	0.039979	0.85682	D	0.000000	T	0.22360	0.0539	L	0.53617	1.68	0.80722	D	1	P;P;P	0.47409	0.71;0.895;0.895	B;P;P	0.44359	0.118;0.447;0.447	T	0.01512	-1.1336	10	0.66056	D	0.02	-27.1948	13.885	0.63704	1.0:0.0:0.0:0.0	.	681;717;734	Q96BJ8;F8W9E7;Q96BJ8-3	ELMO3_HUMAN;.;.	L	717;734	ENSP00000354077:M717L;ENSP00000377566:M734L	ENSP00000354077:M717L	M	+	1	0	ELMO3	65795159	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.317000	0.96327	1.970000	0.57323	0.459000	0.35465	ATG		0.642	ELMO3-001	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000257667.2	NM_024712		3	22	0	0	0	0.115264	0	3	22				
TICAM1	148022	broad.mit.edu	37	19	4816506	4816506	+	Silent	SNP	C	C	A			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr19:4816506C>A	ENST00000248244.5	-	2	2113	c.1884G>T	c.(1882-1884)ccG>ccT	p.P628P		NM_182919.3	NP_891549.1	Q8IUC6	TCAM1_HUMAN	toll-like receptor adaptor molecule 1	628	Pro-rich.|Sufficient to induce apoptosis.				apoptotic signaling pathway (GO:0097190)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of protein homodimerization activity (GO:0043496)|response to exogenous dsRNA (GO:0043330)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|ripoptosome (GO:0097342)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		GTGGCGGCTGCGGGCACCCCG	0.711																																						ENST00000248244.5																			0				NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	26						c.(1882-1884)ccG>ccT		toll-like receptor adaptor molecule 1							14.0	14.0	14.0					19																	4816506		2192	4280	6472	SO:0001819	synonymous_variant	148022				apoptosis|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	protein kinase binding|signal transducer activity	g.chr19:4816506C>A	AB086380	CCDS12136.1	19p13.3	2014-09-17				ENSG00000127666			18348	protein-coding gene	gene with protein product		607601				12539043, 12471095	Standard	NM_182919		Approved	TRIF, TICAM-1, MGC35334, PRVTIRB	uc002mbi.4	Q8IUC6		ENST00000248244.5:c.1884G>T	19.37:g.4816506C>A							p.P628P	NM_182919.3	NP_891549.1	Q8IUC6	TCAM1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)	2	2113	-			628			Pro-rich.|Sufficient to induce apoptosis.		B3Y691|O75532|Q86XP8|Q96GA0	Silent	SNP	ENST00000248244.5	37	c.1884G>T	CCDS12136.1																																																																																				0.711	TICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450435.1	NM_014261		5	22	1	0	0.0215528	0.217242	0.0240159	5	22				
SNTG1	54212	broad.mit.edu	37	8	51569552	51569552	+	Missense_Mutation	SNP	G	G	T			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr8:51569552G>T	ENST00000522124.1	+	14	1594	c.933G>T	c.(931-933)agG>agT	p.R311S	SNTG1_ENST00000276467.5_Missense_Mutation_p.R311S|SNTG1_ENST00000518864.1_Missense_Mutation_p.R311S|SNTG1_ENST00000517473.1_Missense_Mutation_p.R311S	NM_018967.2	NP_061840.1	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	311	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell communication (GO:0007154)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)|syntrophin complex (GO:0016013)	protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(36)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	66		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				TGGCCCTGAGGGGCTCATGTC	0.483																																						ENST00000522124.1																			0				NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(36)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	66						c.(931-933)agG>agT		syntrophin, gamma 1							104.0	96.0	99.0					8																	51569552		2203	4300	6503	SO:0001583	missense	54212				cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding	g.chr8:51569552G>T	AJ003030	CCDS6147.1, CCDS75737.1	8q11-q12	2008-07-03				ENSG00000147481			13740	protein-coding gene	gene with protein product		608714				10747910	Standard	NM_018967		Approved	SYN4, G1SYN	uc003xqs.1	Q9NSN8		ENST00000522124.1:c.933G>T	8.37:g.51569552G>T	ENSP00000429842:p.Arg311Ser					SNTG1_ENST00000276467.5_Missense_Mutation_p.R311S|SNTG1_ENST00000518864.1_Missense_Mutation_p.R311S|SNTG1_ENST00000517473.1_Missense_Mutation_p.R311S	p.R311S	NM_018967.2	NP_061840.1	Q9NSN8	SNTG1_HUMAN			14	1594	+		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)	311			PH.		Q2M3Q0|Q9NY98	Missense_Mutation	SNP	ENST00000522124.1	37	c.933G>T	CCDS6147.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.435683	0.25813	.	.	ENSG00000147481	ENST00000518864;ENST00000522124;ENST00000517473;ENST00000276467	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	5.01	1.67	0.24075	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.45637	0.1352	M	0.63843	1.955	0.58432	D	0.999992	D;D	0.60160	0.971;0.987	P;D	0.66196	0.888;0.942	T	0.19910	-1.0291	10	0.37606	T	0.19	.	10.318	0.43749	0.282:0.0:0.718:0.0	.	311;311	Q9NSN8-2;Q9NSN8	.;SNTG1_HUMAN	S	311	ENSP00000429276:R311S;ENSP00000429842:R311S;ENSP00000431123:R311S;ENSP00000276467:R311S	ENSP00000276467:R311S	R	+	3	2	SNTG1	51732105	1.000000	0.71417	0.152000	0.22495	0.016000	0.09150	1.640000	0.37186	0.158000	0.19367	-1.094000	0.02160	AGG		0.483	SNTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377964.1			9	88	1	0	3.86212e-05	0.361761	5.19388e-05	9	88				
ABCA12	26154	broad.mit.edu	37	2	215820033	215820033	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr2:215820033C>A	ENST00000272895.7	-	43	6505	c.6286G>T	c.(6286-6288)Gga>Tga	p.G2096*	AC072062.1_ENST00000607412.1_RNA|ABCA12_ENST00000389661.4_Nonsense_Mutation_p.G1778*	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2096					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		AAGGCCATTCCTGTTTCATGG	0.418																																					Ovarian(66;664 1488 5121 34295)	ENST00000272895.7																			0				NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139						c.(6286-6288)Gga>Tga		ATP-binding cassette, sub-family A (ABC1), member 12							94.0	84.0	87.0					2																	215820033		2203	4300	6503	SO:0001587	stop_gained	26154				cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity	g.chr2:215820033C>A	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.6286G>T	2.37:g.215820033C>A	ENSP00000272895:p.Gly2096*					ABCA12_ENST00000389661.4_Nonsense_Mutation_p.G1778*|AC072062.1_ENST00000607412.1_RNA	p.G2096*	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)	43	6505	-		Renal(323;0.127)	2096					Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Nonsense_Mutation	SNP	ENST00000272895.7	37	c.6286G>T	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	47	13.252699	0.99730	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	.	.	.	5.97	5.1	0.69264	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	15.4196	0.75000	0.0:0.9333:0.0:0.0667	.	.	.	.	X	2096;1778	.	ENSP00000272895:G2096X	G	-	1	0	ABCA12	215528278	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.961000	0.63681	1.540000	0.49301	-0.143000	0.13931	GGA		0.418	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		4	90	1	0	0.150653	0.150653	0.158797	4	90				
