#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_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_default_gene_name	i_deletion_substructures	i_domain	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_name	i_gene_name_source	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
AKAP8	10270	genome.wustl.edu	37	19	15484149	15484149	+	Missense_Mutation	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr19:15484149G>A	ENST00000269701.2	-	5	434	c.374C>T	c.(373-375)tCc>tTc	p.S125F		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	125					mitotic chromosome condensation (GO:0007076)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)	condensed chromosome (GO:0000793)|female pronucleus (GO:0001939)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)	26						GAAGCGGAAGGAGCTGCAACA	0.597																																					GBM(190;1671 2163 3274 27186 30476)												0													18.0	18.0	18.0					19																	15484149		2203	4300	6503	SO:0001583	missense	10270			Y11997	CCDS12329.1	19p13.12	2012-05-16			ENSG00000105127	ENSG00000105127		"""A-kinase anchor proteins"""	378	protein-coding gene	gene with protein product	"""A-kinase anchor protein, 95kDa"""	604692				9473338	Standard	NM_005858		Approved	AKAP95, DKFZp586B1222	uc002nav.3	O43823		ENST00000269701.2:c.374C>T	19.37:g.15484149G>A	ENSP00000269701:p.Ser125Phe	Somatic		WXS	Illumina HiSeq	Phase_IV		Missense_Mutation	SNP	pfam_AKAP95	p.S125F	ENST00000269701.2	37	c.374	CCDS12329.1	19	.	.	.	.	.	.	.	.	.	.	g	14.39	2.521075	0.44866	.	.	ENSG00000105127	ENST00000269701	T	0.50277	0.75	4.82	3.75	0.43078	.	0.290065	0.25094	N	0.033186	T	0.41581	0.1165	L	0.57536	1.79	0.80722	D	1	B	0.33583	0.418	B	0.26693	0.072	T	0.44697	-0.9311	10	0.72032	D	0.01	-20.3959	11.7557	0.51874	0.0:0.0:0.823:0.177	.	125	O43823	AKAP8_HUMAN	F	125	ENSP00000269701:S125F	ENSP00000269701:S125F	S	-	2	0	AKAP8	15345149	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	4.224000	0.58593	1.121000	0.41925	0.651000	0.88453	TCC	AKAP8	-	NULL		0.597	AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	AKAP8	HGNC	protein_coding	OTTHUMT00000461293.3	G	NM_005858		15484149	-1	no_errors	ENST00000269701	ensembl	human	known	70_37	missense	SNP	1.000	A
ATP13A4	84239	genome.wustl.edu	37	3	193210717	193210717	+	Silent	SNP	T	T	C			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr3:193210717T>C	ENST00000342695.4	-	5	844	c.522A>G	c.(520-522)gaA>gaG	p.E174E	ATP13A4_ENST00000392443.3_Silent_p.E174E|ATP13A4_ENST00000295548.3_Silent_p.E174E	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	174						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		TAATCTCCTGTTCTTCTCTTG	0.318																																																	0													154.0	150.0	151.0					3																	193210717		2203	4300	6503	SO:0001819	synonymous_variant	84239			AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.522A>G	3.37:g.193210717T>C		Somatic		WXS	Illumina HiSeq	Phase_IV	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	pfam_ATPase_P-typ_ATPase-assoc-dom,pfam_Dehalogen-like_hydro,pfam_ATPase_P-typ_cation-transptr_N,superfamily_HAD-like_dom,superfamily_ATPase_cation_domN,smart_ATPase_P-typ_cation-transptr_N,prints_ATPase_P-typ_ion-transptr,prints_ATPase_P-typ_cation-exchng_asu,tigrfam_ATPase_P-typ_unknown-pump-sp,tigrfam_ATPase_P-typ_ion-transptr	p.E174	ENST00000342695.4	37	c.522	CCDS3304.2	3																																																																																			ATP13A4	-	pfam_ATPase_P-typ_cation-transptr_N,smart_ATPase_P-typ_cation-transptr_N,tigrfam_ATPase_P-typ_unknown-pump-sp		0.318	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	ATP13A4	HGNC	protein_coding	OTTHUMT00000157244.4	T	NM_032279		193210717	-1	no_errors	ENST00000342695	ensembl	human	known	70_37	silent	SNP	0.999	C
C2orf71	388939	genome.wustl.edu	37	2	29294044	29294044	+	Silent	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr2:29294044C>T	ENST00000331664.5	-	1	3083	c.3084G>A	c.(3082-3084)acG>acA	p.T1028T		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1028	Pro-rich.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						GGCTGGGGGGCGTCTGCACAG	0.672																																																	0													29.0	35.0	33.0					2																	29294044		1946	4119	6065	SO:0001819	synonymous_variant	388939				CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3084G>A	2.37:g.29294044C>T		Somatic		WXS	Illumina HiSeq	Phase_IV		Silent	SNP	NULL	p.T1028	ENST00000331664.5	37	c.3084	CCDS42669.1	2																																																																																			C2orf71	-	NULL		0.672	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	C2orf71	HGNC	protein_coding	OTTHUMT00000324924.3	C	NM_001029883		29294044	-1	no_errors	ENST00000331664	ensembl	human	novel	70_37	silent	SNP	0.000	T
CACNA1H	8912	genome.wustl.edu	37	16	1246002	1246002	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr16:1246002C>T	ENST00000348261.5	+	5	870	c.622C>T	c.(622-624)Cgc>Tgc	p.R208C	CACNA1H_ENST00000565831.1_Missense_Mutation_p.R208C|CACNA1H_ENST00000358590.4_Missense_Mutation_p.R208C	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	208					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GCGGCCCCTCCGCGCCATCAA	0.667																																																	0													48.0	58.0	55.0					16																	1246002		2033	4173	6206	SO:0001583	missense	8912			AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.622C>T	16.37:g.1246002C>T	ENSP00000334198:p.Arg208Cys	Somatic		WXS	Illumina HiSeq	Phase_IV	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	pfam_Ion_trans_dom,pfam_PKD1_2_channel,prints_VDCC_T_a1su,prints_PKD_2	p.R208C	ENST00000348261.5	37	c.622	CCDS45375.1	16	.	.	.	.	.	.	.	.	.	.	C	15.14	2.746066	0.49151	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.98531	-4.98;-4.98	4.23	2.03	0.26663	Ion transport (1);	0.268553	0.30101	N	0.010414	D	0.99242	0.9736	H	0.98980	4.39	0.44918	D	0.997933	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.984	D	0.98235	1.0485	10	0.87932	D	0	.	8.3643	0.32378	0.292:0.5623:0.1457:0.0	.	208;208	O95180-2;O95180	.;CAC1H_HUMAN	C	208	ENSP00000334198:R208C;ENSP00000351401:R208C	ENSP00000334198:R208C	R	+	1	0	CACNA1H	1186003	0.115000	0.22152	0.739000	0.30968	0.012000	0.07955	0.479000	0.22228	0.866000	0.35629	0.478000	0.44815	CGC	CACNA1H	-	pfam_Ion_trans_dom		0.667	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	CACNA1H	HGNC	protein_coding	OTTHUMT00000421601.1	C	NM_001005407		1246002	+1	no_errors	ENST00000348261	ensembl	human	known	70_37	missense	SNP	1.000	T
CCDC86	79080	genome.wustl.edu	37	11	60610305	60610305	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr11:60610305G>A	ENST00000227520.5	+	1	762	c.708G>A	c.(706-708)ccG>ccA	p.P236P	RP11-804A23.2_ENST00000539897.1_RNA|RP11-804A23.4_ENST00000538705.1_RNA	NM_024098.3	NP_077003.1	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	236					viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.P236P(1)		endometrium(1)|large_intestine(2)|liver(2)|lung(2)|urinary_tract(3)	10						CTGTAATCCCGAAGGGGAAGC	0.567																																																	1	Substitution - coding silent(1)	urinary_tract(1)											21.0	25.0	24.0					11																	60610305		2199	4299	6498	SO:0001819	synonymous_variant	79080			AK025974	CCDS7993.1	11q12.2	2006-03-16			ENSG00000110104	ENSG00000110104			28359	protein-coding gene	gene with protein product		611293					Standard	NM_024098		Approved	MGC2574	uc001nqa.2	Q9H6F5	OTTHUMG00000167706	ENST00000227520.5:c.708G>A	11.37:g.60610305G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	B4DY99	Silent	SNP	NULL	p.P236	ENST00000227520.5	37	c.708	CCDS7993.1	11																																																																																			CCDC86	-	NULL		0.567	CCDC86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CCDC86	HGNC	protein_coding	OTTHUMT00000395743.1	G	NM_024098		60610305	+1	no_errors	ENST00000227520	ensembl	human	known	70_37	silent	SNP	0.012	A
CDH11	1009	genome.wustl.edu	37	16	65006813	65006813	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr16:65006813C>T	ENST00000268603.4	-	9	1999	c.1384G>A	c.(1384-1386)Gaa>Aaa	p.E462K	CDH11_ENST00000566827.1_Missense_Mutation_p.E336K|CDH11_ENST00000394156.3_Missense_Mutation_p.E462K	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	462	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TTACGGATTTCTGCTGCAAAG	0.363			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																														Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	0													125.0	127.0	126.0					16																	65006813		2203	4300	6503	SO:0001583	missense	1009			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.1384G>A	16.37:g.65006813C>T	ENSP00000268603:p.Glu462Lys	Somatic		WXS	Illumina HiSeq	Phase_IV	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.E462K	ENST00000268603.4	37	c.1384	CCDS10803.1	16	.	.	.	.	.	.	.	.	.	.	C	28.6	4.930738	0.92389	.	.	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000538390	T;T	0.52295	0.67;0.67	5.44	5.44	0.79542	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.72867	0.3514	M	0.87827	2.91	0.80722	D	1	D;D	0.76494	0.999;0.985	D;D	0.69142	0.962;0.949	T	0.76252	-0.3027	10	0.51188	T	0.08	.	18.2557	0.90019	0.0:1.0:0.0:0.0	.	462;462	P55287-2;P55287	.;CAD11_HUMAN	K	462;462;445	ENSP00000268603:E462K;ENSP00000377711:E462K	ENSP00000268603:E462K	E	-	1	0	CDH11	63564314	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.468000	0.80943	2.573000	0.86826	0.655000	0.94253	GAA	CDH11	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin		0.363	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH11	HGNC	protein_coding	OTTHUMT00000268755.1	C	NM_033664		65006813	-1	no_errors	ENST00000268603	ensembl	human	known	70_37	missense	SNP	1.000	T
CDH23	64072	genome.wustl.edu	37	10	73569598	73569598	+	Missense_Mutation	SNP	G	G	T	rs58875306		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr10:73569598G>T	ENST00000224721.6	+	60	8764	c.8759G>T	c.(8758-8760)cGc>cTc	p.R2920L	CDH23_ENST00000475158.1_3'UTR|CDH23_ENST00000398788.3_Missense_Mutation_p.R675L	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2915	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						GGCATTCTGCGCACCTTCGAC	0.637																																																	0													104.0	110.0	108.0					10																	73569598		2081	4205	6286	SO:0001583	missense	64072			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.8759G>T	10.37:g.73569598G>T	ENSP00000224721:p.Arg2920Leu	Somatic		WXS	Illumina HiSeq	Phase_IV	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.R2918L	ENST00000224721.6	37	c.8753		10	.	.	.	.	.	.	.	.	.	.	G	19.58	3.855187	0.71719	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	T	0.60672	0.17	5.61	5.61	0.85477	Cadherin (2);Cadherin-like (1);	0.065480	0.64402	D	0.000017	T	0.50956	0.1646	M	0.62723	1.935	0.80722	D	1	P;P	0.42078	0.61;0.77	B;B	0.33196	0.12;0.159	T	0.54655	-0.8261	10	0.07990	T	0.79	.	19.6296	0.95694	0.0:0.0:1.0:0.0	.	2915;2915	E9PEX1;Q9H251	.;CAD23_HUMAN	L	2920;2915;2918;675	ENSP00000381768:R675L	ENSP00000224721:R2920L	R	+	2	0	CDH23	73239604	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	9.818000	0.99354	2.650000	0.89964	0.549000	0.68633	CGC	CDH23	-	superfamily_Cadherin-like,pfscan_Cadherin		0.637	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	CDH23	HGNC	protein_coding	OTTHUMT00000051227.4	G	NM_052836		73569598	+1	no_errors	ENST00000224721	ensembl	human	known	70_37	missense	SNP	1.000	T
CDX2	1045	genome.wustl.edu	37	13	28542887	28542887	+	Missense_Mutation	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr13:28542887G>A	ENST00000381020.7	-	1	2389	c.257C>T	c.(256-258)gCg>gTg	p.A86V	CDX2_ENST00000548877.1_5'Flank	NM_001265.4	NP_001256.3	Q99626	CDX2_HUMAN	caudal type homeobox 2	86	Poly-Ala.				anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|endosome to lysosome transport (GO:0008333)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|labyrinthine layer development (GO:0060711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	condensed nuclear chromosome (GO:0000794)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|large_intestine(1)|lung(6)	9	all_cancers(110;0.191)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155)	Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199)		ggcggcggccgcggcgcctcc	0.741			T	ETV6	AML																																			Dom	yes		13	13q12.3	1045	caudal type homeo box transcription factor 2		L	0													11.0	17.0	15.0					13																	28542887		1703	3294	4997	SO:0001583	missense	1045			Y13709	CCDS9328.1	13q12.2	2012-03-09	2007-07-09		ENSG00000165556	ENSG00000165556		"""Homeoboxes / ANTP class : HOXL subclass"""	1806	protein-coding gene	gene with protein product		600297	"""caudal type homeo box transcription factor 2"""	CDX3		7698771	Standard	NM_001265		Approved		uc001urv.4	Q99626	OTTHUMG00000016640	ENST00000381020.7:c.257C>T	13.37:g.28542887G>A	ENSP00000370408:p.Ala86Val	Somatic		WXS	Illumina HiSeq	Phase_IV	O00503|Q5VTU7|Q969L8|Q9UD92	Missense_Mutation	SNP	pfam_Caudal_activation_dom,pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,pfscan_Homeodomain,prints_HTH_motif,prints_Homeobox_metazoa	p.A86V	ENST00000381020.7	37	c.257	CCDS9328.1	13	.	.	.	.	.	.	.	.	.	.	G	13.06	2.124556	0.37533	.	.	ENSG00000165556	ENST00000381020	T	0.46819	0.86	4.39	3.51	0.40186	Caudal-like activation domain (1);	0.925570	0.09034	N	0.858282	T	0.31451	0.0797	L	0.35854	1.095	0.09310	N	1	P	0.43938	0.822	B	0.30716	0.119	T	0.04723	-1.0931	10	0.19147	T	0.46	-14.6361	9.9847	0.41835	0.0:0.2062:0.7938:0.0	.	86	Q99626	CDX2_HUMAN	V	86	ENSP00000370408:A86V	ENSP00000370408:A86V	A	-	2	0	CDX2	27440887	0.949000	0.32298	0.214000	0.23707	0.447000	0.32167	2.970000	0.49240	1.005000	0.39183	0.407000	0.27541	GCG	CDX2	-	pfam_Caudal_activation_dom		0.741	CDX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDX2	HGNC	protein_coding	OTTHUMT00000044312.5	G			28542887	-1	no_errors	ENST00000381020	ensembl	human	known	70_37	missense	SNP	0.075	A
CHD7	55636	genome.wustl.edu	37	8	61693596	61693596	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr8:61693596C>T	ENST00000423902.2	+	3	2182	c.1703C>T	c.(1702-1704)cCg>cTg	p.P568L	CHD7_ENST00000524602.1_Missense_Mutation_p.P568L|CHD7_ENST00000525508.1_Missense_Mutation_p.P568L	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	568	Pro-rich.				adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.556_871dup(1)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			AAACCAGTGCCGGATATGACT	0.418																																																	1	Insertion - In frame(1)	lung(1)											46.0	45.0	45.0					8																	61693596		1897	4132	6029	SO:0001583	missense	55636			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.1703C>T	8.37:g.61693596C>T	ENSP00000392028:p.Pro568Leu	Somatic		WXS	Illumina HiSeq	Phase_IV	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	pfam_SNF2_N,pfam_BRK_domain,pfam_Chromo_domain,pfam_Helicase_C,superfamily_Chromodomain-like,smart_Chromo_domain/shadow,smart_Helicase_ATP-bd,smart_Helicase_C,smart_BRK_domain,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_Chromo_domain/shadow	p.P568L	ENST00000423902.2	37	c.1703	CCDS47865.1	8	.	.	.	.	.	.	.	.	.	.	C	29.5	5.009246	0.93346	.	.	ENSG00000171316	ENST00000307121;ENST00000423902;ENST00000524602;ENST00000525508	D;T;T	0.81996	-1.56;2.05;-1.2	5.23	5.23	0.72850	.	0.000000	0.45606	D	0.000348	T	0.77942	0.4206	L	0.34521	1.04	0.80722	D	1	D	0.53619	0.961	B	0.41332	0.354	T	0.82018	-0.0665	10	0.72032	D	0.01	-15.2638	19.1535	0.93499	0.0:1.0:0.0:0.0	.	568	Q9P2D1	CHD7_HUMAN	L	568	ENSP00000392028:P568L;ENSP00000437061:P568L;ENSP00000436027:P568L	ENSP00000307304:P568L	P	+	2	0	CHD7	61856150	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.801000	0.62532	2.608000	0.88229	0.650000	0.86243	CCG	CHD7	-	NULL		0.418	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHD7	HGNC	protein_coding	OTTHUMT00000383468.2	C	XM_098762		61693596	+1	no_errors	ENST00000307121	ensembl	human	known	70_37	missense	SNP	1.000	T
CHST3	9469	genome.wustl.edu	37	10	73768164	73768164	+	Missense_Mutation	SNP	G	G	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr10:73768164G>T	ENST00000373115.4	+	3	1812	c.1375G>T	c.(1375-1377)Gcc>Tcc	p.A459S		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	459					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						GGCGCGGGACGCCGCCGCCCT	0.692																																																	0													13.0	12.0	12.0					10																	73768164		2166	4247	6413	SO:0001583	missense	9469			AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"""Sulfotransferases, membrane-bound"""	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.1375G>T	10.37:g.73768164G>T	ENSP00000362207:p.Ala459Ser	Somatic		WXS	Illumina HiSeq	Phase_IV	O75099|Q52M30	Missense_Mutation	SNP	pfam_Sulfotransferase_dom,pirsf_Carbohydrate_sulfotransferase	p.A459S	ENST00000373115.4	37	c.1375	CCDS7312.1	10	.	.	.	.	.	.	.	.	.	.	G	10.89	1.477729	0.26511	.	.	ENSG00000122863	ENST00000373115	D	0.96300	-3.97	5.27	4.3	0.51218	.	0.123056	0.56097	D	0.000039	D	0.92028	0.7474	L	0.33485	1.01	0.09310	N	1	B	0.25007	0.116	B	0.26517	0.07	T	0.82557	-0.0398	10	0.29301	T	0.29	-25.3119	10.2547	0.43390	0.0:0.2099:0.6692:0.1209	.	459	Q7LGC8	CHST3_HUMAN	S	459	ENSP00000362207:A459S	ENSP00000362207:A459S	A	+	1	0	CHST3	73438170	0.155000	0.22806	0.933000	0.37362	0.873000	0.50193	2.333000	0.43912	2.621000	0.88768	0.462000	0.41574	GCC	CHST3	-	pirsf_Carbohydrate_sulfotransferase		0.692	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHST3	HGNC	protein_coding	OTTHUMT00000048563.1	G	NM_004273		73768164	+1	no_errors	ENST00000373115	ensembl	human	known	70_37	missense	SNP	0.031	T
CLK2	1196	genome.wustl.edu	37	1	155239279	155239279	+	Splice_Site	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr1:155239279C>T	ENST00000368361.4	-	3	714	c.399G>A	c.(397-399)tcG>tcA	p.S133S	CLK2_ENST00000497188.1_5'Flank|CLK2_ENST00000361168.5_Splice_Site_p.S133S|CLK2_ENST00000355560.4_Splice_Site_p.S132S|CLK2_ENST00000536801.1_Splice_Site_p.S133S			P49760	CLK2_HUMAN	CDC-like kinase 2	133					negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TGGCACTCACCGAAGATGAGC	0.602								Other conserved DNA damage response genes																																									0													52.0	48.0	49.0					1																	155239279		2203	4300	6503	SO:0001630	splice_region_variant	1196			L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444		"""CDC-like kinases"""	2069	protein-coding gene	gene with protein product		602989				7990150, 9856501	Standard	XM_005244876		Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000368361.4:c.399+1G>A	1.37:g.155239279C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	B1AVS9|B5MBX6|Q96CQ0	Silent	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.S133	ENST00000368361.4	37	c.399		1																																																																																			CLK2	-	NULL		0.602	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	CLK2	HGNC	protein_coding	OTTHUMT00000087391.1	C	NM_003993	Silent	155239279	-1	no_errors	ENST00000368361	ensembl	human	known	70_37	silent	SNP	1.000	T
CMYA5	202333	genome.wustl.edu	37	5	79025497	79025497	+	Missense_Mutation	SNP	G	G	C			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr5:79025497G>C	ENST00000446378.2	+	2	940	c.909G>C	c.(907-909)tgG>tgC	p.W303C		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	303					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TTCCACCCTGGAGAGGCGCAC	0.413																																																	0													81.0	74.0	76.0					5																	79025497		1870	4109	5979	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.909G>C	5.37:g.79025497G>C	ENSP00000394770:p.Trp303Cys	Somatic		WXS	Illumina HiSeq	Phase_IV	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	pfam_Fibronectin_type3,pfam_SPRY_rcpt,superfamily_ConA-like_lec_gl_sf,superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_B30.2/SPRY,pfscan_Fibronectin_type3	p.W303C	ENST00000446378.2	37	c.909	CCDS47238.1	5	.	.	.	.	.	.	.	.	.	.	G	5.879	0.346282	0.11126	.	.	ENSG00000164309	ENST00000446378	T	0.71461	-0.57	5.79	4.92	0.64577	.	0.147317	0.32287	N	0.006309	T	0.57961	0.2089	L	0.34521	1.04	0.44275	D	0.997136	B	0.34200	0.441	B	0.26094	0.066	T	0.61912	-0.6965	10	0.87932	D	0	.	12.8644	0.57932	0.0:0.1635:0.8365:0.0	.	303	Q8N3K9	CMYA5_HUMAN	C	303	ENSP00000394770:W303C	ENSP00000394770:W303C	W	+	3	0	CMYA5	79061253	0.680000	0.27605	0.973000	0.42090	0.159000	0.22180	0.965000	0.29319	1.422000	0.47177	-0.175000	0.13238	TGG	CMYA5	-	NULL		0.413	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CMYA5	HGNC	protein_coding	OTTHUMT00000369497.1	G	NM_153610		79025497	+1	no_errors	ENST00000446378	ensembl	human	known	70_37	missense	SNP	0.999	C
COL15A1	1306	genome.wustl.edu	37	9	101832135	101832135	+	Silent	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr9:101832135C>T	ENST00000375001.3	+	42	4557	c.4134C>T	c.(4132-4134)atC>atT	p.I1378I		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	1378	Nonhelical region 10 (NC10).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)	p.I1378I(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				TCCTATGTATCGAAAACAGTT	0.448																																																	1	Substitution - coding silent(1)	large_intestine(1)											89.0	79.0	82.0					9																	101832135		2203	4300	6503	SO:0001819	synonymous_variant	1306			L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.4134C>T	9.37:g.101832135C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	pfam_Collagenase_NC10/endostatin,pfam_Collagen,superfamily_C-type_lectin_fold,superfamily_ConA-like_lec_gl_sf,smart_Laminin_G	p.I1378	ENST00000375001.3	37	c.4134	CCDS35081.1	9																																																																																			COL15A1	-	pfam_Collagenase_NC10/endostatin,superfamily_C-type_lectin_fold		0.448	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL15A1	HGNC	protein_coding	OTTHUMT00000053386.3	C	NM_001855		101832135	+1	no_errors	ENST00000375001	ensembl	human	known	70_37	silent	SNP	0.912	T
COL5A1	1289	genome.wustl.edu	37	9	137706730	137706730	+	Missense_Mutation	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr9:137706730G>A	ENST00000371817.3	+	50	4408	c.3994G>A	c.(3994-3996)Gat>Aat	p.D1332N		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1332	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		TCCCGGAGATGATGGTCCCAA	0.632																																																	0													25.0	21.0	23.0					9																	137706730		2048	3991	6039	SO:0001583	missense	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.3994G>A	9.37:g.137706730G>A	ENSP00000360882:p.Asp1332Asn	Somatic		WXS	Illumina HiSeq	Phase_IV	Q15094|Q5SUX4	Missense_Mutation	SNP	pfam_Collagen,pfam_Fib_collagen_C,pfam_Laminin_G,superfamily_ConA-like_lec_gl_sf,superfamily_Fibrinogen_a/b/g_C,smart_Laminin_G,smart_Fib_collagen_C	p.D1332N	ENST00000371817.3	37	c.3994	CCDS6982.1	9	.	.	.	.	.	.	.	.	.	.	G	22.3	4.273659	0.80580	.	.	ENSG00000130635	ENST00000371817	D	0.93488	-3.23	4.59	4.59	0.56863	.	0.000000	0.85682	U	0.000000	D	0.94155	0.8125	N	0.25825	0.765	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	D	0.95173	0.8292	10	0.62326	D	0.03	.	17.7432	0.88412	0.0:0.0:1.0:0.0	.	1332	P20908	CO5A1_HUMAN	N	1332	ENSP00000360882:D1332N	ENSP00000360882:D1332N	D	+	1	0	COL5A1	136846551	1.000000	0.71417	0.989000	0.46669	0.914000	0.54420	9.652000	0.98499	2.242000	0.73789	0.643000	0.83706	GAT	COL5A1	-	NULL		0.632	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL5A1	HGNC	protein_coding	OTTHUMT00000054954.2	G	NM_000093		137706730	+1	no_errors	ENST00000371817	ensembl	human	known	70_37	missense	SNP	1.000	A
