#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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
AGPAT5	55326	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	6614716	6614716	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr8:6614716C>T	ENST00000285518.6	+	8	1214	c.902C>T	c.(901-903)cCa>cTa	p.P301L		NM_018361.3	NP_060831.2	Q9NUQ2	PLCE_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 5	301					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.P301L(1)	AGPAT5/MCPH1(2)	endometrium(2)|kidney(2)|large_intestine(4)|lung(3)	11			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)		TCACCAGATCCAGAAAGAAGA	0.323																																																	1	Substitution - Missense(1)	kidney(1)											45.0	46.0	46.0					8																	6614716		2203	4300	6503	SO:0001583	missense	55326			AF375789	CCDS34796.1	8p23.1	2013-02-05	2013-02-05		ENSG00000155189	ENSG00000155189	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	20886	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, epsilon"""	614796	"""1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)"""				Standard	NM_018361		Approved	FLJ11210, LPAAT-e, LPAAT-epsilon	uc003wqo.3	Q9NUQ2	OTTHUMG00000163656	ENST00000285518.6:c.902C>T	8.37:g.6614716C>T	ENSP00000285518:p.Pro301Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q8IZ47|Q9BQG4	Missense_Mutation	SNP	ENST00000285518.6	37	CCDS34796.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.2|22.2	4.253626|4.253626	0.80135|0.80135	.|.	.|.	ENSG00000155189|ENSG00000155189	ENST00000285518|ENST00000518327	T|.	0.62232|.	0.04|.	6.04|6.04	6.04|6.04	0.98038|0.98038	.|.	0.346377|.	0.34725|.	N|.	0.003723|.	T|.	0.75803|.	0.3899|.	M|M	0.70595|0.70595	2.14|2.14	0.58432|0.58432	D|D	0.999999|0.999999	P|.	0.51791|.	0.948|.	B|.	0.43103|.	0.408|.	T|.	0.73167|.	-0.4068|.	10|.	0.11485|.	T|.	0.65|.	-10.8366|-10.8366	18.073|18.073	0.89417|0.89417	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	301|.	Q9NUQ2|.	PLCE_HUMAN|.	L|X	301|118	ENSP00000285518:P301L|.	ENSP00000285518:P301L|.	P|Q	+|+	2|1	0|0	AGPAT5|AGPAT5	6602124|6602124	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.436000|4.436000	0.59948|0.59948	2.873000|2.873000	0.98535|0.98535	0.561000|0.561000	0.74099|0.74099	CCA|CAG		0.323	AGPAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374684.1		NM_018361	
ARID2	196528	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	46245701	46245701	+	Silent	SNP	C	C	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr12:46245701C>A	ENST00000334344.6	+	15	3967	c.3795C>A	c.(3793-3795)gtC>gtA	p.V1265V	ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Silent_p.V1116V|ARID2_ENST00000444670.1_Silent_p.V875V	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1265					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|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.V1265V(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		AAATTGAAGTCATGGAGAACC	0.433			"""N, S, F"""		hepatocellular carcinoma																																			Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	1	Substitution - coding silent(1)	kidney(1)											60.0	57.0	58.0					12																	46245701		2203	4300	6503	SO:0001819	synonymous_variant	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.3795C>A	12.37:g.46245701C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Silent	SNP	ENST00000334344.6	37	CCDS31783.1																																																																																				0.433	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2		XM_350875	
ARL16	339231	hgsc.bcm.edu	37	17	79650800	79650800	+	Frame_Shift_Del	DEL	C	C	-	rs200303242	byFrequency	TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr17:79650800delC	ENST00000397498.4	-	1	154	c.56delG	c.(55-57)ggtfs	p.G20fs	HGS_ENST00000329138.4_5'Flank|ARL16_ENST00000570561.1_5'Flank|ARL16_ENST00000573392.1_5'Flank|ARL16_ENST00000576135.1_5'Flank|ARL16_ENST00000574938.1_5'Flank	NM_001040025.1	NP_001035114.1	Q0P5N6	ARL16_HUMAN	ADP-ribosylation factor-like 16	20					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			central_nervous_system(1)|endometrium(1)|lung(4)|skin(1)	7	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			CTTCGCTCCACCCGGCACCCG	0.652																																																	0													16.0	19.0	18.0					17																	79650800		1907	4101	6008	SO:0001589	frameshift_variant	339231				CCDS45813.1	17q25.3	2014-05-09				ENSG00000214087		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	27902	protein-coding gene	gene with protein product						12477932	Standard	NM_001040025		Approved		uc002kbf.3	Q0P5N6		ENST00000397498.4:c.56delG	17.37:g.79650800delC	ENSP00000380635:p.Gly20fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000397498.4	37	CCDS45813.1																																																																																				0.652	ARL16-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440514.1		XM_290777	
BCL6	604	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	187446848	187446848	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr3:187446848T>C	ENST00000406870.2	-	5	1711	c.1345A>G	c.(1345-1347)Atc>Gtc	p.I449V	BCL6_ENST00000232014.4_Missense_Mutation_p.I449V|BCL6_ENST00000450123.2_Missense_Mutation_p.I449V|RP11-211G3.3_ENST00000437407.1_Intron|RP11-211G3.3_ENST00000449623.1_Intron	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	449					actin cytoskeleton organization (GO:0030036)|B cell differentiation (GO:0030183)|cell morphogenesis (GO:0000902)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte development (GO:0048821)|germinal center formation (GO:0002467)|inflammatory response (GO:0006954)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cellular component movement (GO:0051272)|protein import into nucleus, translocation (GO:0000060)|regulation of germinal center formation (GO:0002634)|regulation of immune response (GO:0050776)|regulation of inflammatory response (GO:0050727)|regulation of memory T cell differentiation (GO:0043380)|regulation of Rho GTPase activity (GO:0032319)|Rho protein signal transduction (GO:0007266)|spermatogenesis (GO:0007283)|type 2 immune response (GO:0042092)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I449V(1)		central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(9)|lung(10)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	40	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		CTGTTAACGATGTTATTGAGC	0.557			"""T, Mis"""	"""IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"""	"""NHL, CLL"""																																			Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	1	Substitution - Missense(1)	kidney(1)											58.0	60.0	59.0					3																	187446848		2203	4300	6503	SO:0001583	missense	604				CCDS3289.1, CCDS46975.1	3q27	2013-01-09	2008-08-01		ENSG00000113916	ENSG00000113916		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	1001	protein-coding gene	gene with protein product		109565	"""zinc finger protein 51"""	ZNF51			Standard	NM_001130845		Approved	ZBTB27, LAZ3, BCL5, BCL6A	uc003frq.2	P41182	OTTHUMG00000156441	ENST00000406870.2:c.1345A>G	3.37:g.187446848T>C	ENSP00000384371:p.Ile449Val	Somatic		WXS	Illumina HiSeq	Phase_I	A7E241|B8PSA7|D3DNV5	Missense_Mutation	SNP	ENST00000406870.2	37	CCDS3289.1	.	.	.	.	.	.	.	.	.	.	T	11.62	1.692518	0.30052	.	.	ENSG00000113916	ENST00000406870;ENST00000232014;ENST00000450123	T;T;T	0.08458	3.09;3.09;3.14	5.61	3.13	0.36017	.	0.089927	0.85682	D	0.000000	T	0.06462	0.0166	L	0.29908	0.895	0.40154	D	0.976985	B;B	0.25312	0.123;0.068	B;B	0.21360	0.034;0.024	T	0.34403	-0.9830	10	0.18710	T	0.47	.	12.2613	0.54652	0.0:0.0:0.3922:0.6078	.	449;449	B8PSA7;P41182	.;BCL6_HUMAN	V	449	ENSP00000384371:I449V;ENSP00000232014:I449V;ENSP00000413122:I449V	ENSP00000232014:I449V	I	-	1	0	BCL6	188929542	1.000000	0.71417	0.978000	0.43139	0.994000	0.84299	2.863000	0.48396	0.451000	0.26802	0.459000	0.35465	ATC		0.557	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1		NM_138931	
CCHCR1	54535	broad.mit.edu;hgsc.bcm.edu	37	6	31122472	31122472	+	Missense_Mutation	SNP	C	C	T	rs576214578	byFrequency	TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr6:31122472C>T	ENST00000376266.5	-	4	457	c.335G>A	c.(334-336)cGg>cAg	p.R112Q	CCHCR1_ENST00000396263.2_Missense_Mutation_p.R112Q|CCHCR1_ENST00000451521.2_Missense_Mutation_p.R165Q|CCHCR1_ENST00000480060.1_Intron|CCHCR1_ENST00000396268.3_Missense_Mutation_p.R201Q	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	112					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R112Q(1)|p.R201Q(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						CGAGGTCTCCCGCAGGAGCCG	0.692													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17147	0.0		0.0	False		,,,				2504	0.0																2	Substitution - Missense(2)	kidney(2)											41.0	50.0	47.0					6																	31122472		1507	2709	4216	SO:0001583	missense	54535			AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.335G>A	6.37:g.31122472C>T	ENSP00000365442:p.Arg112Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.503735	0.44558	.	.	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521;ENST00000448141;ENST00000508683;ENST00000448162;ENST00000513222;ENST00000503420;ENST00000515274;ENST00000507751;ENST00000455279;ENST00000412245;ENST00000503934;ENST00000426967;ENST00000502557;ENST00000507829	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.05139	3.49;3.49;3.49;3.49;3.49;3.49;3.49;3.49;3.49;3.49;3.49;3.49;3.49;3.49;3.49	4.8	3.03	0.35002	.	0.325746	0.22679	N	0.056980	T	0.04634	0.0126	M	0.70595	2.14	0.25487	N	0.987688	D;D;D;D;D	0.63046	0.983;0.978;0.978;0.992;0.979	P;B;B;P;B	0.50082	0.524;0.442;0.442;0.63;0.389	T	0.31447	-0.9943	10	0.30854	T	0.27	-22.6889	6.9406	0.24490	0.0:0.7948:0.0:0.2052	.	112;112;112;165;201	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	Q	201;112;112;112;165;76;76;112;86;76;112;112;112;138;112;210;112;112	ENSP00000379566:R201Q;ENSP00000365442:R112Q;ENSP00000379561:R112Q;ENSP00000401039:R165Q;ENSP00000414323:R76Q;ENSP00000421393:R76Q;ENSP00000390027:R112Q;ENSP00000425682:R86Q;ENSP00000421992:R76Q;ENSP00000420941:R112Q;ENSP00000398715:R112Q;ENSP00000425595:R112Q;ENSP00000402432:R210Q;ENSP00000425377:R112Q;ENSP00000420911:R112Q	ENSP00000365442:R112Q	R	-	2	0	CCHCR1	31230451	0.977000	0.34250	0.949000	0.38748	0.511000	0.34104	0.523000	0.22925	0.646000	0.30693	-0.158000	0.13435	CGG		0.692	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5		NM_019052	
