#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
NUP205	23165	broad.mit.edu	37	7	135279306	135279306	+	Silent	SNP	T	T	C			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr7:135279306T>C	ENST00000285968.6	+	13	1868	c.1842T>C	c.(1840-1842)gcT>gcC	p.A614A	NUP205_ENST00000440390.2_Intron	NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	614					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						GTGAAAATGCTCGCTTGGCAC	0.403																																						ENST00000285968.6																			0				breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						c.(1840-1842)gcT>gcC		nucleoporin 205kDa							93.0	95.0	94.0					7																	135279306		2203	4300	6503	SO:0001819	synonymous_variant	23165				carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding	g.chr7:135279306T>C	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.1842T>C	7.37:g.135279306T>C						NUP205_ENST00000440390.2_Intron	p.A614A	NM_015135.2	NP_055950.1	Q92621	NU205_HUMAN			13	1868	+			614					A6H8X3|Q86YC1	Silent	SNP	ENST00000285968.6	37	c.1842T>C	CCDS34759.1																																																																																				0.403	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			5	67	0	0	0	1	0	5	67				
CTTN	2017	broad.mit.edu	37	11	70282413	70282413	+	3'UTR	SNP	C	C	T	rs200495186		TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr11:70282413C>T	ENST00000301843.8	+	0	3004				CTTN_ENST00000346329.3_3'UTR|CTTN_ENST00000376561.3_Missense_Mutation_p.R602W	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin						negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitotic spindle midzone (GO:1990023)|ruffle (GO:0001726)				breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		CCTGAGGAGCCGGGAGGCTGG	0.607																																						ENST00000376561.3																			0				breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31						c.(1804-1806)Cgg>Tgg		cortactin		C	TRP/ARG,,	1,1745		0,1,872	102.0	100.0	100.0		1804,,	-2.7	0.0	11		100	6,3964		0,6,1979	yes	missense,utr-3,utr-3	CTTN	NM_001184740.1,NM_005231.3,NM_138565.2	101,,	0,7,2851	TT,TC,CC		0.1511,0.0573,0.1225	,,	602/635,,	70282413	7,5709	873	1985	2858	SO:0001624	3_prime_UTR_variant	2017					cell cortex|cytoskeleton|lamellipodium|ruffle|soluble fraction	protein binding	g.chr11:70282413C>T	AJ288897	CCDS8197.1, CCDS41680.1, CCDS53676.1	11q13	2008-02-05	2004-06-08	2004-06-09	ENSG00000085733	ENSG00000085733			3338	protein-coding gene	gene with protein product		164765	"""ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate)"""	EMS1		7685625	Standard	NM_005231		Approved		uc001opu.3	Q14247	OTTHUMG00000134307	ENST00000301843.8:c.*1145C>T	11.37:g.70282413C>T						CTTN_ENST00000346329.3_3'UTR|CTTN_ENST00000301843.8_3'UTR	p.R602W	NM_001184740.1	NP_001171669.1	Q14247	SRC8_HUMAN	BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)	19	1975	+			0					Q8N707|Q96H99	Missense_Mutation	SNP	ENST00000301843.8	37	c.1804C>T	CCDS41680.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.504048	0.26949	5.73E-4	0.001511	ENSG00000085733	ENST00000376561;ENST00000529736	T;T	0.37584	1.19;1.29	4.11	-2.72	0.05968	.	.	.	.	.	T	0.22742	0.0549	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.25152	-1.0140	8	0.87932	D	0	.	4.5347	0.12022	0.0:0.3371:0.2941:0.3688	.	602	Q8N707	.	W	602;233	ENSP00000365745:R602W;ENSP00000431421:R233W	ENSP00000365745:R602W	R	+	1	2	CTTN	69960061	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.307000	0.08167	-0.707000	0.05022	-0.136000	0.14681	CGG		0.607	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565		4	66	0	0	0	1	0	4	66				
PAX9	5083	broad.mit.edu	37	14	37132444	37132444	+	Missense_Mutation	SNP	A	A	G			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr14:37132444A>G	ENST00000361487.6	+	2	572	c.347A>G	c.(346-348)aAt>aGt	p.N116S	PAX9_ENST00000402703.2_Missense_Mutation_p.N116S|PAX9_ENST00000554201.1_5'UTR			P55771	PAX9_HUMAN	paired box 9	116	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				cellular response to growth factor stimulus (GO:0071363)|endoderm development (GO:0007492)|face morphogenesis (GO:0060325)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|regulation of odontogenesis (GO:0042481)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(3)	12	Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.218)		Lung(8;1.12e-09)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.00357)|all cancers(34;0.00998)|LUSC - Lung squamous cell carcinoma(13;0.0189)	GBM - Glioblastoma multiforme(112;0.0181)		GACAAGTACAATGTGCCCTCC	0.607																																						ENST00000361487.6																			0				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(3)	12						c.(346-348)aAt>aGt		paired box 9							88.0	81.0	84.0					14																	37132444		2203	4300	6503	SO:0001583	missense	5083				multicellular organismal development|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding	g.chr14:37132444A>G	AJ238381	CCDS9662.1	14q13.3	2007-07-12	2007-07-12		ENSG00000198807	ENSG00000198807		"""Paired boxes"""	8623	protein-coding gene	gene with protein product		167416	"""paired box gene 9"""			7981748	Standard	NM_006194		Approved		uc001wty.4	P55771	OTTHUMG00000140251	ENST00000361487.6:c.347A>G	14.37:g.37132444A>G	ENSP00000355245:p.Asn116Ser					PAX9_ENST00000402703.2_Missense_Mutation_p.N116S|PAX9_ENST00000554201.1_5'UTR	p.N116S			P55771	PAX9_HUMAN	Lung(8;1.12e-09)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.00357)|all cancers(34;0.00998)|LUSC - Lung squamous cell carcinoma(13;0.0189)	GBM - Glioblastoma multiforme(112;0.0181)	2	572	+	Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.218)		116			Paired.		Q99582|Q9UQR4	Missense_Mutation	SNP	ENST00000361487.6	37	c.347A>G	CCDS9662.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.332645	0.81801	.	.	ENSG00000198807	ENST00000402703;ENST00000361487	D;D	0.99394	-5.82;-5.82	5.25	5.25	0.73442	Paired box protein, N-terminal (3);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98686	0.9559	L	0.31526	0.94	0.80722	D	1	D	0.61080	0.989	D	0.64144	0.922	D	0.99904	1.1174	10	0.62326	D	0.03	.	15.1383	0.72586	1.0:0.0:0.0:0.0	.	116	P55771	PAX9_HUMAN	S	116	ENSP00000384817:N116S;ENSP00000355245:N116S	ENSP00000355245:N116S	N	+	2	0	PAX9	36202195	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.493000	0.81493	1.978000	0.57642	0.459000	0.35465	AAT		0.607	PAX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276733.2			13	117	0	0	0	1	0	13	117				
GRIFIN	402635	broad.mit.edu	37	7	2515600	2515600	+	RNA	SNP	C	C	T			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr7:2515600C>T	ENST00000417742.1	-	0	203							A4D1Z8	GRIFN_HUMAN	galectin-related inter-fiber protein								carbohydrate binding (GO:0030246)						Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;3.23e-14)		AGCTTCCAGCCGGGGGCCAGG	0.706																																						ENST00000417742.1																			0													galectin-related inter-fiber protein							24.0	29.0	28.0					7																	2515600		1940	4119	6059			402635							g.chr7:2515600C>T			7p22.2	2013-01-30			ENSG00000236734	ENSG00000275572			4577	protein-coding gene	gene with protein product						9786891, 18087242	Standard	NM_001291784		Approved			A4D1Z8	OTTHUMG00000152042		7.37:g.2515600C>T													UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;3.23e-14)	0	203	-		Ovarian(82;0.11)							RNA	SNP	ENST00000417742.1	37																																																																																						0.706	GRIFIN-002	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000325020.1			4	52	0	0	0	1	0	4	52				
CCDC87	55231	broad.mit.edu	37	11	66358990	66358990	+	Missense_Mutation	SNP	C	C	T			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr11:66358990C>T	ENST00000333861.3	-	1	1564	c.1497G>A	c.(1495-1497)atG>atA	p.M499I	CCS_ENST00000533244.1_5'Flank|CCS_ENST00000310190.4_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	499					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						AGACATGGCTCATCAACTCCT	0.463																																						ENST00000333861.3																			0				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						c.(1495-1497)atG>atA		coiled-coil domain containing 87							112.0	112.0	112.0					11																	66358990		2200	4295	6495	SO:0001583	missense	55231							g.chr11:66358990C>T	BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.1497G>A	11.37:g.66358990C>T	ENSP00000328487:p.Met499Ile						p.M499I	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN			1	1564	-			499					Q8NE76	Missense_Mutation	SNP	ENST00000333861.3	37	c.1497G>A	CCDS8145.1	.	.	.	.	.	.	.	.	.	.	C	6.241	0.412538	0.11812	.	.	ENSG00000182791	ENST00000333861	T	0.33216	1.42	5.3	3.37	0.38596	.	0.386734	0.22040	N	0.065462	T	0.21509	0.0518	L	0.38531	1.155	0.31495	N	0.665548	B	0.21821	0.061	B	0.15870	0.014	T	0.12760	-1.0535	10	0.38643	T	0.18	-4.3813	7.4557	0.27266	0.0:0.7442:0.1664:0.0894	.	499	Q9NVE4	CCD87_HUMAN	I	499	ENSP00000328487:M499I	ENSP00000328487:M499I	M	-	3	0	CCDC87	66115566	1.000000	0.71417	0.999000	0.59377	0.233000	0.25261	0.664000	0.25068	0.755000	0.32990	0.563000	0.77884	ATG		0.463	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219		21	106	0	0	0	1	0	21	106				
MTOR	2475	broad.mit.edu	37	1	11169351	11169351	+	Silent	SNP	G	G	T			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr1:11169351G>T	ENST00000361445.4	-	56	7600	c.7524C>A	c.(7522-7524)ctC>ctA	p.L2508L	MTOR_ENST00000376838.1_Silent_p.L713L	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2508	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	ACTCACCAGTGAGCTTATCTC	0.428																																						ENST00000361445.4																			0				breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149						c.(7522-7524)ctC>ctA		mechanistic target of rapamycin (serine/threonine kinase)							174.0	152.0	159.0					1																	11169351		2203	4300	6503	SO:0001819	synonymous_variant	2475				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity	g.chr1:11169351G>T	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.7524C>A	1.37:g.11169351G>T						MTOR_ENST00000376838.1_Silent_p.L713L	p.L2508L	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN			56	7600	-			2508			PI3K/PI4K.		Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	c.7524C>A	CCDS127.1																																																																																				0.428	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		4	87	1	0	0.150653	1	0.154001	4	87				