TMEM190	147744	broad.mit.edu	37	19	55889522	55889522	+	Missense_Mutation	SNP	A	A	G			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr19:55889522A>G	ENST00000291934.3	+	5	503	c.485A>G	c.(484-486)gAa>gGa	p.E162G	CTD-2105E13.15_ENST00000595064.1_RNA	NM_139172.1	NP_631911.1	Q8WZ59	TM190_HUMAN	transmembrane protein 190	162					hematopoietic progenitor cell differentiation (GO:0002244)	inner acrosomal membrane (GO:0002079)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	5	Breast(117;0.191)		BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		accgagggggaagggacggag	0.637																																						ENST00000291934.3																			0				large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	5						c.(484-486)gAa>gGa		transmembrane protein 190							42.0	45.0	44.0					19																	55889522		2202	4300	6502	SO:0001583	missense	147744					integral to membrane		g.chr19:55889522A>G	AF442729	CCDS33113.1	19q13.42	2011-09-28				ENSG00000160472			29632	protein-coding gene	gene with protein product						21273369	Standard	NM_139172		Approved	MDAC1	uc002qkt.1	Q8WZ59		ENST00000291934.3:c.485A>G	19.37:g.55889522A>G	ENSP00000291934:p.Glu162Gly						p.E162G	NM_139172.1	NP_631911.1	Q8WZ59	TM190_HUMAN	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)	5	503	+	Breast(117;0.191)		162					A6NJL5	Missense_Mutation	SNP	ENST00000291934.3	37	c.485A>G	CCDS33113.1	.	.	.	.	.	.	.	.	.	.	A	10.42	1.344692	0.24426	.	.	ENSG00000160472	ENST00000291934	.	.	.	2.75	2.75	0.32379	.	0.650998	0.11828	U	0.525489	T	0.40423	0.1116	N	0.24115	0.695	0.09310	N	1	D	0.76494	0.999	D	0.75484	0.986	T	0.15636	-1.0430	9	0.31617	T	0.26	-16.3833	7.3147	0.26493	1.0:0.0:0.0:0.0	.	162	Q8WZ59	TM190_HUMAN	G	162	.	ENSP00000291934:E162G	E	+	2	0	TMEM190	60581334	0.616000	0.27035	0.012000	0.15200	0.053000	0.15095	1.266000	0.33039	1.499000	0.48617	0.260000	0.18958	GAA		0.637	TMEM190-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453042.1	NM_139172		7	52	0	0	0	0.278610	0	7	52				
ARNTL	406	broad.mit.edu	37	11	13387083	13387083	+	Silent	SNP	C	C	A			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr11:13387083C>A	ENST00000403290.1	+	10	851	c.496C>A	c.(496-498)Cga>Aga	p.R166R	ARNTL_ENST00000389707.4_Silent_p.R166R|ARNTL_ENST00000497429.1_3'UTR|ARNTL_ENST00000396441.3_Silent_p.R166R|ARNTL_ENST00000403482.3_Silent_p.R164R|ARNTL_ENST00000361003.4_Silent_p.R166R|ARNTL_ENST00000403510.3_Silent_p.R123R|ARNTL_ENST00000401424.1_Silent_p.R123R|ARNTL_ENST00000389708.3_Silent_p.R166R			O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear translocator-like	166	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of cell cycle (GO:0051726)|regulation of cellular senescence (GO:2000772)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|nuclear body (GO:0016604)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|Hsp90 protein binding (GO:0051879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|signal transducer activity (GO:0004871)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(2)|large_intestine(11)|lung(5)|upper_aerodigestive_tract(1)	20				Epithelial(150;0.0243)		AGGATGTGACCGAGGGAAGAT	0.433																																						ENST00000389708.3																			0				breast(1)|endometrium(2)|large_intestine(11)|lung(5)|upper_aerodigestive_tract(1)	20						c.(496-498)Cga>Aga		aryl hydrocarbon receptor nuclear translocator-like							235.0	188.0	203.0					11																	13387083		2200	4294	6494	SO:0001819	synonymous_variant	406				circadian rhythm|positive regulation of transcription from RNA polymerase II promoter	transcription factor complex	aryl hydrocarbon receptor binding|DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity	g.chr11:13387083C>A	D89722	CCDS31430.1, CCDS44543.1, CCDS73259.1	11p15	2013-05-21			ENSG00000133794	ENSG00000133794		"""Basic helix-loop-helix proteins"""	701	protein-coding gene	gene with protein product		602550				9144434, 9079689	Standard	XM_005252930		Approved	MOP3, JAP3, BMAL1, PASD3, bHLHe5	uc001mkp.3	O00327	OTTHUMG00000150623	ENST00000403290.1:c.496C>A	11.37:g.13387083C>A						ARNTL_ENST00000396441.3_Silent_p.R166R|ARNTL_ENST00000497429.1_3'UTR|ARNTL_ENST00000403290.1_Silent_p.R166R|ARNTL_ENST00000401424.1_Silent_p.R123R|ARNTL_ENST00000403482.3_Silent_p.R164R|ARNTL_ENST00000361003.4_Silent_p.R166R|ARNTL_ENST00000389707.4_Silent_p.R166R|ARNTL_ENST00000403510.3_Silent_p.R123R	p.R166R			O00327	BMAL1_HUMAN		Epithelial(150;0.0243)	10	851	+			166			PAS 1.		A2I2N6|A8K645|B5ME11|B7WPG7|D3DQW6|O00313|O00314|O00315|O00316|O00317|Q4G136|Q8IUT4|Q99631|Q99649	Silent	SNP	ENST00000403290.1	37	c.496C>A																																																																																					0.433	ARNTL-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000319173.1	NM_001178		3	83	1	0	0.000602214	0.184627	0.000757625	3	83				
TM4SF20	79853	broad.mit.edu	37	2	228235653	228235653	+	Missense_Mutation	SNP	G	G	A	rs138005777		TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr2:228235653G>A	ENST00000304568.3	-	2	264	c.227C>T	c.(226-228)gCg>gTg	p.A76V		NM_024795.3	NP_079071.2	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	76						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A76V(1)		breast(1)|kidney(2)|large_intestine(1)|lung(4)|stomach(2)	10		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		GTTGCAGCACGCTCTTTTTCT	0.428																																						ENST00000304568.3																			1	Substitution - Missense(1)	p.A76V(1)	lung(1)	breast(1)|kidney(2)|large_intestine(1)|lung(4)|stomach(2)	10						c.