#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_ENSG_ID	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_Ens_Gene	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GMAF	i_HGNC	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_Normal_Alt_Count	i_Normal_Ref_Count	i_Normal_VAF	i_ORegAnno_bin	i_PurityEst	i_RNA_Tum_Ref_count	i_RNA_Tum_VAF	i_RNA_Tum_Var_count	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Tier	i_Tumor_Alt_Count	i_Tumor_Ref_Count	i_Tumor_VAF	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_WGS_Norm_Ref_count	i_WGS_Norm_VAF	i_WGS_Norm_Var_count	i_WGS_Tum_Ref_count	i_WGS_Tum_VAF	i_WGS_Tum_Var_count	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_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_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_rs_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
AFF2	2334	genome.wustl.edu	37	X	148038143	148038143	+	Splice_Site	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chrX:148038143G>T	ENST00000370460.2	+	11	3047	c.2568G>T	c.(2566-2568)aaG>aaT	p.K856N	AFF2_ENST00000342251.3_Splice_Site_p.K823N|AFF2_ENST00000286437.5_Splice_Site_p.K497N|AFF2_ENST00000370457.5_Splice_Site_p.K823N	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	856					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GTAAGCACAAGGTAAGCTGTC	0.517																																																	0								ENSG00000155966						59.0	58.0	58.0					X																	148038143		2203	4300	6503	AFF2	SO:0001630	splice_region_variant	0			-	HGNC	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.2568+1G>T	X.37:g.148038143G>T		Somatic	0	35	0.00		0.4003313805339589	2	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	43	8.51	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_TF_AF4/FMR2	p.K856N	ENST00000370460.2	37	c.2568	CCDS14684.1	X	.	.	.	.	.	.	.	.	.	.	G	19.93	3.917745	0.73098	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.72394	-0.65;-0.65;-0.65;-0.65	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.85737	0.5766	M	0.81942	2.565	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999;0.999	D	0.86981	0.2104	10	0.72032	D	0.01	.	19.1236	0.93374	0.0:0.0:1.0:0.0	.	497;821;823;817;846;856	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	N	856;823;823;497	ENSP00000359489:K856N;ENSP00000359486:K823N;ENSP00000345459:K823N;ENSP00000286437:K497N	ENSP00000286437:K497N	K	+	3	2	AFF2	147845843	1.000000	0.71417	1.000000	0.80357	0.573000	0.36030	8.223000	0.89779	2.467000	0.83353	0.600000	0.82982	AAG	-	pfam_TF_AF4/FMR2		0.517	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	AFF2	protein_coding	OTTHUMT00000058673.2	G	NM_002025	-	Missense_Mutation	148038143	+1	no_errors	ENST00000370460	ensembl	human	known	74_37	missense	SNP	1.000	T
SH3GLB1	51100	genome.wustl.edu	37	1	87194113	87194113	+	Intron	SNP	G	G	C			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr1:87194113G>C	ENST00000370558.4	+	5	894				SH3GLB1_ENST00000482504.1_Missense_Mutation_p.D200H|SH3GLB1_ENST00000535010.1_Intron	NM_001206651.1|NM_001206653.1|NM_016009.4	NP_001193580.1|NP_001193582.1|NP_057093.1	Q9Y371	SHLB1_HUMAN	SH3-domain GRB2-like endophilin B1						'de novo' posttranslational protein folding (GO:0051084)|apoptotic process (GO:0006915)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|protein complex (GO:0043234)	fatty acid binding (GO:0005504)|identical protein binding (GO:0042802)|lysophosphatidic acid acyltransferase activity (GO:0042171)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|stomach(1)	11		Lung NSC(277;0.209)		all cancers(265;0.0136)|Epithelial(280;0.0414)		CCTTGAAGGAGATAACATTAT	0.358																																																	0								ENSG00000097033						11.0	11.0	11.0					1																	87194113		872	1980	2852	SH3GLB1	SO:0001627	intron_variant	0			-	HGNC	AF263293	CCDS710.1, CCDS55612.1, CCDS55613.1, CCDS72819.1	1p22.3	2012-04-17	