CREBZF	58487	genome.wustl.edu	37	11	85375525	85375525	+	Missense_Mutation	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr11:85375525G>A	ENST00000527447.1	-	1	621	c.395C>T	c.(394-396)tCg>tTg	p.S132L	CREBZF_ENST00000534224.1_Intron|CREBZF_ENST00000398294.2_Missense_Mutation_p.S50L|CREBZF_ENST00000531515.1_Intron	NM_001039618.2	NP_001034707.1	Q9NS37	ZHANG_HUMAN	CREB/ATF bZIP transcription factor	132					negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)				TCCGCCAGACGAGGAGAGAGG	0.657																																					NSCLC(172;674 2044 9050 18334 41735)												0													33.0	38.0	37.0					11																	85375525		1926	4137	6063	SO:0001583	missense	58487			AF039942	CCDS41697.1	11q14.1	2013-01-10			ENSG00000137504	ENSG00000137504		"""basic leucine zipper proteins"""	24905	protein-coding gene	gene with protein product	"""Zhangfei"""	606444				10871379	Standard	NM_001039618		Approved	ZF	uc001pas.2	Q9NS37	OTTHUMG00000133648	ENST00000527447.1:c.395C>T	11.37:g.85375525G>A	ENSP00000433459:p.Ser132Leu	Somatic		WXS	Illumina HiSeq	Phase_IV	B2R8Q9|Q0P5U9|Q52LT3	Missense_Mutation	SNP	pfam_bZIP	p.S132L	ENST00000527447.1	37	c.395	CCDS41697.1	11	.	.	.	.	.	.	.	.	.	.	G	26.2	4.716540	0.89205	.	.	ENSG00000137504	ENST00000398294;ENST00000527447	.	.	.	4.11	4.11	0.48088	.	0.250000	0.22322	N	0.061598	T	0.53481	0.1799	N	0.19112	0.55	0.35184	D	0.772761	D	0.69078	0.997	D	0.67725	0.953	T	0.59989	-0.7350	8	.	.	.	-40.6234	12.0439	0.53469	0.0:0.0:1.0:0.0	.	132	Q9NS37	ZHANG_HUMAN	L	50;132	.	.	S	-	2	0	CREBZF	85053173	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.712000	0.54875	2.289000	0.77006	0.561000	0.74099	TCG	CREBZF	-	NULL		0.657	CREBZF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	CREBZF	HGNC	protein_coding	OTTHUMT00000390191.2	G	NM_001039618		85375525	-1	no_errors	ENST00000525639	ensembl	human	known	70_37	missense	SNP	1.000	A
CRTAC1	55118	genome.wustl.edu	37	10	99770902	99770902	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr10:99770902C>T	ENST00000370597.3	-	2	572	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	CRTAC1_ENST00000370591.2_Missense_Mutation_p.V73M|CRTAC1_ENST00000298819.4_Missense_Mutation_p.V73M	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	73						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		TACCCCGCCACGACGATCTCA	0.488																																																	0													122.0	102.0	109.0					10																	99770902		2203	4300	6503	SO:0001583	missense	55118			AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.217G>A	10.37:g.99770902C>T	ENSP00000359629:p.Val73Met	Somatic		WXS	Illumina HiSeq	Phase_IV	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Missense_Mutation	SNP	pfam_FG-GAP,pfam_UnbV_ASPIC,pfam_EGF-like_Ca-bd,smart_EGF-like_Ca-bd	p.V73M	ENST00000370597.3	37	c.217	CCDS31266.1	10	.	.	.	.	.	.	.	.	.	.	C	27.2	4.813676	0.90790	.	.	ENSG00000095713	ENST00000370597;ENST00000298819;ENST00000309155;ENST00000370591	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	6.17	6.17	0.99709	.	0.067577	0.64402	D	0.000011	T	0.61961	0.2389	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.991;0.998	T	0.60454	-0.7260	10	0.56958	D	0.05	-21.7419	20.8794	0.99867	0.0:1.0:0.0:0.0	.	73;73	Q9NQ79-2;Q9NQ79	.;CRAC1_HUMAN	M	73;73;65;73	ENSP00000359629:V73M;ENSP00000298819:V73M;ENSP00000310810:V65M;ENSP00000359623:V73M	ENSP00000298819:V73M	V	-	1	0	CRTAC1	99760892	1.000000	0.71417	0.974000	0.42286	0.996000	0.88848	7.170000	0.77587	2.941000	0.99782	0.655000	0.94253	GTG	CRTAC1	-	NULL		0.488	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	CRTAC1	HGNC	protein_coding	OTTHUMT00000049754.1	C	NM_018058		99770902	-1	no_errors	ENST00000370597	ensembl	human	known	70_37	missense	SNP	1.000	T
CSMD3	114788	genome.wustl.edu	37	8	113317096	113317096	+	Nonsense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr8:113317096C>T	ENST00000297405.5	-	52	8364	c.8120G>A	c.(8119-8121)tGg>tAg	p.W2707*	CSMD3_ENST00000352409.3_Nonsense_Mutation_p.W2637*|CSMD3_ENST00000455883.2_Intron|CSMD3_ENST00000343508.3_Nonsense_Mutation_p.W2667*	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2707	Sushi 16. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CACAATTCGCCATCTTCCATG	0.393										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																							0													90.0	76.0	81.0					8																	113317096		2203	4300	6503	SO:0001587	stop_gained	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.8120G>A	8.37:g.113317096C>T	ENSP00000297405:p.Trp2707*	Somatic		WXS	Illumina HiSeq	Phase_IV	Q96PZ3	Nonsense_Mutation	SNP	pfam_CUB,pfam_Sushi_SCR_CCP,superfamily_CUB,superfamily_Complement_control_module,smart_CUB,smart_Sushi_SCR_CCP,pfscan_CUB,pfscan_Sushi_SCR_CCP	p.W2707*	ENST00000297405.5	37	c.8120	CCDS6315.1	8	.	.	.	.	.	.	.	.	.	.	C	50	16.582174	0.99867	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000352409	.	.	.	5.18	5.18	0.71444	.	0.000000	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	19.0673	0.93116	0.0:1.0:0.0:0.0	.	.	.	.	X	2667;2707;1977;2637	.	ENSP00000297405:W2707X	W	-	2	0	CSMD3	113386272	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.750000	0.85110	2.547000	0.85894	0.655000	0.94253	TGG	CSMD3	-	pfam_Sushi_SCR_CCP,superfamily_Complement_control_module,smart_Sushi_SCR_CCP,pfscan_Sushi_SCR_CCP		0.393	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CSMD3	HGNC	protein_coding	OTTHUMT00000347141.1	C	NM_052900		113317096	-1	no_errors	ENST00000297405	ensembl	human	known	70_37	nonsense	SNP	1.000	T
CTSK	1513	genome.wustl.edu	37	1	150772083	150772083	+	Nonsense_Mutation	SNP	G	G	A	rs74315303		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr1:150772083G>A	ENST00000271651.3	-	6	831	c.721C>T	c.(721-723)Cga>Tga	p.R241*		NM_000396.3	NP_000387.1	P43235	CATK_HUMAN	cathepsin K	241					bone resorption (GO:0045453)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|intramembranous ossification (GO:0001957)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|proteoglycan binding (GO:0043394)	p.R241*(1)		cervix(1)|endometrium(1)|lung(4)|skin(1)	7	all_cancers(9;2.32e-51)|all_epithelial(9;3.89e-42)|all_lung(15;4.59e-35)|Lung NSC(24;1.7e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Colorectal(459;0.171)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			GGTCCCACTCGGGCCACTGCC	0.512																																																	1	Substitution - Nonsense(1)	endometrium(1)	GRCh37	CM960426	CTSK	M	rs74315303	G	stop/ARG	0,4406		0,0,2203	114.0	111.0	112.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	721	2.7	1.0	1	dbSNP_131	112	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained	CTSK	NM_000396.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		241/330	150772083	1,13005	2203	4300	6503	SO:0001587	stop_gained	1513			BC016058	CCDS969.1	1q21	2008-02-05	2006-12-05		ENSG00000143387	ENSG00000143387		"""Cathepsins"""	2536	protein-coding gene	gene with protein product		601105	"""cathepsin K (pycnodysostosis)"""	CTSO2, CTSO, PYCD		7818555	Standard	NM_000396		Approved	PKND	uc001evp.2	P43235	OTTHUMG00000035008	ENST00000271651.3:c.721C>T	1.37:g.150772083G>A	ENSP00000271651:p.Arg241*	Somatic		WXS	Illumina HiSeq	Phase_IV	Q6FHS6	Nonsense_Mutation	SNP	pfam_Peptidase_C1A_C,pfam_Prot_inhib_I29,pfam_Peptidase_C1B,smart_Prot_inhib_I29,smart_Peptidase_C1A_C,prints_Peptidase_C1A_C	p.R241*	ENST00000271651.3	37	c.721	CCDS969.1	1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.678985	0.88542	0.0	1.16E-4	ENSG00000143387	ENST00000271651	.	.	.	5.93	2.74	0.32292	.	0.175567	0.48767	D	0.000168	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	9.5881	0.39528	0.0753:0.0:0.661:0.2636	.	.	.	.	X	241	.	ENSP00000271651:R241X	R	-	1	2	CTSK	149038707	0.000000	0.05858	0.996000	0.52242	0.823000	0.46562	-0.443000	0.06862	0.845000	0.35118	-0.309000	0.09137	CGA	CTSK	-	pfam_Peptidase_C1A_C,smart_Peptidase_C1A_C		0.512	CTSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CTSK	HGNC	protein_coding	OTTHUMT00000084732.1	G	NM_000396		150772083	-1	no_errors	ENST00000271651	ensembl	human	known	70_37	nonsense	SNP	0.249	A
CXCR4	7852	genome.wustl.edu	37	2	136872366	136872366	+	3'UTR	SNP	C	C	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr2:136872366C>A	ENST00000241393.3	-	0	1236				CXCR4_ENST00000409817.1_3'UTR|CXCR4_ENST00000466288.1_5'UTR	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4						activation of MAPK activity (GO:0000187)|ameboidal cell migration (GO:0001667)|apoptotic process (GO:0006915)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular response to cytokine stimulus (GO:0071345)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|germ cell development (GO:0007281)|germ cell migration (GO:0008354)|inflammatory response (GO:0006954)|motor neuron axon guidance (GO:0008045)|myelin maintenance (GO:0043217)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|neutrophil activation (GO:0042119)|patterning of blood vessels (GO:0001569)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of cell migration (GO:0030334)|regulation of chemotaxis (GO:0050920)|response to hypoxia (GO:0001666)|response to virus (GO:0009615)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)|myosin light chain binding (GO:0032027)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)|Plerixafor(DB06809)	ATTGGTCAGTCTTTTATATCT	0.244																																																	0																																										SO:0001624	3_prime_UTR_variant	7852			AF005058	CCDS33295.1, CCDS46420.1	2q21	2014-09-17	2002-08-22		ENSG00000121966	ENSG00000121966		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	2561	protein-coding gene	gene with protein product		162643	"""chemokine (C-X-C motif), receptor 4 (fusin)"""			9599023, 9379028	Standard	NM_001008540		Approved	LESTR, NPY3R, HM89, NPYY3R, D2S201E, fusin, HSY3RR, NPYR, CD184	uc002tuz.3	P61073	OTTHUMG00000153583	ENST00000241393.3:c.*73G>T	2.37:g.136872366C>A		Somatic		WXS	Illumina HiSeq	Phase_IV	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	RNA	SNP	-	NULL	ENST00000241393.3	37	NULL	CCDS46420.1	2																																																																																			CXCR4	-	-		0.244	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	CXCR4	HGNC	protein_coding	OTTHUMT00000331732.1	C			136872366	-1	no_errors	ENST00000466288	ensembl	human	known	70_37	rna	SNP	1.000	A
CYP26C1	340665	genome.wustl.edu	37	10	94828206	94828206	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr10:94828206C>T	ENST00000285949.5	+	6	1321	c.1321C>T	c.(1321-1323)Cgg>Tgg	p.R441W		NM_183374.2	NP_899230.2	Q6V0L0	CP26C_HUMAN	cytochrome P450, family 26, subfamily C, polypeptide 1	441					anterior/posterior pattern specification (GO:0009952)|central nervous system development (GO:0007417)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|neural crest cell development (GO:0014032)|organelle fusion (GO:0048284)|oxidation-reduction process (GO:0055114)|retinoic acid catabolic process (GO:0034653)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			central_nervous_system(1)|lung(3)|ovary(1)	5		Colorectal(252;0.122)				CGAAGATTCCCGGGGCGCCTC	0.682																																																	0													12.0	15.0	14.0					10																	94828206		2075	4140	6215	SO:0001583	missense	340665				CCDS7425.1	10q23.33	2003-11-20			ENSG00000187553	ENSG00000187553		"""Cytochrome P450s"""	20577	protein-coding gene	gene with protein product		608428					Standard	XR_246086		Approved		uc010qns.2	Q6V0L0	OTTHUMG00000018766	ENST00000285949.5:c.1321C>T	10.37:g.94828206C>T	ENSP00000285949:p.Arg441Trp	Somatic		WXS	Illumina HiSeq	Phase_IV	Q5VXH6	Missense_Mutation	SNP	pfam_Cyt_P450,superfamily_Cyt_P450,prints_Cyt_P450_E_grp-IV,prints_Cyt_P450_E_grp-I,prints_Cyt_P450	p.R441W	ENST00000285949.5	37	c.1321	CCDS7425.1	10	.	.	.	.	.	.	.	.	.	.	C	11.64	1.699236	0.30142	.	.	ENSG00000187553	ENST00000285949	T	0.69306	-0.39	5.17	2.23	0.28157	.	0.490884	0.20477	N	0.091569	T	0.55940	0.1952	N	0.20574	0.59	0.09310	N	1	D	0.56035	0.974	P	0.51266	0.664	T	0.48246	-0.9052	10	0.62326	D	0.03	-0.4072	6.9332	0.24453	0.4359:0.4827:0.0:0.0815	.	441	Q6V0L0	CP26C_HUMAN	W	441	ENSP00000285949:R441W	ENSP00000285949:R441W	R	+	1	2	CYP26C1	94818196	0.000000	0.05858	0.008000	0.14137	0.015000	0.08874	0.226000	0.17776	0.557000	0.29117	-0.276000	0.10085	CGG	CYP26C1	-	pfam_Cyt_P450,superfamily_Cyt_P450		0.682	CYP26C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYP26C1	HGNC	protein_coding	OTTHUMT00000049409.2	C	NM_183374		94828206	+1	no_errors	ENST00000285949	ensembl	human	known	70_37	missense	SNP	0.000	T
CYP4F2	8529	genome.wustl.edu	37	19	16000293	16000293	+	Silent	SNP	G	G	A	rs564383704		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr19:16000293G>A	ENST00000221700.6	-	7	953	c.858C>T	c.(856-858)ttC>ttT	p.F286F	CYP4F2_ENST00000011989.7_Silent_p.F137F	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TGGCTTGGAGGAAGTCATCAA	0.572													.|||	1	0.000199681	0.0	0.0	5008	,	,		19773	0.0		0.0	False		,,,				2504	0.001																0													70.0	67.0	68.0					19																	16000293		2203	4300	6503	SO:0001819	synonymous_variant	8529			U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.858C>T	19.37:g.16000293G>A		Somatic		WXS	Illumina HiSeq	Phase_IV		Silent	SNP	pfam_Cyt_P450,superfamily_Cyt_P450,prints_Cyt_P450_E_grp-I,prints_Cyt_P450_E_grp-IV,prints_Cyt_P450,prints_Cyt_P450_E_grp-II	p.F286	ENST00000221700.6	37	c.858	CCDS12336.1	19																																																																																			CYP4F2	-	pfam_Cyt_P450,superfamily_Cyt_P450		0.572	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYP4F2	HGNC	protein_coding	OTTHUMT00000460372.3	G	NM_001082		16000293	-1	no_errors	ENST00000221700	ensembl	human	known	70_37	silent	SNP	0.221	A
CYR61	3491	genome.wustl.edu	37	1	86048260	86048260	+	Missense_Mutation	SNP	A	A	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr1:86048260A>T	ENST00000451137.2	+	4	1020	c.796A>T	c.(796-798)Att>Ttt	p.I266F		NM_001554.4	NP_001545.2	O00622	CYR61_HUMAN	cysteine-rich, angiogenic inducer, 61	266	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				anatomical structure morphogenesis (GO:0009653)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|cell proliferation (GO:0008283)|chemotaxis (GO:0006935)|chondroblast differentiation (GO:0060591)|chorio-allantoic fusion (GO:0060710)|extracellular matrix organization (GO:0030198)|intussusceptive angiogenesis (GO:0002041)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of apoptotic process (GO:0043066)|osteoblast differentiation (GO:0001649)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|reactive oxygen species metabolic process (GO:0072593)|regulation of cell growth (GO:0001558)|regulation of ERK1 and ERK2 cascade (GO:0070372)|ventricular septum development (GO:0003281)|wound healing, spreading of cells (GO:0044319)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|prostate(1)	5				all cancers(265;0.0216)|Epithelial(280;0.0441)		AGAAACCCGGATTTGTGAGGT	0.532											OREG0013583	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0													68.0	63.0	65.0					1																	86048260		2203	4300	6503	SO:0001583	missense	3491			AF031385	CCDS706.1	1p22.3	2008-02-05			ENSG00000142871	ENSG00000142871			2654	protein-coding gene	gene with protein product		602369		IGFBP10		9135077	Standard	NM_001554		Approved	GIG1, CCN1	uc001dle.3	O00622	OTTHUMG00000010577	ENST00000451137.2:c.796A>T	1.37:g.86048260A>T	ENSP00000398736:p.Ile266Phe	Somatic	1241	WXS	Illumina HiSeq	Phase_IV	O14934|O43775|Q9BZL7	Missense_Mutation	SNP	pfam_Cys_knot,pfam_IGFBP-like,pfam_VWF_C,pfam_Thrombospondin_1_rpt,superfamily_Thrombospondin_1_rpt,smart_IGFBP-like,smart_VWF_C,smart_Thrombospondin_1_rpt,smart_Cys_knot_C,pirsf_IGFBP_CNN,pfscan_Cys_knot_C,pfscan_Thrombospondin_1_rpt,pfscan_VWF_C	p.I266F	ENST00000451137.2	37	c.796	CCDS706.1	1	.	.	.	.	.	.	.	.	.	.	A	12.28	1.890523	0.33348	.	.	ENSG00000142871	ENST00000451137;ENST00000536321;ENST00000360431	T	0.55930	0.49	5.81	5.81	0.92471	.	0.089828	0.85682	D	0.000000	T	0.35068	0.0919	N	0.21097	0.63	0.80722	D	1	P	0.36837	0.571	B	0.42163	0.378	T	0.45440	-0.9261	10	0.87932	D	0	-21.2875	16.1699	0.81801	1.0:0.0:0.0:0.0	.	266	O00622	CYR61_HUMAN	F	266;242;266	ENSP00000398736:I266F	ENSP00000353612:I266F	I	+	1	0	CYR61	85820848	1.000000	0.71417	0.983000	0.44433	0.715000	0.41141	4.961000	0.63681	2.217000	0.71921	0.533000	0.62120	ATT	CYR61	-	pfam_Thrombospondin_1_rpt,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,pirsf_IGFBP_CNN,pfscan_Thrombospondin_1_rpt		0.532	CYR61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYR61	HGNC	protein_coding	OTTHUMT00000029187.1	A	NM_001554		86048260	+1	no_errors	ENST00000451137	ensembl	human	known	70_37	missense	SNP	0.994	T
DCBLD2	131566	genome.wustl.edu	37	3	98518644	98518644	+	Missense_Mutation	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr3:98518644G>A	ENST00000326840.6	-	16	2262	c.1900C>T	c.(1900-1902)Cat>Tat	p.H634Y	DCBLD2_ENST00000326857.9_Missense_Mutation_p.H648Y	NM_080927.3	NP_563615.3	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2	634					cell adhesion (GO:0007155)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell growth (GO:0030308)|wound healing (GO:0042060)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|stomach(2)	25						GATCTTTGATGAAGTGTACCA	0.398																																																	0													89.0	79.0	82.0					3																	98518644		1894	4129	6023	SO:0001583	missense	131566				CCDS46878.1	3q12.2	2006-04-12			ENSG00000057019	ENSG00000057019			24627	protein-coding gene	gene with protein product		608698				11447234	Standard	NM_080927		Approved	CLCP1, ESDN	uc003dtd.3	Q96PD2	OTTHUMG00000151985	ENST00000326840.6:c.1900C>T	3.37:g.98518644G>A	ENSP00000321573:p.His634Tyr	Somatic		WXS	Illumina HiSeq	Phase_IV	B7WNL1|D3DN41|Q8N6M4|Q8TDX2	Missense_Mutation	SNP	pfam_Coagulation_fac_5/8-C_type_dom,pfam_CUB,pfam_LCCL,superfamily_Galactose-bd-like,superfamily_CUB,superfamily_LCCL,smart_CUB,smart_LCCL,smart_Coagulation_fac_5/8-C_type_dom,pfscan_CUB,pfscan_Coagulation_fac_5/8-C_type_dom,pfscan_LCCL	p.H648Y	ENST00000326840.6	37	c.1942	CCDS46878.1	3	.	.	.	.	.	.	.	.	.	.	G	19.04	3.749653	0.69533	.	.	ENSG00000057019	ENST00000326840;ENST00000326857	T;T	0.31510	1.49;1.49	5.51	5.51	0.81932	.	0.190706	0.47455	D	0.000240	T	0.34687	0.0906	N	0.22421	0.69	0.42139	D	0.991507	B;D	0.59357	0.016;0.985	B;P	0.53006	0.009;0.715	T	0.13899	-1.0492	10	0.66056	D	0.02	-22.0623	16.913	0.86144	0.0:0.0:1.0:0.0	.	648;634	Q96PD2-2;Q96PD2	.;DCBD2_HUMAN	Y	634;648	ENSP00000321573:H634Y;ENSP00000321646:H648Y	ENSP00000321573:H634Y	H	-	1	0	DCBLD2	100001334	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.354000	0.73036	2.581000	0.87130	0.655000	0.94253	CAT	DCBLD2	-	NULL		0.398	DCBLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DCBLD2	HGNC	protein_coding	OTTHUMT00000324675.2	G	NM_080927		98518644	-1	no_errors	ENST00000326857	ensembl	human	known	70_37	missense	SNP	1.000	A
DGKI	9162	genome.wustl.edu	37	7	137148328	137148328	+	Missense_Mutation	SNP	C	C	T	rs141499171	byFrequency	TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr7:137148328C>T	ENST00000288490.5	-	28	2666	c.2666G>A	c.(2665-2667)cGg>cAg	p.R889Q	DGKI_ENST00000446122.1_Missense_Mutation_p.R871Q|DGKI_ENST00000424189.2_Missense_Mutation_p.R902Q|DGKI_ENST00000453654.2_Intron	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	889					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						CATGCGTTTCCGCAGGGCAGG	0.507													C|||	4	0.000798722	0.003	0.0	5008	,	,		20198	0.0		0.0	False		,,,				2504	0.0																0								C	GLN/ARG	7,4399	12.9+/-30.5	1,5,2197	83.0	72.0	76.0		2666	5.0	0.9	7	dbSNP_134	76	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DGKI	NM_004717.2	43	1,6,6496	TT,TC,CC		0.0116,0.1589,0.0615	benign	889/1066	137148328	8,12998	2203	4300	6503	SO:0001583	missense	9162			AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"""Ankyrin repeat domain containing"""	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2666G>A	7.37:g.137148328C>T	ENSP00000288490:p.Arg889Gln	Somatic		WXS	Illumina HiSeq	Phase_IV	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	pfam_Diacylglycerol_kin_accessory,pfam_Diacylglycerol_kinase_cat_dom,pfam_Prot_Kinase_C-like_PE/DAG-bd,pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Prot_Kinase_C-like_PE/DAG-bd,smart_Diacylglycerol_kinase_cat_dom,smart_Diacylglycerol_kin_accessory,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	p.R892Q	ENST00000288490.5	37	c.2675	CCDS5845.1	7	.	.	.	.	.	.	.	.	.	.	C	19.68	3.872973	0.72180	0.001589	1.16E-4	ENSG00000157680	ENST00000424189;ENST00000288490;ENST00000446122	T;T	0.34667	1.35;1.54	5.91	5.03	0.67393	.	0.193404	0.37219	N	0.002195	T	0.17492	0.0420	N	0.08118	0	0.38498	D	0.94815	P	0.41546	0.754	B	0.27608	0.081	T	0.12682	-1.0538	10	0.54805	T	0.06	.	14.8654	0.70412	0.0:0.9316:0.0:0.0684	.	889	O75912	DGKI_HUMAN	Q	892;889;871	ENSP00000288490:R889Q;ENSP00000399131:R871Q	ENSP00000288490:R889Q	R	-	2	0	DGKI	136798868	1.000000	0.71417	0.886000	0.34754	0.976000	0.68499	3.577000	0.53885	1.521000	0.48983	0.655000	0.94253	CGG	DGKI	-	NULL		0.507	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	DGKI	HGNC	protein_coding	OTTHUMT00000341286.3	C	NM_004717		137148328	-1	no_errors	ENST00000424189	ensembl	human	known	70_37	missense	SNP	0.999	T
DLEC1	9940	genome.wustl.edu	37	3	38158718	38158718	+	Missense_Mutation	SNP	G	G	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr3:38158718G>T	ENST00000308059.6	+	31	4346	c.4325G>T	c.(4324-4326)gGg>gTg	p.G1442V	DLEC1_ENST00000452631.2_Missense_Mutation_p.G1445V|DLEC1_ENST00000346219.3_Missense_Mutation_p.G1442V					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		GAGATTCCAGGGAAGAGGCAT	0.607																																																	0													59.0	66.0	63.0					3																	38158718		2065	4211	6276	SO:0001583	missense	9940			AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.4325G>T	3.37:g.38158718G>T	ENSP00000308597:p.Gly1442Val	Somatic		WXS	Illumina HiSeq	Phase_IV		Missense_Mutation	SNP	superfamily_PapD-like	p.G1442V	ENST00000308059.6	37	c.4325	CCDS2672.2	3	.	.	.	.	.	.	.	.	.	.	G	17.71	3.456375	0.63401	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.07908	3.2;3.15;3.42	5.07	4.2	0.49525	.	0.144057	0.45126	D	0.000383	T	0.28599	0.0708	M	0.77103	2.36	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.996;0.999;0.996;0.996	T	0.02581	-1.1138	10	0.87932	D	0	-22.9092	12.4049	0.55434	0.084:0.0:0.916:0.0	.	1445;1442;1442;1442	F8W6T4;B7ZW06;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	V	1442;1442;1445	ENSP00000308597:G1442V;ENSP00000315914:G1442V;ENSP00000410427:G1445V	ENSP00000308597:G1442V	G	+	2	0	DLEC1	38133722	1.000000	0.71417	0.155000	0.22561	0.909000	0.53808	5.650000	0.67944	1.136000	0.42199	-0.136000	0.14681	GGG	DLEC1	-	NULL		0.607	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	DLEC1	HGNC	protein_coding	OTTHUMT00000253745.3	G	NM_007337		38158718	+1	no_errors	ENST00000346219	ensembl	human	known	70_37	missense	SNP	0.984	T