(226-228)gCg>gTg		transmembrane 4 L six family member 20		G	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	431.0	400.0	410.0		227	-2.6	0.0	2	dbSNP_134	410	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TM4SF20	NM_024795.3	64	0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308	benign	76/230	228235653	4,13002	2203	4300	6503	SO:0001583	missense	79853					integral to membrane|plasma membrane		g.chr2:228235653G>A	AK026453	CCDS2466.1	2q36.3	2008-02-05			ENSG00000168955	ENSG00000168955			26230	protein-coding gene	gene with protein product		615404				12975309	Standard	NM_024795		Approved	FLJ22800, TCCE518	uc002vpb.2	Q53R12	OTTHUMG00000133187	ENST00000304568.3:c.227C>T	2.37:g.228235653G>A	ENSP00000303028:p.Ala76Val						p.A76V	NM_024795.3	NP_079071.2	Q53R12	T4S20_HUMAN		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)	2	264	-		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)	76					B2RP42|Q5U609|Q6UWS1|Q9H5X9	Missense_Mutation	SNP	ENST00000304568.3	37	c.227C>T	CCDS2466.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.926263	0.34002	4.54E-4	2.33E-4	ENSG00000168955	ENST00000304568	T	0.33216	1.42	6.17	-2.61	0.06171	.	0.960647	0.08635	N	0.916462	T	0.36193	0.0958	M	0.68317	2.08	0.09310	N	1	P	0.40794	0.729	P	0.45276	0.475	T	0.46133	-0.9213	10	0.46703	T	0.11	-0.9901	10.7669	0.46299	0.0:0.4896:0.2257:0.2847	.	76	Q53R12	T4S20_HUMAN	V	76	ENSP00000303028:A76V	ENSP00000303028:A76V	A	-	2	0	TM4SF20	227943897	0.004000	0.15560	0.035000	0.18076	0.007000	0.05969	-0.345000	0.07770	-0.108000	0.12066	-0.833000	0.03075	GCG		0.428	TM4SF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256896.2	NM_024795		52	463	0	0	0	0.870114	0	52	463				
SEPT2	4735	broad.mit.edu	37	2	242277165	242277165	+	Missense_Mutation	SNP	A	A	C			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr2:242277165A>C	ENST00000391973.2	+	7	1082	c.554A>C	c.(553-555)gAc>gCc	p.D185A	SEPT2_ENST00000391971.2_Missense_Mutation_p.D185A|SEPT2_ENST00000360051.3_Missense_Mutation_p.D185A|SEPT2_ENST00000402092.2_Missense_Mutation_p.D185A|SEPT2_ENST00000401990.1_Missense_Mutation_p.D195A|SEPT2_ENST00000407971.1_Missense_Mutation_p.D145A	NM_006155.1	NP_006146.1	Q15019	SEPT2_HUMAN	septin 2	185	Septin-type G.				cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|neuron projection development (GO:0031175)|regulation of L-glutamate transport (GO:0002036)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|synapse (GO:0045202)	enzyme regulator activity (GO:0030234)|GTP binding (GO:0005525)			central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)		GCAAAAGCTGACACTCTCACC	0.498																																						ENST00000391973.2																			0				central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12						c.(553-555)gAc>gCc		septin 2							82.0	77.0	79.0					2																	242277165		2203	4300	6503	SO:0001583	missense	4735				cell division|mitosis	actin cytoskeleton|cleavage furrow|condensed chromosome kinetochore|midbody|nucleolus|septin complex|spindle	GTP binding	g.chr2:242277165A>C	D28540	CCDS2548.1, CCDS63195.1, CCDS74682.1	2q37.3	2013-01-21	2005-01-11	2005-01-12	ENSG00000168385	ENSG00000168385		"""Septins"""	7729	protein-coding gene	gene with protein product		601506	"""neural precursor cell expressed, developmentally down-regulated 5"""	DIFF6, NEDD5		8697812	Standard	XM_005247011		Approved	KIAA0158, hNedd5, Pnutl3	uc002wbd.3	Q15019	OTTHUMG00000133394	ENST00000391973.2:c.554A>C	2.37:g.242277165A>C	ENSP00000375834:p.Asp185Ala					SEPT2_ENST00000407971.1_Missense_Mutation_p.D145A|SEPT2_ENST00000401990.1_Missense_Mutation_p.D195A|SEPT2_ENST00000360051.3_Missense_Mutation_p.D185A|SEPT2_ENST00000391971.2_Missense_Mutation_p.D185A|SEPT2_ENST00000402092.2_Missense_Mutation_p.D185A	p.D185A	NM_006155.1	NP_006146.1	Q15019	SEPT2_HUMAN		Epithelial(32;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)	7	1082	+		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)	185					B4DGE8|Q14132|Q53QU3|Q8IUK9|Q96CB0	Missense_Mutation	SNP	ENST00000391973.2	37	c.554A>C	CCDS2548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.3|24.3	4.514268|4.514268	0.85389|0.85389	.|.	.|.	ENSG00000168385|ENSG00000168385	ENST00000391973;ENST00000428282;ENST00000360051;ENST00000391971;ENST00000401990;ENST00000407971;ENST00000402092;ENST00000391972;ENST00000421717|ENST00000457874	T;T;T;T;T;D;T;D|.	0.96041|.	-1.46;-1.46;-1.46;-1.46;-1.46;-3.89;-1.46;-3.89|.	5.23|5.23	4.05|4.05	0.47172|0.47172	.|.	0.049200|.	0.85682|.	D|.	0.000000|.	D|D	0.88009|0.88009	0.6322|0.6322	H|H	0.98682|0.98682	4.3|4.3	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;0.999;1.0|.	D;D;D|.	0.97110|.	1.0;0.985;0.995|.	D|D	0.90622|0.90622	0.4560|0.4560	10|5	0.87932|.	D|.	0|.	.|.	12.1992|12.1992	0.54315|0.54315	0.8571:0.1429:0.0:0.0|0.8571:0.1429:0.0:0.0	.|.	220;145;185|.	Q15019-2;B5MCX3;Q15019|.	.;.;SEPT2_HUMAN|.	A|P	185;145;185;185;195;145;185;220;40|157	ENSP00000375834:D185A;ENSP00000397195:D145A;ENSP00000353157:D185A;ENSP00000375832:D185A;ENSP00000385109:D195A;ENSP00000384525:D145A;ENSP00000385172:D185A;ENSP00000408296:D40A|.	ENSP00000353157:D185A|.	D|T	+|+	2|1	0|0	SEPT2|SEPT2	241925838|241925838	1.000000|1.000000	0.71417|0.71417	0.874000|0.874000	0.34290|0.34290	0.979000|0.979000	0.70002|0.70002	9.110000|9.110000	0.94302|0.94302	0.813000|0.813000	0.34350|0.34350	0.533000|0.533000	0.62120|0.62120	GAC|ACA		0.498	SEPT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323177.3	NM_006155		6	85	0	0	0	0.278610	0	6	85				
MYH8	4626	broad.mit.edu	37	17	10297708	10297708	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr17:10297708G>A	ENST00000403437.2	-	35	5118	c.5024C>T	c.(5023-5025)gCa>gTa	p.A1675V	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1675					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						CTCCACAATTGCCAGCTGTTC	0.542									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																													ENST00000403437.2																			0				NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						c.(5023-5025)gCa>gTa		myosin, heavy chain 8, skeletal muscle, perinatal							86.0	80.0	82.0					17																	10297708		2203	4300	6503	SO:0001583	missense	4626	Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling	Familial Cancer Database	Carney Complex Variant	muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle	g.chr17:10297708G>A		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.5024C>T	17.37:g.10297708G>A	ENSP00000384330:p.Ala1675Val					CTC-297N7.7_ENST00000587182.1_RNA|CTC-297N7.7_ENST00000581304.1_RNA|CTC-297N7.7_ENST00000399342.2_RNA	p.A1675V	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN			35	5118	-			1675					Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	c.5024C>T	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.592334	0.46214	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.79141	-1.24	5.06	4.09	0.47781	Myosin tail (1);	0.000000	0.41396	U	0.000884	T	0.79857	0.4518	M	0.82517	2.595	0.49051	D	0.999743	B	0.15719	0.014	B	0.24006	0.05	T	0.79205	-0.1899	10	0.62326	D	0.03	.	13.6992	0.62597	0.0743:0.0:0.9257:0.0	.	1675	P13535	MYH8_HUMAN	V	1675	ENSP00000384330:A1675V	ENSP00000252173:A1675V	A	-	2	0	MYH8	10238433	1.000000	0.71417	0.837000	0.33122	0.016000	0.09150	6.542000	0.73869	1.360000	0.45960	0.650000	0.86243	GCA		0.542	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		9	65	0	0	0	0.361761	0	9	65				