2001-12-04		ENSG00000097033	ENSG00000097033		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	10833	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 70"""	609287	"""SH3-domain, GRB2-like, endophilin B1"""			11161816, 11259440	Standard	NM_016009		Approved	CGI-61, KIAA0491, Bif-1, PPP1R70	uc001dly.3	Q9Y371	OTTHUMG00000010257	ENST00000370558.4:c.570+4025G>C	1.37:g.87194113G>C		Somatic	0	46	0.00		0.4003313805339589	4	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	44	8.33	B4E182|Q5H8U5|Q9H3Z0|Q9NR47|Q9NYA9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_BAR_dom,pfam_BAR_dom-cont,pfam_SH3_domain,pfam_SH3_2,superfamily_SH3_domain,smart_BAR_dom,smart_SH3_domain,pfscan_BAR_dom,pfscan_SH3_domain	p.D200H	ENST00000370558.4	37	c.598	CCDS710.1	1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.687891	0.68271	.	.	ENSG00000097033	ENST00000482504	T	0.32515	1.45	5.51	5.51	0.81932	.	0.000000	0.44902	D	0.000408	T	0.17959	0.0431	.	.	.	0.80722	D	1	P	0.41131	0.739	B	0.41332	0.354	T	0.02411	-1.1163	9	0.48119	T	0.1	0.8498	10.5286	0.44963	0.1186:0.0:0.8814:0.0	.	200	Q9Y371-2	.	H	200	ENSP00000418744:D200H	ENSP00000418744:D200H	D	+	1	0	SH3GLB1	86966701	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.522000	0.67092	2.592000	0.87571	0.591000	0.81541	GAT	-	pfam_BAR_dom,pfam_BAR_dom-cont,smart_BAR_dom,pfscan_BAR_dom		0.358	SH3GLB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SH3GLB1	protein_coding	OTTHUMT00000028287.2	G	NM_016009	-		87194113	+1	no_errors	ENST00000482504	ensembl	human	known	74_37	missense	SNP	1.000	C
MMP3	4314	genome.wustl.edu	37	11	102713509	102713509	+	Missense_Mutation	SNP	C	C	T	rs552104362		TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr11:102713509C>T	ENST00000299855.5	-	2	500	c.244G>A	c.(244-246)Gac>Aac	p.D82N		NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	82					cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	TCCAGAGTGTCGGAGTCCAGC	0.502													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16273	0.0		0.0	False		,,,				2504	0.0																0								ENSG00000149968						71.0	61.0	65.0					11																	102713509		2203	4299	6502	MMP3	SO:0001583	missense	0			-	HGNC	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"""matrix metalloproteinase 3 (stromelysin 1, progelatinase)"""	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.244G>A	11.37:g.102713509C>T	ENSP00000299855:p.Asp82Asn	Somatic	0	44	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	44	8.33	B2R8B8|Q3B7S0|Q6GRF8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pirsf_Pept_M10A_Metazoans,pfam_Pept_M10_metallopeptidase,pfam_Hemopexin-like_repeat,pfam_Peptidoglycan-bd-like,superfamily_Hemopexin-like_dom,superfamily_Peptidoglycan-bd-like,smart_Peptidase_Metallo,smart_Hemopexin-like_repeat,prints_Pept_M10A	p.D82N	ENST00000299855.5	37	c.244	CCDS8323.1	11	.	.	.	.	.	.	.	.	.	.	C	1.162	-0.643424	0.03531	.	.	ENSG00000149968	ENST00000299855	T	0.35421	1.31	6.16	-3.62	0.04543	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.636993	0.12802	N	0.437865	T	0.18383	0.0441	N	0.12920	0.275	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32295	-0.9912	10	0.09338	T	0.73	.	15.343	0.74311	0.0:0.4101:0.0:0.5899	.	82	P08254	MMP3_HUMAN	N	82	ENSP00000299855:D82N	ENSP00000299855:D82N	D	-	1	0	MMP3	102218719	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-1.561000	0.02158	-0.648000	0.05437	-0.781000	0.03364	GAC	-	pirsf_Pept_M10A_Metazoans,pfam_Peptidoglycan-bd-like,superfamily_Peptidoglycan-bd-like		0.502	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MMP3	protein_coding	OTTHUMT00000109758.2	C	NM_002422	-		102713509	-1	no_errors	ENST00000299855	ensembl	human	known	74_37	missense	SNP	0.000	T
