#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_BAM_File	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_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	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_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ABCC12	94160	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	48173117	48173117	+	Missense_Mutation	SNP	G	G	A	rs141109408		TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr16:48173117G>A	ENST00000311303.3	-	5	1133	c.788C>T	c.(787-789)gCt>gTt	p.A263V	ABCC12_ENST00000416054.1_Missense_Mutation_p.A263V|ABCC12_ENST00000448542.1_Missense_Mutation_p.A263V	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	263	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.A263V(1)		NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				CCCGATGAGAGCTGTGGGCCC	0.473																																																	1	Substitution - Missense(1)	kidney(1)											132.0	121.0	125.0					16																	48173117		2201	4300	6501	SO:0001583	missense	94160			AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.788C>T	16.37:g.48173117G>A	ENSP00000311030:p.Ala263Val		Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	G	31	5.065508	0.93898	.	.	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000416054	D;D;D	0.89196	-2.48;-2.48;-2.48	5.74	5.74	0.90152	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.93187	0.7830	M	0.68952	2.095	0.80722	D	1	D;D	0.64830	0.994;0.989	D;D	0.66602	0.919;0.945	D	0.90907	0.4773	10	0.25751	T	0.34	.	18.6963	0.91601	0.0:0.0:1.0:0.0	.	263;263	Q96J65-2;Q96J65	.;MRP9_HUMAN	V	263	ENSP00000311030:A263V;ENSP00000401855:A263V;ENSP00000413046:A263V	ENSP00000311030:A263V	A	-	2	0	ABCC12	46730618	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	7.446000	0.80609	2.683000	0.91414	0.655000	0.94253	GCT		0.473	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1		NM_033226	
ACAD11	84129	broad.mit.edu;hgsc.bcm.edu	37	3	132323956	132323956	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr3:132323956C>G	ENST00000264990.6	-	12	2479	c.1508G>C	c.(1507-1509)tGc>tCc	p.C503S	ACAD11_ENST00000355458.3_Missense_Mutation_p.C503S|ACAD11_ENST00000545291.1_Missense_Mutation_p.C28S	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11	503					fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)	p.C503S(1)		breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						CATACAGAAGCAAGAGGTAAT	0.453																																																	1	Substitution - Missense(1)	kidney(1)											163.0	150.0	154.0					3																	132323956		2203	4300	6503	SO:0001583	missense	84129			BC019607	CCDS3074.1	3q22.1	2010-04-30	2010-04-30		ENSG00000240303	ENSG00000240303			30211	protein-coding gene	gene with protein product		614288	"""acyl-Coenzyme A dehydrogenase family, member 11"""				Standard	NM_032169		Approved	FLJ12592		Q709F0	OTTHUMG00000159780	ENST00000264990.6:c.1508G>C	3.37:g.132323956C>G	ENSP00000264990:p.Cys503Ser		Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Missense_Mutation	SNP	ENST00000264990.6	37	CCDS3074.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.529205	0.64860	.	.	ENSG00000240303	ENST00000355458;ENST00000264990;ENST00000545291	D;D;D	0.95272	-3.66;-3.66;-3.66	4.95	0.811	0.18739	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	.	.	.	.	D	0.91915	0.7440	L	0.42487	1.325	0.80722	D	1	P	0.42123	0.771	P	0.44623	0.455	D	0.87620	0.2509	9	0.52906	T	0.07	.	11.4652	0.50235	0.1291:0.5342:0.3366:0.0	.	503	Q709F0	ACD11_HUMAN	S	503;503;28	ENSP00000347636:C503S;ENSP00000264990:C503S;ENSP00000446263:C28S	ENSP00000264990:C503S	C	-	2	0	ACAD11	133806646	1.000000	0.71417	0.514000	0.27761	0.979000	0.70002	1.625000	0.37029	-0.161000	0.10983	0.655000	0.94253	TGC		0.453	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2		NM_032169	
AGFG2	3268	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	100160277	100160277	+	Silent	SNP	C	C	T	rs146791629		TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr7:100160277C>T	ENST00000300176.4	+	8	1181	c.1059C>T	c.(1057-1059)ggC>ggT	p.G353G	AGFG2_ENST00000474713.1_3'UTR|AGFG2_ENST00000262935.4_3'UTR	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	353					regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.G353G(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCGGCGGCGGCGGCAGCAGCA	0.657																																																	1	Substitution - coding silent(1)	kidney(1)						C		2,4402	4.2+/-10.8	0,2,2200	25.0	27.0	26.0		1059	-0.8	0.0	7	dbSNP_134	26	0,8600		0,0,4300	no	coding-synonymous	AGFG2	NM_006076.4		0,2,6500	TT,TC,CC		0.0,0.0454,0.0154		353/482	100160277	2,13002	2202	4300	6502	SO:0001819	synonymous_variant	3268			AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"""ADP-ribosylation factor GTPase activating proteins"""	5177	protein-coding gene	gene with protein product		604019	"""HIV-1 Rev binding protein-like"""	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.1059C>T	7.37:g.100160277C>T			O75429|Q96AB9|Q96GL4	Silent	SNP	ENST00000300176.4	37	CCDS5697.1	.	.	.	.	.	.	.	.	.	.	C	5.664	0.307043	0.10733	4.54E-4	0.0	ENSG00000106351	ENST00000429987	.	.	.	0.377	-0.753	0.11068	.	.	.	.	.	T	0.23492	0.0568	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.26643	-1.0097	3	.	.	.	-65.4676	.	.	.	.	.	.	.	V	95	.	.	A	+	2	0	AGFG2	99998213	0.025000	0.19082	0.003000	0.11579	0.316000	0.28119	0.342000	0.19926	-0.370000	0.08016	0.271000	0.19318	GCG		0.657	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1		NM_006076	
ALPK2	115701	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	56202373	56202373	+	Silent	SNP	T	T	C			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr18:56202373T>C	ENST00000361673.3	-	5	5259	c.5046A>G	c.(5044-5046)aaA>aaG	p.K1682K	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1682						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.K1043K(1)|p.K1682K(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCCTGGACTTTTTCGCACAGC	0.547																																																	2	Substitution - coding silent(2)	kidney(2)											71.0	76.0	74.0					18																	56202373		2203	4300	6503	SO:0001819	synonymous_variant	115701			AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.5046A>G	18.37:g.56202373T>C			Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																				0.547	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1		NM_052947	
BCAR1	9564	broad.mit.edu;hgsc.bcm.edu	37	16	75269312	75269312	+	Missense_Mutation	SNP	C	C	A	rs540154029	byFrequency	TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr16:75269312C>A	ENST00000162330.5	-	5	1611	c.1485G>T	c.(1483-1485)gaG>gaT	p.E495D	BCAR1_ENST00000546196.1_Missense_Mutation_p.E466D|BCAR1_ENST00000535626.2_Missense_Mutation_p.E347D|BCAR1_ENST00000542031.2_Missense_Mutation_p.E493D|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000420641.3_Missense_Mutation_p.E513D|BCAR1_ENST00000538440.2_Missense_Mutation_p.E495D|BCAR1_ENST00000418647.3_Missense_Mutation_p.E541D|BCAR1_ENST00000393422.2_Missense_Mutation_p.E513D|BCAR1_ENST00000393420.6_Missense_Mutation_p.E513D	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	495	Ser-rich.				actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.E495D(1)|p.E513D(1)|p.E541D(1)		breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		GCTCCTGTGGCTCAGAGGGGC	0.697													C|||	4	0.000798722	0.0	0.0	5008	,	,		15049	0.0		0.0	False		,,,				2504	0.0041																3	Substitution - Missense(3)	kidney(3)											14.0	17.0	16.0					16																	75269312		2176	4266	6442	SO:0001583	missense	9564			AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"""Cas scaffolding proteins"""	971	protein-coding gene	gene with protein product	"""Crk-associated substrate"", ""Cas scaffolding protein family member 1"""	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.1485G>T	16.37:g.75269312C>A	ENSP00000162330:p.Glu495Asp		B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Missense_Mutation	SNP	ENST00000162330.5	37	CCDS10915.1	.	.	.	.	.	.	.	.	.	.	C	7.230	0.599057	0.13939	.	.	ENSG00000050820	ENST00000162330;ENST00000393422;ENST00000420641;ENST00000538440;ENST00000418647;ENST00000535626;ENST00000393420;ENST00000542031;ENST00000546196	T;T;T;T;T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92;1.92;1.92;1.92;1.92	3.97	1.76	0.24704	Serine rich protein interaction (1);	0.253027	0.30732	N	0.008993	T	0.26159	0.0638	L	0.31420	0.93	0.26936	N	0.966368	P;P;P;P;P;P;P;P;P	0.45044	0.849;0.557;0.849;0.818;0.609;0.849;0.557;0.849;0.612	D;P;D;D;P;D;P;D;P	0.70935	0.971;0.532;0.971;0.95;0.516;0.971;0.607;0.971;0.642	T	0.25572	-1.0128	10	0.07030	T	0.85	-24.3624	3.0456	0.06152	0.1807:0.5367:0.1763:0.1064	.	513;347;541;493;513;513;495;495;285	B4DIW5;F5GXV6;E9PCL5;F5GXA2;F8WA69;E9PCV2;F5H7Z0;P56945;B3KWE2	.;.;.;.;.;.;.;BCAR1_HUMAN;.	D	495;513;513;495;541;347;513;493;466	ENSP00000162330:E495D;ENSP00000377074:E513D;ENSP00000392708:E513D;ENSP00000443841:E495D;ENSP00000391669:E541D;ENSP00000440370:E347D;ENSP00000377072:E513D;ENSP00000440415:E493D;ENSP00000442161:E466D	ENSP00000162330:E495D	E	-	3	2	BCAR1	73826813	0.991000	0.36638	0.882000	0.34594	0.030000	0.12068	0.569000	0.23638	0.775000	0.33450	-0.514000	0.04452	GAG		0.697	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1		NM_014567	
BCL7A	605	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	122492742	122492742	+	Silent	SNP	G	G	C			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr12:122492742G>C	ENST00000261822.4	+	5	677	c.471G>C	c.(469-471)tcG>tcC	p.S157S	BCL7A_ENST00000538010.1_Silent_p.S157S	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	157					negative regulation of transcription, DNA-templated (GO:0045892)			p.S157S(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		CACAGTCCTCGATGGAACATT	0.552			T	MYC	BNHL						OREG0022214	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									GBM(17;197 467 16477 23242 44349)			Dom	yes		12	12q24.1	605	B-cell CLL/lymphoma 7A		L	1	Substitution - coding silent(1)	kidney(1)											125.0	132.0	130.0					12																	122492742		2203	4300	6503	SO:0001819	synonymous_variant	605			X89984	CCDS9226.1, CCDS53841.1	12q24.1	2008-07-03			ENSG00000110987	ENSG00000110987			1004	protein-coding gene	gene with protein product		601406		BCL7		8605326, 9931421	Standard	NM_020993		Approved		uc001ubo.3	Q4VC05	OTTHUMG00000168951	ENST00000261822.4:c.471G>C	12.37:g.122492742G>C		1519	B4DJN6|B7ZB21|Q13843|Q14CT7	Silent	SNP	ENST00000261822.4	37	CCDS53841.1																																																																																				0.552	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1			
BIRC6	57448	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	32689778	32689778	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr2:32689778G>T	ENST00000421745.2	+	25	5277	c.5143G>T	c.(5143-5145)Gca>Tca	p.A1715S		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1715					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.A1687S(1)|p.A1715S(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					ACCCAATGAAGCAGTTTCCGT	0.458																																					Pancreas(94;175 1509 16028 18060 45422)												2	Substitution - Missense(2)	kidney(2)											144.0	136.0	139.0					2																	32689778		2203	4300	6503	SO:0001583	missense	57448			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.5143G>T	2.37:g.32689778G>T	ENSP00000393596:p.Ala1715Ser		Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	18.32	3.597866	0.66332	.	.	ENSG00000115760	ENST00000421745	T	0.74737	-0.87	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.68201	0.2975	L	0.42245	1.32	0.58432	D	0.999999	P	0.37466	0.596	B	0.29785	0.107	T	0.70375	-0.4889	10	0.54805	T	0.06	.	20.1551	0.98106	0.0:0.0:1.0:0.0	.	1715	Q9NR09	BIRC6_HUMAN	S	1715	ENSP00000393596:A1715S	ENSP00000393596:A1715S	A	+	1	0	BIRC6	32543282	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.876000	0.87215	2.760000	0.94817	0.655000	0.94253	GCA		0.458	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3		NM_016252	
PROSER1	80209	hgsc.bcm.edu;ucsc.edu	37	13	39587067	39587067	+	Frame_Shift_Del	DEL	G	G	-			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr13:39587067delG	ENST00000352251.3	-	11	3155	c.2322delC	c.(2320-2322)ttcfs	p.F774fs	PROSER1_ENST00000350125.3_Frame_Shift_Del_p.F752fs|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	774	Ser-rich.																GAGTAACAGAGAAAAGTGAGG	0.527																																																	0													119.0	125.0	123.0					13																	39587067		2203	4300	6503	SO:0001589	frameshift_variant	0			AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 23"""	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.2322delC	13.37:g.39587067delG	ENSP00000332034:p.Phe774fs		A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Frame_Shift_Del	DEL	ENST00000352251.3	37	CCDS9368.2																																																																																				0.527	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5		NM_025138	
KIAA0930	23313	hgsc.bcm.edu	37	22	45601731	45601731	+	Silent	SNP	C	C	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr22:45601731C>A	ENST00000336156.5	-	3	344	c.279G>T	c.(277-279)ctG>ctT	p.L93L	KIAA0930_ENST00000443310.3_Silent_p.L75L|KIAA0930_ENST00000251993.7_Silent_p.L98L|KIAA0930_ENST00000391627.2_Silent_p.L59L	NM_001009880.1	NP_001009880.1	Q6ICG6	K0930_HUMAN	KIAA0930	93								p.L98L(1)		endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|urinary_tract(1)	15						CAGGGTCTCCCAGGCCTGGCA	0.647																																																	1	Substitution - coding silent(1)	kidney(1)											59.0	53.0	55.0					22																	45601731		2203	4300	6503	SO:0001819	synonymous_variant	0			AK025608	CCDS33665.1, CCDS33666.1	22q13.31	2011-02-23	2011-02-23	2011-02-23	ENSG00000100364	ENSG00000100364			1314	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 9"""	C22orf9		10231032	Standard	NM_015264		Approved	bK268H5.C22.1	uc003bfw.1	Q6ICG6	OTTHUMG00000151263	ENST00000336156.5:c.279G>T	22.37:g.45601731C>A			B0QY17|B0QY19|B3KT48|Q6ZVE5|Q7Z6K9|Q8IZ76|Q9Y2E2	Silent	SNP	ENST00000336156.5	37	CCDS33665.1																																																																																				0.647	KIAA0930-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321975.2		NM_001009880	