DSPP	1834	genome.wustl.edu	37	4	88537225	88537225	+	Missense_Mutation	SNP	C	C	A	rs201608130|rs200679221		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr4:88537225C>A	ENST00000282478.7	+	4	3444	c.3411C>A	c.(3409-3411)gaC>gaA	p.D1137E	DSPP_ENST00000399271.1_Missense_Mutation_p.D1137E|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1137	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472 and 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		atagcagtgacagcagcaaca	0.562																																																	0													23.0	34.0	31.0					4																	88537225		1394	2644	4038	SO:0001583	missense	1834			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3411C>A	4.37:g.88537225C>A	ENSP00000282478:p.Asp1137Glu	Somatic		WXS	Illumina HiSeq	Phase_IV	A8MUI0|O95815	Missense_Mutation	SNP	NULL	p.D1137E	ENST00000282478.7	37	c.3411	CCDS43248.1	4	.	.	.	.	.	.	.	.	.	.	c	0.286	-0.983242	0.02180	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88124	-2.34;-2.34	1.8	-0.124	0.13523	.	1.128020	0.07042	N	0.830287	T	0.77638	0.4160	L	0.34521	1.04	0.09310	N	0.999993	B	0.24768	0.111	B	0.21708	0.036	T	0.62595	-0.6821	10	0.46703	T	0.11	-1.6689	2.3607	0.04307	0.2942:0.5173:0.0:0.1885	.	1137	Q9NZW4	DSPP_HUMAN	E	1137	ENSP00000382213:D1137E;ENSP00000282478:D1137E	ENSP00000282478:D1137E	D	+	3	2	DSPP	88756249	0.765000	0.28485	0.234000	0.24042	0.018000	0.09664	-0.576000	0.05854	-0.053000	0.13289	0.291000	0.19559	GAC	DSPP	-	NULL		0.562	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	DSPP	HGNC	protein_coding	OTTHUMT00000363616.3	C	NM_014208		88537225	+1	no_errors	ENST00000282478	ensembl	human	known	70_37	missense	SNP	0.941	A
EGFL7	51162	genome.wustl.edu	37	9	139564113	139564113	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr9:139564113C>T	ENST00000371699.1	+	5	1164	c.253C>T	c.(253-255)Cgc>Tgc	p.R85C	EGFL7_ENST00000308874.7_Missense_Mutation_p.R85C|EGFL7_ENST00000492002.1_3'UTR|EGFL7_ENST00000371698.3_Missense_Mutation_p.R85C|EGFL7_ENST00000406555.3_Missense_Mutation_p.R85C|MIR126_ENST00000362291.1_RNA			Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7	85	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.				angiogenesis (GO:0001525)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|negative regulation of cell migration (GO:0030336)|negative regulation of Notch signaling pathway (GO:0045746)|positive regulation of endothelial cell proliferation (GO:0001938)|vasculogenesis (GO:0001570)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)			kidney(2)|ovary(1)|prostate(2)|urinary_tract(1)	6	all_cancers(76;0.109)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		TGCCAGGCCTCGCTACGCGTG	0.697																																																	0													15.0	17.0	16.0					9																	139564113		2176	4290	6466	SO:0001583	missense	51162			AF186111	CCDS7002.1	9q34.3	2008-02-05			ENSG00000172889	ENSG00000172889			20594	protein-coding gene	gene with protein product		608582					Standard	NM_016215		Approved	ZNEU1	uc004cih.3	Q9UHF1	OTTHUMG00000020938	ENST00000371699.1:c.253C>T	9.37:g.139564113C>T	ENSP00000360764:p.Arg85Cys	Somatic		WXS	Illumina HiSeq	Phase_IV	B3KRP0|M9VTX9|Q5M7Y5|Q5VUD5|Q96EG0	Missense_Mutation	SNP	pfam_EMI_domain,pfam_EGF-like_Ca-bd,pfam_EGF_extracell,smart_EG-like_dom,smart_EGF-like_Ca-bd,pfscan_EG-like_dom,pfscan_EMI_domain	p.R85C	ENST00000371699.1	37	c.253	CCDS7002.1	9	.	.	.	.	.	.	.	.	.	.	C	15.04	2.714441	0.48622	.	.	ENSG00000172889	ENST00000371699;ENST00000308874;ENST00000406555;ENST00000371698	D;D;D;D	0.96802	-4.13;-4.13;-4.13;-4.13	4.06	4.06	0.47325	EMI domain (2);	0.851494	0.10529	N	0.664054	D	0.96200	0.8761	L	0.44542	1.39	0.42157	D	0.99158	D	0.76494	0.999	P	0.54815	0.761	D	0.94392	0.7615	10	0.45353	T	0.12	-36.6546	15.386	0.74703	0.0:1.0:0.0:0.0	.	85	Q9UHF1	EGFL7_HUMAN	C	85	ENSP00000360764:R85C;ENSP00000307843:R85C;ENSP00000385639:R85C;ENSP00000360763:R85C	ENSP00000307843:R85C	R	+	1	0	EGFL7	138683934	0.002000	0.14202	0.986000	0.45419	0.154000	0.21943	1.718000	0.38001	2.089000	0.63090	0.313000	0.20887	CGC	EGFL7	-	pfam_EMI_domain,pfscan_EMI_domain		0.697	EGFL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EGFL7	HGNC	protein_coding	OTTHUMT00000055094.1	C	NM_016215		139564113	+1	no_errors	ENST00000308874	ensembl	human	known	70_37	missense	SNP	0.674	T
AC008132.13	0	genome.wustl.edu	37	22	18835754	18835754	+	Missense_Mutation	SNP	G	G	A	rs371365085	byFrequency	TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr22:18835754G>A	ENST00000342005.4	+	1	1431	c.1310G>A	c.(1309-1311)cGc>cAc	p.R437H																								AGCCCCTACCGCTCTACGGGA	0.622													g|||	1056	0.210863	0.1732	0.2061	5008	,	,		19004	0.1796		0.2843	False		,,,				2504	0.2219																0																																										SO:0001583	missense	0																														ENST00000342005.4:c.1310G>A	22.37:g.18835754G>A	ENSP00000342394:p.Arg437His	Somatic		WXS	Illumina HiSeq	Phase_IV		Missense_Mutation	SNP	NULL	p.R437H	ENST00000342005.4	37	c.1310		22	.	.	.	.	.	.	.	.	.	.	G	7.576	0.667644	0.14710	.	.	ENSG00000182356	ENST00000427789;ENST00000342005	T	0.11169	2.8	0.75	0.75	0.18387	.	.	.	.	.	T	0.07279	0.0184	.	.	.	.	.	.	B	0.19445	0.036	B	0.06405	0.002	T	0.17410	-1.0370	7	0.62326	D	0.03	.	4.9044	0.13791	0.0:0.0:1.0:0.0	.	437	E2QRI0	.	H	437	ENSP00000342394:R437H	ENSP00000342394:R437H	R	+	2	0	AC008132.13	17215754	0.011000	0.17503	0.003000	0.11579	0.001000	0.01503	0.785000	0.26830	0.729000	0.32403	0.403000	0.27427	CGC	AC008132.13	-	NULL		0.622	AC008132.13-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	ENSG00000182356	Clone_based_vega_gene	protein_coding	OTTHUMT00000316711.1	G			18835754	+1	no_errors	ENST00000427789	ensembl	human	known	70_37	missense	SNP	0.003	A
MT-CYB	4519	genome.wustl.edu	37	M	14705	14705	+	5'Flank	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chrM:14705G>A	ENST00000361789.2	+	0	0				MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b						cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						CCACGACCAATGATATGAAAA	0.383																																																	0																																										SO:0001631	upstream_gene_variant	0					mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156			M.37:g.14705G>A	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_IV	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	RNA	SNP	-	NULL	ENST00000361789.2	37	NULL		MT																																																																																			J01415.20	-	-		0.383	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	ENSG00000210194	Clone_based_ensembl_gene	protein_coding		G	YP_003024038		14705	-1	no_errors	ENST00000387459	ensembl	human	known	70_37	rna	SNP	NULL	A
RP11-764K9.1	0	genome.wustl.edu	37	9	68400475	68400475	+	lincRNA	SNP	T	T	G	rs75317582	byFrequency	TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr9:68400475T>G	ENST00000417843.2	-	0	1344																											CAGGCCACAGTGTGGACtgtt	0.488																																																	0																																												0																															9.37:g.68400475T>G		Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	SNP	-	NULL	ENST00000417843.2	37	NULL		9																																																																																			RP11-764K9.1	-	-		0.488	RP11-764K9.1-001	KNOWN	basic	lincRNA	ENSG00000225411	Clone_based_vega_gene	lincRNA	OTTHUMT00000129817.2	T			68400475	-1	no_errors	ENST00000417843	ensembl	human	known	70_37	rna	SNP	0.010	G
RP11-764K9.1	0	genome.wustl.edu	37	9	68400511	68400511	+	lincRNA	SNP	G	G	A	rs78515312	byFrequency	TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr9:68400511G>A	ENST00000417843.2	-	0	1308																											atagaggaacgccacactttg	0.473																																																	0																																												0																															9.37:g.68400511G>A		Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	SNP	-	NULL	ENST00000417843.2	37	NULL		9																																																																																			RP11-764K9.1	-	-		0.473	RP11-764K9.1-001	KNOWN	basic	lincRNA	ENSG00000225411	Clone_based_vega_gene	lincRNA	OTTHUMT00000129817.2	G			68400511	-1	no_errors	ENST00000417843	ensembl	human	known	70_37	rna	SNP	0.062	A
LOC100287934	100287934	genome.wustl.edu	37	1	741258	741258	+	5'Flank	SNP	C	C	T	rs542632275	byFrequency	TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr1:741258C>T	ENST00000599533.1	-	0	0				RP11-206L10.8_ENST00000447500.1_RNA																							TCCCAAGGTGCAATAGCCATG	0.343													.|||	28	0.00559105	0.0204	0.0	5008	,	,		18867	0.0		0.001	False		,,,				2504	0.0																0																																										SO:0001631	upstream_gene_variant	0																															1.37:g.741258C>T	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	SNP	-	NULL	ENST00000599533.1	37	NULL		1																																																																																			RP11-206L10.8	-	-		0.343	AL669831.1-201	NOVEL	basic|appris_principal	protein_coding	ENSG00000230092	Clone_based_vega_gene	protein_coding		C			741258	-1	no_errors	ENST00000447500	ensembl	human	known	70_37	rna	SNP	1.000	T
IDS	3423	genome.wustl.edu	37	X	148615669	148615669	+	5'Flank	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chrX:148615669C>T	ENST00000422081.2	-	0	0				LINC00893_ENST00000608355.1_RNA|LINC00893_ENST00000431025.1_RNA|IDS_ENST00000541269.1_5'Flank|LINC00893_ENST00000608616.1_RNA|LINC00893_ENST00000430173.1_RNA|LINC00893_ENST00000447209.1_RNA|LINC00893_ENST00000609161.1_RNA|LINC00893_ENST00000608342.1_RNA|LINC00893_ENST00000609314.1_RNA|LINC00893_ENST00000596412.2_RNA|LINC00893_ENST00000437981.1_RNA|LINC00893_ENST00000609369.1_RNA|LINC00893_ENST00000431214.1_RNA|LINC00893_ENST00000451969.1_RNA|LINC00893_ENST00000412882.1_RNA|LINC00893_ENST00000609651.1_RNA|IDS_ENST00000427113.2_5'Flank|LINC00893_ENST00000541582.1_RNA|LINC00893_ENST00000436708.2_RNA			P22304	IDS_HUMAN	iduronate 2-sulfatase						carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	lysosomal lumen (GO:0043202)	iduronate-2-sulfatase activity (GO:0004423)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(5)|large_intestine(2)|lung(8)|prostate(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					caccctatcccgaaggagaaa	0.557																																																	0																																										SO:0001631	upstream_gene_variant	0			M58342	CCDS14685.1, CCDS14686.1	Xq27.3-q28	2012-10-02	2008-08-01		ENSG00000010404	ENSG00000010404	3.1.6.13		5389	protein-coding gene	gene with protein product	"""Hunter syndrome"""	300823		SIDS			Standard	NM_006123		Approved		uc011mxe.2	P22304	OTTHUMG00000022615		X.37:g.148615669C>T	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_IV	D3DWT4|Q14604|Q9BRM3	RNA	SNP	-	NULL	ENST00000422081.2	37	NULL		X																																																																																			AF011889.4	-	-		0.557	IDS-006	PUTATIVE	basic|appris_principal|readthrough_transcript	protein_coding	ENSG00000241769	Clone_based_vega_gene	protein_coding	OTTHUMT00000058694.2	C			148615669	-1	no_errors	ENST00000431214	ensembl	human	known	70_37	rna	SNP	0.000	T
CLRN1-AS1	116933	genome.wustl.edu	37	3	150608642	150608642	+	Intron	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr3:150608642C>T	ENST00000569170.1	-	7	917				CLRN1-AS1_ENST00000476886.1_RNA|FAM188B2_ENST00000397891.3_Intron|RP11-166N6.2_ENST00000469268.1_RNA																							GATGGGGCCCCACCTGCATAC	0.517																																																	0																																										SO:0001627	intron_variant	0																														ENST00000569170.1:c.215+82G>A	3.37:g.150608642C>T		Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	SNP	-	NULL	ENST00000569170.1	37	NULL		3																																																																																			RP11-166N6.2	-	-		0.517	RP11-166N6.3-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_candidate_longest|readthrough_transcript	nonsense_mediated_decay	ENSG00000243273	Clone_based_vega_gene	protein_coding	OTTHUMT00000430534.1	C			150608642	+1	no_errors	ENST00000469268	ensembl	human	known	70_37	rna	SNP	0.000	T
RP11-1166P10.1	0	genome.wustl.edu	37	16	31993404	31993404	+	RNA	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr16:31993404G>A	ENST00000568570.1	+	0	214																											CACGTGTTCCGGCTGACCACC	0.652																																																	0																																												0																															16.37:g.31993404G>A		Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	SNP	-	NULL	ENST00000568570.1	37	NULL		16																																																																																			RP11-1166P10.1	-	-		0.652	RP11-1166P10.1-002	KNOWN	basic	processed_transcript	ENSG00000260628	Clone_based_vega_gene	pseudogene	OTTHUMT00000432457.1	G			31993404	+1	no_errors	ENST00000568570	ensembl	human	known	70_37	rna	SNP	1.000	A
EPB41	2035	genome.wustl.edu	37	1	29379717	29379717	+	Nonsense_Mutation	SNP	A	A	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr1:29379717A>T	ENST00000343067.4	+	12	1865	c.1738A>T	c.(1738-1740)Aaa>Taa	p.K580*	EPB41_ENST00000373797.1_Nonsense_Mutation_p.K580*|EPB41_ENST00000349460.4_Nonsense_Mutation_p.K371*|EPB41_ENST00000398863.2_Nonsense_Mutation_p.K580*|EPB41_ENST00000356093.2_Nonsense_Mutation_p.K580*|EPB41_ENST00000373798.1_Nonsense_Mutation_p.K580*|EPB41_ENST00000347529.3_Nonsense_Mutation_p.K545*|EPB41_ENST00000373800.3_Nonsense_Mutation_p.K371*	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	580	Hydrophilic.				actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		TGCCTCTGCTAAAAAAACAGT	0.542																																																	0													80.0	82.0	82.0					1																	29379717		2203	4300	6503	SO:0001587	stop_gained	2035			BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023			3377	protein-coding gene	gene with protein product		130500	"""elliptocytosis 1, RH-linked"""	EL1			Standard	NM_001166005		Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.1738A>T	1.37:g.29379717A>T	ENSP00000345259:p.Lys580*	Somatic		WXS	Illumina HiSeq	Phase_IV	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	Nonsense_Mutation	SNP	pirsf_Band_41_protein,pfam_Band_4.1_C,pfam_SAB,pfam_FERM_PH-like_C,pfam_FERM_N,pfam_FERM_central,pfam_FERM-adjacent,superfamily_FERM_central,smart_Band_41_domain,prints_Band_41_fam,prints_Ez/rad/moesin,pfscan_FERM_domain	p.K580*	ENST00000343067.4	37	c.1738	CCDS53288.1	1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.114726	0.77210	.	.	ENSG00000159023	ENST00000358989;ENST00000343067;ENST00000356093;ENST00000398863;ENST00000398861;ENST00000398865;ENST00000349460;ENST00000373800;ENST00000347529;ENST00000373798;ENST00000373797	.	.	.	5.5	4.35	0.52113	.	6.762180	0.00166	N	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	10.5406	0.45031	0.8377:0.1623:0.0:0.0	.	.	.	.	X	597;580;580;580;474;580;371;371;545;580;580	.	ENSP00000345259:K580X	K	+	1	0	EPB41	29252304	0.946000	0.32159	0.555000	0.28281	0.007000	0.05969	2.178000	0.42519	0.881000	0.35993	0.533000	0.62120	AAA	EPB41	-	pirsf_Band_41_protein		0.542	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	EPB41	HGNC	protein_coding	OTTHUMT00000010312.1	A	NM_203342		29379717	+1	no_errors	ENST00000343067	ensembl	human	known	70_37	nonsense	SNP	0.796	T
ERN1	2081	genome.wustl.edu	37	17	62149426	62149426	+	Silent	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr17:62149426C>T	ENST00000433197.3	-	6	488	c.393G>A	c.(391-393)ctG>ctA	p.L131L	ERN1_ENST00000577567.1_5'UTR	NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						TCTCTCCGGTCAGGAGGTCAA	0.448																																																	0													53.0	51.0	52.0					17																	62149426		1915	4140	6055	SO:0001819	synonymous_variant	2081			AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"""inositol-requiring enzyme 1"""	604033	"""ER to nucleus signalling 1"""			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.393G>A	17.37:g.62149426C>T		Somatic		WXS	Illumina HiSeq	Phase_IV		Silent	SNP	pfam_Prot_kinase_cat_dom,pfam_KEN_RNase_activator,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_Quinonprotein_ADH-like,smart_PQQ_beta_propeller_repeat,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_PUG-dom,pfscan_Prot_kinase_cat_dom	p.L131	ENST00000433197.3	37	c.393	CCDS45762.1	17																																																																																			ERN1	-	superfamily_Quinonprotein_ADH-like,smart_PQQ_beta_propeller_repeat		0.448	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ERN1	HGNC	protein_coding	OTTHUMT00000443734.2	C	NM_001433		62149426	-1	no_errors	ENST00000433197	ensembl	human	known	70_37	silent	SNP	1.000	T
ERN1	2081	genome.wustl.edu	37	17	62152586	62152586	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr17:62152586C>T	ENST00000433197.3	-	5	399	c.304G>A	c.(304-306)Gaa>Aaa	p.E102K	ERN1_ENST00000577567.1_5'UTR	NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						TGCACCAATTCTGGGATGGTA	0.373																																																	0													19.0	18.0	18.0					17																	62152586		1643	3585	5228	SO:0001583	missense	2081			AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"""inositol-requiring enzyme 1"""	604033	"""ER to nucleus signalling 1"""			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.304G>A	17.37:g.62152586C>T	ENSP00000401445:p.Glu102Lys	Somatic		WXS	Illumina HiSeq	Phase_IV		Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_KEN_RNase_activator,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_Quinonprotein_ADH-like,smart_PQQ_beta_propeller_repeat,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_PUG-dom,pfscan_Prot_kinase_cat_dom	p.E102K	ENST00000433197.3	37	c.304	CCDS45762.1	17	.	.	.	.	.	.	.	.	.	.	C	35	5.491616	0.96339	.	.	ENSG00000178607	ENST00000433197	T	0.20200	2.09	5.87	5.87	0.94306	Quinonprotein alcohol dehydrogenase-like (2);	0.000000	0.85682	D	0.000000	T	0.52158	0.1717	M	0.82323	2.585	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	T	0.46992	-0.9151	10	0.39692	T	0.17	-32.9915	20.1991	0.98252	0.0:1.0:0.0:0.0	.	102	O75460	ERN1_HUMAN	K	102	ENSP00000401445:E102K	ENSP00000401445:E102K	E	-	1	0	ERN1	59506318	1.000000	0.71417	0.894000	0.35097	0.937000	0.57800	7.487000	0.81328	2.775000	0.95449	0.650000	0.86243	GAA	ERN1	-	superfamily_Quinonprotein_ADH-like		0.373	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ERN1	HGNC	protein_coding	OTTHUMT00000443734.2	C	NM_001433		62152586	-1	no_errors	ENST00000433197	ensembl	human	known	70_37	missense	SNP	1.000	T
ESPN	83715	genome.wustl.edu	37	1	6520730	6520730	+	3'UTR	SNP	C	C	G			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr1:6520730C>G	ENST00000377828.1	+	0	3257				TNFRSF25_ENST00000461703.2_5'Flank|ESPN_ENST00000416731.1_3'UTR|ESPN_ENST00000461727.1_3'UTR	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin						locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		GGTTTCCTCTCAGTCATTTGT	0.627																																																	0																																										SO:0001624	3_prime_UTR_variant	83715			AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"""Ankyrin repeat domain containing"""	13281	protein-coding gene	gene with protein product		606351	"""deafness, autosomal recessive 36"""	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.*524C>G	1.37:g.6520730C>G		Somatic		WXS	Illumina HiSeq	Phase_IV	Q6XYB2|Q9H0A2|Q9Y329	RNA	SNP	-	NULL	ENST00000377828.1	37	NULL	CCDS70.1	1																																																																																			ESPN	-	-		0.627	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ESPN	HGNC	protein_coding	OTTHUMT00000001887.3	C	NM_031475		6520730	+1	no_errors	ENST00000468561	ensembl	human	known	70_37	rna	SNP	1.000	G
ESPN	83715	genome.wustl.edu	37	1	6521027	6521027	+	IGR	SNP	C	C	G			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr1:6521027C>G	ENST00000377828.1	+	0	3531				TNFRSF25_ENST00000461703.2_5'Flank	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin						locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		GCGACTTGCTCTCTCCTTCTC	0.642																																																	0																																										SO:0001628	intergenic_variant	83715			AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"""Ankyrin repeat domain containing"""	13281	protein-coding gene	gene with protein product		606351	"""deafness, autosomal recessive 36"""	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753		1.37:g.6521027C>G		Somatic		WXS	Illumina HiSeq	Phase_IV	Q6XYB2|Q9H0A2|Q9Y329	RNA	SNP	-	NULL	ENST00000377828.1	37	NULL	CCDS70.1	1																																																																																			ESPN	-	-		0.642	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ESPN	HGNC	protein_coding	OTTHUMT00000001887.3	C	NM_031475		6521027	+1	no_errors	ENST00000468561	ensembl	human	known	70_37	rna	SNP	0.118	G
EVC2	132884	genome.wustl.edu	37	4	5624288	5624288	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr4:5624288C>T	ENST00000344408.5	-	14	2530	c.2477G>A	c.(2476-2478)cGa>cAa	p.R826Q	EVC2_ENST00000310917.2_Missense_Mutation_p.R746Q|EVC2_ENST00000344938.1_Missense_Mutation_p.R826Q	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	826					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R826Q(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						CTCCCAGCGTCGCAGCTCTGC	0.622																																																	1	Substitution - Missense(1)	large_intestine(1)											74.0	46.0	56.0					4																	5624288		2203	4300	6503	SO:0001583	missense	132884			AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.2477G>A	4.37:g.5624288C>T	ENSP00000342144:p.Arg826Gln	Somatic		WXS	Illumina HiSeq	Phase_IV	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	pfam_Limbin	p.R826Q	ENST00000344408.5	37	c.2477	CCDS3382.2	4	.	.	.	.	.	.	.	.	.	.	C	17.46	3.395695	0.62177	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	D;D;D	0.90844	-2.72;-2.74;-2.73	5.44	5.44	0.79542	.	0.342390	0.34133	N	0.004237	D	0.94798	0.8320	M	0.65498	2.005	0.41571	D	0.988682	D	0.89917	1.0	D	0.87578	0.998	D	0.94949	0.8098	10	0.59425	D	0.04	-25.9408	18.2385	0.89958	0.0:1.0:0.0:0.0	.	826	Q86UK5	LBN_HUMAN	Q	826;746;826	ENSP00000339954:R826Q;ENSP00000311683:R746Q;ENSP00000342144:R826Q	ENSP00000311683:R746Q	R	-	2	0	EVC2	5675189	0.989000	0.36119	0.456000	0.27044	0.001000	0.01503	4.404000	0.59735	2.549000	0.85964	0.462000	0.41574	CGA	EVC2	-	NULL		0.622	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	EVC2	HGNC	protein_coding	OTTHUMT00000289822.2	C	NM_147127		5624288	-1	no_errors	ENST00000344408	ensembl	human	known	70_37	missense	SNP	0.925	T
