#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
CSMD2	114784	broad.mit.edu	37	1	34112373	34112373	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr1:34112373G>A	ENST00000373380.1	-	8	1488	c.1268C>T	c.(1267-1269)cCt>cTt	p.P423L	CSMD2_ENST00000373381.4_Missense_Mutation_p.P1550L|CSMD2_ENST00000373388.2_5'UTR			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1510	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P1510L(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TCCTATGAGAGGGCTGAGAGA	0.562																																						ENST00000373381.4																			1	Substitution - Missense(1)	p.P1510L(1)	prostate(1)	NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246						c.(4648-4650)cCt>cTt		CUB and Sushi multiple domains 2							55.0	53.0	54.0					1																	34112373		2203	4300	6503	SO:0001583	missense	114784					integral to membrane|plasma membrane	protein binding	g.chr1:34112373G>A	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.1268C>T	1.37:g.34112373G>A	ENSP00000362478:p.Pro423Leu		Somatic				CSMD2_ENST00000373388.2_5'UTR|CSMD2_ENST00000373380.1_Missense_Mutation_p.P423L	p.P1550L	NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	WXS	Illumina GAIIx	Phase_I	Q7Z408	CSMD2_HUMAN			29	4825	-		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)	1510			CUB 9.		B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	37	c.4649C>T		.	.	.	.	.	.	.	.	.	.	G	34	5.317123	0.95682	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	T;T	0.32272	1.46;1.46	5.95	5.95	0.96441	CUB (5);	0.000000	0.85682	D	0.000000	T	0.50582	0.1624	M	0.64170	1.965	0.80722	D	1	D;D;D	0.67145	0.97;0.996;0.996	P;D;D	0.70487	0.844;0.969;0.938	T	0.31641	-0.9936	10	0.07990	T	0.79	.	19.3735	0.94500	0.0:0.0:1.0:0.0	.	423;1510;1550	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	L	1550;423	ENSP00000362479:P1550L;ENSP00000362478:P423L	ENSP00000241312:P1510L	P	-	2	0	CSMD2	33884960	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.869000	0.99810	2.825000	0.97269	0.655000	0.94253	CCT		0.562	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		4	35	4	35	---	---	---	---
KIAA0319L	79932	broad.mit.edu	37	1	35915489	35915489	+	Missense_Mutation	SNP	T	T	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr1:35915489T>C	ENST00000325722.3	-	15	2566	c.2332A>G	c.(2332-2334)Acc>Gcc	p.T778A	KIAA0319L_ENST00000485551.1_5'UTR|KIAA0319L_ENST00000373266.4_Missense_Mutation_p.T215A	NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	778	PKD 5. {ECO:0000255|PROSITE- ProRule:PRU00151}.					cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.T778A(2)		breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TCCACAGTGGTCCGGTCTGTG	0.488																																						ENST00000325722.3																			2	Substitution - Missense(2)	p.T778A(2)	prostate(2)	breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34						c.(2332-2334)Acc>Gcc		KIAA0319-like							155.0	113.0	128.0					1																	35915489		2203	4300	6503	SO:0001583	missense	79932					cytoplasmic vesicle part|integral to membrane	protein binding	g.chr1:35915489T>C	AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.2332A>G	1.37:g.35915489T>C	ENSP00000318406:p.Thr778Ala		Somatic				KIAA0319L_ENST00000485551.1_5'UTR|KIAA0319L_ENST00000373266.4_Missense_Mutation_p.T215A	p.T778A	NM_024874.4	NP_079150.3	WXS	Illumina GAIIx	Phase_I	Q8IZA0	K319L_HUMAN			15	2566	-		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)	778			PKD 5.		B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Missense_Mutation	SNP	ENST00000325722.3	37	c.2332A>G	CCDS390.1	.	.	.	.	.	.	.	.	.	.	T	3.554	-0.091023	0.07053	.	.	ENSG00000142687	ENST00000325722;ENST00000373266;ENST00000426982	T;T;T	0.69040	2.62;-0.37;2.62	5.82	0.908	0.19326	PKD/Chitinase domain (1);PKD/REJ-like protein (1);PKD domain (2);	0.304486	0.42420	N	0.000710	T	0.36413	0.0966	N	0.05534	-0.03	0.80722	D	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.34304	-0.9834	10	0.02654	T	1	-1.4002	9.0391	0.36307	0.0:0.3844:0.0:0.6156	.	778;778;220	Q8IZA0-2;Q8IZA0;Q8IZA0-3	.;K319L_HUMAN;.	A	778;215;778	ENSP00000318406:T778A;ENSP00000362363:T215A;ENSP00000395883:T778A	ENSP00000318406:T778A	T	-	1	0	KIAA0319L	35688076	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	1.538000	0.36094	-0.082000	0.12640	0.533000	0.62120	ACC		0.488	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874		22	154	22	154	---	---	---	---
SF3A3	10946	broad.mit.edu	37	1	38442585	38442585	+	Missense_Mutation	SNP	G	G	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr1:38442585G>T	ENST00000373019.4	-	12	1931	c.976C>A	c.(976-978)Cag>Aag	p.Q326K	SF3A3_ENST00000448721.2_Missense_Mutation_p.Q273K|SF3A3_ENST00000489537.1_5'Flank	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	326					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TCATAGATCTGGGCTTCTAGA	0.403																																						ENST00000373019.4																			0				breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12						c.(976-978)Cag>Aag		splicing factor 3a, subunit 3, 60kDa							147.0	148.0	148.0					1																	38442585		2202	4300	6502	SO:0001583	missense	10946				nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nuclear speck	nucleic acid binding|protein binding|zinc ion binding	g.chr1:38442585G>T	U08815	CCDS428.1	1p34.3	2012-06-07	2002-08-29		ENSG00000183431	ENSG00000183431			10767	protein-coding gene	gene with protein product		605596	"""splicing factor 3a, subunit 3, 60kD"""			7816610, 8022796	Standard	NM_006802		Approved	SF3a60, SAP61, PRP9, PRPF9	uc001cci.3	Q12874	OTTHUMG00000004438	ENST00000373019.4:c.976C>A	1.37:g.38442585G>T	ENSP00000362110:p.Gln326Lys		Somatic				SF3A3_ENST00000448721.2_Missense_Mutation_p.Q273K	p.Q326K	NM_006802.2	NP_006793.1	WXS	Illumina GAIIx	Phase_I	Q12874	SF3A3_HUMAN			12	1931	-	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)	326					D3DPT5|Q15460|Q5VT87	Missense_Mutation	SNP	ENST00000373019.4	37	c.976C>A	CCDS428.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.608328	0.28623	.	.	ENSG00000183431	ENST00000373019;ENST00000448721	.	.	.	5.69	5.69	0.88448	Domain of unknown function DUF3449 (1);	0.111433	0.64402	D	0.000006	T	0.40196	0.1107	N	0.13299	0.325	0.58432	D	0.999999	B;B	0.28128	0.001;0.201	B;B	0.28385	0.004;0.089	T	0.36625	-0.9740	9	0.02654	T	1	-14.2306	19.4634	0.94929	0.0:0.0:1.0:0.0	.	273;326	E7EUT8;Q12874	.;SF3A3_HUMAN	K	326;273	.	ENSP00000362110:Q326K	Q	-	1	0	SF3A3	38215172	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.365000	0.97139	2.715000	0.92844	0.585000	0.79938	CAG		0.403	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802		28	185	28	185	---	---	---	---