CD6	923	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	60785461	60785461	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr11:60785461G>A	ENST00000313421.7	+	11	1999	c.1813G>A	c.(1813-1815)Gcc>Acc	p.A605T	CD6_ENST00000352009.5_Missense_Mutation_p.A573T|CD6_ENST00000452451.2_Missense_Mutation_p.A564T|CD6_ENST00000344028.5_Missense_Mutation_p.A573T|CD6_ENST00000346437.4_Missense_Mutation_p.A532T	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	605					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)	p.A605T(2)		endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						CTTGGAGCTGGCCGGCACCCA	0.582																																					Pancreas(169;904 2017 4767 38890 42505)												2	Substitution - Missense(2)	kidney(2)											42.0	47.0	45.0					11																	60785461		2199	4290	6489	SO:0001583	missense	923				CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1813G>A	11.37:g.60785461G>A	ENSP00000323280:p.Ala605Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Missense_Mutation	SNP	ENST00000313421.7	37	CCDS7999.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.626869	0.87560	.	.	ENSG00000013725	ENST00000344028;ENST00000346437;ENST00000313421;ENST00000452451;ENST00000352009	T;T;T;T;T	0.02812	4.21;4.15;4.31;4.44;4.63	5.18	5.18	0.71444	.	1.103240	0.07185	N	0.854712	T	0.16041	0.0386	M	0.66939	2.045	0.28268	N	0.924543	D;D;P;P	0.89917	1.0;1.0;0.836;0.635	D;D;B;B	0.87578	0.998;0.998;0.43;0.081	T	0.13872	-1.0493	10	0.87932	D	0	.	14.1921	0.65644	0.0:0.0:1.0:0.0	.	564;573;605;605	P30203-5;P30203-4;P30203;Q8N4Q7	.;.;CD6_HUMAN;.	T	573;532;605;564;573	ENSP00000344108:A573T;ENSP00000345566:A532T;ENSP00000323280:A605T;ENSP00000390676:A564T;ENSP00000340628:A573T	ENSP00000323280:A605T	A	+	1	0	CD6	60542037	1.000000	0.71417	0.997000	0.53966	0.923000	0.55619	4.680000	0.61656	2.428000	0.82296	0.313000	0.20887	GCC		0.582	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1		NM_006725	
CNTN3	5067	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	74474063	74474063	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr3:74474063C>A	ENST00000263665.6	-	4	414	c.387G>T	c.(385-387)agG>agT	p.R129S		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	129	Ig-like C2-type 2.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.R129S(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		ACACTGTACTCCTCATTTTGG	0.398																																																	1	Substitution - Missense(1)	kidney(1)											70.0	65.0	67.0					3																	74474063		2203	4300	6503	SO:0001583	missense	5067			AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.387G>T	3.37:g.74474063C>A	ENSP00000263665:p.Arg129Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.484767	0.63962	.	.	ENSG00000113805	ENST00000263665	T	0.76060	-0.99	5.18	-1.32	0.09201	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.86468	0.5940	M	0.93808	3.46	0.45272	D	0.998276	D	0.76494	0.999	D	0.74023	0.982	D	0.84989	0.0893	10	0.52906	T	0.07	.	10.5542	0.45107	0.0:0.5308:0.0:0.4692	.	129	Q9P232	CNTN3_HUMAN	S	129	ENSP00000263665:R129S	ENSP00000263665:R129S	R	-	3	2	CNTN3	74556753	0.934000	0.31675	0.847000	0.33407	0.974000	0.67602	-0.077000	0.11394	-0.406000	0.07588	-0.390000	0.06520	AGG		0.398	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1		NM_020872	
CTNNA2	1496	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	80136882	80136882	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr2:80136882C>T	ENST00000402739.4	+	6	1020	c.1015C>T	c.(1015-1017)Cgg>Tgg	p.R339W	CTNNA2_ENST00000541047.1_Missense_Mutation_p.R339W|CTNNA2_ENST00000496558.1_Missense_Mutation_p.R339W|CTNNA2_ENST00000361291.4_Missense_Mutation_p.R373W|CTNNA2_ENST00000540488.1_Missense_Mutation_p.R339W|CTNNA2_ENST00000466387.1_Missense_Mutation_p.R339W	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	339					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)	p.R339W(2)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CAACGCCGTGCGGCAGGCGCT	0.597																																																	2	Substitution - Missense(2)	kidney(2)											43.0	49.0	47.0					2																	80136882		2080	4222	6302	SO:0001583	missense	1496				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.1015C>T	2.37:g.80136882C>T	ENSP00000384638:p.Arg339Trp	Somatic		WXS	Illumina HiSeq	Phase_I	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	37		.	.	.	.	.	.	.	.	.	.	C	25.2	4.616181	0.87359	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01	5.6	4.7	0.59300	.	0.000000	0.64402	D	0.000002	T	0.69566	0.3125	M	0.89658	3.05	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.989;0.988;0.992	T	0.76761	-0.2840	10	0.87932	D	0	.	13.4363	0.61086	0.2852:0.7148:0.0:0.0	.	339;339;339	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	W	339;339;373;339;339;339	ENSP00000418191:R339W;ENSP00000419295:R339W;ENSP00000355398:R373W;ENSP00000384638:R339W;ENSP00000444675:R339W;ENSP00000441705:R339W	ENSP00000355398:R373W	R	+	1	2	CTNNA2	79990393	0.961000	0.32948	0.965000	0.40720	0.998000	0.95712	2.001000	0.40825	1.328000	0.45358	0.591000	0.81541	CGG		0.597	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4		NM_004389	
CPS1	1373	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	211476961	211476961	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr2:211476961G>A	ENST00000233072.5	+	20	2708	c.2512G>A	c.(2512-2514)Gat>Aat	p.D838N	CPS1_ENST00000430249.2_Missense_Mutation_p.D844N|CPS1_ENST00000451903.2_Missense_Mutation_p.D387N	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	838					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)	p.D838N(1)|p.D844N(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	ATCTAATTTAGATCTTAGAAA	0.453																																																	2	Substitution - Missense(2)	kidney(2)											115.0	115.0	115.0					2																	211476961		2202	4300	6502	SO:0001583	missense	1373			AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.2512G>A	2.37:g.211476961G>A	ENSP00000233072:p.Asp838Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	11.86	1.765813	0.31228	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.97455	-4.39;-4.39;-4.39	5.65	4.77	0.60923	Carbamoyl-phosphate synthetase, large subunit, oligomerisation (2);	0.135878	0.64402	D	0.000003	D	0.91310	0.7260	N	0.08118	0	0.40071	D	0.976012	B;B	0.11235	0.004;0.004	B;B	0.09377	0.004;0.004	D	0.87662	0.2535	10	0.52906	T	0.07	-5.592	10.9013	0.47054	0.1441:0.0:0.8559:0.0	.	848;838	Q59HF8;P31327	.;CPSM_HUMAN	N	844;846;838;387	ENSP00000402608:D844N;ENSP00000233072:D838N;ENSP00000406136:D387N	ENSP00000233072:D838N	D	+	1	0	CPS1	211185206	1.000000	0.71417	0.037000	0.18230	0.274000	0.26718	4.572000	0.60886	1.380000	0.46344	0.557000	0.71058	GAT		0.453	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			
DIP2C	22982	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	430563	430563	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr10:430563A>G	ENST00000280886.6	-	15	1766	c.1679T>C	c.(1678-1680)aTg>aCg	p.M560T	DIP2C_ENST00000381496.3_Missense_Mutation_p.M453T	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	560						nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.M560T(1)		breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		GATCACATGCATCATGTTCAT	0.577																																																	1	Substitution - Missense(1)	kidney(1)											180.0	147.0	158.0					10																	430563		2203	4300	6503	SO:0001583	missense	22982			BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.1679T>C	10.37:g.430563A>G	ENSP00000280886:p.Met560Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	37	CCDS7054.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.4|20.4	3.978995|3.978995	0.74360|0.74360	.|.	.|.	ENSG00000151240|ENSG00000151240	ENST00000421992|ENST00000280886;ENST00000381496	.|T;T	.|0.39997	.|1.05;1.05	5.55|5.55	5.55|5.55	0.83447|0.83447	.|AMP-dependent synthetase/ligase (1);	.|0.038788	.|0.85682	.|D	.|0.000000	T|T	0.59321|0.59321	0.2185|0.2185	M|M	0.80746|0.80746	2.51|2.51	0.49798|0.49798	D|D	0.999828|0.999828	.|P;P	.|0.37731	.|0.607;0.482	.|P;P	.|0.50896	.|0.574;0.653	T|T	0.56727|0.56727	-0.7931|-0.7931	5|10	.|0.21540	.|T	.|0.41	-51.3092|-51.3092	15.7042|15.7042	0.77565|0.77565	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|453;560	.|E7EPU2;Q9Y2E4	.|.;DIP2C_HUMAN	R|T	28|560;453	.|ENSP00000280886:M560T;ENSP00000370907:M453T	.|ENSP00000280886:M560T	C|M	-|-	1|2	0|0	DIP2C|DIP2C	420563|420563	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.947000|0.947000	0.59692|0.59692	9.279000|9.279000	0.95777|0.95777	2.113000|2.113000	0.64589|0.64589	0.379000|0.379000	0.24179|0.24179	TGC|ATG		0.577	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1		NM_014974	
EEF1D	1936	hgsc.bcm.edu;ucsc.edu	37	8	144672056	144672056	+	Intron	SNP	G	G	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr8:144672056G>A	ENST00000529272.1	-	2	397				EEF1D_ENST00000419152.2_Intron|EEF1D_ENST00000528610.1_Intron|EEF1D_ENST00000531770.1_5'Flank|EEF1D_ENST00000532400.1_Intron|EEF1D_ENST00000526838.1_Intron|EEF1D_ENST00000532741.1_Missense_Mutation_p.P116S|EEF1D_ENST00000524624.1_Intron|EEF1D_ENST00000317198.6_Intron|EEF1D_ENST00000423316.2_Missense_Mutation_p.P66S|EEF1D_ENST00000395119.3_Intron|EEF1D_ENST00000442189.2_Missense_Mutation_p.P66S|EEF1D_ENST00000531621.1_Intron			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			CCGCCGTCAGGGGCTTCCGCC	0.706																																																	0													15.0	17.0	16.0					8																	144672056		2196	4296	6492	SO:0001627	intron_variant	1936			AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191	ENST00000529272.1:c.4-3037C>T	8.37:g.144672056G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Missense_Mutation	SNP	ENST00000529272.1	37	CCDS6405.1	.	.	.	.	.	.	.	.	.	.	G	3.043	-0.197028	0.06259	.	.	ENSG00000104529	ENST00000532741;ENST00000442189;ENST00000423316;ENST00000356793;ENST00000337369;ENST00000526710;ENST00000531281;ENST00000532596;ENST00000524883;ENST00000531670;ENST00000528519;ENST00000529832;ENST00000530306;ENST00000530545;ENST00000525261;ENST00000534804	.	.	.	3.39	3.39	0.38822	.	1.083410	0.07314	N	0.876453	T	0.34366	0.0895	L	0.44542	1.39	0.25427	N	0.988217	B;B;B	0.30326	0.063;0.276;0.103	B;B;B	0.25140	0.026;0.045;0.058	T	0.24728	-1.0152	9	0.62326	D	0.03	.	6.8291	0.23900	0.0:0.3278:0.4933:0.1789	.	66;116;66	D3DWK1;E9PRY8;P29692-2	.;.;.	S	116;66;66;18;66;66;66;66;66;66;66;66;66;66;66;66	.	ENSP00000338323:P66S	P	-	1	0	EEF1D	144743199	0.000000	0.05858	0.056000	0.19401	0.149000	0.21700	0.167000	0.16602	2.219000	0.72066	0.484000	0.47621	CCT		0.706	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2		NM_032378	