F11	2160	genome.wustl.edu	37	4	187201212	187201212	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr4:187201212C>T	ENST00000403665.2	+	8	1154	c.802C>T	c.(802-804)Cgc>Tgc	p.R268C	F11_ENST00000264692.4_Missense_Mutation_p.R216C	NM_000128.3	NP_000119.1	P03951	FA11_HUMAN	coagulation factor XI	268	Apple 3. {ECO:0000255|PROSITE- ProRule:PRU00315}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	32		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)	GCCCAGTACACGCATTAAAAA	0.393																																																	0			GRCh37	CM035499	F11	M							80.0	80.0	80.0					4																	187201212		2203	4300	6503	SO:0001583	missense	2160			M13142	CCDS3847.1	4q35	2008-08-01	2008-08-01		ENSG00000088926	ENSG00000088926	3.4.21.27		3529	protein-coding gene	gene with protein product	"""plasma thromboplastin antecedent"""	264900					Standard	NM_000128		Approved	FXI	uc003iza.1	P03951	OTTHUMG00000150311	ENST00000403665.2:c.802C>T	4.37:g.187201212C>T	ENSP00000384957:p.Arg268Cys	Somatic		WXS	Illumina HiSeq	Phase_IV	D3DP64|Q4W5C2|Q9Y495	Missense_Mutation	SNP	pfam_Peptidase_S1_S6,pfam_PAN-1_domain,superfamily_Pept_cys/ser_Trypsin-like,smart_Apple,smart_Peptidase_S1_S6,pfscan_Pan_app,pfscan_Peptidase_S1_S6,prints_Apple,prints_Peptidase_S1A	p.R268C	ENST00000403665.2	37	c.802	CCDS3847.1	4	.	.	.	.	.	.	.	.	.	.	C	9.073	0.997466	0.19043	.	.	ENSG00000088926	ENST00000403665;ENST00000264692	D;D	0.90133	-2.62;-2.62	5.63	5.63	0.86233	Apple domain (3);PAN-1 domain (1);Apple-like (1);	0.578150	0.17984	N	0.155446	D	0.93969	0.8069	M	0.77313	2.365	0.09310	N	0.999997	D	0.89917	1.0	D	0.67103	0.949	D	0.87660	0.2534	10	0.37606	T	0.19	.	9.9347	0.41543	0.0:0.7877:0.1397:0.0726	.	268	P03951	FA11_HUMAN	C	268;216	ENSP00000384957:R268C;ENSP00000264692:R216C	ENSP00000264692:R216C	R	+	1	0	F11	187438206	0.001000	0.12720	0.383000	0.26132	0.181000	0.23173	0.865000	0.27940	2.829000	0.97493	0.644000	0.83932	CGC	F11	-	pfam_PAN-1_domain,smart_Apple,pfscan_Pan_app,prints_Apple		0.393	F11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	F11	HGNC	protein_coding	OTTHUMT00000317519.4	C			187201212	+1	no_errors	ENST00000403665	ensembl	human	known	70_37	missense	SNP	0.075	T
FAM96A	84191	genome.wustl.edu	37	15	64385878	64385878	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr15:64385878G>A	ENST00000300030.3	-	1	339	c.90C>T	c.(88-90)ccC>ccT	p.P30P	SNX1_ENST00000560829.1_5'Flank|SNX1_ENST00000353874.4_5'Flank|SNX1_ENST00000559844.1_5'Flank|FAM96A_ENST00000559950.1_Silent_p.P30P|FAM96A_ENST00000380290.3_Silent_p.P30P|SNX1_ENST00000561026.1_5'Flank|FAM96A_ENST00000557835.1_Silent_p.P30P|SNX1_ENST00000261889.5_5'Flank	NM_032231.4	NP_115607.1	Q9H5X1	FA96A_HUMAN	family with sequence similarity 96, member A	30					chromosome segregation (GO:0007059)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	9						CCATGATCCGGGGCTGCCGGG	0.602																																																	0													48.0	51.0	50.0					15																	64385878		2203	4300	6503	SO:0001819	synonymous_variant	84191				CCDS10189.1, CCDS45278.1	15q22.31	2014-01-16			ENSG00000166797	ENSG00000166797			26235	protein-coding gene	gene with protein product						23891004	Standard	NM_032231		Approved	FLJ22875	uc002amt.1	Q9H5X1	OTTHUMG00000132961	ENST00000300030.3:c.90C>T	15.37:g.64385878G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	A6NKS1|B2R5F8|B7Z8Z5	Silent	SNP	pfam_DUF59	p.P30	ENST00000300030.3	37	c.90	CCDS10189.1	15																																																																																			FAM96A	-	NULL		0.602	FAM96A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM96A	HGNC	protein_coding	OTTHUMT00000256520.1	G	NM_032231		64385878	-1	no_errors	ENST00000300030	ensembl	human	known	70_37	silent	SNP	1.000	A
FBXW7	55294	genome.wustl.edu	37	4	153251907	153251907	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr4:153251907G>A	ENST00000281708.4	-	7	2328	c.1099C>T	c.(1099-1101)Cga>Tga	p.R367*	FBXW7_ENST00000263981.5_Nonsense_Mutation_p.R287*|FBXW7_ENST00000296555.5_Nonsense_Mutation_p.R249*|FBXW7_ENST00000603548.1_Nonsense_Mutation_p.R367*|FBXW7_ENST00000603841.1_Nonsense_Mutation_p.R367*|FBXW7_ENST00000393956.3_Nonsense_Mutation_p.R191*	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	367					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R367*(10)|p.R287*(3)|p.R128*(3)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				AGTTCTCCTCGCCTCCAGTTA	0.388			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	17	Substitution - Nonsense(16)|Unknown(1)	large_intestine(10)|upper_aerodigestive_tract(4)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|endometrium(1)											335.0	288.0	304.0					4																	153251907		2203	4300	6503	SO:0001587	stop_gained	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1099C>T	4.37:g.153251907G>A	ENSP00000281708:p.Arg367*	Somatic		WXS	Illumina HiSeq	Phase_IV	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Nonsense_Mutation	SNP	pfam_WD40_repeat,pfam_F-box_dom_cyclin-like,superfamily_WD40_repeat_dom,superfamily_F-box_dom_cyclin-like,smart_F-box_dom_cyclin-like,smart_WD40_repeat,pfscan_F-box_dom_cyclin-like,pfscan_WD40_repeat,pfscan_WD40_repeat_dom,prints_G-protein_beta_WD-40_rep	p.R367*	ENST00000281708.4	37	c.1099	CCDS3777.1	4	.	.	.	.	.	.	.	.	.	.	G	37	6.344024	0.97489	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	.	.	.	6.07	5.22	0.72569	.	0.052867	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	-12.733	16.6928	0.85326	0.0:0.0:0.8693:0.1307	.	.	.	.	X	367;249;287;191	.	ENSP00000263981:R287X	R	-	1	2	FBXW7	153471357	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.642000	0.46596	1.556000	0.49512	0.650000	0.86243	CGA	FBXW7	-	superfamily_WD40_repeat_dom,superfamily_F-box_dom_cyclin-like		0.388	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FBXW7	HGNC	protein_coding	OTTHUMT00000469956.1	G			153251907	-1	no_errors	ENST00000281708	ensembl	human	known	70_37	nonsense	SNP	1.000	A
FOXD4L5	653427	genome.wustl.edu	37	9	70176944	70176944	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr9:70176944C>T	ENST00000377420.1	-	1	1871	c.1040G>A	c.(1039-1041)cGa>cAa	p.R347Q		NM_001126334.1	NP_001119806.1	Q5VV16	FX4L5_HUMAN	forkhead box D4-like 5	347					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|lung(2)	7						TCCACGCGGTCGGGGACAAAC	0.632																																																	0													0.0	1.0	1.0					9																	70176944		0	17	17	SO:0001583	missense	653427				CCDS47977.1	9q13	2008-07-21			ENSG00000204779	ENSG00000204779			18522	protein-coding gene	gene with protein product						12234674	Standard	NM_001126334		Approved	bA15J10.2, OTTHUMG00000013332	uc010moc.3	Q5VV16	OTTHUMG00000013332	ENST00000377420.1:c.1040G>A	9.37:g.70176944C>T	ENSP00000366637:p.Arg347Gln	Somatic		WXS	Illumina HiSeq	Phase_IV		Missense_Mutation	SNP	pfam_TF_fork_head,smart_TF_fork_head,pfscan_TF_fork_head,prints_TF_fork_head	p.R347Q	ENST00000377420.1	37	c.1040	CCDS47977.1	9	.	.	.	.	.	.	.	.	.	.	c	10.98	1.504061	0.26949	.	.	ENSG00000204779	ENST00000377420	D	0.95980	-3.87	1.07	-2.14	0.07123	.	0.216748	0.22176	U	0.063565	D	0.87997	0.6319	L	0.34521	1.04	0.09310	N	1	B	0.30634	0.288	B	0.14578	0.011	T	0.77983	-0.2382	10	0.45353	T	0.12	.	6.6701	0.23064	0.0:0.5532:0.4468:0.0	.	347	Q5VV16	FX4L5_HUMAN	Q	347	ENSP00000366637:R347Q	ENSP00000366637:R347Q	R	-	2	0	FOXD4L5	69466764	0.000000	0.05858	0.049000	0.19019	0.395000	0.30598	-1.377000	0.02558	-0.737000	0.04824	0.074000	0.15403	CGA	FOXD4L5	-	NULL		0.632	FOXD4L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FOXD4L5	HGNC	protein_coding	OTTHUMT00000037122.1	C	NM_001126334		70176944	-1	no_errors	ENST00000377420	ensembl	human	known	70_37	missense	SNP	0.009	T
GAK	2580	genome.wustl.edu	37	4	870335	870335	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr4:870335G>A	ENST00000314167.4	-	18	2147	c.2037C>T	c.(2035-2037)acC>acT	p.T679T	GAK_ENST00000511163.1_Silent_p.T600T	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	679	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		ATTTCACAGTGGTGGCGTTCC	0.592																																																	0													159.0	131.0	140.0					4																	870335		2203	4300	6503	SO:0001819	synonymous_variant	2580			D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.2037C>T	4.37:g.870335G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	Q5U4P5|Q9BVY6	Silent	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Tensin_phosphatase_C2-dom,pfam_DnaJ_N,superfamily_Kinase-like_dom,superfamily_DnaJ_N,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_DnaJ_N,pfscan_Prot_kinase_cat_dom,pfscan_Phosphatase_tensin-typ,pfscan_Tensin_phosphatase_C2-dom,pfscan_DnaJ_N	p.T679	ENST00000314167.4	37	c.2037	CCDS3340.1	4																																																																																			GAK	-	pfam_Tensin_phosphatase_C2-dom,superfamily_C2_Ca/lipid-bd_dom_CaLB,pfscan_Tensin_phosphatase_C2-dom		0.592	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GAK	HGNC	protein_coding	OTTHUMT00000239188.1	G	NM_005255		870335	-1	no_errors	ENST00000314167	ensembl	human	known	70_37	silent	SNP	0.743	A
GDF5	8200	genome.wustl.edu	37	20	34022246	34022246	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr20:34022246C>T	ENST00000374372.1	-	4	1470	c.967G>A	c.(967-969)Gac>Aac	p.D323N	GDF5_ENST00000374369.3_Missense_Mutation_p.D323N|GDF5OS_ENST00000374375.1_Missense_Mutation_p.S97F			P43026	GDF5_HUMAN	growth differentiation factor 5	323					cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			CCACGGAGGTCCACGGCCCTG	0.632																																																	0													22.0	24.0	23.0					20																	34022246		2200	4298	6498	SO:0001583	missense	8200			X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"""cartilage-derived morphogenetic protein-1"""	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.967G>A	20.37:g.34022246C>T	ENSP00000363492:p.Asp323Asn	Somatic		WXS	Illumina HiSeq	Phase_IV	E1P5Q2|Q96SB1	Missense_Mutation	SNP	pfam_TGF-b_C,pfam_TGF-b_N,smart_TGF-b_C	p.D323N	ENST00000374372.1	37	c.967	CCDS13254.1	20	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.62|18.62	3.662662|3.662662	0.67700|0.67700	.|.	.|.	ENSG00000125965|ENSG00000204183	ENST00000374369;ENST00000374372|ENST00000374375	T;T|.	0.64991|.	-0.13;-0.13|.	4.65|4.65	4.65|4.65	0.58169|0.58169	Transforming growth factor-beta, N-terminal (1);|.	0.055842|.	0.64402|.	D|.	0.000002|.	T|T	0.73923|0.73923	0.3649|0.3649	L|L	0.61387|0.61387	1.9|1.9	0.80722|0.80722	D|D	1|1	B;B|.	0.22003|.	0.036;0.063|.	B;B|.	0.24848|.	0.056;0.043|.	T|T	0.77670|0.77670	-0.2501|-0.2501	10|6	0.48119|0.87932	T|D	0.1|0	.|.	17.6966|17.6966	0.88283|0.88283	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	323;323|.	F1T0J1;P43026|.	.;GDF5_HUMAN|.	N|F	323|97	ENSP00000363489:D323N;ENSP00000363492:D323N|.	ENSP00000363489:D323N|ENSP00000363495:S97F	D|S	-|+	1|2	0|0	GDF5|GDF5OS	33485660|33485660	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.842000|0.842000	0.47809|0.47809	7.651000|7.651000	0.83577|0.83577	2.399000|2.399000	0.81585|0.81585	0.491000|0.491000	0.48974|0.48974	GAC|TCC	GDF5	-	pfam_TGF-b_N		0.632	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GDF5	HGNC	protein_coding	OTTHUMT00000078875.2	C			34022246	-1	no_errors	ENST00000374369	ensembl	human	known	70_37	missense	SNP	1.000	T
GJD2	57369	genome.wustl.edu	37	15	35045326	35045326	+	Missense_Mutation	SNP	G	G	A	rs202150693		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr15:35045326G>A	ENST00000290374.4	-	2	795	c.319C>T	c.(319-321)Cgc>Tgc	p.R107C	RP11-814P5.1_ENST00000503496.1_RNA|RP11-814P5.1_ENST00000558707.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	107					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)	p.R107C(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		GAGTAGCGGCGTTCTCGCTGC	0.582																																																	1	Substitution - Missense(1)	pancreas(1)											83.0	84.0	83.0					15																	35045326		2201	4298	6499	SO:0001583	missense	57369			AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"""Ion channels / Gap junction proteins (connexins)"""	19154	protein-coding gene	gene with protein product	"""connexin 36"""	607058	"""gap junction protein, alpha 9, 36kDa"""	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.319C>T	15.37:g.35045326G>A	ENSP00000290374:p.Arg107Cys	Somatic		WXS	Illumina HiSeq	Phase_IV	Q2M241|Q9P2R0	Missense_Mutation	SNP	pfam_Connexin_N,pfam_Connexin_CCC,smart_Connexin_N,prints_Connexin,prints_Connexin36	p.R107C	ENST00000290374.4	37	c.319	CCDS10040.1	15	.	.	.	.	.	.	.	.	.	.	G	18.09	3.545828	0.65198	.	.	ENSG00000159248	ENST00000290374	D	0.99129	-5.46	4.9	4.9	0.64082	Connexin, N-terminal (1);	0.000000	0.53938	D	0.000059	D	0.98422	0.9475	L	0.54323	1.7	0.80722	D	1	D	0.69078	0.997	P	0.54270	0.747	D	0.98061	1.0393	10	0.59425	D	0.04	.	13.5912	0.61961	0.0:0.0:0.8448:0.1552	.	107	Q9UKL4	CXD2_HUMAN	C	107	ENSP00000290374:R107C	ENSP00000290374:R107C	R	-	1	0	GJD2	32832618	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.467000	0.53078	2.717000	0.92951	0.650000	0.86243	CGC	GJD2	-	pfam_Connexin_N		0.582	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GJD2	HGNC	protein_coding	OTTHUMT00000251875.2	G			35045326	-1	no_errors	ENST00000290374	ensembl	human	known	70_37	missense	SNP	1.000	A
GPLD1	2822	genome.wustl.edu	37	6	24447152	24447152	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr6:24447152G>A	ENST00000230036.1	-	18	1844	c.1734C>T	c.(1732-1734)tcC>tcT	p.S578S		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	578					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						ATCCAAACCAGGAGAAGTCTT	0.493																																																	0													126.0	111.0	116.0					6																	24447152		2203	4300	6503	SO:0001819	synonymous_variant	2822			L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.1734C>T	6.37:g.24447152G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Silent	SNP	pfam_FG-GAP,smart_Int_alpha_beta-p,prints_Gprt_PLipase_D	p.S578	ENST00000230036.1	37	c.1734	CCDS4553.1	6																																																																																			GPLD1	-	smart_Int_alpha_beta-p		0.493	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPLD1	HGNC	protein_coding	OTTHUMT00000043315.1	G	NM_001503		24447152	-1	no_errors	ENST00000230036	ensembl	human	known	70_37	silent	SNP	0.884	A
GPR35	2859	genome.wustl.edu	37	2	241569402	241569402	+	Silent	SNP	C	C	T	rs548753085		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr2:241569402C>T	ENST00000319838.5	+	6	975	c.33C>T	c.(31-33)agC>agT	p.S11S	GPR35_ENST00000407714.1_Silent_p.S11S|GPR35_ENST00000403859.1_Silent_p.S11S|GPR35_ENST00000438013.2_Silent_p.S42S|GPR35_ENST00000430267.1_Silent_p.S11S	NM_001195381.1	NP_001182310.1	Q9HC97	GPR35_HUMAN	G protein-coupled receptor 35	11					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|cervix(1)|endometrium(1)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	17		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;5.29e-32)|all cancers(36;1.38e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.02e-06)|Lung(119;0.00163)|Colorectal(34;0.00463)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.031)		GTGGCTCCAGCGACCTCACCT	0.652													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18052	0.0		0.0	False		,,,				2504	0.0																0													58.0	61.0	60.0					2																	241569402		2203	4300	6503	SO:0001819	synonymous_variant	2859				CCDS2541.1, CCDS56174.1	2q37.3	2012-08-21			ENSG00000178623	ENSG00000178623		"""GPCR / Class A : Orphans"""	4492	protein-coding gene	gene with protein product		602646				9479505	Standard	NM_005301		Approved		uc021vze.1	Q9HC97	OTTHUMG00000133356	ENST00000319838.5:c.33C>T	2.37:g.241569402C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	J3KR30|O43495|Q17R58|Q4VBN5|Q4ZFV2|Q6FHI8|Q86UH4	Silent	SNP	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_GPCR_Rhodpsn	p.S42	ENST00000319838.5	37	c.126	CCDS2541.1	2																																																																																			GPR35	-	NULL		0.652	GPR35-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	GPR35	HGNC	protein_coding	OTTHUMT00000325631.1	C	NM_001195382		241569402	+1	no_errors	ENST00000438013	ensembl	human	known	70_37	silent	SNP	0.000	T
HAS1	3036	genome.wustl.edu	37	19	52222789	52222789	+	Silent	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr19:52222789C>T	ENST00000222115.1	-	2	406	c.372G>A	c.(370-372)ccG>ccA	p.P124P	HAS1_ENST00000601714.1_Silent_p.P131P|HAS1_ENST00000540069.2_Silent_p.P123P|HAS1_ENST00000594621.1_5'Flank	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	124					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GCCGCGCGCGCGGGTACAGCA	0.711																																					NSCLC(132;636 2450 45807 47979)												0													5.0	5.0	5.0					19																	52222789		1929	3731	5660	SO:0001819	synonymous_variant	3036			U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.372G>A	19.37:g.52222789C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	Q14470|Q9NS49	Silent	SNP	pfam_Chitin_synth_fng,pfam_Glyco_trans_2	p.P124	ENST00000222115.1	37	c.372	CCDS12838.1	19																																																																																			HAS1	-	NULL		0.711	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	HAS1	HGNC	protein_coding	OTTHUMT00000466953.1	C	NM_001523		52222789	-1	no_errors	ENST00000222115	ensembl	human	known	70_37	silent	SNP	0.459	T
HIST1H3J	8356	genome.wustl.edu	37	6	27858549	27858549	+	Missense_Mutation	SNP	C	C	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr6:27858549C>A	ENST00000359303.2	-	1	21	c.22G>T	c.(22-24)Gct>Tct	p.A8S	HIST1H3J_ENST00000479986.1_5'UTR|HIST1H2BO_ENST00000303806.4_5'Flank	NM_003535.2	NP_003526.1	P68431	H31_HUMAN	histone cluster 1, H3j	8					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	8						GACTTGCGAGCTGTCTGCTTC	0.572																																																	0													29.0	32.0	31.0					6																	27858549		2199	4291	6490	SO:0001583	missense	8356			Z83737	CCDS4638.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197153	ENSG00000197153		"""Histones / Replication-dependent"""	4774	protein-coding gene	gene with protein product		602817	"""H3 histone family, member J"", ""histone 1, H3j"""	H3FJ		9439656, 12408966	Standard	NM_003535		Approved	H3/j	uc003nka.3	P68431	OTTHUMG00000016185	ENST00000359303.2:c.22G>T	6.37:g.27858549C>A	ENSP00000352252:p.Ala8Ser	Somatic		WXS	Illumina HiSeq	Phase_IV	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	pfam_Histone_core_D,superfamily_Histone-fold,smart_Histone_H3,prints_Histone_H3	p.A8S	ENST00000359303.2	37	c.22	CCDS4638.1	6	.	.	.	.	.	.	.	.	.	.	C	10.80	1.451421	0.26074	.	.	ENSG00000197153	ENST00000359303	T	0.48201	0.82	4.06	4.06	0.47325	.	.	.	.	.	T	0.56891	0.2016	.	.	.	0.46823	D	0.999211	.	.	.	.	.	.	T	0.62374	-0.6868	6	0.87932	D	0	.	16.036	0.80628	0.0:1.0:0.0:0.0	.	.	.	.	S	8	ENSP00000352252:A8S	ENSP00000352252:A8S	A	-	1	0	HIST1H3J	27966528	1.000000	0.71417	0.163000	0.22734	0.137000	0.21094	7.296000	0.78790	2.560000	0.86352	0.655000	0.94253	GCT	HIST1H3J	-	superfamily_Histone-fold,prints_Histone_H3		0.572	HIST1H3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HIST1H3J	HGNC	protein_coding	OTTHUMT00000043453.2	C	NM_003535		27858549	-1	no_errors	ENST00000359303	ensembl	human	known	70_37	missense	SNP	0.998	A
HTT	3064	genome.wustl.edu	37	4	3122961	3122961	+	Missense_Mutation	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr4:3122961G>A	ENST00000355072.5	+	9	1220	c.1075G>A	c.(1075-1077)Gaa>Aaa	p.E359K		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	359					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CTAGGTTTATGAACTGACGTT	0.438																																																	0													52.0	53.0	53.0					4																	3122961		1939	4149	6088	SO:0001583	missense	3064			L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.1075G>A	4.37:g.3122961G>A	ENSP00000347184:p.Glu359Lys	Somatic		WXS	Illumina HiSeq	Phase_IV	Q9UQB7	Missense_Mutation	SNP	pfam_Huntingtin_middle-repeat,pfam_HEAT,superfamily_ARM-type_fold,prints_Huntingtin	p.E359K	ENST00000355072.5	37	c.1075	CCDS43206.1	4	.	.	.	.	.	.	.	.	.	.	G	22.7	4.322102	0.81580	.	.	ENSG00000197386	ENST00000355072	T	0.67171	-0.25	4.82	4.82	0.62117	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.67316	0.2880	M	0.78637	2.42	0.80722	D	1	P	0.37015	0.578	B	0.31442	0.13	T	0.74487	-0.3649	10	0.66056	D	0.02	.	17.5029	0.87737	0.0:0.0:1.0:0.0	.	359	P42858	HD_HUMAN	K	359	ENSP00000347184:E359K	ENSP00000347184:E359K	E	+	1	0	HTT	3092759	1.000000	0.71417	0.993000	0.49108	0.979000	0.70002	7.410000	0.80065	2.233000	0.73108	0.655000	0.94253	GAA	HTT	-	superfamily_ARM-type_fold		0.438	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HTT	HGNC	protein_coding	OTTHUMT00000358234.2	G	NM_002111		3122961	+1	no_errors	ENST00000355072	ensembl	human	known	70_37	missense	SNP	1.000	A
IRX5	10265	genome.wustl.edu	37	16	54967571	54967571	+	Missense_Mutation	SNP	C	C	T	rs568146590	byFrequency	TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr16:54967571C>T	ENST00000394636.4	+	3	1575	c.1238C>T	c.(1237-1239)aCg>aTg	p.T413M	IRX5_ENST00000558597.1_Missense_Mutation_p.T347M|IRX5_ENST00000560154.1_Missense_Mutation_p.T193M|CTD-3032H12.2_ENST00000560487.1_lincRNA|IRX5_ENST00000320990.5_Missense_Mutation_p.T412M			P78411	IRX5_HUMAN	iroquois homeobox 5	413					embryonic cranial skeleton morphogenesis (GO:0048701)|gonad development (GO:0008406)|neuron maturation (GO:0042551)|regulation of heart rate (GO:0002027)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|vitamin D binding (GO:0005499)	p.T413M(1)		kidney(3)|large_intestine(6)|lung(4)|prostate(1)	14						CCCGGCTACACGAACTATGGC	0.657																																																	1	Substitution - Missense(1)	large_intestine(1)											25.0	31.0	29.0					16																	54967571		2196	4291	6487	SO:0001583	missense	10265			U90309	CCDS10751.1, CCDS58462.1	16q12.2	2011-06-20	2007-07-13		ENSG00000176842	ENSG00000176842		"""Homeoboxes / TALE class"""	14361	protein-coding gene	gene with protein product		606195					Standard	NM_005853		Approved	IRX-2a	uc002ehv.3	P78411	OTTHUMG00000133201	ENST00000394636.4:c.1238C>T	16.37:g.54967571C>T	ENSP00000378132:p.Thr413Met	Somatic		WXS	Illumina HiSeq	Phase_IV	H0YMS7|P78416|Q7Z2E1	Missense_Mutation	SNP	pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,smart_Iroquois_homeo,pfscan_Homeodomain	p.T413M	ENST00000394636.4	37	c.1238	CCDS10751.1	16	.	.	.	.	.	.	.	.	.	.	C	16.43	3.121274	0.56613	.	.	ENSG00000176842	ENST00000394636;ENST00000320990	T;T	0.52295	0.67;0.67	4.54	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.63212	0.2492	L	0.52573	1.65	0.80722	D	1	D	0.89917	1.0	D	0.69142	0.962	T	0.67507	-0.5653	10	0.87932	D	0	-17.8814	17.4716	0.87647	0.0:1.0:0.0:0.0	.	413	P78411	IRX5_HUMAN	M	413;412	ENSP00000378132:T413M;ENSP00000316250:T412M	ENSP00000316250:T412M	T	+	2	0	IRX5	53525072	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.207000	0.77899	2.340000	0.79590	0.650000	0.86243	ACG	IRX5	-	NULL		0.657	IRX5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	IRX5	HGNC	protein_coding	OTTHUMT00000256911.2	C			54967571	+1	no_errors	ENST00000394636	ensembl	human	known	70_37	missense	SNP	1.000	T