JAG1	182	genome.wustl.edu	37	20	10620502	10620502	+	Missense_Mutation	SNP	T	T	C			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr20:10620502T>C	ENST00000254958.5	-	26	3816	c.3301A>G	c.(3301-3303)Agc>Ggc	p.S1101G	JAG1_ENST00000423891.2_Missense_Mutation_p.S942G	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	1101					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						TGTGTGTGGCTGCCCGGCTTC	0.562									Alagille Syndrome																																								0								ENSG00000101384						77.0	72.0	73.0					20																	10620502		2203	4300	6503	JAG1	SO:0001583	missense	0	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	-	HGNC	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.3301A>G	20.37:g.10620502T>C	ENSP00000254958:p.Ser1101Gly	Somatic	0	56	0.00		0.4003313805339589	53	31.17	24	WXS	Illumina HiSeq 2500	Phase_IV	tier1	9	66	12.00	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_EG-like_dom,pfam_Notch_ligand_N,pfam_DSL,pfam_EGF_extracell,pfam_EGF-like_Ca-bd_dom,smart_DSL,smart_EG-like_dom,smart_EGF-like_Ca-bd_dom,smart_VWC_out,smart_VWF_C,pfscan_DSL,pfscan_EG-like_dom	p.S1101G	ENST00000254958.5	37	c.3301	CCDS13112.1	20	.	.	.	.	.	.	.	.	.	.	T	10.80	1.451877	0.26074	.	.	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.86230	-2.07;-2.09	5.65	5.65	0.86999	.	0.077210	0.85682	D	0.000000	T	0.81987	0.4939	L	0.27053	0.805	0.58432	D	0.999997	B	0.28552	0.215	B	0.32465	0.146	T	0.79172	-0.1913	10	0.37606	T	0.19	.	16.17	0.81801	0.0:0.0:0.0:1.0	.	1101	P78504	JAG1_HUMAN	G	1101;942	ENSP00000254958:S1101G;ENSP00000389519:S942G	ENSP00000254958:S1101G	S	-	1	0	JAG1	10568502	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	4.637000	0.61346	2.279000	0.76181	0.533000	0.62120	AGC	-	NULL		0.562	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	JAG1	protein_coding		T	NM_000214	-		10620502	-1	no_errors	ENST00000254958	ensembl	human	known	74_37	missense	SNP	1.000	C
PCLO	27445	genome.wustl.edu	37	7	82784690	82784690	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr7:82784690G>T	ENST00000333891.9	-	2	1604	c.1267C>A	c.(1267-1269)Caa>Aaa	p.Q423K	PCLO_ENST00000423517.2_Missense_Mutation_p.Q423K	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CCAGGTTGTTGAGCTAGGGGT	0.582																																																	0								ENSG00000186472						123.0	125.0	124.0					7																	82784690		2015	4178	6193	PCLO	SO:0001583	missense	0			-	HGNC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.1267C>A	7.37:g.82784690G>T	ENSP00000334319:p.Gln423Lys	Somatic	0	30	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	42	8.70		Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Znf_piccolo,pfam_C2_dom,pfam_PDZ,superfamily_C2_dom,superfamily_PDZ,superfamily_Znf_FYVE_PHD,smart_PDZ,smart_C2_dom,pfscan_C2_dom,pfscan_PDZ	p.Q423K	ENST00000333891.9	37	c.1267	CCDS47630.1	7	.	.	.	.	.	.	.	.	.	.	G	8.742	0.919202	0.17982	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17054	2.34;2.3	5.31	5.31	0.75309	.	.	.	.	.	T	0.19208	0.0461	M	0.62723	1.935	0.80722	D	1	P;P	0.35272	0.493;0.493	B;B	0.30495	0.116;0.116	T	0.01940	-1.1243	9	0.87932	D	0	.	12.6755	0.56891	0.0757:0.0:0.9243:0.0	.	423;423	Q9Y6V0-5;Q9Y6V0-6	.;.	K	423	ENSP00000334319:Q423K;ENSP00000388393:Q423K	ENSP00000334319:Q423K	Q	-	1	0	PCLO	82622626	0.795000	0.28851	0.349000	0.25694	0.099000	0.18886	1.631000	0.37092	2.653000	0.90120	0.655000	0.94253	CAA	-	NULL		0.582	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	PCLO	protein_coding	OTTHUMT00000337368.5	G	NM_014510	-		82784690	-1	no_errors	ENST00000333891	ensembl	human	known	74_37	missense	SNP	0.826	T