HELZ2	85441	broad.mit.edu	37	20	62194306	62194306	+	Missense_Mutation	SNP	C	C	T	rs530022156		TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr20:62194306C>T	ENST00000467148.1	-	8	5938	c.5869G>A	c.(5869-5871)Gcg>Acg	p.A1957T	HELZ2_ENST00000427522.2_Missense_Mutation_p.A1388T	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1957					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										TCGGCAACCGCGCCGGTGGCC	0.687													C|||	1	0.000199681	0.0	0.0	5008	,	,		16689	0.001		0.0	False		,,,				2504	0.0					ENST00000467148.1																			0											c.(5869-5871)Gcg>Acg		helicase with zinc finger 2, transcriptional coactivator							14.0	11.0	12.0					20																	62194306		2151	4261	6412	SO:0001583	missense	85441							g.chr20:62194306C>T	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.5869G>A	20.37:g.62194306C>T	ENSP00000417401:p.Ala1957Thr					HELZ2_ENST00000427522.2_Missense_Mutation_p.A1388T	p.A1957T	NM_001037335.2	NP_001032412.2					8	5938	-								Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	c.5869G>A	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068884	0.76301	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.85702	-2.02;-1.85	4.75	4.75	0.60458	.	0.181457	0.46145	D	0.000302	D	0.91250	0.7242	M	0.71581	2.175	0.54753	D	0.999985	D;D	0.76494	0.998;0.999	P;D	0.65140	0.856;0.932	D	0.92450	0.5969	10	0.72032	D	0.01	-22.0306	17.736	0.88392	0.0:1.0:0.0:0.0	.	1957;1388	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	T	1388;1957	ENSP00000393257:A1388T;ENSP00000417401:A1957T	ENSP00000393257:A1388T	A	-	1	0	RP4-697K14.7	61664750	1.000000	0.71417	0.005000	0.12908	0.003000	0.03518	5.323000	0.65858	2.192000	0.70111	0.491000	0.48974	GCG		0.687	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		5	4	0	0	0	0.184627	0	5	4				
GPNMB	10457	broad.mit.edu	37	7	23313757	23313757	+	Missense_Mutation	SNP	C	C	T			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr7:23313757C>T	ENST00000381990.2	+	11	1794	c.1633C>T	c.(1633-1635)Ctc>Ttc	p.L545F	GPNMB_ENST00000478451.1_3'UTR|GPNMB_ENST00000258733.4_Missense_Mutation_p.L533F|GPNMB_ENST00000453162.2_Missense_Mutation_p.L487F|GPNMB_ENST00000539136.1_Missense_Mutation_p.L434F	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	545					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			GAGTGTCTTTCTCAACCGTGC	0.403																																						ENST00000258733.4																			0				breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41						c.(1597-1599)Ctc>Ttc		glycoprotein (transmembrane) nmb							88.0	89.0	89.0					7																	23313757		2203	4300	6503	SO:0001583	missense	10457				negative regulation of cell proliferation	melanosome		g.chr7:23313757C>T	X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"""transmembrane glycoprotein"", ""glycoprotein NMB"", ""glycoprotein nmb-like protein"", ""osteoactivin"""	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.1633C>T	7.37:g.23313757C>T	ENSP00000371420:p.Leu545Phe					GPNMB_ENST00000381990.2_Missense_Mutation_p.L545F|GPNMB_ENST00000539136.1_Missense_Mutation_p.L434F|GPNMB_ENST00000453162.2_Missense_Mutation_p.L487F|GPNMB_ENST00000478451.1_3'UTR	p.L533F			Q14956	GPNMB_HUMAN	GBM - Glioblastoma multiforme(13;0.154)		11	1892	+			545					A4D155|Q6UVX1|Q8N1A1	Missense_Mutation	SNP	ENST00000381990.2	37	c.1597C>T	CCDS34610.1	.	.	.	.	.	.	.	.	.	.	C	1.644	-0.515665	0.04200	.	.	ENSG00000136235	ENST00000258733;ENST00000435486;ENST00000381990;ENST00000425903;ENST00000539136;ENST00000453162	T;T;T;T	0.18016	2.3;2.27;2.28;2.24	6.07	1.15	0.20763	.	0.448765	0.20944	N	0.082871	T	0.09730	0.0239	L	0.35723	1.085	0.09310	N	1	B;B;B;B	0.19583	0.004;0.007;0.003;0.037	B;B;B;B	0.22386	0.009;0.006;0.006;0.039	T	0.24977	-1.0145	10	0.24483	T	0.36	-6.9588	0.7253	0.00948	0.1543:0.2326:0.2434:0.3697	.	434;487;545;533	F6SKP1;F5GY20;Q14956;Q14956-2	.;.;GPNMB_HUMAN;.	F	533;580;545;428;434;487	ENSP00000258733:L533F;ENSP00000371420:L545F;ENSP00000445266:L434F;ENSP00000405586:L487F	ENSP00000258733:L533F	L	+	1	0	GPNMB	23280282	0.580000	0.26733	0.002000	0.10522	0.018000	0.09664	0.141000	0.16076	0.293000	0.22520	0.655000	0.94253	CTC		0.403	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340		6	99	0	0	0	0.248553	0	6	99				
GIGYF2	26058	broad.mit.edu	37	2	233675977	233675977	+	Missense_Mutation	SNP	C	C	T			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr2:233675977C>T	ENST00000409547.1	+	19	2233	c.1922C>T	c.(1921-1923)gCc>gTc	p.A641V	GIGYF2_ENST00000373563.4_Missense_Mutation_p.A641V|GIGYF2_ENST00000409196.3_Missense_Mutation_p.A635V|GIGYF2_ENST00000373566.3_Missense_Mutation_p.A663V|GIGYF2_ENST00000409480.1_Missense_Mutation_p.A663V|GIGYF2_ENST00000409451.3_Missense_Mutation_p.A662V|GIGYF2_ENST00000452341.2_Missense_Mutation_p.A472V	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	641	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		CAGGTTTTGGCCCAACAGCAG	0.428																																						ENST00000373566.3																			0				NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63						c.(1987-1989)gCc>gTc		GRB10 interacting GYF protein 2							133.0	117.0	123.0					2																	233675977		2203	4300	6503	SO:0001583	missense	26058				cell death		protein binding	g.chr2:233675977C>T	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.1922C>T	2.37:g.233675977C>T	ENSP00000386537:p.Ala641Val					GIGYF2_ENST00000409480.1_Missense_Mutation_p.A663V|GIGYF2_ENST00000409547.1_Missense_Mutation_p.A641V|GIGYF2_ENST00000452341.2_Missense_Mutation_p.A472V|GIGYF2_ENST00000409451.3_Missense_Mutation_p.A662V|GIGYF2_ENST00000409196.3_Missense_Mutation_p.A635V|GIGYF2_ENST00000373563.4_Missense_Mutation_p.A641V	p.A663V			Q6Y7W6	PERQ2_HUMAN		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)	18	2185	+		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)	641			Gln-rich.		