SYNE3	161176	broad.mit.edu	37	14	95921914	95921914	+	Missense_Mutation	SNP	G	G	A	rs201816324	byFrequency	TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr14:95921914G>A	ENST00000334258.5	-	5	951	c.937C>T	c.(937-939)Cgc>Tgc	p.R313C	SYNE3_ENST00000553340.1_Missense_Mutation_p.R313C|SYNE3_ENST00000557275.1_Missense_Mutation_p.R313C|SYNE3_ENST00000554873.1_Missense_Mutation_p.R70C	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	313					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						CAGAGGGCGCGCAGCTTCTCC	0.617													G|||	3	0.000599042	0.0	0.0	5008	,	,		17818	0.002		0.001	False		,,,				2504	0.0					ENST00000334258.5																			0				breast(1)|endometrium(2)|lung(25)	28						c.(937-939)Cgc>Tgc		spectrin repeat containing, nuclear envelope family member 3		G	CYS/ARG	0,4406		0,0,2203	82.0	88.0	86.0		937	1.4	0.3	14		86	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C14orf49	NM_152592.3	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	313/976	95921914	1,13005	2203	4300	6503	SO:0001583	missense	161176							g.chr14:95921914G>A	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.937C>T	14.37:g.95921914G>A	ENSP00000334308:p.Arg313Cys					SYNE3_ENST00000553340.1_Missense_Mutation_p.R313C|SYNE3_ENST00000554873.1_Missense_Mutation_p.R70C|SYNE3_ENST00000557275.1_Missense_Mutation_p.R313C	p.R313C	NM_152592.3	NP_689805.3					5	951	-								A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	c.937C>T	CCDS9935.1	2	9.157509157509158E-4	0	0.0	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	G	13.49	2.253119	0.39797	0.0	1.16E-4	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275;ENST00000553340	T;T;T;T	0.35421	3.41;1.31;3.4;2.82	4.99	1.38	0.22167	.	0.539289	0.13989	N	0.348960	T	0.51890	0.1701	M	0.70595	2.14	0.43622	D	0.996004	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.68765	0.96;0.927;0.912	T	0.49943	-0.8885	10	0.66056	D	0.02	-4.8666	6.2119	0.20633	0.1151:0.0:0.2845:0.6004	.	313;313;313	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	C	313;70;313;313	ENSP00000334308:R313C;ENSP00000452154:R70C;ENSP00000450562:R313C;ENSP00000450774:R313C	ENSP00000334308:R313C	R	-	1	0	C14orf49	94991667	0.997000	0.39634	0.285000	0.24819	0.108000	0.19459	0.977000	0.29475	0.373000	0.24621	0.455000	0.32223	CGC		0.617	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		6	157	0	0	0	1	0	6	157				
CYFIP1	23191	broad.mit.edu	37	15	22933658	22933658	+	Splice_Site	SNP	G	G	T			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr15:22933658G>T	ENST00000313077.7	+	7	791		c.e7+1		CYFIP1_ENST00000560848.1_Splice_Site	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		GATCACACAGGTAAGGCTGGT	0.537																																						ENST00000313077.7																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						c.e7+1		cytoplasmic FMR1 interacting protein 1							104.0	90.0	95.0					15																	22933658		2203	4300	6503	SO:0001630	splice_region_variant	23191				axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization	cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome	actin filament binding|Rac GTPase binding	g.chr15:22933658G>T	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.666+1G>T	15.37:g.22933658G>T						CYFIP1_ENST00000560848.1_Splice_Site		NM_014608.2	NP_055423.1	Q7L576	CYFP1_HUMAN		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)	7	791	+		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)							Splice_Site	SNP	ENST00000313077.7	37		CCDS10009.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.414946	0.42817	.	.	ENSG00000068793	ENST00000313077;ENST00000412127	.	.	.	5.94	5.02	0.67125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4843	0.84180	0.0:0.0:0.8679:0.1321	.	.	.	.	.	-1	.	.	.	+	.	.	CYFIP1	20485099	1.000000	0.71417	0.186000	0.23195	0.210000	0.24377	9.705000	0.98719	1.498000	0.48600	0.650000	0.86243	.		0.537	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608	Intron	4	65	1	0	1	1	1	4	65				
HLA-DRB6	3128	broad.mit.edu	37	6	32522465	32522465	+	RNA	SNP	A	A	G			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr6:32522465A>G	ENST00000411500.1	-	0	740					NR_001298.1				major histocompatibility complex, class II, DR beta 6 (pseudogene)																		AAAGCTGCTCACTCCATTCCA	0.498																																						ENST00000411500.1																			0																																																			0							g.chr6:32522465A>G	L76566		6p21.3	2011-07-08			ENSG00000229391	ENSG00000229391		"""Histocompatibility complex"""	4954	pseudogene	pseudogene						1529427, 10436177	Standard	NR_001298		Approved		uc003obn.1		OTTHUMG00000031028		6.37:g.32522465A>G								NR_001298.1						0	740	-									RNA	SNP	ENST00000411500.1	37																																																																																						0.498	HLA-DRB6-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000272900.1	NR_001298		6	147	0	0	0	1	0	6	147				
LRRIQ3	127255	broad.mit.edu	37	1	74507071	74507071	+	Missense_Mutation	SNP	C	C	T	rs534493116	byFrequency	TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr1:74507071C>T	ENST00000395089.1	-	6	1543	c.1544G>A	c.(1543-1545)cGt>cAt	p.R515H	LRRIQ3_ENST00000354431.4_Missense_Mutation_p.R515H			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	515								p.R515H(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						AACTAATAAACGCTCTGAAGC	0.363													C|||	2	0.000399361	0.0	0.0029	5008	,	,		15266	0.0		0.0	False		,,,				2504	0.0					ENST00000354431.4																			1	Substitution - Missense(1)	p.R515H(1)	large_intestine(1)	NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						c.(1543-1545)cGt>cAt		leucine-rich repeats and IQ motif containing 3							102.0	100.0	101.0					1																	74507071		1797	4070	5867	SO:0001583	missense	127255							g.chr1:74507071C>T	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"""leucine rich repeat containing 44"""	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.1544G>A	1.37:g.74507071C>T	ENSP00000378524:p.Arg515His					LRRIQ3_ENST00000395089.1_Missense_Mutation_p.R515H	p.R515H	NM_001105659.1	NP_001099129.1	A6PVS8	LRIQ3_HUMAN			7	1735	-			515					A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Missense_Mutation	SNP	ENST00000395089.1	37	c.1544G>A	CCDS41350.1	.	.	.	.	.	.	.	.	.	.	C	6.084	0.383714	0.11524	.	.	ENSG00000162620	ENST00000395089;ENST00000354431	T;T	0.10382	2.88;2.88	5.86	2.52	0.30459	.	.	.	.	.	T	0.02047	0.0064	L	0.29908	0.895	0.09310	N	1	B	0.34255	0.445	B	0.20184	0.028	T	0.44452	-0.9327	9	0.35671	T	0.21	.	8.4238	0.32716	0.0:0.7631:0.0:0.2369	.	515	A6PVS8	LRIQ3_HUMAN	H	515	ENSP00000378524:R515H;ENSP00000346414:R515H	ENSP00000346414:R515H	R	-	2	0	LRRIQ3	74279659	0.273000	0.24181	0.016000	0.15963	0.029000	0.11900	0.609000	0.24238	0.295000	0.22570	0.650000	0.86243	CGT		0.363	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		5	82	0	0	0	1	0	5	82				
BEND6	221336	broad.mit.edu	37	6	56819267	56819267	+	5'Flank	SNP	C	C	T			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr6:56819267C>T	ENST00000370746.3	+	0	0				BEND6_ENST00000370748.3_5'Flank|BEND6_ENST00000370745.1_5'Flank|DST_ENST00000370754.5_Missense_Mutation_p.R40H|BEND6_ENST00000370750.2_5'Flank	NM_152731.2	NP_689944.2	Q5SZJ8	BEND6_HUMAN	BEN domain containing 6						negative regulation of transcription from RNA polymerase II promoter (GO:0000122)		RNA polymerase II transcription corepressor activity (GO:0001106)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	17						CTGGAGCTTGCGGTGCCAGCA	0.582																																						ENST00000370754.5																			0				NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105						c.(118-120)cGc>cAc		dystonin							43.0	44.0	43.0					6																	56819267		1568	3582	5150	SO:0001631	upstream_gene_variant	667				cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity	g.chr6:56819267C>T	AK054724	CCDS43476.1	6p12.1	2012-11-22	2008-10-03	2008-10-03	ENSG00000151917	ENSG00000151917		"""BEN domain containing"""	20871	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 65"""	C6orf65			Standard	NM_152731		Approved	FLJ30162, bA203B9.1	uc010kab.3	Q5SZJ8	OTTHUMG00000014914		6.37:g.56819267C>T	Exception_encountered						p.R40H			Q03001	DYST_HUMAN	LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)		1	118	-	Lung NSC(77;0.103)		0			Actin-binding.|CH 1.		Q4G0W8|Q8N662|Q96NS6	Missense_Mutation	SNP	ENST00000370746.3	37	c.119G>A	CCDS43476.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.284925	0.80803	.	.	ENSG00000151914	ENST00000370754;ENST00000449297	T;D	0.96651	-1.45;-4.08	4.12	4.12	0.48240	.	.	.	.	.	D	0.97860	0.9297	.	.	.	.	.	.	D	0.89917	1.0	D	0.78314	0.991	D	0.98871	1.0766	7	0.87932	D	0	.	16.1918	0.81996	0.0:1.0:0.0:0.0	.	40	E9PEB9	.	H	40	ENSP00000359790:R40H;ENSP00000393082:R40H	ENSP00000359790:R40H	R	-	2	0	DST	56927226	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.608000	0.74168	2.111000	0.64477	0.563000	0.77884	CGC		0.582	BEND6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041032.4	NM_152731		3	31	0	0	0	1	0	3	31				
