#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_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
CLCA2	9635	broad.mit.edu	37	1	86916415	86916415	+	Splice_Site	SNP	C	C	T	rs140158852		TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr1:86916415C>T	ENST00000370565.4	+	12	2316	c.2154C>T	c.(2152-2154)aaC>aaT	p.N718N	CLCA2_ENST00000498802.1_3'UTR	NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	718					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)	p.N718N(1)		NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		ACACAGCAAACGGTAAGAACC	0.448																																					Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	ENST00000370565.4																			1	Substitution - coding silent(1)	p.N718N(1)	prostate(1)	NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42						c.(2152-2154)aaC>aaT		chloride channel accessory 2		C		0,4406		0,0,2203	140.0	125.0	130.0		2154	-10.7	0.0	1	dbSNP_134	130	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous-near-splice	CLCA2	NM_006536.5		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		718/944	86916415	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	9635				cell adhesion	basal plasma membrane|cell junction|extracellular region|integral to plasma membrane	chloride channel activity	g.chr1:86916415C>T		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2155+1C>T	1.37:g.86916415C>T			Somatic				CLCA2_ENST00000498802.1_3'UTR	p.N718N	NM_006536.5	NP_006527.1	WXS	Illumina GAIIx	Phase_I	Q9UQC9	CLCA2_HUMAN		all cancers(265;0.0233)|Epithelial(280;0.0452)	12	2316	+		Lung NSC(277;0.238)	718					A8K2T3|Q9Y6N2	Splice_Site	SNP	ENST00000370565.4	37	c.2154C>T	CCDS708.1																																																																																				0.448	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	Silent	31	203	31	203	---	---	---	---
SEMA6C	10500	broad.mit.edu	37	1	151105861	151105861	+	Missense_Mutation	SNP	C	C	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr1:151105861C>T	ENST00000341697.3	-	19	3583	c.1892G>A	c.(1891-1893)cGc>cAc	p.R631H	RP11-68I18.10_ENST00000563624.1_RNA|SEMA6C_ENST00000479820.1_5'Flank			Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	631					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.R631H(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCGGTGGGCGCGGCGACAAGC	0.716																																						ENST00000341697.3																			1	Substitution - Missense(1)	p.R631H(1)	prostate(1)	central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28						c.(1891-1893)cGc>cAc		sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C							19.0	22.0	21.0					1																	151105861		2196	4290	6486	SO:0001583	missense	10500					integral to membrane	receptor activity	g.chr1:151105861C>T	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"""Semaphorins"""	10740	protein-coding gene	gene with protein product	"""m-Sema Y2"""	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.1892G>A	1.37:g.151105861C>T	ENSP00000344148:p.Arg631His		Somatic					p.R631H			WXS	Illumina GAIIx	Phase_I	Q9H3T2	SEM6C_HUMAN	UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)		19	3583	-	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		631					D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Missense_Mutation	SNP	ENST00000341697.3	37	c.1892G>A	CCDS984.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.504477	0.26949	.	.	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697	T;T;T;T	0.55234	0.53;0.53;0.53;0.53	3.99	1.92	0.25849	.	0.757669	0.12812	N	0.437127	T	0.09247	0.0228	N	0.02011	-0.69	0.29020	N	0.886361	B;B;B	0.21309	0.054;0.003;0.032	B;B;B	0.14023	0.01;0.005;0.004	T	0.22068	-1.0227	10	0.38643	T	0.18	.	7.1287	0.25488	0.0:0.7498:0.0:0.2502	.	623;663;631	Q9H3T2-2;Q9H3T2-3;Q9H3T2	.;.;SEM6C_HUMAN	H	631;623;663;631	ENSP00000357910:R631H;ENSP00000357908:R623H;ENSP00000357909:R663H;ENSP00000344148:R631H	ENSP00000344148:R631H	R	-	2	0	SEMA6C	149372485	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	2.272000	0.43373	0.882000	0.36016	0.561000	0.74099	CGC		0.716	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913		3	24	3	24	---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	185880818	185880818	+	Missense_Mutation	SNP	A	A	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr1:185880818A>C	ENST00000271588.4	+	6	1035	c.806A>C	c.(805-807)aAa>aCa	p.K269T	HMCN1_ENST00000367492.2_Missense_Mutation_p.K269T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	269					response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.K269T(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AAGCTGATAAAAAAGGGATTT	0.393																																						ENST00000271588.4																			1	Substitution - Missense(1)	p.K269T(1)	prostate(1)	NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						c.(805-807)aAa>aCa		hemicentin 1							213.0	227.0	222.0					1																	185880818		2203	4300	6503	SO:0001583	missense	83872				response to stimulus|visual perception	basement membrane	calcium ion binding	g.chr1:185880818A>C	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.806A>C	1.37:g.185880818A>C	ENSP00000271588:p.Lys269Thr		Somatic				HMCN1_ENST00000367492.2_Missense_Mutation_p.K269T	p.K269T	NM_031935.2	NP_114141.2	WXS	Illumina GAIIx	Phase_I	Q96RW7	HMCN1_HUMAN			6	1035	+			269					A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	c.806A>C	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	8.351	0.830991	0.16820	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.62639	0.01;0.01	5.63	5.63	0.86233	.	0.212444	0.51477	D	0.000096	T	0.33990	0.0882	N	0.04203	-0.255	0.30931	N	0.726908	B	0.17852	0.024	B	0.13407	0.009	T	0.31724	-0.9933	10	0.14656	T	0.56	.	6.9181	0.24371	0.7671:0.152:0.0809:0.0	.	269	Q96RW7	HMCN1_HUMAN	T	269	ENSP00000271588:K269T;ENSP00000356462:K269T	ENSP00000271588:K269T	K	+	2	0	HMCN1	184147441	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.047000	0.41269	2.269000	0.75478	0.454000	0.30748	AAA		0.393	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		24	389	24	389	---	---	---	---
CPS1	1373	broad.mit.edu	37	2	211421556	211421556	+	Silent	SNP	A	A	G			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr2:211421556A>G	ENST00000233072.5	+	1	295	c.99A>G	c.(97-99)agA>agG	p.R33R	CPS1_ENST00000430249.2_Silent_p.R39R	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	33					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)	p.R33R(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	AATTTTCAAGACCTGGCATCA	0.403																																						ENST00000233072.5																			1	Substitution - coding silent(1)	p.R33R(1)	prostate(1)	breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142						c.(97-99)agA>agG		carbamoyl-phosphate synthase 1, mitochondrial							104.0	104.0	104.0					2																	211421556		2203	4299	6502	SO:0001819	synonymous_variant	1373				carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity	g.chr2:211421556A>G	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.99A>G	2.37:g.211421556A>G			Somatic				CPS1_ENST00000430249.2_Silent_p.R39R	p.R33R	NM_001875.4	NP_001866.2	WXS	Illumina GAIIx	Phase_I	P31327	CPSM_HUMAN		Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	1	295	+			33					B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Silent	SNP	ENST00000233072.5	37	c.99A>G	CCDS2393.1																																																																																				0.403	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			13	235	13	235	---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215914419	215914419	+	Missense_Mutation	SNP	G	G	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr2:215914419G>T	ENST00000272895.7	-	6	843	c.624C>A	c.