CALHM1	255022	hgsc.bcm.edu	37	10	105218252	105218259	+	Frame_Shift_Del	DEL	AGCGGCCG	AGCGGCCG	-	rs4918016|rs576980684|rs386747134|rs151031063|rs2986017	byFrequency	TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	AGCGGCCG	AGCGGCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr10:105218252_105218259delAGCGGCCG	ENST00000329905.5	-	1	386_393	c.250_257delCGGCCGCT	c.(250-258)cggccgctgfs	p.RPL84fs	RP11-225H22.4_ENST00000411906.1_RNA	NM_001001412.3	NP_001001412.3	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	84					ATP transport (GO:0015867)|cation transport (GO:0006812)|protein homooligomerization (GO:0051260)|regulation of ion transmembrane transport (GO:0034765)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|identical protein binding (GO:0042802)|voltage-gated ion channel activity (GO:0005244)			large_intestine(2)|liver(1)|lung(5)|ovary(1)	9						CCGGCGGCCCAGCGGCCGCTTCCACTCT	0.663																																																	0			GRCh37	CM082516	CALHM1	M																																				SO:0001589	frameshift_variant	255022			BC036208	CCDS7550.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000185933	ENSG00000185933			23494	protein-coding gene	gene with protein product		612234	"""family with sequence similarity 26, member C"""	FAM26C		18585350	Standard	NM_001001412		Approved		uc001kxe.2	Q8IU99	OTTHUMG00000018991	ENST00000329905.5:c.250_257delCGGCCGCT	10.37:g.105218252_105218259delAGCGGCCG	ENSP00000329926:p.Arg84fs		Q5W091	Frame_Shift_Del	DEL	ENST00000329905.5	37	CCDS7550.1																																																																																				0.663	CALHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050165.1		NM_001001412	
CCDC89	220388	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	85396828	85396828	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr11:85396828C>T	ENST00000316398.3	-	1	492	c.346G>A	c.(346-348)Ggt>Agt	p.G116S	CREBZF_ENST00000534224.1_5'Flank|CREBZF_ENST00000531515.1_5'Flank	NM_152723.1	NP_689936.1	Q8N998	CCD89_HUMAN	coiled-coil domain containing 89	116						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.G116S(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	15		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				CTGTACTCACCCTGGGCCTTG	0.532																																																	1	Substitution - Missense(1)	kidney(1)											114.0	89.0	98.0					11																	85396828		2203	4299	6502	SO:0001583	missense	220388			AK095478	CCDS8270.1	11q14.1	2006-03-16			ENSG00000179071	ENSG00000179071			26762	protein-coding gene	gene with protein product						12477932	Standard	NM_152723		Approved	FLJ38159	uc001pau.1	Q8N998	OTTHUMG00000166976	ENST00000316398.3:c.346G>A	11.37:g.85396828C>T	ENSP00000320649:p.Gly116Ser			Missense_Mutation	SNP	ENST00000316398.3	37	CCDS8270.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.437215	0.01098	.	.	ENSG00000179071	ENST00000316398	.	.	.	5.44	-1.58	0.08479	.	0.907596	0.09432	N	0.802917	T	0.08802	0.0218	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30851	-0.9964	8	.	.	.	6.566	2.3695	0.04327	0.2379:0.0675:0.2473:0.4473	.	116	Q8N998	CCD89_HUMAN	S	116	.	.	G	-	1	0	CCDC89	85074476	0.600000	0.26899	0.001000	0.08648	0.003000	0.03518	0.852000	0.27764	-0.566000	0.06054	-1.087000	0.02190	GGT		0.532	CCDC89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392182.1		NM_152723	
CDK17	5128	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	96683053	96683053	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr12:96683053G>A	ENST00000261211.3	-	11	1613	c.1010C>T	c.(1009-1011)gCc>gTc	p.A337V	CDK17_ENST00000553042.1_5'UTR|CDK17_ENST00000542666.1_Missense_Mutation_p.A284V|CDK17_ENST00000543119.2_Missense_Mutation_p.A337V	NM_001170464.2|NM_002595.4	NP_001163935.1|NP_002586.2	Q00537	CDK17_HUMAN	cyclin-dependent kinase 17	337	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)	p.A337V(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(11)|ovary(4)|prostate(2)|skin(1)	37						AACTGACTTGGCTCGGGCTAG	0.443																																																	1	Substitution - Missense(1)	kidney(1)											183.0	158.0	167.0					12																	96683053		2203	4300	6503	SO:0001583	missense	5128				CCDS9061.1, CCDS53819.1	12q23.1	2011-11-08	2009-12-16	2009-12-16		ENSG00000059758		"""Cyclin-dependent kinases"""	8750	protein-coding gene	gene with protein product		603440	"""PCTAIRE protein kinase 2"""	PCTK2		9370357, 19884882	Standard	NM_001170464		Approved	PCTAIRE2	uc009ztk.3	Q00537		ENST00000261211.3:c.1010C>T	12.37:g.96683053G>A	ENSP00000261211:p.Ala337Val		A8K1U6|B2RCQ2|Q8NEB8	Missense_Mutation	SNP	ENST00000261211.3	37	CCDS9061.1	.	.	.	.	.	.	.	.	.	.	G	35	5.523989	0.96431	.	.	ENSG00000059758	ENST00000261211;ENST00000543119;ENST00000542666	T;T;T	0.64991	-0.13;-0.13;-0.13	5.29	5.29	0.74685	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.67646	0.2915	N	0.17901	0.54	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.65323	0.934;0.934	T	0.72750	-0.4199	10	0.87932	D	0	-6.3589	19.2862	0.94072	0.0:0.0:1.0:0.0	.	337;337	A8K1U6;Q00537	.;CDK17_HUMAN	V	337;337;284	ENSP00000261211:A337V;ENSP00000444459:A337V;ENSP00000442926:A284V	ENSP00000261211:A337V	A	-	2	0	CDK17	95207184	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.813000	0.99286	2.621000	0.88768	0.563000	0.77884	GCC		0.443	CDK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408751.1		NM_002595	
CES5A	221223	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	55907817	55907817	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr16:55907817G>A	ENST00000290567.9	-	2	327	c.206C>T	c.(205-207)tCc>tTc	p.S69F	CES5A_ENST00000518005.1_5'UTR|CES5A_ENST00000520435.1_Missense_Mutation_p.S69F|CES5A_ENST00000521992.1_Missense_Mutation_p.S98F|CES5A_ENST00000319165.9_Missense_Mutation_p.S69F|CES5A_ENST00000541580.1_Intron	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	69						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)	p.S69F(1)|p.S98F(1)		breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						AAATCGCAGGGATCCCAGCGG	0.602																																																	2	Substitution - Missense(2)	kidney(2)											78.0	72.0	74.0					16																	55907817		2198	4300	6498	SO:0001583	missense	221223			AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"""Carboxylesterases"""	26459	protein-coding gene	gene with protein product			"""carboxylesterase 7"""	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.206C>T	16.37:g.55907817G>A	ENSP00000290567:p.Ser69Phe		B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.094575	0.56075	.	.	ENSG00000159398	ENST00000521992;ENST00000319165;ENST00000290567;ENST00000520435	T;T;T;T	0.08807	3.05;3.05;3.05;3.05	5.7	1.21	0.21127	Carboxylesterase, type B (1);	0.768149	0.11565	N	0.551350	T	0.08802	0.0218	L	0.49571	1.57	0.09310	N	1	P;B	0.35894	0.526;0.396	B;B	0.37304	0.246;0.155	T	0.29397	-1.0013	10	0.87932	D	0	.	4.6796	0.12729	0.1634:0.0:0.4245:0.4121	.	69;69	Q6NT32;Q6NT32-2	EST5A_HUMAN;.	F	98;69;69;69	ENSP00000428864:S98F;ENSP00000324271:S69F;ENSP00000290567:S69F;ENSP00000428887:S69F	ENSP00000290567:S69F	S	-	2	0	CES5A	54465318	0.073000	0.21202	0.001000	0.08648	0.111000	0.19643	2.064000	0.41432	0.411000	0.25702	0.655000	0.94253	TCC		0.602	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3		NM_145024	
CHSY1	22856	hgsc.bcm.edu	37	15	101717654	101717655	+	Frame_Shift_Ins	INS	-	-	C			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr15:101717654_101717655insC	ENST00000254190.3	-	3	2822_2823	c.2347_2348insG	c.(2347-2349)gaafs	p.E783fs	CHSY1_ENST00000543813.1_5'UTR	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	783					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of ossification (GO:0030279)|response to nutrient levels (GO:0031667)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			ATCATTTTTTTCCAGCCACATC	0.436																																																	0																																										SO:0001589	frameshift_variant	22856			AB023207	CCDS10390.1	15q26.3	2013-02-19	2008-01-24	2008-01-24	ENSG00000131873	ENSG00000131873	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	17198	protein-coding gene	gene with protein product		608183	"""carbohydrate (chondroitin) synthase 1"""			11514575	Standard	NM_014918		Approved	KIAA0990, CSS1	uc021sxt.1	Q86X52	OTTHUMG00000149873	ENST00000254190.3:c.2348dupG	15.37:g.101717656_101717656dupC	ENSP00000254190:p.Glu783fs		Q6UX38|Q7LFU5|Q9Y2J5	Frame_Shift_Ins	INS	ENST00000254190.3	37	CCDS10390.1																																																																																				0.436	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1		NM_014918	
CLINT1	9685	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	157232998	157232998	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr5:157232998G>T	ENST00000411809.2	-	7	1022	c.818C>A	c.(817-819)aCc>aAc	p.T273N	CLINT1_ENST00000523094.1_Missense_Mutation_p.T255N|CLINT1_ENST00000530742.1_Missense_Mutation_p.T255N|CLINT1_ENST00000296951.5_Missense_Mutation_p.T255N|CLINT1_ENST00000523908.1_Missense_Mutation_p.T273N	NM_014666.3	NP_055481.1	Q14677	EPN4_HUMAN	clathrin interactor 1	273					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|lipid binding (GO:0008289)	p.T255N(2)		breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|urinary_tract(1)	21	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTTGTGTCTGGTTGTGGTGGT	0.478																																					Colon(22;427 587 2170 6147 14291)												2	Substitution - Missense(2)	kidney(2)											263.0	266.0	265.0					5																	157232998		2150	4244	6394	SO:0001583	missense	9685			AF434813	CCDS47330.1, CCDS56388.1, CCDS56389.1	5q33.3	2006-06-13			ENSG00000113282	ENSG00000113282			23186	protein-coding gene	gene with protein product		607265				12213833, 12429846	Standard	NM_014666		Approved	ENTH, KIAA0171, EPNR, CLINT	uc011ddv.2	Q14677	OTTHUMG00000163527	ENST00000411809.2:c.818C>A	5.37:g.157232998G>T	ENSP00000388340:p.Thr273Asn		B7Z6F8|D3DQJ6|Q8NAF1|Q96E05	Missense_Mutation	SNP	ENST00000411809.2	37	CCDS47330.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.735753	0.69189	.	.	ENSG00000113282	ENST00000523094;ENST00000530742;ENST00000411809;ENST00000296951;ENST00000523908	T;T;T;T;T	0.49139	0.8;0.8;0.83;0.8;0.79	5.63	5.63	0.86233	.	0.043535	0.85682	D	0.000000	T	0.41026	0.1141	L	0.55990	1.75	0.51012	D	0.999909	B;P	0.40794	0.28;0.729	B;B	0.39258	0.156;0.295	T	0.17623	-1.0363	10	0.17369	T	0.5	-13.1452	11.12	0.48284	0.0709:0.1302:0.7989:0.0	.	273;273	B7Z6F8;Q14677	.;EPN4_HUMAN	N	255;255;273;255;273	ENSP00000429345:T255N;ENSP00000433419:T255N;ENSP00000388340:T273N;ENSP00000296951:T255N;ENSP00000429824:T273N	ENSP00000296951:T255N	T	-	2	0	CLINT1	157165576	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	4.189000	0.58358	2.656000	0.90262	0.557000	0.71058	ACC		0.478	CLINT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374001.1		NM_014666	
DDX25	29118	broad.mit.edu	37	11	125786947	125786947	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr11:125786947C>T	ENST00000263576.6	+	9	994	c.839C>T	c.(838-840)gCa>gTa	p.A280V	RP11-680F20.9_ENST00000533033.2_RNA|DDX25_ENST00000525943.1_3'UTR	NM_013264.4	NP_037396.3	Q9UHL0	DDX25_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 25	280	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)	p.A280V(1)|p.A166V(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)	10	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0203)|Lung NSC(97;0.0203)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.14e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.046)		CTCTTTTCAGCAACCTTTGAG	0.493																																																	2	Substitution - Missense(2)	kidney(2)											102.0	100.0	101.0					11																	125786947		2069	4206	6275	SO:0001583	missense	29118			AF155140	CCDS44766.1	11q24	2012-02-23	2012-02-23		ENSG00000109832	ENSG00000109832		"""DEAD-boxes"""	18698	protein-coding gene	gene with protein product	"""gonadotropin-regulated testicular RNA helicase"""	607663	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 25"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 25"""			10608860, 15096601	Standard	NM_013264		Approved	GRTH	uc001qcz.5	Q9UHL0	OTTHUMG00000165859	ENST00000263576.6:c.839C>T	11.37:g.125786947C>T	ENSP00000263576:p.Ala280Val		B2R6Z0|Q5XVN2|Q86W81|Q8IYP1	Missense_Mutation	SNP	ENST00000263576.6	37	CCDS44766.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.650195	0.67472	.	.	ENSG00000109832	ENST00000525943;ENST00000263576;ENST00000526875	T;T	0.32272	1.46;2.58	5.79	5.79	0.91817	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.60547	0.2277	H	0.95780	3.72	0.80722	D	1	D;D	0.63880	0.993;0.993	P;P	0.50352	0.638;0.638	T	0.74598	-0.3612	10	0.87932	D	0	-7.6423	19.6367	0.95736	0.0:1.0:0.0:0.0	.	280;280	B4DHI6;Q9UHL0	.;DDX25_HUMAN	V	166;280;146	ENSP00000263576:A280V;ENSP00000436087:A146V	ENSP00000263576:A280V	A	+	2	0	DDX25	125292157	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	7.412000	0.80091	2.735000	0.93741	0.655000	0.94253	GCA		0.493	DDX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386736.3		NM_013264	
