#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
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_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000457356.4_3'UTR|MSC_ENST00000518440.1_5'Flank|RP11-383H13.1_ENST00000521467.1_Intron	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					RP11-383H13.1_ENST00000521467.1_Intron|RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000457356.4_3'UTR|RP11-383H13.1_ENST00000524152.1_Intron	p.R15W	NM_005098.3	NP_005089.2	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	0	0	0	0.150653	0	4	21				
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_ENST00000573648.1_Missense_Mutation_p.A360V|SLC13A5_ENST00000381074.4_Missense_Mutation_p.A317V	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					SLC13A5_ENST00000293800.6_Missense_Mutation_p.A343V|SLC13A5_ENST00000573648.1_Missense_Mutation_p.A360V|SLC13A5_ENST00000381074.4_Missense_Mutation_p.A317V	p.A360V	NM_177550.3	NP_808218.1	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	0	0	0	0.248553	0	6	28				
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		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	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	0	0	0	0.115264	0	3	32				
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	NPEPL1_ENST00000525967.1_Silent_p.A453A|NPEPL1_ENST00000525817.1_Silent_p.A433A|STX16-NPEPL1_ENST00000530122.1_3'UTR	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						STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Silent_p.A453A|NPEPL1_ENST00000525817.1_Silent_p.A433A	p.A481A	NM_024663.3	NP_078939.3	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	0	0	0	0.184627	0	5	9				
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						p.R1584I	NM_002976.3	NP_002967.2	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	1	0	2.31418e-15	0.870114	3.00844e-15	51	357				
LINC01410	103352539	broad.mit.edu	37	9	66466226	66466226	+	lincRNA	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.chr9:66466226A>G	ENST00000424345.1	+	0	859																											cctagcggagagagagccgga	0.453																																						ENST00000424345.1																			0																																																			0							g.chr9:66466226A>G																													9.37:g.66466226A>G														0	859	+									RNA	SNP	ENST00000424345.1	37																																																																																						0.453	RP11-262H14.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000128851.1			2	6	0	0	0	0.115264	0	2	6				
HERC2P9	440248	broad.mit.edu	37	15	28929317	28929317	+	RNA	SNP	T	T	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.chr15:28929317T>G	ENST00000528584.1	+	0	1854					NR_036443.1				hect domain and RLD 2 pseudogene 9																		AGAATTATATTGAGATCTACT	0.363																																						ENST00000528584.1																			0																																																			0							g.chr15:28929317T>G	BC047911		15q13.1	2011-05-24			ENSG00000206149	ENSG00000206149			30495	pseudogene	pseudogene							Standard	NR_036443		Approved	FLJ59185	uc010azc.3		OTTHUMG00000167114		15.37:g.28929317T>G								NR_036443.1						0	1854	+									RNA	SNP	ENST00000528584.1	37																																																																																						0.363	HERC2P9-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000393268.1	NR_036443		6	30	0	0	0	0.217242	0	6	30				
SV2C	22987	broad.mit.edu	37	5	75427791	75427791	+	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.chr5:75427791C>T	ENST00000502798.2	+	2	658	c.216C>T	c.(214-216)gaC>gaT	p.D72D	SV2C_ENST00000322285.7_Silent_p.D72D	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	72					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)	p.D72D(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		CCAACGATGACGAAGGCTCAA	0.498																																						ENST00000502798.2																			1	Substitution - coding silent(1)	p.D72D(1)	prostate(1)	NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						c.(214-216)gaC>gaT		synaptic vesicle glycoprotein 2C							84.0	87.0	86.0					5																	75427791		2084	4235	6319	SO:0001819	synonymous_variant	22987				neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity	g.chr5:75427791C>T	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.216C>T	5.37:g.75427791C>T						SV2C_ENST00000322285.7_Silent_p.D72D	p.D72D	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)	2	658	+		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)	72					Q496K1|Q9UPU8	Silent	SNP	ENST00000502798.2	37	c.216C>T	CCDS43331.1																																																																																				0.498	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4			7	52	0	0	0	0.278610	0	7	52				
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*						p.C1423*	NM_006269.1	NP_006260.1	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	0	0	0	0.500413	0	15	110				
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_ENST00000373388.2_5'UTR|CSMD2_ENST00000373381.4_Missense_Mutation_p.P1550L			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					CSMD2_ENST00000373380.1_Missense_Mutation_p.P423L|CSMD2_ENST00000373388.2_5'UTR	p.P1550L	NM_052896.3	NP_443128.2	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	0	0	0	0.150653	0	4	35				
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					ZFYVE9_ENST00000361625.1_Missense_Mutation_p.D360H|ZFYVE9_ENST00000371591.1_Missense_Mutation_p.D360H|ZFYVE9_ENST00000357206.2_Missense_Mutation_p.D360H	p.D360H	NM_004799.2	NP_004790.2	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	0	0	0	0.557998	0	17	206				