(622-624)aaC>aaA	p.N208K		NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	208					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.N208K(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GGCAAAATTTGTTAAAAACAT	0.383																																					Ovarian(66;664 1488 5121 34295)	ENST00000272895.7																			1	Substitution - Missense(1)	p.N208K(1)	prostate(1)	NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139						c.(622-624)aaC>aaA		ATP-binding cassette, sub-family A (ABC1), member 12							84.0	83.0	83.0					2																	215914419		2203	4300	6503	SO:0001583	missense	26154				cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity	g.chr2:215914419G>T	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.624C>A	2.37:g.215914419G>T	ENSP00000272895:p.Asn208Lys		Somatic					p.N208K	NM_173076.2	NP_775099.2	WXS	Illumina GAIIx	Phase_I	Q86UK0	ABCAC_HUMAN		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)	6	843	-		Renal(323;0.127)	208					Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	c.624C>A	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	G	0.184	-1.059470	0.01950	.	.	ENSG00000144452	ENST00000272895	D	0.87650	-2.28	6.05	3.33	0.38152	.	0.416026	0.25380	N	0.031094	T	0.73690	0.3619	N	0.19112	0.55	0.44149	D	0.996944	B	0.26318	0.146	B	0.19666	0.026	T	0.63107	-0.6711	10	0.33141	T	0.24	.	5.4346	0.16474	0.2339:0.1453:0.6208:0.0	.	208	Q86UK0	ABCAC_HUMAN	K	208	ENSP00000272895:N208K	ENSP00000272895:N208K	N	-	3	2	ABCA12	215622664	0.056000	0.20664	0.997000	0.53966	0.509000	0.34042	0.010000	0.13242	0.470000	0.27294	0.655000	0.94253	AAC		0.383	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		28	103	28	103	---	---	---	---
XXbac-BPG308J9.3	0	broad.mit.edu	37	6	29231318	29231318	+	lincRNA	SNP	G	G	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr6:29231318G>A	ENST00000441381.1	+	0	79																		p.S180F(1)									GACCATTGCAGATATTTCACA	0.433																																						ENST00000441381.1																			1	Substitution - Missense(1)	p.S180F(1)	prostate(1)																	58.0	55.0	56.0					6																	29231318		1861	4100	5961			101929006							g.chr6:29231318G>A																													6.37:g.29231318G>A			Somatic								WXS	Illumina GAIIx	Phase_I					0	79	+									RNA	SNP	ENST00000441381.1	37																																																																																						0.433	XXbac-BPG308J9.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000192829.1			48	118	48	118	---	---	---	---
MICB	4277	broad.mit.edu	37	6	31477560	31477560	+	Splice_Site	SNP	G	G	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr6:31477560G>T	ENST00000252229.6	+	6	1105	c.1026G>T	c.(1024-1026)gaG>gaT	p.E342D	MICB_ENST00000538442.1_Splice_Site_p.E310D|MICB_ENST00000399150.3_Splice_Site_p.E299D	NM_005931.3	NP_005922.2			MHC class I polypeptide-related sequence B									p.E342D(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						CTTCTCCAGAGCTTGTGAGCC	0.522																																						ENST00000252229.6																			1	Substitution - Missense(1)	p.E342D(1)	prostate(1)	NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						c.(1024-1026)gaG>gaT		MHC class I polypeptide-related sequence B							125.0	122.0	123.0					6																	31477560		1238	2576	3814	SO:0001630	splice_region_variant	4277				antigen processing and presentation|cytolysis|gamma-delta T cell activation|immune response|immune response-activating cell surface receptor signaling pathway|interspecies interaction between organisms|negative regulation of defense response to virus by host|response to heat|response to oxidative stress|response to retinoic acid	integral to plasma membrane|MHC class I protein complex	natural killer cell lectin-like receptor binding	g.chr6:31477560G>T		CCDS43449.1, CCDS75422.1, CCDS75423.1	6p21.3	2013-01-11			ENSG00000204516	ENSG00000204516		"""Immunoglobulin superfamily / C1-set domain containing"""	7091	protein-coding gene	gene with protein product		602436				8022771	Standard	NM_005931		Approved	PERB11.2	uc003ntn.4	Q29980	OTTHUMG00000031074	ENST00000252229.6:c.1025-1G>T	6.37:g.31477560G>T			Somatic				MICB_ENST00000538442.1_Splice_Site_p.E310D|MICB_ENST00000399150.3_Splice_Site_p.E299D	p.E342D	NM_005931.3	NP_005922.2	WXS	Illumina GAIIx	Phase_I	Q29980	MICB_HUMAN			6	1105	+			342						Splice_Site	SNP	ENST00000252229.6	37	c.1026G>T	CCDS43449.1	.	.	.	.	.	.	.	.	.	.	N	11.39	1.625924	0.28889	.	.	ENSG00000204516	ENST00000538442;ENST00000399150;ENST00000252229	T;T;T	0.00949	5.51;5.56;5.62	1.11	-0.991	0.10235	.	.	.	.	.	T	0.00695	0.0023	L	0.32530	0.975	0.09310	N	1	D;D;D	0.64830	0.974;0.994;0.994	D;D;D	0.70716	0.969;0.97;0.97	T	0.51576	-0.8688	9	0.59425	D	0.04	.	1.8088	0.03086	0.2375:0.0:0.4389:0.3236	.	310;299;342	F5H7Q8;A2AC57;Q29980	.;.;MICB_HUMAN	D	310;299;342	ENSP00000442345:E310D;ENSP00000382103:E299D;ENSP00000252229:E342D	ENSP00000252229:E342D	E	+	3	2	MICB	31585539	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	-0.379000	0.07437	-0.390000	0.07774	0.313000	0.20887	GAG		0.522	MICB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076102.3	NM_005931	Missense_Mutation	30	136	30	136	---	---	---	---
FAM83B	222584	broad.mit.edu	37	6	54735357	54735357	+	Missense_Mutation	SNP	G	G	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr6:54735357G>A	ENST00000306858.7	+	2	429	c.313G>A	c.(313-315)Gac>Aac	p.D105N		NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	105								p.D105N(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					TCCAAATCTTGACTTAGGCTG	0.463																																						ENST00000306858.7																			1	Substitution - Missense(1)	p.D105N(1)	prostate(1)	autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71						c.(313-315)Gac>Aac		family with sequence similarity 83, member B							110.0	111.0	111.0					6																	54735357		2203	4300	6503	SO:0001583	missense	222584							g.chr6:54735357G>A	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.313G>A	6.37:g.54735357G>A	ENSP00000304078:p.Asp105Asn		Somatic					p.D105N	NM_001010872.1	NP_001010872.1	WXS	Illumina GAIIx	Phase_I	Q5T0W9	FA83B_HUMAN			2	429	+	Lung NSC(77;0.0178)|Renal(3;0.122)		105					Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	c.313G>A	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.043898	0.75732	.	.	ENSG00000168143	ENST00000306858	T	0.14516	2.5	5.66	5.66	0.87406	.	0.209958	0.48286	D	0.000184	T	0.36248	0.0960	M	0.84511	2.7	0.80722	D	1	D	0.63880	0.993	D	0.65323	0.934	T	0.22800	-1.0206	10	0.72032	D	0.01	-27.2773	20.0973	0.97856	0.0:0.0:1.0:0.0	.	105	Q5T0W9	FA83B_HUMAN	N	105	ENSP00000304078:D105N	ENSP00000304078:D105N	D	+	1	0	FAM83B	54843316	1.000000	0.71417	0.952000	0.39060	0.090000	0.18270	9.525000	0.98039	2.830000	0.97506	0.585000	0.79938	GAC		0.463	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139		114	216	114	216	---	---	---	---