ZFYVE9	9372	broad.mit.edu	37	1	52704167	52704167	+	Missense_Mutation	SNP	G	G	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr1:52704167G>C	ENST00000371591.1	+	3	1209	c.1078G>C	c.(1078-1080)Gat>Cat	p.D360H	ZFYVE9_ENST00000357206.2_Missense_Mutation_p.D360H|ZFYVE9_ENST00000287727.3_Missense_Mutation_p.D360H	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	360					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)	p.D360H(1)		breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						ACGGTGTTCAGATTGCCTTGT	0.428																																						ENST00000287727.3																			1	Substitution - Missense(1)	p.D360H(1)	prostate(1)	breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						c.(1078-1080)Gat>Cat		zinc finger, FYVE domain containing 9							127.0	115.0	119.0					1																	52704167		2203	4300	6503	SO:0001583	missense	9372				endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	early endosome membrane	metal ion binding|protein binding|receptor activity|serine-type peptidase activity	g.chr1:52704167G>C	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"""Zinc fingers, FYVE domain containing"""	6775	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 173"""	603755	"""MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"""	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.1078G>C	1.37:g.52704167G>C	ENSP00000360647:p.Asp360His		Somatic				ZFYVE9_ENST00000357206.2_Missense_Mutation_p.D360H|ZFYVE9_ENST00000371591.1_Missense_Mutation_p.D360H	p.D360H			WXS	Illumina GAIIx	Phase_I	O95405	ZFYV9_HUMAN			4	1250	+			360					Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	37	c.1078G>C	CCDS563.1	.	.	.	.	.	.	.	.	.	.	G	7.706	0.694215	0.15039	.	.	ENSG00000157077	ENST00000357206;ENST00000361625;ENST00000287727;ENST00000371591	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	4.88	2.86	0.33363	.	0.315721	0.25997	N	0.026967	T	0.50616	0.1626	N	0.19112	0.55	0.09310	N	1	D;P;D	0.89917	0.958;0.93;1.0	P;P;D	0.69479	0.66;0.635;0.964	T	0.28267	-1.0049	10	0.72032	D	0.01	.	5.8759	0.18828	0.1794:0.0:0.6535:0.1671	.	360;360;360	O95405-2;O95405;O95405-3	.;ZFYV9_HUMAN;.	H	360	ENSP00000349737:D360H;ENSP00000355358:D360H;ENSP00000287727:D360H;ENSP00000360647:D360H	ENSP00000287727:D360H	D	+	1	0	ZFYVE9	52476755	1.000000	0.71417	1.000000	0.80357	0.254000	0.26022	2.465000	0.45075	1.291000	0.44653	0.655000	0.94253	GAT		0.428	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		17	206	17	206	---	---	---	---
SCN7A	6332	broad.mit.edu	37	2	167262388	167262388	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr2:167262388C>A	ENST00000409855.1	-	25	4877	c.4751G>T	c.(4750-4752)aGa>aTa	p.R1584I		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1584					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.R1584I(3)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	ACCCATAACTCTCTTTGTAAA	0.428																																						ENST00000409855.1																			3	Substitution - Missense(3)	p.R1584I(3)	prostate(3)	breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44						c.(4750-4752)aGa>aTa		sodium channel, voltage-gated, type VII, alpha subunit							163.0	162.0	163.0					2																	167262388		1898	4123	6021	SO:0001583	missense	6332				muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity	g.chr2:167262388C>A	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.4751G>T	2.37:g.167262388C>A	ENSP00000386796:p.Arg1584Ile		Somatic					p.R1584I	NM_002976.3	NP_002967.2	WXS	Illumina GAIIx	Phase_I	Q01118	SCN7A_HUMAN			25	4877	-			1584						Missense_Mutation	SNP	ENST00000409855.1	37	c.4751G>T	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	C	18.63	3.665903	0.67700	.	.	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.97114	-4.25	4.51	4.51	0.55191	.	0.000000	0.52532	D	0.000066	D	0.98261	0.9424	M	0.87269	2.87	0.45883	D	0.998736	D	0.67145	0.996	P	0.61874	0.895	D	0.98920	1.0783	10	0.87932	D	0	.	15.1081	0.72336	0.0:1.0:0.0:0.0	.	1584	Q01118	SCN7A_HUMAN	I	1584	ENSP00000386796:R1584I	ENSP00000259060:R1584I	R	-	2	0	SCN7A	166970634	0.004000	0.15560	0.997000	0.53966	0.857000	0.48899	1.741000	0.38238	2.514000	0.84764	0.655000	0.94253	AGA		0.428	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			51	357	51	357	---	---	---	---
CDKN2AIPNL	91368	broad.mit.edu	37	5	133747428	133747428	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr5:133747428G>A	ENST00000458198.2	-	1	161	c.118C>T	c.(118-120)Cgc>Tgc	p.R40C	CDKN2AIPNL_ENST00000395009.3_Missense_Mutation_p.R40C	NM_080656.2	NP_542387.1	Q96HQ2	C2AIL_HUMAN	CDKN2A interacting protein N-terminal like	40								p.R40C(1)		central_nervous_system(1)|kidney(2)|prostate(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AATTCCATGCGGGCCTTCCAT	0.677											OREG0016789	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000458198.2																			1	Substitution - Missense(1)	p.R40C(1)	prostate(1)	central_nervous_system(1)|kidney(2)|prostate(1)	4						c.(118-120)Cgc>Tgc		CDKN2A interacting protein N-terminal like							14.0	19.0	17.0					5																	133747428		2201	4296	6497	SO:0001583	missense	91368							g.chr5:133747428G>A	BC008293	CCDS4175.1	5q31.1	2008-02-05			ENSG00000237190	ENSG00000237190			30545	protein-coding gene	gene with protein product						12477932	Standard	NM_080656		Approved	MGC13017	uc011cxs.2	Q96HQ2	OTTHUMG00000129123	ENST00000458198.2:c.118C>T	5.37:g.133747428G>A	ENSP00000394183:p.Arg40Cys		Somatic	OREG0016789	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1605	CDKN2AIPNL_ENST00000395009.3_Missense_Mutation_p.R40C	p.R40C	NM_080656.2	NP_542387.1	WXS	Illumina GAIIx	Phase_I	Q96HQ2	C2AIL_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		1	161	-			40					Q8WVE3	Missense_Mutation	SNP	ENST00000458198.2	37	c.118C>T	CCDS4175.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.665154	0.88251	.	.	ENSG00000237190	ENST00000458198;ENST00000395009	.	.	.	4.46	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.78368	0.4272	M	0.74467	2.265	0.58432	D	0.999996	D;D	0.89917	0.999;1.0	P;D	0.75020	0.871;0.985	T	0.81602	-0.0858	9	0.87932	D	0	-4.3739	16.3909	0.83537	0.0:0.0:1.0:0.0	.	40;40	Q96HQ2;Q96HQ2-2	C2AIL_HUMAN;.	C	40	.	ENSP00000378456:R40C	R	-	1	0	CDKN2AIPNL	133775327	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.760000	0.47581	2.503000	0.84419	0.491000	0.48974	CGC		0.677	CDKN2AIPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251171.2	NM_080656		3	32	3	32	---	---	---	---