ISL1	3670	genome.wustl.edu	37	5	50683468	50683468	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr5:50683468G>A	ENST00000230658.7	+	3	948	c.363G>A	c.(361-363)gcG>gcA	p.A121A	ISL1_ENST00000505475.2_3'UTR|ISL1_ENST00000511384.1_Silent_p.A121A	NM_002202.2	NP_002193.2	P61371	ISL1_HUMAN	ISL LIM homeobox 1	121	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				atrial septum morphogenesis (GO:0060413)|axon regeneration (GO:0031103)|cardiac cell fate determination (GO:0060913)|cardiac muscle cell myoblast differentiation (GO:0060379)|cardiac right ventricle morphogenesis (GO:0003215)|cellular response to glucocorticoid stimulus (GO:0071385)|endocardial cushion morphogenesis (GO:0003203)|innervation (GO:0060384)|mesenchymal cell differentiation (GO:0048762)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of protein homodimerization activity (GO:0090074)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate specification (GO:0048665)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|pancreas development (GO:0031016)|peripheral nervous system neuron axonogenesis (GO:0048936)|pharyngeal system development (GO:0060037)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of granulocyte colony-stimulating factor production (GO:0071657)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 alpha production (GO:0032730)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage colony-stimulating factor production (GO:1901258)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|retinal ganglion cell axon guidance (GO:0031290)|secondary heart field specification (GO:0003139)|sensory system development (GO:0048880)|spinal cord motor neuron cell fate specification (GO:0021520)|spinal cord motor neuron differentiation (GO:0021522)|trigeminal nerve development (GO:0021559)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(11)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		Lung NSC(810;0.000845)|Breast(144;0.0411)				ACGAATTTGCGCTTCGGGAGG	0.637																																																	0													54.0	57.0	56.0					5																	50683468		2094	4209	6303	SO:0001819	synonymous_variant	3670			BC031213	CCDS43314.1	5q11.2	2012-03-09	2007-07-13		ENSG00000016082	ENSG00000016082		"""Homeoboxes / LIM class"""	6132	protein-coding gene	gene with protein product		600366	"""ISL1 transcription factor, LIM/homeodomain, (islet-1)"""			7912209	Standard	NM_002202		Approved	Isl-1, ISLET1	uc003jor.3	P61371	OTTHUMG00000162281	ENST00000230658.7:c.363G>A	5.37:g.50683468G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	P20663|P47894	Silent	SNP	pfam_Znf_LIM,pfam_Homeodomain,superfamily_Homeodomain-like,smart_Znf_LIM,smart_Homeodomain,pfscan_Znf_LIM,pfscan_Homeodomain	p.A121	ENST00000230658.7	37	c.363	CCDS43314.1	5	.	.	.	.	.	.	.	.	.	.	G	10.91	1.484882	0.26598	.	.	ENSG00000016082	ENST00000505475	.	.	.	5.53	2.79	0.32731	.	0.058204	0.64402	N	0.000002	T	0.61527	0.2354	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59716	-0.7402	6	0.87932	D	0	.	5.8079	0.18450	0.2846:0.132:0.5834:0.0	.	.	.	.	T	68	.	ENSP00000421737:A68T	A	+	1	0	ISL1	50719225	0.823000	0.29233	1.000000	0.80357	0.976000	0.68499	-0.108000	0.10857	0.299000	0.22661	0.555000	0.69702	GCT	ISL1	-	pfam_Znf_LIM,smart_Znf_LIM,pfscan_Znf_LIM		0.637	ISL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ISL1	HGNC	protein_coding	OTTHUMT00000368413.3	G	NM_002202		50683468	+1	no_errors	ENST00000230658	ensembl	human	known	70_37	silent	SNP	0.997	A
KDM4A	9682	genome.wustl.edu	37	1	44132112	44132112	+	Intron	SNP	C	C	G			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr1:44132112C>G	ENST00000372396.3	+	7	807				KDM4A_ENST00000463151.1_Intron	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A						cardiac muscle hypertrophy in response to stress (GO:0014898)|histone demethylation (GO:0016577)|histone H3-K36 demethylation (GO:0070544)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|methylated histone binding (GO:0035064)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(13)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	37						TGTACCCTTTCAATTAAATAG	0.463																																																	0													60.0	54.0	56.0					1																	44132112		2203	4300	6503	SO:0001627	intron_variant	9682			AB014577	CCDS491.1	1p34.1	2013-01-23	2009-04-06	2009-04-06	ENSG00000066135	ENSG00000066135		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	22978	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 3A"", ""tudor domain containing 14A"""	609764	"""jumonji domain containing 2"", ""jumonji domain containing 2A"""	JMJD2, JMJD2A		9734811, 15138608	Standard	XM_005271354		Approved	KIAA0677, JHDM3A, TDRD14A	uc001cjx.3	O75164	OTTHUMG00000007560	ENST00000372396.3:c.674-11C>G	1.37:g.44132112C>G		Somatic		WXS	Illumina HiSeq	Phase_IV	Q5VVB1	RNA	SNP	-	NULL	ENST00000372396.3	37	NULL	CCDS491.1	1																																																																																			KDM4A	-	-		0.463	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KDM4A	HGNC	protein_coding	OTTHUMT00000019960.1	C	NM_014663		44132112	+1	no_errors	ENST00000472265	ensembl	human	known	70_37	rna	SNP	0.000	G
KNDC1	85442	genome.wustl.edu	37	10	135024981	135024981	+	Missense_Mutation	SNP	G	G	A	rs559717203		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr10:135024981G>A	ENST00000304613.3	+	22	3985	c.3964G>A	c.(3964-3966)Gtc>Atc	p.V1322I	KNDC1_ENST00000368572.2_Missense_Mutation_p.V1324I			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1322	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		GAGCCTCTGCGTCCTGCAGGC	0.637													.|||	1	0.000199681	0.0	0.0	5008	,	,		12543	0.0		0.0	False		,,,				2504	0.001																0													73.0	73.0	73.0					10																	135024981		2203	4300	6503	SO:0001583	missense	85442			AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.3964G>A	10.37:g.135024981G>A	ENSP00000304437:p.Val1322Ile	Somatic		WXS	Illumina HiSeq	Phase_IV	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	pfam_RasGRF_CDC25,pfam_Ras-like_Gua-exchang_fac_N,superfamily_Ras_GEF_dom,superfamily_Kinase-like_dom,smart_KIND,smart_Ras-like_Gua-exchang_fac_N,smart_RasGRF_CDC25,pfscan_RasGRF_CDC25,pfscan_Ras-like_Gua-exchang_fac_N	p.V1324I	ENST00000304613.3	37	c.3970	CCDS7674.1	10	.	.	.	.	.	.	.	.	.	.	G	4.122	0.020874	0.08006	.	.	ENSG00000171798	ENST00000304613;ENST00000368572	T;T	0.34667	1.35;1.35	3.94	1.52	0.23074	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.272710	0.29172	U	0.012934	T	0.10895	0.0266	N	0.04959	-0.14	0.26818	N	0.968851	B	0.21147	0.052	B	0.14578	0.011	T	0.18335	-1.0340	10	0.06494	T	0.89	-21.4415	0.9097	0.01291	0.2035:0.3346:0.2924:0.1695	.	1322	Q76NI1	VKIND_HUMAN	I	1322;1324	ENSP00000304437:V1322I;ENSP00000357561:V1324I	ENSP00000304437:V1322I	V	+	1	0	KNDC1	134874971	0.954000	0.32549	0.992000	0.48379	0.706000	0.40770	0.347000	0.20014	0.780000	0.33566	0.297000	0.19635	GTC	KNDC1	-	pfam_Ras-like_Gua-exchang_fac_N,superfamily_Ras_GEF_dom,smart_Ras-like_Gua-exchang_fac_N,pfscan_Ras-like_Gua-exchang_fac_N		0.637	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	KNDC1	HGNC	protein_coding	OTTHUMT00000277044.3	G	NM_152643		135024981	+1	no_errors	ENST00000368572	ensembl	human	known	70_37	missense	SNP	0.993	A
KPNA1	3836	genome.wustl.edu	37	3	122145813	122145813	+	3'UTR	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr3:122145813G>A	ENST00000344337.6	-	0	1812				RP11-299J3.8_ENST00000609469.1_RNA|RP11-299J3.8_ENST00000608346.1_RNA|RP11-299J3.8_ENST00000608015.1_RNA|RP11-299J3.8_ENST00000608756.1_RNA|KPNA1_ENST00000466923.1_5'UTR	NM_002264.3	NP_002255.3	P52294	IMA5_HUMAN	karyopherin alpha 1 (importin alpha 5)						apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|regulation of DNA recombination (GO:0000018)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	21				GBM - Glioblastoma multiforme(114;0.0898)		ACACAGGTACGTGAAAGCAGA	0.493																																					Melanoma(12;340 801 11196 19797)												0													121.0	100.0	107.0					3																	122145813		2203	4300	6503	SO:0001624	3_prime_UTR_variant	3836			S75295	CCDS3013.1	3q21	2013-02-14			ENSG00000114030	ENSG00000114030		"""Importins"", ""Armadillo repeat containing"""	6394	protein-coding gene	gene with protein product		600686				8052633	Standard	NM_002264		Approved	SRP1, RCH2, NPI-1, IPOA5	uc003efe.2	P52294	OTTHUMG00000159487	ENST00000344337.6:c.*19C>T	3.37:g.122145813G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	D3DN93|Q6IBQ9|Q9BQ56	RNA	SNP	-	NULL	ENST00000344337.6	37	NULL	CCDS3013.1	3																																																																																			KPNA1	-	-		0.493	KPNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KPNA1	HGNC	protein_coding	OTTHUMT00000355740.1	G	NM_002264		122145813	-1	no_errors	ENST00000466923	ensembl	human	known	70_37	rna	SNP	0.927	A
LAMA3	3909	genome.wustl.edu	37	18	21453031	21453031	+	Intron	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr18:21453031C>T	ENST00000313654.9	+	38	5239				LAMA3_ENST00000587184.1_Missense_Mutation_p.S8L|LAMA3_ENST00000269217.6_Missense_Mutation_p.S8L|LAMA3_ENST00000399516.3_Intron	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3						cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GTGAGGCGGTCAGCCTGCAGC	0.622																																																	0													80.0	76.0	78.0					18																	21453031		2203	4300	6503	SO:0001627	intron_variant	3909			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.4998+1406C>T	18.37:g.21453031C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	pfam_Laminin_G,pfam_Laminin_I,pfam_Laminin_II,pfam_EGF_laminin,superfamily_ConA-like_lec_gl_sf,superfamily_STAT_TF_coiled-coil,smart_EGF_laminin,smart_Laminin_G,pfscan_EGF_laminin,pfscan_Laminin_G	p.S8L	ENST00000313654.9	37	c.23	CCDS42419.1	18	.	.	.	.	.	.	.	.	.	.	C	8.374	0.836066	0.16891	.	.	ENSG00000053747	ENST00000269217	T	0.03889	3.77	5.7	1.7	0.24286	.	.	.	.	.	T	0.03520	0.0101	N	0.24115	0.695	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42716	-0.9435	9	0.40728	T	0.16	.	5.6689	0.17711	0.0:0.5257:0.3058:0.1685	.	8;8	Q6VU69;B0YJ33	.;.	L	8	ENSP00000269217:S8L	ENSP00000269217:S8L	S	+	2	0	LAMA3	19707029	0.006000	0.16342	0.004000	0.12327	0.003000	0.03518	0.747000	0.26290	0.344000	0.23847	-0.172000	0.13284	TCA	LAMA3	-	NULL		0.622	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LAMA3	HGNC	protein_coding	OTTHUMT00000254824.3	C	NM_000227, NM_198129		21453031	+1	no_errors	ENST00000269217	ensembl	human	known	70_37	missense	SNP	0.001	T
LMTK2	22853	genome.wustl.edu	37	7	97833404	97833404	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr7:97833404G>A	ENST00000297293.5	+	13	4682	c.4389G>A	c.(4387-4389)ccG>ccA	p.P1463P		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	1463				Missing (in Ref. 2; BAA83031). {ECO:0000305}.	early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					AGAGCTGGCCGCACTCGGCGC	0.597																																																	0													80.0	88.0	85.0					7																	97833404		2203	4300	6503	SO:0001819	synonymous_variant	22853			AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.4389G>A	7.37:g.97833404G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	A4D272|Q75MG7|Q9UPS3	Silent	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.P1463	ENST00000297293.5	37	c.4389	CCDS5654.1	7																																																																																			LMTK2	-	NULL		0.597	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LMTK2	HGNC	protein_coding	OTTHUMT00000334560.1	G	NM_014916		97833404	+1	no_errors	ENST00000297293	ensembl	human	known	70_37	silent	SNP	0.003	A
HNRNPA1P48	642659	genome.wustl.edu	37	16	51680381	51680381	+	RNA	SNP	G	G	A	rs569666544		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr16:51680381G>A	ENST00000562726.1	+	0	715					NR_002944.2|NR_003277.1				heterogeneous nuclear ribonucleoprotein A1 pseudogene 48																		aacttcggtcgtggaggaaac	0.532													-|||	1	0.000199681	0.0008	0.0	5008	,	,		19201	0.0		0.0	False		,,,				2504	0.0																0																																												728643					16q12.1	2013-06-13			ENSG00000224578	ENSG00000224578			48778	pseudogene	pseudogene							Standard	NG_005530		Approved				OTTHUMG00000173250		16.37:g.51680381G>A		Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	SNP	-	NULL	ENST00000562726.1	37	NULL		16																																																																																			CTD-2119F7.2	-	-		0.532	HNRNPA1P48-002	KNOWN	basic	processed_transcript	LOC728643	Clone_based_vega_gene	pseudogene	OTTHUMT00000422613.1	G			51680381	+1	no_errors	ENST00000562726	ensembl	human	known	70_37	rna	SNP	0.034	A
MCF2L	23263	genome.wustl.edu	37	13	113708711	113708711	+	Intron	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr13:113708711G>A	ENST00000375608.3	+	6	517				MCF2L_ENST00000423482.2_Intron|MCF2L_ENST00000375601.3_Intron|MCF2L_ENST00000535094.2_Intron|MCF2L_ENST00000421756.1_Intron|MCF2L_ENST00000375604.2_Intron|MCF2L_ENST00000375597.4_Intron|MCF2L_ENST00000397030.1_Intron|MCF2L_ENST00000442652.2_Intron|MCF2L_ENST00000434480.2_Intron			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like						apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				CACGGCAGCGGCCATTCTGAG	0.562																																																	0																																										SO:0001627	intron_variant	23263			AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.460-6196G>A	13.37:g.113708711G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	RNA	SNP	-	NULL	ENST00000375608.3	37	NULL		13																																																																																			MCF2L	-	-		0.562	MCF2L-001	KNOWN	basic	protein_coding	MCF2L	HGNC	protein_coding	OTTHUMT00000045849.4	G			113708711	+1	no_errors	ENST00000494043	ensembl	human	known	70_37	rna	SNP	0.001	A
MRPL21	219927	genome.wustl.edu	37	11	68671240	68671240	+	Silent	SNP	C	C	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr11:68671240C>A	ENST00000362034.2	-	1	48	c.39G>T	c.(37-39)ctG>ctT	p.L13L	MRPL21_ENST00000450904.2_5'UTR|IGHMBP2_ENST00000255078.3_5'Flank|IGHMBP2_ENST00000539224.1_5'Flank|MRPL21_ENST00000567045.1_5'UTR	NM_181514.1|NM_181515.1	NP_852615.1|NP_852616.1	Q7Z2W9	RM21_HUMAN	mitochondrial ribosomal protein L21	13					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(6)|prostate(1)	8			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			ACGCGGACGCCAGCCGCCCTA	0.687																																																	0													56.0	65.0	62.0					11																	68671240		2199	4290	6489	SO:0001819	synonymous_variant	219927			AK096756	CCDS8186.1, CCDS44662.1	11q13.3	2012-09-13			ENSG00000197345	ENSG00000197345		"""Mitochondrial ribosomal proteins / large subunits"""	14479	protein-coding gene	gene with protein product		611834				11551941	Standard	NM_181514		Approved		uc001ooi.3	Q7Z2W9	OTTHUMG00000167893	ENST00000362034.2:c.39G>T	11.37:g.68671240C>A		Somatic		WXS	Illumina HiSeq	Phase_IV	A6NKU0|C9JPR2	Silent	SNP	pfam_Ribosomal_L21,tigrfam_Ribosomal_L21	p.L13	ENST00000362034.2	37	c.39	CCDS8186.1	11																																																																																			MRPL21	-	NULL		0.687	MRPL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MRPL21	HGNC	protein_coding	OTTHUMT00000396856.1	C	NM_181512		68671240	-1	no_errors	ENST00000362034	ensembl	human	known	70_37	silent	SNP	0.882	A
MT-CO2	4513	genome.wustl.edu	37	M	8119	8119	+	Silent	SNP	T	T	C			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chrM:8119T>C	ENST00000361739.1	+	1	534	c.534T>C	c.(532-534)cgT>cgC	p.R178R	MT-CO3_ENST00000362079.2_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND3_ENST00000361227.2_5'Flank|MT-ATP6_ENST00000361899.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank			P00403	COX2_HUMAN	mitochondrially encoded cytochrome c oxidase II	178					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|respiratory chain complex IV (GO:0045277)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)			endometrium(5)|kidney(8)|lung(2)|pancreas(3)|prostate(1)	19						ATTCCCGGACGTCTAAACCAA	0.473																																																	0																																										SO:0001819	synonymous_variant	4513					mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198712	ENSG00000198712		"""Mitochondrial respiratory chain complex / Complex IV"""	7421	protein-coding gene	gene with protein product		516040	"""cytochrome c oxidase II"""	MTCO2		1712754, 1989603	Standard			Approved	COX2, CO2		P00403		ENST00000361739.1:c.534T>C	M.37:g.8119T>C		Somatic		WXS	Illumina HiSeq	Phase_IV	Q37526	Silent	SNP	pfam_Cyt_c_oxidase_su2_C,pfam_Cyt_c_oxidase_su2_TM_dom,superfamily_Cupredoxin,superfamily_Cyt_c_oxidase_su2-like_TM_dom,pfscan_Cyt_c_oxidase_su2_TM_dom,pfscan_Cyt_c_oxidase_su2_C,tigrfam_Cyt_c_oxidase_su2	p.R178	ENST00000361739.1	37	c.534		MT																																																																																			MT-CO2	-	pfam_Cyt_c_oxidase_su2_C,superfamily_Cupredoxin,pfscan_Cyt_c_oxidase_su2_C,tigrfam_Cyt_c_oxidase_su2		0.473	MT-CO2-201	KNOWN	basic|appris_principal	protein_coding	MT-CO2	HGNC	protein_coding		T	YP_003024029		8119	+1	no_errors	ENST00000361739	ensembl	human	known	70_37	silent	SNP	NULL	C
MTIF2	4528	genome.wustl.edu	37	2	55470638	55470638	+	Missense_Mutation	SNP	C	C	T	rs188291557		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr2:55470638C>T	ENST00000263629.4	-	12	1793	c.1478G>A	c.(1477-1479)cGg>cAg	p.R493Q	MTIF2_ENST00000403721.1_Missense_Mutation_p.R493Q|MTIF2_ENST00000394600.3_Missense_Mutation_p.R493Q	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	493					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						TTCTAAAAACCGTAGAATTGA	0.343																																																	0													149.0	149.0	149.0					2																	55470638		2203	4300	6503	SO:0001583	missense	4528			L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.1478G>A	2.37:g.55470638C>T	ENSP00000263629:p.Arg493Gln	Somatic		WXS	Illumina HiSeq	Phase_IV	D6W5D0	Missense_Mutation	SNP	pfam_EF_GTP-bd_dom,pfam_TIF_IF2_dom3,pfam_Transl_elong_EFTu/EF1A_2,pfam_MIRO-like,pfam_GTP_binding_domain,pfam_Small_GTPase,pfam_SRP_receptor_beta_su,superfamily_TIF_IF2_dom3,superfamily_Transl_elong_init/rib_B-barrel,tigrfam_Small_GTP-bd_dom	p.R493Q	ENST00000263629.4	37	c.1478	CCDS1853.1	2	.	.	.	.	.	.	.	.	.	.	C	2.104	-0.405266	0.04832	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000418823	T;T;T;T	0.58358	0.34;0.34;0.34;0.91	5.6	1.76	0.24704	.	0.574220	0.18261	N	0.146628	T	0.22360	0.0539	N	0.04018	-0.295	0.23215	N	0.998105	B	0.06786	0.001	B	0.06405	0.002	T	0.12837	-1.0532	10	0.19147	T	0.46	-1.5114	2.9042	0.05715	0.2013:0.0808:0.1004:0.6175	.	493	P46199	IF2M_HUMAN	Q	493;493;493;171	ENSP00000384481:R493Q;ENSP00000263629:R493Q;ENSP00000378099:R493Q;ENSP00000403492:R171Q	ENSP00000263629:R493Q	R	-	2	0	MTIF2	55324142	0.972000	0.33761	0.065000	0.19835	0.000000	0.00434	2.814000	0.48010	0.081000	0.16988	-2.404000	0.00223	CGG	MTIF2	-	NULL		0.343	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MTIF2	HGNC	protein_coding	OTTHUMT00000251486.4	C	NM_002453		55470638	-1	no_errors	ENST00000263629	ensembl	human	known	70_37	missense	SNP	0.678	T
MTMR7	9108	genome.wustl.edu	37	8	17188743	17188743	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr8:17188743C>T	ENST00000180173.5	-	7	815	c.781G>A	c.(781-783)Gac>Aac	p.D261N	MTMR7_ENST00000521857.1_Missense_Mutation_p.D261N	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	261	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		GAATAATTGTCTTCATTCTCA	0.393																																																	0													199.0	170.0	180.0					8																	17188743		2203	4300	6503	SO:0001583	missense	9108			AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.781G>A	8.37:g.17188743C>T	ENSP00000180173:p.Asp261Asn	Somatic		WXS	Illumina HiSeq	Phase_IV	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	pfam_Myotub-related,smart_Tyr_Pase_cat,pfscan_Tyr/Dual-specificity_Pase	p.D261N	ENST00000180173.5	37	c.781	CCDS34851.1	8	.	.	.	.	.	.	.	.	.	.	C	33	5.235119	0.95207	.	.	ENSG00000003987	ENST00000180173;ENST00000521857	D;D	0.90385	-2.66;-2.66	4.84	4.84	0.62591	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.000000	0.85682	D	0.000000	D	0.92603	0.7650	L	0.48642	1.525	0.80722	D	1	D;B	0.54772	0.968;0.1	P;B	0.60789	0.879;0.224	D	0.90935	0.4793	10	0.31617	T	0.26	.	18.5404	0.91025	0.0:1.0:0.0:0.0	.	261;261	Q9Y216-2;Q9Y216	.;MTMR7_HUMAN	N	261	ENSP00000180173:D261N;ENSP00000429733:D261N	ENSP00000180173:D261N	D	-	1	0	MTMR7	17233114	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.630000	0.83225	2.683000	0.91414	0.655000	0.94253	GAC	MTMR7	-	pfam_Myotub-related		0.393	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MTMR7	HGNC	protein_coding	OTTHUMT00000375311.1	C	NM_004686		17188743	-1	no_errors	ENST00000180173	ensembl	human	known	70_37	missense	SNP	1.000	T
MTRNR2L1	100462977	genome.wustl.edu	37	17	22024729	22024729	+	IGR	SNP	T	T	C			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr17:22024729T>C	ENST00000540040.1	+	0	1555				MTND1P15_ENST00000579693.1_RNA|RP11-846F4.12_ENST00000483901.2_RNA	NM_001190452.1	NP_001177381.1			MT-RNR2-like 1																		TTCGCCCTATTCTTTATAGCC	0.383																																																	0																																										SO:0001628	intergenic_variant	100288998			CR612552	CCDS54097.1	17p11.2	2014-02-18			ENSG00000256618	ENSG00000256618			37155	protein-coding gene	gene with protein product	"""humanin-like 1"""					19477263	Standard	NM_001190452		Approved		uc002gzb.2	P0CJ68	OTTHUMG00000179068		17.37:g.22024729T>C		Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	SNP	-	NULL	ENST00000540040.1	37	NULL	CCDS54097.1	17																																																																																			MTND1P15	-	-		0.383	MTRNR2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MTND1P15	HGNC	protein_coding	OTTHUMT00000444600.2	T	NM_001190452		22024729	+1	no_errors	ENST00000579693	ensembl	human	known	70_37	rna	SNP	1.000	C