COL21A1	81578	broad.mit.edu	37	6	56035897	56035897	+	Missense_Mutation	SNP	C	C	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr6:56035897C>A	ENST00000244728.5	-	4	1067	c.670G>T	c.(670-672)Gca>Tca	p.A224S	COL21A1_ENST00000370819.1_Missense_Mutation_p.A224S|COL21A1_ENST00000535941.1_Missense_Mutation_p.A224S	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	224					extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.A224S(2)		breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			TCACGAGCTGCCACTGGAATT	0.318																																						ENST00000244728.5																			2	Substitution - Missense(2)	p.A224S(2)	prostate(2)	breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41						c.(670-672)Gca>Tca		collagen, type XXI, alpha 1							85.0	79.0	80.0					6																	56035897		1833	4080	5913	SO:0001583	missense	81578				cell adhesion	collagen|cytoplasm	structural molecule activity	g.chr6:56035897C>A	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"""Collagens"""	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.670G>T	6.37:g.56035897C>A	ENSP00000244728:p.Ala224Ser		Somatic				COL21A1_ENST00000370819.1_Missense_Mutation_p.A224S|COL21A1_ENST00000535941.1_Missense_Mutation_p.A224S	p.A224S	NM_030820.3	NP_110447.2	WXS	Illumina GAIIx	Phase_I	Q96P44	COLA1_HUMAN	LUSC - Lung squamous cell carcinoma(124;0.181)		4	1067	-	Lung NSC(77;0.0483)		224					A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	c.670G>T	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.604364	0.46423	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811	D;D;D	0.88975	-2.45;-2.4;-2.45	4.17	4.17	0.49024	.	0.000000	0.50627	U	0.000105	D	0.90741	0.7094	L	0.53249	1.67	0.80722	D	1	D;D	0.69078	0.993;0.997	P;D	0.75020	0.775;0.985	D	0.89374	0.3677	10	0.32370	T	0.25	.	16.8146	0.85730	0.0:1.0:0.0:0.0	.	224;224	Q96P44-3;Q96P44	.;COLA1_HUMAN	S	224	ENSP00000244728:A224S;ENSP00000359855:A224S;ENSP00000444384:A224S	ENSP00000244728:A224S	A	-	1	0	COL21A1	56143856	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.631000	0.46502	2.024000	0.59613	0.585000	0.79938	GCA		0.318	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			36	92	36	92	---	---	---	---
TTYH3	80727	broad.mit.edu	37	7	2698620	2698620	+	Missense_Mutation	SNP	C	C	G			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr7:2698620C>G	ENST00000258796.7	+	13	1676	c.1471C>G	c.(1471-1473)Ctc>Gtc	p.L491V	TTYH3_ENST00000407643.1_Missense_Mutation_p.L459V|TTYH3_ENST00000403167.1_Missense_Mutation_p.L320V	NM_025250.2	NP_079526.1	Q9C0H2	TTYH3_HUMAN	tweety family member 3	491					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|intracellular calcium activated chloride channel activity (GO:0005229)	p.L491V(1)		kidney(1)|large_intestine(3)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	17		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		GAACACCCCACTCATTGGGCG	0.647																																						ENST00000258796.7																			1	Substitution - Missense(1)	p.L491V(1)	prostate(1)	kidney(1)|large_intestine(3)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	17						c.(1471-1473)Ctc>Gtc		tweety family member 3							124.0	121.0	122.0					7																	2698620		2203	4300	6503	SO:0001583	missense	80727					chloride channel complex|plasma membrane	chloride channel activity	g.chr7:2698620C>G		CCDS34588.1	7p22	2013-09-02	2013-09-02		ENSG00000136295	ENSG00000136295			22222	protein-coding gene	gene with protein product		608919	"""tweety homolog 3 (Drosophila)"""				Standard	NM_025250		Approved	KIAA1691	uc003smp.3	Q9C0H2	OTTHUMG00000152050	ENST00000258796.7:c.1471C>G	7.37:g.2698620C>G	ENSP00000258796:p.Leu491Val		Somatic				TTYH3_ENST00000407643.1_Missense_Mutation_p.L459V|TTYH3_ENST00000403167.1_Missense_Mutation_p.L320V	p.L491V	NM_025250.2	NP_079526.1	WXS	Illumina GAIIx	Phase_I	Q9C0H2	TTYH3_HUMAN		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)	13	1676	+		Ovarian(82;0.0112)	491					A4D201|B7WP98|Q6L749|Q6ZVG3|Q8TEG6	Missense_Mutation	SNP	ENST00000258796.7	37	c.1471C>G	CCDS34588.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.170929	0.78452	.	.	ENSG00000136295	ENST00000258796;ENST00000407643;ENST00000403167;ENST00000429448	T;T;T;T	0.58940	0.3;0.3;0.3;1.12	4.11	4.11	0.48088	.	0.000000	0.64402	U	0.000001	T	0.71634	0.3363	M	0.68317	2.08	0.51767	D	0.999938	D;D	0.89917	0.998;1.0	D;D	0.83275	0.996;0.994	T	0.74393	-0.3680	10	0.66056	D	0.02	.	11.3844	0.49776	0.0:0.9104:0.0:0.0896	.	320;491	Q9C0H2-3;Q9C0H2	.;TTYH3_HUMAN	V	491;459;320;151	ENSP00000258796:L491V;ENSP00000385316:L459V;ENSP00000385015:L320V;ENSP00000413757:L151V	ENSP00000258796:L491V	L	+	1	0	TTYH3	2665146	1.000000	0.71417	0.994000	0.49952	0.996000	0.88848	5.561000	0.67339	2.004000	0.58718	0.462000	0.41574	CTC		0.647	TTYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325082.2	XM_166523		16	175	16	175	---	---	---	---
KMT2C	58508	broad.mit.edu	37	7	151845693	151845693	+	Missense_Mutation	SNP	T	T	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr7:151845693T>C	ENST00000262189.6	-	52	13537	c.13319A>G	c.(13318-13320)tAt>tGt	p.Y4440C	KMT2C_ENST00000355193.2_Missense_Mutation_p.Y4497C	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4440					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.Y4497C(1)|p.Y4440C(1)									CTGAGTCTCATAGACCTCCGT	0.507																																						ENST00000355193.2																			2	Substitution - Missense(2)	p.Y4497C(1)|p.Y4440C(1)	prostate(2)								c.(13489-13491)tAt>tGt		lysine (K)-specific methyltransferase 2C							115.0	112.0	113.0					7																	151845693		2203	4300	6503	SO:0001583	missense	58508							g.chr7:151845693T>C	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.13319A>G	7.37:g.151845693T>C	ENSP00000262189:p.Tyr4440Cys		Somatic				KMT2C_ENST00000262189.6_Missense_Mutation_p.Y4440C	p.Y4497C			WXS	Illumina GAIIx	Phase_I					53	13708	-								Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	c.13490A>G	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	15.93	2.977861	0.53720	.	.	ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877	T;T;T	0.70986	-0.53;-0.53;-0.53	5.24	5.24	0.73138	.	0.000000	0.39407	U	0.001380	D	0.82508	0.5052	M	0.69358	2.11	0.80722	D	1	D;D;D	0.89917	0.988;1.0;1.0	D;D;D	0.91635	0.993;0.999;0.999	D	0.84097	0.0393	10	0.59425	D	0.04	.	15.4242	0.75038	0.0:0.0:0.0:1.0	.	4440;3558;4497	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	MLL3_HUMAN;.;.	C	4440;4497;1057	ENSP00000262189:Y4440C;ENSP00000347325:Y4497C;ENSP00000410411:Y1057C	ENSP00000262189:Y4440C	Y	-	2	0	MLL3	151476626	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.997000	0.88414	2.103000	0.63969	0.455000	0.32223	TAT		0.507	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			70	195	70	195	---	---	---	---
ARHGEF39	84904	broad.mit.edu	37	9	35662634	35662635	+	Missense_Mutation	DNP	GC	GC	TT			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr9:35662634_35662635GC>TT	ENST00000378387.3	-	7	894_895	c.777_778GC>AA	c.(775-780)aaGCct>aaAAct	p.P260T	ARHGEF39_ENST00000378395.2_Missense_Mutation_p.P224T|ARHGEF39_ENST00000343259.3_Intron|ARHGEF39_ENST00000490970.1_5'UTR	NM_032818.2	NP_116207.2	Q8N4T4	ARG39_HUMAN	Rho guanine nucleotide exchange factor (GEF) 39	260	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of cell migration (GO:0030335)	plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.P260T(1)|p.K259K(1)									GGAGGCCGAGGCTTGGCCATGA	0.634																																						ENST00000378387.3																			2	Substitution - Missense(1)|Substitution - coding silent(1)	p.P260T(1)|p.K259K(1)	prostate(2)								c.(778-780)Cct>Act|c.(775-777)aaG>aaA		Rho guanine nucleotide exchange factor (GEF) 39																																				SO:0001583	missense	84904							g.chr9:35662634G>T|g.chr9:35662635C>T	AK001187	CCDS6584.2	9p13.3	2012-08-08	2012-08-08	2012-08-08	ENSG00000137135	ENSG00000137135			25909	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 100"""	C9orf100		22327280	Standard	XR_242516		Approved	FLJ14642	uc003zxm.1	Q8N4T4	OTTHUMG00000019869	ENST00000378387.3:c.777_778delinsTT	9.37:g.35662634_35662635delinsTT	ENSP00000367638:p.Pro260Thr		Somatic				ARHGEF39_ENST00000343259.3_Intron|ARHGEF39_ENST00000378395.2_Missense_Mutation_p.P224T|ARHGEF39_ENST00000490970.1_5'UTR|ARHGEF39_ENST00000343259.3_Intron|ARHGEF39_ENST00000378395.2_Silent_p.K223K|ARHGEF39_ENST00000490970.1_5'UTR	p.P260T|p.K259K	NM_032818.2	NP_116207.2	WXS	Illumina GAIIx	Phase_I					7	895|894	-								Q49AG0|Q6TPQ2|Q96ST6	Missense_Mutation|Silent	SNP	ENST00000378387.3	37	c.778C>A|c.777G>A	CCDS6584.2																																																																																				0.634	ARHGEF39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052330.1	NM_032818		21|20	23	20	23	---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94486051	94486051	+	Missense_Mutation	SNP	C	C	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr9:94486051C>T	ENST00000375708.3	-	9	2923	c.2725G>A	c.