UBR1	197131	broad.mit.edu	37	15	43276106	43276106	+	Missense_Mutation	SNP	C	C	T	rs536630830		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.chr15:43276106C>T	ENST00000290650.4	-	37	4217	c.4139G>A	c.(4138-4140)cGt>cAt	p.R1380H	UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1380					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R1380H(1)		NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		TGATAGAAGACGAACCAGATG	0.348													C|||	1	0.000199681	0.0	0.0	5008	,	,		12419	0.0		0.0	False		,,,				2504	0.001					ENST00000290650.4																			1	Substitution - Missense(1)	p.R1380H(1)	prostate(1)	NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58						c.(4138-4140)cGt>cAt		ubiquitin protein ligase E3 component n-recognin 1							71.0	63.0	66.0					15																	43276106		2203	4299	6502	SO:0001583	missense	197131				cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding	g.chr15:43276106C>T		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.4139G>A	15.37:g.43276106C>T	ENSP00000290650:p.Arg1380His					UBR1_ENST00000382177.2_3'UTR	p.R1380H	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)	37	4217	-		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)	1380					O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	c.4139G>A	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	33	5.226800	0.95173	.	.	ENSG00000159459	ENST00000290650	T	0.49432	0.78	5.84	5.84	0.93424	.	0.289878	0.40554	N	0.001071	T	0.62392	0.2424	M	0.68952	2.095	0.80722	D	1	D	0.71674	0.998	P	0.55667	0.781	T	0.60702	-0.7211	10	0.44086	T	0.13	-22.8504	18.3196	0.90232	0.0:1.0:0.0:0.0	.	1380	Q8IWV7	UBR1_HUMAN	H	1380	ENSP00000290650:R1380H	ENSP00000290650:R1380H	R	-	2	0	UBR1	41063398	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.752000	0.55172	2.764000	0.94973	0.655000	0.94253	CGT		0.348	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		5	50	0	0	0	0.217242	0	5	50				
ANK2	287	broad.mit.edu	37	4	114251487	114251487	+	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.chr4:114251487C>T	ENST00000357077.4	+	27	3039	c.2986C>T	c.(2986-2988)Cgg>Tgg	p.R996W	ANK2_ENST00000264366.6_Missense_Mutation_p.R996W|ANK2_ENST00000509550.1_Missense_Mutation_p.R205W|ANK2_ENST00000506722.1_Missense_Mutation_p.R987W|ANK2_ENST00000394537.3_Missense_Mutation_p.R996W	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	996	Interaction with SPTBN1.|ZU5 1. {ECO:0000255|PROSITE- ProRule:PRU00485}.				atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.R996W(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TATTCCACCTCGGAAATGTAC	0.512																																						ENST00000357077.4																			1	Substitution - Missense(1)	p.R996W(1)	prostate(1)	NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248						c.(2986-2988)Cgg>Tgg		ankyrin 2, neuronal							75.0	68.0	70.0					4																	114251487		2203	4300	6503	SO:0001583	missense	287				axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding	g.chr4:114251487C>T	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.2986C>T	4.37:g.114251487C>T	ENSP00000349588:p.Arg996Trp					ANK2_ENST00000264366.6_Missense_Mutation_p.R996W|ANK2_ENST00000509550.1_Missense_Mutation_p.R205W|ANK2_ENST00000394537.3_Missense_Mutation_p.R996W|ANK2_ENST00000506722.1_Missense_Mutation_p.R987W	p.R996W	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)	27	3039	+		Ovarian(17;0.0448)|Hepatocellular(203;0.218)	996			Interaction with SPTBN1.|ZU5.		Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	c.2986C>T	CCDS3702.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.9|24.9	4.578400|4.578400	0.86645|0.86645	.|.	.|.	ENSG00000145362|ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000431447;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056;ENST00000509550|ENST00000514960	T;T;T;T;T;T;T;T|.	0.47177|.	0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85|.	5.93|5.93	5.08|5.08	0.68730|0.68730	ZU5 (3);|.	0.000000|.	0.49916|.	D|.	0.000131|.	T|T	0.66915|0.66915	0.2838|0.2838	L|L	0.46157|0.46157	1.445|1.445	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;0.996|.	D;D;D;D;D;D;P|.	0.85130|.	0.98;0.997;0.991;0.961;0.994;0.967;0.802|.	T|T	0.64262|0.64262	-0.6449|-0.6449	10|5	0.87932|.	D|.	0|.	.|.	16.4059|16.4059	0.83670|0.83670	0.1328:0.8672:0.0:0.0|0.1328:0.8672:0.0:0.0	.|.	205;996;41;996;996;987;987|.	E9PCH6;Q01484;Q7Z344;Q01484-2;Q01484-4;Q01484-5;F8WEF9|.	.;ANK2_HUMAN;.;.;.;.;.|.	W|L	975;942;987;75;1011;996;996;996;987;205|41	ENSP00000423799:R975W;ENSP00000421011:R942W;ENSP00000421067:R987W;ENSP00000424722:R1011W;ENSP00000378044:R996W;ENSP00000349588:R996W;ENSP00000264366:R996W;ENSP00000426944:R205W|.	ENSP00000264366:R996W|.	R|S	+|+	1|2	2|0	ANK2|ANK2	114470936|114470936	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.950000|0.950000	0.60333|0.60333	4.039000|4.039000	0.57325|0.57325	1.467000|1.467000	0.48044|0.48044	0.563000|0.563000	0.77884|0.77884	CGG|TCG		0.512	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		7	59	0	0	0	0.307466	0	7	59				
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					MARK4_ENST00000262891.4_Missense_Mutation_p.P31L	p.P31L	NM_031417.3	NP_113605.2	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	0	0	0	0.278610	0	6	26				
POM121L9P	29774	broad.mit.edu	37	22	24659809	24659809	+	RNA	SNP	G	G	A	rs376621154		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.chr22:24659809G>A	ENST00000414583.2	+	0	3334					NR_003714.1				POM121 transmembrane nucleoporin-like 9, pseudogene																		CCCTATCTGCGCACCCGGAGG	0.612																																						ENST00000414583.2																			0																																																			0							g.chr22:24659809G>A	AL040062, AL117401		22q11.22	2012-03-13	2012-03-13		ENSG00000128262	ENSG00000128262			30080	pseudogene	pseudogene			"""POM121 membrane glycoprotein-like 9, pseudogene"""				Standard	NR_003714		Approved				OTTHUMG00000150763		22.37:g.24659809G>A								NR_003714.1						0	3334	+									RNA	SNP	ENST00000414583.2	37																																																																																						0.612	POM121L9P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000319991.1	NM_014549		3	8	0	0	0	0.115264	0	3	8				