ELAC2	60528	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	12920219	12920219	+	Silent	SNP	G	G	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr17:12920219G>A	ENST00000338034.4	-	3	566	c.327C>T	c.(325-327)ttC>ttT	p.F109F	ELAC2_ENST00000609345.1_5'UTR|ELAC2_ENST00000426905.3_Silent_p.F109F|ELAC2_ENST00000578071.1_Silent_p.F109F|ELAC2_ENST00000395962.2_Silent_p.F90F	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	109					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.F109F(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						TTCGTGTCAGGAATATGTTGT	0.413																																																	1	Substitution - coding silent(1)	kidney(1)											120.0	109.0	112.0					17																	12920219		2203	4300	6503	SO:0001819	synonymous_variant	60528			AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"""tRNase Z (long form)"""	605367	"""elaC (E. coli) homolog 2"", ""elaC homolog 2 (E. coli)"""			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.327C>T	17.37:g.12920219G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Silent	SNP	ENST00000338034.4	37	CCDS11164.1																																																																																				0.413	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5			
EMILIN1	11117	hgsc.bcm.edu;ucsc.edu	37	2	27308027	27308032	+	Splice_Site	DEL	GGAGTG	GGAGTG	-	rs113364468	byFrequency	TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	GGAGTG	GGAGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr2:27308027_27308032delGGAGTG	ENST00000380320.4	+	7	3074_3079	c.2575_2580delGGAGTG	c.(2575-2580)ggagtgdel	p.GV859del	KHK_ENST00000260598.5_5'Flank|KHK_ENST00000260599.6_5'Flank	NM_007046.3	NP_008977	Q9Y6C2	EMIL1_HUMAN	elastin microfibril interfacer 1	859	Collagen-like.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(14)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	26	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCCCACTCAGGAGTGGAGGGGGCAC	0.641																																																	0																																										SO:0001630	splice_region_variant	11117			AF088916	CCDS1733.1	2p23.3-p23.2	2008-02-05			ENSG00000138080	ENSG00000138080		"""EMI domain containing"""	19880	protein-coding gene	gene with protein product		130660					Standard	NM_007046		Approved	DKFZp586M121, gp115	uc002rii.4	Q9Y6C2	OTTHUMG00000097069	ENST00000380320.4:c.2576-1GGAGTG>-	2.37:g.27308027_27308032delGGAGTG		Somatic		WXS	Illumina HiSeq	Phase_I	A5PL03|H0Y7A0|Q53SY9|Q96G58|Q96IH6|Q9UG76	Frame_Shift_Del	DEL	ENST00000380320.4	37	CCDS1733.1																																																																																				0.641	EMILIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214185.1		NM_007046	In_Frame_Del
FGFR3	2261	hgsc.bcm.edu	37	4	1807542	1807543	+	Frame_Shift_Ins	INS	-	-	G			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr4:1807542_1807543insG	ENST00000260795.2	+	12	1813_1814	c.1711_1712insG	c.(1711-1713)cggfs	p.R571fs	FGFR3_ENST00000412135.2_Frame_Shift_Ins_p.R459fs|FGFR3_ENST00000481110.2_Frame_Shift_Ins_p.R572fs|FGFR3_ENST00000352904.1_Frame_Shift_Ins_p.R459fs|FGFR3_ENST00000440486.2_Frame_Shift_Ins_p.R571fs|FGFR3_ENST00000340107.4_Frame_Shift_Ins_p.R573fs			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	571	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	gcgggcgcggcggcccccgggc	0.703		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome																															Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	0																																										SO:0001589	frameshift_variant	2261	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.1713dupG	4.37:g.1807544_1807544dupG	ENSP00000260795:p.Arg571fs	Somatic		WXS	Illumina HiSeq	Phase_I	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Frame_Shift_Ins	INS	ENST00000260795.2	37	CCDS3353.1																																																																																				0.703	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2		NM_000142	
FUT11	170384	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	75533416	75533416	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr10:75533416G>C	ENST00000372841.3	+	2	1220	c.1177G>C	c.(1177-1179)Gac>Cac	p.D393H	FUT11_ENST00000465695.1_3'UTR|FUT11_ENST00000394790.1_Missense_Mutation_p.D393H|RMRPP1_ENST00000517236.1_RNA|AC022400.2_ENST00000595757.1_5'Flank	NM_173540.2	NP_775811.2	Q495W5	FUT11_HUMAN	fucosyltransferase 11 (alpha (1,3) fucosyltransferase)	393					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)	p.D393H(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	7	Prostate(51;0.0112)					TTTCGTCTGTGACTACGAACT	0.572																																																	1	Substitution - Missense(1)	kidney(1)											93.0	92.0	92.0					10																	75533416		2203	4300	6503	SO:0001583	missense	170384			BC036037	CCDS7333.1, CCDS60558.1	10q22.3	2014-01-02			ENSG00000196968	ENSG00000196968		"""Fucosyltransferases"""	19233	protein-coding gene	gene with protein product						11698403, 24318988	Standard	NM_173540		Approved	MGC33202	uc001jva.3	Q495W5	OTTHUMG00000018483	ENST00000372841.3:c.1177G>C	10.37:g.75533416G>C	ENSP00000361932:p.Asp393His	Somatic		WXS	Illumina HiSeq	Phase_I	Q495W7|Q8IYE4	Missense_Mutation	SNP	ENST00000372841.3	37	CCDS7333.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.841180	0.91197	.	.	ENSG00000196968	ENST00000372841;ENST00000394790	T;T	0.24908	1.83;1.83	5.68	5.68	0.88126	.	0.042189	0.85682	D	0.000000	T	0.44286	0.1286	M	0.83483	2.645	0.80722	D	1	P;P	0.42248	0.774;0.732	P;B	0.44897	0.463;0.333	T	0.49698	-0.8912	10	0.72032	D	0.01	-32.6689	19.786	0.96437	0.0:0.0:1.0:0.0	.	393;393	Q495W5;Q495W5-2	FUT11_HUMAN;.	H	393	ENSP00000361932:D393H;ENSP00000378270:D393H	ENSP00000361932:D393H	D	+	1	0	FUT11	75203422	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.062000	0.89475	2.676000	0.91093	0.563000	0.77884	GAC		0.572	FUT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048689.1		NM_173540	
GAS6	2621	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	114549554	114549554	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr13:114549554T>G	ENST00000327773.6	-	4	435	c.289A>C	c.(289-291)Aac>Cac	p.N97H	GAS6_ENST00000355761.4_Missense_Mutation_p.N43H|GAS6_ENST00000357389.3_Missense_Mutation_p.N97H|GAS6_ENST00000476291.1_5'Flank	NM_000820.2	NP_000811.1	Q14393	GAS6_HUMAN	growth arrest-specific 6	97					activation of protein kinase B activity (GO:0032148)|apoptotic cell clearance (GO:0043277)|B cell chemotaxis (GO:0035754)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to interferon-alpha (GO:0035457)|cellular response to starvation (GO:0009267)|cellular response to vitamin K (GO:0071307)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|extracellular matrix assembly (GO:0085029)|fusion of virus membrane with host plasma membrane (GO:0019064)|hematopoietic stem cell migration to bone marrow (GO:0097241)|leukocyte migration (GO:0050900)|macrophage cytokine production (GO:0010934)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of oligodendrocyte apoptotic process (GO:1900142)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of renal albumin absorption (GO:2000533)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|peptidyl-serine phosphorylation (GO:0018105)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phagocytosis (GO:0050766)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of TOR signaling (GO:0032008)|post-translational protein modification (GO:0043687)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein targeting to plasma membrane (GO:0072661)|proteolysis (GO:0006508)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|viral entry into host cell (GO:0046718)|viral genome replication (GO:0019079)	cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|platelet alpha granule lumen (GO:0031093)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|phosphatidylserine binding (GO:0001786)|protein tyrosine kinase activator activity (GO:0030296)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|voltage-gated calcium channel activity (GO:0005245)	p.N97H(1)		central_nervous_system(4)|ovary(1)	5	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0176)|all_epithelial(44;0.0104)|all_lung(25;0.0249)|Lung NSC(25;0.0908)|Breast(118;0.188)				CCATACTTGTTGATGCAGTCT	0.542																																																	1	Substitution - Missense(1)	kidney(1)											174.0	152.0	160.0					13																	114549554		2203	4300	6503	SO:0001583	missense	2621				CCDS45072.1	13q34	2008-07-18			ENSG00000183087	ENSG00000183087			4168	protein-coding gene	gene with protein product	"""AXL stimulatory factor"""	600441		AXLLG		8336730	Standard	NM_000820		Approved	AXSF, FLJ34709, DKFZp666G247	uc001vud.3	Q14393	OTTHUMG00000017395	ENST00000327773.6:c.289A>C	13.37:g.114549554T>G	ENSP00000331831:p.Asn97His	Somatic		WXS	Illumina HiSeq	Phase_I	B3KRQ7|B3KVL4|E9PBL7|Q6IMN1|Q7Z7N3	Missense_Mutation	SNP	ENST00000327773.6	37	CCDS45072.1	.	.	.	.	.	.	.	.	.	.	T	6.883	0.532357	0.13127	.	.	ENSG00000183087	ENST00000357389;ENST00000355761;ENST00000327773	D;D;D	0.99771	-6.71;-2.3;-6.71	3.81	-0.607	0.11615	.	.	.	.	.	D	0.98924	0.9635	M	0.75777	2.31	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	D	0.99978	1.2340	9	0.34782	T	0.22	0.1569	5.4147	0.16368	0.0:0.1042:0.3281:0.5677	.	97	Q14393-2	.	H	97;43;97	ENSP00000349962:N97H;ENSP00000348003:N43H;ENSP00000331831:N97H	ENSP00000331831:N97H	N	-	1	0	GAS6	113564389	0.070000	0.21116	0.000000	0.03702	0.002000	0.02628	0.141000	0.16076	-0.116000	0.11893	-2.436000	0.00213	AAC		0.542	GAS6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045946.2		NM_000820	