RAB37	326624	broad.mit.edu	37	17	72736966	72736966	+	Silent	SNP	C	C	T	rs530556816		TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr17:72736966C>T	ENST00000392613.5	+	2	209	c.153C>T	c.(151-153)gaC>gaT	p.D51D	RAB37_ENST00000392615.5_Intron|RAB37_ENST00000528438.1_Silent_p.D24D|RAB37_ENST00000392610.1_Silent_p.D51D|RAB37_ENST00000392612.3_Intron|RAB37_ENST00000402449.4_Intron|RAB37_ENST00000392614.4_Silent_p.D56D|RAB37_ENST00000340415.3_Intron	NM_001006638.2	NP_001006639.1	Q96AX2	RAB37_HUMAN	RAB37, member RAS oncogene family	51					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|secretory granule (GO:0030141)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	12						AATTCAAAGACGGGGCCTTCC	0.587																																						ENST00000392610.1																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	12						c.(151-153)gaC>gaT		RAB37, member RAS oncogene family							140.0	139.0	139.0					17																	72736966		2203	4300	6503	SO:0001819	synonymous_variant	326624				protein transport|small GTPase mediated signal transduction	ER-Golgi intermediate compartment	GTP binding	g.chr17:72736966C>T	BC040547	CCDS11703.1, CCDS32722.1, CCDS54161.1, CCDS54162.1	17q25.2	2008-02-05			ENSG00000172794	ENSG00000172794		"""RAB, member RAS oncogene"""	30268	protein-coding gene	gene with protein product		609956				10722846	Standard	NM_175738		Approved		uc002jlk.3	Q96AX2	OTTHUMG00000134282	ENST00000392613.5:c.153C>T	17.37:g.72736966C>T						RAB37_ENST00000392613.5_Silent_p.D51D|RAB37_ENST00000402449.4_Intron|RAB37_ENST00000392612.3_Intron|RAB37_ENST00000528438.1_Silent_p.D24D|RAB37_ENST00000392614.4_Silent_p.D56D|RAB37_ENST00000392615.5_Intron|RAB37_ENST00000340415.3_Intron	p.D51D			Q96AX2	RAB37_HUMAN			2	194	+			51					A8MXF5|A8MYT0|Q8IWA7	Silent	SNP	ENST00000392613.5	37	c.153C>T	CCDS32722.1																																																																																				0.587	RAB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258872.2	NM_175738		18	190	0	0	0	1	0	18	190				
PKHD1L1	93035	broad.mit.edu	37	8	110442248	110442248	+	Missense_Mutation	SNP	G	G	A			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr8:110442248G>A	ENST00000378402.5	+	27	3315	c.3211G>A	c.(3211-3213)Gcg>Acg	p.A1071T		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1071	IPT/TIG 4.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CCTAGTCTTGGCGATAAGCCC	0.368										HNSCC(38;0.096)																												ENST00000378402.5																			0				NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263						c.(3211-3213)Gcg>Acg		polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1							121.0	107.0	111.0					8																	110442248		1870	4113	5983	SO:0001583	missense	93035				immune response	cytosol|extracellular space|integral to membrane	receptor activity	g.chr8:110442248G>A	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.3211G>A	8.37:g.110442248G>A	ENSP00000367655:p.Ala1071Thr	HNSCC(38;0.096)					p.A1071T	NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)		27	3315	+			1071			IPT/TIG 4.		Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	c.3211G>A	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	9.042	0.989916	0.18966	.	.	ENSG00000205038	ENST00000378402	T	0.78003	-1.14	5.44	0.0583	0.14327	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.842433	0.10435	N	0.674990	T	0.57577	0.2063	N	0.25332	0.735	0.09310	N	1	B	0.10296	0.003	B	0.13407	0.009	T	0.35773	-0.9775	10	0.12766	T	0.61	.	2.9311	0.05800	0.2832:0.0:0.3849:0.332	.	1071	Q86WI1	PKHL1_HUMAN	T	1071	ENSP00000367655:A1071T	ENSP00000367655:A1071T	A	+	1	0	PKHD1L1	110511424	0.000000	0.05858	0.000000	0.03702	0.085000	0.17905	0.416000	0.21198	0.054000	0.16065	0.650000	0.86243	GCG		0.368	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		3	22	0	0	0	1	0	3	22				
PLCB1	23236	broad.mit.edu	37	20	8639228	8639228	+	Missense_Mutation	SNP	G	G	A			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr20:8639228G>A	ENST00000338037.6	+	9	766	c.739G>A	c.(739-741)Gat>Aat	p.D247N	PLCB1_ENST00000378637.2_Missense_Mutation_p.D247N|PLCB1_ENST00000378641.3_Missense_Mutation_p.D247N	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	247					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						TCAGATGATGGATTTTATCAA	0.333																																						ENST00000378641.3																			0				NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						c.(739-741)Gat>Aat		phospholipase C, beta 1 (phosphoinositide-specific)							106.0	102.0	104.0					20																	8639228		2203	4300	6503	SO:0001583	missense	23236				activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity	g.chr20:8639228G>A	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.739G>A	20.37:g.8639228G>A	ENSP00000338185:p.Asp247Asn					PLCB1_ENST00000378637.2_Missense_Mutation_p.D247N|PLCB1_ENST00000338037.6_Missense_Mutation_p.D247N	p.D247N	NM_182734.1	NP_877398.1	Q9NQ66	PLCB1_HUMAN			9	1214	+			247					D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	37	c.739G>A	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.391924	0.83011	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.17528	2.27;2.27;2.27	5.95	5.95	0.96441	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);EF-hand-like domain (1);	0.044614	0.85682	D	0.000000	T	0.19208	0.0461	N	0.25201	0.72	0.53005	D	0.999964	B;P	0.45176	0.063;0.852	B;P	0.45753	0.044;0.492	T	0.00653	-1.1625	10	0.37606	T	0.19	.	20.3921	0.98947	0.0:0.0:1.0:0.0	.	247;247	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	N	247;247;247;167;167	ENSP00000367908:D247N;ENSP00000338185:D247N;ENSP00000367904:D247N	ENSP00000338185:D247N	D	+	1	0	PLCB1	8587228	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.751000	0.98889	2.822000	0.97130	0.650000	0.86243	GAT		0.333	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			9	48	0	0	0	1	0	9	48				
CYB561A3	220002	broad.mit.edu	37	11	61118523	61118523	+	Silent	SNP	G	G	A			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr11:61118523G>A	ENST00000294072.4	-	6	1322	c.645C>T	c.(643-645)ctC>ctT	p.L215L	CYB561A3_ENST00000536915.1_Silent_p.L215L|CYB561A3_ENST00000539890.1_Missense_Mutation_p.S94F|CYB561A3_ENST00000426130.2_Silent_p.L232L|CYB561A3_ENST00000540317.1_5'UTR|CYB561A3_ENST00000546151.1_3'UTR|CYB561A3_ENST00000447532.2_Silent_p.L215L|CYB561A3_ENST00000544118.1_Missense_Mutation_p.S89F	NM_001161452.1|NM_153611.4	NP_001154924.1|NP_705839.3	Q8NBI2	CYAC3_HUMAN	cytochrome b561 family, member A3	215	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.					integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)										GAAGGATGTAGAGCACCAGCA	0.607																																						ENST00000544118.1																			0											c.(265-267)tCt>tTt		cytochrome b561 family, member A3							60.0	59.0	59.0					11																	61118523		2203	4299	6502	SO:0001819	synonymous_variant	220002							g.chr11:61118523G>A	AK024953	CCDS8004.1, CCDS53639.1, CCDS73296.1	11q12.2	2013-03-14	2013-03-14	2013-03-14		ENSG00000162144		"""Cytochrome b genes"""	23014	protein-coding gene	gene with protein product			"""cytochrome b, ascorbate dependent 3"""	CYBASC3		23249217	Standard	NM_153611		Approved		uc001nrf.4	Q8NBI2		ENST00000294072.4:c.645C>T	11.37:g.61118523G>A						CYB561A3_ENST00000536915.1_Silent_p.L215L|CYB561A3_ENST00000539890.1_Missense_Mutation_p.S94F|CYB561A3_ENST00000294072.4_Silent_p.L215L|CYB561A3_ENST00000447532.2_Silent_p.L215L|CYB561A3_ENST00000426130.2_Silent_p.L232L|CYB561A3_ENST00000546151.1_3'UTR|CYB561A3_ENST00000540317.1_5'UTR	p.S89F							4	493	-								B3KPU2|B4DLN9|J3KQH4|Q6PK96	Missense_Mutation	SNP	ENST00000294072.4	37	c.266C>T	CCDS8004.1	.	.	.	.	.	.	.	.	.	.	G	15.60	2.882470	0.51908	.	.	ENSG00000162144	ENST00000544118;ENST00000539890	.	.	.	5.68	3.75	0.43078	.	.	.	.	.	T	0.70596	0.3242	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71846	-0.4469	5	0.87932	D	0	-35.8401	10.5811	0.45257	0.0741:0.4816:0.4442:0.0	.	.	.	.	F	89;94	.	ENSP00000443756:S94F	S	-	2	0	CYBASC3	60875099	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	1.166000	0.31834	0.706000	0.31912	0.563000	0.77884	TCT		0.607	CYB561A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398714.2	NM_153611		5	27	0	0	0	1	0	5	27				
SHROOM1	134549	broad.mit.edu	37	5	132158689	132158689	+	Silent	SNP	C	C	T			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr5:132158689C>T	ENST00000378679.3	-	10	3162	c.2358G>A	c.(2356-2358)ctG>ctA	p.L786L	SHROOM1_ENST00000378676.1_Silent_p.L717L|SHROOM1_ENST00000488072.1_5'Flank|SHROOM1_ENST00000319854.3_Silent_p.L781L	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	786	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AATAGACGCGCAGCTCCTCCA	0.706																																						ENST00000378679.3																			0				endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17						c.(2356-2358)ctG>ctA		shroom family member 1							32.0	30.0	31.0					5																	132158689		2200	4298	6498	SO:0001819	synonymous_variant	134549				actin filament bundle assembly|cell morphogenesis	cytoplasm|microtubule	actin filament binding	g.chr5:132158689C>T	AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.2358G>A	5.37:g.132158689C>T						SHROOM1_ENST00000319854.3_Silent_p.L781L|SHROOM1_ENST00000378676.1_Silent_p.L717L	p.L786L	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		10	3162	-			786			ASD2.		B7WP40|B7ZL01|Q8TDP0|Q8TF41	Silent	SNP	ENST00000378679.3	37	c.2358G>A	CCDS54902.1																																																																																				0.706	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		4	39	0	0	0	1	0	4	39				
GRIP1	23426	broad.mit.edu	37	12	66788097	66788097	+	Missense_Mutation	SNP	C	C	T			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr12:66788097C>T	ENST00000398016.3	-	16	1932	c.1864G>A	c.(1864-1866)Gtg>Atg	p.V622M	GRIP1_ENST00000286445.7_Missense_Mutation_p.V674M|GRIP1_ENST00000542021.1_5'Flank|GRIP1_ENST00000359742.4_Missense_Mutation_p.V674M	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		TTAAGCTCCACGGTGTAAATA	0.413																																						ENST00000359742.4																			0				NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50						c.(2020-2022)Gtg>Atg		glutamate receptor interacting protein 1							77.0	73.0	74.0					12																	66788097		1815	4074	5889	SO:0001583	missense	23426				androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity	g.chr12:66788097C>T	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.1864G>A	12.37:g.66788097C>T	ENSP00000381098:p.Val622Met					GRIP1_ENST00000398016.3_Missense_Mutation_p.V622M|GRIP1_ENST00000286445.7_Missense_Mutation_p.V674M	p.V674M			Q9Y3R0	GRIP1_HUMAN	GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)	17	2260	-			674			PDZ 6.		B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	37	c.2020G>A	CCDS41807.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.815383	0.90790	.	.	ENSG00000155974	ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215	T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96	4.2	4.2	0.49525	PDZ/DHR/GLGF (3);	0.250432	0.39146	N	0.001446	T	0.71584	0.3357	M	0.92122	3.275	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;0.997;0.999	D;D;P;D	0.66979	0.921;0.92;0.908;0.948	T	0.80070	-0.1536	9	.	.	.	-18.3282	17.8456	0.88729	0.0:1.0:0.0:0.0	.	622;674;622;674	F5H4N6;Q9Y3R0;Q9Y3R0-3;Q9Y3R0-2	.;GRIP1_HUMAN;.;.	M	622;674;674;622;566;514	ENSP00000381098:V622M;ENSP00000352780:V674M;ENSP00000286445:V674M;ENSP00000446047:V622M;ENSP00000446024:V566M;ENSP00000446011:V514M	.	V	-	1	0	GRIP1	65074364	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	7.609000	0.82925	2.644000	0.89710	0.655000	0.94253	GTG		0.413	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			7	55	0	0	0	1	0	7	55				