DNAH9	1770	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	11757612	11757612	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr17:11757612C>A	ENST00000262442.4	+	50	9868	c.9800C>A	c.(9799-9801)tCc>tAc	p.S3267Y	DNAH9_ENST00000454412.2_Missense_Mutation_p.S3267Y	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3267	Stalk. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.S3267Y(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GGCCTCTGCTCCTGGGTCATC	0.547																																																	1	Substitution - Missense(1)	kidney(1)											119.0	117.0	118.0					17																	11757612		2203	4300	6503	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.9800C>A	17.37:g.11757612C>A	ENSP00000262442:p.Ser3267Tyr		A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	17.51	3.406725	0.62399	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.80304	-1.36;-1.36	5.55	5.55	0.83447	Dynein heavy chain, coiled coil stalk (1);	0.121587	0.56097	D	0.000022	D	0.92414	0.7592	M	0.92691	3.335	0.80722	D	1	D	0.63880	0.993	D	0.72075	0.976	D	0.93406	0.6764	10	0.87932	D	0	.	19.6941	0.96016	0.0:1.0:0.0:0.0	.	3267	Q9NYC9	DYH9_HUMAN	Y	3267;3267;1849	ENSP00000262442:S3267Y;ENSP00000414874:S3267Y	ENSP00000262442:S3267Y	S	+	2	0	DNAH9	11698337	1.000000	0.71417	0.983000	0.44433	0.281000	0.26958	7.278000	0.78587	2.885000	0.99019	0.655000	0.94253	TCC		0.547	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2		NM_001372	
DSCR10	259234	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	39580489	39580489	+	lincRNA	SNP	G	G	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr21:39580489G>A	ENST00000432141.1	+	0	611					NR_027695.1		P59022	DSC10_HUMAN	Down syndrome critical region gene 10 (non-protein coding)																		GTCACTGTGTGTCACCTTCAA	0.507																																																	0													346.0	312.0	323.0					21																	39580489		2203	4300	6503			259234			AB066291		21q22.13	2012-10-16	2011-02-24		ENSG00000233316	ENSG00000233316		"""Long non-coding RNAs"""	16302	non-coding RNA	RNA, long non-coding			"""Down syndrome critical region gene 10"""			12168953	Standard	NR_027695		Approved		uc010gnt.2	P59022	OTTHUMG00000090611		21.37:g.39580489G>A			Q52LN2	RNA	SNP	ENST00000432141.1	37																																																																																					0.507	DSCR10-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000207199.1		NR_027695.1	
FAM122C	159091	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	133941717	133941717	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chrX:133941717C>A	ENST00000370784.4	+	1	495	c.89C>A	c.(88-90)gCc>gAc	p.A30D	FAM122C_ENST00000475361.1_3'UTR|FAM122C_ENST00000414371.2_Missense_Mutation_p.A66D|FAM122C_ENST00000445123.1_5'UTR|FAM122C_ENST00000370785.3_Missense_Mutation_p.A30D	NM_001170779.1	NP_001164250.1	Q6P4D5	F222C_HUMAN	family with sequence similarity 122C	30								p.A30D(2)		endometrium(2)|kidney(1)|lung(2)	5	Acute lymphoblastic leukemia(192;0.000127)					GTCAACAGTGCCCCTTTGATC	0.532																																																	2	Substitution - Missense(2)	kidney(2)											80.0	68.0	72.0					X																	133941717		2203	4300	6503	SO:0001583	missense	159091			BC017868	CCDS14644.1, CCDS55500.1, CCDS55501.1, CCDS76028.1	Xq26.3	2008-02-05	2006-07-11		ENSG00000156500	ENSG00000156500			25202	protein-coding gene	gene with protein product						12477932	Standard	NM_138819		Approved	RP3-473B4.1	uc004exz.2	Q6P4D5	OTTHUMG00000022716	ENST00000370784.4:c.89C>A	X.37:g.133941717C>A	ENSP00000359820:p.Ala30Asp		F5H036|Q8WVK9	Missense_Mutation	SNP	ENST00000370784.4	37	CCDS55501.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.037388	0.54896	.	.	ENSG00000156500	ENST00000414371;ENST00000370784;ENST00000370785	T;T;T	0.58060	0.36;0.36;0.36	4.44	-1.26	0.09376	.	0.296367	0.36200	N	0.002727	T	0.41719	0.1171	L	0.58510	1.815	0.19775	N	0.999952	B;B;B;B	0.27679	0.185;0.185;0.185;0.185	B;B;B;B	0.29716	0.106;0.106;0.106;0.106	T	0.37384	-0.9708	10	0.87932	D	0	.	3.9335	0.09296	0.1659:0.4001:0.0:0.434	.	66;30;30;30	F5H036;Q6P4D5;Q6P4D5-2;Q6P187	.;F222C_HUMAN;.;.	D	66;30;30	ENSP00000402477:A66D;ENSP00000359820:A30D;ENSP00000359821:A30D	ENSP00000359820:A30D	A	+	2	0	FAM122C	133769383	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.231000	0.09069	-0.562000	0.06086	-0.232000	0.12228	GCC		0.532	FAM122C-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			NM_138819	
LECT2	3950	hgsc.bcm.edu	37	5	135276202	135276204	+	5'UTR	DEL	GTT	GTT	-	rs553770840|rs1160982|rs568134250	byFrequency	TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr5:135276202_135276204delGTT	ENST00000471827.1	-	0	557_559				FBXL21_ENST00000297158.9_RNA|FBXL21_ENST00000467490.1_RNA|LECT2_ENST00000522943.1_Intron			O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2						chemotaxis (GO:0006935)|negative regulation of Wnt signaling pathway (GO:0030178)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	identical protein binding (GO:0042802)			large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGCACTTACAGTTGTTTTTATCA	0.291														3677	0.734225	0.6437	0.7637	5008	,	,		15660	0.7817		0.7078	False		,,,				2504	0.8139																0										2327,1203		774,779,212						-5.4	1.0		dbSNP_87	50	5563,2261		2004,1555,353	no	coding	FBXL21	NM_012159.4		2778,2334,565	A1A1,A1R,RR		28.8983,34.0793,30.5091				7890,3464				SO:0001623	5_prime_UTR_variant	26223			AB007546	CCDS4190.1	5q31.1	2008-05-15			ENSG00000145826	ENSG00000145826			6550	protein-coding gene	gene with protein product		602882				9545637	Standard	NM_002302		Approved	chm-II, chm2	uc003lbe.1	O14960	OTTHUMG00000129146	ENST00000471827.1:c.-255AAC>-	5.37:g.135276205_135276207delGTT			B2RA90|O14565|Q52M49	In_Frame_Del	DEL	ENST00000471827.1	37																																																																																					0.291	LECT2-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000342497.1		NM_002302	
FCRL5	83416	hgsc.bcm.edu	37	1	157485438	157485438	+	3'UTR	DEL	A	A	-			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr1:157485438delA	ENST00000361835.3	-	0	3118				FCRL5_ENST00000356953.4_3'UTR|FCRL5_ENST00000461387.1_5'UTR	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5						negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				GCAGAGGCTGAAACAGCAGTT	0.532																																																	0													135.0	151.0	146.0					1																	157485438		2203	4300	6503	SO:0001624	3_prime_UTR_variant	83416			AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.*27T>-	1.37:g.157485438delA			A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Frame_Shift_Del	DEL	ENST00000361835.3	37	CCDS1165.1																																																																																				0.532	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1		NM_031281	
GALK2	2585	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	49611861	49611861	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr15:49611861T>C	ENST00000560031.1	+	9	1335	c.1028T>C	c.(1027-1029)cTc>cCc	p.L343P	GALK2_ENST00000327171.3_Missense_Mutation_p.L332P|GALK2_ENST00000561014.1_3'UTR|GALK2_ENST00000543495.1_3'UTR|GALK2_ENST00000544523.1_Missense_Mutation_p.L319P|GALK2_ENST00000396509.2_Missense_Mutation_p.L319P|GALK2_ENST00000559454.1_Missense_Mutation_p.L319P			Q01415	GALK2_HUMAN	galactokinase 2	343					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)	p.L332P(1)|p.L343P(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)		GCGCGAGTGCTCCAGTTTAAG	0.507																																																	2	Substitution - Missense(2)	kidney(2)											92.0	84.0	87.0					15																	49611861		2196	4295	6491	SO:0001583	missense	2585				CCDS32236.1, CCDS42034.1, CCDS73724.1	15q21.1-q21.2	2013-09-20			ENSG00000156958	ENSG00000156958	2.7.1.6		4119	protein-coding gene	gene with protein product		137028					Standard	XM_005254279		Approved	GK2	uc001zxj.1	Q01415	OTTHUMG00000172325	ENST00000560031.1:c.1028T>C	15.37:g.49611861T>C	ENSP00000453129:p.Leu343Pro		Q7Z4Q4	Missense_Mutation	SNP	ENST00000560031.1	37	CCDS42034.1	.	.	.	.	.	.	.	.	.	.	T	14.49	2.550791	0.45383	.	.	ENSG00000156958	ENST00000327171;ENST00000396509;ENST00000544523	D;D	0.87256	-2.23;-2.22	5.89	5.89	0.94794	.	0.119478	0.64402	D	0.000017	D	0.93288	0.7861	M	0.85859	2.78	0.80722	D	1	D;B	0.63880	0.993;0.185	P;B	0.60886	0.88;0.089	D	0.94056	0.7322	10	0.66056	D	0.02	-17.8486	16.3043	0.82842	0.0:0.0:0.0:1.0	.	343;332	Q01415;Q7Z4Q4	GALK2_HUMAN;.	P	332;343;319	ENSP00000316632:L332P;ENSP00000440312:L319P	ENSP00000316632:L332P	L	+	2	0	GALK2	47399153	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.070000	0.57548	2.231000	0.72958	0.533000	0.62120	CTC		0.507	GALK2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417854.1			
GRIN3B	116444	hgsc.bcm.edu	37	19	1007860	1007861	+	Frame_Shift_Ins	INS	-	-	C	rs545736648	byFrequency	TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr19:1007860_1007861insC	ENST00000234389.3	+	5	2223_2224	c.2204_2205insC	c.(2203-2208)gaccccfs	p.DP735fs		NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	735					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AGCAGGAGCGACCCCCCCAAGC	0.708													|||unknown(ALL_OTHER_Ns)	3	0.000599042	0.0	0.0	5008	,	,		5748	0.0		0.003	False		,,,				2504	0.0																0										21,4213		0,21,2096						3.2	1.0			17	12,8192		0,12,4090	no	frameshift	GRIN3B	NM_138690.1		0,33,6186	A1A1,A1R,RR		0.1463,0.496,0.2653				33,12405				SO:0001589	frameshift_variant	116444				CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.2211dupC	19.37:g.1007867_1007867dupC	ENSP00000234389:p.Asp735fs		Q5EAK7|Q7RTW9	Frame_Shift_Ins	INS	ENST00000234389.3	37	CCDS32861.1																																																																																				0.708	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2			
ARHGAP35	2909	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	47424189	47424189	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr19:47424189C>T	ENST00000404338.3	+	1	2257	c.2257C>T	c.(2257-2259)Caa>Taa	p.Q753*		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	753					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)	p.Q753*(2)									GCAAATCAGTCAAGTTTTGAA	0.428																																																	2	Substitution - Nonsense(2)	kidney(2)											90.0	87.0	88.0					19																	47424189		1944	4153	6097	SO:0001587	stop_gained	0			M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"""Rho GTPase activating proteins"""	4591	protein-coding gene	gene with protein product		605277	"""glucocorticoid receptor DNA binding factor 1"""	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.2257C>T	19.37:g.47424189C>T	ENSP00000385720:p.Gln753*		A7E2A4|Q14452|Q9C0E1	Nonsense_Mutation	SNP	ENST00000404338.3	37	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	C	39	7.511961	0.98329	.	.	ENSG00000160007	ENST00000317082;ENST00000404338	.	.	.	5.39	5.39	0.77823	.	0.054276	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-17.1931	18.2664	0.90053	0.0:1.0:0.0:0.0	.	.	.	.	X	753	.	ENSP00000324820:Q753X	Q	+	1	0	ARHGAP35	52116029	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	4.920000	0.63390	2.684000	0.91462	0.655000	0.94253	CAA		0.428	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1		NM_004491	
GSPT2	23708	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	51488138	51488138	+	Silent	SNP	T	T	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chrX:51488138T>A	ENST00000340438.4	+	1	1658	c.1416T>A	c.(1414-1416)gtT>gtA	p.V472V		NM_018094.4	NP_060564.2	Q8IYD1	ERF3B_HUMAN	G1 to S phase transition 2	472					cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational termination (GO:0006415)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.V472V(1)		breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Ovarian(276;0.236)					ATGTAGAAGTTCTTGGAATAC	0.433																																																	1	Substitution - coding silent(1)	kidney(1)											64.0	56.0	59.0					X																	51488138		2203	4300	6503	SO:0001819	synonymous_variant	23708			AI285711	CCDS14336.1	Xp11.22	2008-05-14			ENSG00000189369	ENSG00000189369			4622	protein-coding gene	gene with protein product		300418				10575220	Standard	NM_018094		Approved	eRF3b, FLJ10441	uc004dpl.3	Q8IYD1	OTTHUMG00000021538	ENST00000340438.4:c.1416T>A	X.37:g.51488138T>A			Q9H909|Q9NVY0|Q9NY44	Silent	SNP	ENST00000340438.4	37	CCDS14336.1																																																																																				0.433	GSPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056587.1			
HJURP	55355	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	234749963	234749963	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr2:234749963G>A	ENST00000411486.2	-	8	1528	c.1463C>T	c.(1462-1464)cCt>cTt	p.P488L	HJURP_ENST00000432087.1_Missense_Mutation_p.P434L|HJURP_ENST00000441687.1_Missense_Mutation_p.P403L|HJURP_ENST00000434039.1_5'Flank	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	488					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)	p.P488L(1)		NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		TTTGCTGGAAGGTAAACTCAG	0.527																																																	1	Substitution - Missense(1)	kidney(1)											84.0	87.0	86.0					2																	234749963		2203	4300	6503	SO:0001583	missense	55355				CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.1463C>T	2.37:g.234749963G>A	ENSP00000414109:p.Pro488Leu		A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.138904	0.37728	.	.	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924	T;T;T;T	0.28069	1.83;1.88;1.86;1.63	4.53	1.79	0.24919	.	1.134810	0.06472	N	0.731406	T	0.21631	0.0521	N	0.24115	0.695	0.09310	N	1	B;B;B	0.23735	0.09;0.09;0.054	B;B;B	0.23419	0.046;0.046;0.021	T	0.30179	-0.9987	10	0.44086	T	0.13	-0.4596	6.6315	0.22859	0.2866:0.0:0.7134:0.0	.	403;434;488	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	L	488;434;403;403	ENSP00000414109:P488L;ENSP00000407208:P434L;ENSP00000401944:P403L;ENSP00000393253:P403L	ENSP00000414109:P488L	P	-	2	0	HJURP	234414702	0.001000	0.12720	0.001000	0.08648	0.107000	0.19398	0.625000	0.24477	0.423000	0.26033	0.655000	0.94253	CCT		0.527	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6		NM_018410	
HOMEZ	57594	hgsc.bcm.edu	37	14	23745517	23745518	+	Frame_Shift_Ins	INS	-	-	G			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr14:23745517_23745518insG	ENST00000357460.5	-	2	1083_1084	c.919_920insC	c.(919-921)cagfs	p.Q307fs	HOMEZ_ENST00000431326.2_Frame_Shift_Ins_p.Q309fs|HOMEZ_ENST00000561013.1_Frame_Shift_Ins_p.Q309fs	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	307					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		GCCTAGTGGCTGGAGGGGTTTA	0.54																																																	0																																										SO:0001589	frameshift_variant	57594			AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.920dupC	14.37:g.23745519_23745519dupG	ENSP00000350049:p.Gln307fs		A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Frame_Shift_Ins	INS	ENST00000357460.5	37	CCDS45085.1																																																																																				0.540	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2		NM_020834	