A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	c.1988C>T	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.393974	0.42410	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000452341	T;T;T;T;T;T;T;T;T	0.75938	-0.82;-0.83;-0.82;-0.83;-0.97;-0.83;-0.83;-0.98;-0.7	5.89	4.03	0.46877	.	0.125476	0.53938	D	0.000054	T	0.74680	0.3748	L	0.45581	1.43	0.40122	D	0.976616	D;D;B;D	0.56968	0.978;0.968;0.437;0.958	P;P;B;B	0.52066	0.689;0.477;0.115;0.423	T	0.75494	-0.3298	10	0.56958	D	0.05	-0.7447	11.4929	0.50391	0.1411:0.7234:0.1355:0.0	.	472;662;641;635	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	V	663;584;641;663;641;641;584;635;662;635;472	ENSP00000362667:A663V;ENSP00000362664:A641V;ENSP00000386765:A663V;ENSP00000386537:A641V;ENSP00000404195:A584V;ENSP00000387070:A635V;ENSP00000387170:A662V;ENSP00000410297:A635V;ENSP00000411505:A472V	ENSP00000362664:A641V	A	+	2	0	GIGYF2	233384221	1.000000	0.71417	0.840000	0.33206	0.263000	0.26337	3.541000	0.53618	0.762000	0.33152	0.561000	0.74099	GCC		0.428	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		3	43	0	0	0	0.115264	0	3	43				
SPATA16	83893	broad.mit.edu	37	3	172835272	172835272	+	Missense_Mutation	SNP	G	G	A	rs202106536		TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr3:172835272G>A	ENST00000351008.3	-	2	433	c.250C>T	c.(250-252)Cgg>Tgg	p.R84W		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	84					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			TCTGCCTTCCGTTTAAAGGCT	0.398													G|||	1	0.000199681	0.0	0.0	5008	,	,		22879	0.0		0.001	False		,,,				2504	0.0					ENST00000351008.3																			0				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43						c.(250-252)Cgg>Tgg		spermatogenesis associated 16							390.0	362.0	372.0					3																	172835272		2203	4300	6503	SO:0001583	missense	83893				cell differentiation|multicellular organismal development|spermatogenesis	Golgi apparatus	binding	g.chr3:172835272G>A	AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.250C>T	3.37:g.172835272G>A	ENSP00000341765:p.Arg84Trp						p.R84W	NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)		2	433	-	Ovarian(172;0.00319)|Breast(254;0.197)		84					Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Missense_Mutation	SNP	ENST00000351008.3	37	c.250C>T	CCDS3221.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	15.15	2.749245	0.49257	.	.	ENSG00000144962	ENST00000351008	T	0.17370	2.28	5.27	1.98	0.26296	.	0.274679	0.25698	N	0.028883	T	0.09113	0.0225	N	0.17082	0.46	0.32572	N	0.529682	B	0.28667	0.219	B	0.21360	0.034	T	0.14117	-1.0484	10	0.40728	T	0.16	-12.531	8.983	0.35977	0.0919:0.0:0.6251:0.283	.	84	Q9BXB7	SPT16_HUMAN	W	84	ENSP00000341765:R84W	ENSP00000341765:R84W	R	-	1	2	SPATA16	174317966	0.580000	0.26733	0.997000	0.53966	0.996000	0.88848	-0.266000	0.08631	0.148000	0.19059	0.650000	0.86243	CGG		0.398	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955		12	268	0	0	0	0.435327	0	12	268				
LINC00969	440993	broad.mit.edu	37	3	195395399	195395399	+	lincRNA	SNP	G	G	A	rs62287990	byFrequency	TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr3:195395399G>A	ENST00000445430.1	+	0	806									long intergenic non-protein coding RNA 969																		GGCTACGGGCGCACCTACTTG	0.607																																						ENST00000445430.1																			0																																																			440993							g.chr3:195395399G>A	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195395399G>A														0	806	+									RNA	SNP	ENST00000445430.1	37																																																																																						0.607	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			5	42	0	0	0	0.335167	0	5	42				
POTEF	728378	broad.mit.edu	37	2	130832473	130832473	+	Missense_Mutation	SNP	C	C	T	rs201025840		TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr2:130832473C>T	ENST00000409914.2	-	17	2971	c.2572G>A	c.(2572-2574)Ggg>Agg	p.G858R	POTEF_ENST00000357462.5_Missense_Mutation_p.G858R	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	858	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						TGGGTGACCCCGTCACCAGAG	0.607													.|||	1	0.000199681	0.0	0.0	5008	,	,		16851	0.0		0.001	False		,,,				2504	0.0					ENST00000357462.5																			0				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						c.(2572-2574)Ggg>Agg		POTE ankyrin domain family, member F							50.0	60.0	57.0					2																	130832473		2177	4259	6436	SO:0001583	missense	728378					cell cortex	ATP binding	g.chr2:130832473C>T	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2572G>A	2.37:g.130832473C>T	ENSP00000386786:p.Gly858Arg					POTEF_ENST00000409914.2_Missense_Mutation_p.G858R	p.G858R			A5A3E0	POTEF_HUMAN			15	2665	-			858			Actin-like.		A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	c.2572G>A	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	15.05	2.717493	0.48622	.	.	ENSG00000196604	ENST00000357462;ENST00000409914	T;T	0.12361	2.69;2.69	.	.	.	.	.	.	.	.	T	0.44705	0.1306	H	0.96604	3.85	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.39035	-0.9633	8	0.87932	D	0	.	5.9051	0.18992	0.0:0.9992:0.0:8.0E-4	.	858	A5A3E0	POTEF_HUMAN	R	858	ENSP00000350052:G858R;ENSP00000386786:G858R	ENSP00000350052:G858R	G	-	1	0	POTEF	130548943	1.000000	0.71417	0.088000	0.20740	0.089000	0.18198	5.244000	0.65400	0.119000	0.18210	0.121000	0.15741	GGG		0.607	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		8	78	0	0	0	0.307466	0	8	78				
MUC2	4583	broad.mit.edu	37	11	1092904	1092904	+	Missense_Mutation	SNP	C	C	A			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr11:1092904C>A	ENST00000441003.2	+	30	4750	c.4723C>A	c.(4723-4725)Ccc>Acc	p.P1575T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.P1576T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	aaccccaacacccaccggcac	0.642																																						ENST00000441003.2																			0				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102						c.(4723-4725)Ccc>Acc		mucin 2, oligomeric mucus/gel-forming	Pranlukast(DB01411)						102.0	143.0	129.0					11																	1092904		1946	3630	5576	SO:0001583	missense	4583					inner mucus layer|outer mucus layer	protein binding	g.chr11:1092904C>A	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4723C>A	11.37:g.1092904C>A	ENSP00000415183:p.Pro1575Thr					MUC2_ENST00000359061.5_Missense_Mutation_p.P1576T|MUC2_ENST00000361558.6_Intron	p.P1575T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	30	4750	+		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)	1578			Approximate repeats.		Q14878	Missense_Mutation	SNP	ENST00000441003.2	37	c.4723C>A		.	.	.	.	.	.	.	.	.	.	C	2.217	-0.379205	0.05000	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12569	2.68;2.67	1.49	-1.15	0.09709	.	23.387500	0.00794	U	0.001367	T	0.05777	0.0151	.	.	.	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.25257	-1.0137	9	0.09084	T	0.74	.	3.3129	0.07022	0.4211:0.4141:0.0:0.1648	.	1575	E7EUV1	.	T	1575;1576	ENSP00000415183:P1575T;ENSP00000351956:P1576T	ENSP00000351956:P1576T	P	+	1	0	MUC2	1082904	0.000000	0.05858	0.003000	0.11579	0.097000	0.18754	-2.401000	0.01048	-0.076000	0.12775	0.121000	0.15741	CCC		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		2	2	1	0	0.0016	0.115264	0.00195	2	2				