MYH7B	57644	genome.wustl.edu	37	20	33568502	33568502	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr20:33568502C>T	ENST00000262873.7	+	6	682	c.590C>T	c.(589-591)gCg>gTg	p.A197V	MYH7B_ENST00000481922.1_3'UTR	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	155	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			CATATATATGCGGTGGCGGAC	0.612																																																	0													67.0	75.0	72.0					20																	33568502		2114	4242	6356	SO:0001583	missense	57644			AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.590C>T	20.37:g.33568502C>T	ENSP00000262873:p.Ala197Val	Somatic		WXS	Illumina HiSeq	Phase_IV	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	pfam_Myosin_tail,pfam_Myosin_head_motor_dom,pfam_Myosin_N,superfamily_Myosin_S1_N,superfamily_Prefoldin,superfamily_tRNA-bd_arm,superfamily_t-SNARE,smart_Myosin_head_motor_dom,pfscan_IQ_motif_EF-hand-BS,prints_Myosin_head_motor_dom	p.A197V	ENST00000262873.7	37	c.590	CCDS42869.1	20	.	.	.	.	.	.	.	.	.	.	C	20.5	3.999227	0.74818	.	.	ENSG00000078814	ENST00000262873	D	0.89681	-2.55	4.46	4.46	0.54185	Myosin head, motor domain (2);	0.207473	0.24206	N	0.040574	D	0.94417	0.8204	H	0.98701	4.305	0.51767	D	0.999936	D	0.57571	0.98	B	0.43990	0.438	D	0.97044	0.9759	10	0.87932	D	0	.	17.6559	0.88177	0.0:1.0:0.0:0.0	.	155	A7E2Y1	MYH7B_HUMAN	V	197	ENSP00000262873:A197V	ENSP00000262873:A197V	A	+	2	0	MYH7B	33032163	1.000000	0.71417	0.451000	0.26982	0.011000	0.07611	7.651000	0.83577	2.472000	0.83506	0.655000	0.94253	GCG	MYH7B	-	pfam_Myosin_head_motor_dom,smart_Myosin_head_motor_dom		0.612	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MYH7B	HGNC	protein_coding	OTTHUMT00000078833.2	C	NM_020884		33568502	+1	no_errors	ENST00000262873	ensembl	human	novel	70_37	missense	SNP	1.000	T
NAT14	57106	genome.wustl.edu	37	19	55997216	55997216	+	Intron	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr19:55997216C>T	ENST00000205194.4	+	2	375				NAT14_ENST00000591590.1_Silent_p.H47H|NAT14_ENST00000592719.1_Intron|NAT14_ENST00000587400.1_Intron|SSC5D_ENST00000587166.1_5'Flank|SSC5D_ENST00000389623.6_5'Flank	NM_020378.3	NP_065111.1	Q8WUY8	NAT14_HUMAN	N-acetyltransferase 14 (GCN5-related, putative)						DNA-templated transcription, initiation (GO:0006352)|positive regulation of transcription, DNA-templated (GO:0045893)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|N-acetyltransferase activity (GO:0008080)			central_nervous_system(1)|large_intestine(1)|ovary(1)|pancreas(1)	4	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0527)		GATTCAGCCACCCCCTCCCAC	0.647																																																	0																																										SO:0001627	intron_variant	57106			AB055059	CCDS12926.1	19q13.42	2011-11-25	2008-09-24		ENSG00000090971	ENSG00000090971			28918	protein-coding gene	gene with protein product	"""K562 cells-derived leucine zipper-like protein 1"""		"""N-acetyltransferase 14"""			10873651	Standard	NM_020378		Approved	KLP1	uc002qle.2	Q8WUY8		ENST00000205194.4:c.72+69C>T	19.37:g.55997216C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	Q8TDY7|Q9NS72	Silent	SNP	NULL	p.H47	ENST00000205194.4	37	c.141	CCDS12926.1	19																																																																																			NAT14	-	NULL		0.647	NAT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NAT14	HGNC	protein_coding	OTTHUMT00000453339.1	C	NM_020378		55997216	+1	no_errors	ENST00000591590	ensembl	human	putative	70_37	silent	SNP	0.007	T
NHSL1	57224	genome.wustl.edu	37	6	138745300	138745300	+	Missense_Mutation	SNP	G	G	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr6:138745300G>T	ENST00000427025.2	-	7	5379	c.4751C>A	c.(4750-4752)cCc>cAc	p.P1584H	NHSL1_ENST00000343505.5_Missense_Mutation_p.P1580H	NM_020464.1	NP_065197.1	Q5SYE7	NHSL1_HUMAN	NHS-like 1	1584										breast(2)|endometrium(4)|kidney(1)	7						CACAGGGCCGGGGGCCTGGGG	0.682																																																	0													5.0	9.0	8.0					6																	138745300		658	1548	2206	SO:0001583	missense	57224			AB037778	CCDS47487.1, CCDS55063.1	6q23.3	2009-02-18	2004-10-07	2004-10-07	ENSG00000135540	ENSG00000135540			21021	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 63"""	C6orf63			Standard	NM_001144060		Approved	bA43P8.1, KIAA1357	uc011edp.2	Q5SYE7	OTTHUMG00000016321	ENST00000427025.2:c.4751C>A	6.37:g.138745300G>T	ENSP00000394546:p.Pro1584His	Somatic		WXS	Illumina HiSeq	Phase_IV	Q3ZCS5|Q5SYE8|Q9P2J0	Missense_Mutation	SNP	NULL	p.P1584H	ENST00000427025.2	37	c.4751	CCDS55063.1	6	.	.	.	.	.	.	.	.	.	.	G	11.61	1.689791	0.29962	.	.	ENSG00000135540	ENST00000427025;ENST00000343505	T;T	0.38722	1.12;1.61	4.64	0.629	0.17687	.	0.000000	0.35615	N	0.003084	T	0.14614	0.0353	L	0.36672	1.1	0.09310	N	1	P;P	0.44816	0.844;0.844	B;B	0.42555	0.391;0.391	T	0.10451	-1.0629	10	0.72032	D	0.01	-5.2268	5.8365	0.18609	0.1684:0.2972:0.5344:0.0	.	1580;1584	E2QRJ1;Q5SYE7	.;NHSL1_HUMAN	H	1584;1580	ENSP00000394546:P1584H;ENSP00000344672:P1580H	ENSP00000344672:P1580H	P	-	2	0	NHSL1	138786993	0.006000	0.16342	0.000000	0.03702	0.005000	0.04900	1.385000	0.34408	-0.204000	0.10235	-0.812000	0.03155	CCC	NHSL1	-	NULL		0.682	NHSL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	NHSL1	HGNC	protein_coding	OTTHUMT00000043700.2	G	XM_050421		138745300	-1	no_errors	ENST00000427025	ensembl	human	known	70_37	missense	SNP	0.000	T
NIPBL	25836	genome.wustl.edu	37	5	36955658	36955658	+	Missense_Mutation	SNP	T	T	C			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr5:36955658T>C	ENST00000282516.8	+	3	648	c.149T>C	c.(148-150)gTg>gCg	p.V50A	NIPBL_ENST00000448238.2_Missense_Mutation_p.V50A	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	50					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			GCAGAAGAGGTGAACTGCCTT	0.408																																																	0													138.0	126.0	130.0					5																	36955658		2203	4300	6503	SO:0001583	missense	25836			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.149T>C	5.37:g.36955658T>C	ENSP00000282516:p.Val50Ala	Somatic		WXS	Illumina HiSeq	Phase_IV	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.V50A	ENST00000282516.8	37	c.149	CCDS3920.1	5	.	.	.	.	.	.	.	.	.	.	T	19.27	3.794976	0.70452	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.92249	-3.0;-3.0	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.91808	0.7408	L	0.27975	0.815	0.49687	D	0.99981	D;D	0.61697	0.984;0.99	D;D	0.73380	0.956;0.98	D	0.88366	0.2991	10	0.07990	T	0.79	.	15.5202	0.75859	0.0:0.0:0.0:1.0	.	50;50	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	A	50	ENSP00000282516:V50A;ENSP00000406266:V50A	ENSP00000282516:V50A	V	+	2	0	NIPBL	36991415	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.651000	0.83577	2.075000	0.62263	0.477000	0.44152	GTG	NIPBL	-	NULL		0.408	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NIPBL	HGNC	protein_coding	OTTHUMT00000207582.1	T	NM_015384		36955658	+1	no_errors	ENST00000282516	ensembl	human	known	70_37	missense	SNP	1.000	C
OR1L4	254973	genome.wustl.edu	37	9	125487177	125487177	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr9:125487177G>A	ENST00000259466.1	+	1	909	c.909G>A	c.(907-909)aaG>aaA	p.K303K		NM_001005235.1	NP_001005235.1	Q8NGR5	OR1L4_HUMAN	olfactory receptor, family 1, subfamily L, member 4	303						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K303K(1)		breast(2)|large_intestine(3)|lung(13)|prostate(1)|skin(1)	20						GGGGTTTGAAGAAATTAAGAC	0.398																																																	1	Substitution - coding silent(1)	breast(1)											46.0	46.0	46.0					9																	125487177		2203	4300	6503	SO:0001819	synonymous_variant	254973				CCDS35129.1	9q33.2	2013-09-20			ENSG00000136939	ENSG00000136939		"""GPCR / Class A : Olfactory receptors"""	8216	protein-coding gene	gene with protein product				OR1L5			Standard	NM_001005235		Approved	OR9-E	uc004bmu.1	Q8NGR5	OTTHUMG00000020620	ENST00000259466.1:c.909G>A	9.37:g.125487177G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	Q6IFN0|Q96R81	Silent	SNP	pfam_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.K303	ENST00000259466.1	37	c.909	CCDS35129.1	9																																																																																			OR1L4	-	NULL		0.398	OR1L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR1L4	HGNC	protein_coding	OTTHUMT00000053951.1	G			125487177	+1	no_errors	ENST00000259466	ensembl	human	known	70_37	silent	SNP	0.089	A
OR4C5	79346	genome.wustl.edu	37	11	48387825	48387825	+	Missense_Mutation	SNP	T	T	G	rs75650204	byFrequency	TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr11:48387825T>G	ENST00000319813.3	-	1	192	c.193A>C	c.(193-195)Atc>Ctc	p.I65L				Q8NGB2	OR4C5_HUMAN	olfactory receptor, family 4, subfamily C, member 5	65						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)										ACCACAATGATTAGGTTGTCT	0.463																																																	0																																										SO:0001583	missense	79346					11p11.2	2013-03-27	2004-03-04	2004-03-05	ENSG00000176540	ENSG00000176540		"""GPCR / Class A : Olfactory receptors"""	14702	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 5 pseudogene"""	OR4C5P			Standard	NG_002247		Approved	OR4C5Q		Q8NGB2	OTTHUMG00000169462	ENST00000319813.3:c.193A>C	11.37:g.48387825T>G	ENSP00000321338:p.Ile65Leu	Somatic		WXS	Illumina HiSeq	Phase_IV	Q6IFB2	Missense_Mutation	SNP	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.I65L	ENST00000319813.3	37	c.193		11	.	.	.	.	.	.	.	.	.	.	T	0.013	-1.613559	0.00835	.	.	ENSG00000176540	ENST00000319813	T	0.00570	6.51	5.03	1.92	0.25849	.	0.124718	0.36665	N	0.002466	T	0.00210	0.0006	.	.	.	0.18873	N	0.999988	.	.	.	.	.	.	T	0.42241	-0.9463	7	0.02654	T	1	.	6.4039	0.21654	0.0868:0.0:0.4795:0.4337	.	.	.	.	L	65	ENSP00000321338:I65L	ENSP00000321338:I65L	I	-	1	0	OR4C5	48344401	0.000000	0.05858	0.949000	0.38748	0.198000	0.23893	-0.236000	0.09003	0.640000	0.30582	-1.398000	0.01145	ATC	OR4C5	-	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_GPCR_Rhodpsn		0.463	OR4C5-001	KNOWN	basic|appris_principal	protein_coding	OR4C5	HGNC	protein_coding	OTTHUMT00000404174.1	T	NG_002247		48387825	-1	no_errors	ENST00000319813	ensembl	human	known	70_37	missense	SNP	0.945	G
OR4C5	79346	genome.wustl.edu	37	11	48387833	48387833	+	Missense_Mutation	SNP	T	T	C	rs79515387	byFrequency	TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr11:48387833T>C	ENST00000319813.3	-	1	184	c.185A>G	c.(184-186)gAc>gGc	p.D62G				Q8NGB2	OR4C5_HUMAN	olfactory receptor, family 4, subfamily C, member 5	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)										GATTAGGTTGTCTACCATGGT	0.458																																																	0																																										SO:0001583	missense	79346					11p11.2	2013-03-27	2004-03-04	2004-03-05	ENSG00000176540	ENSG00000176540		"""GPCR / Class A : Olfactory receptors"""	14702	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 5 pseudogene"""	OR4C5P			Standard	NG_002247		Approved	OR4C5Q		Q8NGB2	OTTHUMG00000169462	ENST00000319813.3:c.185A>G	11.37:g.48387833T>C	ENSP00000321338:p.Asp62Gly	Somatic		WXS	Illumina HiSeq	Phase_IV	Q6IFB2	Missense_Mutation	SNP	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.D62G	ENST00000319813.3	37	c.185		11	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.647783	0.00792	.	.	ENSG00000176540	ENST00000319813	T	0.00482	7.1	5.03	5.03	0.67393	.	0.000000	0.64402	N	0.000016	T	0.00178	0.0005	.	.	.	0.19300	N	0.999976	.	.	.	.	.	.	T	0.31280	-0.9949	7	0.02654	T	1	.	7.7889	0.29108	0.0:0.7491:0.1625:0.0884	.	.	.	.	G	62	ENSP00000321338:D62G	ENSP00000321338:D62G	D	-	2	0	OR4C5	48344409	0.002000	0.14202	0.851000	0.33527	0.073000	0.16967	0.308000	0.19314	1.283000	0.44513	-0.374000	0.07098	GAC	OR4C5	-	pfscan_GPCR_Rhodpsn_7TM,prints_GPCR_Rhodpsn		0.458	OR4C5-001	KNOWN	basic|appris_principal	protein_coding	OR4C5	HGNC	protein_coding	OTTHUMT00000404174.1	T	NG_002247		48387833	-1	no_errors	ENST00000319813	ensembl	human	known	70_37	missense	SNP	0.972	C
OR4C5	79346	genome.wustl.edu	37	11	48387850	48387850	+	Nonsense_Mutation	SNP	G	G	T	rs73460781	byFrequency	TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr11:48387850G>T	ENST00000319813.3	-	1	167	c.168C>A	c.(166-168)taC>taA	p.Y56*				Q8NGB2	OR4C5_HUMAN	olfactory receptor, family 4, subfamily C, member 5	56						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)										TGGTGAGAAAGTAGATGAGTG	0.448																																																	0																																										SO:0001587	stop_gained	79346					11p11.2	2013-03-27	2004-03-04	2004-03-05	ENSG00000176540	ENSG00000176540		"""GPCR / Class A : Olfactory receptors"""	14702	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 5 pseudogene"""	OR4C5P			Standard	NG_002247		Approved	OR4C5Q		Q8NGB2	OTTHUMG00000169462	ENST00000319813.3:c.168C>A	11.37:g.48387850G>T	ENSP00000321338:p.Tyr56*	Somatic		WXS	Illumina HiSeq	Phase_IV	Q6IFB2	Nonsense_Mutation	SNP	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.Y56*	ENST00000319813.3	37	c.168		11	.	.	.	.	.	.	.	.	.	.	G	10.40	1.338755	0.24253	.	.	ENSG00000176540	ENST00000319813	.	.	.	5.03	3.15	0.36227	.	0.000000	0.52532	D	0.000078	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7439	0.40435	0.1725:0.0:0.8275:0.0	.	.	.	.	X	56	.	ENSP00000321338:Y56X	Y	-	3	2	OR4C5	48344426	0.000000	0.05858	0.515000	0.27774	0.046000	0.14306	-0.066000	0.11598	0.649000	0.30751	0.465000	0.42564	TAC	OR4C5	-	prints_GPCR_Rhodpsn		0.448	OR4C5-001	KNOWN	basic|appris_principal	protein_coding	OR4C5	HGNC	protein_coding	OTTHUMT00000404174.1	G	NG_002247		48387850	-1	no_errors	ENST00000319813	ensembl	human	known	70_37	nonsense	SNP	0.968	T
ORMDL2	29095	genome.wustl.edu	37	12	56213206	56213206	+	Silent	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr12:56213206C>T	ENST00000243045.5	+	3	450	c.255C>T	c.(253-255)caC>caT	p.H85H	ORMDL2_ENST00000548974.1_Silent_p.H85H|RP11-762I7.5_ENST00000552719.1_Intron|ORMDL2_ENST00000550836.1_5'UTR|SARNP_ENST00000552080.1_5'Flank|SARNP_ENST00000336133.3_5'Flank|ORMDL2_ENST00000552672.1_Silent_p.H51H|RP11-762I7.5_ENST00000546837.1_Intron|SARNP_ENST00000444631.2_5'Flank	NM_014182.4	NP_054901.1	Q53FV1	ORML2_HUMAN	ORMDL sphingolipid biosynthesis regulator 2	85					ceramide metabolic process (GO:0006672)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|lung(3)	4						TACTGACACACTGGGAGCAAA	0.517																																																	0													220.0	189.0	200.0					12																	56213206		2203	4300	6503	SO:0001819	synonymous_variant	29095			AF395707	CCDS8893.1	12q13.2	2014-06-16	2014-06-16			ENSG00000123353			16037	protein-coding gene	gene with protein product		610074	"""ORM1 (S. cerevisiae)-like 2"", ""ORM1-like 2 (S. cerevisiae)"""			12093374, 23066021	Standard	NM_014182		Approved	HSPC160, adoplin-2, MST095, MSTP095	uc001shw.1	Q53FV1		ENST00000243045.5:c.255C>T	12.37:g.56213206C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	B2RA58|Q7Z4E5|Q8NFX0|Q9P004	Silent	SNP	pfam_ORMDL,pirsf_ORMDL	p.H85	ENST00000243045.5	37	c.255	CCDS8893.1	12																																																																																			ORMDL2	-	pfam_ORMDL,pirsf_ORMDL		0.517	ORMDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ORMDL2	HGNC	protein_coding	OTTHUMT00000407934.1	C	NM_014182		56213206	+1	no_errors	ENST00000243045	ensembl	human	known	70_37	silent	SNP	1.000	T
PCBP3	54039	genome.wustl.edu	37	21	47333873	47333873	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr21:47333873G>A	ENST00000400314.1	+	10	947	c.609G>A	c.(607-609)ccG>ccA	p.P203P	PCBP3_ENST00000400304.1_Silent_p.P171P|PCBP3_ENST00000400310.1_Silent_p.P203P|PCBP3_ENST00000400308.1_Intron|PCBP3_ENST00000449640.1_Silent_p.P203P|PCBP3_ENST00000400309.1_Silent_p.P203P			P57721	PCBP3_HUMAN	poly(rC) binding protein 3	203					mRNA metabolic process (GO:0016071)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		AGTCCCCACCGAAAGGTGCCA	0.642																																																	0													71.0	82.0	78.0					21																	47333873		2011	4165	6176	SO:0001819	synonymous_variant	54039			AF176329	CCDS42974.2, CCDS46652.1	21q22.3	2013-07-16	2001-11-28		ENSG00000183570	ENSG00000183570			8651	protein-coding gene	gene with protein product		608502	"""poly(rC)-binding protein 3"""			10936052	Standard	NM_020528		Approved		uc002zhq.2	P57721	OTTHUMG00000090399	ENST00000400314.1:c.609G>A	21.37:g.47333873G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	A8MPS2|A8MQ26|B7WNN9|B7WPC1|Q8N9K6|Q96EP6	Silent	SNP	pfam_KH_dom_type_1,pfam_KH_dom_type_2,smart_KH_dom,pfscan_KH_dom_type_1	p.P203	ENST00000400314.1	37	c.609	CCDS42974.2	21																																																																																			PCBP3	-	NULL		0.642	PCBP3-001	KNOWN	basic|CCDS	protein_coding	PCBP3	HGNC	protein_coding	OTTHUMT00000206808.2	G			47333873	+1	no_errors	ENST00000400314	ensembl	human	known	70_37	silent	SNP	1.000	A
PCDHB14	56122	genome.wustl.edu	37	5	140605131	140605131	+	Missense_Mutation	SNP	C	C	G	rs149493075	byFrequency	TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr5:140605131C>G	ENST00000239449.4	+	1	2054	c.2054C>G	c.(2053-2055)tCc>tGc	p.S685C	PCDHB14_ENST00000515856.2_Missense_Mutation_p.S532C	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	685					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGGCCGACTCCCTCACCGTC	0.706																																					Ovarian(141;50 1831 27899 33809 37648)												0													73.0	82.0	79.0					5																	140605131		2194	4285	6479	SO:0001583	missense	56122			AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.2054C>G	5.37:g.140605131C>G	ENSP00000239449:p.Ser685Cys	Somatic		WXS	Illumina HiSeq	Phase_IV	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.S685C	ENST00000239449.4	37	c.2054	CCDS4256.1	5	.	.	.	.	.	.	.	.	.	.	-	12.67	2.007020	0.35415	.	.	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.54866	0.55;0.56	4.17	1.03	0.20045	.	.	.	.	.	T	0.61337	0.2339	M	0.89715	3.055	0.09310	N	1	D	0.55172	0.97	P	0.48089	0.566	T	0.55431	-0.8142	9	0.66056	D	0.02	.	5.1744	0.15127	0.1332:0.3937:0.3917:0.0815	.	685	Q9Y5E9	PCDBE_HUMAN	C	532;685	ENSP00000444518:S532C;ENSP00000239449:S685C	ENSP00000239449:S685C	S	+	2	0	PCDHB14	140585315	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	0.091000	0.15046	-0.042000	0.13535	0.650000	0.86243	TCC	PCDHB14	-	NULL		0.706	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHB14	HGNC	protein_coding	OTTHUMT00000251814.2	C	NM_018934		140605131	+1	no_errors	ENST00000239449	ensembl	human	known	70_37	missense	SNP	0.000	G
PCDHGA5	56110	genome.wustl.edu	37	5	140745349	140745349	+	Silent	SNP	C	C	T	rs369080489		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr5:140745349C>T	ENST00000518069.1	+	1	1452	c.1452C>T	c.(1450-1452)aaC>aaT	p.N484N	PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	484	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGGCGACAACGCTCGAGTCA	0.537																																																	0								C	,,,,,,,	0,4104		0,0,2052	132.0	147.0	142.0		,,,,1452,,,1452	-10.4	0.0	5		142	3,8415		0,3,4206	no	intron,intron,intron,intron,coding-synonymous,intron,intron,coding-synonymous	PCDHGB2,PCDHGB1,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018922.2,NM_018923.2,NM_032054.1	,,,,,,,	0,3,6258	TT,TC,CC		0.0356,0.0,0.024	,,,,,,,	,,,,484/932,,,484/814	140745349	3,12519	2052	4209	6261	SO:0001819	synonymous_variant	56110			AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"""Cadherins / Protocadherins : Clustered"""	8703	other	protocadherin	"""cadherin ME3"""	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.1452C>T	5.37:g.140745349C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	Q2M3F5|Q9Y5D2	Silent	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.N484	ENST00000518069.1	37	c.1452	CCDS54925.1	5																																																																																			PCDHGA5	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin		0.537	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHGA5	HGNC	protein_coding	OTTHUMT00000374742.1	C	NM_018918		140745349	+1	no_errors	ENST00000518069	ensembl	human	known	70_37	silent	SNP	0.076	T
PEAR1	375033	genome.wustl.edu	37	1	156875139	156875139	+	Missense_Mutation	SNP	G	G	A	rs367928332		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr1:156875139G>A	ENST00000338302.3	+	5	455	c.230G>A	c.(229-231)cGt>cAt	p.R77H	PEAR1_ENST00000292357.7_Missense_Mutation_p.R77H			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	77	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ACCGTGTACCGTCAGGTGGTG	0.657																																																	0								G	HIS/ARG	0,4406		0,0,2203	66.0	58.0	61.0		230	2.0	1.0	1		61	1,8599	1.2+/-3.3	0,1,4299	no	missense	PEAR1	NM_001080471.1	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	77/1038	156875139	1,13005	2203	4300	6503	SO:0001583	missense	375033			AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.230G>A	1.37:g.156875139G>A	ENSP00000344465:p.Arg77His	Somatic		WXS	Illumina HiSeq	Phase_IV	Q8TEK2	Missense_Mutation	SNP	pfam_EGF_laminin,superfamily_Growth_fac_rcpt,smart_EG-like_dom,smart_EGF_laminin,pfscan_EG-like_dom,pfscan_EMI_domain	p.R77H	ENST00000338302.3	37	c.230	CCDS30892.1	1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.822319	0.50739	0.0	1.16E-4	ENSG00000187800	ENST00000338302;ENST00000455314;ENST00000292357	D;T;D	0.90732	-2.72;0.54;-2.72	3.92	2.01	0.26516	EMI domain (1);	0.180201	0.27035	N	0.021250	T	0.71651	0.3365	L	0.36672	1.1	0.46954	D	0.999267	P	0.40050	0.7	B	0.26094	0.066	T	0.70920	-0.4741	10	0.87932	D	0	.	8.25	0.31712	0.2038:0.0:0.7962:0.0	.	77	Q5VY43	PEAR1_HUMAN	H	77	ENSP00000344465:R77H;ENSP00000389742:R77H;ENSP00000292357:R77H	ENSP00000292357:R77H	R	+	2	0	PEAR1	155141763	1.000000	0.71417	0.969000	0.41365	0.894000	0.52154	6.979000	0.76154	0.311000	0.23014	-0.150000	0.13652	CGT	PEAR1	-	superfamily_Growth_fac_rcpt,pfscan_EMI_domain		0.657	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PEAR1	HGNC	protein_coding	OTTHUMT00000098937.2	G	NM_001080471		156875139	+1	no_errors	ENST00000292357	ensembl	human	known	70_37	missense	SNP	0.990	A
PHLPP2	23035	genome.wustl.edu	37	16	71697826	71697826	+	Missense_Mutation	SNP	T	T	C			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr16:71697826T>C	ENST00000568954.1	-	13	2339	c.1961A>G	c.(1960-1962)aAt>aGt	p.N654S	RNU6-208P_ENST00000362431.1_RNA|PHLPP2_ENST00000356272.3_Missense_Mutation_p.N654S|PHLPP2_ENST00000567016.1_Missense_Mutation_p.N689S|PHLPP2_ENST00000393524.2_Intron|RP11-432I5.6_ENST00000567077.1_RNA|PHLPP2_ENST00000540628.1_5'UTR|PHLPP2_ENST00000360429.3_Missense_Mutation_p.N654S			Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein phosphatase 2	654					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment membrane (GO:0042622)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						CTGTAACTGATTGTTTGCAAG	0.408																																																	0													96.0	91.0	93.0					16																	71697826		2198	4300	6498	SO:0001583	missense	23035			BX647823	CCDS32479.1, CCDS73910.1	16q22.2	2013-01-11	2009-05-26	2009-05-26	ENSG00000040199	ENSG00000040199		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"", ""Pleckstrin homology (PH) domain containing"""	29149	protein-coding gene	gene with protein product		611066	"""PH domain and leucine rich repeat protein phosphatase-like"""	PHLPPL		17386267	Standard	NM_001289003		Approved	KIAA0931	uc002fax.3	Q6ZVD8		ENST00000568954.1:c.1961A>G	16.37:g.71697826T>C	ENSP00000457991:p.Asn654Ser	Somatic		WXS	Illumina HiSeq	Phase_IV	A1L374|Q9NV17|Q9Y2E3	Missense_Mutation	SNP	pfam_PP2C-like,pfam_Leu-rich_rpt,superfamily_PP2C-like,smart_Leu-rich_rpt_typical-subtyp,smart_PP2C-like	p.N654S	ENST00000568954.1	37	c.1961	CCDS32479.1	16	.	.	.	.	.	.	.	.	.	.	T	27.2	4.806009	0.90623	.	.	ENSG00000040199	ENST00000299971;ENST00000360429;ENST00000356272	T;T	0.72615	-0.67;-0.67	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.88351	0.6413	H	0.94542	3.55	0.58432	D	0.999999	D	0.76494	0.999	D	0.83275	0.996	D	0.91401	0.5143	10	0.72032	D	0.01	-21.381	15.086	0.72155	0.0:0.0:0.0:1.0	.	654	Q6ZVD8	PHLP2_HUMAN	S	461;654;654	ENSP00000353610:N654S;ENSP00000348611:N654S	ENSP00000299971:N461S	N	-	2	0	PHLPP2	70255327	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.825000	0.86693	2.149000	0.67028	0.377000	0.23210	AAT	PHLPP2	-	pfam_Leu-rich_rpt,smart_Leu-rich_rpt_typical-subtyp		0.408	PHLPP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	PHLPP2	HGNC	protein_coding	OTTHUMT00000434139.1	T	NM_015020		71697826	-1	no_errors	ENST00000356272	ensembl	human	known	70_37	missense	SNP	1.000	C