HSPG2	3339	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	22168731	22168731	+	Splice_Site	SNP	C	C	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr1:22168731C>T	ENST00000374695.3	-	68	9132		c.e68+1			NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2						angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.?(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCCATACTCACGGTAGGAAGA	0.652																																																	1	Unknown(1)	kidney(1)											54.0	52.0	53.0					1																	22168731		2203	4300	6503	SO:0001630	splice_region_variant	3339			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.9052+1G>A	1.37:g.22168731C>T			Q16287|Q5SZI3|Q9H3V5	Splice_Site	SNP	ENST00000374695.3	37	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.580352	0.46006	.	.	ENSG00000142798	ENST00000374695	.	.	.	4.95	3.97	0.46021	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4558	0.61197	0.0:0.8417:0.1583:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HSPG2	22041318	1.000000	0.71417	1.000000	0.80357	0.523000	0.34469	4.215000	0.58534	2.276000	0.75962	0.462000	0.41574	.		0.652	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1		NM_005529	Intron
IL17RA	23765	hgsc.bcm.edu	37	22	17589955	17589955	+	Missense_Mutation	SNP	G	G	A	rs375421722		TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr22:17589955G>A	ENST00000319363.6	+	13	1979	c.1846G>A	c.(1846-1848)Ggc>Agc	p.G616S		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	616					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)			endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		TCCGGGAACCGGCATCGTGAA	0.647																																																	0								G	SER/GLY	0,4364		0,0,2182	10.0	9.0	9.0		1846	3.0	0.0	22		9	1,8547		0,1,4273	no	missense	IL17RA	NM_014339.5	56	0,1,6455	AA,AG,GG		0.0117,0.0,0.0077	probably-damaging	616/867	17589955	1,12911	2182	4274	6456	SO:0001583	missense	23765			U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"""Interleukins and interleukin receptors"", ""CD molecules"""	5985	protein-coding gene	gene with protein product		605461	"""interleukin 17 receptor"""	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.1846G>A	22.37:g.17589955G>A	ENSP00000320936:p.Gly616Ser		O43844|Q20WK1	Missense_Mutation	SNP	ENST00000319363.6	37	CCDS13739.1	.	.	.	.	.	.	.	.	.	.	G	17.21	3.332649	0.60853	0.0	1.17E-4	ENSG00000177663	ENST00000425985;ENST00000319363	T	0.08102	3.13	5.1	2.97	0.34412	.	0.421756	0.26383	N	0.024681	T	0.16041	0.0386	M	0.67953	2.075	0.09310	N	1	D;D	0.69078	0.997;0.991	P;P	0.56088	0.791;0.627	T	0.07233	-1.0783	10	0.30854	T	0.27	-25.8352	6.8933	0.24243	0.1455:0.0:0.7146:0.14	.	564;616	D3YTB4;Q96F46	.;I17RA_HUMAN	S	564;616	ENSP00000320936:G616S	ENSP00000320936:G616S	G	+	1	0	IL17RA	15969955	0.698000	0.27777	0.010000	0.14722	0.043000	0.13939	1.202000	0.32271	0.636000	0.30508	0.561000	0.74099	GGC		0.647	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1		NM_014339	
IWS1	55677	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	128252517	128252517	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr2:128252517A>C	ENST00000295321.4	-	8	1989	c.1730T>G	c.(1729-1731)tTg>tGg	p.L577W	IWS1_ENST00000455721.2_3'UTR|AC010976.2_ENST00000599001.1_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	577	Interaction with SUPT6H and ALYREF.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.L577W(1)		cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		TTGATTGTTCAACTGTCTGTC	0.259																																																	1	Substitution - Missense(1)	kidney(1)											77.0	82.0	80.0					2																	128252517		2201	4292	6493	SO:0001583	missense	55677			AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.1730T>G	2.37:g.128252517A>C	ENSP00000295321:p.Leu577Trp		Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Missense_Mutation	SNP	ENST00000295321.4	37	CCDS2146.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.406193	0.83230	.	.	ENSG00000163166	ENST00000295321;ENST00000433551	T	0.52526	0.66	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.71392	0.3334	M	0.83774	2.66	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	T	0.74682	-0.3583	10	0.52906	T	0.07	-3.9598	16.1809	0.81898	1.0:0.0:0.0:0.0	.	577	Q96ST2	IWS1_HUMAN	W	577;530	ENSP00000295321:L577W	ENSP00000295321:L577W	L	-	2	0	IWS1	127968987	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	9.281000	0.95811	2.229000	0.72834	0.383000	0.25322	TTG		0.259	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2		NM_017969	
KDM5C	8242	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	53228213	53228213	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chrX:53228213C>A	ENST00000375401.3	-	15	2721	c.2189G>T	c.(2188-2190)tGc>tTc	p.C730F	KDM5C_ENST00000404049.3_Missense_Mutation_p.C729F|KDM5C_ENST00000375379.3_Missense_Mutation_p.C730F|KDM5C_ENST00000465402.1_5'Flank|KDM5C_ENST00000375383.3_Missense_Mutation_p.C689F|KDM5C_ENST00000452825.3_Missense_Mutation_p.C663F	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	730					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|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)	p.C663F(1)|p.C730F(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						GTGGGAAAGGCAGACAAGGCC	0.572			"""N, F, S"""		clear cell renal carcinoma																																			Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	2	Substitution - Missense(2)	kidney(2)											141.0	107.0	118.0					X																	53228213		2203	4300	6503	SO:0001583	missense	8242			Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11114	protein-coding gene	gene with protein product		314690	"""Jumonji, AT rich interactive domain 1C (RBP2-like)"", ""Smcy homolog, X-linked (mouse)"", ""jumonji, AT rich interactive domain 1C"", ""mental retardation, X-linked 13"""	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.2189G>T	X.37:g.53228213C>A	ENSP00000364550:p.Cys730Phe		B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Missense_Mutation	SNP	ENST00000375401.3	37	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	c	21.9	4.219087	0.79464	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	D;D;D;D;D	0.99791	-6.76;-6.76;-6.76;-6.76;-6.76	4.69	4.69	0.59074	Zinc finger, C5HC2-type (1);	0.000000	0.85682	D	0.000000	D	0.99799	0.9914	M	0.92738	3.34	0.80722	D	1	D;D;D	0.61697	0.99;0.973;0.973	D;D;D	0.69824	0.943;0.966;0.966	D	0.96827	0.9608	10	0.87932	D	0	-4.307	14.2463	0.65990	0.0:1.0:0.0:0.0	.	663;729;730	F5H3T1;B0QZ44;P41229	.;.;KDM5C_HUMAN	F	663;730;729;730;689	ENSP00000445176:C663F;ENSP00000364550:C730F;ENSP00000385394:C729F;ENSP00000364528:C730F;ENSP00000364532:C689F	ENSP00000364528:C730F	C	-	2	0	KDM5C	53244938	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.716000	0.84723	1.935000	0.56089	0.519000	0.50382	TGC		0.572	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2		NM_004187	
MTCL1	23255	broad.mit.edu	37	18	8786001	8786001	+	Missense_Mutation	SNP	G	G	T	rs373511257		TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr18:8786001G>T	ENST00000306329.11	+	6	2879	c.2879G>T	c.(2878-2880)cGc>cTc	p.R960L	SOGA2_ENST00000306285.7_5'UTR|SOGA2_ENST00000517570.1_Missense_Mutation_p.R600L|SOGA2_ENST00000400050.3_Missense_Mutation_p.R600L|SOGA2_ENST00000359865.3_Missense_Mutation_p.R600L														p.R600L(1)									GAGAGCCTGCGCCTCCGAGCC	0.692																																																	1	Substitution - Missense(1)	kidney(1)											14.0	16.0	16.0					18																	8786001		2190	4266	6456	SO:0001583	missense	0																														ENST00000306329.11:c.2879G>T	18.37:g.8786001G>T	ENSP00000305027:p.Arg960Leu			Missense_Mutation	SNP	ENST00000306329.11	37		.	.	.	.	.	.	.	.	.	.	G	8.706	0.910787	0.17833	.	.	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050	T;T;T	0.39997	1.05;1.05;1.05	5.29	1.18	0.20946	.	0.583503	0.15639	N	0.251969	T	0.25865	0.0630	L	0.29908	0.895	0.26514	N	0.974546	P;P	0.42620	0.678;0.785	B;B	0.37346	0.125;0.247	T	0.12319	-1.0552	10	0.21540	T	0.41	-2.3846	9.2781	0.37711	0.5502:0.0:0.4498:0.0	.	621;600	A8MQ54;Q9Y4B5-3	.;.	L	621;600;600;600	ENSP00000429556:R600L;ENSP00000352927:R600L;ENSP00000382924:R600L	ENSP00000305027:R621L	R	+	2	0	CCDC165	8776001	0.013000	0.17824	0.000000	0.03702	0.105000	0.19272	0.808000	0.27154	-0.088000	0.12506	-0.150000	0.13652	CGC		0.692	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			
KIF1B	23095	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	10363881	10363881	+	Intron	SNP	G	G	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr1:10363881G>T	ENST00000377086.1	+	22	2317				KIF1B_ENST00000377081.1_Intron|KIF1B_ENST00000263934.6_Intron|KIF1B_ENST00000377083.1_Missense_Mutation_p.A880S|RN7SL731P_ENST00000584329.1_RNA|KIF1B_ENST00000377093.4_Missense_Mutation_p.A880S			O60333	KIF1B_HUMAN	kinesin family member 1B						anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.A880S(1)		breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		GCCTGTTGGTGCTGGTGTTAG	0.438																																																	1	Substitution - Missense(1)	kidney(1)											45.0	49.0	48.0					1																	10363881		2203	4300	6503	SO:0001627	intron_variant	23095			AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.2115+6577G>T	1.37:g.10363881G>T			A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		.	.	.	.	.	.	.	.	.	.	G	0.188	-1.055978	0.01965	.	.	ENSG00000054523	ENST00000377093;ENST00000377083	T;T	0.72942	-0.7;-0.7	5.47	3.58	0.41010	.	.	.	.	.	T	0.56688	0.2002	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.51741	-0.8667	8	0.26408	T	0.33	.	12.2836	0.54779	0.1249:0.0:0.8751:0.0	.	880	O60333-3	.	S	880	ENSP00000366297:A880S;ENSP00000366287:A880S	ENSP00000366287:A880S	A	+	1	0	KIF1B	10286468	0.998000	0.40836	0.064000	0.19789	0.032000	0.12392	3.947000	0.56652	2.553000	0.86117	0.655000	0.94253	GCT		0.438	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			
L1TD1	54596	hgsc.bcm.edu	37	1	62676248	62676251	+	Frame_Shift_Del	DEL	AACT	AACT	-	rs202029696	byFrequency	TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	AACT	AACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr1:62676248_62676251delAACT	ENST00000498273.1	+	4	2097_2100	c.1802_1805delAACT	c.(1801-1806)gaactafs	p.EL601fs	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	601										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						CACACAGAAGAACTAACATCCaaa	0.348														29	0.00579073	0.0	0.0043	5008	,	,		23431	0.0		0.0179	False		,,,				2504	0.0082																0									,	16,4250		1,14,2118					,	-0.2	0.0			38	119,8135		7,105,4015	no	frameshift,frameshift	L1TD1	NM_019079.4,NM_001164835.1	,	8,119,6133	A1A1,A1R,RR		1.4417,0.3751,1.0783	,	,		135,12385				SO:0001589	frameshift_variant	54596			BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1802_1805delAACT	1.37:g.62676248_62676251delAACT	ENSP00000419901:p.Glu601fs		Q8NDA1|Q9NUV8|Q9NV78	Frame_Shift_Del	DEL	ENST00000498273.1	37	CCDS619.1																																																																																				0.348	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1		NM_019079	
LAMB2	3913	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	49160288	49160288	+	Silent	SNP	G	G	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr3:49160288G>A	ENST00000418109.1	-	28	4586	c.4422C>T	c.(4420-4422)ctC>ctT	p.L1474L	USP19_ENST00000417901.1_5'Flank|USP19_ENST00000398892.3_5'Flank|LAMB2_ENST00000464891.1_5'Flank|USP19_ENST00000488993.1_5'Flank|LAMB2_ENST00000305544.4_Silent_p.L1474L|USP19_ENST00000434032.2_5'Flank|USP19_ENST00000453664.1_5'Flank|USP19_ENST00000398888.2_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1474	Domain I.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.L1474L(1)		NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCACTCTGCTGAGGATGCTAC	0.662																																																	1	Substitution - coding silent(1)	kidney(1)											62.0	62.0	62.0					3																	49160288		2203	4300	6503	SO:0001819	synonymous_variant	3913				CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.4422C>T	3.37:g.49160288G>A			Q16321	Silent	SNP	ENST00000418109.1	37	CCDS2789.1																																																																																				0.662	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1		NM_002292	
LRRC37A16P	651250	broad.mit.edu	37	17	66123801	66123801	+	RNA	SNP	C	C	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr17:66123801C>A	ENST00000590019.1	-	0	371									leucine rich repeat containing 37, member A16, pseudogene																		TTTGAAGGGCCTTTTCTGGAT	0.537																																																	0																																												0					17q24.2	2012-10-18				ENSG00000267023			43820	pseudogene	pseudogene							Standard	NG_023507		Approved				OTTHUMG00000180160		17.37:g.66123801C>A				RNA	SNP	ENST00000590019.1	37																																																																																					0.537	LRRC37A16P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000450078.1			