KIAA1324L	222223	broad.mit.edu	37	7	86556150	86556150	+	Missense_Mutation	SNP	T	T	C			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr7:86556150T>C	ENST00000450689.2	-	9	1357	c.1172A>G	c.(1171-1173)gAg>gGg	p.E391G	KIAA1324L_ENST00000297222.6_Missense_Mutation_p.E151G|KIAA1324L_ENST00000444627.1_Missense_Mutation_p.E391G|KIAA1324L_ENST00000416314.1_Missense_Mutation_p.E224G	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	391						integral component of membrane (GO:0016021)		p.E151G(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					ATCCTTCTTCTCTCCAGAAGG	0.428																																						ENST00000450689.2																			1	Substitution - Missense(1)	p.E151G(1)	prostate(1)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						c.(1171-1173)gAg>gGg		KIAA1324-like							123.0	123.0	123.0					7																	86556150		2203	4300	6503	SO:0001583	missense	222223					integral to membrane		g.chr7:86556150T>C	AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"""EIG121-like"""	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.1172A>G	7.37:g.86556150T>C	ENSP00000413445:p.Glu391Gly		Somatic				KIAA1324L_ENST00000297222.6_Missense_Mutation_p.E151G|KIAA1324L_ENST00000416314.1_Missense_Mutation_p.E224G|KIAA1324L_ENST00000444627.1_Missense_Mutation_p.E391G	p.E391G	NM_001142749.2	NP_001136221.1	WXS	Illumina GAIIx	Phase_I	A8MWY0	K132L_HUMAN			9	1357	-	Esophageal squamous(14;0.0058)		391					A4D1C9|B4DJV3|Q17RI6|Q96DP2	Missense_Mutation	SNP	ENST00000450689.2	37	c.1172A>G	CCDS47632.1	.	.	.	.	.	.	.	.	.	.	T	14.76	2.631921	0.46944	.	.	ENSG00000164659	ENST00000450689;ENST00000297222;ENST00000444627;ENST00000416314	T;T;T;T	0.24723	2.53;1.84;2.53;2.53	5.53	5.53	0.82687	Growth factor, receptor (1);	0.214093	0.48767	D	0.000169	T	0.25568	0.0622	L	0.49350	1.555	0.51482	D	0.999929	P;P;P	0.39940	0.696;0.617;0.617	B;B;B	0.38842	0.283;0.242;0.121	T	0.02983	-1.1086	10	0.22109	T	0.4	.	14.8389	0.70209	0.0:0.0:0.0:1.0	.	391;151;224	A8MWY0;A8MWY0-2;B4DJV3	K132L_HUMAN;.;.	G	391;151;391;224	ENSP00000413445:E391G;ENSP00000297222:E151G;ENSP00000397377:E391G;ENSP00000402390:E224G	ENSP00000297222:E151G	E	-	2	0	KIAA1324L	86394086	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.179000	0.71974	2.098000	0.63641	0.460000	0.39030	GAG		0.428	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748		14	265	14	265	---	---	---	---
MET	4233	broad.mit.edu	37	7	116340051	116340051	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr7:116340051A>G	ENST00000318493.6	+	2	1100	c.913A>G	c.(913-915)Aaa>Gaa	p.K305E	MET_ENST00000436117.2_Missense_Mutation_p.K305E|MET_ENST00000397752.3_Missense_Mutation_p.K305E			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K305E(2)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			AGAAAAGAGAAAAAAGAGATC	0.428			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																													ENST00000397752.3				Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	Mis	met proto-oncogene (hepatocyte growth factor receptor)			E		papillary renal	"""papillary renal, head-neck squamous cell """		2	Substitution - Missense(2)	p.K305E(2)	prostate(2)	NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233						c.(913-915)Aaa>Gaa		met proto-oncogene							63.0	61.0	61.0					7																	116340051		1847	4092	5939	SO:0001583	missense	4233	Hereditary Papillary Renal Carcinoma (type 1)	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding	g.chr7:116340051A>G	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.913A>G	7.37:g.116340051A>G	ENSP00000317272:p.Lys305Glu		Somatic				MET_ENST00000436117.2_Missense_Mutation_p.K305E|MET_ENST00000318493.6_Missense_Mutation_p.K305E	p.K305E	NM_000245.2|NM_001127500.1	NP_000236.2|NP_001120972.1	WXS	Illumina GAIIx	Phase_I	P08581	MET_HUMAN	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)		2	1113	+	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	305			Sema.		A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	c.913A>G	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	A	8.816	0.936454	0.18206	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000436117	T;T;T	0.11063	2.81;2.81;2.81	6.17	5.0	0.66597	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.092574	0.64402	D	0.000001	T	0.09379	0.0231	N	0.22421	0.69	0.80722	D	1	B;B;P;B;B;B;B;B;B;B;B;B;B	0.39044	0.09;0.134;0.656;0.177;0.177;0.134;0.3;0.177;0.44;0.11;0.134;0.034;0.034	B;B;B;B;B;B;B;B;B;B;B;B;B	0.37731	0.089;0.174;0.243;0.174;0.174;0.174;0.257;0.174;0.174;0.068;0.174;0.119;0.119	T	0.08911	-1.0699	10	0.87932	D	0	.	13.5284	0.61607	0.8699:0.1301:0.0:0.0	.	305;305;305;305;305;305;305;305;305;305;305;305;305	B5A929;E7EQ94;B5A930;B5A934;B5A936;B5A937;B5A939;B5A941;B5A940;P08581-2;B5A942;P08581;A1L467	.;.;.;.;.;.;.;.;.;.;.;MET_HUMAN;.	E	305	ENSP00000380860:K305E;ENSP00000317272:K305E;ENSP00000410980:K305E	ENSP00000317272:K305E	K	+	1	0	MET	116127287	1.000000	0.71417	0.995000	0.50966	0.150000	0.21749	4.483000	0.60264	1.119000	0.41883	0.533000	0.62120	AAA		0.428	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			11	202	11	202	---	---	---	---