AXIN2	8313	broad.mit.edu	37	17	63554729	63554729	+	Missense_Mutation	SNP	C	C	A			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr17:63554729C>A	ENST00000375702.5	-	1	118	c.10G>T	c.(10-12)Gct>Tct	p.A4S	AXIN2_ENST00000307078.5_Missense_Mutation_p.A4S|CTD-2535L24.2_ENST00000577662.1_3'UTR			Q9Y2T1	AXIN2_HUMAN	axin 2	4					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						ACCAACATAGCGCTACTCATG	0.592									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																													ENST00000307078.5																			0				NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						c.(10-12)Gct>Tct		axin 2							23.0	27.0	26.0					17																	63554729		2200	4294	6494	SO:0001583	missense	8313	Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding	g.chr17:63554729C>A	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"""conductin"", ""axil"""	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.10G>T	17.37:g.63554729C>A	ENSP00000364854:p.Ala4Ser					AXIN2_ENST00000375702.5_Missense_Mutation_p.A4S|CTD-2535L24.2_ENST00000577662.1_3'UTR	p.A4S	NM_004655.3	NP_004646.3	Q9Y2T1	AXIN2_HUMAN			2	323	-			4					Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	ENST00000375702.5	37	c.10G>T		.	.	.	.	.	.	.	.	.	.	C	9.740	1.164525	0.21538	.	.	ENSG00000168646	ENST00000307078;ENST00000544103;ENST00000375702	T;T;T	0.78364	-0.21;-1.17;-0.22	4.61	2.62	0.31277	.	0.259107	0.28964	N	0.013574	T	0.62392	0.2424	L	0.32530	0.975	0.28610	N	0.908701	B;B;B	0.22909	0.077;0.008;0.077	B;B;B	0.17098	0.017;0.016;0.017	T	0.53837	-0.8382	10	0.44086	T	0.13	-4.4115	5.1076	0.14793	0.1643:0.657:0.0:0.1788	.	4;4;4	B7ZKL5;Q9Y2T1;E7ES00	.;AXIN2_HUMAN;.	S	4	ENSP00000302625:A4S;ENSP00000441151:A4S;ENSP00000364854:A4S	ENSP00000302625:A4S	A	-	1	0	AXIN2	60985191	1.000000	0.71417	0.006000	0.13384	0.882000	0.50991	3.331000	0.52075	0.385000	0.24970	0.462000	0.41574	GCT		0.592	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655		3	35	1	0	0.004672	1	0.00488436	3	35				
FGA	2243	broad.mit.edu	37	4	155510000	155510000	+	Silent	SNP	A	A	G			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr4:155510000A>G	ENST00000302053.3	-	3	387	c.309T>C	c.(307-309)caT>caC	p.H103H	FGA_ENST00000403106.3_Silent_p.H103H	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	103					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	TGGTCAACGAATGAGAATCCT	0.299																																					NSCLC(143;340 1922 20892 22370 48145)	ENST00000302053.3																			0				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73						c.(307-309)caT>caC		fibrinogen alpha chain	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)						141.0	154.0	150.0					4																	155510000		2202	4299	6501	SO:0001819	synonymous_variant	2243				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding	g.chr4:155510000A>G		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3661	protein-coding gene	gene with protein product		134820	"""fibrinogen, A alpha polypeptide"""				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.309T>C	4.37:g.155510000A>G						FGA_ENST00000403106.3_Silent_p.H103H	p.H103H	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN			3	387	-	all_hematologic(180;0.215)	Renal(120;0.0458)	103					A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Silent	SNP	ENST00000302053.3	37	c.309T>C	CCDS3787.1																																																																																				0.299	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508		8	100	0	0	0	1	0	8	100				
ROS1	6098	broad.mit.edu	37	6	117662426	117662426	+	Missense_Mutation	SNP	C	C	T			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr6:117662426C>T	ENST00000368508.3	-	30	5149	c.4951G>A	c.(4951-4953)Gtc>Atc	p.V1651I	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.V1645I	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1651	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		TCCACAGTGACAGGATGACTC	0.408			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																	ENST00000368508.3				Dom	yes		6	6q22	6098	T	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)			"""O, E"""	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""		"""glioblastoma, NSCLC"""	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	0				NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162						c.(4951-4953)Gtc>Atc		c-ros oncogene 1 , receptor tyrosine kinase							130.0	123.0	125.0					6																	117662426		2203	4300	6503	SO:0001583	missense	6098				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity	g.chr6:117662426C>T	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.4951G>A	6.37:g.117662426C>T	ENSP00000357494:p.Val1651Ile					GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.V1645I	p.V1651I	NM_002944.2	NP_002935.2	P08922	ROS_HUMAN		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)	30	5149	-		all_cancers(87;0.00846)|all_epithelial(87;0.0242)	1651			Fibronectin type-III 7.		Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	c.4951G>A	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	C	17.68	3.448983	0.63178	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.71817	-0.6;-0.6	5.1	4.22	0.49857	.	0.109437	0.40144	N	0.001168	T	0.65502	0.2697	L	0.32530	0.975	0.54753	D	0.999985	D	0.58970	0.984	D	0.70016	0.967	T	0.69453	-0.5141	10	0.52906	T	0.07	.	9.469	0.38831	0.0:0.9008:0.0:0.0992	.	1651	P08922	ROS1_HUMAN	I	1651;1645	ENSP00000357494:V1651I;ENSP00000357493:V1645I	ENSP00000357493:V1645I	V	-	1	0	ROS1	117769119	0.994000	0.37717	1.000000	0.80357	0.923000	0.55619	3.458000	0.53014	1.149000	0.42402	0.650000	0.86243	GTC		0.408	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			4	71	0	0	0	1	0	4	71				
PAG1	55824	broad.mit.edu	37	8	81897133	81897133	+	Missense_Mutation	SNP	G	G	C			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr8:81897133G>C	ENST00000220597.4	-	7	1464	c.754C>G	c.(754-756)Cca>Gca	p.P252A		NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	252					epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			TCCTCTTCTGGATCACATGAA	0.478																																						ENST00000220597.4																			0				breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11						c.(754-756)Cca>Gca		phosphoprotein associated with glycosphingolipid microdomains 1							146.0	143.0	144.0					8																	81897133		2203	4300	6503	SO:0001583	missense	55824				epidermal growth factor receptor signaling pathway|intracellular signal transduction|T cell receptor signaling pathway	integral to membrane|intracellular|membrane raft|plasma membrane	SH2 domain binding|SH3/SH2 adaptor activity	g.chr8:81897133G>C	AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30						30043	protein-coding gene	gene with protein product	"""Csk-binding protein"", ""transmembrane adaptor protein PAG"""	605767	"""phosphoprotein associated with glycosphingolipid microdomains 1"""			10790433	Standard	XM_006716461		Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.754C>G	8.37:g.81897133G>C	ENSP00000220597:p.Pro252Ala						p.P252A	NM_018440.3	NP_060910.3	Q9NWQ8	PAG1_HUMAN	BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)		7	1464	-	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		252					A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	Missense_Mutation	SNP	ENST00000220597.4	37	c.754C>G	CCDS6227.1	.	.	.	.	.	.	.	.	.	.	G	6.274	0.418577	0.11870	.	.	ENSG00000076641	ENST00000220597	.	.	.	5.33	-2.09	0.07232	.	1.435330	0.04031	N	0.301427	T	0.52191	0.1719	L	0.47716	1.5	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.52245	-0.8601	9	0.17369	T	0.5	1.4441	23.3323	0.99982	0.0:0.6698:0.3302:0.0	.	252	Q9NWQ8	PAG1_HUMAN	A	252	.	ENSP00000220597:P252A	P	-	1	0	PAG1	82059688	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.295000	0.08298	-0.247000	0.09597	-0.181000	0.13052	CCA		0.478	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379352.3	NM_018440		7	93	0	0	0	1	0	7	93				
SMARCA1	6594	broad.mit.edu	37	X	128599496	128599496	+	Splice_Site	SNP	C	C	T			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chrX:128599496C>T	ENST00000371122.4	-	23	3160		c.e23+1		SMARCA1_ENST00000371123.1_Splice_Site|SMARCA1_ENST00000371121.3_Splice_Site	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1						ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						GGAATACATACCATGGCAGTC	0.353																																						ENST00000371122.4																			0				biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						c.e23+1		SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1							144.0	130.0	135.0					X																	128599496		2203	4300	6503	SO:0001630	splice_region_variant	6594				ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding	g.chrX:128599496C>T	M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.3030+1G>A	X.37:g.128599496C>T						SMARCA1_ENST00000371123.1_Splice_Site|SMARCA1_ENST00000371121.3_Splice_Site		NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN			23	3160	-								Q5JV41|Q5JV42	Splice_Site	SNP	ENST00000371122.4	37		CCDS14612.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.596193	0.86953	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6879	0.91571	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SMARCA1	128427177	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.769000	0.85360	2.358000	0.79984	0.538000	0.68166	.		0.353	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069	Intron	12	38	0	0	0	1	0	12	38				