(2725-2727)Gtg>Atg	p.V909M	ROR2_ENST00000375715.1_Intron|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	909					cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)	p.V909M(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GCTTCCTGCACGGTGCTCTGG	0.637																																						ENST00000375708.3																			1	Substitution - Missense(1)	p.V909M(1)	prostate(1)	autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						c.(2725-2727)Gtg>Atg		receptor tyrosine kinase-like orphan receptor 2							83.0	84.0	84.0					9																	94486051		2203	4300	6503	SO:0001583	missense	4920				negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding	g.chr9:94486051C>T	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.2725G>A	9.37:g.94486051C>T	ENSP00000364860:p.Val909Met		Somatic				ROR2_ENST00000550066.1_5'UTR|ROR2_ENST00000375715.1_Intron	p.V909M	NM_004560.3	NP_004551.2	WXS	Illumina GAIIx	Phase_I	Q01974	ROR2_HUMAN			9	2923	-			909					Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	37	c.2725G>A	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	C	10.95	1.495711	0.26774	.	.	ENSG00000169071	ENST00000375708	T	0.78481	-1.18	4.75	4.75	0.60458	.	0.000000	0.38005	N	0.001857	T	0.70316	0.3210	N	0.08118	0	0.39472	D	0.967735	D	0.67145	0.996	P	0.51453	0.67	T	0.77453	-0.2582	10	0.51188	T	0.08	.	17.9502	0.89051	0.0:1.0:0.0:0.0	.	909	Q01974	ROR2_HUMAN	M	909	ENSP00000364860:V909M	ENSP00000364860:V909M	V	-	1	0	ROR2	93525872	1.000000	0.71417	0.997000	0.53966	0.020000	0.10135	4.545000	0.60698	2.466000	0.83321	0.561000	0.74099	GTG		0.637	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			39	185	39	185	---	---	---	---
TTLL11	158135	broad.mit.edu	37	9	124752018	124752018	+	Missense_Mutation	SNP	C	C	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr9:124752018C>A	ENST00000373776.3	-	4	1182	c.995G>T	c.(994-996)tGg>tTg	p.W332L	TTLL11_ENST00000321582.5_Missense_Mutation_p.W332L|TTLL11_ENST00000474723.1_5'UTR	NM_194252.2	NP_919228.2	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	332	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)	p.W332L(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1)	18						AGTGGGCTTCCAGGAGGGGTC	0.512																																						ENST00000321582.5																			1	Substitution - Missense(1)	p.W332L(1)	prostate(1)	breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1)	18						c.(994-996)tGg>tTg		tubulin tyrosine ligase-like family, member 11							108.0	118.0	114.0					9																	124752018		2199	4298	6497	SO:0001583	missense	158135				protein modification process	cilium|microtubule basal body	tubulin-tyrosine ligase activity	g.chr9:124752018C>A	AF521886	CCDS6834.2, CCDS48012.1	9q34.11	2013-02-14	2005-07-28	2005-07-28	ENSG00000175764	ENSG00000175764		"""Tubulin tyrosine ligase-like family"""	18113	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 20"""	C9orf20		15890843	Standard	NM_001139442		Approved	bA244O19.1	uc011lyl.2	Q8NHH1	OTTHUMG00000020597	ENST00000373776.3:c.995G>T	9.37:g.124752018C>A	ENSP00000362881:p.Trp332Leu		Somatic				TTLL11_ENST00000373776.3_Missense_Mutation_p.W332L|TTLL11_ENST00000474723.1_5'UTR	p.W332L	NM_001139442.1	NP_001132914.1	WXS	Illumina GAIIx	Phase_I	Q8NHH1	TTL11_HUMAN			4	1182	-			332			TTL.			Missense_Mutation	SNP	ENST00000373776.3	37	c.995G>T	CCDS6834.2	.	.	.	.	.	.	.	.	.	.	C	13.53	2.264390	0.39995	.	.	ENSG00000175764	ENST00000321582;ENST00000373776	T;T	0.06068	3.49;3.35	4.89	4.89	0.63831	.	0.232836	0.23237	U	0.050391	T	0.05547	0.0146	N	0.17800	0.525	0.48696	D	0.999691	B;B	0.17852	0.014;0.024	B;B	0.24155	0.014;0.051	T	0.37126	-0.9719	10	0.10377	T	0.69	.	17.1382	0.86745	0.0:1.0:0.0:0.0	.	332;332	F8W6M1;Q8NHH1	.;TTL11_HUMAN	L	332	ENSP00000321346:W332L;ENSP00000362881:W332L	ENSP00000321346:W332L	W	-	2	0	TTLL11	123791839	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.748000	0.55142	2.283000	0.76528	0.549000	0.68633	TGG		0.512	TTLL11-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053907.1	XM_088486		66	240	66	240	---	---	---	---
MKI67	4288	broad.mit.edu	37	10	129900972	129900972	+	Silent	SNP	G	G	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr10:129900972G>C	ENST00000368654.3	-	13	9507	c.9132C>G	c.(9130-9132)ccC>ccG	p.P3044P	MKI67_ENST00000368653.3_Silent_p.P2684P	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3044					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.P3044P(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TGATGACCACGGGTTCGGATG	0.517																																						ENST00000368654.3																			1	Substitution - coding silent(1)	p.P3044P(1)	prostate(1)	NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159						c.(9130-9132)ccC>ccG		marker of proliferation Ki-67							156.0	148.0	151.0					10																	129900972		2203	4300	6503	SO:0001819	synonymous_variant	4288				cell proliferation	nucleolus	ATP binding|protein C-terminus binding	g.chr10:129900972G>C	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.9132C>G	10.37:g.129900972G>C			Somatic				MKI67_ENST00000368653.3_Silent_p.P2684P	p.P3044P	NM_002417.4	NP_002408.3	WXS	Illumina GAIIx	Phase_I	P46013	KI67_HUMAN			13	9507	-		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)	3044					Q5VWH2	Silent	SNP	ENST00000368654.3	37	c.9132C>G	CCDS7659.1																																																																																				0.517	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		10	296	10	296	---	---	---	---
EED	8726	broad.mit.edu	37	11	85968564	85968564	+	Missense_Mutation	SNP	T	T	G			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr11:85968564T>G	ENST00000263360.6	+	6	1246	c.560T>G	c.(559-561)gTt>gGt	p.V187G	EED_ENST00000528180.1_Missense_Mutation_p.V187G|EED_ENST00000327320.4_Missense_Mutation_p.V187G|EED_ENST00000351625.6_Missense_Mutation_p.V187G	NM_003797.3	NP_003788.2	O75530	EED_HUMAN	embryonic ectoderm development	187	Interaction with EZH2. {ECO:0000250}.|Required for interaction with the matrix protein MA of HIV-1.				negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K27 methylation (GO:0061087)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|identical protein binding (GO:0042802)	p.V187G(1)		haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	21		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				TAGCACTATGTTGGCCATGGA	0.303																																						ENST00000263360.6																			1	Substitution - Missense(1)	p.V187G(1)	prostate(1)	haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	21						c.