RP1	6101	broad.mit.edu	37	8	55540711	55540711	+	Nonsense_Mutation	SNP	T	T	A	rs540468439		TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr8:55540711T>A	ENST00000220676.1	+	4	4417	c.4269T>A	c.(4267-4269)tgT>tgA	p.C1423*		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1423					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.C1423*(1)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TTGAAAATTGTTCACTAAGGA	0.363																																					Colon(91;1014 1389 7634 14542 40420)	ENST00000220676.1																			1	Substitution - Nonsense(1)	p.C1423*(1)	prostate(1)	NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169						c.(4267-4269)tgT>tgA		retinitis pigmentosa 1 (autosomal dominant)							53.0	57.0	55.0					8																	55540711		2201	4297	6498	SO:0001587	stop_gained	6101				axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding	g.chr8:55540711T>A	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.4269T>A	8.37:g.55540711T>A	ENSP00000220676:p.Cys1423*		Somatic					p.C1423*	NM_006269.1	NP_006260.1	WXS	Illumina GAIIx	Phase_I	P56715	RP1_HUMAN	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)		4	4417	+		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	1423						Nonsense_Mutation	SNP	ENST00000220676.1	37	c.4269T>A	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	T	42	9.388276	0.99156	.	.	ENSG00000104237	ENST00000220676	.	.	.	5.41	2.99	0.34606	.	0.766385	0.11747	N	0.533445	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.2621	0.10745	0.141:0.2522:0.0:0.6068	.	.	.	.	X	1423	.	ENSP00000220676:C1423X	C	+	3	2	RP1	55703264	0.001000	0.12720	0.001000	0.08648	0.812000	0.45895	0.942000	0.29017	0.343000	0.23821	0.496000	0.49642	TGT		0.363	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		15	110	15	110	---	---	---	---
MSC	9242	broad.mit.edu	37	8	72756371	72756371	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr8:72756371G>A	ENST00000325509.4	-	1	332	c.43C>T	c.(43-45)Cgg>Tgg	p.R15W	RP11-383H13.1_ENST00000521467.1_Intron|RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000457356.4_3'UTR|RP11-383H13.1_ENST00000537896.1_Intron|MSC_ENST00000518440.1_5'Flank	NM_005098.3	NP_005089.2	O60682	MUSC_HUMAN	musculin	15					branchiomeric skeletal muscle development (GO:0014707)|diaphragm development (GO:0060539)|palate development (GO:0060021)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.R15W(1)		endometrium(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(4)|skin(2)	26	Breast(64;0.176)		Epithelial(68;0.137)|BRCA - Breast invasive adenocarcinoma(89;0.203)			TGCAGCCCCCGAAGCTCCATC	0.692																																						ENST00000325509.4																			1	Substitution - Missense(1)	p.R15W(1)	prostate(1)	endometrium(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(4)|skin(2)	26						c.(43-45)Cgg>Tgg		musculin							18.0	20.0	19.0					8																	72756371		1633	3511	5144	SO:0001583	missense	9242				transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity	g.chr8:72756371G>A		CCDS43746.1	8q13.3	2013-06-07	2010-04-28		ENSG00000178860	ENSG00000178860		"""Basic helix-loop-helix proteins"""	7321	protein-coding gene	gene with protein product	"""activated B-cell factor-1"""	603628	"""musculin (activated B-cell factor-1)"""			9584154, 10198176	Standard	NM_005098		Approved	ABF-1, bHLHa22	uc003xyx.1	O60682	OTTHUMG00000164489	ENST00000325509.4:c.43C>T	8.37:g.72756371G>A	ENSP00000321445:p.Arg15Trp		Somatic				RP11-383H13.1_ENST00000521467.1_Intron|RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000457356.4_3'UTR	p.R15W	NM_005098.3	NP_005089.2	WXS	Illumina GAIIx	Phase_I	O60682	MUSC_HUMAN	Epithelial(68;0.137)|BRCA - Breast invasive adenocarcinoma(89;0.203)		1	332	-	Breast(64;0.176)		15					O75946|Q53XZ2|Q9BRE7	Missense_Mutation	SNP	ENST00000325509.4	37	c.43C>T	CCDS43746.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.217506	0.79352	.	.	ENSG00000178860	ENST00000325509	D	0.98381	-4.9	4.11	3.22	0.36961	.	0.326796	0.24991	N	0.033998	D	0.95831	0.8643	L	0.29908	0.895	0.42120	D	0.991422	D	0.60575	0.988	P	0.46339	0.513	D	0.94818	0.7984	10	0.72032	D	0.01	.	11.4207	0.49980	0.0:0.0:0.6745:0.3255	.	15	O60682	MUSC_HUMAN	W	15	ENSP00000321445:R15W	ENSP00000321445:R15W	R	-	1	2	MSC	72918925	0.818000	0.29161	0.999000	0.59377	0.980000	0.70556	1.301000	0.33447	0.905000	0.36596	0.561000	0.74099	CGG		0.692	MSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378974.1	NM_005098		4	21	4	21	---	---	---	---
RNF26	79102	broad.mit.edu	37	11	119207000	119207000	+	Missense_Mutation	SNP	G	G	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr11:119207000G>T	ENST00000311413.4	+	1	1764	c.1168G>T	c.(1168-1170)Gtg>Ttg	p.V390L	C1QTNF5_ENST00000525657.1_5'Flank|RP11-334E6.10_ENST00000501918.2_RNA	NM_032015.4	NP_114404.1	Q9BY78	RNF26_HUMAN	ring finger protein 26	390						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.V390L(1)		cervix(1)|endometrium(1)|kidney(1)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.8e-05)		GAGCAAGACAGTGTTGCTCCT	0.607																																						ENST00000311413.4																			1	Substitution - Missense(1)	p.V390L(1)	prostate(1)	cervix(1)|endometrium(1)|kidney(1)|lung(7)|ovary(1)|prostate(1)	12						c.(1168-1170)Gtg>Ttg		ring finger protein 26							98.0	84.0	89.0					11																	119207000		2199	4295	6494	SO:0001583	missense	79102						zinc ion binding	g.chr11:119207000G>T	AB055622	CCDS8419.1	11q23	2008-07-21				ENSG00000173456		"""RING-type (C3HC4) zinc fingers"""	14646	protein-coding gene	gene with protein product	"""ring finger protein with leucine zipper"""	606130				11352657	Standard	NM_032015		Approved	MGC2642	uc001pwh.3	Q9BY78		ENST00000311413.4:c.1168G>T	11.37:g.119207000G>T	ENSP00000312439:p.Val390Leu		Somatic				RP11-334E6.10_ENST00000501918.2_RNA	p.V390L	NM_032015.4	NP_114404.1	WXS	Illumina GAIIx	Phase_I	Q9BY78	RNF26_HUMAN		BRCA - Breast invasive adenocarcinoma(274;3.8e-05)	1	1764	+		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)	390					Q542Y8	Missense_Mutation	SNP	ENST00000311413.4	37	c.1168G>T	CCDS8419.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.420200	0.83559	.	.	ENSG00000173456	ENST00000311413	T	0.80994	-1.44	5.57	5.57	0.84162	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.000000	0.64402	D	0.000014	D	0.89375	0.6697	M	0.71036	2.16	0.51233	D	0.999912	D	0.76494	0.999	D	0.77557	0.99	D	0.89946	0.4076	10	0.72032	D	0.01	-15.9898	18.5437	0.91039	0.0:0.0:1.0:0.0	.	390	Q9BY78	RNF26_HUMAN	L	390	ENSP00000312439:V390L	ENSP00000312439:V390L	V	+	1	0	RNF26	118712210	1.000000	0.71417	0.959000	0.39883	0.975000	0.68041	7.795000	0.85887	2.619000	0.88677	0.491000	0.48974	GTG		0.607	RNF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388220.1	NM_032015		16	95	16	95	---	---	---	---