PLIN2	123	genome.wustl.edu	37	9	19108575	19108575	+	RNA	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr9:19108575C>T	ENST00000583933.1	-	0	0									RNA, 7SL, cytoplasmic 158, pseudogene																		ATACAAATTGCGTATTCAACC	0.353																																																	0																																												123					9p22.1	2013-04-02			ENSG00000264126			"""ncRNAs / Small cytoplasmic RNAs"""	46174	pseudogene	RNA, pseudogene							Standard			Approved						9.37:g.19108575C>T		Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	SNP	-	NULL	ENST00000583933.1	37	NULL		9																																																																																			PLIN2	-	-		0.353	RN7SL158P-201	KNOWN	basic	misc_RNA	PLIN2	HGNC	misc_RNA		C			19108575	-1	no_errors	ENST00000464326	ensembl	human	known	70_37	rna	SNP	0.000	T
PLXNA4	91584	genome.wustl.edu	37	7	132192823	132192823	+	Silent	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr7:132192823C>T	ENST00000359827.3	-	2	1592	c.630G>A	c.(628-630)gcG>gcA	p.A210A	PLXNA4_ENST00000321063.4_Silent_p.A210A|PLXNA4_ENST00000423507.2_Silent_p.A210A|PLXNA4_ENST00000378539.5_Silent_p.A210A			Q9HCM2	PLXA4_HUMAN	plexin A4	210	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						ACATGCCATCCGCCTCAGAGT	0.517																																																	0													147.0	140.0	142.0					7																	132192823		2203	4300	6503	SO:0001819	synonymous_variant	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.630G>A	7.37:g.132192823C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	pfam_Plexin_cytoplasmic_RasGAP_dom,pfam_Semaphorin/CD100_Ag,pfam_IPT_TIG_rcpt,pfam_Plexin_repeat,superfamily_Semaphorin/CD100_Ag,superfamily_Rho_GTPase_activation_prot,superfamily_Ig_E-set,superfamily_Plexin-like_fold,smart_Semaphorin/CD100_Ag,smart_Plexin-like,smart_IPT_TIG_rcpt,pfscan_Semaphorin/CD100_Ag	p.A210	ENST00000359827.3	37	c.630	CCDS43646.1	7																																																																																			PLXNA4	-	pfam_Semaphorin/CD100_Ag,superfamily_Semaphorin/CD100_Ag,smart_Semaphorin/CD100_Ag,pfscan_Semaphorin/CD100_Ag		0.517	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLXNA4	HGNC	protein_coding	OTTHUMT00000338422.2	C	NM_181775		132192823	-1	no_errors	ENST00000321063	ensembl	human	known	70_37	silent	SNP	0.000	T
PNPLA1	285848	genome.wustl.edu	37	6	36270034	36270034	+	Frame_Shift_Del	DEL	C	C	-			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr6:36270034delC	ENST00000394571.2	+	6	1172	c.1172delC	c.(1171-1173)accfs	p.T391fs	PNPLA1_ENST00000388715.3_Frame_Shift_Del_p.T296fs|PNPLA1_ENST00000312917.5_Frame_Shift_Del_p.T305fs	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	391	Pro-rich.				lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						TCACTGCCCACCCCACCACCT	0.577											OREG0017382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0													177.0	152.0	160.0					6																	36270034		2203	4300	6503	SO:0001589	frameshift_variant	285848				CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"""Patatin-like phospholipase domain containing"""	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.1172delC	6.37:g.36270034delC	ENSP00000378072:p.Thr391fs	Somatic	861	WXS	Illumina HiSeq	Phase_IV	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Frame_Shift_Del	DEL	pfam_Patatin/PLipase_A2-rel,superfamily_Acyl_Trfase/lysoPLipase	p.P393fs	ENST00000394571.2	37	c.1175	CCDS54997.1	6																																																																																			PNPLA1	-	NULL		0.577	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	PNPLA1	HGNC	protein_coding		C	NM_173676		36270034	+1	no_errors	ENST00000457797	ensembl	human	known	70_37	frame_shift_del	DEL	0.000	-
PTCH1	5727	genome.wustl.edu	37	9	98211363	98211363	+	Silent	SNP	G	G	A	rs144312968		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr9:98211363G>A	ENST00000331920.6	-	22	4091	c.3792C>T	c.(3790-3792)ttC>ttT	p.F1264F	PTCH1_ENST00000421141.1_Silent_p.F1113F|PTCH1_ENST00000375274.2_Silent_p.F1263F|PTCH1_ENST00000430669.2_Silent_p.F1198F|PTCH1_ENST00000437951.1_Silent_p.F1198F|PTCH1_ENST00000418258.1_Silent_p.F1113F|PTCH1_ENST00000429896.2_Silent_p.F1113F	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	1264					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				TGGAGTGGGCGAAGACGGGGT	0.652													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16570	0.0		0.0	False		,,,				2504	0.0																0								G	,,,,,,	3,4403	6.2+/-15.9	0,3,2200	32.0	34.0	33.0		3792,3594,3789,3339,3339,3339,3339	-4.6	0.9	9	dbSNP_134	33	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTCH1	NM_000264.3,NM_001083602.1,NM_001083603.1,NM_001083604.1,NM_001083605.1,NM_001083606.1,NM_001083607.1	,,,,,,	0,4,6498	AA,AG,GG		0.0116,0.0681,0.0308	,,,,,,	1264/1448,1198/1382,1263/1447,1113/1297,1113/1297,1113/1297,1113/1297	98211363	4,13000	2203	4299	6502	SO:0001819	synonymous_variant	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.3792C>T	9.37:g.98211363G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	pfam_Patched,pfscan_SSD,tigrfam_TM_rcpt_patched	p.F1264	ENST00000331920.6	37	c.3792	CCDS6714.1	9																																																																																			PTCH1	-	NULL		0.652	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTCH1	HGNC	protein_coding	OTTHUMT00000053229.2	G	NM_000264		98211363	-1	no_errors	ENST00000331920	ensembl	human	known	70_37	silent	SNP	0.950	A
QARS	5859	genome.wustl.edu	37	3	49137041	49137041	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr3:49137041G>A	ENST00000306125.6	-	16	1765	c.1428C>T	c.(1426-1428)gtC>gtT	p.V476V	QARS_ENST00000414533.1_Silent_p.V465V|QARS_ENST00000470225.1_5'Flank			P47897	SYQ_HUMAN	glutaminyl-tRNA synthetase	476					brain development (GO:0007420)|gene expression (GO:0010467)|glutaminyl-tRNA aminoacylation (GO:0006425)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|glutamine-tRNA ligase activity (GO:0004819)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)	L-Glutamine(DB00130)	CAGGGCAATAGACGTCCAGTG	0.557																																																	0													73.0	73.0	73.0					3																	49137041		2203	4300	6503	SO:0001819	synonymous_variant	5859			X76013	CCDS2788.1, CCDS63633.1	3p21.31	2011-07-01			ENSG00000172053	ENSG00000172053	6.1.1.18	"""Aminoacyl tRNA synthetases / Class I"""	9751	protein-coding gene	gene with protein product	"""glutamine tRNA ligase"""	603727				8078941, 10393422	Standard	NM_005051		Approved		uc003cvx.4	P47897	OTTHUMG00000156774	ENST00000306125.6:c.1428C>T	3.37:g.49137041G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	B4DWJ2	Silent	SNP	pfam_Glu/Gln-tRNA-synth_Ib_cat-dom,pfam_Gln-tRNA-synth_Ib_RNA-bd_N,pfam_Glu/Gln-tRNA-synth_Ib_codon-bd,pfam_Gln-tRNA-synth_Ib_RNA-bd_2,superfamily_Ribosomal_L25/Gln-tRNA_synth,prints_Glu/Gln-tRNA-synth_Ib,tigrfam_Gln-tRNA-synth_Ib	p.V476	ENST00000306125.6	37	c.1428	CCDS2788.1	3																																																																																			QARS	-	pfam_Glu/Gln-tRNA-synth_Ib_cat-dom,tigrfam_Gln-tRNA-synth_Ib		0.557	QARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	QARS	HGNC	protein_coding	OTTHUMT00000345689.2	G	NM_005051		49137041	-1	no_errors	ENST00000306125	ensembl	human	known	70_37	silent	SNP	0.779	A
RBM6	10180	genome.wustl.edu	37	3	50005813	50005813	+	Missense_Mutation	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr3:50005813G>A	ENST00000266022.4	+	3	1214	c.955G>A	c.(955-957)Gac>Aac	p.D319N	RBM6_ENST00000539992.1_Intron|RBM6_ENST00000422955.1_Intron|RBM6_ENST00000442092.1_Intron|RBM6_ENST00000441115.1_Intron|RBM6_ENST00000443081.1_Missense_Mutation_p.D187N	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	319					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		ATCCACACATGACCATACGAT	0.423																																																	0													74.0	68.0	70.0					3																	50005813		2203	4300	6503	SO:0001583	missense	10180			AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.955G>A	3.37:g.50005813G>A	ENSP00000266022:p.Asp319Asn	Somatic		WXS	Illumina HiSeq	Phase_IV	O60549|O75524|Q86SS3	Missense_Mutation	SNP	pfam_G_patch_dom,smart_RRM_dom,smart_G_patch_dom,pfscan_G_patch_dom,pfscan_RRM_dom	p.D319N	ENST00000266022.4	37	c.955	CCDS2809.1	3	.	.	.	.	.	.	.	.	.	.	G	5.711	0.315713	0.10789	.	.	ENSG00000004534	ENST00000266022;ENST00000443081	T;T	0.30714	1.52;1.54	6.04	6.04	0.98038	.	0.649667	0.15667	N	0.250587	T	0.19366	0.0465	N	0.19112	0.55	0.80722	D	1	P	0.35433	0.501	B	0.33042	0.157	T	0.05666	-1.0871	9	.	.	.	-17.5673	10.4186	0.44338	0.0682:0.0:0.798:0.1338	.	319	P78332	RBM6_HUMAN	N	319;187	ENSP00000266022:D319N;ENSP00000396466:D187N	.	D	+	1	0	RBM6	49980817	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	3.816000	0.55658	2.873000	0.98535	0.561000	0.74099	GAC	RBM6	-	NULL		0.423	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RBM6	HGNC	protein_coding	OTTHUMT00000345528.4	G	NM_005777		50005813	+1	no_errors	ENST00000266022	ensembl	human	known	70_37	missense	SNP	1.000	A
REEP6	92840	genome.wustl.edu	37	19	1496286	1496286	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr19:1496286C>A	ENST00000233596.3	+	4	455	c.351C>A	c.(349-351)tgC>tgA	p.C117*		NM_138393.1	NP_612402.1	Q96HR9	REEP6_HUMAN	receptor accessory protein 6	117					regulation of intracellular transport (GO:0032386)	apical part of cell (GO:0045177)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				lung(1)|ovary(1)	2		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCTGCAGTGCGCCTTCCTGT	0.672																																																	0													69.0	54.0	59.0					19																	1496286		2202	4299	6501	SO:0001587	stop_gained	92840			BC008201	CCDS12070.1	19p13.3	2012-12-20	2006-02-08	2006-02-07	ENSG00000115255	ENSG00000115255		"""Receptor accessory proteins"""	30078	protein-coding gene	gene with protein product	"""polyposis locus protein 1-like 1"", ""deleted in polyposis 1-like 1"""	609346	"""chromosome 19 open reading frame 32"""	C19orf32		16271481, 15550249	Standard	NM_138393		Approved	DP1L1, FLJ25383	uc002ltc.3	Q96HR9	OTTHUMG00000180072	ENST00000233596.3:c.351C>A	19.37:g.1496286C>A	ENSP00000233596:p.Cys117*	Somatic		WXS	Illumina HiSeq	Phase_IV	B2RE01|D6W5Z0|Q96LM0	Nonsense_Mutation	SNP	pfam_TB2_DP1_HVA22	p.C117*	ENST00000233596.3	37	c.351	CCDS12070.1	19	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.81|19.81	3.897446|3.897446	0.72639|0.72639	.|.	.|.	ENSG00000115255|ENSG00000115255	ENST00000233596;ENST00000395479|ENST00000395484	.|.	.|.	.|.	4.97|4.97	1.41|1.41	0.22369|0.22369	.|.	.|.	.|.	.|.	.|.	.|T	.|0.48624	.|0.1510	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.59053	.|-0.7526	.|4	0.02654|0.62326	T|D	1|0.03	-9.4907|-9.4907	7.5145|7.5145	0.27593|0.27593	0.0:0.576:0.0:0.424|0.0:0.576:0.0:0.424	.|.	.|.	.|.	.|.	X|S	117|185	.|.	ENSP00000233596:C117X|ENSP00000378865:R185S	C|R	+|+	3|1	2|0	REEP6|REEP6	1447286|1447286	0.969000|0.969000	0.33509|0.33509	1.000000|1.000000	0.80357|0.80357	0.105000|0.105000	0.19272|0.19272	1.876000|1.876000	0.39588|0.39588	0.517000|0.517000	0.28361|0.28361	-0.267000|-0.267000	0.10333|0.10333	TGC|CGC	REEP6	-	pfam_TB2_DP1_HVA22		0.672	REEP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	REEP6	HGNC	protein_coding	OTTHUMT00000449623.1	C	NM_138393		1496286	+1	no_errors	ENST00000233596	ensembl	human	known	70_37	nonsense	SNP	0.979	A
RNF10	9921	genome.wustl.edu	37	12	121014518	121014518	+	3'UTR	SNP	T	T	G			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr12:121014518T>G	ENST00000325954.4	+	0	2946				RNF10_ENST00000542701.1_3'UTR|RNF10_ENST00000413266.2_3'UTR|POP5_ENST00000542776.1_5'Flank	NM_014868.4	NP_055683.3	Q8N5U6	RNF10_HUMAN	ring finger protein 10						negative regulation of Schwann cell proliferation (GO:0010626)|positive regulation of myelination (GO:0031643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autoubiquitination (GO:0051865)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	27	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TTTTTGTTTTTTTTTCCCCCA	0.453																																																	0													81.0	82.0	82.0					12																	121014518		2203	4300	6503	SO:0001624	3_prime_UTR_variant	9921			AB027196	CCDS9201.1	12q23-q24	2013-01-09			ENSG00000022840	ENSG00000022840		"""RING-type (C3HC4) zinc fingers"""	10055	protein-coding gene	gene with protein product							Standard	NM_014868		Approved	KIAA0262, RIE2	uc001typ.4	Q8N5U6	OTTHUMG00000168999	ENST00000325954.4:c.*49T>G	12.37:g.121014518T>G		Somatic		WXS	Illumina HiSeq	Phase_IV	Q92550|Q9NPP8|Q9ULW4	RNA	SNP	-	NULL	ENST00000325954.4	37	NULL	CCDS9201.1	12																																																																																			RNF10	-	-		0.453	RNF10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	RNF10	HGNC	protein_coding	OTTHUMT00000401898.4	T			121014518	+1	no_errors	ENST00000535470	ensembl	human	known	70_37	rna	SNP	0.180	G
RPS6KA6	27330	genome.wustl.edu	37	X	83372122	83372122	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chrX:83372122C>T	ENST00000262752.2	-	11	902	c.895G>A	c.(895-897)Gaa>Aaa	p.E299K	RPS6KA6_ENST00000543399.1_Missense_Mutation_p.E299K	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	299	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|central nervous system development (GO:0007417)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation of embryonic development (GO:0045992)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of mesoderm development (GO:2000381)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(26)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	46						CTTTGTGCTTCAGCACTAAGA	0.318																																																	0													51.0	48.0	49.0					X																	83372122		2201	4296	6497	SO:0001583	missense	27330			AF184965	CCDS14451.1	Xq21.1	2011-04-05	2002-08-29		ENSG00000072133	ENSG00000072133			10435	protein-coding gene	gene with protein product		300303	"""ribosomal protein S6 kinase, 90kD, polypeptide 6"""			10644430	Standard	NM_014496		Approved	RSK4	uc004eej.2	Q9UK32	OTTHUMG00000021923	ENST00000262752.2:c.895G>A	X.37:g.83372122C>T	ENSP00000262752:p.Glu299Lys	Somatic		WXS	Illumina HiSeq	Phase_IV	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Pkinase_C,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_AGC-kinase_C,pirsf_Ribosomal_S6_kinase_II,pfscan_Prot_kinase_cat_dom	p.E299K	ENST00000262752.2	37	c.895	CCDS14451.1	X	.	.	.	.	.	.	.	.	.	.	C	26.1	4.702921	0.88924	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	T;T	0.52754	0.65;0.65	4.64	4.64	0.57946	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.60560	0.2278	M	0.76002	2.32	0.80722	D	1	P;P	0.38250	0.624;0.624	P;B	0.47251	0.542;0.439	T	0.65549	-0.6141	10	0.54805	T	0.06	.	17.0306	0.86460	0.0:1.0:0.0:0.0	.	299;299	B7ZL90;Q9UK32	.;KS6A6_HUMAN	K	299	ENSP00000262752:E299K;ENSP00000440830:E299K	ENSP00000262752:E299K	E	-	1	0	RPS6KA6	83258778	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.552000	0.82192	2.028000	0.59812	0.600000	0.82982	GAA	RPS6KA6	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Ribosomal_S6_kinase_II,pfscan_Prot_kinase_cat_dom		0.318	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RPS6KA6	HGNC	protein_coding	OTTHUMT00000057372.1	C	NM_014496		83372122	-1	no_errors	ENST00000262752	ensembl	human	known	70_37	missense	SNP	1.000	T
SEMA5A	9037	genome.wustl.edu	37	5	9197373	9197373	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr5:9197373G>A	ENST00000382496.5	-	10	1640	c.975C>T	c.(973-975)agC>agT	p.S325S		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	325	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						GCGCGATGGCGCTCAGGTTGA	0.597																																																	0													80.0	80.0	80.0					5																	9197373		2203	4300	6503	SO:0001819	synonymous_variant	9037			U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"""Semaphorins"""	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.975C>T	5.37:g.9197373G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	D3DTC6|O60408|Q1RLL9	Silent	SNP	pfam_Semaphorin/CD100_Ag,pfam_Thrombospondin_1_rpt,superfamily_Semaphorin/CD100_Ag,superfamily_Thrombospondin_1_rpt,superfamily_Plexin-like_fold,smart_Semaphorin/CD100_Ag,smart_Plexin-like,smart_Thrombospondin_1_rpt,pfscan_Semaphorin/CD100_Ag,pfscan_Thrombospondin_1_rpt	p.S325	ENST00000382496.5	37	c.975	CCDS3875.1	5																																																																																			SEMA5A	-	pfam_Semaphorin/CD100_Ag,superfamily_Semaphorin/CD100_Ag,smart_Semaphorin/CD100_Ag,pfscan_Semaphorin/CD100_Ag		0.597	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SEMA5A	HGNC	protein_coding	OTTHUMT00000206989.2	G			9197373	-1	no_errors	ENST00000382496	ensembl	human	known	70_37	silent	SNP	0.763	A
SGSM1	129049	genome.wustl.edu	37	22	25297862	25297862	+	Silent	SNP	C	C	T	rs577535941		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr22:25297862C>T	ENST00000400359.4	+	21	2845	c.2838C>T	c.(2836-2838)tgC>tgT	p.C946C	SNORD56_ENST00000362913.1_RNA|SGSM1_ENST00000400358.4_Silent_p.C891C	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	946	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						TGCAGAGGTGCGACCGCAACT	0.592													C|||	1	0.000199681	0.0008	0.0	5008	,	,		13158	0.0		0.0	False		,,,				2504	0.0																0													45.0	43.0	43.0					22																	25297862		2203	4300	6503	SO:0001819	synonymous_variant	129049			AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.2838C>T	22.37:g.25297862C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	pfam_Run,pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Run,smart_Rab-GTPase-TBC_dom,pfscan_Run,pfscan_Rab-GTPase-TBC_dom	p.C946	ENST00000400359.4	37	c.2838	CCDS46674.1	22																																																																																			SGSM1	-	pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom		0.592	SGSM1-004	KNOWN	basic|CCDS	protein_coding	SGSM1	HGNC	protein_coding	OTTHUMT00000320282.1	C	XM_059318		25297862	+1	no_errors	ENST00000400359	ensembl	human	known	70_37	silent	SNP	0.244	T
SLC44A2	57153	genome.wustl.edu	37	19	10741799	10741799	+	Missense_Mutation	SNP	C	C	G			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr19:10741799C>G	ENST00000335757.5	+	5	688	c.312C>G	c.(310-312)ttC>ttG	p.F104L	SLC44A2_ENST00000586078.1_Missense_Mutation_p.F104L|SLC44A2_ENST00000407327.4_Missense_Mutation_p.F102L			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	104					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	TGCTGGAATTCCAATGTCCCA	0.507																																																	0													100.0	92.0	95.0					19																	10741799		2203	4300	6503	SO:0001583	missense	57153			AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353		"""Solute carriers"""	17292	protein-coding gene	gene with protein product		606106				10677542, 15715662	Standard	NM_001145056		Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000335757.5:c.312C>G	19.37:g.10741799C>G	ENSP00000336888:p.Phe104Leu	Somatic		WXS	Illumina HiSeq	Phase_IV	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Missense_Mutation	SNP	pfam_Choline_transptr-like	p.F104L	ENST00000335757.5	37	c.312	CCDS12245.1	19	.	.	.	.	.	.	.	.	.	.	C	0.026	-1.373425	0.01214	.	.	ENSG00000129353	ENST00000407327;ENST00000335757;ENST00000380614	T;T	0.10192	2.9;2.9	4.69	1.25	0.21368	.	0.051219	0.85682	D	0.000000	T	0.05686	0.0149	L	0.28458	0.855	0.44417	D	0.99733	B;B	0.06786	0.001;0.001	B;B	0.11329	0.006;0.005	T	0.33033	-0.9884	10	0.02654	T	1	.	7.1307	0.25499	0.0:0.6053:0.0:0.3947	.	104;102	Q8IWA5;Q8IWA5-3	CTL2_HUMAN;.	L	102;104;104	ENSP00000385135:F102L;ENSP00000336888:F104L	ENSP00000336888:F104L	F	+	3	2	SLC44A2	10602799	0.973000	0.33851	1.000000	0.80357	0.249000	0.25844	0.152000	0.16302	0.592000	0.29728	0.456000	0.33151	TTC	SLC44A2	-	NULL		0.507	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC44A2	HGNC	protein_coding	OTTHUMT00000452045.1	C			10741799	+1	no_errors	ENST00000335757	ensembl	human	known	70_37	missense	SNP	1.000	G
SRCIN1	80725	genome.wustl.edu	37	17	36719744	36719744	+	Silent	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr17:36719744C>T	ENST00000264659.7	-	5	779	c.555G>A	c.(553-555)ctG>ctA	p.L185L	SRCIN1_ENST00000398579.4_5'UTR|SRCIN1_ENST00000578925.1_Silent_p.L219L	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	57					exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						CCCCGAACTGCAGGAACAGCA	0.672																																																	0													28.0	32.0	30.0					17																	36719744		2107	4133	6240	SO:0001819	synonymous_variant	80725				CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"""p130Cas-associated protein"", ""SNAP-25-interacting protein"""	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.555G>A	17.37:g.36719744C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	Q75T46|Q8N4W8	Silent	SNP	pfam_AIP3_C	p.L185	ENST00000264659.7	37	c.555	CCDS45660.1	17																																																																																			SRCIN1	-	pfam_AIP3_C		0.672	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	SRCIN1	HGNC	protein_coding	OTTHUMT00000441878.4	C	NM_025248		36719744	-1	no_errors	ENST00000264659	ensembl	human	known	70_37	silent	SNP	1.000	T
STAG3L4	64940	genome.wustl.edu	37	7	66785110	66785110	+	RNA	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr7:66785110C>T	ENST00000416602.2	+	0	740					NR_040586.1		Q8TBR4	ST3L4_HUMAN	stromal antigen 3-like 4 (pseudogene)											endometrium(2)|lung(5)	7		Lung NSC(55;0.0839)|all_lung(88;0.181)				ACTACATTGTCAAAGACAAAG	0.373																																																	0													75.0	66.0	69.0					7																	66785110		1838	4083	5921			64940					7q11.21	2013-06-26	2013-06-26		ENSG00000106610	ENSG00000106610			33887	pseudogene	pseudogene			"""stromal antigen 3-like 4"""				Standard	NR_040585		Approved	FLJ13195, STAG3L4P	uc010laj.3	Q8TBR4	OTTHUMG00000156920		7.37:g.66785110C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	Q9H8W0	RNA	SNP	-	NULL	ENST00000416602.2	37	NULL		7																																																																																			STAG3L4	-	-		0.373	STAG3L4-001	KNOWN	basic	processed_transcript	STAG3L4	HGNC	pseudogene	OTTHUMT00000346611.1	C	NM_022906		66785110	+1	no_errors	ENST00000416602	ensembl	human	known	70_37	rna	SNP	0.998	T