(559-561)gTt>gGt		embryonic ectoderm development							86.0	79.0	81.0					11																	85968564		2202	4299	6501	SO:0001583	missense	8726				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|identical protein binding	g.chr11:85968564T>G	AF078933	CCDS8273.1, CCDS8274.1	11q14.2-q22.3	2013-01-10			ENSG00000074266	ENSG00000074266		"""WD repeat domain containing"""	3188	protein-coding gene	gene with protein product	"""WD protein associating with integrin cytoplasmic tails 1"""	605984				9765275, 9806832	Standard	NM_003797		Approved	WAIT-1, HEED	uc001pbp.3	O75530	OTTHUMG00000167209	ENST00000263360.6:c.560T>G	11.37:g.85968564T>G	ENSP00000263360:p.Val187Gly		Somatic				EED_ENST00000351625.6_Missense_Mutation_p.V187G|EED_ENST00000528180.1_Missense_Mutation_p.V187G|EED_ENST00000327320.4_Missense_Mutation_p.V187G	p.V187G	NM_003797.3	NP_003788.2	WXS	Illumina GAIIx	Phase_I	O75530	EED_HUMAN			6	1246	+		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)	187			Interaction with EZH2 (By similarity).|Required for interaction with the matrix protein MA of HIV-1.		A8K7V5|O00149|Q6NTH2|Q7LDA5|Q7LDG8|Q86VV2|Q9UNY7	Missense_Mutation	SNP	ENST00000263360.6	37	c.560T>G	CCDS8273.1	.	.	.	.	.	.	.	.	.	.	T	18.21	3.573196	0.65765	.	.	ENSG00000074266	ENST00000263360;ENST00000528180;ENST00000351625;ENST00000327320	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.31	5.31	0.75309	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.48750	0.1517	L	0.56199	1.76	0.80722	D	1	P;P;D;P	0.63046	0.8;0.92;0.992;0.69	P;P;D;P	0.65010	0.618;0.723;0.931;0.666	T	0.40194	-0.9576	9	.	.	.	-18.1676	15.5428	0.76070	0.0:0.0:0.0:1.0	.	187;187;187;187	O75530-3;E9PJK2;O75530-2;O75530	.;.;.;EED_HUMAN	G	187	ENSP00000263360:V187G;ENSP00000431778:V187G;ENSP00000338186:V187G;ENSP00000315587:V187G	.	V	+	2	0	EED	85646212	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.693000	0.84214	2.136000	0.66102	0.533000	0.62120	GTT		0.303	EED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393733.1	NM_003797		4	90	4	90	---	---	---	---
PKP2	5318	broad.mit.edu	37	12	32975445	32975445	+	Missense_Mutation	SNP	T	T	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr12:32975445T>C	ENST00000070846.6	-	9	1951	c.1927A>G	c.(1927-1929)Aaa>Gaa	p.K643E	PKP2_ENST00000340811.4_Missense_Mutation_p.K599E	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	643					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)	p.K643E(1)		NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					CCAATACTTTTGTTGTTGTCA	0.403																																						ENST00000340811.4																			1	Substitution - Missense(1)	p.K643E(1)	prostate(1)	NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50						c.(1795-1797)Aaa>Gaa		plakophilin 2							128.0	121.0	123.0					12																	32975445		2203	4300	6503	SO:0001583	missense	5318				cell-cell adhesion	desmosome|integral to membrane|nucleus	binding	g.chr12:32975445T>C	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"""Armadillo repeat containing"""	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.1927A>G	12.37:g.32975445T>C	ENSP00000070846:p.Lys643Glu		Somatic				PKP2_ENST00000070846.6_Missense_Mutation_p.K643E	p.K599E	NM_001005242.2	NP_001005242.2	WXS	Illumina GAIIx	Phase_I	Q99959	PKP2_HUMAN			8	1903	-	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)		643					A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	c.1795A>G	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	T	10.63	1.403312	0.25291	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.74947	-0.89;-0.89	5.05	5.05	0.67936	Armadillo-like helical (1);Armadillo-type fold (1);	0.407398	0.26244	N	0.025493	T	0.61850	0.2380	L	0.33485	1.01	0.33762	D	0.622018	B;B;B	0.17268	0.006;0.004;0.021	B;B;B	0.15052	0.01;0.004;0.012	T	0.63139	-0.6704	10	0.12103	T	0.63	-11.5073	13.3952	0.60849	0.0:0.0:0.0:1.0	.	599;599;643	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	E	599;643;643	ENSP00000342800:K599E;ENSP00000070846:K643E	ENSP00000070846:K643E	K	-	1	0	PKP2	32866712	1.000000	0.71417	0.991000	0.47740	0.911000	0.54048	2.490000	0.45294	1.888000	0.54679	0.460000	0.39030	AAA		0.403	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		11	125	11	125	---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124395093	124395093	+	Silent	SNP	G	G	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr12:124395093G>A	ENST00000409039.3	+	58	9679	c.9654G>A	c.(9652-9654)aaG>aaA	p.K3218K		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3218	Stalk. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.K1810K(1)|p.K3218K(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GCCTCTTGAAGACTCTTAATA	0.388																																						ENST00000409039.3																			2	Substitution - coding silent(2)	p.K1810K(1)|p.K3218K(1)	prostate(2)	breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						c.(9652-9654)aaG>aaA		dynein, axonemal, heavy chain 10							117.0	119.0	118.0					12																	124395093		1880	4110	5990	SO:0001819	synonymous_variant	196385				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity	g.chr12:124395093G>A	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.9654G>A	12.37:g.124395093G>A			Somatic					p.K3218K	NM_207437.3	NP_997320.2	WXS	Illumina GAIIx	Phase_I	Q8IVF4	DYH10_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)	58	9679	+	all_neural(191;0.101)|Medulloblastoma(191;0.163)		3218			Stalk (By similarity).		C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	c.9654G>A	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	0.657	-0.807122	0.02819	.	.	ENSG00000197653	ENST00000540041	.	.	.	5.2	5.2	0.72013	.	.	.	.	.	T	0.74696	0.3750	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73861	-0.3849	4	.	.	.	.	18.7279	0.91722	0.0:0.0:1.0:0.0	.	.	.	.	K	146	.	.	R	+	2	0	DNAH10	122961046	1.000000	0.71417	1.000000	0.80357	0.085000	0.17905	4.521000	0.60532	2.420000	0.82092	0.655000	0.94253	AGA		0.388	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			12	219	12	219	---	---	---	---
TYRO3	7301	broad.mit.edu	37	15	41860444	41860444	+	Missense_Mutation	SNP	G	G	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr15:41860444G>A	ENST00000263798.3	+	8	1215	c.991G>A	c.(991-993)Gcc>Acc	p.A331T	TYRO3_ENST00000559066.1_Missense_Mutation_p.A286T	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	331	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.A331T(1)|p.A323T(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		AAACCTCCATGCCATCCGCAC	0.572																																						ENST00000263798.3																			2	Substitution - Missense(2)	p.A331T(1)|p.A323T(1)	prostate(2)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43						c.(991-993)Gcc>Acc		TYRO3 protein tyrosine kinase							60.0	58.0	59.0					15																	41860444		2203	4300	6503	SO:0001583	missense	7301					integral to plasma membrane	ATP binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity	g.chr15:41860444G>A	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.991G>A	15.37:g.41860444G>A	ENSP00000263798:p.Ala331Thr		Somatic				TYRO3_ENST00000559066.1_Missense_Mutation_p.A286T	p.A331T	NM_006293.3	NP_006284.2	WXS	Illumina GAIIx	Phase_I	Q06418	TYRO3_HUMAN		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)	8	1215	+		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)	331			Fibronectin type-III 2.		O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	37	c.991G>A	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.213082	0.58452	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	T	0.60299	0.2	4.96	4.96	0.65561	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.40640	N	0.001045	T	0.51584	0.1683	L	0.58101	1.795	0.32350	N	0.558623	P	0.35124	0.485	B	0.37550	0.253	T	0.62148	-0.6915	10	0.39692	T	0.17	-14.7784	7.3749	0.26823	0.1782:0.0:0.8217:0.0	.	331	Q06418	TYRO3_HUMAN	T	263;331	ENSP00000263798:A331T	ENSP00000263798:A331T	A	+	1	0	TYRO3	39647736	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	2.667000	0.46808	2.586000	0.87340	0.563000	0.77884	GCC		0.572	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2			17	74	17	74	---	---	---	---