BIN2	51411	broad.mit.edu	37	12	51696475	51696475	+	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.chr12:51696475C>T	ENST00000267012.4	-	4	368	c.307G>A	c.(307-309)Gta>Ata	p.V103I	BIN2_ENST00000544402.1_Missense_Mutation_p.V77I|BIN2_ENST00000604560.1_Missense_Mutation_p.V76I|BIN2_ENST00000452142.2_Missense_Mutation_p.V103I	NM_016293.2	NP_057377.2	Q9UBW5	BIN2_HUMAN	bridging integrator 2	103	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				cell chemotaxis (GO:0060326)|membrane tubulation (GO:0097320)|phagocytosis, engulfment (GO:0006911)|podosome assembly (GO:0071800)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|podosome (GO:0002102)	phospholipid binding (GO:0005543)	p.V103I(1)		NS(2)|breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(3)	31						CTTACCCATACGATGGCCTTC	0.448																																						ENST00000267012.4																			1	Substitution - Missense(1)	p.V103I(1)	prostate(1)	NS(2)|breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(3)	31						c.(307-309)Gta>Ata		bridging integrator 2							220.0	197.0	205.0					12																	51696475		2203	4300	6503	SO:0001583	missense	51411					cytoplasm	protein binding	g.chr12:51696475C>T	AF146531	CCDS8811.1	12q13.13	2012-01-23			ENSG00000110934	ENSG00000110934			1053	protein-coding gene	gene with protein product		605936				10903846	Standard	XM_005268957		Approved	BRAP-1	uc001ryg.3	Q9UBW5		ENST00000267012.4:c.307G>A	12.37:g.51696475C>T	ENSP00000267012:p.Val103Ile					BIN2_ENST00000544402.1_Missense_Mutation_p.V77I|BIN2_ENST00000604560.1_Missense_Mutation_p.V76I|BIN2_ENST00000452142.2_Missense_Mutation_p.V103I	p.V103I	NM_016293.2	NP_057377.2	Q9UBW5	BIN2_HUMAN			4	368	-			103			BAR.		Q86VV0|Q9NWK4|Q9UKN4	Missense_Mutation	SNP	ENST00000267012.4	37	c.307G>A	CCDS8811.1	.	.	.	.	.	.	.	.	.	.	C	0.095	-1.160371	0.01686	.	.	ENSG00000110934	ENST00000452142;ENST00000267012;ENST00000544402	T;T;T	0.64618	0.23;-0.11;-0.11	5.18	2.96	0.34315	BAR (3);	0.683102	0.14180	N	0.336134	T	0.42966	0.1226	N	0.24115	0.695	0.09310	N	1	B;B;P	0.34587	0.403;0.403;0.458	B;B;B	0.26202	0.04;0.04;0.067	T	0.13683	-1.0500	10	0.33940	T	0.23	-0.5784	10.3319	0.43827	0.0:0.8108:0.0:0.1892	.	77;103;103	F5H0W4;Q9UBW5-2;Q9UBW5	.;.;BIN2_HUMAN	I	103;103;77	ENSP00000410217:V103I;ENSP00000267012:V103I;ENSP00000445874:V77I	ENSP00000267012:V103I	V	-	1	0	BIN2	49982742	0.000000	0.05858	0.575000	0.28536	0.096000	0.18686	0.465000	0.22004	0.608000	0.30000	0.655000	0.94253	GTA		0.448	BIN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000469800.1			47	320	0	0	0	0.870114	0	47	320				
SNPH	9751	broad.mit.edu	37	20	1276943	1276943	+	Intron	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.chr20:1276943C>A	ENST00000381873.3	+	3	189				RAD21L1_ENST00000402452.1_Intron|SNPH_ENST00000381867.1_Silent_p.G20G|RAD21L1_ENST00000381882.2_Intron	NM_014723.2	NP_055538.2	O15079	SNPH_HUMAN	syntaphilin						brain development (GO:0007420)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|synaptic vesicle docking involved in exocytosis (GO:0016081)	cell junction (GO:0030054)|cytoplasmic microtubule (GO:0005881)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)	syntaxin-1 binding (GO:0017075)	p.G20G(1)		endometrium(2)|large_intestine(4)|lung(10)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TTTCTGCGGGCCCCCCAACCC	0.687																																						ENST00000381867.1																			1	Substitution - coding silent(1)	p.G20G(1)	prostate(1)	endometrium(2)|large_intestine(4)|lung(10)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						c.(58-60)ggC>ggA		syntaphilin							28.0	27.0	27.0					20																	1276943		692	1591	2283	SO:0001627	intron_variant	9751				synaptic vesicle docking involved in exocytosis	cell junction|integral to membrane|synapse|synaptosome	syntaxin-1 binding	g.chr20:1276943C>A		CCDS13012.1	20p13	2008-07-02			ENSG00000101298	ENSG00000101298			15931	protein-coding gene	gene with protein product		604942				10707983	Standard	NM_014723		Approved	bA314N13.5	uc002wes.3	O15079	OTTHUMG00000031662	ENST00000381873.3:c.-47-26C>A	20.37:g.1276943C>A						RAD21L1_ENST00000381882.2_Intron|SNPH_ENST00000381873.3_Intron|RAD21L1_ENST00000402452.1_Intron	p.G20G			O15079	SNPH_HUMAN			4	702	+			0					Q8IYI3	Silent	SNP	ENST00000381873.3	37	c.60C>A	CCDS13012.1																																																																																				0.687	SNPH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145240.2	NM_014723		4	7	1	0	0.00909568	0.150653	0.0102821	4	7				
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	0	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					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	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	0	0	0	0.361761	0	11	202				
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							p.L380L	NM_018036.5	NP_060506.5	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	0	0	0	0.184627	0	4	165				
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|SIGLECL1_ENST00000593968.1_Intron|CTD-3187F8.2_ENST00000597569.1_RNA	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					CTD-3187F8.2_ENST00000597569.1_RNA|SIGLECL1_ENST00000593968.1_Intron|SIGLECL1_ENST00000597824.1_Intron	p.P35L	NM_173635.1	NP_775906.1					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	0	0	0	0.717897	0	29	152				
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						p.G2120R	NM_000138.4	NP_000129.3	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	0	0	0	0.115264	0	3	59				
CLMN	79789	broad.mit.edu	37	14	95670136	95670136	+	Missense_Mutation	SNP	C	C	T	rs78561092	byFrequency	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.chr14:95670136C>T	ENST00000298912.4	-	9	1663	c.1550G>A	c.(1549-1551)cGc>cAc	p.R517H		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	517					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.R517H(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		TTCATCGTGGCGGGCTGTACT	0.458													C|||	13	0.00259585	0.0	0.0014	5008	,	,		18763	0.0119		0.0	False		,,,				2504	0.0					ENST00000298912.4																			1	Substitution - Missense(1)	p.R517H(1)	prostate(1)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44						c.(1549-1551)cGc>cAc		calmin (calponin-like, transmembrane)		C	HIS/ARG	0,4406		0,0,2203	69.0	72.0	71.0		1550	0.4	0.0	14	dbSNP_131	71	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CLMN	NM_024734.3	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	517/1003	95670136	2,13004	2203	4300	6503	SO:0001583	missense	79789					integral to membrane	actin binding	g.chr14:95670136C>T	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.1550G>A	14.37:g.95670136C>T	ENSP00000298912:p.Arg517His						p.R517H	NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN		Epithelial(152;0.193)	9	1663	-			517					B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	37	c.1550G>A	CCDS9933.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	11	0.019230769230769232	0	0.0	C	12.46	1.945266	0.34283	0.0	2.33E-4	ENSG00000165959	ENST00000298912	D	0.92752	-3.1	5.76	0.394	0.16299	.	1.379260	0.04685	N	0.413178	T	0.70150	0.3191	N	0.08118	0	0.09310	N	1	B	0.27117	0.168	B	0.10450	0.005	T	0.68473	-0.5399	10	0.49607	T	0.09	.	4.7041	0.12841	0.1415:0.5438:0.0:0.3147	.	517	Q96JQ2	CLMN_HUMAN	H	517	ENSP00000298912:R517H	ENSP00000298912:R517H	R	-	2	0	CLMN	94739889	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.006000	0.13152	0.034000	0.15491	-0.126000	0.14955	CGC		0.458	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			11	112	0	0	0	0.361761	0	11	112				