TEP1	7011	genome.wustl.edu	37	14	20841447	20841447	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr14:20841447G>A	ENST00000262715.5	-	47	6836	c.6796C>T	c.(6796-6798)Cag>Tag	p.Q2266*	TEP1_ENST00000556935.1_Nonsense_Mutation_p.Q2158*|TEP1_ENST00000545983.1_Nonsense_Mutation_p.Q604*	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2266					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		TTAGGAACCTGCCAGAGCCGT	0.562																																																	0													97.0	102.0	100.0					14																	20841447		2203	4300	6503	SO:0001587	stop_gained	7011				CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.6796C>T	14.37:g.20841447G>A	ENSP00000262715:p.Gln2266*	Somatic		WXS	Illumina HiSeq	Phase_IV	A0AUV9	Nonsense_Mutation	SNP	pfam_TROVE,pfam_TEP1_N,pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_NACHT_NTPase,pfscan_TROVE,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.Q2266*	ENST00000262715.5	37	c.6796	CCDS9548.1	14	.	.	.	.	.	.	.	.	.	.	G	44	10.562190	0.99428	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000545983	.	.	.	5.06	4.1	0.47936	.	0.703990	0.13931	N	0.352913	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-12.6632	10.9571	0.47364	0.0:0.1894:0.8106:0.0	.	.	.	.	X	2266;2266;2158;604	.	ENSP00000262715:Q2266X	Q	-	1	0	TEP1	19911287	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.849000	0.39318	2.508000	0.84585	0.655000	0.94253	CAG	TEP1	-	superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom		0.562	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TEP1	HGNC	protein_coding	OTTHUMT00000073563.2	G	NM_007110		20841447	-1	no_errors	ENST00000262715	ensembl	human	known	70_37	nonsense	SNP	1.000	A
THBS3	7059	genome.wustl.edu	37	1	155166959	155166959	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr1:155166959G>A	ENST00000368378.3	-	21	2565	c.2545C>T	c.(2545-2547)Ctg>Ttg	p.L849L	RP11-263K19.4_ENST00000454348.1_RNA|RP11-263K19.4_ENST00000453136.1_RNA|MIR92B_ENST00000607575.1_RNA|RP11-263K19.4_ENST00000436772.1_RNA|RP11-263K19.4_ENST00000447623.1_RNA|THBS3_ENST00000541576.1_Silent_p.L246L|THBS3_ENST00000541990.1_Silent_p.L378L|THBS3_ENST00000457183.2_Silent_p.L729L	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	849	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GTATGCCACAGGGCATTTCGG	0.577																																																	0													93.0	87.0	89.0					1																	155166959		2203	4300	6503	SO:0001819	synonymous_variant	7059			L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.2545C>T	1.37:g.155166959G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	B1AVR8|B4DQ20|Q8WV34	Silent	SNP	pfam_Thrombospondin_C,pfam_Thbs/COMP_coiled-coil,pfam_Thrombospondin_3-like_rpt,pfam_EGF-like_Ca-bd,superfamily_ConA-like_lec_gl_sf,smart_Laminin_G,smart_EG-like_dom,smart_EGF-like_Ca-bd,pfscan_EG-like_dom	p.L849	ENST00000368378.3	37	c.2545	CCDS1099.1	1																																																																																			THBS3	-	pfam_Thrombospondin_C,superfamily_ConA-like_lec_gl_sf		0.577	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	THBS3	HGNC	protein_coding	OTTHUMT00000086856.1	G	NM_007112		155166959	-1	no_errors	ENST00000368378	ensembl	human	known	70_37	silent	SNP	0.999	A
TMEM178B	100507421	genome.wustl.edu	37	7	141137413	141137413	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr7:141137413C>T	ENST00000565468.1	+	3	581	c.502C>T	c.(502-504)Cgc>Tgc	p.R168C		NM_001195278.1	NP_001182207.1	H3BS89	T178B_HUMAN	transmembrane protein 178B	168						integral component of membrane (GO:0016021)											CACAGACCTGCGCAGAATGAC	0.642																																																	0																																										SO:0001583	missense	100507421				CCDS59086.1	7q34	2012-06-29			ENSG00000261115	ENSG00000261115			44112	protein-coding gene	gene with protein product							Standard	NM_001195278		Approved	DKFZp547G036	uc003vwg.2	H3BS89	OTTHUMG00000172737	ENST00000565468.1:c.502C>T	7.37:g.141137413C>T	ENSP00000456594:p.Arg168Cys	Somatic		WXS	Illumina HiSeq	Phase_IV		Missense_Mutation	SNP	NULL	p.R168C	ENST00000565468.1	37	c.502	CCDS59086.1	7																																																																																			TMEM178B	-	NULL		0.642	TMEM178B-001	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	TMEM178B	HGNC	protein_coding	OTTHUMT00000420337.4	C			141137413	+1	no_errors	ENST00000565468	ensembl	human	putative	70_37	missense	SNP	1.000	T
TRAIP	10293	genome.wustl.edu	37	3	49867119	49867119	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr3:49867119G>A	ENST00000331456.2	-	13	1280	c.1167C>T	c.(1165-1167)gtC>gtT	p.V389V	TRAIP_ENST00000469027.1_Silent_p.V234V	NM_005879.2	NP_005870.2	Q9BWF2	TRAIP_HUMAN	TRAF interacting protein	389	Interaction with CYLD.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|receptor signaling protein activity (GO:0005057)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TGGCATTCCGGACAAAAATAG	0.592																																																	0													63.0	64.0	63.0					3																	49867119		2203	4300	6503	SO:0001819	synonymous_variant	10293			BC019283	CCDS2806.1	3p21.31	2013-01-09			ENSG00000183763	ENSG00000183763		"""RING-type (C3HC4) zinc fingers"""	30764	protein-coding gene	gene with protein product	"""ring finger protein 206"""	605958				9104814	Standard	NM_005879		Approved	TRIP, RNF206	uc003cxs.1	Q9BWF2	OTTHUMG00000158269	ENST00000331456.2:c.1167C>T	3.37:g.49867119G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	B5BU84|B5BUL3|O00467	Silent	SNP	pfam_Znf_C3HC4_RING-type,superfamily_Prefoldin,smart_Znf_RING,pfscan_Znf_RING	p.V389	ENST00000331456.2	37	c.1167	CCDS2806.1	3																																																																																			TRAIP	-	NULL		0.592	TRAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRAIP	HGNC	protein_coding	OTTHUMT00000350518.1	G	NM_005879		49867119	-1	no_errors	ENST00000331456	ensembl	human	known	70_37	silent	SNP	1.000	A
TRIM11	81559	genome.wustl.edu	37	1	228588758	228588758	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr1:228588758G>A	ENST00000284551.6	-	3	920	c.642C>T	c.(640-642)ggC>ggT	p.G214G	TRIM11_ENST00000366699.3_Silent_p.G214G|TRIM11_ENST00000460651.1_5'UTR|TRIM11_ENST00000493030.2_Silent_p.G89G	NM_145214.2	NP_660215.1	Q96F44	TRI11_HUMAN	tripartite motif containing 11	214					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of neurogenesis (GO:0050768)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of viral entry into host cell (GO:0046598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	18		Prostate(94;0.0724)				GGTGGGCTGCGCCCTCCCGCA	0.692																																																	0													17.0	20.0	19.0					1																	228588758		2203	4299	6502	SO:0001819	synonymous_variant	81559			AF220125	CCDS31048.1	1q42.13	2013-01-09	2011-01-25		ENSG00000154370	ENSG00000154370		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16281	protein-coding gene	gene with protein product		607868	"""tripartite motif-containing 11"""			11331580	Standard	NM_145214		Approved	RNF92, BIA1	uc001hss.3	Q96F44	OTTHUMG00000039773	ENST00000284551.6:c.642C>T	1.37:g.228588758G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	A6NKE2|B2RB82|B3KUS3|B4DX88|Q5VSU1|Q8NCA6|Q9C022	Silent	SNP	pfam_SPRY_rcpt,pfam_Znf_C3HC4_RING-type,pfam_Znf_B-box,superfamily_ConA-like_lec_gl_sf,smart_Znf_RING,smart_Znf_B-box,smart_PRY,smart_SPla/RYanodine_receptor_subgr,pfscan_B30.2/SPRY,pfscan_Znf_B-box,pfscan_Znf_RING,prints_Butyrophylin	p.G214	ENST00000284551.6	37	c.642	CCDS31048.1	1																																																																																			TRIM11	-	NULL		0.692	TRIM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRIM11	HGNC	protein_coding	OTTHUMT00000095995.3	G	NM_145214		228588758	-1	no_errors	ENST00000284551	ensembl	human	known	70_37	silent	SNP	0.000	A
TRIM9	114088	genome.wustl.edu	37	14	51467500	51467500	+	Silent	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr14:51467500G>A	ENST00000298355.3	-	6	2486	c.1365C>T	c.(1363-1365)aaC>aaT	p.N455N	TRIM9_ENST00000338969.5_Silent_p.N451N|TRIM9_ENST00000360392.4_Silent_p.N455N	NM_015163.5	NP_055978.4	Q9C026	TRIM9_HUMAN	tripartite motif containing 9	455	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of SNARE complex assembly (GO:0035544)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|synaptic vesicle (GO:0008021)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_epithelial(31;0.00418)|Breast(41;0.148)					TAGCGCTGTTGTTGTGGGTAC	0.527																																																	0													157.0	138.0	145.0					14																	51467500		2203	4300	6503	SO:0001819	synonymous_variant	114088			AF220036	CCDS9703.1, CCDS45105.1	14q21.3	2013-02-11	2011-01-25		ENSG00000100505	ENSG00000100505		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16288	protein-coding gene	gene with protein product		606555	"""tripartite motif-containing 9"""			11331580, 11524423	Standard	NM_015163		Approved	SPRING, RNF91	uc001wyx.4	Q9C026	OTTHUMG00000140291	ENST00000298355.3:c.1365C>T	14.37:g.51467500G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	D3DSB7|D3DSB8|Q92557|Q96D24|Q96NI4|Q9C025|Q9C027	Silent	SNP	pfam_SPRY_rcpt,pfam_Fibronectin_type3,pfam_Znf_B-box,pfam_Znf_C3HC4_RING-type,superfamily_ConA-like_lec_gl_sf,superfamily_Fibronectin_type3,superfamily_Znf_FYVE_PHD,smart_Znf_RING,smart_Znf_B-box,smart_Bbox_C,smart_Fibronectin_type3,smart_SPla/RYanodine_receptor_subgr,pfscan_B30.2/SPRY,pfscan_Fibronectin_type3,pfscan_Znf_B-box,pfscan_Znf_RING	p.N451	ENST00000298355.3	37	c.1353	CCDS9703.1	14																																																																																			TRIM9	-	pfam_Fibronectin_type3,superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_Fibronectin_type3		0.527	TRIM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRIM9	HGNC	protein_coding	OTTHUMT00000276874.1	G	NM_015163		51467500	-1	no_errors	ENST00000338969	ensembl	human	known	70_37	silent	SNP	1.000	A
TRPC3	7222	genome.wustl.edu	37	4	122828660	122828660	+	Missense_Mutation	SNP	C	C	G			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr4:122828660C>G	ENST00000379645.3	-	7	1928	c.1855G>C	c.(1855-1857)Gtt>Ctt	p.V619L	TRPC3_ENST00000513531.1_Missense_Mutation_p.V491L|TRPC3_ENST00000264811.5_Missense_Mutation_p.V546L	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	534					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)			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						CTGAGCACAACAGCTATGGCA	0.438																																																	0													89.0	88.0	89.0					4																	122828660		2203	4299	6502	SO:0001583	missense	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.1855G>C	4.37:g.122828660C>G	ENSP00000368966:p.Val619Leu	Somatic		WXS	Illumina HiSeq	Phase_IV	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	pfam_Ion_trans_dom,pfam_TRP_dom,pfam_PKD1_2_channel,superfamily_Ankyrin_rpt-contain_dom,superfamily_ARM-type_fold,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,prints_TRPC3_channel,prints_TRPC_channel,tigrfam_TRP_channel	p.V619L	ENST00000379645.3	37	c.1855	CCDS47130.1	4	.	.	.	.	.	.	.	.	.	.	C	20.1	3.939809	0.73557	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	D;D;D	0.98437	-4.93;-4.93;-4.93	5.3	5.3	0.74995	Ion transport (1);	0.000000	0.64402	D	0.000004	D	0.98915	0.9632	M	0.84948	2.725	0.51233	D	0.999911	B;P;D	0.56287	0.417;0.786;0.975	B;P;D	0.67382	0.374;0.688;0.951	D	0.99490	1.0950	10	0.30078	T	0.28	-32.4163	18.9622	0.92681	0.0:1.0:0.0:0.0	.	534;491;619	Q13507;E9PCJ9;Q5G1L5	TRPC3_HUMAN;.;.	L	546;619;491	ENSP00000264811:V546L;ENSP00000368966:V619L;ENSP00000426899:V491L	ENSP00000264811:V546L	V	-	1	0	TRPC3	123048110	1.000000	0.71417	0.077000	0.20336	0.990000	0.78478	6.005000	0.70716	2.465000	0.83290	0.655000	0.94253	GTT	TRPC3	-	pfam_Ion_trans_dom,pfam_PKD1_2_channel,tigrfam_TRP_channel		0.438	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TRPC3	HGNC	protein_coding	OTTHUMT00000364252.1	C	NM_003305		122828660	-1	no_errors	ENST00000379645	ensembl	human	known	70_37	missense	SNP	0.993	G
TTN	7273	genome.wustl.edu	37	2	179567367	179567367	+	Missense_Mutation	SNP	G	G	A	rs377714947		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr2:179567367G>A	ENST00000591111.1	-	105	29520	c.29296C>T	c.(29296-29298)Cgc>Tgc	p.R9766C	TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R10083C|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R8839C|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13844	Ig-like 79.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R8839S(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCTGTATGCGCTTTGTAAAC	0.393													G|||	1	0.000199681	0.0	0.0	5008	,	,		19455	0.001		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	lung(1)						G	CYS/ARG,,,	1,3915		0,1,1957	115.0	109.0	111.0		26515,,,	5.8	1.0	2		111	0,8300		0,0,4150	no	missense,intron,intron,intron	TTN	NM_133378.4,NM_003319.4,NM_133432.3,NM_133437.3	180,,,	0,1,6107	AA,AG,GG		0.0,0.0255,0.0082	probably-damaging,,,	8839/33424,,,	179567367	1,12215	1958	4150	6108	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.29296C>T	2.37:g.179567367G>A	ENSP00000465570:p.Arg9766Cys	Somatic		WXS	Illumina HiSeq	Phase_IV	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Fibronectin_type3,pfam_Immunoglobulin,pfam_Ig_V-set,pfam_Titin_Z,pfam_PPAK_motif,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,superfamily_Calpain_domain_III,superfamily_RNaseH-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_Prot_kinase_cat_dom,pfscan_Ig-like	p.R8839C	ENST00000591111.1	37	c.26515		2	.	.	.	.	.	.	.	.	.	.	G	13.90	2.375072	0.42105	2.55E-4	0.0	ENSG00000155657	ENST00000342992	T	0.68025	-0.3	5.84	5.84	0.93424	Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.79370	0.4434	M	0.75264	2.295	0.80722	D	1	D	0.76494	0.999	D	0.63597	0.916	T	0.81182	-0.1049	9	0.87932	D	0	.	13.0931	0.59176	0.0:0.0:0.7352:0.2648	.	9766	Q8WZ42	TITIN_HUMAN	C	8839	ENSP00000343764:R8839C	ENSP00000343764:R8839C	R	-	1	0	TTN	179275612	1.000000	0.71417	0.991000	0.47740	0.931000	0.56810	5.000000	0.63940	2.764000	0.94973	0.655000	0.94253	CGC	TTN	-	pfam_Ig_I-set,superfamily_Calpain_domain_III,superfamily_RNaseH-like_dom,pfscan_Ig-like		0.393	TTN-019	PUTATIVE	basic	protein_coding	TTN	HGNC	protein_coding	OTTHUMT00000460310.1	G	NM_133378		179567367	-1	no_errors	ENST00000342992	ensembl	human	known	70_37	missense	SNP	1.000	A
TUBA4B	80086	genome.wustl.edu	37	2	220136719	220136719	+	RNA	SNP	G	G	A	rs535207947	byFrequency	TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr2:220136719G>A	ENST00000490341.1	+	0	1189					NR_003063.1		Q9H853	TBA4B_HUMAN	tubulin, alpha 4b (pseudogene)						microtubule-based process (GO:0007017)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|structural constituent of cytoskeleton (GO:0005200)										CCAAGAGGGCGTTTGGGCACT	0.557													G|||	3	0.000599042	0.0023	0.0	5008	,	,		20223	0.0		0.0	False		,,,				2504	0.0																0																																												80086			AK024002		2q35	2014-03-20	2007-03-16	2007-02-12	ENSG00000243910	ENSG00000243910		"""Tubulins"""	18637	pseudogene	pseudogene			"""tubulin, alpha 4"", ""tubulin, alpha 4b"""	TUBA4		3785200	Standard	NR_003063		Approved	FLJ13940	uc002vkv.1	Q9H853	OTTHUMG00000154516		2.37:g.220136719G>A		Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	SNP	-	NULL	ENST00000490341.1	37	NULL		2																																																																																			TUBA4B	-	-		0.557	TUBA4B-001	KNOWN	basic	processed_transcript	TUBA4B	HGNC	pseudogene	OTTHUMT00000335637.1	G	NR_003063		220136719	+1	no_errors	ENST00000473885	ensembl	human	known	70_37	rna	SNP	0.899	A
VPS39	23339	genome.wustl.edu	37	15	42454321	42454321	+	Missense_Mutation	SNP	C	C	T	rs149062725		TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr15:42454321C>T	ENST00000348544.4	-	24	2401	c.2402G>A	c.(2401-2403)cGc>cAc	p.R801H	VPS39_ENST00000318006.5_Missense_Mutation_p.R790H			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	801					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		CAGGAAGATGCGTATGTCATT	0.468																																																	0								C	HIS/ARG	0,4406		0,0,2203	161.0	147.0	152.0		2369	5.2	1.0	15	dbSNP_134	152	1,8597	1.2+/-3.3	0,1,4298	no	missense	VPS39	NM_015289.2	29	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	790/876	42454321	1,13003	2203	4299	6502	SO:0001583	missense	23339			AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"""vacuolar protein sorting 39 (yeast)"""			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.2402G>A	15.37:g.42454321C>T	ENSP00000335193:p.Arg801His	Somatic		WXS	Illumina HiSeq	Phase_IV	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Missense_Mutation	SNP	pfam_Citron,pfam_VPS39/TGF_beta_rcpt-assoc_2,pfam_VPS39/TGF_beta_rcpt-assoc_1,pfam_Clathrin_H-chain/VPS_repeat,superfamily_WD40_repeat_dom,smart_Citron	p.R801H	ENST00000348544.4	37	c.2402	CCDS10083.1	15	.	.	.	.	.	.	.	.	.	.	C	15.03	2.711816	0.48517	0.0	1.16E-4	ENSG00000166887	ENST00000318006;ENST00000348544	T;T	0.44482	0.92;0.93	5.21	5.21	0.72293	Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 2 (1);	0.113873	0.64402	D	0.000008	T	0.26231	0.0640	N	0.22421	0.69	0.50632	D	0.99988	B;B	0.29909	0.261;0.065	B;B	0.23419	0.046;0.017	T	0.07616	-1.0763	10	0.15499	T	0.54	-16.0948	12.4737	0.55801	0.0:0.9232:0.0:0.0768	.	801;790	Q96JC1;Q96JC1-2	VPS39_HUMAN;.	H	790;801	ENSP00000326534:R790H;ENSP00000335193:R801H	ENSP00000326534:R790H	R	-	2	0	VPS39	40241613	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.010000	0.49559	2.598000	0.87819	0.561000	0.74099	CGC	VPS39	-	pfam_VPS39/TGF_beta_rcpt-assoc_2		0.468	VPS39-002	KNOWN	basic|CCDS	protein_coding	VPS39	HGNC	protein_coding	OTTHUMT00000420472.1	C	NM_015289		42454321	-1	no_errors	ENST00000348544	ensembl	human	known	70_37	missense	SNP	1.000	T
VPS41	27072	genome.wustl.edu	37	7	38805239	38805239	+	Missense_Mutation	SNP	T	T	C			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr7:38805239T>C	ENST00000310301.4	-	16	1324	c.1270A>G	c.(1270-1272)Aaa>Gaa	p.K424E	VPS41_ENST00000395969.2_Missense_Mutation_p.K399E	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	424					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)			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						GCTGCATTTTTCCCAAGAATT	0.323																																																	0													62.0	65.0	64.0					7																	38805239		2203	4298	6501	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.1270A>G	7.37:g.38805239T>C	ENSP00000309457:p.Lys424Glu	Somatic		WXS	Illumina HiSeq	Phase_IV	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	pfam_Clathrin_H-chain/VPS_repeat,superfamily_WD40_repeat_dom,superfamily_ARM-type_fold,smart_Clathrin_H-chain/VPS_repeat,pirsf_VPS41,pfscan_Znf_RING	p.K424E	ENST00000310301.4	37	c.1270	CCDS5457.1	7	.	.	.	.	.	.	.	.	.	.	T	17.48	3.400122	0.62177	.	.	ENSG00000006715	ENST00000310301;ENST00000395969	T;T	0.17528	2.27;2.27	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.12944	0.0314	L	0.33485	1.01	0.80722	D	1	B;B;B	0.29188	0.236;0.236;0.236	B;B;B	0.24848	0.056;0.056;0.056	T	0.06499	-1.0823	10	0.09084	T	0.74	-28.91	15.5539	0.76177	0.0:0.0:0.0:1.0	.	424;399;424	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	E	424;399	ENSP00000309457:K424E;ENSP00000379297:K399E	ENSP00000309457:K424E	K	-	1	0	VPS41	38771764	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.790000	0.85794	2.089000	0.63090	0.377000	0.23210	AAA	VPS41	-	pirsf_VPS41		0.323	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VPS41	HGNC	protein_coding	OTTHUMT00000226986.3	T			38805239	-1	no_errors	ENST00000310301	ensembl	human	known	70_37	missense	SNP	1.000	C
XPR1	9213	genome.wustl.edu	37	1	180853188	180853188	+	Missense_Mutation	SNP	G	G	A			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr1:180853188G>A	ENST00000367590.4	+	15	2275	c.2077G>A	c.(2077-2079)Gaa>Aaa	p.E693K	XPR1_ENST00000367589.3_Missense_Mutation_p.E628K	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	693					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						CACAGATGATGAAGCTAACAC	0.408																																																	0													217.0	193.0	201.0					1																	180853188		2203	4300	6503	SO:0001583	missense	9213			AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"""xenotropic and polytropic retrovirus receptor"""			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.2077G>A	1.37:g.180853188G>A	ENSP00000356562:p.Glu693Lys	Somatic		WXS	Illumina HiSeq	Phase_IV	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Missense_Mutation	SNP	pfam_EXS_C,pfam_SPX_N	p.E693K	ENST00000367590.4	37	c.2077	CCDS1340.1	1	.	.	.	.	.	.	.	.	.	.	G	19.79	3.892442	0.72524	.	.	ENSG00000143324	ENST00000367590;ENST00000367589	T	0.46451	0.87	5.61	5.61	0.85477	.	0.049230	0.85682	D	0.000000	T	0.38746	0.1052	L	0.44542	1.39	0.43403	D	0.995537	P;P	0.46395	0.481;0.877	B;B	0.37731	0.158;0.257	T	0.39860	-0.9593	10	0.66056	D	0.02	-11.194	19.237	0.93864	0.0:0.0:1.0:0.0	.	628;693	Q9UBH6-2;Q9UBH6	.;XPR1_HUMAN	K	693;628	ENSP00000356562:E693K	ENSP00000356561:E628K	E	+	1	0	XPR1	179119811	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.976000	0.93442	2.640000	0.89533	0.655000	0.94253	GAA	XPR1	-	NULL		0.408	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	XPR1	HGNC	protein_coding	OTTHUMT00000084996.2	G	NM_004736		180853188	+1	no_errors	ENST00000367590	ensembl	human	known	70_37	missense	SNP	1.000	A
ZNF512B	57473	genome.wustl.edu	37	20	62595898	62595898	+	Silent	SNP	C	C	T			TCGA-EK-A3GN-01A-11D-A20U-09	TCGA-EK-A3GN-10A-01D-A20U-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d8016a3d-d2e9-45ba-ac10-9587913f76ef	5e78de9c-5e9e-4a85-9952-cacd7592adad	g.chr20:62595898C>T	ENST00000450537.1	-	6	1266	c.1206G>A	c.(1204-1206)ctG>ctA	p.L402L	ZNF512B_ENST00000369888.1_Silent_p.L402L|ZNF512B_ENST00000217130.3_Silent_p.L402L			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	402					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CTGCAGCCTTCAGTGCCTCCA	0.687																																																	0													36.0	36.0	36.0					20																	62595898		2202	4299	6501	SO:0001819	synonymous_variant	57473			AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.1206G>A	20.37:g.62595898C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	Q08AK9|Q9ULM4	Silent	SNP	smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.L402	ENST00000450537.1	37	c.1206	CCDS13548.1	20																																																																																			ZNF512B	-	NULL		0.687	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF512B	HGNC	protein_coding	OTTHUMT00000080246.1	C	NM_020713		62595898	-1	no_errors	ENST00000217130	ensembl	human	known	70_37	silent	SNP	0.000	T