IPO9	55705	broad.mit.edu;ucsc.edu	37	1	201845133	201845133	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr1:201845133G>T	ENST00000361565.4	+	24	3146	c.3077G>T	c.(3076-3078)gGc>gTc	p.G1026V		NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	1026					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)	p.G1026V(1)		cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						ATGTTTTCAGGCCACCTTAAT	0.483											OREG0014090	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											251.0	247.0	249.0					1																	201845133		2203	4300	6503	SO:0001583	missense	55705			AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700		"""Importins"""	19425	protein-coding gene	gene with protein product						11823430, 10574461	Standard	NM_018085		Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.3077G>T	1.37:g.201845133G>T	ENSP00000354742:p.Gly1026Val	Somatic	2124	WXS	Illumina GAIIx	Phase_I	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Missense_Mutation	SNP	ENST00000361565.4	37	CCDS1415.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.18|16.18	3.050019|3.050019	0.55218|0.55218	.|.	.|.	ENSG00000198700|ENSG00000198700	ENST00000456707|ENST00000361565	.|T	.|0.67171	.|-0.25	5.67|5.67	5.67|5.67	0.87782|0.87782	.|Armadillo-type fold (1);	.|0.250711	.|0.48767	.|D	.|0.000161	T|T	0.50377|0.50377	0.1612|0.1612	N|N	0.22421|0.22421	0.69|0.69	0.58432|0.58432	D|D	0.999998|0.999998	.|B	.|0.06786	.|0.001	.|B	.|0.04013	.|0.001	T|T	0.42531|0.42531	-0.9446|-0.9446	6|10	0.72032|0.27785	D|T	0.01|0.31	.|.	10.9707|10.9707	0.47438|0.47438	0.0851:0.0:0.9149:0.0|0.0851:0.0:0.9149:0.0	.|.	.|1026	.|Q96P70	.|IPO9_HUMAN	S|V	81|1026	.|ENSP00000354742:G1026V	ENSP00000387761:A81S|ENSP00000354742:G1026V	A|G	+|+	1|2	0|0	IPO9|IPO9	200111756|200111756	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.854000|4.854000	0.62918|0.62918	2.835000|2.835000	0.97688|0.97688	0.591000|0.591000	0.81541|0.81541	GCC|GGC		0.483	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1		NM_018085	
KDM5C	8242	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	53228204	53228204	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chrX:53228204T>G	ENST00000375401.3	-	15	2730	c.2198A>C	c.(2197-2199)cAc>cCc	p.H733P	KDM5C_ENST00000375379.3_Missense_Mutation_p.H733P|KDM5C_ENST00000375383.3_Missense_Mutation_p.H692P|KDM5C_ENST00000465402.1_5'Flank|KDM5C_ENST00000404049.3_Missense_Mutation_p.H732P|KDM5C_ENST00000452825.3_Missense_Mutation_p.H666P	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	733					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.H666P(1)|p.H733P(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						ATCATTGATGTGGGAAAGGCA	0.577			"""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)											135.0	103.0	114.0					X																	53228204		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.2198A>C	X.37:g.53228204T>G	ENSP00000364550:p.His733Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Missense_Mutation	SNP	ENST00000375401.3	37	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	t	20.8	4.047081	0.75846	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	D;D;D;D;D	0.95821	-3.82;-3.82;-3.82;-3.82;-3.82	4.69	4.69	0.59074	Zinc finger, C5HC2-type (1);	0.000000	0.85682	D	0.000000	D	0.97967	0.9331	M	0.92507	3.315	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.999	D	0.98528	1.0626	10	0.87932	D	0	-8.6508	11.2689	0.49127	0.0:0.0:0.0:1.0	.	666;732;733	F5H3T1;B0QZ44;P41229	.;.;KDM5C_HUMAN	P	666;733;732;733;692	ENSP00000445176:H666P;ENSP00000364550:H733P;ENSP00000385394:H732P;ENSP00000364528:H733P;ENSP00000364532:H692P	ENSP00000364528:H733P	H	-	2	0	KDM5C	53244929	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.161000	0.71868	1.556000	0.49512	0.422000	0.28245	CAC		0.577	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2		NM_004187	
KRT27	342574	broad.mit.edu;ucsc.edu	37	17	38933946	38933946	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr17:38933946A>T	ENST00000301656.3	-	6	1051	c.1011T>A	c.(1009-1011)agT>agA	p.S337R	KRT27_ENST00000540723.1_5'UTR	NM_181537.3	NP_853515.2			keratin 27									p.S337R(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				CACAGTAGTTACTCTCGGTCT	0.527																																																	1	Substitution - Missense(1)	kidney(1)											147.0	146.0	147.0					17																	38933946		2203	4300	6503	SO:0001583	missense	342574			AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30841	protein-coding gene	gene with protein product			"""keratin 25C"""	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.1011T>A	17.37:g.38933946A>T	ENSP00000301656:p.Ser337Arg	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000301656.3	37	CCDS11375.1	.	.	.	.	.	.	.	.	.	.	a	9.507	1.104668	0.20632	.	.	ENSG00000171446	ENST00000301656	D	0.88431	-2.38	5.7	1.25	0.21368	Filament (1);	0.085006	0.51477	D	0.000089	T	0.78413	0.4279	L	0.31294	0.92	0.23162	N	0.998192	B	0.06786	0.001	B	0.08055	0.003	T	0.67650	-0.5616	10	0.72032	D	0.01	.	3.422	0.07397	0.194:0.2089:0.4902:0.107	.	337	Q7Z3Y8	K1C27_HUMAN	R	337	ENSP00000301656:S337R	ENSP00000301656:S337R	S	-	3	2	KRT27	36187472	0.000000	0.05858	1.000000	0.80357	0.140000	0.21249	-1.281000	0.02802	0.438000	0.26450	-0.802000	0.03209	AGT		0.527	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1		NM_181537	
KSR2	283455	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	118020150	118020150	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr12:118020150G>C	ENST00000339824.5	-	6	1913	c.1186C>G	c.(1186-1188)Cca>Gca	p.P396A	KSR2_ENST00000302438.5_Missense_Mutation_p.P93A|KSR2_ENST00000425217.1_Missense_Mutation_p.P367A|KSR2_ENST00000545002.1_5'UTR			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	396					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.P428A(1)|p.P93A(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GACCAGCGTGGCACTGACAGT	0.582																																																	2	Substitution - Missense(2)	kidney(2)											115.0	119.0	118.0					12																	118020150		2112	4228	6340	SO:0001583	missense	283455			AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.1186C>G	12.37:g.118020150G>C	ENSP00000339952:p.Pro396Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A0PJT2|Q3B828|Q8N775	Missense_Mutation	SNP	ENST00000339824.5	37		.	.	.	.	.	.	.	.	.	.	G	13.88	2.369413	0.42003	.	.	ENSG00000171435	ENST00000425217;ENST00000339824;ENST00000302438;ENST00000542378	T;T;T	0.58940	0.3;0.3;0.3	4.94	3.1	0.35709	.	0.062089	0.64402	D	0.000003	T	0.46502	0.1396	L	0.39898	1.24	0.54753	D	0.999989	P	0.42871	0.792	B	0.39339	0.297	T	0.40308	-0.9570	10	0.54805	T	0.06	.	10.1663	0.42882	0.1678:0.0:0.8322:0.0	.	396	Q6VAB6	KSR2_HUMAN	A	367;396;93;68	ENSP00000389715:P367A;ENSP00000339952:P396A;ENSP00000305466:P93A	ENSP00000305466:P93A	P	-	1	0	KSR2	116504533	1.000000	0.71417	0.971000	0.41717	0.194000	0.23727	8.891000	0.92485	0.495000	0.27882	0.313000	0.20887	CCA		0.582	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2		NM_173598	
LAMP3	27074	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	182871600	182871600	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr3:182871600G>A	ENST00000265598.3	-	2	884	c.629C>T	c.(628-630)aCg>aTg	p.T210M	LAMP3_ENST00000466939.1_Missense_Mutation_p.T186M	NM_014398.3	NP_055213.2	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3	210	Thr-rich.				cell proliferation (GO:0008283)|immune system process (GO:0002376)	alveolar lamellar body membrane (GO:0097233)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)		p.T210M(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(2)	28	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)			CCCAGGAACCGTGGAGGCAGG	0.557																																																	1	Substitution - Missense(1)	kidney(1)											101.0	100.0	100.0					3																	182871600		2203	4300	6503	SO:0001583	missense	27074			AB013924	CCDS3242.1	3q26.3-q27	2011-11-24			ENSG00000078081	ENSG00000078081		"""CD molecules"""	14582	protein-coding gene	gene with protein product		605883				9721848	Standard	NM_014398		Approved	LAMP, TSC403, DC-LAMP, DCLAMP, CD208	uc003flh.4	Q9UQV4	OTTHUMG00000158387	ENST00000265598.3:c.629C>T	3.37:g.182871600G>A	ENSP00000265598:p.Thr210Met	Somatic		WXS	Illumina HiSeq	Phase_I	D3DNS4|O94781|Q8NEC8	Missense_Mutation	SNP	ENST00000265598.3	37	CCDS3242.1	.	.	.	.	.	.	.	.	.	.	g	15.11	2.736649	0.49045	.	.	ENSG00000078081	ENST00000265598;ENST00000466939	T;T	0.36520	1.25;1.25	5.81	-3.86	0.04230	.	1.431570	0.04239	N	0.336618	T	0.28466	0.0704	L	0.45581	1.43	0.09310	N	1	P	0.39520	0.676	B	0.35413	0.202	T	0.26916	-1.0089	10	0.38643	T	0.18	4.6752	7.935	0.29925	0.5882:0.1196:0.2922:0.0	.	210	Q9UQV4	LAMP3_HUMAN	M	210;186	ENSP00000265598:T210M;ENSP00000418912:T186M	ENSP00000265598:T210M	T	-	2	0	LAMP3	184354294	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.123000	0.10611	-1.317000	0.02292	-0.136000	0.14681	ACG		0.557	LAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350863.1			
MAGEE2	139599	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	75004670	75004670	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chrX:75004670C>A	ENST00000373359.2	-	1	409	c.217G>T	c.(217-219)Gac>Tac	p.D73Y		NM_138703.4	NP_619648.1	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	73								p.D73Y(2)		autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GACTGCTCGTCGATCAGGACC	0.557																																																	2	Substitution - Missense(2)	autonomic_ganglia(1)|kidney(1)											40.0	38.0	39.0					X																	75004670		2203	4300	6503	SO:0001583	missense	139599			AF490509	CCDS14431.1	Xq13	2008-02-05			ENSG00000186675	ENSG00000186675			24935	protein-coding gene	gene with protein product		300760				11454705	Standard	NM_138703		Approved	HCA3	uc004ecj.2	Q8TD90	OTTHUMG00000021870	ENST00000373359.2:c.217G>T	X.37:g.75004670C>A	ENSP00000362457:p.Asp73Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JSI5	Missense_Mutation	SNP	ENST00000373359.2	37	CCDS14431.1	.	.	.	.	.	.	.	.	.	.	C	8.446	0.852016	0.17034	.	.	ENSG00000186675	ENST00000373359	T	0.04234	3.67	2.87	1.09	0.20402	.	.	.	.	.	T	0.04003	0.0112	N	0.19112	0.55	0.18873	N	0.999986	D	0.53885	0.963	P	0.45310	0.476	T	0.41910	-0.9482	9	0.66056	D	0.02	.	4.6539	0.12608	0.0:0.6797:0.0:0.3203	.	73	Q8TD90	MAGE2_HUMAN	Y	73	ENSP00000362457:D73Y	ENSP00000362457:D73Y	D	-	1	0	MAGEE2	74921395	0.252000	0.23972	0.357000	0.25798	0.875000	0.50365	0.303000	0.19210	0.169000	0.19679	-0.305000	0.09177	GAC		0.557	MAGEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057288.1		NM_138703	
MINK1	50488	broad.mit.edu;hgsc.bcm.edu	37	17	4794820	4794820	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr17:4794820G>A	ENST00000355280.6	+	16	2006	c.1810G>A	c.(1810-1812)Gac>Aac	p.D604N	MINK1_ENST00000453408.3_Missense_Mutation_p.D584N|MINK1_ENST00000347992.7_Missense_Mutation_p.D604N	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1									p.D604N(2)		central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						GTCCCTGCAGGACCAGCCCAC	0.677																																																	2	Substitution - Missense(2)	kidney(2)											39.0	51.0	47.0					17																	4794820		2088	4213	6301	SO:0001583	missense	50488			AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"""misshapen/NIK-related kinase"""	609426	"""misshapen-like kinase 1 (zebrafish)"""			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.1810G>A	17.37:g.4794820G>A	ENSP00000347427:p.Asp604Asn	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000355280.6	37	CCDS45588.1	.	.	.	.	.	.	.	.	.	.	G	33	5.231166	0.95207	.	.	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;T	0.47177	0.85;0.85;0.85	5.02	5.02	0.67125	.	0.111770	0.64402	D	0.000019	T	0.63977	0.2557	L	0.55481	1.735	0.58432	D	0.999998	D;D;D;D	0.67145	0.996;0.996;0.993;0.996	D;D;D;D	0.73708	0.981;0.981;0.956;0.981	T	0.65973	-0.6038	10	0.72032	D	0.01	.	15.8757	0.79159	0.0:0.0:1.0:0.0	.	604;584;604;604	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	N	604;584;604	ENSP00000347427:D604N;ENSP00000406487:D584N;ENSP00000269296:D604N	ENSP00000269296:D604N	D	+	1	0	MINK1	4735596	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.120000	0.94369	2.615000	0.88500	0.561000	0.74099	GAC		0.677	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1		NM_015716	