SMAD3	4088	broad.mit.edu	37	15	67477178	67477178	+	Missense_Mutation	SNP	G	G	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr15:67477178G>T	ENST00000327367.4	+	7	1295	c.985G>T	c.(985-987)Gcc>Tcc	p.A329S	SMAD3_ENST00000439724.3_Missense_Mutation_p.A285S|SMAD3_ENST00000540846.2_Missense_Mutation_p.A224S|SMAD3_ENST00000537194.2_Missense_Mutation_p.A134S	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	329	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.A329S(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		CTGGCACCCGGCCACCGTCTG	0.597																																						ENST00000327367.4																			1	Substitution - Missense(1)	p.A329S(1)	prostate(1)	autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						c.(985-987)Gcc>Tcc		SMAD family member 3							86.0	76.0	79.0					15																	67477178		2201	4299	6500	SO:0001583	missense	4088				activation of caspase activity|cell cycle arrest|cell-cell junction organization|evasion of host defenses by virus|immune response|induction of apoptosis|negative regulation of cell growth|negative regulation of mitotic cell cycle|negative regulation of protein catabolic process|negative regulation of protein phosphorylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|protein stabilization|regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|transport|wound healing	cytosol|nuclear inner membrane|receptor complex	beta-catenin binding|co-SMAD binding|metal ion binding|protein homodimerization activity|protein kinase binding|R-SMAD binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor binding|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding	g.chr15:67477178G>T	BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"""SMADs"""	6769	protein-coding gene	gene with protein product		603109	"""MAD, mothers against decapentaplegic homolog 3 (Drosophila)"", ""SMAD, mothers against DPP homolog 3 (Drosophila)"""	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.985G>T	15.37:g.67477178G>T	ENSP00000332973:p.Ala329Ser		Somatic				SMAD3_ENST00000540846.2_Missense_Mutation_p.A224S|SMAD3_ENST00000537194.2_Missense_Mutation_p.A134S|SMAD3_ENST00000439724.3_Missense_Mutation_p.A285S	p.A329S	NM_005902.3	NP_005893.1	WXS	Illumina GAIIx	Phase_I	P84022	SMAD3_HUMAN		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)	7	1295	+			329			MH2.		A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Missense_Mutation	SNP	ENST00000327367.4	37	c.985G>T	CCDS10222.1	.	.	.	.	.	.	.	.	.	.	G	33	5.259644	0.95368	.	.	ENSG00000166949	ENST00000327367;ENST00000535241;ENST00000540846;ENST00000439724;ENST00000537194	D;D;D;D	0.97041	-4.22;-4.22;-4.22;-4.22	5.19	5.19	0.71726	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.97040	0.9033	L	0.33792	1.035	0.80722	D	1	P;D	0.61080	0.903;0.989	P;D	0.67103	0.88;0.949	D	0.96378	0.9279	10	0.29301	T	0.29	.	18.7296	0.91730	0.0:0.0:1.0:0.0	.	285;329	B7Z4Z5;P84022	.;SMAD3_HUMAN	S	329;329;224;285;134	ENSP00000332973:A329S;ENSP00000437757:A224S;ENSP00000401133:A285S;ENSP00000445348:A134S	ENSP00000332973:A329S	A	+	1	0	SMAD3	65264232	1.000000	0.71417	0.958000	0.39756	0.995000	0.86356	9.633000	0.98432	2.412000	0.81896	0.650000	0.86243	GCC		0.597	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902		7	36	7	36	---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93524064	93524064	+	Missense_Mutation	SNP	G	G	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr15:93524064G>C	ENST00000394196.4	+	23	3964	c.2896G>C	c.(2896-2898)Gaa>Caa	p.E966Q	CHD2_ENST00000557381.1_Missense_Mutation_p.E966Q	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	966	Glu-rich.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)	p.E966Q(2)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TTTTAATAAAGAAGAGCTGAC	0.368																																						ENST00000394196.4																			2	Substitution - Missense(2)	p.E966Q(2)	prostate(2)	breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47						c.(2896-2898)Gaa>Caa		chromodomain helicase DNA binding protein 2							43.0	47.0	46.0					15																	93524064		2192	4295	6487	SO:0001583	missense	1106				regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding	g.chr15:93524064G>C	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.2896G>C	15.37:g.93524064G>C	ENSP00000377747:p.Glu966Gln		Somatic				CHD2_ENST00000557381.1_Missense_Mutation_p.E966Q	p.E966Q	NM_001271.3	NP_001262.3	WXS	Illumina GAIIx	Phase_I	O14647	CHD2_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)		23	3964	+	Lung NSC(78;0.00976)|all_lung(78;0.016)		966			Glu-rich.		C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	c.2896G>C	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	G	28.4	4.913709	0.92178	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	T;T	0.77489	-1.1;-1.1	5.38	5.38	0.77491	.	0.000000	0.35067	U	0.003462	T	0.76456	0.3990	L	0.46567	1.45	0.80722	D	1	B;B	0.32338	0.109;0.365	B;B	0.36186	0.013;0.219	T	0.76277	-0.3018	10	0.54805	T	0.06	-27.9263	19.137	0.93431	0.0:0.0:1.0:0.0	.	966;966	O14647;O14647-2	CHD2_HUMAN;.	Q	966	ENSP00000377747:E966Q;ENSP00000451366:E966Q	ENSP00000377747:E966Q	E	+	1	0	CHD2	91325068	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.835000	0.99442	2.532000	0.85374	0.561000	0.74099	GAA		0.368	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		12	105	12	105	---	---	---	---
SMARCE1	6605	broad.mit.edu	37	17	38792754	38792754	+	Missense_Mutation	SNP	T	T	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr17:38792754T>C	ENST00000348513.6	-	6	1042	c.262A>G	c.(262-264)Aac>Gac	p.N88D	KRT222_ENST00000476049.1_3'UTR|SMARCE1_ENST00000580419.1_Missense_Mutation_p.N53D|SMARCE1_ENST00000544009.1_Missense_Mutation_p.N18D|SMARCE1_ENST00000578044.1_Missense_Mutation_p.N18D|SMARCE1_ENST00000377808.4_Missense_Mutation_p.N53D|SMARCE1_ENST00000431889.2_Missense_Mutation_p.N70D|SMARCE1_ENST00000400122.3_Missense_Mutation_p.N18D	NM_003079.4	NP_003070.3	Q969G3	SMCE1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	88					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|metabolic process (GO:0008152)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|N-acetyltransferase activity (GO:0008080)|protein N-terminus binding (GO:0047485)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)	p.N88D(1)		large_intestine(1)	1		Breast(137;0.000812)				AGGTCAGGGTTGGAAGCCTTT	0.363																																						ENST00000348513.6																			1	Substitution - Missense(1)	p.N88D(1)	prostate(1)	large_intestine(1)	1						c.(262-264)Aac>Gac		SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1							110.0	102.0	105.0					17																	38792754		2203	4300	6503	SO:0001583	missense	6605				chromatin modification|negative regulation of transcription, DNA-dependent|nervous system development|nucleosome disassembly|regulation of transcription from RNA polymerase II promoter	nBAF complex|npBAF complex|nuclear chromosome|SWI/SNF complex|transcriptional repressor complex	chromatin binding|DNA binding|N-acetyltransferase activity|protein binding|protein N-terminus binding|transcription coactivator activity	g.chr17:38792754T>C	AF035262	CCDS11370.1	17q21.2	2006-09-20			ENSG00000073584	ENSG00000073584			11109	protein-coding gene	gene with protein product		603111				9435219	Standard	NM_003079		Approved	BAF57	uc002hux.2	Q969G3	OTTHUMG00000133367	ENST00000348513.6:c.262A>G	17.37:g.38792754T>C	ENSP00000323967:p.Asn88Asp		Somatic				SMARCE1_ENST00000400122.3_Missense_Mutation_p.N18D|SMARCE1_ENST00000578044.1_Missense_Mutation_p.N18D|SMARCE1_ENST00000431889.2_Missense_Mutation_p.N70D|KRT222_ENST00000476049.1_3'UTR|SMARCE1_ENST00000580419.1_Missense_Mutation_p.N53D|SMARCE1_ENST00000377808.4_Missense_Mutation_p.N53D|SMARCE1_ENST00000544009.1_Missense_Mutation_p.N18D	p.N88D	NM_003079.4	NP_003070.3	WXS	Illumina GAIIx	Phase_I	Q969G3	SMCE1_HUMAN			6	1042	-		Breast(137;0.000812)	88					B3KMC1|B4DFR4|C0IMW4|C0IMW5|C0IMW7|H7C3F6|O43539	Missense_Mutation	SNP	ENST00000348513.6	37	c.262A>G	CCDS11370.