TRO	7216	broad.mit.edu	37	X	54955458	54955458	+	Silent	SNP	C	C	T			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chrX:54955458C>T	ENST00000173898.7	+	12	2413	c.2301C>T	c.(2299-2301)gcC>gcT	p.A767A	TRO_ENST00000375022.4_Intron|TRO_ENST00000399736.1_Intron|TRO_ENST00000375041.2_Silent_p.A370A|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000420798.2_Silent_p.A298A|TRO_ENST00000319167.8_Intron	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	767	62 X 10 AA approximate tandem repeats.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						GCACCAGTGCCAGCTTCAGCA	0.542																																						ENST00000173898.7																			0				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						c.(2299-2301)gcC>gcT		trophinin							63.0	66.0	65.0					X																	54955458		2141	4234	6375	SO:0001819	synonymous_variant	7216				embryo implantation|homophilic cell adhesion	integral to plasma membrane		g.chrX:54955458C>T	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.2301C>T	X.37:g.54955458C>T						TRO_ENST00000319167.8_Intron|TRO_ENST00000375022.4_Intron|TRO_ENST00000399736.1_Intron|TRO_ENST00000375041.2_Silent_p.A370A|TRO_ENST00000420798.2_Silent_p.A298A	p.A767A	NM_001039705.1	NP_001034794.1	Q12816	TROP_HUMAN			12	2413	+			767			62 X 10 AA approximate tandem repeats.		B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Silent	SNP	ENST00000173898.7	37	c.2301C>T	CCDS43959.1																																																																																				0.542	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		7	41	0	0	0	0.248553	0	7	41				
ARID1A	8289	broad.mit.edu	37	1	27105895	27105896	+	Frame_Shift_Ins	INS	-	-	A			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr1:27105895_27105896insA	ENST00000324856.7	+	20	5877_5878	c.5506_5507insA	c.(5506-5508)gagfs	p.E1836fs	ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.E1453fs|ARID1A_ENST00000540690.1_Frame_Shift_Ins_p.E164fs|ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.E1619fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1836					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GCGTGTGCAGGAGTTTGACAGT	0.535			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																	ENST00000324856.7				Rec	yes		1	1p35.3	8289	"""Mis, N, F, S, D"""	AT rich interactive domain 1A (SWI-like)			E			"""clear cell ovarian carcinoma, RCC"""	ARID1A/MAST2_ENST00000361297(2)	0				NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411						c.(5506-5508)gttfs		AT rich interactive domain 1A (SWI-like)																																				SO:0001589	frameshift_variant	8289				androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding	g.chr1:27105895_27105896insA	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5507dupA	1.37:g.27105896_27105896dupA	ENSP00000320485:p.Glu1836fs					ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.V1619fs|ARID1A_ENST00000540690.1_Frame_Shift_Ins_p.V164fs|ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.V1453fs	p.V1836fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)	20	5877_5878	+		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)	1836					D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Ins	INS	ENST00000324856.7	37	c.5506_5507insA	CCDS285.1																																																																																				0.535	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		7	100						7	100	---	---	---	---
BAP1	8314	broad.mit.edu	37	3	52437530	52437533	+	Frame_Shift_Del	DEL	ATGC	ATGC	-			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr3:52437530_52437533delATGC	ENST00000460680.1	-	13	2099_2102	c.1628_1631delGCAT	c.(1627-1632)tgcatafs	p.CI543fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.CI525fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GTTGTAGCGTATGCAGTCAACACG	0.618			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															GBM(101;493 1458 7992 21037 25532)	ENST00000460680.1				Rec	yes		3	3p21.31-p21.2	8314	"""N, Mis, F, S, O"""	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)			E		"""mesothelioma, uveal melanoma"""	"""uveal melanoma, breast, NSCLC, RCC"""		0				NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180						c.(1627-1632)tafs		BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)																																				SO:0001589	frameshift_variant	8314				monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	g.chr3:52437530_52437533delATGC	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1628_1631delGCAT	3.37:g.52437530_52437533delATGC	ENSP00000417132:p.Cys543fs					BAP1_ENST00000296288.5_Frame_Shift_Del_p.CI525fs	p.CI543fs	NM_004656.2	NP_004647.1	Q92560	BAP1_HUMAN		BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	13	2099_2102	-			543					B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	37	c.1628_1631delGCAT	CCDS2853.1																																																																																				0.618	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			9	75						9	75	---	---	---	---