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_ENST00000373266.4_Missense_Mutation_p.T215A|KIAA0319L_ENST00000485551.1_5'UTR	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					KIAA0319L_ENST00000373266.4_Missense_Mutation_p.T215A|KIAA0319L_ENST00000485551.1_5'UTR	p.T778A	NM_024874.4	NP_079150.3	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	0	0	0	0.608945	0	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_ENST00000489537.1_5'Flank|SF3A3_ENST00000448721.2_Missense_Mutation_p.Q273K	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					SF3A3_ENST00000448721.2_Missense_Mutation_p.Q273K	p.Q326K	NM_006802.2	NP_006793.1	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	1	0	1.88708e-17	0.729181	2.51611e-17	28	185				
CSF3R	1441	broad.mit.edu	37	1	36935383	36935383	+	Silent	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.chr1:36935383G>T	ENST00000373106.1	-	11	1891	c.1344C>A	c.(1342-1344)ggC>ggA	p.G448G	CSF3R_ENST00000418048.2_Silent_p.G448G|CSF3R_ENST00000338937.5_Silent_p.G448G|CSF3R_ENST00000373104.1_Silent_p.G448G|CSF3R_ENST00000361632.4_Silent_p.G448G|CSF3R_ENST00000373103.1_Silent_p.G448G|CSF3R_ENST00000440588.2_Silent_p.G448G|CSF3R_ENST00000331941.5_Silent_p.G448G|CSF3R_ENST00000487540.2_5'UTR	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	448	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|defense response (GO:0006952)|neutrophil chemotaxis (GO:0030593)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.G448G(2)		central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	GGGGCTCCCAGCCTACCCAGA	0.602																																						ENST00000373103.1																			2	Substitution - coding silent(2)	p.G448G(2)	prostate(2)	central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						c.(1342-1344)ggC>ggA		colony stimulating factor 3 receptor (granulocyte)	Filgrastim(DB00099)|Pegfilgrastim(DB00019)						34.0	38.0	36.0					1																	36935383		2203	4300	6503	SO:0001819	synonymous_variant	1441				cell adhesion|defense response	extracellular region|integral to plasma membrane	cytokine receptor activity	g.chr1:36935383G>T	M59820	CCDS412.1, CCDS413.1, CCDS414.1	1p35-p34.3	2014-09-17			ENSG00000119535	ENSG00000119535		"""CD molecules"", ""Fibronectin type III domain containing"""	2439	protein-coding gene	gene with protein product		138971		CD114		1371413	Standard	NM_000760		Approved	GCSFR	uc001cax.2	Q99062	OTTHUMG00000008010	ENST00000373106.1:c.1344C>A	1.37:g.36935383G>T						CSF3R_ENST00000418048.2_Silent_p.G448G|CSF3R_ENST00000487540.2_5'UTR|CSF3R_ENST00000373104.1_Silent_p.G448G|CSF3R_ENST00000373106.1_Silent_p.G448G|CSF3R_ENST00000361632.4_Silent_p.G448G|CSF3R_ENST00000338937.5_Silent_p.G448G|CSF3R_ENST00000331941.5_Silent_p.G448G|CSF3R_ENST00000440588.2_Silent_p.G448G	p.G448G	NM_156039.3	NP_724781.1	Q99062	CSF3R_HUMAN			11	1891	-		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)	448			Fibronectin type-III 4.			Silent	SNP	ENST00000373106.1	37	c.1344C>A	CCDS413.1	.	.	.	.	.	.	.	.	.	.	G	9.501	1.103148	0.20632	.	.	ENSG00000119535	ENST00000464465	.	.	.	5.62	-1.16	0.09678	.	.	.	.	.	T	0.39600	0.1084	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29579	-1.0007	4	.	.	.	-8.5794	1.0777	0.01636	0.3526:0.1361:0.3562:0.155	.	.	.	.	D	34	.	.	A	-	2	0	CSF3R	36707970	0.995000	0.38212	0.997000	0.53966	0.785000	0.44390	0.172000	0.16704	0.062000	0.16340	-0.140000	0.14226	GCT		0.602	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039		5	74	1	0	0.000602214	0.184627	0.000711708	5	74				
SEMA4A	64218	broad.mit.edu	37	1	156131152	156131152	+	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.chr1:156131152G>A	ENST00000368285.3	+	9	1093	c.826G>A	c.(826-828)Gaa>Aaa	p.E276K	SEMA4A_ENST00000368282.1_Missense_Mutation_p.E276K|SEMA4A_ENST00000368284.1_Missense_Mutation_p.E144K|SEMA4A_ENST00000368286.2_Missense_Mutation_p.E144K|SEMA4A_ENST00000487358.1_3'UTR|SEMA4A_ENST00000355014.2_Missense_Mutation_p.E276K	NM_001193300.1|NM_022367.3	NP_001180229.1|NP_071762.2	Q9H3S1	SEM4A_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	276	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|regulation of cell shape (GO:0008360)|regulation of endothelial cell migration (GO:0010594)|semaphorin-plexin signaling pathway (GO:0071526)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.E276K(1)		breast(1)|ovary(2)|skin(2)	5	Hepatocellular(266;0.158)					CGTGGGCGGCGAAAAGCTGCT	0.726																																						ENST00000368285.3																			1	Substitution - Missense(1)	p.E276K(1)	prostate(1)	breast(1)|ovary(2)|skin(2)	5						c.(826-828)Gaa>Aaa		sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A							36.0	35.0	35.0					1																	156131152		2203	4300	6503	SO:0001583	missense	64218				axon guidance	integral to membrane|plasma membrane	receptor activity	g.chr1:156131152G>A	AK022416	CCDS1132.1, CCDS53378.1	1q22	2014-01-28			ENSG00000196189	ENSG00000196189		"""Semaphorins"""	10729	protein-coding gene	gene with protein product		607292		SEMAB		7748561	Standard	NM_022367		Approved	SemB, FLJ12287, CORD10	uc009wrq.3	Q9H3S1	OTTHUMG00000014042	ENST00000368285.3:c.826G>A	1.37:g.156131152G>A	ENSP00000357268:p.Glu276Lys					SEMA4A_ENST00000487358.1_3'UTR|SEMA4A_ENST00000355014.2_Missense_Mutation_p.E276K|SEMA4A_ENST00000368286.2_Missense_Mutation_p.E144K|SEMA4A_ENST00000368282.1_Missense_Mutation_p.E276K|SEMA4A_ENST00000368284.1_Missense_Mutation_p.E144K	p.E276K	NM_001193300.1|NM_022367.3	NP_001180229.1|NP_071762.2	Q9H3S1	SEM4A_HUMAN			9	1093	+	Hepatocellular(266;0.158)		276			Sema.		