TRIM51HP	440041	broad.mit.edu	37	11	55065705	55065705	+	RNA	SNP	G	G	A			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr11:55065705G>A	ENST00000526016.1	-	0	3					NR_038174.2				tripartite motif-containing 51H, pseudogene																		GATGGGACAGGTGAGTTCCCT	0.483																																						ENST00000526016.1																			0																																																			0							g.chr11:55065705G>A			11q11	2012-11-02			ENSG00000166007	ENSG00000166007		"""Triparite motif-containing / Pseudogenes"""	43977	pseudogene	pseudogene							Standard	NR_038174		Approved		uc021qjb.1		OTTHUMG00000166775		11.37:g.55065705G>A								NR_038174.2						0	3	-									RNA	SNP	ENST00000526016.1	37																																																																																						0.483	TRIM51HP-002	PUTATIVE	basic|exp_conf	processed_transcript	pseudogene	OTTHUMT00000391438.1			4	56	0	0	0	1	0	4	56				
NPC2	10577	broad.mit.edu	37	14	74959974	74959974	+	Missense_Mutation	SNP	G	G	A			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr14:74959974G>A	ENST00000555619.1	-	1	241	c.4C>T	c.(4-6)Cgt>Tgt	p.R2C	NPC2_ENST00000434013.2_Missense_Mutation_p.R2C|NPC2_ENST00000541064.1_Missense_Mutation_p.R2C|NPC2_ENST00000557510.1_Missense_Mutation_p.R2C|NPC2_ENST00000238633.2_Missense_Mutation_p.R2C|ISCA2_ENST00000554924.1_5'Flank|ISCA2_ENST00000556816.1_5'Flank|ISCA2_ENST00000298818.8_5'Flank	NM_006432.3	NP_006423.1	P61916	NPC2_HUMAN	Niemann-Pick disease, type C2	2					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|glycolipid transport (GO:0046836)|intracellular cholesterol transport (GO:0032367)|intracellular sterol transport (GO:0032366)|phospholipid transport (GO:0015914)|regulation of isoprenoid metabolic process (GO:0019747)|response to virus (GO:0009615)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	cholesterol binding (GO:0015485)|enzyme binding (GO:0019899)			breast(1)|endometrium(2)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(2)	7				BRCA - Breast invasive adenocarcinoma(234;0.00149)		GCCAGGAAACGCATCGCGGAT	0.667																																					Pancreas(93;260 1497 8575 30964 48133)	ENST00000541064.1																			0				breast(1)|endometrium(2)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(2)	7						c.(4-6)Cgt>Tgt		Niemann-Pick disease, type C2							34.0	38.0	37.0					14																	74959974		2203	4300	6503	SO:0001583	missense	10577				cholesterol efflux|cholesterol homeostasis|glycolipid transport|intracellular cholesterol transport|phospholipid transport|regulation of isoprenoid metabolic process|response to virus	extracellular region|lysosome	cholesterol binding|enzyme binding	g.chr14:74959974G>A	X67698	CCDS32121.1	14q24.3	2009-09-12				ENSG00000119655			14537	protein-coding gene	gene with protein product	"""epididymal protein 1"""	601015				8418812, 11125141	Standard	NM_006432		Approved	HE1, NP-C2, EDDM1	uc001xpy.3	P61916		ENST00000555619.1:c.4C>T	14.37:g.74959974G>A	ENSP00000451112:p.Arg2Cys					NPC2_ENST00000238633.2_Missense_Mutation_p.R2C|NPC2_ENST00000557510.1_Missense_Mutation_p.R2C|NPC2_ENST00000555619.1_Missense_Mutation_p.R2C|NPC2_ENST00000434013.2_Missense_Mutation_p.R2C	p.R2C			P61916	NPC2_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.00149)	1	10	-			2					B4DQV7|Q15668|Q29413	Missense_Mutation	SNP	ENST00000555619.1	37	c.4C>T	CCDS32121.1	.	.	.	.	.	.	.	.	.	.	G	17.17	3.321316	0.60634	.	.	ENSG00000119655	ENST00000434013;ENST00000541064;ENST00000555619;ENST00000238633;ENST00000553490;ENST00000557510;ENST00000555592	D;D;D;D;D;D;D	0.90788	-2.7;-2.55;-2.52;-2.53;-2.73;-2.6;-2.53	5.07	-1.7	0.08159	.	1.408580	0.03784	N	0.261798	D	0.84188	0.5417	L	0.34521	1.04	0.22446	N	0.9991	B;B	0.09022	0.002;0.002	B;B	0.04013	0.001;0.001	T	0.68985	-0.5265	10	0.66056	D	0.02	-0.0712	4.4954	0.11835	0.0765:0.1251:0.2859:0.5125	.	2;2	B4DQV7;P61916	.;NPC2_HUMAN	C	2	ENSP00000412103:R2C;ENSP00000442488:R2C;ENSP00000451112:R2C;ENSP00000238633:R2C;ENSP00000451180:R2C;ENSP00000451206:R2C;ENSP00000450887:R2C	ENSP00000238633:R2C	R	-	1	0	NPC2	74029727	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	-1.206000	0.03011	-0.408000	0.07565	-0.989000	0.02550	CGT		0.667	NPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412346.1	NM_006432		3	18	0	0	0	1	0	3	18				
HLA-A	3105	broad.mit.edu	37	6	29910693	29910693	+	Missense_Mutation	SNP	A	A	G	rs41559716	byFrequency	TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr6:29910693A>G	ENST00000396634.1	+	4	574	c.233A>G	c.(232-234)cAg>cGg	p.Q78R	HLA-A_ENST00000376802.2_Missense_Mutation_p.Q78R|HLA-A_ENST00000376809.5_Missense_Mutation_p.Q78R|HLA-A_ENST00000376806.5_Missense_Mutation_p.Q78R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	78	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.Q78R(2)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TGGATAGAGCAGGAGGGGCCG	0.657									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																												ENST00000396634.1																			2	Substitution - Missense(2)	p.Q78R(2)	lung(1)|endometrium(1)	central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						c.(232-234)cAg>cGg		major histocompatibility complex, class I, A							54.0	57.0	56.0					6																	29910693		2203	4299	6502	SO:0001583	missense	3105	Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity	g.chr6:29910693A>G	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.233A>G	6.37:g.29910693A>G	ENSP00000379873:p.Gln78Arg	Multiple Myeloma(9;0.094)				HLA-A_ENST00000376806.5_Missense_Mutation_p.Q78R|HLA-A_ENST00000376802.2_Missense_Mutation_p.Q78R|HLA-A_ENST00000376809.5_Missense_Mutation_p.Q78R	p.Q78R			P30443	1A01_HUMAN			4	574	+			78			Alpha-1.		O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	c.233A>G	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	9.798	1.179669	0.21787	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00784	5.7;5.7;5.7;5.7	3.72	-4.39	0.03611	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	1.398580	0.06189	N	0.681068	T	0.00815	0.0027	L	0.56280	1.765	0.09310	N	1	B;P;B;P;B	0.42483	0.0;0.781;0.0;0.781;0.0	B;D;B;D;B	0.71184	0.006;0.972;0.01;0.972;0.01	T	0.44952	-0.9294	10	0.87932	D	0	.	0.9552	0.01384	0.3504:0.1689:0.3159:0.1647	rs41559716	78;78;78;78;78	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	R	78	ENSP00000379873:Q78R;ENSP00000366002:Q78R;ENSP00000366005:Q78R;ENSP00000365998:Q78R	ENSP00000348012:Q78R	Q	+	2	0	HLA-A	30018672	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	-0.990000	0.03732	-0.910000	0.03847	-0.450000	0.05554	CAG		0.657	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		5	37	0	0	0	1	0	5	37				
ZNRD1-AS1	80862	broad.mit.edu	37	6	29974845	29974845	+	RNA	SNP	G	G	C	rs200291839		TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr6:29974845G>C	ENST00000376797.3	-	0	1346				ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA			Q2KJ03	ZRAS1_HUMAN	ZNRD1 antisense RNA 1																		AGAGCGAGGCGGGTGAGTGAC	0.667																																						ENST00000376797.3																			0																																																			0							g.chr6:29974845G>C	AF032110		6p21.33	2014-08-14	2012-08-15	2010-11-25	ENSG00000204623	ENSG00000204623		"""Long non-coding RNAs"""	13924	non-coding RNA	RNA, long non-coding		615714	"""chromosome 6 open reading frame 12"", ""non-protein coding RNA 171"", ""ZNRD1 antisense RNA (non-protein coding)"", ""ZNRD1 antisense RNA 1 (non-protein coding)"""	C6orf12, NCRNA00171, ZNRD1AS, ZNRD1-AS		9553157, 11130983, 25110835	Standard	NR_026751		Approved	HTEX4, Em:AB023056.3	uc003rto.3	Q2KJ03	OTTHUMG00000031109		6.37:g.29974845G>C						ZNRD1-AS1_ENST00000448093.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA								0	1346	-									RNA	SNP	ENST00000376797.3	37																																																																																						0.667	ZNRD1-AS1-006	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000253083.1	NR_026751		3	15	0	0	0	1	0	3	15				
FGD5	152273	broad.mit.edu	37	3	14861542	14861542	+	Missense_Mutation	SNP	G	G	A			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr3:14861542G>A	ENST00000285046.5	+	1	1074	c.964G>A	c.(964-966)Gag>Aag	p.E322K	FGD5_ENST00000543601.1_Missense_Mutation_p.E81K	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	322	Glu-rich.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						TGAGTCCGCCGAGGAGAGCTG	0.552																																						ENST00000285046.5																			0				NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						c.(964-966)Gag>Aag		FYVE, RhoGEF and PH domain containing 5							71.0	76.0	74.0					3																	14861542		2004	4182	6186	SO:0001583	missense	152273				actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding	g.chr3:14861542G>A	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.964G>A	3.37:g.14861542G>A	ENSP00000285046:p.Glu322Lys					FGD5_ENST00000543601.1_Missense_Mutation_p.E81K	p.E322K	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN			1	1074	+			322			Glu-rich.		B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	37	c.964G>A	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	G	17.03	3.284211	0.59867	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.78003	-1.14;-1.02	5.34	5.34	0.76211	.	0.212230	0.32624	N	0.005845	T	0.74951	0.3784	L	0.29908	0.895	0.35240	D	0.777746	D;D	0.62365	0.991;0.991	P;P	0.50617	0.646;0.646	T	0.82673	-0.0341	10	0.62326	D	0.03	-32.7299	14.3506	0.66699	0.0729:0.0:0.9271:0.0	.	81;322	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	K	322;81	ENSP00000285046:E322K;ENSP00000445949:E81K	ENSP00000285046:E322K	E	+	1	0	FGD5	14836546	1.000000	0.71417	0.986000	0.45419	0.046000	0.14306	5.319000	0.65835	2.492000	0.84095	0.655000	0.94253	GAG		0.552	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		4	61	0	0	0	1	0	4	61				