KMT2B	9757	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	36219945	36219945	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr19:36219945C>T	ENST00000222270.7	+	21	4747	c.4747C>T	c.(4747-4749)Ctc>Ttc	p.L1583F	KMT2B_ENST00000420124.1_Missense_Mutation_p.L1583F|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1583					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.L1585F(1)									TCAGTGTGCACTCTGCCTCAA	0.592																																																	1	Substitution - Missense(1)	kidney(1)											78.0	81.0	80.0					19																	36219945		2072	4210	6282	SO:0001583	missense	9757			AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.4747C>T	19.37:g.36219945C>T	ENSP00000222270:p.Leu1583Phe	Somatic		WXS	Illumina HiSeq	Phase_I	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	37	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.750094	0.49257	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.87809	-2.3;-2.3	5.13	5.13	0.70059	.	0.000000	0.40385	N	0.001114	D	0.84047	0.5386	L	0.49350	1.555	0.58432	D	0.999994	P	0.48503	0.911	B	0.42916	0.402	T	0.81632	-0.0845	10	0.18710	T	0.47	.	16.1185	0.81325	0.0:1.0:0.0:0.0	.	1583	Q9UMN6	MLL4_HUMAN	F	1583	ENSP00000222270:L1583F;ENSP00000398837:L1583F	ENSP00000222270:L1583F	L	+	1	0	AD000671.1	40911785	0.958000	0.32768	0.982000	0.44146	0.826000	0.46750	2.126000	0.42026	2.669000	0.90835	0.655000	0.94253	CTC		0.592	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_014727	
MLLT4	4301	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	168297599	168297599	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr6:168297599C>T	ENST00000447894.2	+	10	1264	c.1264C>T	c.(1264-1266)Cag>Tag	p.Q422*	MLLT4_ENST00000392112.1_Nonsense_Mutation_p.Q406*|MLLT4_ENST00000351017.4_Nonsense_Mutation_p.Q422*|MLLT4_ENST00000400822.3_Nonsense_Mutation_p.Q421*|MLLT4_ENST00000344191.4_Nonsense_Mutation_p.Q422*|MLLT4_ENST00000392108.3_Nonsense_Mutation_p.Q422*|MLLT4_ENST00000366806.2_Nonsense_Mutation_p.Q422*			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	422					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)	p.Q406*(2)|p.Q422*(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		TTACCGCCTTCAGTTAAGTGT	0.428			T	MLL	AL																																			Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	3	Substitution - Nonsense(3)	kidney(2)|breast(1)											106.0	98.0	101.0					6																	168297599		2203	4300	6503	SO:0001587	stop_gained	4301			AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.1264C>T	6.37:g.168297599C>T	ENSP00000404595:p.Gln422*	Somatic		WXS	Illumina HiSeq	Phase_I	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Nonsense_Mutation	SNP	ENST00000447894.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.157943|8.157943	0.98683|0.98683	.|.	.|.	ENSG00000130396|ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894|ENST00000423229	.|.	.|.	.|.	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.69006	.|0.3063	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.67806	.|-0.5575	.|3	0.24483|.	T|.	0.36|.	-4.1676|-4.1676	18.8669|18.8669	0.92296|0.92296	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	422;422;422;422;406;422;421;422|120	.|.	ENSP00000345834:Q422X|.	Q|S	+|+	1|2	0|0	MLLT4|MLLT4	168040448|168040448	1.000000|1.000000	0.71417|0.71417	0.358000|0.358000	0.25811|0.25811	0.965000|0.965000	0.64279|0.64279	7.508000|7.508000	0.81686|0.81686	2.447000|2.447000	0.82792|0.82792	0.591000|0.591000	0.81541|0.81541	CAG|TCA		0.428	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1		NM_005936	
MRPS21	54460	broad.mit.edu;hgsc.bcm.edu	37	1	150266811	150266811	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr1:150266811G>A	ENST00000369084.5	+	1	472	c.25G>A	c.(25-27)Gcc>Acc	p.A9T	MRPS21_ENST00000309092.7_Missense_Mutation_p.A9T	NM_018997.3	NP_061870.1	P82921	RT21_HUMAN	mitochondrial ribosomal protein S21	9					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.A9T(1)		kidney(1)|large_intestine(1)|lung(1)|pancreas(1)	4	Lung NSC(24;5.57e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			GAAGTTCATCGCCAGGACTGT	0.473																																																	1	Substitution - Missense(1)	kidney(1)											108.0	94.0	99.0					1																	150266811		2203	4300	6503	SO:0001583	missense	54460			AB051353	CCDS950.1	1q21	2012-09-13			ENSG00000187145			"""Mitochondrial ribosomal proteins / small subunits"""	14046	protein-coding gene	gene with protein product		611984					Standard	NM_031901		Approved		uc001euk.3	P82921	OTTHUMG00000012544	ENST00000369084.5:c.25G>A	1.37:g.150266811G>A	ENSP00000358080:p.Ala9Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TB11|Q9BST6	Missense_Mutation	SNP	ENST00000369084.5	37	CCDS950.1	.	.	.	.	.	.	.	.	.	.	G	32	5.122348	0.94429	.	.	ENSG00000187145	ENST00000309092;ENST00000369084	T;T	0.35048	1.33;1.33	5.41	5.41	0.78517	.	.	.	.	.	T	0.47229	0.1434	.	.	.	0.42650	D	0.99344	D	0.76494	0.999	P	0.58266	0.836	T	0.42172	-0.9467	8	0.52906	T	0.07	.	16.2255	0.82286	0.0:0.0:1.0:0.0	.	9	P82921	RT21_HUMAN	T	9	ENSP00000312395:A9T;ENSP00000358080:A9T	ENSP00000312395:A9T	A	+	1	0	MRPS21	148533435	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.988000	0.56951	2.826000	0.97356	0.655000	0.94253	GCC		0.473	MRPS21-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035813.1		NM_018997	
MUC16	94025	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	9009312	9009313	+	Missense_Mutation	DNP	GA	GA	AT	rs553681175		TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr19:9009312_9009313GA>AT	ENST00000397910.4	-	40	39363_39364	c.39160_39161TC>AT	c.(39160-39162)TCc>ATc	p.S13054I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13056	SEA 7. {ECO:0000255|PROSITE- ProRule:PRU00188}.				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.S13054F(1)|p.S206F(1)|p.S206I(1)|p.S13054I(1)|p.S13054T(1)|p.S206T(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						GCCGACACTGGAGTTCTTGAAC	0.52																																																	6	Substitution - Missense(6)	kidney(6)																																								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.39160_39161delinsAT	19.37:g.9009312_9009313delinsAT	ENSP00000381008:p.Ser13054Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.520	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1		NM_024690	
NCKAP5	344148	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	133541011	133541011	+	Missense_Mutation	SNP	C	C	A	rs371372513		TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr2:133541011C>A	ENST00000409261.1	-	14	3746	c.3373G>T	c.(3373-3375)Gcc>Tcc	p.A1125S	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.A1125S	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1125	Ser-rich.							p.A1125S(1)		NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						TGGCTTTTGGCGGGTGATGAG	0.502																																																	1	Substitution - Missense(1)	kidney(1)						C	SER/ALA,	0,4188		0,0,2094	157.0	164.0	162.0		3373,	1.5	0.0	2		162	1,8453		0,1,4226	no	missense,intron	NCKAP5	NM_207363.2,NM_207481.3	99,	0,1,6320	AA,AC,CC		0.0118,0.0,0.0079	benign,	1125/1910,	133541011	1,12641	2094	4227	6321	SO:0001583	missense	344148			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.3373G>T	2.37:g.133541011C>A	ENSP00000387128:p.Ala1125Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	c	0.208	-1.039366	0.02013	0.0	1.18E-4	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.08720	3.06;3.06	5.24	1.46	0.22682	.	0.992366	0.08158	N	0.988883	T	0.03095	0.0091	N	0.03608	-0.345	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.47459	-0.9116	10	0.18710	T	0.47	.	1.7347	0.02939	0.5677:0.1727:0.095:0.1646	.	1125	O14513	NCKP5_HUMAN	S	1125	ENSP00000387128:A1125S;ENSP00000380603:A1125S	ENSP00000380603:A1125S	A	-	1	0	NCKAP5	133257481	0.000000	0.05858	0.003000	0.11579	0.028000	0.11728	0.367000	0.20382	0.091000	0.17302	-0.291000	0.09656	GCC		0.502	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1		NM_207481	
OR4M2	390538	broad.mit.edu;hgsc.bcm.edu	37	15	22369272	22369272	+	Nonsense_Mutation	SNP	G	G	T			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr15:22369272G>T	ENST00000332663.2	+	1	795	c.697G>T	c.(697-699)Gag>Tag	p.E233*	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E233*(1)		NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		AGGCTCAGGTGAGAATACCAA	0.463																																																	1	Substitution - Nonsense(1)	kidney(1)											328.0	225.0	259.0					15																	22369272		2203	4300	6503	SO:0001587	stop_gained	390538			AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"""GPCR / Class A : Olfactory receptors"""	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.697G>T	15.37:g.22369272G>T	ENSP00000329467:p.Glu233*	Somatic		WXS	Illumina HiSeq	Phase_I	B9EH16|Q6IEY2	Nonsense_Mutation	SNP	ENST00000332663.2	37	CCDS32172.1	.	.	.	.	.	.	.	.	.	.	.	20.9	4.069657	0.76301	.	.	ENSG00000182974	ENST00000332663	.	.	.	2.5	1.56	0.23342	.	0.147283	0.32068	N	0.006636	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-13.618	3.1274	0.06412	0.1553:0.0:0.5837:0.261	.	.	.	.	X	233	.	ENSP00000329467:E233X	E	+	1	0	OR4M2	19870636	0.000000	0.05858	0.746000	0.31095	0.854000	0.48673	-0.049000	0.11924	0.390000	0.25115	0.448000	0.29417	GAG		0.463	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1			