FBXO2	26232	genome.wustl.edu	37	1	11710779	11710780	+	In_Frame_Ins	INS	-	-	GCG	rs148874459|rs571719627|rs538764329	byFrequency	TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr1:11710779_11710780insGCG	ENST00000354287.4	-	2	475_476	c.134_135insCGC	c.(133-135)gcg>gcCGCg	p.45_45A>AA	FBXO2_ENST00000475961.1_5'Flank	NM_012168.5	NP_036300.2	Q9UK22	FBX2_HUMAN	F-box protein 2	45	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.			Missing (in Ref. 1; AAF01822). {ECO:0000305}.	cellular protein modification process (GO:0006464)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of protein ubiquitination (GO:0031396)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|SCF ubiquitin ligase complex (GO:0019005)	beta-amyloid binding (GO:0001540)|carbohydrate binding (GO:0030246)|ubiquitin-protein transferase activity (GO:0004842)			kidney(1)|large_intestine(1)|lung(4)	6	Ovarian(185;0.249)	Lung NSC(185;9.37e-06)|all_lung(284;1.39e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|BRCA - Breast invasive adenocarcinoma(304;1.88e-06)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|Lung(427;0.0146)|LUSC - Lung squamous cell carcinoma(448;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)		CGTCCAGGTACGCGGCGGCGGc	0.757																																																	0								ENSG00000116661																																			FBXO2	SO:0001652	inframe_insertion	0				HGNC	AF174594	CCDS130.1	1p36.21	2010-04-21	2004-06-15		ENSG00000116661	ENSG00000116661		"""F-boxes /  ""other"""""	13581	protein-coding gene	gene with protein product		607112	"""F-box only protein 2"", ""organ of Corti protein 1"""	OCP1		10531035, 10531037	Standard	NM_012168		Approved	FBX2, Nfb42, Fbs1, Fbg1	uc001asj.3	Q9UK22	OTTHUMG00000002072	ENST00000354287.4:c.132_134dupCGC	1.37:g.11710786_11710788dupGCG	ENSP00000346240:p.Ala45dup	Somatic	0	13	0.00		0.4003313805339589	5	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	19	17.39	B2R7K7|Q5TGY0|Q6FGJ7|Q8TB29|Q9UKC6	In_Frame_Ins	INS	NA	NA	NA	NA	NA	NA	pfam_F-box-assoc_dom,pfam_F-box_dom,superfamily_Galactose-bd-like,superfamily_F-box_dom,pfscan_F-box_dom,pfscan_F-box-assoc_dom	p.46in_frame_insA	ENST00000354287.4	37	c.135_134	CCDS130.1	1																																																																																			-	superfamily_F-box_dom,pfscan_F-box_dom		0.757	FBXO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FBXO2	protein_coding	OTTHUMT00000005764.1	-	NM_012168			11710780	-1	no_errors	ENST00000354287	ensembl	human	known	74_37	in_frame_ins	INS	0.915:0.821	GCG
NEB	4703	genome.wustl.edu	37	2	152512817	152512817	+	Silent	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr2:152512817G>T	ENST00000172853.10	-	49	6492	c.6345C>A	c.(6343-6345)acC>acA	p.T2115T	NEB_ENST00000397345.3_Silent_p.T2115T|NEB_ENST00000604864.1_Silent_p.T2115T|NEB_ENST00000427231.2_Silent_p.T2115T|NEB_ENST00000603639.1_Silent_p.T2115T|NEB_ENST00000409198.1_Silent_p.T2115T			P20929	NEBU_HUMAN	nebulin	2115					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGTCGGCAGGGGTGTGGTAGC	0.478																																																	0								ENSG00000183091						261.0	262.0	262.0					2																	152512817		2103	4230	6333	NEB	SO:0001819	synonymous_variant	0			-	HGNC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.6345C>A	2.37:g.152512817G>T		Somatic	0	30	0.00		0.4003313805339589	492	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	31	11.11	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Nebulin_35r-motif,pfam_SH3_domain,pfam_SH3_2,superfamily_SH3_domain,superfamily_Adhesion_dom,superfamily_6-PGluconate_DH_C-like,smart_Nebulin_35r-motif,smart_SH3_domain,pfscan_Nebulin_35r-motif,pfscan_SH3_domain,prints_Nebulin	p.T2115	ENST00000172853.10	37	c.6345		2																																																																																			-	smart_Nebulin_35r-motif		0.478	NEB-201	KNOWN	basic	protein_coding	NEB	protein_coding		G	NM_004543	-		152512817	-1	no_errors	ENST00000397345	ensembl	human	known	74_37	silent	SNP	0.951	T