LRRK2	120892	hgsc.bcm.edu;ucsc.edu	37	12	40702937	40702937	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr12:40702937C>A	ENST00000298910.7	+	30	4277	c.4219C>A	c.(4219-4221)Cat>Aat	p.H1407N		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1407	Roc. {ECO:0000255|PROSITE- ProRule:PRU00758}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.H1407N(2)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TACTCATCCCCATTTTATGAC	0.378																																																	2	Substitution - Missense(2)	kidney(2)											96.0	92.0	93.0					12																	40702937		2203	4300	6503	SO:0001583	missense	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.4219C>A	12.37:g.40702937C>A	ENSP00000298910:p.His1407Asn		A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.380267	0.61845	.	.	ENSG00000188906	ENST00000298910	T	0.80304	-1.36	5.63	5.63	0.86233	ROC GTPase (1);Small GTP-binding protein domain (1);Mitochondrial Rho-like (1);	0.000000	0.85682	D	0.000000	D	0.86314	0.5903	L	0.41632	1.29	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	D	0.84484	0.0607	10	0.36615	T	0.2	.	19.6816	0.95965	0.0:1.0:0.0:0.0	.	1407;1407	Q17RV3;Q5S007	.;LRRK2_HUMAN	N	1407	ENSP00000298910:H1407N	ENSP00000298910:H1407N	H	+	1	0	LRRK2	38989204	1.000000	0.71417	0.998000	0.56505	0.806000	0.45545	7.335000	0.79234	2.654000	0.90174	0.655000	0.94253	CAT		0.378	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1		XM_058513	
MALAT1	378938	broad.mit.edu;hgsc.bcm.edu	37	11	65273309	65273309	+	lincRNA	SNP	A	A	G			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr11:65273309A>G	ENST00000534336.1	+	0	8077					NR_002819.2		Q9UHZ2	MALAT_HUMAN	metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)																		CATGTTCAAGAACTGTAATGC	0.398																																																	0													120.0	113.0	115.0					11																	65273309		874	1988	2862			378938			AF001540		11q13.1	2013-12-11	2007-11-20		ENSG00000251562	ENSG00000251562		"""Long non-coding RNAs"", ""-"""	29665	non-coding RNA	RNA, long non-coding	"""metastasis associated in lung adenocarcinoma transcript 1"", ""non-protein coding RNA 47"", ""hepcarcin"", ""nuclear enriched abundant transcript 2"", ""nuclear paraspeckle assembly transcript 2 (non-protein coding)"", ""long intergenic non-protein coding RNA 47"""	607924				12970751, 22560368	Standard	NR_002819		Approved	PRO1073, MALAT-1, NCRNA00047, HCN, NEAT2, LINC00047, mascRNA	uc010roh.3	Q9UHZ2	OTTHUMG00000166322		11.37:g.65273309A>G				RNA	SNP	ENST00000534336.1	37																																																																																					0.398	MALAT1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000389143.1		NR_002819	
MTHFR	4524	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	11855302	11855302	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr1:11855302C>A	ENST00000376592.1	-	5	1012	c.884G>T	c.(883-885)cGc>cTc	p.R295L	MTHFR_ENST00000376585.1_Missense_Mutation_p.R336L|MTHFR_ENST00000376590.3_Missense_Mutation_p.R295L|MTHFR_ENST00000376583.3_Missense_Mutation_p.R336L			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	295					blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)	p.R295L(1)		NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	GCCATAGTTGCGGATGGCAGC	0.582																																																	1	Substitution - Missense(1)	kidney(1)											107.0	99.0	101.0					1																	11855302		2203	4300	6503	SO:0001583	missense	4524			BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.884G>T	1.37:g.11855302C>A	ENSP00000365777:p.Arg295Leu		B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Missense_Mutation	SNP	ENST00000376592.1	37	CCDS137.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892619	0.91889	.	.	ENSG00000177000	ENST00000376592;ENST00000376583;ENST00000376590;ENST00000376585	D;D;D;D	0.92299	-3.01;-3.01;-3.01;-3.01	4.97	4.06	0.47325	.	0.049455	0.85682	D	0.000000	D	0.95667	0.8591	M	0.87971	2.92	0.58432	D	0.999993	P;D	0.55172	0.948;0.97	P;P	0.62184	0.887;0.899	D	0.95912	0.8924	10	0.87932	D	0	.	12.5744	0.56355	0.0:0.9192:0.0:0.0808	.	295;336	P42898;Q5SNW6	MTHR_HUMAN;.	L	295;336;295;336	ENSP00000365777:R295L;ENSP00000365767:R336L;ENSP00000365775:R295L;ENSP00000365770:R336L	ENSP00000365767:R336L	R	-	2	0	MTHFR	11777889	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.399000	0.66314	1.222000	0.43521	0.462000	0.41574	CGC		0.582	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1		NM_005957	
MST1L	11223	broad.mit.edu	37	1	17085795	17085795	+	RNA	SNP	G	G	T	rs1057379	byFrequency	TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr1:17085795G>T	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.I332I(2)|p.I342I(2)									TACAACGCCGGATCTGGTAGC	0.687																																																	4	Substitution - coding silent(4)	kidney(2)|endometrium(2)																																										0			U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17085795G>T			B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																					0.687	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1		NM_001271733	
MUC16	94025	broad.mit.edu	37	19	9067792	9067792	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	T	T	T	C	T	T	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr19:9067792T>C	ENST00000397910.4	-	3	19857	c.19654A>G	c.(19654-19656)Acc>Gcc	p.T6552A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6554	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.T6552A(2)|p.T2185A(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATATCTGTGGTCTTCACTAGG	0.478																																																	3	Substitution - Missense(3)	kidney(3)											88.0	78.0	81.0					19																	9067792		1920	4118	6038	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.19654A>G	19.37:g.9067792T>C	ENSP00000381008:p.Thr6552Ala		Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	5.068	0.198141	0.09652	.	.	ENSG00000181143	ENST00000397910	T	0.27104	1.69	1.47	1.47	0.22746	.	.	.	.	.	T	0.20659	0.0497	L	0.52573	1.65	.	.	.	B	0.24368	0.102	B	0.18263	0.021	T	0.22243	-1.0222	8	0.87932	D	0	.	5.0941	0.14723	0.0:0.0:0.0:1.0	.	6552	B5ME49	.	A	6552	ENSP00000381008:T6552A	ENSP00000381008:T6552A	T	-	1	0	MUC16	8928792	0.000000	0.05858	0.003000	0.11579	0.034000	0.12701	-0.001000	0.12947	0.944000	0.37579	0.149000	0.16113	ACC		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1		NM_024690	
MYL9	10398	broad.mit.edu	37	20	35177531	35177531	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr20:35177531G>A	ENST00000279022.2	+	4	502	c.398G>A	c.(397-399)cGc>cAc	p.R133H	RP5-977B1.11_ENST00000561134.1_RNA|RP5-977B1.7_ENST00000439595.1_RNA|MYL9_ENST00000346786.2_Missense_Mutation_p.R79H|RP5-977B1.7_ENST00000425233.1_RNA	NM_006097.4	NP_006088.2	P24844	MYL9_HUMAN	myosin, light chain 9, regulatory	133	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				axon guidance (GO:0007411)|muscle contraction (GO:0006936)|platelet aggregation (GO:0070527)|regulation of muscle contraction (GO:0006937)	cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)	p.R133H(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(2)	8	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				ATGGGTGACCGCTTCACAGAT	0.572																																																	1	Substitution - Missense(1)	kidney(1)											102.0	88.0	93.0					20																	35177531		2203	4300	6503	SO:0001583	missense	10398			J02854	CCDS13276.1, CCDS13277.1	20q11.23	2013-01-10	2006-09-29		ENSG00000101335	ENSG00000101335		"""Myosins / Light chain"", ""EF-hand domain containing"""	15754	protein-coding gene	gene with protein product	"""myosin regulatory light chain 2, smooth muscle isoform"", ""myosin regulatory light chain 1"""	609905	"""myosin, light polypeptide 9, regulatory"""			2526655	Standard	NM_006097		Approved	MYRL2, MLC2, LC20, MRLC1	uc002xfl.2	P24844	OTTHUMG00000032387	ENST00000279022.2:c.398G>A	20.37:g.35177531G>A	ENSP00000279022:p.Arg133His		E1P5T6|Q9BQL9|Q9BUF9|Q9H136	Missense_Mutation	SNP	ENST00000279022.2	37	CCDS13276.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.516496	0.85495	.	.	ENSG00000101335	ENST00000279022;ENST00000346786	T;T	0.79141	-1.24;-1.18	4.7	4.7	0.59300	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.79627	0.4478	M	0.84156	2.68	0.80722	D	1	B;B	0.26775	0.001;0.159	B;B	0.20184	0.0;0.028	T	0.80830	-0.1207	10	0.66056	D	0.02	.	16.5838	0.84722	0.0:0.0:1.0:0.0	.	79;133	Q9BUF9;P24844	.;MYL9_HUMAN	H	133;79	ENSP00000279022:R133H;ENSP00000217313:R79H	ENSP00000279022:R133H	R	+	2	0	MYL9	34610945	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	9.759000	0.98931	2.317000	0.78254	0.655000	0.94253	CGC		0.572	MYL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079015.2		NM_006097	
NTSR1	4923	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	61341142	61341142	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr20:61341142G>A	ENST00000370501.3	+	1	954	c.583G>A	c.(583-585)Gcc>Acc	p.A195T		NM_002531.2	NP_002522.2	P30989	NTR1_HUMAN	neurotensin receptor 1 (high affinity)	195					adult locomotory behavior (GO:0008344)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)	p.A195T(2)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(16)|prostate(1)|skin(3)	27	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;3.63e-06)			CATCTGGCTCGCCTCGGCCCT	0.667																																					GBM(37;400 780 6403 19663 35669)												2	Substitution - Missense(2)	lung(1)|kidney(1)											67.0	55.0	59.0					20																	61341142		2203	4300	6503	SO:0001583	missense	4923				CCDS13502.1	20q13	2012-08-08			ENSG00000101188	ENSG00000101188		"""GPCR / Class A : Neurotensin receptors"""	8039	protein-coding gene	gene with protein product		162651				8075503	Standard	NM_002531		Approved	NTR	uc002ydf.3	P30989	OTTHUMG00000032932	ENST00000370501.3:c.583G>A	20.37:g.61341142G>A	ENSP00000359532:p.Ala195Thr		Q9H4H1|Q9H4T5	Missense_Mutation	SNP	ENST00000370501.3	37	CCDS13502.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.575434	0.45902	.	.	ENSG00000101188	ENST00000370501	T	0.72835	-0.69	5.15	3.03	0.35002	GPCR, rhodopsin-like superfamily (1);	0.272196	0.33732	N	0.004601	T	0.58466	0.2124	L	0.48642	1.525	0.36981	D	0.894291	B	0.20368	0.044	B	0.16722	0.016	T	0.57154	-0.7860	10	0.30078	T	0.28	-34.4698	7.1983	0.25866	0.0773:0.13:0.6743:0.1185	.	195	P30989	NTR1_HUMAN	T	195	ENSP00000359532:A195T	ENSP00000359532:A195T	A	+	1	0	NTSR1	60811587	0.994000	0.37717	0.995000	0.50966	0.995000	0.86356	2.210000	0.42816	1.170000	0.42753	0.561000	0.74099	GCC		0.667	NTSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080061.1			
OR5I1	10798	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	55703464	55703464	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr11:55703464A>C	ENST00000301532.3	-	1	412	c.413T>G	c.(412-414)aTg>aGg	p.M138R		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	138					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M138R(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						GCCCCTAGACATCACAACTGT	0.438																																																	1	Substitution - Missense(1)	kidney(1)											76.0	79.0	78.0					11																	55703464		2201	4295	6496	SO:0001583	missense	10798			BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"""GPCR / Class A : Olfactory receptors"""	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.413T>G	11.37:g.55703464A>C	ENSP00000301532:p.Met138Arg		Q6IEU4	Missense_Mutation	SNP	ENST00000301532.3	37	CCDS7949.1	.	.	.	.	.	.	.	.	.	.	A	14.76	2.630392	0.46944	.	.	ENSG00000167825	ENST00000301532	T	0.00601	6.29	4.94	3.8	0.43715	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000020	T	0.04634	0.0126	H	0.97852	4.09	0.36041	D	0.840122	D	0.55800	0.973	D	0.66196	0.942	T	0.01269	-1.1400	10	0.87932	D	0	.	9.1148	0.36750	0.9113:0.0:0.0887:0.0	.	138	Q13606	OR5I1_HUMAN	R	138	ENSP00000301532:M138R	ENSP00000301532:M138R	M	-	2	0	OR5I1	55460040	1.000000	0.71417	0.828000	0.32881	0.456000	0.32438	4.590000	0.61013	0.819000	0.34492	0.519000	0.50382	ATG		0.438	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1		NM_006637	
OR10W1	81341	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	58034733	58034733	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr11:58034733C>T	ENST00000395079.2	-	1	999	c.598G>A	c.(598-600)Gtg>Atg	p.V200M		NM_207374.3	NP_997257.2	Q8NGF6	O10W1_HUMAN	olfactory receptor, family 10, subfamily W, member 1	200						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V200M(1)		kidney(2)|large_intestine(2)|lung(19)|ovary(2)|skin(1)	26		Breast(21;0.0589)				AAGAAAGGCACAGCAATGGCT	0.547																																																	1	Substitution - Missense(1)	kidney(1)											105.0	88.0	93.0					11																	58034733		2201	4295	6496	SO:0001583	missense	81341			AB065850	CCDS7968.1	11q12.1	2012-08-09	2004-03-04	2004-03-05		ENSG00000172772		"""GPCR / Class A : Olfactory receptors"""	15139	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily W, member 1 pseudogene"""	OR10W1P			Standard	NM_207374		Approved		uc001nmq.1	Q8NGF6		ENST00000395079.2:c.598G>A	11.37:g.58034733C>T	ENSP00000378516:p.Val200Met		A2RUD2|A8MTE1|Q6UXQ2	Missense_Mutation	SNP	ENST00000395079.2	37	CCDS7968.1	.	.	.	.	.	.	.	.	.	.	c	12.45	1.941847	0.34283	.	.	ENSG00000172772	ENST00000395079	T	0.40225	1.04	5.86	1.01	0.19927	GPCR, rhodopsin-like superfamily (1);	0.575172	0.14732	N	0.301707	T	0.37865	0.1019	L	0.60845	1.875	0.09310	N	1	B	0.31125	0.309	B	0.33620	0.167	T	0.38394	-0.9663	10	0.66056	D	0.02	.	8.1651	0.31222	0.0:0.6231:0.1774:0.1996	.	200	Q8NGF6	O10W1_HUMAN	M	200	ENSP00000378516:V200M	ENSP00000378516:V200M	V	-	1	0	OR10W1	57791309	0.000000	0.05858	0.897000	0.35233	0.931000	0.56810	-1.527000	0.02227	0.833000	0.34828	-0.126000	0.14955	GTG		0.547	OR10W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394704.1		NM_207374	