PCDHA2	56146	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	140174870	140174870	+	Silent	SNP	G	G	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr5:140174870G>A	ENST00000526136.1	+	1	321	c.321G>A	c.(319-321)gaG>gaA	p.E107E	PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000520672.2_Silent_p.E107E|PCDHA2_ENST00000378132.1_Silent_p.E107E	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	107	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E107E(2)		NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCACGTGGAGGTGATCGTGG	0.517																																																	2	Substitution - coding silent(2)	kidney(2)											108.0	123.0	118.0					5																	140174870		2203	4300	6503	SO:0001819	synonymous_variant	56146			AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"""Cadherins / Protocadherins : Clustered"""	8668	other	complex locus constituent	"""KIAA0345-like 12"""	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.321G>A	5.37:g.140174870G>A		Somatic		WXS	Illumina HiSeq	Phase_I	O75287|Q9BTV3	Silent	SNP	ENST00000526136.1	37	CCDS54914.1																																																																																				0.517	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3		NM_018905	
PEPD	5184	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	33902626	33902626	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr19:33902626C>A	ENST00000244137.7	-	11	803	c.770G>T	c.(769-771)gGa>gTa	p.G257V	PEPD_ENST00000436370.3_Missense_Mutation_p.G193V|PEPD_ENST00000397032.4_Missense_Mutation_p.G216V	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	257					cellular amino acid metabolic process (GO:0006520)|collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)	aminopeptidase activity (GO:0004177)|dipeptidase activity (GO:0016805)|manganese ion binding (GO:0030145)|metallocarboxypeptidase activity (GO:0004181)	p.G257V(1)		endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	17	Esophageal squamous(110;0.137)					TCCGGCGTGTCCGTAGTGTAG	0.597																																																	1	Substitution - Missense(1)	kidney(1)											49.0	54.0	52.0					19																	33902626		2036	4171	6207	SO:0001583	missense	5184			BC015027	CCDS42544.1, CCDS54244.1, CCDS54245.1	19q13.11	2008-02-05				ENSG00000124299	3.4.13.9		8840	protein-coding gene	gene with protein product	"""prolidase"""	613230				2925654, 1972707	Standard	NM_000285		Approved		uc002nur.4	P12955		ENST00000244137.7:c.770G>T	19.37:g.33902626C>A	ENSP00000244137:p.Gly257Val	Somatic		WXS	Illumina HiSeq	Phase_I	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	Missense_Mutation	SNP	ENST00000244137.7	37	CCDS42544.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.974274	0.53720	.	.	ENSG00000124299	ENST00000244137;ENST00000397032;ENST00000436370	T;T;T	0.75367	-0.93;-0.93;-0.93	5.06	5.06	0.68205	Peptidase M24, structural domain (3);	0.000000	0.85682	D	0.000000	T	0.80778	0.4688	L	0.41710	1.295	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.82619	-0.0368	10	0.87932	D	0	-14.0637	13.9282	0.63975	0.0:1.0:0.0:0.0	.	193;216;257	E9PCE8;A8MX47;P12955	.;.;PEPD_HUMAN	V	257;216;193	ENSP00000244137:G257V;ENSP00000380226:G216V;ENSP00000391890:G193V	ENSP00000244137:G257V	G	-	2	0	PEPD	38594466	1.000000	0.71417	0.901000	0.35422	0.064000	0.16182	6.020000	0.70826	2.352000	0.79861	0.561000	0.74099	GGA		0.597	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3		NM_000285	
PLA2G12A	81579	broad.mit.edu;hgsc.bcm.edu	37	4	110650931	110650931	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr4:110650931A>G	ENST00000243501.5	-	1	302	c.35T>C	c.(34-36)cTg>cCg	p.L12P	PLA2G12A_ENST00000502283.1_Missense_Mutation_p.L12P	NM_030821.4	NP_110448.2	Q9BZM1	PG12A_HUMAN	phospholipase A2, group XIIA	12					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)	p.L12P(1)		kidney(1)|lung(1)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000268)		GAGGAGGAGCAGGAGGGTGAG	0.701																																																	1	Substitution - Missense(1)	kidney(1)											25.0	21.0	23.0					4																	110650931		2185	4269	6454	SO:0001583	missense	81579				CCDS3686.1	4q25	2010-11-24	2004-01-13	2004-01-14	ENSG00000123739	ENSG00000123739	3.1.1.4		18554	protein-coding gene	gene with protein product		611652	"""phospholipase A2, group XII"""	PLA2G12		11031251	Standard	NM_030821		Approved		uc003hzp.3	Q9BZM1	OTTHUMG00000131915	ENST00000243501.5:c.35T>C	4.37:g.110650931A>G	ENSP00000243501:p.Leu12Pro	Somatic		WXS	Illumina HiSeq	Phase_I	Q9BZ89	Missense_Mutation	SNP	ENST00000243501.5	37	CCDS3686.1	.	.	.	.	.	.	.	.	.	.	A	17.24	3.338442	0.60963	.	.	ENSG00000123739	ENST00000243501;ENST00000502283	.	.	.	3.72	2.54	0.30619	.	0.685334	0.13048	N	0.417950	T	0.46151	0.1378	L	0.44542	1.39	0.80722	D	1	B;B	0.10296	0.003;0.003	B;B	0.14023	0.01;0.01	T	0.43130	-0.9410	9	0.66056	D	0.02	-24.887	5.2494	0.15514	0.7239:0.1786:0.0974:0.0	.	12;12	Q542Y6;Q9BZM1	.;PG12A_HUMAN	P	12	.	ENSP00000243501:L12P	L	-	2	0	PLA2G12A	110870380	0.973000	0.33851	0.650000	0.29550	0.324000	0.28378	2.505000	0.45424	0.607000	0.29982	0.260000	0.18958	CTG		0.701	PLA2G12A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254868.3			
POSTN	10631	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	38154095	38154095	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr13:38154095C>A	ENST00000379747.4	-	12	1680	c.1563G>T	c.(1561-1563)ttG>ttT	p.L521F	POSTN_ENST00000541179.1_Missense_Mutation_p.L521F|POSTN_ENST00000541481.1_Missense_Mutation_p.L521F|POSTN_ENST00000379742.4_Missense_Mutation_p.L521F|POSTN_ENST00000379743.4_Missense_Mutation_p.L521F|POSTN_ENST00000379749.4_Missense_Mutation_p.L521F	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	521	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)	p.L521F(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		GGAGCTCTTTCAAGTCTGCAG	0.398																																																	1	Substitution - Missense(1)	kidney(1)											166.0	149.0	155.0					13																	38154095		2203	4300	6503	SO:0001583	missense	10631			D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.1563G>T	13.37:g.38154095C>A	ENSP00000369071:p.Leu521Phe	Somatic		WXS	Illumina HiSeq	Phase_I	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	37	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.630754	0.67015	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	D;D;D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.27;-3.27;-3.27	5.42	4.58	0.56647	FAS1 domain (4);	0.124470	0.56097	D	0.000032	D	0.97018	0.9026	M	0.92604	3.325	0.51233	D	0.999915	D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.999;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.999;0.995;0.999;0.996;0.995;0.995	D	0.96819	0.9602	10	0.49607	T	0.09	-3.8608	10.9396	0.47266	0.0:0.8011:0.0:0.1989	.	521;521;521;521;521;521;521	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	F	521	ENSP00000437959:L521F;ENSP00000369073:L521F;ENSP00000369071:L521F;ENSP00000369067:L521F;ENSP00000369066:L521F;ENSP00000437953:L521F	ENSP00000369066:L521F	L	-	3	2	POSTN	37052095	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.455000	0.44988	1.420000	0.47138	0.591000	0.81541	TTG		0.398	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2		NM_006475	
RAG2	5897	hgsc.bcm.edu	37	11	36614395	36614396	+	Frame_Shift_Ins	INS	-	-	G	rs370624669		TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr11:36614395_36614396insG	ENST00000311485.3	-	2	1484_1485	c.1323_1324insC	c.(1321-1326)cccgccfs	p.A442fs	C11orf74_ENST00000534635.1_5'Flank|C11orf74_ENST00000347206.4_5'Flank|RAG2_ENST00000528428.1_5'Flank|C11orf74_ENST00000446510.2_5'Flank|C11orf74_ENST00000334307.5_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	442					B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				TAGATCATGGCGGGTTTGTTGA	0.495									Familial Hemophagocytic Lymphohistiocytosis																																								0																																										SO:0001589	frameshift_variant	5897	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.1324dupC	11.37:g.36614398_36614398dupG	ENSP00000308620:p.Ala442fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K9E9|Q8TBL4	Frame_Shift_Ins	INS	ENST00000311485.3	37	CCDS7903.1																																																																																				0.495	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1		NM_000536	
RPL31	6160	broad.mit.edu;hgsc.bcm.edu	37	2	101622534	101622534	+	Splice_Site	SNP	G	G	C			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr2:101622534G>C	ENST00000264258.3	+	4	947		c.e4+1		RPL31_ENST00000409028.4_Splice_Site|RPL31_ENST00000409650.1_Splice_Site|RPL31_ENST00000409038.1_Splice_Site|RPL31_ENST00000409733.1_Splice_Site|RPL31_ENST00000409711.1_3'UTR|RPL31_ENST00000409320.3_Missense_Mutation_p.S116T	NM_000993.4	NP_000984.1	P62899	RL31_HUMAN	ribosomal protein L31						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)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.?(1)		kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(3)	8						ACTTTCAAAAGTAAGTTCTCC	0.378																																																	1	Unknown(1)	kidney(1)											47.0	45.0	46.0					2																	101622534		2203	4300	6503	SO:0001630	splice_region_variant	6160			X15940	CCDS2049.1, CCDS46373.1, CCDS46374.1	2q11.2	2011-04-06			ENSG00000071082	ENSG00000071082		"""L ribosomal proteins"""	10334	protein-coding gene	gene with protein product						2780320, 11875025	Standard	NM_000993		Approved	L31	uc010fiu.1	P62899	OTTHUMG00000130687	ENST00000264258.3:c.346+1G>C	2.37:g.101622534G>C		Somatic		WXS	Illumina HiSeq	Phase_I	B7Z4K2|D3DVJ4|P12947|Q53SQ5|Q6IRZ0|Q6LBJ6	Missense_Mutation	SNP	ENST00000264258.3	37	CCDS2049.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.2|23.2	4.384501|4.384501	0.82792|0.82792	.|.	.|.	ENSG00000071082|ENSG00000071082	ENST00000264258;ENST00000409028;ENST00000409733;ENST00000409650;ENST00000409038;ENST00000441435|ENST00000409320	.|.	.|.	.|.	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	.|.	.|.	.|.	.|.	.|T	.|0.51618	.|0.1685	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	.|T	.|0.43245	.|-0.9403	.|6	.|.	.|.	.|.	.|.	18.5932|18.5932	0.91222|0.91222	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|116	.|Q6IRZ0	.|.	.|T	-1|116	.|.	.|.	.|S	+|+	.|2	.|0	RPL31|RPL31	100988966|100988966	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	9.448000|9.448000	0.97600|0.97600	2.610000|2.610000	0.88304|0.88304	0.563000|0.563000	0.77884|0.77884	.|AGT		0.378	RPL31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253182.3		NM_001098577	Intron