B2RDH8|B3KR76|Q5TCI5|Q5TCJ6|Q8WUA9	Missense_Mutation	SNP	ENST00000368285.3	37	c.826G>A	CCDS1132.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.034904	0.93575	.	.	ENSG00000196189	ENST00000435124;ENST00000414683;ENST00000355014;ENST00000368285;ENST00000368284;ENST00000368283;ENST00000544376;ENST00000368286;ENST00000368282	T;T;T;T;T;T;T	0.10573	2.86;2.86;2.86;2.86;2.86;2.86;2.86	5.42	5.42	0.78866	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.330856	0.31156	N	0.008149	T	0.09730	0.0239	L	0.35644	1.08	0.58432	D	0.999993	D;P	0.53312	0.959;0.916	P;P	0.51974	0.686;0.612	T	0.23511	-1.0186	10	0.25106	T	0.35	.	17.7936	0.88562	0.0:0.0:1.0:0.0	.	144;276	Q5TCJ6;Q9H3S1	.;SEM4A_HUMAN	K	276;177;276;276;144;238;238;144;276	ENSP00000401391:E276K;ENSP00000399230:E177K;ENSP00000347117:E276K;ENSP00000357268:E276K;ENSP00000357267:E144K;ENSP00000357269:E144K;ENSP00000357265:E276K	ENSP00000347117:E276K	E	+	1	0	SEMA4A	154397776	1.000000	0.71417	0.881000	0.34555	0.551000	0.35334	6.211000	0.72182	2.535000	0.85469	0.455000	0.32223	GAA		0.726	SEMA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039484.2	NM_022367		10	59	0	0	0	0.335167	0	10	59				
PRSS3P2	154754	broad.mit.edu	37	7	142482229	142482229	+	RNA	SNP	T	T	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.chr7:142482229T>A	ENST00000603901.1	+	0	609					NR_001296.3		Q8NHM4	TRY6_HUMAN	protease, serine, 3 pseudogene 2						endothelial cell migration (GO:0043542)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.P203P(1)									CTGGTGGCCCTGTGGTCTGCA	0.493																																						ENST00000603901.1																			1	Substitution - coding silent(1)	p.P203P(1)	prostate(1)																																																0							g.chr7:142482229T>A			7q34	2012-03-06			ENSG00000250606	ENSG00000275896			43788	pseudogene	pseudogene	"""trypsinogen C"""						Standard	NR_001296		Approved	TRY6	uc011ksq.2	Q8NHM4	OTTHUMG00000158904		7.37:g.142482229T>A								NR_001296.3						0	609	+									RNA	SNP	ENST00000603901.1	37																																																																																						0.493	PRSS3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000470000.1	NR_001296		4	65	0	0	0	0.307466	0	4	65				
LINC01410	103352539	broad.mit.edu	37	9	66459820	66459820	+	lincRNA	SNP	G	G	C	rs371375365		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.chr9:66459820G>C	ENST00000424345.1	+	0	80				RNA5SP283_ENST00000365604.1_RNA																							tttgtccccagtgccttattt	0.353																																						ENST00000424345.1																			0																																																			0							g.chr9:66459820G>C																													9.37:g.66459820G>C														0	80	+									RNA	SNP	ENST00000424345.1	37																																																																																						0.353	RP11-262H14.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000128851.1			2	2	0	0	0	0.184627	0	2	2				
MRPL28	10573	broad.mit.edu	37	16	418564	418564	+	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.chr16:418564C>T	ENST00000199706.8	-	4	548	c.513G>A	c.(511-513)cgG>cgA	p.R171R	MRPL28_ENST00000389675.2_Silent_p.R171R|MRPL28_ENST00000429738.1_Intron	NM_006428.4	NP_006419.2	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28	171					translation (GO:0006412)	cytoplasm (GO:0005737)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.R171R(1)		breast(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)	5		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)				GGGGGTCCTGCCGGGCAAGCC	0.657																																						ENST00000199706.8																			1	Substitution - coding silent(1)	p.R171R(1)	prostate(1)	breast(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)	5						c.(511-513)cgG>cgA		mitochondrial ribosomal protein L28							45.0	51.0	49.0					16																	418564		2203	4300	6503	SO:0001819	synonymous_variant	10573				translation	mitochondrial ribosome	protein binding|structural constituent of ribosome	g.chr16:418564C>T	U19796	CCDS32349.1	16p13.12	2012-09-26	2002-11-13		ENSG00000086504	ENSG00000086504		"""Mitochondrial ribosomal proteins / large subunits"""	14484	protein-coding gene	gene with protein product		604853	"""melanoma-associated antigen recognised by cytotoxic T lymphocytes"""	MAAT1		11551941, 19753307	Standard	NM_006428		Approved	p15	uc002cgs.2	Q13084	OTTHUMG00000047994	ENST00000199706.8:c.513G>A	16.37:g.418564C>T						MRPL28_ENST00000429738.1_Intron|MRPL28_ENST00000389675.2_Silent_p.R171R	p.R171R	NM_006428.4	NP_006419.2	Q13084	RM28_HUMAN			4	548	-		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)	171					B2RCM4|D3DU46|Q4TT39|Q96S26|Q9BQD8|Q9BR04	Silent	SNP	ENST00000199706.8	37	c.513G>A	CCDS32349.1																																																																																				0.657	MRPL28-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139285.2			7	64	0	0	0	0.307466	0	7	64				
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	SBNO1_ENST00000602750.1_Silent_p.I26I|SBNO1_ENST00000420886.2_Silent_p.I26I|SBNO1_ENST00000267176.4_Silent_p.I26I|Y_RNA_ENST00000384460.1_RNA			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						SBNO1_ENST00000602398.1_Silent_p.I26I|SBNO1_ENST00000267176.4_Silent_p.I26I|SBNO1_ENST00000602750.1_Silent_p.I26I	p.I26I	NM_001167856.1	NP_001161328.1	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	0	0	0	0.520397	0	16	386				
TNN	63923	broad.mit.edu	37	1	175046577	175046577	+	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.chr1:175046577G>A	ENST00000239462.4	+	2	136	c.23G>A	c.(22-24)cGc>cAc	p.R8H		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	8					axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)		p.R8H(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GAGATGTTCCGCTTCCCTATG	0.572																																						ENST00000239462.4																			1	Substitution - Missense(1)	p.R8H(1)	prostate(1)	NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156						c.(22-24)cGc>cAc		tenascin N							83.0	89.0	87.0					1																	175046577		2203	4298	6501	SO:0001583	missense	63923				cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix		g.chr1:175046577G>A	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.23G>A	1.37:g.175046577G>A	ENSP00000239462:p.Arg8His						p.R8H	NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)	2	136	+		Breast(1374;0.000962)	8					B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	c.23G>A	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	G	0.377	-0.930581	0.02359	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.25749	1.78	5.21	1.06	0.20224	.	1.265810	0.04920	N	0.454766	T	0.12774	0.0310	N	0.14661	0.345	0.09310	N	1	B;B	0.31931	0.0;0.347	B;B	0.17722	0.0;0.019	T	0.22347	-1.0219	10	0.15952	T	0.53	.	7.2197	0.25979	0.1635:0.4143:0.4222:0.0	.	8;8	B3KXB6;Q9UQP3	.;TENN_HUMAN	H	8	ENSP00000239462:R8H	ENSP00000239462:R8H	R	+	2	0	TNN	173313200	0.006000	0.16342	0.162000	0.22713	0.020000	0.10135	0.144000	0.16135	0.275000	0.22094	-0.140000	0.14226	CGC		0.572	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		8	239	0	0	0	0.278610	0	8	239				