SBNO1	55206	broad.mit.edu	37	12	123834911	123834911	+	Silent	SNP	A	A	G			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr12:123834911A>G	ENST00000602398.1	-	2	205	c.78T>C	c.(76-78)atT>atC	p.I26I	Y_RNA_ENST00000384460.1_RNA|SBNO1_ENST00000420886.2_Silent_p.I26I|SBNO1_ENST00000602750.1_Silent_p.I26I|SBNO1_ENST00000267176.4_Silent_p.I26I			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	26					regulation of transcription, DNA-templated (GO:0006355)			p.I26I(2)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		CTCCACCATCAATATCAAAGA	0.438																																						ENST00000420886.2																			2	Substitution - coding silent(2)	p.I26I(2)	prostate(2)	NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62						c.(76-78)atT>atC		strawberry notch homolog 1 (Drosophila)							205.0	201.0	203.0					12																	123834911		2203	4300	6503	SO:0001819	synonymous_variant	55206						ATP binding|DNA binding|hydrolase activity	g.chr12:123834911A>G	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"""sno, strawberry notch homolog 1 (Drosophila)"""				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.78T>C	12.37:g.123834911A>G			Somatic				SBNO1_ENST00000267176.4_Silent_p.I26I|SBNO1_ENST00000602398.1_Silent_p.I26I|SBNO1_ENST00000602750.1_Silent_p.I26I	p.I26I	NM_001167856.1	NP_001161328.1	WXS	Illumina GAIIx	Phase_I	A3KN83	SBNO1_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)	1	77	-	all_neural(191;0.101)|Medulloblastoma(191;0.163)		26					Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	37	c.78T>C	CCDS53844.1																																																																																				0.438	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		16	386	16	386	---	---	---	---
INTS6	26512	broad.mit.edu	37	13	51942011	51942011	+	Missense_Mutation	SNP	G	G	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr13:51942011G>T	ENST00000311234.4	-	17	2972	c.2500C>A	c.(2500-2502)Ctg>Atg	p.L834M	INTS6_ENST00000463928.1_3'UTR|INTS6_ENST00000490542.1_Missense_Mutation_p.L518M|INTS6_ENST00000425000.1_Missense_Mutation_p.L402M|INTS6_ENST00000497989.1_Missense_Mutation_p.L656M|INTS6_ENST00000398119.2_Missense_Mutation_p.L821M	NM_012141.2	NP_036273.1	Q9UL03	INT6_HUMAN	integrator complex subunit 6	834					signal transduction (GO:0007165)|snRNA processing (GO:0016180)	actin cytoskeleton (GO:0015629)|integrator complex (GO:0032039)|nucleus (GO:0005634)	transmembrane signaling receptor activity (GO:0004888)	p.L834M(1)		NS(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)		ACATGCTTCAGTAAAGTGAAG	0.269																																						ENST00000311234.4																			1	Substitution - Missense(1)	p.L834M(1)	prostate(1)	NS(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						c.(2500-2502)Ctg>Atg		integrator complex subunit 6							76.0	72.0	74.0					13																	51942011		2201	4281	6482	SO:0001583	missense	26512				snRNA processing	actin cytoskeleton|integrator complex	protein binding|transmembrane receptor activity	g.chr13:51942011G>T	AF097645	CCDS9428.1, CCDS41890.1, CCDS45048.1	13q14.3	2010-08-20	2006-03-15	2006-03-15	ENSG00000102786	ENSG00000102786		"""DEAD-boxes"""	14879	protein-coding gene	gene with protein product		604331	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26"""	DDX26		10467397, 16239144	Standard	XM_005266340		Approved	DICE1, HDB, Notchl2, DBI-1, DDX26A, INT6	uc001vfk.3	Q9UL03	OTTHUMG00000016945	ENST00000311234.4:c.2500C>A	13.37:g.51942011G>T	ENSP00000310260:p.Leu834Met		Somatic				INTS6_ENST00000497989.1_Missense_Mutation_p.L656M|INTS6_ENST00000425000.1_Missense_Mutation_p.L402M|INTS6_ENST00000463928.1_3'UTR|INTS6_ENST00000490542.1_Missense_Mutation_p.L518M|INTS6_ENST00000398119.2_Missense_Mutation_p.L821M	p.L834M	NM_012141.2	NP_036273.1	WXS	Illumina GAIIx	Phase_I	Q9UL03	INT6_HUMAN		GBM - Glioblastoma multiforme(99;7.7e-08)	17	2972	-		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)	834					Q0P664|Q6PJP4|Q9UFK0|Q9Y5M9	Missense_Mutation	SNP	ENST00000311234.4	37	c.2500C>A	CCDS9428.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.296695	0.81025	.	.	ENSG00000102786	ENST00000311234;ENST00000398119;ENST00000497989;ENST00000425000;ENST00000490542	.	.	.	5.37	4.51	0.55191	.	0.071477	0.56097	D	0.000022	T	0.77968	0.4210	M	0.80847	2.515	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.78937	-0.2007	9	0.48119	T	0.1	-5.5668	12.6253	0.56626	0.0796:0.0:0.9204:0.0	.	834	Q9UL03	INT6_HUMAN	M	834;821;656;402;518	.	ENSP00000310260:L834M	L	-	1	2	INTS6	50840012	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.697000	0.54764	2.524000	0.85096	0.650000	0.86243	CTG		0.269	INTS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045023.1	NM_012141		3	76	3	76	---	---	---	---
PRMT5	10419	broad.mit.edu	37	14	23397824	23397824	+	Splice_Site	SNP	C	C	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr14:23397824C>A	ENST00000324366.8	-	2	334	c.111G>T	c.(109-111)ggG>ggT	p.G37G	PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000553641.1_5'UTR|PRMT5_ENST00000538452.1_Intron|PRMT5_ENST00000397440.4_Splice_Site_p.G20G|RP11-298I3.1_ENST00000548819.1_RNA|PRMT5-AS1_ENST00000587245.2_RNA|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5_ENST00000216350.8_Splice_Site_p.G20G|PRMT5-AS1_ENST00000595662.1_RNA|RP11-298I3.1_ENST00000548322.1_RNA|PRMT5_ENST00000553897.1_Splice_Site_p.G37G|PRMT5_ENST00000397441.2_Splice_Site_p.G20G	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	37	TIM barrel. {ECO:0000269|PubMed:23071334}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)	p.G37G(1)|p.G20G(1)		endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		GGAAATCAAACCTACAACCGC	0.512																																						ENST00000324366.8																			2	Substitution - coding silent(2)	p.G37G(1)|p.G20G(1)	prostate(2)	endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25						c.