SCD5	79966	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	83719638	83719638	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr4:83719638T>G	ENST00000319540.4	-	1	372	c.53A>C	c.(52-54)gAa>gCa	p.E18A	SCD5_ENST00000273908.4_Missense_Mutation_p.E18A|SCD5_ENST00000282709.4_Missense_Mutation_p.E18A	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	18					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)	p.E18A(2)		endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				ACGGATTTCTTCCTTGGCGTC	0.721																																																	2	Substitution - Missense(2)	kidney(2)											19.0	21.0	20.0					4																	83719638		2201	4294	6495	SO:0001583	missense	79966			AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"""Fatty acid desaturases"""	21088	protein-coding gene	gene with protein product		608370	"""stearoyl-CoA desaturase 4"""	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.53A>C	4.37:g.83719638T>G	ENSP00000316329:p.Glu18Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	37	CCDS34024.1	.	.	.	.	.	.	.	.	.	.	T	12.51	1.959683	0.34565	.	.	ENSG00000145284	ENST00000319540;ENST00000273908;ENST00000282709	T	0.46819	0.86	4.2	2.92	0.33932	.	0.277510	0.20085	U	0.099567	T	0.22244	0.0536	N	0.08118	0	0.09310	N	1	B;P;B	0.41673	0.288;0.759;0.131	B;B;B	0.34590	0.063;0.186;0.027	T	0.07616	-1.0763	10	0.37606	T	0.19	-10.4899	8.6817	0.34212	0.0:0.0:0.1915:0.8085	.	18;18;18	Q9BSN4;Q86SK9-2;Q86SK9	.;.;SCD5_HUMAN	A	18	ENSP00000316329:E18A	ENSP00000273908:E18A	E	-	2	0	SCD5	83938662	0.096000	0.21769	0.286000	0.24833	0.664000	0.39144	1.019000	0.30014	1.747000	0.51819	0.386000	0.25728	GAA		0.721	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1		NM_024906	
SCRN3	79634	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	175289230	175289230	+	Silent	SNP	G	G	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr2:175289230G>A	ENST00000272732.6	+	7	1027	c.945G>A	c.(943-945)gtG>gtA	p.V315V	SCRN3_ENST00000548921.1_3'UTR|SCRN3_ENST00000409673.3_Silent_p.V308V	NM_001193528.1|NM_024583.4	NP_001180457.1|NP_078859.2	Q0VDG4	SCRN3_HUMAN	secernin 3	315							dipeptidase activity (GO:0016805)	p.V315V(1)|p.V308V(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|urinary_tract(3)	13			OV - Ovarian serous cystadenocarcinoma(117;0.229)			TCATATTTGTGCCACATATTT	0.299																																																	2	Substitution - coding silent(2)	kidney(2)											62.0	57.0	59.0					2																	175289230		2203	4299	6502	SO:0001819	synonymous_variant	79634			AF279776	CCDS2258.1, CCDS54420.1	2q31	2008-02-05			ENSG00000144306	ENSG00000144306			30382	protein-coding gene	gene with protein product		614967				12221138	Standard	NM_024583		Approved	FLJ23142	uc002uiq.3	Q0VDG4	OTTHUMG00000132332	ENST00000272732.6:c.945G>A	2.37:g.175289230G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B4DI11|C9JPC1|D3DPE0|Q7L1C5|Q9H5R5	Silent	SNP	ENST00000272732.6	37	CCDS2258.1																																																																																				0.299	SCRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255451.2		NM_024583	
SLC13A2	9058	hgsc.bcm.edu	37	17	26822695	26822696	+	Frame_Shift_Ins	INS	-	-	G			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr17:26822695_26822696insG	ENST00000314669.5	+	10	1751_1752	c.1331_1332insG	c.(1330-1335)ctgggafs	p.LG444fs	SLC13A2_ENST00000537681.1_Frame_Shift_Ins_p.LG373fs|SLC13A2_ENST00000444914.3_Frame_Shift_Ins_p.LG493fs|SLC13A2_ENST00000545060.1_Frame_Shift_Ins_p.LG401fs	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	444					dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	TCAGAGTGGCTGGGAAACAAGC	0.619																																																	0																																										SO:0001589	frameshift_variant	9058			U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"""Solute carriers"""	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.1334dupG	17.37:g.26822698_26822698dupG	ENSP00000316202:p.Leu444fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Frame_Shift_Ins	INS	ENST00000314669.5	37	CCDS11231.1																																																																																				0.619	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1		NM_003984	
IGFLR1	79713	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	36231433	36231433	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr19:36231433C>T	ENST00000592537.1	-	3	290	c.190G>A	c.(190-192)Gac>Aac	p.D64N	IGFLR1_ENST00000588992.1_Intron|IGFLR1_ENST00000344990.3_Intron|IGFLR1_ENST00000592889.1_Intron|AD000671.6_ENST00000589807.1_3'UTR|IGFLR1_ENST00000587101.1_5'UTR|IGFLR1_ENST00000246532.1_Missense_Mutation_p.D64N|KMT2B_ENST00000607650.1_RNA			Q9H665	IGFR1_HUMAN	IGF-like family receptor 1	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D64N(1)		endometrium(2)|kidney(3)|large_intestine(1)|lung(8)|prostate(1)	15						TCGCCGTGGTCATTGAGTCCG	0.657																																																	1	Substitution - Missense(1)	kidney(1)											39.0	34.0	35.0					19																	36231433		2203	4300	6503	SO:0001583	missense	0			AK026226	CCDS12472.1	19q13.12	2012-10-02	2011-04-04	2011-04-04	ENSG00000126246	ENSG00000126246			23620	protein-coding gene	gene with protein product		614143	"""U2(RNU2) small nuclear RNA auxiliary factor 1-like 4"", ""transmembrane protein 149"""	U2AF1L4, TMEM149		21454693	Standard	NM_024660		Approved	FLJ22573	uc002obd.4	Q9H665		ENST00000592537.1:c.190G>A	19.37:g.36231433C>T	ENSP00000466181:p.Asp64Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q8N5X0	Missense_Mutation	SNP	ENST00000592537.1	37	CCDS12472.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520528	0.85495	.	.	ENSG00000126246	ENST00000246532	D	0.92397	-3.03	4.76	3.72	0.42706	.	0.065095	0.56097	N	0.000021	D	0.86732	0.6003	L	0.34521	1.04	0.37381	D	0.912024	B	0.27498	0.18	B	0.31442	0.13	D	0.85496	0.1188	10	0.49607	T	0.09	-18.3714	9.1812	0.37143	0.0:0.8999:0.0:0.1001	.	64	Q9H665	IGFR1_HUMAN	N	64	ENSP00000246532:D64N	ENSP00000246532:D64N	D	-	1	0	IGFLR1	40923273	0.002000	0.14202	0.055000	0.19348	0.297000	0.27493	0.841000	0.27613	1.372000	0.46190	0.561000	0.74099	GAC		0.657	IGFLR1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459077.1		NM_024660	
TRPC3	7222	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	122853762	122853762	+	Silent	SNP	G	G	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr4:122853762G>A	ENST00000379645.3	-	2	724	c.651C>T	c.(649-651)gaC>gaT	p.D217D	TRPC3_ENST00000264811.5_Silent_p.D144D|TRPC3_ENST00000513531.1_Silent_p.D144D	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	132					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.D144D(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						AGAAGTCGTCGTCCTGCAGCT	0.627																																																	1	Substitution - coding silent(1)	kidney(1)											81.0	73.0	75.0					4																	122853762		2203	4300	6503	SO:0001819	synonymous_variant	7222			Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.651C>T	4.37:g.122853762G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Silent	SNP	ENST00000379645.3	37	CCDS47130.1																																																																																				0.627	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1		NM_003305	
VPS13D	55187	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	12566928	12566928	+	Silent	SNP	T	T	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr1:12566928T>A	ENST00000358136.3	+	69	12946	c.12816T>A	c.(12814-12816)atT>atA	p.I4272I	VPS13D_ENST00000471923.1_5'UTR|SNORA59A_ENST00000459326.1_RNA|VPS13D_ENST00000543766.1_Silent_p.I270I|VPS13D_ENST00000543710.1_Silent_p.I76I|VPS13D_ENST00000356315.4_Silent_p.I4247I|VPS13D_ENST00000496628.1_3'UTR	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)									p.I4272I(1)		NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TGGAGAACATTGACAGCTACT	0.537																																																	1	Substitution - coding silent(1)	kidney(1)											81.0	79.0	80.0					1																	12566928		2203	4300	6503	SO:0001819	synonymous_variant	55187			AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.12816T>A	1.37:g.12566928T>A		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000358136.3	37	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	T	11.20	1.568906	0.28003	.	.	ENSG00000048707	ENST00000011700	.	.	.	5.78	0.084	0.14436	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.9104	0.09201	0.3515:0.3433:0.0:0.3052	.	.	.	.	X	3094	.	.	L	+	2	0	VPS13D	12489515	0.002000	0.14202	0.907000	0.35723	0.969000	0.65631	-1.494000	0.02296	-0.249000	0.09569	-0.408000	0.06270	TTG		0.537	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2		NM_015378	
VPS41	27072	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	38803128	38803128	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr7:38803128G>C	ENST00000310301.4	-	17	1403	c.1349C>G	c.(1348-1350)cCa>cGa	p.P450R	VPS41_ENST00000395969.2_Missense_Mutation_p.P425R	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	450					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)	p.P450R(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						ATCACCTCTTGGCAAATAAGG	0.333																																																	1	Substitution - Missense(1)	kidney(1)											94.0	86.0	89.0					7																	38803128		2203	4300	6503	SO:0001583	missense	27072			U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.1349C>G	7.37:g.38803128G>C	ENSP00000309457:p.Pro450Arg	Somatic		WXS	Illumina HiSeq	Phase_I	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	37	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.726275	0.89298	.	.	ENSG00000006715	ENST00000310301;ENST00000395969	T;T	0.60299	0.21;0.2	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.81264	0.4786	M	0.90198	3.095	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.997	D;D;D	0.66716	0.946;0.946;0.946	D	0.83471	0.0059	10	0.62326	D	0.03	-10.2242	20.3398	0.98759	0.0:0.0:1.0:0.0	.	450;425;450	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	R	450;425	ENSP00000309457:P450R;ENSP00000379297:P425R	ENSP00000309457:P450R	P	-	2	0	VPS41	38769653	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.811000	0.96726	0.557000	0.71058	CCA		0.333	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3			
HCFC1	3054	broad.mit.edu	37	X	153236256	153236256	+	Silent	SNP	C	C	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chrX:153236256C>A	ENST00000310441.7	-	1	1002	c.36G>T	c.(34-36)gcG>gcT	p.A12A	HCFC1_ENST00000369984.4_Silent_p.A12A|HCFC1-AS1_ENST00000438219.1_RNA|HCFC1_ENST00000354233.3_Silent_p.A12A|TMEM187_ENST00000369982.4_5'Flank	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	12					cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.A12A(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GCAGAAGCACCGCTGGCAAGT	0.677																																																	1	Substitution - coding silent(1)	kidney(1)											13.0	12.0	13.0					X																	153236256		1863	4022	5885	SO:0001819	synonymous_variant	3054				CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.36G>T	X.37:g.153236256C>A		Somatic		WXS	Illumina GAIIx	Phase_I	Q6P4G5	Silent	SNP	ENST00000310441.7	37	CCDS44020.1																																																																																				0.677	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4		NM_005334	