PAX3	5077	broad.mit.edu;hgsc.bcm.edu	37	2	223066808	223066808	+	Silent	SNP	C	C	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr2:223066808C>A	ENST00000350526.4	-	8	1411	c.1275G>T	c.(1273-1275)gtG>gtT	p.V425V	PAX3_ENST00000392069.2_Silent_p.V425V|PAX3_ENST00000409551.3_Silent_p.V424V|PAX3_ENST00000336840.6_Intron|PAX3_ENST00000464706.1_5'UTR|PAX3_ENST00000344493.4_Intron|PAX3_ENST00000392070.2_Silent_p.V425V	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	425					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V425V(1)	PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCTGGCCGACACCGTGGTGG	0.572			T	"""FOXO1A, NCOA1"""	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																																	Dom	yes		2	2q35	5077	paired box gene 3	yes	M	1	Substitution - coding silent(1)	kidney(1)											101.0	90.0	94.0					2																	223066808		2203	4300	6503	SO:0001819	synonymous_variant	5077				CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"""Paired boxes"", ""Homeoboxes / PRD class"""	8617	protein-coding gene	gene with protein product		606597	"""Waardenburg syndrome 1"", ""paired box gene 3 (Waardenburg syndrome 1)"""	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.1275G>T	2.37:g.223066808C>A			G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Silent	SNP	ENST00000350526.4	37	CCDS42826.1																																																																																				0.572	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52595787	52595787	+	Nonsense_Mutation	SNP	A	A	C			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr3:52595787A>C	ENST00000296302.7	-	25	4285	c.4284T>G	c.(4282-4284)taT>taG	p.Y1428*	PBRM1_ENST00000337303.4_Nonsense_Mutation_p.Y1428*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.Y1443*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.Y1443*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.Y1428*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.Y1396*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.Y1403*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.Y1376*|RNU6ATAC16P_ENST00000408591.1_RNA|SMIM4_ENST00000476842.1_Intron			Q86U86	PB1_HUMAN	polybromo 1	1428					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.Y1428*(2)|p.Y1396*(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		ATTTACCTTCATATTCTGCTT	0.498			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	3	Substitution - Nonsense(3)	kidney(3)											265.0	270.0	268.0					3																	52595787		2203	4300	6503	SO:0001587	stop_gained	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.4284T>G	3.37:g.52595787A>C	ENSP00000296302:p.Tyr1428*		A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	A	42	9.572483	0.99208	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351	.	.	.	5.89	2.25	0.28309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.4144	8.4849	0.33065	0.72:0.0:0.28:0.0	.	.	.	.	X	1396;1376;1428;1428;1428;1403;1443;1443;1427	.	ENSP00000296302:Y1428X	Y	-	3	2	PBRM1	52570827	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.286000	0.43496	0.477000	0.27464	0.455000	0.32223	TAT		0.498	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PGPEP1L	145814	hgsc.bcm.edu	37	15	99511804	99511805	+	Frame_Shift_Ins	INS	-	-	C	rs398043625|rs5814919	byFrequency	TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr15:99511804_99511805insC	ENST00000378919.6	-	5	698_699	c.493_494insG	c.(493-495)gtcfs	p.V165fs	RP11-654A16.3_ENST00000559468.1_RNA|PGPEP1L_ENST00000535714.1_Frame_Shift_Ins_p.V111fs	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	165							cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						CTGGATGATGACTCTCAAGGCT	0.574													C|C|CC|insertion	2217	0.442692	0.1558	0.4914	5008	,	,		17754	0.4841		0.5716	False		,,,				2504	0.6207																0									,	816,2946		112,592,1177					,	1.6	0.2		dbSNP_114	44	4130,3796		1081,1968,914	no	frameshift,frameshift	PGPEP1L	NM_001167902.1,NM_001102612.2	,	1193,2560,2091	A1A1,A1R,RR		47.893,21.6906,42.3169	,	,		4946,6742				SO:0001589	frameshift_variant	145814				CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.494dupG	15.37:g.99511805_99511805dupC	ENSP00000368199:p.Val165fs		H0YF86	Frame_Shift_Ins	INS	ENST00000378919.6	37	CCDS53977.1																																																																																				0.574	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1		NM_001102612.2	
PPFIA1	8500	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	70218604	70218604	+	Silent	SNP	T	T	C			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr11:70218604T>C	ENST00000253925.7	+	23	3278	c.3063T>C	c.(3061-3063)atT>atC	p.I1021I	PPFIA1_ENST00000530548.1_3'UTR|PPFIA1_ENST00000389547.3_Silent_p.I1021I|AP000487.5_ENST00000530690.1_RNA|AP000487.5_ENST00000500185.2_RNA	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	1021	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)	p.I1021I(1)		breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			AGTGTGGAATTATGTGCCTGA	0.323																																																	1	Substitution - coding silent(1)	kidney(1)											91.0	96.0	95.0					11																	70218604		2200	4294	6494	SO:0001819	synonymous_variant	8500			U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"""Sterile alpha motif (SAM) domain containing"""	9245	protein-coding gene	gene with protein product	"""Liprin-alpha1"""	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.3063T>C	11.37:g.70218604T>C			A6NLE3|Q13135|Q14567|Q8N4I2	Silent	SNP	ENST00000253925.7	37	CCDS31627.1																																																																																				0.323	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1		NM_003626	
PRDM13	59336	broad.mit.edu	37	6	100057184	100057184	+	Splice_Site	SNP	G	G	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr6:100057184G>A	ENST00000369215.4	+	3	702		c.e3+1			NM_021620.3	NP_067633.2	Q9H4Q3	PRD13_HUMAN	PR domain containing 13						negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.?(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(1)	17		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)		GACGAGAAAGGTACCCATTCC	0.532																																																	1	Unknown(1)	kidney(1)											56.0	62.0	60.0					6																	100057184		2135	4259	6394	SO:0001630	splice_region_variant	59336			AY004253	CCDS43487.1	6q16.2	2012-03-28			ENSG00000112238	ENSG00000112238			13998	protein-coding gene	gene with protein product							Standard	NM_021620		Approved		uc003pqg.1	Q9H4Q3	OTTHUMG00000015269	ENST00000369215.4:c.397+1G>A	6.37:g.100057184G>A			Q5TGC1|Q5TGC2	Splice_Site	SNP	ENST00000369215.4	37	CCDS43487.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.015793	0.54468	.	.	ENSG00000112238	ENST00000369215;ENST00000369214	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9252	0.92541	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PRDM13	100163905	1.000000	0.71417	1.000000	0.80357	0.339000	0.28857	9.430000	0.97488	2.579000	0.87056	0.558000	0.71614	.		0.532	PRDM13-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041619.2			Intron
RBFOX1	54715	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	7568337	7568337	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr16:7568337C>A	ENST00000550418.1	+	5	1204	c.216C>A	c.(214-216)caC>caA	p.H72Q	RBFOX1_ENST00000547338.1_Missense_Mutation_p.H72Q|RBFOX1_ENST00000553186.1_Missense_Mutation_p.H72Q|RBFOX1_ENST00000311745.5_Missense_Mutation_p.H92Q|RBFOX1_ENST00000535565.2_Missense_Mutation_p.H108Q|RBFOX1_ENST00000552089.1_Missense_Mutation_p.H108Q|RBFOX1_ENST00000355637.4_Missense_Mutation_p.H92Q|RBFOX1_ENST00000547372.1_Missense_Mutation_p.H115Q|RBFOX1_ENST00000422070.4_Missense_Mutation_p.H115Q|RBFOX1_ENST00000436368.2_Missense_Mutation_p.H92Q|RBFOX1_ENST00000340209.4_Missense_Mutation_p.H77Q	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	72					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)	p.H92Q(2)|p.H72Q(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						CCCAGACGCACTCCGAGCAGA	0.652																																					Ovarian(157;934 2567 15163 39509)												3	Substitution - Missense(3)	kidney(3)											111.0	106.0	107.0					16																	7568337		2197	4300	6497	SO:0001583	missense	54715			AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"""RNA binding motif (RRM) containing"""	18222	protein-coding gene	gene with protein product	"""ataxin 2-binding protein 1"", ""hexaribonucleotide binding protein 1"""	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.216C>A	16.37:g.7568337C>A	ENSP00000450031:p.His72Gln		Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Missense_Mutation	SNP	ENST00000550418.1	37	CCDS55983.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.158469	0.57368	.	.	ENSG00000078328	ENST00000547605;ENST00000550418;ENST00000553186;ENST00000547372;ENST00000422070;ENST00000535565;ENST00000552089;ENST00000551752;ENST00000547338;ENST00000436368;ENST00000311745;ENST00000355637;ENST00000352951;ENST00000340209	T;T;T;T;T;T;T;T;T;T;T	0.30182	2.05;1.54;1.91;1.84;1.86;1.95;1.54;1.68;1.86;1.86;1.54	4.67	3.48	0.39840	.	0.000000	0.85682	D	0.000000	T	0.50888	0.1642	M	0.66939	2.045	0.52099	D	0.999944	P;D;P;D;B;D;B;P;P	0.76494	0.913;0.998;0.93;0.999;0.389;0.987;0.389;0.643;0.562	B;D;B;D;B;D;B;B;P	0.85130	0.391;0.969;0.351;0.997;0.198;0.981;0.343;0.318;0.544	T	0.49716	-0.8910	10	0.37606	T	0.19	-13.1793	13.6593	0.62357	0.0:0.9099:0.0:0.0901	.	92;108;115;92;92;92;72;72;115	F8WAC5;F5H0M1;B7Z1U7;Q9NWB1-2;Q9NWB1-4;Q9NWB1-5;Q9NWB1-3;Q9NWB1;F8VZG9	.;.;.;.;.;.;.;RFOX1_HUMAN;.	Q	72;72;72;115;115;108;108;72;72;92;92;92;92;77	ENSP00000450402:H72Q;ENSP00000450031:H72Q;ENSP00000447753:H72Q;ENSP00000446842:H115Q;ENSP00000391269:H115Q;ENSP00000447281:H72Q;ENSP00000447717:H72Q;ENSP00000402745:H92Q;ENSP00000309117:H92Q;ENSP00000347855:H92Q;ENSP00000344196:H77Q	ENSP00000309117:H92Q	H	+	3	2	RBFOX1	7508338	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	3.370000	0.52372	2.129000	0.65627	0.557000	0.71058	CAC		0.652	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2		NM_145891	
SDK2	54549	broad.mit.edu;hgsc.bcm.edu	37	17	71344797	71344797	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr17:71344797G>A	ENST00000392650.3	-	44	6106	c.6106C>T	c.(6106-6108)Ctc>Ttc	p.L2036F	SDK2_ENST00000410094.1_5'UTR|SDK2_ENST00000388726.3_Missense_Mutation_p.L2017F	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	2036					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.L2036F(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						GCAGGGATGAGGTCGTTGTAT	0.647																																																	1	Substitution - Missense(1)	kidney(1)											76.0	66.0	69.0					17																	71344797		2203	4299	6502	SO:0001583	missense	54549			AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.6106C>T	17.37:g.71344797G>A	ENSP00000376421:p.Leu2036Phe		A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.372943	0.82573	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893;ENST00000410094	T;T;T	0.59772	0.24;0.26;1.52	4.81	4.81	0.61882	.	0.000000	0.64402	D	0.000006	T	0.54532	0.1864	L	0.44542	1.39	0.58432	D	0.999998	P;P	0.44281	0.74;0.831	B;P	0.45998	0.304;0.5	T	0.49390	-0.8945	10	0.13853	T	0.58	.	16.6634	0.85247	0.0:0.0:1.0:0.0	.	2036;2017	Q58EX2;Q58EX2-3	SDK2_HUMAN;.	F	1660;2036;2017;1193;2036;377	ENSP00000376421:L2036F;ENSP00000373378:L2017F;ENSP00000407098:L1193F	ENSP00000324967:L2036F	L	-	1	0	SDK2	68856392	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.067000	0.71193	2.204000	0.70986	0.563000	0.77884	CTC		0.647	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2		NM_019064	
SELE	6401	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	169697008	169697008	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr1:169697008G>A	ENST00000333360.7	-	9	1479	c.1340C>T	c.(1339-1341)cCt>cTt	p.P447L	SELE_ENST00000367782.4_Intron|SELE_ENST00000367779.4_Intron|SELE_ENST00000367774.1_Intron|SELE_ENST00000367781.4_Missense_Mutation_p.P384L|SELE_ENST00000367776.1_Missense_Mutation_p.P384L|SELE_ENST00000367775.1_Missense_Mutation_p.P322L|SELE_ENST00000367777.1_Intron|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367780.4_Missense_Mutation_p.P322L	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	447	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				actin filament-based process (GO:0030029)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of receptor internalization (GO:0002092)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)	caveola (GO:0005901)|coated pit (GO:0005905)|cortical cytoskeleton (GO:0030863)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	oligosaccharide binding (GO:0070492)|phospholipase binding (GO:0043274)|sialic acid binding (GO:0033691)|transmembrane signaling receptor activity (GO:0004888)	p.P447L(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				Carvedilol(DB01136)	TTCTCCAATAGGGGAATGAGC	0.488																																																	1	Substitution - Missense(1)	kidney(1)											100.0	95.0	97.0					1																	169697008		2203	4300	6503	SO:0001583	missense	6401			M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908		"""CD molecules"""	10718	protein-coding gene	gene with protein product		131210	"""endothelial adhesion molecule 1"""	ELAM1, ELAM		1375831	Standard	NM_000450		Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.1340C>T	1.37:g.169697008G>A	ENSP00000331736:p.Pro447Leu		A2RRD6|P16111	Missense_Mutation	SNP	ENST00000333360.7	37	CCDS1283.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.874730	0.51695	.	.	ENSG00000007908	ENST00000367781;ENST00000367780;ENST00000333360;ENST00000367775;ENST00000367776	T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69;-0.69	5.9	2.94	0.34122	Complement control module (2);Sushi/SCR/CCP (3);	1.436570	0.04558	N	0.391037	T	0.45438	0.1342	L	0.54908	1.71	0.20563	N	0.999884	P	0.36909	0.573	B	0.34590	0.186	T	0.35549	-0.9784	10	0.32370	T	0.25	-1.3324	6.956	0.24572	0.081:0.0:0.5874:0.3316	.	447	P16581	LYAM2_HUMAN	L	384;322;447;322;384	ENSP00000356755:P384L;ENSP00000356754:P322L;ENSP00000331736:P447L;ENSP00000356749:P322L;ENSP00000356750:P384L	ENSP00000331736:P447L	P	-	2	0	SELE	167963632	0.000000	0.05858	0.006000	0.13384	0.539000	0.34962	0.053000	0.14184	0.345000	0.23873	0.650000	0.86243	CCT		0.488	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1		NM_000450	