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.143819	0.57044	.	.	ENSG00000073584	ENST00000348513;ENST00000544009;ENST00000431889;ENST00000377808	D;D;D;D	0.98381	-4.9;-4.9;-4.9;-4.9	5.74	5.74	0.90152	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.042264	0.85682	D	0.000000	D	0.98988	0.9655	M	0.87547	2.89	0.80722	D	1	D;D;D;D	0.71674	0.996;0.992;0.998;0.997	D;D;D;D	0.71414	0.965;0.942;0.965;0.973	D	0.99705	1.1005	10	0.66056	D	0.02	.	16.3305	0.83010	0.0:0.0:0.0:1.0	.	53;70;53;88	C0IMW5;B4DGM3;C0IMW4;Q969G3	.;.;.;SMCE1_HUMAN	D	88;18;70;53	ENSP00000323967:N88D;ENSP00000441857:N18D;ENSP00000445370:N70D;ENSP00000367039:N53D	ENSP00000323967:N88D	N	-	1	0	SMARCE1	36046280	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.920000	0.87521	2.317000	0.78254	0.459000	0.35465	AAC		0.363	SMARCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257203.1	NM_003079		68	179	68	179	---	---	---	---
NAGS	162417	broad.mit.edu	37	17	42085837	42085837	+	Silent	SNP	C	C	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr17:42085837C>T	ENST00000293404.3	+	7	1591	c.1473C>T	c.(1471-1473)ggC>ggT	p.G491G		NM_153006.2	NP_694551.1	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	491	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial matrix (GO:0005759)	acetyl-CoA:L-glutamate N-acetyltransferase activity (GO:0004042)	p.G491G(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)		ACAGTGATGGCAGCTTCTCCA	0.498																																						ENST00000293404.3																			1	Substitution - coding silent(1)	p.G491G(1)	prostate(1)	endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						c.(1471-1473)ggC>ggT		N-acetylglutamate synthase	L-Glutamic Acid(DB00142)						317.0	308.0	311.0					17																	42085837		2203	4300	6503	SO:0001819	synonymous_variant	162417				arginine biosynthetic process|urea cycle	mitochondrial matrix	acetyl-CoA:L-glutamate N-acetyltransferase activity	g.chr17:42085837C>T	AY116537	CCDS11473.1	17q21.31	2008-02-05				ENSG00000161653			17996	protein-coding gene	gene with protein product		608300				15050968, 12459178	Standard	NM_153006		Approved	AGAS, ARGA, NAT7	uc002ies.3	Q8N159		ENST00000293404.3:c.1473C>T	17.37:g.42085837C>T			Somatic					p.G491G	NM_153006.2	NP_694551.1	WXS	Illumina GAIIx	Phase_I	Q8N159	NAGS_HUMAN		BRCA - Breast invasive adenocarcinoma(366;0.113)	7	1591	+		Breast(137;0.00536)|Prostate(33;0.0724)	491			N-acetyltransferase.		B2RAZ9|Q8IWR4	Silent	SNP	ENST00000293404.3	37	c.1473C>T	CCDS11473.1																																																																																				0.498	NAGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457660.1	NM_153006		27	320	27	320	---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61864525	61864525	+	Missense_Mutation	SNP	T	T	C			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr17:61864525T>C	ENST00000578681.1	+	3	717	c.116T>C	c.(115-117)tTt>tCt	p.F39S	DDX42_ENST00000583590.1_Missense_Mutation_p.F39S|DDX42_ENST00000457800.2_Missense_Mutation_p.F39S|DDX42_ENST00000359353.5_Intron|DDX42_ENST00000389924.2_Missense_Mutation_p.F39S	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	39					protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.F39S(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						CACAGTGCCTTTGGGGCAACC	0.502																																						ENST00000578681.1																			1	Substitution - Missense(1)	p.F39S(1)	prostate(1)	NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						c.(115-117)tTt>tCt		DEAD (Asp-Glu-Ala-Asp) box helicase 42							126.0	121.0	123.0					17																	61864525		2203	4300	6503	SO:0001583	missense	11325				protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding	g.chr17:61864525T>C	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"""DEAD-boxes"""	18676	protein-coding gene	gene with protein product	"""splicing factor 3b, subunit 8"""	613369	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"""			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.116T>C	17.37:g.61864525T>C	ENSP00000464050:p.Phe39Ser		Somatic				DDX42_ENST00000457800.2_Missense_Mutation_p.F39S|DDX42_ENST00000389924.2_Missense_Mutation_p.F39S|DDX42_ENST00000583590.1_Missense_Mutation_p.F39S|DDX42_ENST00000359353.5_Intron	p.F39S	NM_007372.2	NP_031398.2	WXS	Illumina GAIIx	Phase_I	Q86XP3	DDX42_HUMAN			3	717	+			39					A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	ENST00000578681.1	37	c.116T>C	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.174005	0.78452	.	.	ENSG00000198231	ENST00000389924;ENST00000457800	T;T	0.20738	2.05;2.05	5.57	5.57	0.84162	.	0.901057	0.09784	N	0.756306	T	0.21921	0.0528	L	0.50333	1.59	0.80722	D	1	P	0.48911	0.917	B	0.41135	0.348	T	0.10200	-1.0640	10	0.08381	T	0.77	-11.5982	14.9045	0.70709	0.0:0.0:0.0:1.0	.	39	Q86XP3	DDX42_HUMAN	S	39	ENSP00000374574:F39S;ENSP00000390121:F39S	ENSP00000374574:F39S	F	+	2	0	DDX42	59218257	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.967000	0.87967	2.107000	0.64212	0.454000	0.30748	TTT		0.502	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372		15	222	15	222	---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54591238	54591238	+	Silent	SNP	G	G	A	rs149456946	byFrequency	TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr18:54591238G>A	ENST00000254442.3	+	22	3823	c.3612G>A	c.(3610-3612)ctG>ctA	p.L1204L	WDR7_ENST00000357574.3_Silent_p.L1171L|WDR7_ENST00000589935.1_Intron	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	1204					hematopoietic progenitor cell differentiation (GO:0002244)			p.L1204L(1)		NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		CCATTGATCTGATTGGACGTG	0.498																																						ENST00000254442.3																			1	Substitution - coding silent(1)	p.L1204L(1)	prostate(1)	NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78						c.(3610-3612)ctG>ctA		WD repeat domain 7							172.0	143.0	153.0					18																	54591238		2203	4300	6503	SO:0001819	synonymous_variant	23335							g.chr18:54591238G>A	AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"""WD repeat domain containing"""	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.3612G>A	18.37:g.54591238G>A			Somatic				WDR7_ENST00000589935.1_Intron|WDR7_ENST00000357574.3_Silent_p.L1171L	p.L1204L	NM_015285.2	NP_056100.2	WXS	Illumina GAIIx	Phase_I	Q9Y4E6	WDR7_HUMAN		Lung(128;0.0238)|Colorectal(16;0.0296)	22	3823	+			1204					A7E2C8|Q86UX5|Q86VP2|Q96PS7	Silent	SNP	ENST00000254442.3	37	c.3612G>A	CCDS11962.1																																																																																				0.498	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1			10	122	10	122	---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9056757	9056757	+	Missense_Mutation	SNP	G	G	T			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr19:9056757G>T	ENST00000397910.4	-	3	30892	c.30689C>A	c.(30688-30690)cCc>cAc	p.P10230H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10232	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.P5863H(1)|p.P10230H(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGCATTAAAGGGGGTGATTAT	0.448																																						ENST00000397910.4																			2	Substitution - Missense(2)	p.P5863H(1)|p.P10230H(1)	prostate(2)	NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						c.(30688-30690)cCc>cAc		mucin 16, cell surface associated							90.0	89.0	90.0					19																	9056757		1908	4136	6044	SO:0001583	missense	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:9056757G>T	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.30689C>A	19.37:g.9056757G>T	ENSP00000381008:p.Pro10230His		Somatic					p.P10230H	NM_024690.2	NP_078966.2	WXS	Illumina GAIIx	Phase_I	Q8WXI7	MUC16_HUMAN			3	30892	-			10232			Ser-rich.|Thr-rich.		Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	c.30689C>A	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	7.784	0.710095	0.15239	.	.	ENSG00000181143	ENST00000397910	T	0.03301	3.98	3.24	-2.13	0.07144	.	.	.	.	.	T	0.01730	0.0055	N	0.08118	0	.	.	.	B	0.14438	0.01	B	0.10450	0.005	T	0.46884	-0.9159	8	0.87932	D	0	.	0.2379	0.00188	0.3589:0.1401:0.2138:0.2872	.	10230	B5ME49	.	H	10230	ENSP00000381008:P10230H	ENSP00000381008:P10230H	P	-	2	0	MUC16	8917757	0.000000	0.05858	0.000000	0.03702	0.333000	0.28666	-3.014000	0.00646	-0.492000	0.06687	0.467000	0.42956	CCC		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		10	94	10	94	---	---	---	---