BTNL9	153579	broad.mit.edu	37	5	180486849	180486849	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr5:180486849delT	ENST00000327705.9	+	11	1826	c.1595delT	c.(1594-1596)ctgfs	p.L532fs	BTNL9_ENST00000376842.3_Frame_Shift_Del_p.L533fs	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	532						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GACCCCGCCCTGGACTGGTGG	0.711																																						ENST00000327705.9																			0				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19						c.(1594-1596)cgfs		butyrophilin-like 9							6.0	8.0	7.0					5																	180486849		2156	4247	6403	SO:0001589	frameshift_variant	153579					integral to membrane		g.chr5:180486849delT	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.1595delT	5.37:g.180486849delT	ENSP00000330200:p.Leu532fs					BTNL9_ENST00000376842.3_Frame_Shift_Del_p.L533fs	p.L532fs	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		11	1826	+	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	532					A6NL42|Q6P660|Q96DM5	Frame_Shift_Del	DEL	ENST00000327705.9	37	c.1595delT	CCDS4460.2																																																																																				0.711	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547		2	4						2	4	---	---	---	---
POM121C	100101267	broad.mit.edu	37	7	75045497	75045497	+	IGR	DEL	G	G	-	rs201842651	byFrequency	TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr7:75045497delG	ENST00000257665.5	-	0	5700				NSUN5P1_ENST00000393633.2_RNA			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C						mRNA transport (GO:0051028)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14						GGGTCGTGGAGGGGGGGGATG	0.657													|||unknown(NO_COVERAGE)	508	0.101438	0.2995	0.0317	5008	,	,		10857	0.001		0.0398	False		,,,				2504	0.0501					ENST00000393633.2																			0				large_intestine(1)|lung(1)	2												589,1955		269,51,952	7.0	15.0	12.0			2.1	0.0	7	dbSNP_114	12	725,5999		314,97,2951	no	near-gene-3				583,148,3903	A1A1,A1R,RR		10.7823,23.1525,14.1778			75045497	1314,7954	2010	4158	6168	SO:0001628	intergenic_variant	155400							g.chr7:75045497delG		CCDS47617.1	7q11.23	2012-03-13	2012-03-13		ENSG00000135213	ENSG00000272391			34005	protein-coding gene	gene with protein product		615754	"""POM121 membrane glycoprotein C"""			17900573	Standard	NM_001099415		Approved		uc003udk.4	A8CG34	OTTHUMG00000156238		7.37:g.75045497delG														0	4280	+								O75115|Q9Y2N3|Q9Y4S7	RNA	DEL	ENST00000257665.5	37																																																																																						0.657	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415		2	4						2	4	---	---	---	---
FRMPD2	143162	broad.mit.edu	37	10	49379224	49379224	+	Frame_Shift_Del	DEL	T	T	-	rs568453728		TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr10:49379224delT	ENST00000374201.3	-	26	3553	c.3251delA	c.(3250-3252)aagfs	p.K1084fs	FRMPD2_ENST00000463706.1_5'UTR|FRMPD2_ENST00000407470.4_Frame_Shift_Del_p.K1052fs|FRMPD2_ENST00000474573.1_Frame_Shift_Del_p.K36fs|FRMPD2_ENST00000305531.3_Frame_Shift_Del_p.K1059fs	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	1084	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		ATTGGCATTCTTTTTTAGTTT	0.398																																						ENST00000374201.3																			0				NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66						c.(3250-3252)agfs		FERM and PDZ domain containing 2				2,1164		1,0,582	2.0	2.0	2.0			2.4	1.0	10		2	16,1814		7,2,906	no	frameshift	FRMPD2	NM_001018071.3		8,2,1488	A1A1,A1R,RR		0.8743,0.1715,0.6008			49379224	18,2978	812	1396	2208	SO:0001589	frameshift_variant	143162				tight junction assembly	basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction	1-phosphatidylinositol binding|protein binding	g.chr10:49379224delT	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.3251delA	10.37:g.49379224delT	ENSP00000363317:p.Lys1084fs					FRMPD2_ENST00000407470.4_Frame_Shift_Del_p.K1052fs|FRMPD2_ENST00000463706.1_5'UTR|FRMPD2_ENST00000474573.1_Frame_Shift_Del_p.K36fs|FRMPD2_ENST00000305531.3_Frame_Shift_Del_p.K1059fs	p.K1084fs	NM_001018071.3	NP_001018081.3	Q68DX3	FRPD2_HUMAN		Kidney(211;0.201)	26	3553	-			1084			PDZ 3.		B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Frame_Shift_Del	DEL	ENST00000374201.3	37	c.3251delA	CCDS31195.1																																																																																				0.398	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		4	2						4	2	---	---	---	---
POU4F1	5457	broad.mit.edu	37	13	79176484	79176486	+	In_Frame_Del	DEL	TGG	TGG	-	rs371388366		TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr13:79176484_79176486delTGG	ENST00000377208.5	-	2	535_537	c.324_326delCCA	c.(322-327)caccag>cag	p.H108del	RNF219-AS1_ENST00000607860.1_RNA|RNF219-AS1_ENST00000606376.1_RNA|RP11-52L5.6_ENST00000607269.1_RNA|RNF219-AS1_ENST00000444769.3_RNA|RNF219-AS1_ENST00000607205.1_RNA|RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000606124.1_RNA|RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000430549.2_RNA|RNF219-AS1_ENST00000607220.1_RNA	NM_006237.3	NP_006228.3	Q01851	PO4F1_HUMAN	POU class 4 homeobox 1	108	Poly-His.				axonogenesis (GO:0007409)|cell migration in hindbrain (GO:0021535)|central nervous system neuron differentiation (GO:0021953)|habenula development (GO:0021986)|innervation (GO:0060384)|mesoderm development (GO:0007498)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|peripheral nervous system neuron development (GO:0048935)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proprioception involved in equilibrioception (GO:0051355)|regulation of neurogenesis (GO:0050767)|sensory system development (GO:0048880)|suckling behavior (GO:0001967)|synapse assembly (GO:0007416)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)|ventricular compact myocardium morphogenesis (GO:0003223)	neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)	p.H108delH(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)	16		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.129)		TTCGAGCGCCtggtggtggtggt	0.729																																					Melanoma(109;347 2166 14574 42843)|Ovarian(81;1394 1854 22417 48351)	ENST00000377208.5																			1	Deletion - In frame(1)	p.H108delH(1)	central_nervous_system(1)	central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)	16						c.(322-327)cag>ca		POU class 4 homeobox 1																																				SO:0001651	inframe_deletion	5457				axonogenesis|regulation of transcription from RNA polymerase II promoter|synapse assembly	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr13:79176484_79176486delTGG	X64624	CCDS31996.1	13q31.1	2011-06-20	2007-07-13		ENSG00000152192	ENSG00000152192		"""Homeoboxes / POU class"""	9218	protein-coding gene	gene with protein product		601632	"""POU domain class 4, transcription factor 1"""	BRN3A		1357630	Standard	NM_006237		Approved	RDC-1	uc001vkv.3	Q01851	OTTHUMG00000017119	ENST00000377208.5:c.324_326delCCA	13.37:g.79176493_79176495delTGG	ENSP00000366413:p.His108del					RNF219-AS1_ENST00000430549.2_RNA|RNF219-AS1_ENST00000607220.1_RNA|RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000606376.1_RNA|RNF219-AS1_ENST00000606124.1_RNA|RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000607860.1_RNA|RNF219-AS1_ENST00000444769.3_RNA|RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000607205.1_RNA	p.HQ108del	NM_006237.3	NP_006228.3	Q01851	PO4F1_HUMAN		GBM - Glioblastoma multiforme(99;0.129)	2	535_537	-		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)	108			Poly-His.		Q14986|Q15318|Q5T227	In_Frame_Del	DEL	ENST00000377208.5	37	c.324_326delCCA	CCDS31996.1																																																																																				0.729	POU4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045360.3			2	4						2	4	---	---	---	---