SETD2	29072	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	47125380	47125380	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr3:47125380C>A	ENST00000409792.3	-	12	5932	c.5890G>T	c.(5890-5892)Gag>Tag	p.E1964*	SETD2_ENST00000492397.1_5'UTR	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1964					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.E1461*(1)|p.E1964*(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CCGTTGCTCTCTTTGGGCTCT	0.443			"""N, F, S, Mis"""		clear cell renal carcinoma																																			Rec	yes		3	3p21.31	29072	SET domain containing 2		E	2	Substitution - Nonsense(2)	kidney(2)											257.0	220.0	233.0					3																	47125380		2203	4300	6503	SO:0001587	stop_gained	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5890G>T	3.37:g.47125380C>A	ENSP00000386759:p.Glu1964*		O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Nonsense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	47	13.198478	0.99726	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	.	.	.	5.69	4.81	0.61882	.	0.213333	0.32593	N	0.005889	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	14.8476	0.70272	0.0:0.9308:0.0:0.0692	.	.	.	.	X	1964	.	ENSP00000386759:E1964X	E	-	1	0	SETD2	47100384	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	2.691000	0.47010	1.387000	0.46486	0.650000	0.86243	GAG		0.443	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2		NM_014159	
SLC9A4	389015	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	103120167	103120167	+	Splice_Site	SNP	G	G	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr2:103120167G>A	ENST00000295269.4	+	3	1437		c.e3+1			NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4						epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)	p.?(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						GCATCCTGGCGTGAGTACAAA	0.433																																																	1	Unknown(1)	kidney(1)											102.0	100.0	100.0					2																	103120167		2203	4300	6503	SO:0001630	splice_region_variant	389015				CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.980+1G>A	2.37:g.103120167G>A			Q69YK0	Splice_Site	SNP	ENST00000295269.4	37	CCDS33264.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.510328	0.85389	.	.	ENSG00000180251	ENST00000295269	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0018	0.97417	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC9A4	102486599	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.813000	0.99286	2.793000	0.96121	0.655000	0.94253	.		0.433	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1		NM_001011552.3	Intron
SLC23A3	151295	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	220033819	220033819	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr2:220033819G>A	ENST00000409878.3	-	4	456	c.424C>T	c.(424-426)Ctc>Ttc	p.L142F	SLC23A3_ENST00000295738.7_Missense_Mutation_p.L142F|SLC23A3_ENST00000455516.2_Missense_Mutation_p.L150F|SLC23A3_ENST00000396775.3_Missense_Mutation_p.L84F	NM_001144889.1	NP_001138361.1	Q6PIS1	S23A3_HUMAN	solute carrier family 23, member 3	142					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.L150F(1)|p.L142F(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	11		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGCAGCATGAGGGAGGCTAGG	0.562																																																	2	Substitution - Missense(2)	kidney(2)											82.0	85.0	84.0					2																	220033819		2035	4193	6228	SO:0001583	missense	151295			BC030243	CCDS42819.1, CCDS46517.1, CCDS46518.1	2q35	2013-07-18	2013-07-18		ENSG00000213901	ENSG00000213901		"""Solute carriers"""	20601	protein-coding gene	gene with protein product							Standard	NM_144712		Approved	SVCT3, FLJ31168, Yspl1	uc010zkr.2	Q6PIS1	OTTHUMG00000154616	ENST00000409878.3:c.424C>T	2.37:g.220033819G>A	ENSP00000386473:p.Leu142Phe		B7Z512|Q2PYN6|Q96NA6	Missense_Mutation	SNP	ENST00000409878.3	37	CCDS46518.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.843270	0.51057	.	.	ENSG00000213901	ENST00000396775;ENST00000295738;ENST00000409878;ENST00000455516;ENST00000409370;ENST00000430764	T;T;T;T;T	0.50277	0.75;2.13;2.11;0.75;2.13	5.0	3.19	0.36642	.	0.850231	0.10280	N	0.693664	T	0.51568	0.1682	L	0.32530	0.975	0.30783	N	0.741769	P;P;D	0.69078	0.873;0.873;0.997	B;B;P	0.62184	0.419;0.419;0.899	T	0.47289	-0.9129	9	.	.	.	.	7.7013	0.28625	0.0882:0.165:0.7468:0.0	.	142;150;142	Q6PIS1;B7Z512;Q6PIS1-2	S23A3_HUMAN;.;.	F	84;142;142;150;142;97	ENSP00000295738:L142F;ENSP00000386473:L142F;ENSP00000406546:L150F;ENSP00000386989:L142F;ENSP00000388907:L97F	.	L	-	1	0	SLC23A3	219742063	0.016000	0.18221	0.978000	0.43139	0.727000	0.41649	0.422000	0.21296	0.693000	0.31634	0.655000	0.94253	CTC		0.562	SLC23A3-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336331.2		NM_144712	
SSPO	23145	broad.mit.edu	37	7	149482073	149482073	+	RNA	SNP	G	G	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr7:149482073G>T	ENST00000378016.2	+	0	2861							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)	p.A290S(1)				Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			AGTACTGATGGCTGTGTCTGT	0.627																																																	1	Substitution - Missense(1)	kidney(1)											27.0	30.0	29.0					7																	149482073		2084	4202	6286			23145			AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149482073G>T			Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																					0.627	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				
TNK1	8711	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	7291994	7291994	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr17:7291994G>T	ENST00000576812.1	+	11	2131	c.1762G>T	c.(1762-1764)Gat>Tat	p.D588Y	TNK1_ENST00000570896.1_Missense_Mutation_p.D583Y|TNK1_ENST00000311668.2_Missense_Mutation_p.D583Y	NM_001251902.1	NP_001238831.1			tyrosine kinase, non-receptor, 1									p.D588Y(1)|p.D588N(1)		central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(2)|pancreas(1)	16		Prostate(122;0.157)				CCTCTTGTCCGATCCTGAGTT	0.592																																																	2	Substitution - Missense(2)	kidney(2)											39.0	43.0	42.0					17																	7291994		1920	4147	6067	SO:0001583	missense	8711			U43408	CCDS45602.1, CCDS58510.1	17p13.1	2005-09-22				ENSG00000174292			11940	protein-coding gene	gene with protein product		608076				8632913	Standard	NM_003985		Approved		uc002ggi.4	Q13470		ENST00000576812.1:c.1762G>T	17.37:g.7291994G>T	ENSP00000459799:p.Asp588Tyr			Missense_Mutation	SNP	ENST00000576812.1	37	CCDS58510.1	.	.	.	.	.	.	.	.	.	.	G	11.30	1.598696	0.28445	.	.	ENSG00000174292	ENST00000311668	T	0.78595	-1.19	5.0	0.96	0.19631	.	0.414645	0.20788	N	0.085680	D	0.82360	0.5020	L	0.54323	1.7	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.72401	-0.4305	10	0.72032	D	0.01	.	8.7905	0.34848	0.274:0.0:0.726:0.0	.	583;588	Q13470-2;Q13470	.;TNK1_HUMAN	Y	583	ENSP00000312309:D583Y	ENSP00000312309:D583Y	D	+	1	0	TNK1	7232718	0.908000	0.30866	0.003000	0.11579	0.358000	0.29455	1.707000	0.37888	0.014000	0.14944	-0.302000	0.09304	GAT		0.592	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2		NM_003985	
TPST1	8460	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	65705680	65705680	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr7:65705680G>T	ENST00000304842.5	+	2	693	c.268G>T	c.(268-270)Gac>Tac	p.D90Y	TPST1_ENST00000480281.1_Intron	NM_003596.3	NP_003587.1	O60507	TPST1_HUMAN	tyrosylprotein sulfotransferase 1	90					inflammatory response (GO:0006954)|peptidyl-tyrosine sulfation (GO:0006478)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)	p.D90Y(1)		NS(1)|biliary_tract(1)|breast(1)|kidney(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						GGCCATGCTGGACGCACATCC	0.502																																																	1	Substitution - Missense(1)	kidney(1)											99.0	91.0	93.0					7																	65705680		2203	4300	6503	SO:0001583	missense	8460			AF038009	CCDS5533.1	7q11.21	2012-12-13			ENSG00000169902	ENSG00000169902	2.8.2.20	"""Sulfotransferases, membrane-bound"""	12020	protein-coding gene	gene with protein product	"""transport and golgi organization 13 homolog A (Drosophila)"""	603125				9501187	Standard	NM_003596		Approved	TANGO13A	uc003tuw.3	O60507	OTTHUMG00000023871	ENST00000304842.5:c.268G>T	7.37:g.65705680G>T	ENSP00000302413:p.Asp90Tyr		A4D2M0|Q6FGM7	Missense_Mutation	SNP	ENST00000304842.5	37	CCDS5533.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.510621	0.85389	.	.	ENSG00000169902	ENST00000304842;ENST00000544114;ENST00000451388	T;T	0.46451	0.87;0.87	5.93	5.93	0.95920	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.75177	0.3814	M	0.93594	3.435	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80605	-0.1308	10	0.66056	D	0.02	-22.6521	19.3279	0.94270	0.0:0.0:1.0:0.0	.	90;90	F5H7U7;O60507	.;TPST1_HUMAN	Y	90	ENSP00000302413:D90Y;ENSP00000391338:D90Y	ENSP00000302413:D90Y	D	+	1	0	TPST1	65343115	1.000000	0.71417	0.983000	0.44433	0.964000	0.63967	8.786000	0.91826	2.803000	0.96430	0.585000	0.79938	GAC		0.502	TPST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251705.2		NM_003596	
TPX2	22974	broad.mit.edu;ucsc.edu	37	20	30365398	30365398	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr20:30365398A>C	ENST00000300403.6	+	9	1367	c.839A>C	c.(838-840)gAa>gCa	p.E280A	TPX2_ENST00000340513.4_Missense_Mutation_p.E280A	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	280					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)	p.E280A(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			GAATATAAGGAAGTGAACTTT	0.388																																																	1	Substitution - Missense(1)	kidney(1)											132.0	109.0	117.0					20																	30365398		2203	4300	6503	SO:0001583	missense	22974			AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"""chromosome 20 open reading frame 1"", ""TPX2, microtubule-associated, homolog (Xenopus laevis)"""	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.839A>C	20.37:g.30365398A>C	ENSP00000300403:p.Glu280Ala		Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Missense_Mutation	SNP	ENST00000300403.6	37	CCDS13190.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.092255	0.55968	.	.	ENSG00000088325	ENST00000300403;ENST00000340513	T	0.37752	1.18	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.30634	0.0771	L	0.46157	1.445	0.80722	D	1	P;P	0.49862	0.816;0.929	B;B	0.39299	0.1;0.296	T	0.07139	-1.0788	10	0.20046	T	0.44	-9.3842	14.841	0.70223	1.0:0.0:0.0:0.0	.	280;280	Q96RR5;Q9ULW0	.;TPX2_HUMAN	A	280	ENSP00000341145:E280A	ENSP00000300403:E280A	E	+	2	0	TPX2	29829059	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.027000	0.76463	2.161000	0.67846	0.533000	0.62120	GAA		0.388	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2			
UBE2O	63893	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	74392798	74392798	+	Silent	SNP	G	G	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr17:74392798G>A	ENST00000319380.7	-	14	2284	c.2220C>T	c.(2218-2220)agC>agT	p.S740S	UBE2O_ENST00000587581.1_5'Flank	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	740					positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.S740S(2)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						CCGTCTCCCAGCTGTCACTAT	0.587																																																	2	Substitution - coding silent(2)	kidney(2)											125.0	111.0	116.0					17																	74392798		2203	4300	6503	SO:0001819	synonymous_variant	63893			AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.2220C>T	17.37:g.74392798G>A			A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Silent	SNP	ENST00000319380.7	37	CCDS32742.1																																																																																				0.587	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1		NM_022066	
USP31	57478	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	23079995	23079995	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr16:23079995G>T	ENST00000219689.7	-	16	3430	c.3431C>A	c.(3430-3432)cCt>cAt	p.P1144H	USP31_ENST00000567975.1_Missense_Mutation_p.P437H	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.P1144H(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		GCTCTTCCCAGGTGGGAAAGG	0.587																																																	1	Substitution - Missense(1)	kidney(1)											63.0	66.0	65.0					16																	23079995		2197	4300	6497	SO:0001583	missense	57478			AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.3431C>A	16.37:g.23079995G>T	ENSP00000219689:p.Pro1144His		B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	G	10.08	1.251433	0.22880	.	.	ENSG00000103404	ENST00000219689	T	0.07444	3.19	5.8	2.64	0.31445	.	1.584560	0.03865	N	0.274686	T	0.08403	0.0209	N	0.14661	0.345	0.09310	N	1	B;B	0.33448	0.412;0.25	B;B	0.39379	0.125;0.298	T	0.41484	-0.9506	10	0.49607	T	0.09	-2.3607	8.0573	0.30612	0.1434:0.1313:0.7253:0.0	.	1144;437	Q70CQ4;B3KS48	UBP31_HUMAN;.	H	1144	ENSP00000219689:P1144H	ENSP00000219689:P1144H	P	-	2	0	USP31	22987496	0.348000	0.24861	0.265000	0.24526	0.736000	0.42039	3.376000	0.52417	0.801000	0.34066	0.655000	0.94253	CCT		0.587	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1		NM_020718	