GPR112	139378	broad.mit.edu	37	X	135431329	135431329	+	Missense_Mutation	SNP	C	C	A			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chrX:135431329C>A	ENST00000394143.1	+	6	5755	c.5464C>A	c.(5464-5466)Cca>Aca	p.P1822T	GPR112_ENST00000370652.1_Missense_Mutation_p.P1822T|GPR112_ENST00000287534.4_Missense_Mutation_p.P1759T|GPR112_ENST00000412101.1_Missense_Mutation_p.P1617T|GPR112_ENST00000394141.1_Missense_Mutation_p.P1617T	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1822					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P1822T(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TTCATACCCTCCATGGACCCC	0.408																																						ENST00000394143.1																			1	Substitution - Missense(1)	p.P1822T(1)	prostate(1)	NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199						c.(5464-5466)Cca>Aca		G protein-coupled receptor 112							139.0	127.0	131.0					X																	135431329		2203	4300	6503	SO:0001583	missense	139378				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chrX:135431329C>A	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.5464C>A	X.37:g.135431329C>A	ENSP00000377699:p.Pro1822Thr		Somatic				GPR112_ENST00000412101.1_Missense_Mutation_p.P1617T|GPR112_ENST00000370652.1_Missense_Mutation_p.P1822T|GPR112_ENST00000394141.1_Missense_Mutation_p.P1617T|GPR112_ENST00000287534.4_Missense_Mutation_p.P1759T	p.P1822T	NM_153834.3	NP_722576.3	WXS	Illumina GAIIx	Phase_I	Q8IZF6	GP112_HUMAN			6	5755	+	Acute lymphoblastic leukemia(192;0.000127)		1822					A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	c.5464C>A	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	c	2.137	-0.397754	0.04899	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.27104	1.72;1.72;1.69;1.83;1.69	3.71	-2.15	0.07102	.	.	.	.	.	T	0.12475	0.0303	N	0.24115	0.695	0.09310	N	1	B;B;B	0.25312	0.123;0.103;0.063	B;B;B	0.25140	0.042;0.058;0.026	T	0.32824	-0.9892	9	0.23302	T	0.38	.	2.6312	0.04945	0.3648:0.2418:0.0:0.3934	.	1759;1617;1822	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	T	1822;1822;1617;1759;1617	ENSP00000377699:P1822T;ENSP00000359686:P1822T;ENSP00000416526:P1617T;ENSP00000287534:P1759T;ENSP00000377697:P1617T	ENSP00000287534:P1759T	P	+	1	0	GPR112	135258995	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.287000	0.02785	-0.215000	0.10063	-0.369000	0.07265	CCA		0.408	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			15	143	15	143	---	---	---	---
C10orf55	414236	broad.mit.edu	37	10	75673298	75673298	+	Intron	DEL	A	A	-			TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr10:75673298delA	ENST00000409178.1	-	3	268				C10orf55_ENST00000412307.2_Intron|PLAU_ENST00000494287.1_3'UTR|PLAU_ENST00000446342.1_Splice_Site_p.G137fs|PLAU_ENST00000372762.4_Splice_Site_p.G118fs|PLAU_ENST00000372764.3_Splice_Site_p.G154fs	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55											endometrium(1)	1	Prostate(51;0.0112)					GTCCTCCAGGAAAAAAGCCCT	0.517																																						ENST00000446342.1																			0				cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(3)|ovary(2)	16						c.(409-411)gga>gg		plasminogen activator, urokinase	Amiloride(DB00594)|Urokinase(DB00013)						156.0	188.0	177.0					10																	75673298		2203	4300	6503	SO:0001627	intron_variant	5328				blood coagulation|chemotaxis|fibrinolysis|proteolysis|regulation of cell adhesion mediated by integrin|regulation of receptor activity|regulation of smooth muscle cell migration|regulation of smooth muscle cell-matrix adhesion|signal transduction	cell surface|extracellular space|plasma membrane	serine-type endopeptidase activity	g.chr10:75673298delA		CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.73-465T>-	10.37:g.75673298delA			Somatic				PLAU_ENST00000372764.3_Splice_Site_p.G154fs|C10orf55_ENST00000412307.2_Intron|C10orf55_ENST00000409178.1_Intron|PLAU_ENST00000372762.4_Splice_Site_p.G118fs|PLAU_ENST00000494287.1_3'UTR	p.G137fs	NM_001145031.1	NP_001138503	WXS	Illumina GAIIx	Phase_I	P00749	UROK_HUMAN			6	893	+	Prostate(51;0.0112)		154			Kringle.		Q3KRG4|Q8NAK4	Splice_Site	DEL	ENST00000409178.1	37	c.411delA	CCDS53541.1																																																																																				0.517	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791		7	790	7	790	---	---	---	---
ARHGAP11A	9824	broad.mit.edu	37	15	32920998	32921007	+	Splice_Site	DEL	GAATTGGTAG	GAATTGGTAG	-	rs372419991		TCGA-EJ-5524-01A-01D-1576-08	TCGA-EJ-5524-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb32ee2b-3ed2-4a8b-a7ed-89ef4bef7661	75bec014-53c0-49e0-88d8-fcd261d22ec1	g.chr15:32920998_32921007delGAATTGGTAG	ENST00000361627.3	+	7	1654_1659	c.932_937delGAATTGGTAG	c.(931-939)agaattggt>agt	p.RIG311fs	ARHGAP11A_ENST00000563864.1_Splice_Site_p.RIG311fs|ARHGAP11A_ENST00000565905.1_Splice_Site_p.RIG122fs|ARHGAP11A_ENST00000543522.1_Splice_Site_p.RIG122fs|ARHGAP11A_ENST00000567348.1_Splice_Site_p.RIG311fs	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	311					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.A313P(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		CAAGAAGAAAGAATTGGTAGGTATTTATTA	0.238																																					Colon(45;757 1134 30003 36652)	ENST00000361627.3																			1	Substitution - Missense(1)	p.A313P(1)	large_intestine(1)	breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						c.(931-939)agaattggt>agt		Rho GTPase activating protein 11A																																				SO:0001630	splice_region_variant	9824				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity	g.chr15:32920998_32921007delGAATTGGTAG	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"""Rho GTPase activating proteins"""	15783	protein-coding gene	gene with protein product	"""GAP (1-12)"""	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.937+1GAATTGGTAG>-	15.37:g.32920998_32921007delGAATTGGTAG			Somatic				ARHGAP11A_ENST00000565905.1_Splice_Site_p.RIG122fs|ARHGAP11A_ENST00000543522.1_Splice_Site_p.RIG122fs|ARHGAP11A_ENST00000563864.1_Splice_Site_p.RIG311fs|ARHGAP11A_ENST00000567348.1_Splice_Site_p.RIG311fs	p.RIG311fs	NM_014783.3	NP_055598.1	WXS	Illumina GAIIx	Phase_I	Q6P4F7	RHGBA_HUMAN		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	7	1654_1659	+		all_lung(180;1.3e-11)	311					B4DZN9|Q6PI96|Q9Y3S6	Splice_Site	DEL	ENST00000361627.3	37	c.932_937delGAATTGGTAG	CCDS10028.1																																																																																				0.238	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783	Frame_Shift_Del	13	141	13	141	---	---	---	---