IGHV3-23	28442	broad.mit.edu	37	14	106725714	106725715	+	RNA	INS	-	-	G	rs376179032		TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr14:106725714_106725715insG	ENST00000390609.2	-	0	18_19									immunoglobulin heavy variable 3-23																		ATCCCAGGGCTGGGCTCCTCTC	0.5																																						ENST00000390609.2																			0																																																			28442							g.chr14:106725714_106725715insG	M99660		14q32.33	2012-02-08			ENSG00000211949	ENSG00000211949		"""Immunoglobulins / IGH locus"""	5588	other	immunoglobulin gene		611939					Standard	NG_001019		Approved				OTTHUMG00000152091		14.37:g.106725717_106725717dupG														0	18_19	-									RNA	INS	ENST00000390609.2	37																																																																																						0.500	IGHV3-23-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000325188.1	NG_001019		7	55						7	55	---	---	---	---
ZNF559	84527	broad.mit.edu	37	19	9452027	9452028	+	Intron	DEL	CT	CT	-	rs55837495|rs201124569|rs398059552	byFrequency	TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr19:9452027_9452028delCT	ENST00000393883.2	+	5	891				ZNF177_ENST00000602856.1_Intron|ZNF177_ENST00000605471.1_Intron|ZNF177_ENST00000541595.2_Intron|ZNF559_ENST00000538743.1_Intron|ZNF559_ENST00000592896.1_Intron|ZNF559_ENST00000586255.1_Intron|ZNF559_ENST00000603380.1_Intron|ZNF559_ENST00000592504.1_Frame_Shift_Del_p.T137fs|ZNF559_ENST00000317221.7_Intron|ZNF559_ENST00000587557.1_Intron|ZNF559_ENST00000585352.1_Intron|ZNF177_ENST00000602738.1_Intron|ZNF177_ENST00000446085.4_Intron	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						TTGACAAACACTCTAAACATCC	0.347														2623	0.523762	0.5166	0.5317	5008	,	,		18993	0.4514		0.5606	False		,,,				2504	0.5644					ENST00000592504.1																			0				endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						c.(409-411)afs		zinc finger protein 559																																				SO:0001627	intron_variant	84527				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:9452027_9452028delCT	AL389937	CCDS12211.1, CCDS59349.1, CCDS62531.1, CCDS62532.1	19p13.2	2013-09-20			ENSG00000188321	ENSG00000188321		"""Zinc fingers, C2H2-type"", ""-"""	28197	protein-coding gene	gene with protein product						12477932	Standard	NM_001202406		Approved	MGC13105	uc002mle.4	Q9BR84	OTTHUMG00000179942	ENST00000393883.2:c.243+167CT>-	19.37:g.9452029_9452030delCT						ZNF177_ENST00000602738.1_Intron|ZNF177_ENST00000605471.1_Intron|ZNF177_ENST00000602856.1_Intron|ZNF559_ENST00000592896.1_Intron|ZNF559_ENST00000393883.2_Intron|ZNF177_ENST00000446085.4_Intron|ZNF559_ENST00000587557.1_Intron|ZNF559_ENST00000603380.1_Intron|ZNF559_ENST00000586255.1_Intron|ZNF559_ENST00000585352.1_Intron|ZNF177_ENST00000541595.2_Intron|ZNF559_ENST00000538743.1_Intron|ZNF559_ENST00000317221.7_Intron	p.T137fs			Q9BR84	ZN559_HUMAN			6	665_666	+			0					K7EMG6	Frame_Shift_Del	DEL	ENST00000393883.2	37	c.410_411delCT	CCDS12211.1																																																																																				0.347	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497		2	4						2	4	---	---	---	---
U2AF2	11338	broad.mit.edu	37	19	56185302	56185302	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CW-6097-01A-11D-1669-08	TCGA-CW-6097-11A-01D-1669-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d3cfe810-7b8c-4c3e-a49a-eea4d1ae9533	c3a6d147-8cb9-4088-b340-278ccad97903	g.chr19:56185302delC	ENST00000308924.4	+	12	1336	c.1296delC	c.(1294-1296)atcfs	p.I432fs	EPN1_ENST00000270460.6_5'Flank|CTD-2537I9.12_ENST00000589456.1_RNA|EPN1_ENST00000411543.2_5'Flank|U2AF2_ENST00000450554.2_Frame_Shift_Del_p.I428fs|CTD-2537I9.13_ENST00000592252.1_RNA|U2AF2_ENST00000590551.1_Frame_Shift_Del_p.I264fs|CTD-2537I9.12_ENST00000585940.1_RNA|EPN1_ENST00000085079.7_5'Flank			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	432	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		CCCCACAGATCTTTGTGGAGT	0.567																																						ENST00000450554.2																			0				biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21						c.(1282-1284)atfs		U2 small nuclear RNA auxiliary factor 2							96.0	85.0	89.0					19																	56185302		2203	4300	6503	SO:0001589	frameshift_variant	11338				mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	nucleoplasm|spliceosomal complex	enzyme binding|nucleotide binding|RNA binding	g.chr19:56185302delC	BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"""RNA binding motif (RRM) containing"""	23156	protein-coding gene	gene with protein product	"""U2 small nuclear ribonucleoprotein auxiliary factor (65kD)"", ""splicing factor U2AF 65 kD subunit"", ""U2 snRNP auxiliary factor large subunit"""	191318	"""U2 (RNU2) small nuclear RNA auxiliary factor 2"""			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.1296delC	19.37:g.56185302delC	ENSP00000307863:p.Ile432fs					CTD-2537I9.12_ENST00000585940.1_RNA|CTD-2537I9.12_ENST00000589456.1_RNA|U2AF2_ENST00000308924.4_Frame_Shift_Del_p.I432fs|U2AF2_ENST00000590551.1_Frame_Shift_Del_p.I264fs	p.I428fs	NM_001012478.1|NM_007279.2	NP_001012496.1|NP_009210.1	P26368	U2AF2_HUMAN	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)	12	2243	+		Colorectal(82;0.00244)|Ovarian(87;0.133)	432			RRM 3.		Q96HC5	Frame_Shift_Del	DEL	ENST00000308924.4	37	c.1284delC	CCDS12933.1																																																																																				0.567	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		12	104						12	104	---	---	---	---