(109-111)ggG>ggT		protein arginine methyltransferase 5							105.0	98.0	100.0					14																	23397824		2203	4300	6503	SO:0001630	splice_region_variant	10419				cell proliferation|histone H4-R3 methylation|ncRNA metabolic process|regulation of mitosis|spliceosomal snRNP assembly|transcription, DNA-dependent	cytosol|nucleus	histone-arginine N-methyltransferase activity|protein binding|protein-arginine omega-N symmetric methyltransferase activity|ribonucleoprotein binding	g.chr14:23397824C>A	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"""Protein arginine methyltransferases"""	10894	protein-coding gene	gene with protein product		604045	"""skb1 (S. pombe) homolog"", ""SKB1 homolog (S. pombe)"""	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.111-1G>T	14.37:g.23397824C>A			Somatic				PRMT5_ENST00000538452.1_Intron|PRMT5_ENST00000553897.1_Splice_Site_p.G37G|PRMT5_ENST00000553641.1_5'UTR|PRMT5_ENST00000216350.8_Splice_Site_p.G20G|PRMT5_ENST00000397440.4_Splice_Site_p.G20G|PRMT5_ENST00000397441.2_Splice_Site_p.G20G	p.G37G	NM_006109.3	NP_006100.2	WXS	Illumina GAIIx	Phase_I	O14744	ANM5_HUMAN		GBM - Glioblastoma multiforme(265;0.0126)	2	334	-	all_cancers(95;2.76e-05)		37					A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Splice_Site	SNP	ENST00000324366.8	37	c.111G>T	CCDS9579.1																																																																																				0.512	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3		Silent	4	100	4	100	---	---	---	---
ATG2B	55102	broad.mit.edu	37	14	96800092	96800092	+	Silent	SNP	G	G	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr14:96800092G>A	ENST00000359933.4	-	8	2033	c.1140C>T	c.(1138-1140)ctC>ctT	p.L380L		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	380					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)		p.L380L(1)		breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		CACCCACAGAGAGGGAATCTT	0.413																																						ENST00000359933.4																			1	Substitution - coding silent(1)	p.L380L(1)	prostate(1)	breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64						c.(1138-1140)ctC>ctT		autophagy related 2B							121.0	114.0	116.0					14																	96800092		1840	4094	5934	SO:0001819	synonymous_variant	55102							g.chr14:96800092G>A	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.1140C>T	14.37:g.96800092G>A			Somatic					p.L380L	NM_018036.5	NP_060506	WXS	Illumina GAIIx	Phase_I	Q96BY7	ATG2B_HUMAN		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)	8	2033	-		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)	380					Q6ZRE7|Q96DQ3|Q9NW80	Silent	SNP	ENST00000359933.4	37	c.1140C>T	CCDS9944.2																																																																																				0.413	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		4	165	4	165	---	---	---	---
FBN1	2200	broad.mit.edu	37	15	48729540	48729540	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr15:48729540C>T	ENST00000316623.5	-	52	6813	c.6358G>A	c.(6358-6360)Gga>Aga	p.G2120R		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2120					extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.G2120R(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TCATCAGGTCCCACGATGATC	0.423																																						ENST00000316623.5																			1	Substitution - Missense(1)	p.G2120R(1)	prostate(1)	NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139						c.(6358-6360)Gga>Aga		fibrillin 1							71.0	72.0	71.0					15																	48729540		2198	4296	6494	SO:0001583	missense	2200				heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding	g.chr15:48729540C>T	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.6358G>A	15.37:g.48729540C>T	ENSP00000325527:p.Gly2120Arg		Somatic					p.G2120R	NM_000138.4	NP_000129	WXS	Illumina GAIIx	Phase_I	P35555	FBN1_HUMAN		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)	52	6813	-		all_lung(180;0.00279)	2120					B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	c.6358G>A	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.991710	0.74703	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.90900	-2.75	5.55	5.55	0.83447	Matrix fibril-associated (1);	0.279473	0.40818	N	0.001007	D	0.89146	0.6632	L	0.53617	1.68	0.80722	D	1	B	0.27229	0.172	B	0.21917	0.037	D	0.86317	0.1690	10	0.62326	D	0.03	.	19.2868	0.94082	0.0:1.0:0.0:0.0	.	2120	P35555	FBN1_HUMAN	R	2120;688;1010	ENSP00000325527:G2120R	ENSP00000325527:G2120R	G	-	1	0	FBN1	46516832	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.224000	0.58593	2.885000	0.99019	0.655000	0.94253	GGA		0.423	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			3	59	3	59	---	---	---	---
SLC13A5	284111	broad.mit.edu	37	17	6597493	6597493	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr17:6597493G>A	ENST00000433363.2	-	8	1312	c.1079C>T	c.(1078-1080)gCc>gTc	p.A360V	SLC13A5_ENST00000293800.6_Missense_Mutation_p.A343V|SLC13A5_ENST00000381074.4_Missense_Mutation_p.A317V|SLC13A5_ENST00000573648.1_Missense_Mutation_p.A360V	NM_001284510.1|NM_177550.3	NP_001271439.1|NP_808218.1	Q86YT5	S13A5_HUMAN	solute carrier family 13 (sodium-dependent citrate transporter), member 5	360					transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	citrate transmembrane transporter activity (GO:0015137)|sodium:dicarboxylate symporter activity (GO:0017153)|succinate transmembrane transporter activity (GO:0015141)	p.A360V(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|prostate(5)|skin(3)|urinary_tract(1)	26						CACAAAGATGGCCACAGTGGC	0.522																																						ENST00000433363.2																			1	Substitution - Missense(1)	p.A360V(1)	prostate(1)	breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|prostate(5)|skin(3)|urinary_tract(1)	26						c.(1078-1080)gCc>gTc		solute carrier family 13 (sodium-dependent citrate transporter), member 5							83.0	69.0	74.0					17																	6597493		2203	4300	6503	SO:0001583	missense	284111					integral to membrane	citrate transmembrane transporter activity	g.chr17:6597493G>A	AJ489980	CCDS11079.1, CCDS45593.1, CCDS67136.1, CCDS67137.1	17p13.1	2013-05-22			ENSG00000141485	ENSG00000141485		"""Solute carriers"""	23089	protein-coding gene	gene with protein product		608305				12445824	Standard	NM_001284510		Approved	NACT	uc002gdj.3	Q86YT5	OTTHUMG00000102052	ENST00000433363.2:c.1079C>T	17.37:g.6597493G>A	ENSP00000406220:p.Ala360Val		Somatic				SLC13A5_ENST00000293800.6_Missense_Mutation_p.A343V|SLC13A5_ENST00000573648.1_Missense_Mutation_p.A360V|SLC13A5_ENST00000381074.4_Missense_Mutation_p.A317V	p.A360V	NM_001284510.1|NM_177550.3	NP_001271439.1|NP_808218.1	WXS	Illumina GAIIx	Phase_I	Q86YT5	S13A5_HUMAN			8	1312	-			360					B3KXR0|B7Z4P2|B7ZLB4|F8W7N2|Q6ZMG1	Missense_Mutation	SNP	ENST00000433363.2	37	c.1079C>T	CCDS11079.1	.	