SSX2IP	117178	broad.mit.edu	37	1	85127952	85127952	+	Missense_Mutation	SNP	T	T	C			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr1:85127952T>C	ENST00000342203.3	-	8	1119	c.856A>G	c.(856-858)Aag>Gag	p.K286E	SSX2IP_ENST00000603677.1_Intron|SSX2IP_ENST00000605755.1_Missense_Mutation_p.K259E|SSX2IP_ENST00000437941.2_Missense_Mutation_p.K259E|SSX2IP_ENST00000370612.4_Missense_Mutation_p.K286E	NM_001166293.1|NM_001166294.1|NM_014021.3	NP_001159765.1|NP_001159766.1|NP_054740.3	Q9Y2D8	ADIP_HUMAN	synovial sarcoma, X breakpoint 2 interacting protein	286					cell adhesion (GO:0007155)|centrosome organization (GO:0051297)|regulation of cell motility (GO:2000145)|regulation of Rac protein signal transduction (GO:0035020)	cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|centriolar satellite (GO:0034451)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|urinary_tract(1)	19				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		ATCATTTCCTTTTTCATTTGT	0.328																																						ENST00000437941.2																			0				endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|urinary_tract(1)	19						c.(775-777)Aag>Gag		synovial sarcoma, X breakpoint 2 interacting protein							157.0	175.0	169.0					1																	85127952		2203	4300	6503	SO:0001583	missense	117178				cell adhesion	nucleus|protein complex		g.chr1:85127952T>C		CCDS699.1, CCDS53337.1	1p22.3	2008-02-05			ENSG00000117155	ENSG00000117155			16509	protein-coding gene	gene with protein product		608690					Standard	NM_014021		Approved		uc001dkj.3	Q9Y2D8	OTTHUMG00000009926	ENST00000342203.3:c.856A>G	1.37:g.85127952T>C	ENSP00000340279:p.Lys286Glu					SSX2IP_ENST00000370612.4_Missense_Mutation_p.K286E|SSX2IP_ENST00000342203.3_Missense_Mutation_p.K286E|SSX2IP_ENST00000605755.1_Missense_Mutation_p.K259E|SSX2IP_ENST00000603677.1_Intron	p.K259E	NM_001166295.1|NM_001166417.1	NP_001159767.1|NP_001159889.1	Q9Y2D8	ADIP_HUMAN		all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)	7	1127	-			286					A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Missense_Mutation	SNP	ENST00000342203.3	37	c.775A>G	CCDS699.1	.	.	.	.	.	.	.	.	.	.	T	16.68	3.190426	0.58017	.	.	ENSG00000117155	ENST00000342203;ENST00000437941;ENST00000544699;ENST00000370612	T;T	0.48522	0.81;0.81	5.48	5.48	0.80851	.	0.178498	0.64402	D	0.000019	T	0.40694	0.1127	M	0.65975	2.015	0.36455	D	0.866333	P;P;P	0.40619	0.724;0.604;0.604	B;B;B	0.41988	0.372;0.205;0.205	T	0.52533	-0.8563	10	0.66056	D	0.02	-0.6298	15.5628	0.76262	0.0:0.0:0.0:1.0	.	282;286;259	F5H549;Q9Y2D8;B4DFE3	.;ADIP_HUMAN;.	E	286;259;282;286	ENSP00000340279:K286E;ENSP00000412781:K259E	ENSP00000340279:K286E	K	-	1	0	SSX2IP	84900540	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.750000	0.62162	2.096000	0.63516	0.482000	0.46254	AAG		0.328	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	NM_014021		4	88	0	0	0	1	0	4	88				
PRSS38	339501	broad.mit.edu	37	1	228003856	228003856	+	Missense_Mutation	SNP	C	C	T			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr1:228003856C>T	ENST00000366757.3	+	2	238	c.214C>T	c.(214-216)Ccg>Tcg	p.P72S		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	72	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						GAGGAAGTGGCCGTGGCAGGT	0.652																																						ENST00000366757.3																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						c.(214-216)Ccg>Tcg		protease, serine, 38							68.0	76.0	73.0					1																	228003856		2203	4299	6502	SO:0001583	missense	339501				proteolysis	extracellular region	serine-type endopeptidase activity	g.chr1:228003856C>T		CCDS1563.1	1q42.13	2010-05-07			ENSG00000185888	ENSG00000185888		"""Serine peptidases / Serine peptidases"""	29625	protein-coding gene	gene with protein product	"""marapsin 2"""					12838346	Standard	NM_183062		Approved	MPN2	uc001hrh.3	A1L453	OTTHUMG00000037701	ENST00000366757.3:c.214C>T	1.37:g.228003856C>T	ENSP00000355719:p.Pro72Ser						p.P72S	NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN			2	238	+			72			Peptidase S1.		Q7RTY6	Missense_Mutation	SNP	ENST00000366757.3	37	c.214C>T	CCDS1563.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.293713	0.60086	.	.	ENSG00000185888	ENST00000366757	D	0.85484	-1.99	4.13	4.13	0.48395	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.41001	D	0.000965	D	0.94039	0.8090	H	0.94503	3.545	0.54753	D	0.99998	D	0.89917	1.0	D	0.97110	1.0	D	0.95440	0.8524	10	0.87932	D	0	.	13.9194	0.63921	0.0:1.0:0.0:0.0	.	72	A1L453	PRS38_HUMAN	S	72	ENSP00000355719:P72S	ENSP00000355719:P72S	P	+	1	0	PRSS38	226070479	1.000000	0.71417	0.993000	0.49108	0.244000	0.25665	4.256000	0.58810	2.140000	0.66376	0.467000	0.42956	CCG		0.652	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062		4	130	0	0	0	1	0	4	130				
OR12D2	26529	broad.mit.edu	37	6	29365088	29365088	+	Silent	SNP	T	T	C			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr6:29365088T>C	ENST00000383555.2	+	1	673	c.612T>C	c.(610-612)atT>atC	p.I204I	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	204						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						CGGGGACAATTGCCATGGGCC	0.443																																						ENST00000383555.2																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						c.(610-612)atT>atC		olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)							158.0	161.0	160.0					6																	29365088		1511	2709	4220	SO:0001819	synonymous_variant	26529				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr6:29365088T>C		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.612T>C	6.37:g.29365088T>C						OR5V1_ENST00000377154.1_Intron	p.I204I	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN			1	673	+			204					B0S862|Q5SUN9|Q6IET9	Silent	SNP	ENST00000383555.2	37	c.612T>C	CCDS4659.1																																																																																				0.443	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2			4	110	0	0	0	1	0	4	110				
SAMD9	54809	broad.mit.edu	37	7	92734007	92734007	+	Silent	SNP	T	T	C			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr7:92734007T>C	ENST00000379958.2	-	3	1673	c.1404A>G	c.(1402-1404)gtA>gtG	p.V468V		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	468						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			GTTCTACATATACACTTGGAA	0.403																																						ENST00000379958.2																			0				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						c.(1402-1404)gtA>gtG		sterile alpha motif domain containing 9							67.0	64.0	65.0					7																	92734007		2203	4299	6502	SO:0001819	synonymous_variant	54809					cytoplasm		g.chr7:92734007T>C	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.1404A>G	7.37:g.92734007T>C							p.V468V	NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	STAD - Stomach adenocarcinoma(171;0.000302)		3	1673	-	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		468					A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Silent	SNP	ENST00000379958.2	37	c.1404A>G	CCDS34680.1																																																																																				0.403	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		7	32	0	0	0	1	0	7	32				
SPOP	8405	broad.mit.edu	37	17	47696426	47696426	+	Missense_Mutation	SNP	A	A	C			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr17:47696426A>C	ENST00000393328.2	-	6	762	c.397T>G	c.(397-399)Ttc>Gtc	p.F133V	SPOP_ENST00000513080.1_5'Flank|SPOP_ENST00000504102.1_Missense_Mutation_p.F133V|SPOP_ENST00000347630.2_Missense_Mutation_p.F133V|SPOP_ENST00000503676.1_Missense_Mutation_p.F133V|SPOP_ENST00000393331.3_Missense_Mutation_p.F133V	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	133	Important for binding substrate proteins.|MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.|Required for nuclear localization.				glucose homeostasis (GO:0042593)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)	p.F133V(4)		endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						AATTTCTTGAATCCCCAGTCT	0.448										Prostate(2;0.17)																												ENST00000393331.3																			4	Substitution - Missense(4)	p.F133V(4)	prostate(4)	endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						c.(397-399)Ttc>Gtc		speckle-type POZ protein							119.0	121.0	120.0					17																	47696426		2203	4300	6503	SO:0001583	missense	8405				mRNA processing	nucleus	protein binding	g.chr17:47696426A>C	AJ000644	CCDS11551.1	17q21.33	2013-01-09			ENSG00000121067	ENSG00000121067		"""BTB/POZ domain containing"""	11254	protein-coding gene	gene with protein product		602650				9414087	Standard	NM_001007227		Approved	TEF2, BTBD32	uc002ipg.3	O43791	OTTHUMG00000161496	ENST00000393328.2:c.397T>G	17.37:g.47696426A>C	ENSP00000377001:p.Phe133Val	Prostate(2;0.17)				SPOP_ENST00000504102.1_Missense_Mutation_p.F133V|SPOP_ENST00000503676.1_Missense_Mutation_p.F133V|SPOP_ENST00000393328.2_Missense_Mutation_p.F133V|SPOP_ENST00000347630.2_Missense_Mutation_p.F133V	p.F133V	NM_001007226.1|NM_001007227.1	NP_001007227.1|NP_001007228.1	O43791	SPOP_HUMAN			7	867	-			133			MATH.|Required for nuclear localization.		B2R6S3|D3DTW7|Q53HJ1	Missense_Mutation	SNP	ENST00000393328.2	37	c.397T>G	CCDS11551.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.550963	0.86127	.	.	ENSG00000121067	ENST00000393328;ENST00000393331;ENST00000347630;ENST00000504102;ENST00000503536;ENST00000503676;ENST00000513872;ENST00000509079;ENST00000505581;ENST00000507970;ENST00000514121	T;T;T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.41	5.41	0.78517	TRAF-type (1);TRAF-like (1);MATH (3);	0.000000	0.85682	D	0.000000	T	0.68632	0.3022	M	0.94021	3.485	0.80722	D	1	P	0.35155	0.487	P	0.49637	0.617	T	0.74861	-0.3520	10	0.66056	D	0.02	-9.6576	15.258	0.73599	1.0:0.0:0.0:0.0	.	133	O43791	SPOP_HUMAN	V	133;133;133;133;17;133;86;133;133;133;133	ENSP00000377001:F133V;ENSP00000377004:F133V;ENSP00000240327:F133V;ENSP00000425905:F133V;ENSP00000420908:F133V;ENSP00000426986:F133V;ENSP00000420960:F133V;ENSP00000426262:F133V;ENSP00000424119:F133V	ENSP00000240327:F133V	F	-	1	0	SPOP	45051425	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.131000	0.94446	2.261000	0.74972	0.460000	0.39030	TTC		0.448	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563		11	105	0	0	0	1	0	11	105				