LSM11	134353	broad.mit.edu	37	5	157170976	157170976	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr5:157170976G>A	ENST00000286307.5	+	1	274	c.218G>A	c.(217-219)gGg>gAg	p.G73E		NM_173491.2	NP_775762.1	P83369	LSM11_HUMAN	LSM11, U7 small nuclear RNA associated	73					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	histone pre-mRNA 3'end processing complex (GO:0071204)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U7 snRNP (GO:0005683)	U7 snRNA binding (GO:0071209)	p.G73E(1)		breast(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	7	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ggcgggcgcgggcgcgggcgg	0.786																																																	1	Substitution - Missense(1)	kidney(1)											2.0	3.0	3.0					5																	157170976		1499	3263	4762	SO:0001583	missense	134353			AK095592	CCDS4342.1	5q33.3	2008-02-05	2004-04-28		ENSG00000155858	ENSG00000155858			30860	protein-coding gene	gene with protein product			"""LSM11 homolog, U7 small nuclear RNA associated (S. cerevisiae)"""			12975319	Standard	NM_173491		Approved	FLJ38273	uc003lxe.1	P83369	OTTHUMG00000130255	ENST00000286307.5:c.218G>A	5.37:g.157170976G>A	ENSP00000286307:p.Gly73Glu	Somatic		WXS	Illumina GAIIx	Phase_I	A0AVQ1|Q7Z7P0|Q8N975	Missense_Mutation	SNP	ENST00000286307.5	37	CCDS4342.1	.	.	.	.	.	.	.	.	.	.	G	1.172	-0.640718	0.03557	.	.	ENSG00000155858	ENST00000286307	.	.	.	2.37	1.39	0.22231	.	.	.	.	.	T	0.20129	0.0484	L	0.38175	1.15	0.39608	D	0.969842	P	0.47841	0.901	B	0.34590	0.186	T	0.21075	-1.0256	8	0.12430	T	0.62	.	2.6712	0.05067	0.2472:0.3021:0.4507:0.0	.	73	P83369	LSM11_HUMAN	E	73	.	ENSP00000286307:G73E	G	+	2	0	LSM11	157103554	0.999000	0.42202	0.278000	0.24718	0.049000	0.14656	2.034000	0.41145	0.278000	0.22164	0.306000	0.20318	GGG		0.786	LSM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252580.2		NM_173491	
MUC6	4588	broad.mit.edu	37	11	1017647	1017647	+	Silent	SNP	G	G	T			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr11:1017647G>T	ENST00000421673.2	-	31	5204	c.5154C>A	c.(5152-5154)ccC>ccA	p.P1718P		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1718	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.P1718P(4)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGTACTGGTGGGGTTGGGGG	0.517																																																	4	Substitution - coding silent(4)	lung(2)|kidney(2)											557.0	554.0	555.0					11																	1017647		2192	4277	6469	SO:0001819	synonymous_variant	4588			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5154C>A	11.37:g.1017647G>T		Somatic		WXS	Illumina GAIIx	Phase_I	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																				0.517	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2		XM_290540	
SFRP1	6422	broad.mit.edu	37	8	41166638	41166640	+	In_Frame_Del	DEL	GCT	GCT	-	rs3055861|rs3832595	byFrequency	TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr8:41166638_41166640delGCT	ENST00000220772.3	-	1	376_378	c.39_41delAGC	c.(37-42)gcagcc>gcc	p.13_14AA>A	SFRP1_ENST00000379845.3_5'Flank	NM_003012.4	NP_003003.3	Q8N474	SFRP1_HUMAN	secreted frizzled-related protein 1	13				Missing (in Ref. 1 and 3). {ECO:0000305}.	bone trabecula formation (GO:0060346)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to BMP stimulus (GO:0071773)|cellular response to estradiol stimulus (GO:0071392)|cellular response to estrogen stimulus (GO:0071391)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heparin (GO:0071504)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to prostaglandin E stimulus (GO:0071380)|cellular response to starvation (GO:0009267)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vitamin D (GO:0071305)|cellular response to X-ray (GO:0071481)|convergent extension involved in somitogenesis (GO:0090246)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral axis specification (GO:0009950)|female gonad development (GO:0008585)|gonad development (GO:0008406)|hematopoietic progenitor cell differentiation (GO:0002244)|hematopoietic stem cell differentiation (GO:0060218)|male gonad development (GO:0008584)|menstrual cycle phase (GO:0022601)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of bone remodeling (GO:0046851)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000080)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000054)|neural crest cell fate commitment (GO:0014034)|neural tube closure (GO:0001843)|osteoblast differentiation (GO:0001649)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of non-canonical Wnt signaling pathway (GO:2000052)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|proteolysis (GO:0006508)|regulation of angiogenesis (GO:0045765)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell cycle process (GO:0010564)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|somatic stem cell maintenance (GO:0035019)|stromal-epithelial cell signaling involved in prostate gland development (GO:0044345)|ureteric bud development (GO:0001657)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cysteine-type endopeptidase activity (GO:0004197)|drug binding (GO:0008144)|frizzled binding (GO:0005109)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|central_nervous_system(1)|large_intestine(2)|liver(1)|lung(1)|skin(1)	7	Breast(1;9.19e-13)|Ovarian(28;0.00769)|Colorectal(14;0.0305)|Lung SC(25;0.211)	all_lung(54;0.0034)|Lung NSC(58;0.0134)|Hepatocellular(245;0.023)|Esophageal squamous(32;0.0559)	BRCA - Breast invasive adenocarcinoma(1;1.11e-10)|LUSC - Lung squamous cell carcinoma(45;0.00894)|COAD - Colon adenocarcinoma(11;0.0174)			CACGCCCAGGGCTGCCCCGCGGC	0.764														1558	0.311102	0.0401	0.389	5008	,	,		9448	0.4038		0.3956	False		,,,				2504	0.4397																0										337,0,3741		45,0,247,0,0,1747						1.6	0.3		dbSNP_107	8	2693,2,5163		669,0,1355,0,2,1903	no	codingComplex	SFRP1	NM_003012.4		714,0,1602,0,2,3650	A1A1,A1A2,A1R,A2A2,A2R,RR		34.2963,8.2639,25.4021				3030,2,8904				SO:0001651	inframe_deletion	6422			AF017987	CCDS34886.1	8p11.21	2006-12-15			ENSG00000104332	ENSG00000104332		"""Secreted frizzled-related proteins"""	10776	protein-coding gene	gene with protein product		604156				9391078, 9192640	Standard	NM_003012		Approved	SARP2, FRP, FRP-1	uc003xnt.3	Q8N474	OTTHUMG00000164074	ENST00000220772.3:c.39_41delAGC	8.37:g.41166638_41166640delGCT	ENSP00000220772:p.Ala14del	Somatic		WXS	Illumina GAIIx	Phase_I	O00546|O14779	In_Frame_Del	DEL	ENST00000220772.3	37	CCDS34886.1																																																																																				0.764	SFRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377132.1		NM_003012	
VHL	7428	broad.mit.edu	37	3	10183715	10183716	+	Frame_Shift_Del	DEL	GT	GT	-			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	GT	GT	GT	-	GT	GT	Unknown	Valid	Somatic	Phase_I	WXS	Illumina Miseq;PacBio			Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr3:10183715_10183716delGT	ENST00000256474.2	+	1	1024_1025	c.184_185delGT	c.(184-186)gtgfs	p.V62fs	snoU13_ENST00000458986.1_RNA|VHL_ENST00000345392.2_Frame_Shift_Del_p.V62fs	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	62					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.V62fs*68(2)|p.E52_S65del(2)|p.?(1)|p.G57fs*69(1)|p.A56_R69>G(1)|p.R60fs*35(1)|p.P61fs*61(1)|p.P61fs*70(1)|p.G57fs*4(1)|p.R60fs*70(1)|p.V62fs*5(1)|p.V62fs*3(1)|p.V62fs*1(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)		GCCGCGGCCCGTGCTGCGCTCG	0.733		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"""	15	Deletion - Frameshift(9)|Complex - frameshift(2)|Deletion - In frame(2)|Complex - deletion inframe(1)|Unknown(1)	kidney(15)																																								SO:0001589	frameshift_variant	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.184_185delGT	3.37:g.10183715_10183716delGT	ENSP00000256474:p.Val62fs	Somatic		WXS	Illumina GAIIx	Phase_I	B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.733	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
DST	667	broad.mit.edu	37	6	56373344	56373344	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-5190-01A-01D-1429-08	TCGA-BP-5190-11A-01D-1429-08	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454	.		Illumina GAIIx	5491645b-552c-47a9-b081-e8e508d1df3d	d2f881a8-f629-40a3-a179-3f8749a51d48	g.chr6:56373344G>C	ENST00000361203.3	-	70	18269	c.18262C>G	c.(18262-18264)Cag>Gag	p.Q6088E	DST_ENST00000446842.2_Missense_Mutation_p.Q5873E|DST_ENST00000340834.4_5'UTR|DST_ENST00000370788.2_Missense_Mutation_p.Q4002E|DST_ENST00000370769.4_Missense_Mutation_p.Q6199E|DST_ENST00000421834.2_Missense_Mutation_p.Q4111E|DST_ENST00000370754.5_Missense_Mutation_p.Q6377E|DST_ENST00000244364.6_Missense_Mutation_p.Q3785E|DST_ENST00000312431.6_3'UTR			Q03001	DYST_HUMAN	dystonin	6078					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.Q3785E(1)|p.Q6199E(1)		NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GCTTCTTGCTGTTGTTTTACT	0.373																																						.											2	Substitution - Missense(2)	kidney(2)											153.0	148.0	150.0					6																	56373344		1860	4096	5956	SO:0001583	missense	667			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.18262C>G	6.37:g.56373344G>C	ENSP00000354508:p.Gln6088Glu	Somatic		WXS	Illumina GAIIx	Phase_I	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	G	19.87	3.906668	0.72868	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203;ENST00000537444	T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.91	5.91	0.95273	.	0.121784	0.37261	N	0.002179	T	0.66346	0.2780	M	0.75777	2.31	0.30190	N	0.79957	D;D;D;P;D	0.76494	0.991;0.998;0.996;0.773;0.999	D;D;D;B;D	0.83275	0.991;0.996;0.989;0.389;0.992	T	0.65150	-0.6238	9	0.52906	T	0.07	.	20.3011	0.98612	0.0:0.0:1.0:0.0	.	4111;6199;6377;6197;3785	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	E	3785;6377;6199;4111;5873;4002;6088;201	ENSP00000244364:Q3785E;ENSP00000359790:Q6377E;ENSP00000359805:Q6199E;ENSP00000400883:Q4111E;ENSP00000393645:Q5873E;ENSP00000359824:Q4002E;ENSP00000354508:Q6088E	ENSP00000244364:Q3785E	Q	-	1	0	DST	56481303	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	9.869000	0.99810	2.804000	0.96469	0.650000	0.86243	CAG		0.373	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3		NM_001723	