.	.	.	.	.	.	.	.	.	G	34	5.320833	0.95682	.	.	ENSG00000141485	ENST00000293800;ENST00000433363;ENST00000381074	T;T	0.04970	3.52;3.52	5.61	5.61	0.85477	.	0.046540	0.85682	D	0.000000	T	0.22085	0.0532	M	0.78637	2.42	0.80722	D	1	P;P;P;P	0.48998	0.745;0.918;0.745;0.87	P;P;P;P	0.55508	0.609;0.596;0.609;0.777	T	0.00032	-1.2276	10	0.48119	T	0.1	.	17.5007	0.87731	0.0:0.0:1.0:0.0	.	360;317;343;360	B7ZLB4;F8W7N2;B3KXR0;Q86YT5	.;.;.;S13A5_HUMAN	V	360;360;317	ENSP00000406220:A360V;ENSP00000370464:A317V	ENSP00000293800:A360V	A	-	2	0	SLC13A5	6538217	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.628000	0.90979	2.815000	0.96918	0.561000	0.74099	GCC		0.522	SLC13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219853.2	NM_177550		6	28	6	28	---	---	---	---
MARK4	57787	broad.mit.edu	37	19	45762287	45762287	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr19:45762287C>T	ENST00000262891.4	+	2	423	c.92C>T	c.(91-93)cCg>cTg	p.P31L	MARK4_ENST00000300843.4_Missense_Mutation_p.P31L	NM_001199867.1	NP_001186796.1	Q96L34	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4	31					microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nervous system development (GO:0007399)|positive regulation of programmed cell death (GO:0043068)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)|ubiquitin binding (GO:0043130)	p.P31L(2)		NS(1)|biliary_tract(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	31		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		GACAAAGGCCCGTCCTGGTCC	0.672																																						ENST00000300843.4																			2	Substitution - Missense(2)	p.P31L(2)	prostate(2)	NS(1)|biliary_tract(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	31						c.(91-93)cCg>cTg		MAP/microtubule affinity-regulating kinase 4							32.0	27.0	29.0					19																	45762287		2203	4300	6503	SO:0001583	missense	57787				microtubule bundle formation|nervous system development|positive regulation of programmed cell death	centrosome|neuron projection	ATP binding|gamma-tubulin binding|microtubule binding|protein serine/threonine kinase activity|tau-protein kinase activity|ubiquitin binding	g.chr19:45762287C>T	AB049127	CCDS12658.1, CCDS56097.1	19q13.32	2014-04-07	2002-06-12	2002-06-14	ENSG00000007047	ENSG00000007047	2.7.11.1		13538	protein-coding gene	gene with protein product		606495	"""MAP/microtubule affinity-regulating kinase like 1"""	MARKL1		23400999, 11326310, 9108484	Standard	NM_001199867		Approved	Nbla00650, FLJ90097, KIAA1860, PAR-1D	uc002paz.2	Q96L34	OTTHUMG00000181769	ENST00000262891.4:c.92C>T	19.37:g.45762287C>T	ENSP00000262891:p.Pro31Leu		Somatic				MARK4_ENST00000262891.4_Missense_Mutation_p.P31L	p.P31L	NM_031417.3	NP_113605.2	WXS	Illumina GAIIx	Phase_I	Q96L34	MARK4_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.0102)	2	389	+		all_neural(266;0.224)|Ovarian(192;0.231)	31					Q8NG37|Q96JG7|Q96SQ2|Q9BYD8	Missense_Mutation	SNP	ENST00000262891.4	37	c.92C>T	CCDS56097.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.270035	0.59540	.	.	ENSG00000007047	ENST00000262893;ENST00000262891;ENST00000300843	T;T	0.71698	-0.53;-0.59	4.88	3.84	0.44239	.	0.168708	0.38959	N	0.001518	T	0.55625	0.1932	N	0.24115	0.695	0.49051	D	0.999742	B;B	0.14012	0.002;0.009	B;B	0.09377	0.002;0.004	T	0.55147	-0.8186	10	0.62326	D	0.03	.	10.9592	0.47374	0.0:0.9089:0.0:0.0911	.	31;31	Q96L34;Q96L34-2	MARK4_HUMAN;.	L	31	ENSP00000262891:P31L;ENSP00000300843:P31L	ENSP00000262891:P31L	P	+	2	0	MARK4	50454127	1.000000	0.71417	0.464000	0.27143	0.966000	0.64601	5.494000	0.66905	1.284000	0.44531	0.555000	0.69702	CCG		0.672	MARK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457537.1	NM_031417		6	26	6	26	---	---	---	---
SIGLECL1	284369	broad.mit.edu	37	19	51768703	51768703	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr19:51768703C>T	ENST00000316401.7	+	3	485	c.104C>T	c.(103-105)cCc>cTc	p.P35L	SIGLECL1_ENST00000597824.1_Intron|CTD-3187F8.2_ENST00000597569.1_RNA|SIGLECL1_ENST00000593968.1_Intron	NM_173635.1	NP_775906.1	Q96PQ1	SIG12_HUMAN	SIGLEC family like 1	409	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.P35L(1)									ATTCCCACACCCTCTGTGCAG	0.587																																						ENST00000316401.7																			1	Substitution - Missense(1)	p.P35L(1)	prostate(1)								c.(103-105)cCc>cTc		SIGLEC family like 1							93.0	84.0	87.0					19																	51768703		2203	4300	6503	SO:0001583	missense	284369							g.chr19:51768703C>T	AK097554	CCDS12827.1	19q13.33	2013-03-20	2012-07-20	2012-07-20	ENSG00000179213	ENSG00000179213			26856	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 75"", ""sialic acid binding Ig-like lectin 23, pseudogene"", ""sialic acid binding Ig-like lectin, pseudogene 7"""	C19orf75, SIGLEC23P, SIGLECP7			Standard	NM_173635		Approved	FLJ40235	uc002pwb.1	Q8N7X8	OTTHUMG00000182881	ENST00000316401.7:c.104C>T	19.37:g.51768703C>T	ENSP00000321249:p.Pro35Leu		Somatic				SIGLECL1_ENST00000597824.1_Intron|CTD-3187F8.2_ENST00000597569.1_RNA|SIGLECL1_ENST00000593968.1_Intron	p.P35L	NM_173635.1	NP_775906.1	WXS	Illumina GAIIx	Phase_I					3	485	+								Q8IYH7	Missense_Mutation	SNP	ENST00000316401.7	37	c.104C>T	CCDS12827.1	.	.	.	.	.	.	.	.	.	.	C	12.97	2.096586	0.36952	.	.	ENSG00000179213	ENST00000316401	D	0.86366	-2.11	3.81	2.77	0.32553	Immunoglobulin-like fold (1);	0.000000	0.37669	N	0.001994	D	0.92064	0.7485	M	0.83118	2.625	0.09310	N	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.83599	0.0127	10	0.87932	D	0	-6.7576	7.2243	0.26005	0.0:0.8755:0.0:0.1245	.	35	Q8N7X8	CS075_HUMAN	L	35	ENSP00000321249:P35L	ENSP00000321249:P35L	P	+	2	0	C19orf75	56460515	0.001000	0.12720	0.109000	0.21407	0.449000	0.32228	0.609000	0.24238	0.923000	0.37045	0.650000	0.86243	CCC		0.587	SIGLECL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464161.2	NM_173635		29	152	29	152	---	---	---	---