PDGFRA	5156	broad.mit.edu	37	4	55138618	55138618	+	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.chr4:55138618C>T	ENST00000257290.5	+	9	1626	c.1295C>T	c.(1294-1296)aCg>aTg	p.T432M	FIP1L1_ENST00000507166.1_Intron	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	432	Ig-like C2-type 5.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.T432M(2)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	GGGGGACAGACGGTGAGGTGC	0.473			"""Mis, O, T"""	FIP1L1	"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											Pancreas(151;208 1913 7310 23853 37092)	ENST00000257290.5				Dom	yes		4	4q11-q13	5156	"""Mis, O, T"""	"""platelet-derived growth factor, alpha-receptor"""			"""L, M, O"""	FIP1L1		"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""		2	Substitution - Missense(2)	p.T432M(2)	prostate(2)	NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967						c.(1294-1296)aCg>aTg		platelet-derived growth factor receptor, alpha polypeptide	Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)						159.0	145.0	150.0					4																	55138618		2203	4300	6503	SO:0001583	missense	5156	Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity	g.chr4:55138618C>T	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.1295C>T	4.37:g.55138618C>T	ENSP00000257290:p.Thr432Met	TSP Lung(21;0.16)				FIP1L1_ENST00000507166.1_Intron	p.T432M	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		9	1626	+	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		432			Ig-like C2-type 5.		B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	37	c.1295C>T	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	C	9.499	1.102670	0.20632	.	.	ENSG00000134853	ENST00000257290	T	0.79352	-1.26	6.17	2.41	0.29592	Immunoglobulin-like fold (1);	0.248587	0.20666	N	0.087927	T	0.69513	0.3119	M	0.70275	2.135	0.80722	D	1	P;B	0.45396	0.857;0.261	B;B	0.35182	0.197;0.033	T	0.65780	-0.6085	10	0.42905	T	0.14	.	7.8483	0.29440	0.1122:0.6978:0.0:0.19	.	432;432	P16234-3;P16234	.;PGFRA_HUMAN	M	432	ENSP00000257290:T432M	ENSP00000257290:T432M	T	+	2	0	PDGFRA	54833375	0.948000	0.32251	0.676000	0.29932	0.004000	0.04260	1.634000	0.37123	0.435000	0.26365	-0.126000	0.14955	ACG		0.473	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		17	118	0	0	0	0.539581	0	17	118				
DMD	1756	broad.mit.edu	37	X	31676189	31676189	+	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.chrX:31676189G>A	ENST00000357033.4	-	54	8151	c.7945C>T	c.(7945-7947)Cgg>Tgg	p.R2649W	DMD_ENST00000378677.2_Missense_Mutation_p.R2645W|DMD_ENST00000541735.1_Missense_Mutation_p.R189W|DMD_ENST00000343523.2_Missense_Mutation_p.R189W|DMD_ENST00000359836.1_Missense_Mutation_p.R189W|DMD_ENST00000474231.1_Missense_Mutation_p.R189W|DMD_ENST00000378707.3_Missense_Mutation_p.R189W	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2649					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.R189W(2)|p.R2645W(2)|p.R2644W(1)|p.R1308W(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GAATAATCCCGGAGAAGTTTC	0.393																																						ENST00000357033.4																			6	Substitution - Missense(6)	p.R189W(2)|p.R2645W(2)|p.R2644W(1)|p.R1308W(1)	prostate(6)	NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77						c.(7945-7947)Cgg>Tgg		dystrophin							93.0	85.0	88.0					X																	31676189		2202	4300	6502	SO:0001583	missense	1756				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding	g.chrX:31676189G>A	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.7945C>T	X.37:g.31676189G>A	ENSP00000354923:p.Arg2649Trp					DMD_ENST00000359836.1_Missense_Mutation_p.R189W|DMD_ENST00000343523.2_Missense_Mutation_p.R189W|DMD_ENST00000378707.3_Missense_Mutation_p.R189W|DMD_ENST00000378677.2_Missense_Mutation_p.R2645W|DMD_ENST00000541735.1_Missense_Mutation_p.R189W|DMD_ENST00000474231.1_Missense_Mutation_p.R189W	p.R2649W	NM_000109.3|NM_004006.2|NM_004007.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997.1|NP_003998.1|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN			54	8151	-		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)	2649					E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	c.7945C>T	CCDS14233.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.0|22.0	4.232620|4.232620	0.79688|0.79688	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000465285|ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000474231	.|T;T;T;T;T;T;T;T	.|0.36157	.|1.27;1.27;1.27;1.27;1.27;1.27;1.27;1.27	5.29|5.29	4.41|4.41	0.53225|0.53225	.|.	.|0.000000	.|0.32901	.|U	.|0.005517	T|T	0.54983|0.54983	0.1892|0.1892	L|L	0.55481|0.55481	1.735|1.735	0.44104|0.44104	D|D	0.996873|0.996873	.|D;D;D;D;D;D;D;D;D;D	.|0.89917	.|0.996;1.0;1.0;1.0;1.0;0.999;0.999;0.999;1.0;0.999	.|D;D;D;D;D;D;D;D;D;D	.|0.87578	.|0.974;0.987;0.998;0.986;0.986;0.913;0.967;0.967;0.965;0.941	T|T	0.56697|0.56697	-0.7936|-0.7936	5|10	.|0.62326	.|D	.|0.03	.|.	14.442|14.442	0.67323|0.67323	0.0:0.0:0.8515:0.1485|0.0:0.0:0.8515:0.1485	.|.	.|2641;2649;2645;1308;1305;189;189;189;189;189	.|P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3	.|.;DMD_HUMAN;.;.;.;.;.;.;.;.	L|W	377|2641;1308;1305;345;2645;2649;189;189;2649;2526;189;189;189	.|ENSP00000350765:R345W;ENSP00000367948:R2645W;ENSP00000354923:R2649W;ENSP00000352894:R189W;ENSP00000340057:R189W;ENSP00000367979:R189W;ENSP00000444119:R189W;ENSP00000417123:R189W	.|ENSP00000340057:R189W	P|R	-|-	2|1	0|2	DMD|DMD	31586110|31586110	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.447000|4.447000	0.60020|0.60020	0.987000|0.987000	0.38709|0.38709	0.529000|0.529000	0.55759|0.55759	CCG|CGG		0.393	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		38	113	0	0	0	0.796494	0	38	113				