VHL	7428	broad.mit.edu;ucsc.edu	37	3	10188200	10188200	+	Missense_Mutation	SNP	C	C	T	rs5030812|rs5030811		TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr3:10188200C>T	ENST00000256474.2	+	2	1183	c.343C>T	c.(343-345)Cac>Tac	p.H115Y	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	115	Involved in binding to CCT complex.		H -> Q (in VHLD; type II). {ECO:0000269|PubMed:9829912}.|H -> R (in VHLD; type II; dbSNP:rs5030812).|H -> Y (in VHLD; type I; dbSNP:rs5030811). {ECO:0000269|PubMed:8956040}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.H115N(7)|p.H115Y(5)|p.?(3)|p.H115fs*15(1)|p.H115D(1)|p.H115fs*41(1)|p.H115fs*42(1)|p.H115fs*44(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CCCGATAGGTCACCTTTGGCT	0.532		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	20	Substitution - Missense(13)|Deletion - Frameshift(4)|Unknown(3)	kidney(19)|pancreas(1)	GRCh37	CM961423|CM982005	VHL	M	rs5030811						167.0	155.0	159.0					3																	10188200		2203	4300	6503	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.343C>T	3.37:g.10188200C>T	ENSP00000256474:p.His115Tyr		B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.188235	0.57909	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99963	-9.62	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.000000	0.85682	D	0.000000	D	0.99966	0.9987	M	0.84511	2.7	0.80722	D	1	D	0.69078	0.997	D	0.67231	0.95	D	0.95010	0.8151	10	0.66056	D	0.02	0.1733	16.3181	0.82935	0.0:1.0:0.0:0.0	rs5030811	115	P40337	VHL_HUMAN	Y	115;33	ENSP00000256474:H115Y	ENSP00000256474:H115Y	H	+	1	0	VHL	10163200	1.000000	0.71417	1.000000	0.80357	0.141000	0.21300	5.806000	0.69150	2.530000	0.85305	0.563000	0.77884	CAC		0.532	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VWF	7450	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	6219564	6219564	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr12:6219564C>T	ENST00000261405.5	-	5	762	c.508G>A	c.(508-510)Gaa>Aaa	p.E170K	VWF_ENST00000572068.1_Missense_Mutation_p.E207K	NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	170	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.E170K(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	AAGTCATCTTCAGCAAAGATG	0.453																																																	1	Substitution - Missense(1)	kidney(1)											151.0	152.0	151.0					12																	6219564		2203	4300	6503	SO:0001583	missense	7450				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.508G>A	12.37:g.6219564C>T	ENSP00000261405:p.Glu170Lys		Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	.	26.5	4.748577	0.89753	.	.	ENSG00000110799	ENST00000261405	T	0.59906	0.23	5.81	5.81	0.92471	von Willebrand factor, type D domain (3);	0.457882	0.17387	N	0.176069	T	0.72843	0.3511	L	0.56280	1.765	0.58432	D	0.999999	P;P;D	0.64830	0.685;0.872;0.994	B;P;D	0.78314	0.26;0.615;0.991	T	0.65709	-0.6102	10	0.27785	T	0.31	.	19.0435	0.93011	0.0:1.0:0.0:0.0	.	170;207;170	B4DNX0;Q8TCE8;P04275	.;.;VWF_HUMAN	K	170	ENSP00000261405:E170K	ENSP00000261405:E170K	E	-	1	0	VWF	6089825	1.000000	0.71417	0.997000	0.53966	0.972000	0.66771	6.355000	0.73041	2.753000	0.94483	0.655000	0.94253	GAA		0.453	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1		NM_000552	
YIF1B	90522	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	38799931	38799931	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr19:38799931T>A	ENST00000339413.6	-	3	380	c.335A>T	c.(334-336)tAc>tTc	p.Y112F	YIF1B_ENST00000587361.1_5'UTR|YIF1B_ENST00000591784.1_Missense_Mutation_p.Y81F|YIF1B_ENST00000392124.3_Missense_Mutation_p.Y81F|YIF1B_ENST00000591755.1_Missense_Mutation_p.Y109F|YIF1B_ENST00000329420.8_Missense_Mutation_p.Y97F|YIF1B_ENST00000592694.1_Missense_Mutation_p.Y81F|YIF1B_ENST00000592246.1_Intron|YIF1B_ENST00000337679.8_Missense_Mutation_p.Y109F	NM_001039672.2|NM_001039673.2	NP_001034761.1|NP_001034762.1	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B (S. cerevisiae)	112						integral component of membrane (GO:0016021)		p.Y109F(1)|p.Y112F(1)|p.Y81F(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)	10	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CACAGCAAAGTAATACTTGAG	0.592																																																	3	Substitution - Missense(3)	kidney(3)											173.0	169.0	170.0					19																	38799931		2203	4300	6503	SO:0001583	missense	90522			AL833382	CCDS12512.1, CCDS33010.1, CCDS46066.1, CCDS46067.1	19q13.2	2008-02-05							30511	protein-coding gene	gene with protein product						12975309	Standard	NM_001039672		Approved	FinGER8	uc002ohz.2	Q5BJH7		ENST00000339413.6:c.335A>T	19.37:g.38799931T>A	ENSP00000343435:p.Tyr112Phe		H7BXS8|Q5JPC2|Q8WY70|Q96C02|Q96IC4	Missense_Mutation	SNP	ENST00000339413.6	37	CCDS33010.1	.	.	.	.	.	.	.	.	.	.	T	17.82	3.482954	0.63962	.	.	ENSG00000167645	ENST00000339413;ENST00000329420;ENST00000392124;ENST00000337679	T;T;T;T	0.74106	-0.41;-0.35;-0.26;-0.81	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.82066	0.4956	L	0.55213	1.73	0.58432	D	0.999999	D;D;D;D;P	0.76494	0.998;0.981;0.998;0.999;0.495	D;P;D;D;B	0.85130	0.987;0.86;0.994;0.997;0.389	T	0.82587	-0.0383	10	0.51188	T	0.08	-12.3006	12.3334	0.55051	0.0:0.0:0.0:1.0	.	81;109;109;112;109	Q5BJH7-2;Q5BJH7-5;Q5BJH7-4;Q5BJH7;Q5BJH7-3	.;.;.;YIF1B_HUMAN;.	F	112;97;81;109	ENSP00000343435:Y112F;ENSP00000329559:Y97F;ENSP00000375971:Y81F;ENSP00000337411:Y109F	ENSP00000329559:Y97F	Y	-	2	0	YIF1B	43491771	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	4.645000	0.61404	1.813000	0.52934	0.334000	0.21626	TAC		0.592	YIF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460511.1		NM_033557	
ZCCHC3	85364	broad.mit.edu	37	20	278688	278690	+	In_Frame_Del	DEL	CGG	CGG	-	rs11468351|rs5839847|rs6147263	byFrequency	TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr20:278688_278690delCGG	ENST00000382352.3	+	1	952_954	c.461_463delCGG	c.(460-465)ccggcg>ccg	p.A159del		NM_033089.6	NP_149080	Q9NUD5	ZCHC3_HUMAN	zinc finger, CCHC domain containing 3	159	Poly-Ala.						poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A159delA(3)		endometrium(2)|large_intestine(1)|lung(3)|prostate(2)	8		all_cancers(10;0.000209)|Lung NSC(37;0.0417)|all_lung(30;0.0713)|all_epithelial(17;0.0748)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			CAGGATGAgccggcggcggcggc	0.768														4335	0.865615	0.8343	0.9395	5008	,	,		8937	0.8065		0.9423	False		,,,				2504	0.8374																3	Deletion - In frame(3)	prostate(2)|large_intestine(1)																																								SO:0001651	inframe_deletion	85364			AL034548	CCDS42844.1	20p13-p12.2	2014-04-10	2004-07-14	2004-07-14	ENSG00000177764	ENSG00000247315		"""Zinc fingers, CCHC domain containing"""	16230	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 99"""	C20orf99			Standard	NM_033089		Approved	dJ1103G7.7	uc002wdf.3	Q9NUD5	OTTHUMG00000188280	ENST00000382352.3:c.461_463delCGG	20.37:g.278697_278699delCGG	ENSP00000371789:p.Ala159del		Q3B7J3|Q6NT79	In_Frame_Del	DEL	ENST00000382352.3	37	CCDS42844.1																																																																																				0.768	ZCCHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077447.1			
ZMYM4	9202	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	35857906	35857906	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr1:35857906G>C	ENST00000314607.6	+	16	2761	c.2681G>C	c.(2680-2682)aGt>aCt	p.S894T	ZMYM4_ENST00000373297.2_Missense_Mutation_p.S805T	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	894					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.S894T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TCATTGGCAAGTGCCCCTGCT	0.433																																																	1	Substitution - Missense(1)	kidney(1)											80.0	73.0	75.0					1																	35857906		2203	4300	6503	SO:0001583	missense	9202			AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"""Zinc fingers, MYM type"""	13055	protein-coding gene	gene with protein product		613568	"""zinc finger protein 262"""	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.2681G>C	1.37:g.35857906G>C	ENSP00000322915:p.Ser894Thr		A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.72|13.72	2.320135|2.320135	0.41096|0.41096	.|.	.|.	ENSG00000146463|ENSG00000146463	ENST00000457946|ENST00000314607;ENST00000373297	.|T;T	.|0.23147	.|1.92;1.95	4.79|4.79	3.87|3.87	0.44632|0.44632	.|.	.|0.207606	.|0.50627	.|D	.|0.000109	T|T	0.25494|0.25494	0.0620|0.0620	L|L	0.51422|0.51422	1.61|1.61	0.45097|0.45097	D|D	0.99811|0.99811	.|B	.|0.14438	.|0.01	.|B	.|0.17098	.|0.017	T|T	0.05053|0.05053	-1.0909|-1.0909	5|10	.|0.49607	.|T	.|0.09	-6.579|-6.579	13.104|13.104	0.59237|0.59237	0.0787:0.0:0.9213:0.0|0.0787:0.0:0.9213:0.0	.|.	.|894	.|Q5VZL5	.|ZMYM4_HUMAN	N|T	553|894;805	.|ENSP00000322915:S894T;ENSP00000362394:S805T	.|ENSP00000322915:S894T	K|S	+|+	3|2	2|0	ZMYM4|ZMYM4	35630493|35630493	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	5.102000|5.102000	0.64572|0.64572	1.133000|1.133000	0.42147|0.42147	0.591000|0.591000	0.81541|0.81541	AAG|AGT		0.433	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3		NM_005095	
ZNF3	7551	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	99668973	99668973	+	Silent	SNP	G	G	C			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr7:99668973G>C	ENST00000424697.1	-	6	1440	c.1134C>G	c.(1132-1134)acC>acG	p.T378T	ZNF3_ENST00000299667.4_Silent_p.T378T|ZNF3_ENST00000303915.6_Silent_p.T378T|ZNF3_ENST00000413658.2_Intron	NM_001278284.1|NM_001278287.1|NM_001278290.1|NM_001278291.1|NM_001278292.1|NM_032924.3	NP_001265213.1|NP_001265216.1|NP_001265219.1|NP_001265220.1|NP_001265221.1|NP_116313.3	P17036	ZNF3_HUMAN	zinc finger protein 3	378				GEKPYECNECGKAFSQSSHLYQHQRIHTGEKPYECMECGGK FTYSSGLIQHQ -> EALPTFVTLIRLLPSVDPIVTNEAAF PAESLATIFALIWRLFCVHSLMFKKV (in Ref. 2; BAA91019). {ECO:0000305}.	cell differentiation (GO:0030154)|leukocyte activation (GO:0045321)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)	p.T378T(1)		NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	25	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			CTGAACTGTAGGTAAACTTTC	0.502																																																	1	Substitution - coding silent(1)	kidney(1)											106.0	115.0	112.0					7																	99668973		2202	4300	6502	SO:0001819	synonymous_variant	7551			AF027136	CCDS43618.1, CCDS43619.1	7q22.1	2013-01-08	2006-05-05					"""Zinc fingers, C2H2-type"", ""-"""	13089	protein-coding gene	gene with protein product		194510	"""zinc finger protein 3 (A8-51)"""				Standard	NM_032924		Approved	A8-51, KOX25, PP838, FLJ20216, HF.12, Zfp113	uc003usr.4	P17036		ENST00000424697.1:c.1134C>G	7.37:g.99668973G>C			D6W5U0|P13683|Q9HBR4|Q9NNX8|Q9NXJ1|Q9UC15|Q9UC16	Silent	SNP	ENST00000424697.1	37	CCDS43619.1																																																																																				0.502	ZNF3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336247.3		NM_017715	
ZNF572	137209	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	125989952	125989952	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr8:125989952C>G	ENST00000319286.5	+	3	1596	c.1442C>G	c.(1441-1443)gCc>gGc	p.A481G		NM_152412.2	NP_689625.2	Q7Z3I7	ZN572_HUMAN	zinc finger protein 572	481					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A481G(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	31	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			AGCAGAAGTGCCTACCTCAGT	0.468										HNSCC(60;0.17)																																							1	Substitution - Missense(1)	kidney(1)											133.0	138.0	137.0					8																	125989952		2203	4300	6503	SO:0001583	missense	137209			BX537876	CCDS6354.1	8q24.13	2013-09-20			ENSG00000180938	ENSG00000180938		"""Zinc fingers, C2H2-type"""	26758	protein-coding gene	gene with protein product							Standard	NM_152412		Approved	FLJ38002	uc003yrr.3	Q7Z3I7	OTTHUMG00000164988	ENST00000319286.5:c.1442C>G	8.37:g.125989952C>G	ENSP00000319305:p.Ala481Gly		A1L4F1|Q8N1Q0	Missense_Mutation	SNP	ENST00000319286.5	37	CCDS6354.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.635844	0.47049	.	.	ENSG00000180938	ENST00000319286	T	0.60424	0.19	4.9	4.9	0.64082	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.140255	0.32836	N	0.005585	T	0.46718	0.1407	L	0.27053	0.805	0.24529	N	0.994125	B	0.17465	0.022	B	0.14023	0.01	T	0.48514	-0.9029	10	0.66056	D	0.02	-1.8627	15.6104	0.76713	0.0:1.0:0.0:0.0	.	481	Q7Z3I7	ZN572_HUMAN	G	481	ENSP00000319305:A481G	ENSP00000319305:A481G	A	+	2	0	ZNF572	126059133	0.000000	0.05858	1.000000	0.80357	0.990000	0.78478	0.720000	0.25896	2.543000	0.85770	0.563000	0.77884	GCC		0.468	ZNF572-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381359.1		NM_152412	
ZNF783	100289678	broad.mit.edu;hgsc.bcm.edu	37	7	148979329	148979329	+	Silent	SNP	C	C	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr7:148979329C>T	ENST00000434415.1	+	6	1699	c.1536C>T	c.(1534-1536)caC>caT	p.H512H	ZNF783_ENST00000489518.1_Intron	NM_001195220.1	NP_001182149.1	Q6ZMS7	ZN783_HUMAN	zinc finger family member 783	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.H512H(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)	22	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.0014)			TGGCCGTGCACATGCAGACCC	0.731																																																	1	Substitution - coding silent(1)	kidney(1)											13.0	16.0	15.0					7																	148979329		2147	4234	6381	SO:0001819	synonymous_variant	100289678			AK131504	CCDS56519.1	7q36.1	2013-01-08	2008-05-28		ENSG00000204946	ENSG00000204946		"""Zinc fingers, C2H2-type"", ""-"""	27222	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001195220		Approved	DKFZp667J212	uc011kuo.2	Q6ZMS7	OTTHUMG00000158969	ENST00000434415.1:c.1536C>T	7.37:g.148979329C>T			C9J9J2	Silent	SNP	ENST00000434415.1	37	CCDS56519.1																																																																																				0.731	ZNF783-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352715.1		NM_001195220	
AIM1	202	ucsc.edu	37	6	106960877	106960877	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5169-01A-01D-1429-08	TCGA-BP-5169-11A-01D-1429-08	G	G	G	T	G	G	Unknown	Valid	Somatic	.	WXS	454	.		Illumina HiSeq	3527b21e-972b-4c31-b5de-8c394ce0e500	5ea7625d-1eb6-45d7-add0-a91070f4ebcb	g.chr6:106960877G>T	ENST00000369066.3	+	1	1148	c.661G>T	c.(661-663)Ggc>Tgc	p.G221C		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0			Missing (in OCA4). {ECO:0000269|PubMed:14722913}.		developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.G221C(1)		breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GAACCATTTCGGCGTGGGCAG	0.657																																						.											1	Substitution - Missense(1)	kidney(1)											14.0	17.0	16.0					6																	106960877		2199	4294	6493	SO:0001583	missense	202			U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.661G>T	6.37:g.106960877G>T	ENSP00000358062:p.Gly221Cys		Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.472751	0.63737	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.74002	-0.8	5.09	5.09	0.68999	.	0.465636	0.16044	N	0.232290	T	0.81240	0.4781	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82540	-0.0406	10	0.72032	D	0.01	.	15.6621	0.77197	0.0:0.0:1.0:0.0	.	221	Q9Y4K1	AIM1_HUMAN	C	629;221	ENSP00000358062:G221C	ENSP00000285105:G629C	G	+	1	0	AIM1	107067570	1.000000	0.71417	0.310000	0.25168	0.474000	0.32979	5.630000	0.67805	2.365000	0.80145	0.655000	0.94253	GGC		0.657	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			