NPEPL1	79716	broad.mit.edu	37	20	57290253	57290253	+	Silent	SNP	C	C	T			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr20:57290253C>T	ENST00000356091.6	+	12	1731	c.1443C>T	c.(1441-1443)gcC>gcT	p.A481A	STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Silent_p.A453A|NPEPL1_ENST00000525817.1_Silent_p.A433A	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	481						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)	p.A481A(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			TCGGTGTGGCCCTCCTGCTGG	0.672																																						ENST00000356091.6																			1	Substitution - coding silent(1)	p.A481A(1)	prostate(1)	endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14						c.(1441-1443)gcC>gcT		aminopeptidase-like 1							24.0	28.0	27.0					20																	57290253		2092	4213	6305	SO:0001819	synonymous_variant	79716				proteolysis	cytoplasm	aminopeptidase activity|manganese ion binding|metalloexopeptidase activity	g.chr20:57290253C>T	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.1443C>T	20.37:g.57290253C>T			Somatic				NPEPL1_ENST00000525817.1_Silent_p.A433A|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Silent_p.A453A	p.A481A	NM_024663.3	NP_078939.3	WXS	Illumina GAIIx	Phase_I	Q8NDH3	PEPL1_HUMAN	BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)		12	1731	+	all_lung(29;0.0175)		481					A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Silent	SNP	ENST00000356091.6	37	c.1443C>T	CCDS46621.1																																																																																				0.672	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		5	9	5	9	---	---	---	---
CDR1	1038	broad.mit.edu	37	X	139866376	139866376	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chrX:139866376C>A	ENST00000370532.2	-	1	347	c.156G>T	c.(154-156)ttG>ttT	p.L52F		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	52	23 X 6 AA approximate repeats.							p.L52F(1)		breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				CCACGTCTTCCAACAAAGCCA	0.438																																						ENST00000370532.2																			1	Substitution - Missense(1)	p.L52F(1)	prostate(1)	breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25						c.(154-156)ttG>ttT		cerebellar degeneration-related protein 1, 34kDa							125.0	117.0	120.0					X																	139866376		2203	4300	6503	SO:0001583	missense	1038							g.chrX:139866376C>A		CCDS14670.1	Xq27.1	2013-06-13	2002-08-29		ENSG00000184258	ENSG00000184258			1798	protein-coding gene	gene with protein product	"""Cerebellar degeneration-related protein-1 (34kD)"""	302650	"""cerebellar degeneration-related protein (34kD)"""	CDR		2326268	Standard	NM_004065		Approved	CDR62A, CDR34	uc004fbg.1	P51861	OTTHUMG00000137398	ENST00000370532.2:c.156G>T	X.37:g.139866376C>A	ENSP00000359563:p.Leu52Phe		Somatic					p.L52F	NM_004065.2	NP_004056.2	WXS	Illumina GAIIx	Phase_I	P51861	CDR1_HUMAN			1	347	-	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)	52			23 X 6 AA approximate repeats.		Q5JXH6	Missense_Mutation	SNP	ENST00000370532.2	37	c.156G>T	CCDS14670.1	.	.	.	.	.	.	.	.	.	.	C	15.71	2.914580	0.52546	.	.	ENSG00000184258	ENST00000370532	T	0.29397	1.57	4.45	3.31	0.37934	.	.	.	.	.	T	0.33235	0.0856	N	0.19112	0.55	0.25724	N	0.985345	D	0.76494	0.999	D	0.87578	0.998	T	0.12451	-1.0547	8	.	.	.	.	4.0306	0.09708	0.0:0.6595:0.0:0.3405	.	52	P51861	CDR1_HUMAN	F	52	ENSP00000359563:L52F	.	L	-	3	2	CDR1	139694042	0.009000	0.17119	0.979000	0.43373	0.050000	0.14768	0.586000	0.23894	1.940000	0.56252	0.544000	0.68410	TTG		0.438	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065		37	101	37	101	---	---	---	---
NEUROD2	4761	broad.mit.edu	37	17	37762300	37762308	+	In_Frame_Del	DEL	GGTCTGGCC	GGTCTGGCC	-			TCGA-CH-5771-01A-21D-1576-08	TCGA-CH-5771-11A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87e1ffee-a8cd-4d75-937e-ed415cf43546	d75f9a49-dfc3-493b-b9dd-4940d9803cfd	g.chr17:37762300_37762308delGGTCTGGCC	ENST00000302584.4	-	2	765_773	c.545_553delGGCCAGACC	c.(544-555)cggccagaccta>cta	p.RPD182del		NM_006160.3	NP_006151.3	Q15784	NDF2_HUMAN	neuronal differentiation 2	182					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|cellular response to calcium ion (GO:0071277)|cellular response to electrical stimulus (GO:0071257)|cerebellar cortex development (GO:0021695)|negative regulation of synapse maturation (GO:2000297)|nervous system development (GO:0007399)|neuron development (GO:0048666)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)	8	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Lung(15;0.00549)|LUAD - Lung adenocarcinoma(14;0.0664)			TAGGACACTAGGTCTGGCCGCTTGCCGGA	0.603																																						ENST00000302584.4																			0				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)	8						c.(544-555)cggccagaccta>cta		neuronal differentiation 2																																				SO:0001651	inframe_deletion	4761				cellular response to calcium ion|cellular response to electrical stimulus|cerebellar cortex development|negative regulation of synapse maturation|positive regulation of calcium-mediated signaling|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of synapse maturation|positive regulation of synaptic plasticity|protein ubiquitination|regulation of transcription from RNA polymerase II promoter	nucleus	E-box binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription corepressor activity	g.chr17:37762300_37762308delGGTCTGGCC	U58681	CCDS11338.1	17q12	2013-05-21	2012-02-22		ENSG00000171532	ENSG00000171532		"""Basic helix-loop-helix proteins"""	7763	protein-coding gene	gene with protein product		601725	"""neurogenic differentiation 2"""			9119405	Standard	XM_005257409		Approved	NDRF, bHLHa1	uc002hry.3	Q15784	OTTHUMG00000133211	ENST00000302584.4:c.545_553delGGCCAGACC	17.37:g.37762300_37762308delGGTCTGGCC	ENSP00000306754:p.Arg182_Asp184del		Somatic					p.RPD182del	NM_006160.3	NP_006151.3	WXS	Illumina GAIIx	Phase_I	Q15784	NDF2_HUMAN	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Lung(15;0.00549)|LUAD - Lung adenocarcinoma(14;0.0664)		2	765_773	-	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		182					Q8TBI7|Q9UQC6	In_Frame_Del	DEL	ENST00000302584.4	37	c.545_553delGGCCAGACC	CCDS11338.1																																																																																				0.603	NEUROD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256931.2	NM_006160		8	81	8	81	---	---	---	---