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						p.L52F	NM_004065.2	NP_004056.2	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	1	0	1.26612e-14	0.779181	1.56757e-14	37	101				
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_ENST00000444627.1_Missense_Mutation_p.E391G|KIAA1324L_ENST00000416314.1_Missense_Mutation_p.E224G|KIAA1324L_ENST00000297222.6_Missense_Mutation_p.E151G	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					KIAA1324L_ENST00000416314.1_Missense_Mutation_p.E224G|KIAA1324L_ENST00000444627.1_Missense_Mutation_p.E391G|KIAA1324L_ENST00000297222.6_Missense_Mutation_p.E151G	p.E391G	NM_001142749.2	NP_001136221.1	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	0	0	0	0.457914	0	14	265				
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					RP11-334E6.10_ENST00000501918.2_RNA	p.V390L	NM_032015.4	NP_114404.1	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	1	0	4.75885e-15	0.520397	6.03561e-15	16	95				
PRAMEF7	441871	broad.mit.edu	37	1	12979764	12979764	+	Missense_Mutation	SNP	G	G	A	rs369932937		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.chr1:12979764G>A	ENST00000361079.2	+	4	1039	c.956G>A	c.(955-957)cGt>cAt	p.R319H	RNU6-1072P_ENST00000384703.1_RNA			Q5VXH5	PRAM7_HUMAN	PRAME family member 7	319					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.R319H(2)		endometrium(2)|kidney(5)|large_intestine(3)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)	18	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CCGAGCATCCGTCAATTAAAG	0.587																																						ENST00000361079.2																			2	Substitution - Missense(2)	p.R319H(2)	prostate(2)	endometrium(2)|kidney(5)|large_intestine(3)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)	18						c.(955-957)cGt>cAt		PRAME family member 7		G	HIS/ARG	1,4403		0,1,2201	89.0	82.0	85.0		956	-0.3	0.0	1		85	0,8592		0,0,4296	no	missense	PRAMEF7	NM_001012277.1	29	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	319/475	12979764	1,12995	2202	4296	6498	SO:0001583	missense	441871							g.chr1:12979764G>A		CCDS30593.1	1p36.21	2013-01-17			ENSG00000204510	ENSG00000204510		"""-"""	28415	protein-coding gene	gene with protein product							Standard	NM_001012277		Approved			Q5VXH5	OTTHUMG00000001982	ENST00000361079.2:c.956G>A	1.37:g.12979764G>A	ENSP00000354371:p.Arg319His						p.R319H						UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)	4	1039	+	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)						B9EIP0	Missense_Mutation	SNP	ENST00000361079.2	37	c.956G>A	CCDS30593.1	.	.	.	.	.	.	.	.	.	.	.	10.93	1.490801	0.26774	2.27E-4	0.0	ENSG00000204510	ENST00000361079;ENST00000330881	T;T	0.09255	3.0;3.0	1.68	-0.352	0.12598	.	0.979768	0.08388	N	0.953488	T	0.09992	0.0245	N	0.15975	0.35	0.09310	N	1	D	0.76494	0.999	P	0.61132	0.884	T	0.23547	-1.0185	10	0.15499	T	0.54	.	1.9777	0.03419	0.3601:0.0:0.3772:0.2627	.	319	Q5VXH5	PRAM7_HUMAN	H	319	ENSP00000354371:R319H;ENSP00000328915:R319H	ENSP00000328915:R319H	R	+	2	0	PRAMEF7	12902351	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.739000	0.04866	-0.101000	0.12219	0.306000	0.20318	CGT		0.587	PRAMEF7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001012277		8	309	0	0	0	0.307466	0	8	309				
AC144450.1	0	broad.mit.edu	37	2	1600084	1600087	+	RNA	DEL	CAGA	CAGA	-			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.chr2:1600084_1600087delCAGA	ENST00000438247.1	-	0	515																											gcacacagatcagacacacacaag	0.485																																						ENST00000438247.1																			0																																																			0							g.chr2:1600084_1600087delCAGA																													2.37:g.1600084_1600087delCAGA														0	515	-									RNA	DEL	ENST00000438247.1	37																																																																																						0.485	AC144450.1-001	KNOWN	basic	antisense	antisense	OTTHUMT00000322440.1			2	4						2	4	---	---	---	---
DOK7	285489	broad.mit.edu	37	4	3494670	3494671	+	Frame_Shift_Ins	INS	-	-	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.chr4:3494670_3494671insA	ENST00000340083.5	+	7	1022_1023	c.957_958insA	c.(958-960)aagfs	p.K320fs	DOK7_ENST00000389653.2_Frame_Shift_Ins_p.K320fs|DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000507039.1_3'UTR	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	320	Ser-rich.				neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GGCCACCCCCCAAGCCGCTGCG	0.688																																						ENST00000340083.5																			0				kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5						c.(955-960)ccagccfs		docking protein 7			,	350,3410		47,256,1577					,	-1.8	0.0			6	591,6803		70,451,3176	no	frameshift,utr-3	DOK7	NM_173660.4,NM_001164673.1	,	117,707,4753	A1A1,A1R,RR		7.993,9.3085,8.4364	,	,		941,10213				SO:0001589	frameshift_variant	285489				positive regulation of protein tyrosine kinase activity	cell junction|synapse	insulin receptor binding|protein kinase binding	g.chr4:3494670_3494671insA	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"""chromosome 4 open reading frame 25"""	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.959dupA	4.37:g.3494672_3494672dupA	ENSP00000344432:p.Lys320fs					DOK7_ENST00000389653.2_Frame_Shift_Ins_p.A320fs|DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000507039.1_3'UTR	p.A320fs	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (64;0.163)	7	1022_1023	+			320			Ser-rich.		A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Frame_Shift_Ins	INS	ENST00000340083.5	37	c.957_958insA	CCDS3370.2																																																																																				0.688	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660		3	5						3	5	---	---	---	---