IQCG	84223	broad.mit.edu	37	3	197665464	197665464	+	Missense_Mutation	SNP	T	T	A			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr3:197665464T>A	ENST00000265239.6	-	5	894	c.470A>T	c.(469-471)cAg>cTg	p.Q157L	IQCG_ENST00000455191.1_Missense_Mutation_p.Q157L|IQCG_ENST00000453254.1_Missense_Mutation_p.Q157L|IQCG_ENST00000480302.1_5'Flank	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	IQ motif containing G	157						extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		CATGATGGTCTGCCTTGTAGG	0.428																																						ENST00000265239.6																			0				autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						c.(469-471)cAg>cTg		IQ motif containing G							266.0	256.0	260.0					3																	197665464		2203	4300	6503	SO:0001583	missense	84223							g.chr3:197665464T>A	AL136889	CCDS3331.1	3q29	2014-07-18			ENSG00000114473	ENSG00000114473			25251	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 9"""	612477				11230166, 23427265, 24362311	Standard	NM_032263		Approved	DKFZp434B227, DRC9, CFAP122	uc003fyo.3	Q9H095	OTTHUMG00000155408	ENST00000265239.6:c.470A>T	3.37:g.197665464T>A	ENSP00000265239:p.Gln157Leu					IQCG_ENST00000455191.1_Missense_Mutation_p.Q157L|IQCG_ENST00000453254.1_Missense_Mutation_p.Q157L	p.Q157L	NM_032263.3	NP_115639.1	Q9H095	IQCG_HUMAN	Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)	5	894	-	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		157					Q9BST2|Q9HAG8	Missense_Mutation	SNP	ENST00000265239.6	37	c.470A>T	CCDS3331.1	.	.	.	.	.	.	.	.	.	.	T	14.55	2.569766	0.45798	.	.	ENSG00000114473	ENST00000265239;ENST00000455191;ENST00000453254;ENST00000416896	T;T;T;T	0.56776	0.68;0.68;0.95;0.44	5.5	5.5	0.81552	.	0.237398	0.36066	N	0.002807	T	0.69788	0.3150	M	0.80746	2.51	0.36109	D	0.844656	D;D	0.76494	0.999;0.969	D;P	0.69479	0.964;0.59	T	0.76977	-0.2759	10	0.41790	T	0.15	-21.269	10.0768	0.42366	0.0:0.0:0.1683:0.8317	.	157;157	C9JKX8;Q9H095	.;IQCG_HUMAN	L	157;157;157;138	ENSP00000265239:Q157L;ENSP00000407736:Q157L;ENSP00000389897:Q157L;ENSP00000406411:Q138L	ENSP00000265239:Q157L	Q	-	2	0	IQCG	199149861	0.998000	0.40836	0.441000	0.26858	0.199000	0.23934	1.640000	0.37186	2.227000	0.72691	0.456000	0.33151	CAG		0.428	IQCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339730.1	NM_032263		17	198	0	0	0	1	0	17	198				
MBNL2	10150	broad.mit.edu	37	13	98043657	98043657	+	Missense_Mutation	SNP	A	A	G			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr13:98043657A>G	ENST00000376673.3	+	8	1857	c.1076A>G	c.(1075-1077)tAc>tGc	p.Y359C	MBNL2_ENST00000397601.1_Missense_Mutation_p.Y347C|MBNL2_ENST00000345429.6_3'UTR|MBNL2_ENST00000445661.2_Missense_Mutation_p.Y192C|MBNL2_ENST00000343600.4_Missense_Mutation_p.Y347C			Q5VZF2	MBNL2_HUMAN	muscleblind-like splicing regulator 2	359					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)			TACTGTACATACTATCCTGTT	0.363																																						ENST00000376673.3																			0				endometrium(4)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	17						c.(1075-1077)tAc>tGc		muscleblind-like splicing regulator 2							178.0	155.0	163.0					13																	98043657		2203	4300	6503	SO:0001583	missense	10150				mRNA processing|regulation of RNA splicing|RNA splicing	cytoplasm|nucleus	RNA binding|zinc ion binding	g.chr13:98043657A>G	AF061261	CCDS9483.1, CCDS9484.1	13q31.1	2013-01-18	2012-02-23		ENSG00000139793	ENSG00000139793		"""Zinc fingers, CCCH-type domain containing"""	16746	protein-coding gene	gene with protein product		607327	"""muscleblind-like 2 (Drosophila)"""			11929853	Standard	NM_207304		Approved	MBLL, MBLL39	uc001vmz.4	Q5VZF2	OTTHUMG00000017239	ENST00000376673.3:c.1076A>G	13.37:g.98043657A>G	ENSP00000365861:p.Tyr359Cys					MBNL2_ENST00000343600.4_Missense_Mutation_p.Y347C|MBNL2_ENST00000445661.2_Missense_Mutation_p.Y192C|MBNL2_ENST00000397601.1_Missense_Mutation_p.Y347C|MBNL2_ENST00000345429.6_3'UTR	p.Y359C			Q5VZF2	MBNL2_HUMAN	BRCA - Breast invasive adenocarcinoma(86;0.218)		8	1857	+	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		359					Q3SXY5|Q58F19|Q8NEV3|Q8TD82	Missense_Mutation	SNP	ENST00000376673.3	37	c.1076A>G		.	.	.	.	.	.	.	.	.	.	A	19.69	3.875122	0.72180	.	.	ENSG00000139793	ENST00000397601;ENST00000343600;ENST00000376673;ENST00000445661	T;T;T;T	0.57595	0.48;0.48;0.45;0.39	5.27	5.27	0.74061	.	0.350601	0.28119	N	0.016535	T	0.54175	0.1842	N	0.08118	0	0.37493	D	0.916463	D;B;D	0.71674	0.998;0.0;0.998	D;B;D	0.77557	0.966;0.002;0.99	T	0.68059	-0.5509	10	0.87932	D	0	.	15.4911	0.75605	1.0:0.0:0.0:0.0	.	192;359;347	B4E3F7;Q5VZF2;A2A3S3	.;MBNL2_HUMAN;.	C	347;347;359;192	ENSP00000380726:Y347C;ENSP00000344214:Y347C;ENSP00000365861:Y359C;ENSP00000406842:Y192C	ENSP00000344214:Y347C	Y	+	2	0	MBNL2	96841658	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.135000	0.77276	2.122000	0.65172	0.379000	0.24179	TAC		0.363	MBNL2-202	KNOWN	basic	protein_coding	protein_coding		NM_144778		6	66	0	0	0	1	0	6	66				
CLASP2	23122	broad.mit.edu	37	3	33552238	33552238	+	Missense_Mutation	SNP	C	C	T			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr3:33552238C>T	ENST00000468888.2	-	37	4199	c.4153G>A	c.(4153-4155)Gaa>Aaa	p.E1385K	CLASP2_ENST00000539981.1_3'UTR|CLASP2_ENST00000307312.7_Missense_Mutation_p.E866K|CLASP2_ENST00000480013.1_Missense_Mutation_p.E1164K|CLASP2_ENST00000359576.5_Missense_Mutation_p.E1376K|CLASP2_ENST00000461133.3_Missense_Mutation_p.E1144K|CLASP2_ENST00000399362.4_Missense_Mutation_p.E1384K			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1165					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						GATGCCGCTTCCTCAGCAGAT	0.383																																						ENST00000399362.4																			0				breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						c.(4150-4152)Gaa>Aaa		cytoplasmic linker associated protein 2							64.0	54.0	57.0					3																	33552238		1931	4132	6063	SO:0001583	missense	23122							g.chr3:33552238C>T	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.4153G>A	3.37:g.33552238C>T	ENSP00000419974:p.Glu1385Lys					CLASP2_ENST00000359576.5_Missense_Mutation_p.E1376K|CLASP2_ENST00000307312.7_Missense_Mutation_p.E866K|CLASP2_ENST00000539981.1_3'UTR|CLASP2_ENST00000480013.1_Missense_Mutation_p.E1164K|CLASP2_ENST00000468888.2_Missense_Mutation_p.E1385K|CLASP2_ENST00000461133.3_Missense_Mutation_p.E1144K	p.E1384K	NM_015097.2	NP_055912.2	B2RTR1	B2RTR1_HUMAN			37	4503	-			1386					Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	37	c.4150G>A		.	.	.	.	.	.	.	.	.	.	C	35	5.413111	0.96072	.	.	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576;ENST00000307312;ENST00000480013;ENST00000461133	T;T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2	6.08	6.08	0.98989	.	0.047128	0.85682	D	0.000000	T	0.78685	0.4322	M	0.70903	2.155	0.80722	D	1	P;D	0.89917	0.882;1.0	P;D	0.91635	0.6;0.999	T	0.70802	-0.4773	10	0.18276	T	0.48	-24.7863	20.6634	0.99662	0.0:1.0:0.0:0.0	.	1376;1384	F5H604;E7ERI8	.;.	K	1385;1384;1376;866;1164;1144	ENSP00000419974:E1385K;ENSP00000382297:E1384K;ENSP00000352581:E1376K;ENSP00000304743:E866K;ENSP00000417518:E1164K;ENSP00000419305:E1144K	ENSP00000304743:E866K	E	-	1	0	CLASP2	33527242	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.506000	0.81665	2.894000	0.99253	0.655000	0.94253	GAA		0.383	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		3	17	0	0	0	1	0	3	17				
ZNRD1-AS1	80862	broad.mit.edu	37	6	29977342	29977342	+	RNA	SNP	A	A	T	rs113017032	byFrequency	TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr6:29977342A>T	ENST00000376797.3	-	0	731				ZNRD1-AS1_ENST00000444051.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA			Q2KJ03	ZRAS1_HUMAN	ZNRD1 antisense RNA 1																		TGGGACTGAGAGGCAAGATTT	0.438													A|||	16	0.00319489	0.003	0.0029	5008	,	,		21762	0.0		0.003	False		,,,				2504	0.0072					ENST00000376797.3																			0																																																			0							g.chr6:29977342A>T	AF032110		6p21.33	2014-08-14	2012-08-15	2010-11-25	ENSG00000204623	ENSG00000204623		"""Long non-coding RNAs"""	13924	non-coding RNA	RNA, long non-coding		615714	"""chromosome 6 open reading frame 12"", ""non-protein coding RNA 171"", ""ZNRD1 antisense RNA (non-protein coding)"", ""ZNRD1 antisense RNA 1 (non-protein coding)"""	C6orf12, NCRNA00171, ZNRD1AS, ZNRD1-AS		9553157, 11130983, 25110835	Standard	NR_026751		Approved	HTEX4, Em:AB023056.3	uc003rto.3	Q2KJ03	OTTHUMG00000031109		6.37:g.29977342A>T						ZNRD1-AS1_ENST00000448093.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA								0	731	-									RNA	SNP	ENST00000376797.3	37																																																																																						0.438	ZNRD1-AS1-006	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000253083.1	NR_026751		3	33	0	0	0	1	0	3	33				
TRIM51HP	440041	broad.mit.edu	37	11	55065601	55065601	+	RNA	SNP	C	C	G	rs4100282		TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr11:55065601C>G	ENST00000526016.1	-	0	107					NR_038174.2				tripartite motif-containing 51H, pseudogene																		CACTGAGCAACAACTGCCATG	0.488																																						ENST00000526016.1																			0																																																			0							g.chr11:55065601C>G			11q11	2012-11-02			ENSG00000166007	ENSG00000166007		"""Triparite motif-containing / Pseudogenes"""	43977	pseudogene	pseudogene							Standard	NR_038174		Approved		uc021qjb.1		OTTHUMG00000166775		11.37:g.55065601C>G								NR_038174.2						0	107	-									RNA	SNP	ENST00000526016.1	37																																																																																						0.488	TRIM51HP-002	PUTATIVE	basic|exp_conf	processed_transcript	pseudogene	OTTHUMT00000391438.1			3	33	0	0	0	1	0	3	33				