KDM7A	80853	broad.mit.edu	37	7	139878082	139878089	+	5'Flank	DEL	TCCCTCCC	TCCCTCCC	-	rs146325560|rs57191915|rs56784277|rs151002849|rs142303955|rs386718447|rs144362124|rs139263707	byFrequency	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.chr7:139878082_139878089delTCCCTCCC	ENST00000397560.2	-	0	0				JHDM1D_ENST00000006967.5_5'Flank|JHDM1D-AS1_ENST00000566699.1_RNA	NM_030647.1	NP_085150.1	Q6ZMT4	KDM7A_HUMAN							histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|midbrain development (GO:0030901)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)	22	Melanoma(164;0.0142)					cttccttccttccctccctccCTTTCCT	0.471																																						ENST00000566699.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr7:139878082_139878089delTCCCTCCC																													7.37:g.139878082_139878089delTCCCTCCC	Exception_encountered							NR_024451.1						0	1022_1029	+								A4D1S9|C9JJH9|C9JQU2|Q6MZL8|Q9C0E5	RNA	DEL	ENST00000397560.2	37		CCDS43658.1																																																																																				0.471	JHDM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348460.1			2	4						2	4	---	---	---	---
LINC00475	158314	broad.mit.edu	37	9	94904432	94904432	+	RNA	DEL	G	G	-	rs34310564	byFrequency	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.chr9:94904432delG	ENST00000416438.2	+	0	184				snoU13_ENST00000459125.1_RNA	NR_027341.1				long intergenic non-protein coding RNA 475																		GGCCTTCTTTGGGGGGGGGGT	0.612													|||unknown(HR)	1764	0.352236	0.3396	0.4957	5008	,	,		14095	0.371		0.2286	False		,,,				2504	0.3753					ENST00000416438.2																			0																																																			0							g.chr9:94904432delG	AK023662		9q22.31	2012-10-12	2011-08-31	2011-08-31	ENSG00000225511	ENSG00000225511		"""Long non-coding RNAs"""	23569	non-coding RNA	RNA, long non-coding			"""chromosome 9 open reading frame 44"""	C9orf44			Standard	NR_027341		Approved		uc004arp.1		OTTHUMG00000020216		9.37:g.94904432delG								NR_027341.1						0	184	+									RNA	DEL	ENST00000416438.2	37																																																																																						0.612	LINC00475-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000053051.2			3	3						3	3	---	---	---	---
LINC01572	101927957	broad.mit.edu	37	16	72564152	72564155	+	lincRNA	DEL	TGTG	TGTG	-	rs60858703|rs71784649|rs33998319|rs57250995|rs376669009	byFrequency	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.chr16:72564152_72564155delTGTG	ENST00000561611.2	-	0	113																											CACTATTTTAtgtgtgtgtgtgtg	0.402														1026	0.204872	0.1044	0.4236	5008	,	,		15150	0.375		0.0905	False		,,,				2504	0.1278					ENST00000561611.2																			0																																																			0							g.chr16:72564152_72564155delTGTG																													16.37:g.72564160_72564163delTGTG														0	113	-									RNA	DEL	ENST00000561611.2	37																																																																																						0.402	AC004158.2-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000423195.2			3	3						3	3	---	---	---	---
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)cta>c		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						p.RPDL182del	NM_006160.3	NP_006151.3	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	---	---	---	---
LINC00669	647946	broad.mit.edu	37	18	37248431	37248454	+	lincRNA	DEL	AGGGAGGAAGGAAGGAAGGAAGGA	AGGGAGGAAGGAAGGAAGGAAGGA	-	rs374466776|rs200479778|rs140841760|rs150930477|rs200157609|rs371433352		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.chr18:37248431_37248454delAGGGAGGAAGGAAGGAAGGAAGGA	ENST00000591629.1	-	0	282					NR_024391.1				long intergenic non-protein coding RNA 669																		ggagggagggagggaggaaggaaggaaggaaggaaggaaggaag	0.402																																						ENST00000591629.1																			0																																																			0							g.chr18:37248431_37248454delAGGGAGGAAGGAAGGAAGGAAGGA	AK090603, BG220862, DB038664		18q12.2-q12.3	2012-10-12				ENSG00000267374		"""Long non-coding RNAs"""	44332	non-coding RNA	RNA, long non-coding							Standard	NR_024391		Approved		uc002lak.1				18.37:g.37248431_37248454delAGGGAGGAAGGAAGGAAGGAAGGA								NR_024391.1						0	282	-									RNA	DEL	ENST00000591629.1	37																																																																																						0.402	LINC00669-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000441462.1	NR_024391		4	6						4	6	---	---	---	---
ARFGAP3	26286	broad.mit.edu	37	22	43213780	43213780	+	Frame_Shift_Del	DEL	T	T	-	rs552164906		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.chr22:43213780delT	ENST00000263245.5	-	10	1115	c.896delA	c.(895-897)aatfs	p.N299fs	ARFGAP3_ENST00000429508.2_Frame_Shift_Del_p.N227fs|ARFGAP3_ENST00000437119.2_Frame_Shift_Del_p.N255fs	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	299					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|protein secretion (GO:0009306)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						TGAGTCAACATTTTTTTTGCC	0.363																																					GBM(58;544 1030 21460 27159 48838)	ENST00000263245.5																			0				breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						c.(895-897)atfs		ADP-ribosylation factor GTPase activating protein 3							317.0	285.0	296.0					22																	43213780		2203	4300	6503	SO:0001589	frameshift_variant	26286				intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport	cytosol|Golgi membrane	ARF GTPase activator activity|protein transporter activity|zinc ion binding	g.chr22:43213780delT	AK002083	CCDS14042.1, CCDS46722.1	22q13.2	2009-11-30	2002-08-20	2002-08-23	ENSG00000242247	ENSG00000242247		"""ADP-ribosylation factor GTPase activating proteins"""	661	protein-coding gene	gene with protein product		612439	"""ADP-ribosylation factor GTPase activating protein 1"""	ARFGAP1		10704287, 11172815	Standard	NM_014570		Approved		uc003bdd.2	Q9NP61	OTTHUMG00000150718	ENST00000263245.5:c.896delA	22.37:g.43213780delT	ENSP00000263245:p.Asn299fs					ARFGAP3_ENST00000429508.2_Frame_Shift_Del_p.N227fs|ARFGAP3_ENST00000437119.2_Frame_Shift_Del_p.N255fs	p.N299fs	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN			10	1115	-			299					E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Frame_Shift_Del	DEL	ENST00000263245.5	37	c.896delA	CCDS14042.1																																																																																				0.363	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570		7	389						7	389	---	---	---	---