ERBB3	2065	broad.mit.edu	37	12	56492616	56492616	+	Silent	SNP	C	C	T			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr12:56492616C>T	ENST00000267101.3	+	23	3206	c.2766C>T	c.(2764-2766)gaC>gaT	p.D922D	ERBB3_ENST00000549832.1_Silent_p.D42D|ERBB3_ENST00000553131.1_Silent_p.D163D|RP11-603J24.9_ENST00000548861.1_5'Flank|ERBB3_ENST00000415288.2_Silent_p.D863D|ERBB3_ENST00000450146.2_Silent_p.D279D	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	922	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			AAGTACCAGACCTGCTAGAGA	0.532																																						ENST00000267101.3																			0				central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8						c.(2764-2766)gaC>gaT		v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3							129.0	115.0	120.0					12																	56492616		2203	4300	6503	SO:0001819	synonymous_variant	2065				cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity	g.chr12:56492616C>T	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"""lethal congenital contracture syndrome 2"""	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.2766C>T	12.37:g.56492616C>T						ERBB3_ENST00000553131.1_Silent_p.D163D|ERBB3_ENST00000450146.2_Silent_p.D279D|ERBB3_ENST00000415288.2_Silent_p.D863D|ERBB3_ENST00000549832.1_Silent_p.D42D	p.D922D	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	OV - Ovarian serous cystadenocarcinoma(18;0.112)		23	3206	+			922			Protein kinase.		A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Silent	SNP	ENST00000267101.3	37	c.2766C>T	CCDS31833.1																																																																																				0.532	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			4	78	0	0	0	1	0	4	78				
THRAP3	9967	broad.mit.edu	37	1	36748270	36748273	+	Frame_Shift_Del	DEL	TCTC	TCTC	-			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr1:36748270_36748273delTCTC	ENST00000354618.5	+	3	330_333	c.106_109delTCTC	c.(106-111)tctctcfs	p.SL36fs	THRAP3_ENST00000469141.2_Frame_Shift_Del_p.SL36fs	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	36	Arg-rich.|Required for mRNA splicing activation.|Ser-rich.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CCGAAGCCGATCTCTCTCTCGTTC	0.446			T	USP6	aneurysmal bone cysts																																Pancreas(129;785 1795 20938 23278 32581)	ENST00000354618.5				Dom	yes		1	1p34.3	9967	T	thyroid hormone receptor associated protein 3 (TRAP150)			M	USP6		aneurysmal bone cysts		0				breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37						c.(106-111)tcfs		thyroid hormone receptor associated protein 3																																				SO:0001589	frameshift_variant	9967				androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding	g.chr1:36748270_36748273delTCTC	AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.106_109delTCTC	1.37:g.36748274_36748277delTCTC	ENSP00000346634:p.Ser36fs					THRAP3_ENST00000469141.2_Frame_Shift_Del_p.SL36fs	p.SL36fs	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN			3	330_333	+		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)	36			Arg-rich.|Ser-rich.		D3DPS5|Q5VTK6	Frame_Shift_Del	DEL	ENST00000354618.5	37	c.106_109delTCTC	CCDS405.1																																																																																				0.446	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119		9	64						9	64	---	---	---	---
CTC-338M12.9	0	broad.mit.edu	37	5	180708776	180708777	+	lincRNA	INS	-	-	G	rs140221514|rs61118356		TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr5:180708776_180708777insG	ENST00000412295.2	+	0	238																											gggcggtaggagggggctggag	0.728																																						ENST00000412295.2																			0																																																			0							g.chr5:180708776_180708777insG																													5.37:g.180708781_180708781dupG														0	238	+									RNA	INS	ENST00000412295.2	37																																																																																						0.728	CTC-338M12.9-001	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000372940.1			3	5						3	5	---	---	---	---
CCT6P3	643180	broad.mit.edu	37	7	64528813	64528814	+	RNA	INS	-	-	T			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr7:64528813_64528814insT	ENST00000426828.1	+	0	621				SNORA15_ENST00000384334.1_RNA|SNORA22_ENST00000384614.1_RNA	NR_033416.1				chaperonin containing TCP1, subunit 6 (zeta) pseudogene 3																		CTTTCTGTAACTTTTTTTTTTT	0.317																																						ENST00000426828.1																			0																																																			0							g.chr7:64528813_64528814insT			7q11.21	2010-06-29			ENSG00000234585	ENSG00000234585			35137	pseudogene	pseudogene							Standard	NR_033416		Approved		uc010kzt.1		OTTHUMG00000156630		7.37:g.64528824_64528824dupT								NR_033416.1						0	621	+									RNA	INS	ENST00000426828.1	37																																																																																						0.317	CCT6P3-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000344862.1			4	5						4	5	---	---	---	---
CFL1	1072	broad.mit.edu	37	11	65623504	65623504	+	Frame_Shift_Del	DEL	A	A	-			TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr11:65623504delA	ENST00000525451.2	-	3	928	c.213delT	c.(211-213)tttfs	p.F71fs	CFL1_ENST00000531413.1_Frame_Shift_Del_p.F54fs|CFL1_ENST00000531407.1_Frame_Shift_Del_p.F54fs|CFL1_ENST00000524553.1_Frame_Shift_Del_p.F54fs|CFL1_ENST00000308162.5_Frame_Shift_Del_p.F71fs|CFL1_ENST00000527344.1_Frame_Shift_Del_p.F54fs|CFL1_ENST00000534769.1_Frame_Shift_Del_p.F109fs			P23528	COF1_HUMAN	cofilin 1 (non-muscle)	71	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				actin cytoskeleton organization (GO:0030036)|actin filament depolymerization (GO:0030042)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytoskeleton organization (GO:0007010)|establishment of cell polarity (GO:0030010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|mitotic cytokinesis (GO:0000281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell size (GO:0045792)|neural crest cell migration (GO:0001755)|neural fold formation (GO:0001842)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of actin filament depolymerization (GO:0030836)|protein import into nucleus (GO:0006606)|protein phosphorylation (GO:0006468)|regulation of cell morphogenesis (GO:0022604)|response to amino acid (GO:0043200)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)	cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				breast(1)|kidney(1)|large_intestine(2)|lung(2)	6				READ - Rectum adenocarcinoma(159;0.169)		GCATCTTGACAAAGGTGGCGT	0.537																																					Esophageal Squamous(90;820 1366 3932 32351 42291)	ENST00000525451.2																			0				breast(1)|kidney(1)|large_intestine(2)|lung(2)	6						c.(211-213)ttfs		cofilin 1 (non-muscle)							157.0	142.0	147.0					11																	65623504		2201	4297	6498	SO:0001589	frameshift_variant	1072				actin cytoskeleton organization|anti-apoptosis|axon guidance|platelet activation|platelet degranulation|response to virus|Rho protein signal transduction	cytoplasm|cytoskeleton|nuclear matrix	actin binding	g.chr11:65623504delA	X95404	CCDS8114.1	11q13.1	2010-12-03			ENSG00000172757	ENSG00000172757			1874	protein-coding gene	gene with protein product		601442		CFL		8800436	Standard	NM_005507		Approved		uc001ofs.3	P23528		ENST00000525451.2:c.213delT	11.37:g.65623504delA	ENSP00000432660:p.Phe71fs					CFL1_ENST00000531407.1_Frame_Shift_Del_p.F54fs|CFL1_ENST00000531413.1_Frame_Shift_Del_p.F54fs|CFL1_ENST00000524553.1_Frame_Shift_Del_p.F54fs|CFL1_ENST00000527344.1_Frame_Shift_Del_p.F54fs|CFL1_ENST00000308162.5_Frame_Shift_Del_p.F71fs|CFL1_ENST00000534769.1_Frame_Shift_Del_p.F109fs	p.F71fs			P23528	COF1_HUMAN		READ - Rectum adenocarcinoma(159;0.169)	3	928	-			71			ADF-H.		B3KUQ1|Q53Y87|Q9UCA2	Frame_Shift_Del	DEL	ENST00000525451.2	37	c.213delT	CCDS8114.1																																																																																				0.537	CFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390701.3	NM_005507		16	121						16	121	---	---	---	---
IGHV3-48	28424	broad.mit.edu	37	14	106993939	106993941	+	RNA	DEL	TAC	TAC	-	rs199815306|rs144292224	byFrequency	TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr14:106993939_106993941delTAC	ENST00000390624.2	-	0	302_304									immunoglobulin heavy variable 3-48																		TAGTATATGGTACTACTACTACT	0.502																																						ENST00000390624.2																			0																	307,3283		14,279,1502						-5.2	0.0		dbSNP_134	157	272,7558		29,214,3672	no	intergenic				43,493,5174	A1A1,A1R,RR		3.4738,8.5515,5.0701				579,10841						0							g.chr14:106993939_106993941delTAC	M99675		14q32.33	2012-02-08			ENSG00000211964	ENSG00000211964		"""Immunoglobulins / IGH locus"""	5606	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151959		14.37:g.106993948_106993950delTAC														0	302_304	-									RNA	DEL	ENST00000390624.2	37																																																																																						0.502	IGHV3-48-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000324605.1	NG_001019		8	286						8	286	---	---	---	---
RP11-252A24.2	0	broad.mit.edu	37	16	74372915	74372915	+	RNA	DEL	T	T	-	rs397827801|rs11353924|rs532713769|rs398078750		TCGA-J4-A6G3-01A-11D-A30X-08	TCGA-J4-A6G3-10A-01D-A30X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68b542b2-f763-47c4-9df4-3f92060c8495	5f191346-ea91-4227-861e-18f4cd4ecc5f	g.chr16:74372915delT	ENST00000429810.2	-	0	1404																											ACGTAGtttgttttttttttt	0.438																																						ENST00000429810.2																			0																																																			0							g.chr16:74372915delT																													16.37:g.74372915delT														0	1404	-									RNA	DEL	ENST00000429810.2	37																																																																																						0.438	RP11-252A24.2-003	KNOWN	basic	retained_intron	pseudogene	OTTHUMT00000434683.1			3	5						3	5	---	---	---	---