MBOAT4	619373	genome.wustl.edu	37	8	29989494	29989494	+	Silent	SNP	A	A	G			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr8:29989494A>G	ENST00000320542.3	-	3	1357	c.1273T>C	c.(1273-1275)Ttg>Ctg	p.L425L	LEPROTL1_ENST00000523116.1_Intron|LEPROTL1_ENST00000442880.2_Intron	NM_001100916.1	NP_001094386.1	Q96T53	MBOA4_HUMAN	membrane bound O-acyltransferase domain containing 4	425					cellular protein metabolic process (GO:0044267)|peptidyl-serine octanoylation (GO:0018191)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	serine O-acyltransferase activity (GO:0016412)			endometrium(1)	1						GCCAATAGCAAAAGCAGAATA	0.453																																																	0								ENSG00000177669						110.0	89.0	96.0					8																	29989494		692	1591	2283	MBOAT4	SO:0001819	synonymous_variant	0			-	HGNC	AF359269	CCDS47835.1	8p12	2008-08-04	2006-06-29	2006-06-29	ENSG00000177669	ENSG00000177669			32311	protein-coding gene	gene with protein product	"""ghrelin O-acyltransferase"""	611940	"""O-acyltransferase (membrane bound) domain containing 4"""	OACT4		18443287	Standard	NM_001100916		Approved	FKSG89, GOAT	uc010lvg.3	Q96T53	OTTHUMG00000163824	ENST00000320542.3:c.1273T>C	8.37:g.29989494A>G		Somatic	0	41	0.00		0.4003313805339589	1	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	39	11.36	B1Q003	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_MBOAT_fam	p.L425	ENST00000320542.3	37	c.1273	CCDS47835.1	8																																																																																			-	NULL		0.453	MBOAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MBOAT4	protein_coding	OTTHUMT00000375795.1	A		-		29989494	-1	no_errors	ENST00000320542	ensembl	human	known	74_37	silent	SNP	0.060	G
TP53	7157	genome.wustl.edu	37	17	7577142	7577142	+	Missense_Mutation	SNP	C	C	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr17:7577142C>T	ENST00000269305.4	-	8	985	c.796G>A	c.(796-798)Gga>Aga	p.G266R	TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.G266R|TP53_ENST00000420246.2_Missense_Mutation_p.G266R|TP53_ENST00000445888.2_Missense_Mutation_p.G266R|TP53_ENST00000455263.2_Missense_Mutation_p.G266R	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	266	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		G -> A (in sporadic cancers; somatic mutation).|G -> E (in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G266R(46)|p.G266*(14)|p.0?(8)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.G262_S269delGNLLGRNS(2)|p.G266fs*79(2)|p.N263fs*5(1)|p.G266T(1)|p.L265_K305del41(1)|p.G266_E271delGRNSFE(1)|p.E258fs*71(1)|p.G266fs*9(1)|p.L265_R267delLGR(1)|p.G266_N268delGRN(1)|p.G262fs*2(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTGTTCCGTCCCAGTAGATTA	0.517		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	86	Substitution - Missense(47)|Substitution - Nonsense(14)|Deletion - In frame(8)|Whole gene deletion(8)|Deletion - Frameshift(5)|Unknown(3)|Insertion - Frameshift(1)	lung(16)|large_intestine(11)|ovary(8)|central_nervous_system(6)|urinary_tract(6)|oesophagus(6)|upper_aerodigestive_tract(5)|breast(5)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|stomach(3)|liver(2)|skin(2)|pancreas(2)|biliary_tract(1)|peritoneum(1)|salivary_gland(1)|endometrium(1)|eye(1)|pleura(1)						ENSG00000141510						49.0	44.0	46.0					17																	7577142		2203	4300	6503	TP53	SO:0001583	missense	0	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	-	HGNC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.796G>A	17.37:g.7577142C>T	ENSP00000269305:p.Gly266Arg	Somatic	0	23	0.00		0.4003313805339589	77	22.22	22	WXS	Illumina HiSeq 2500	Phase_IV	tier1	9	46	16.36	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_p53_DNA-bd,pfam_p53_tetrameristn,pfam_p53_transactivation_domain,superfamily_p53-like_TF_DNA-bd,superfamily_p53_tetrameristn,prints_p53_tumour_suppressor	p.G266R	ENST00000269305.4	37	c.796	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	C	24.5	4.539769	0.85917	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99900	-7.63;-7.63;-7.63;-7.63;-7.63;-7.63	5.13	5.13	0.70059	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99906	0.9955	M	0.92367	3.3	0.80722	D	1	D;D;D;D	0.89917	0.996;1.0;0.986;0.997	D;D;D;D	0.97110	0.978;1.0;0.962;0.958	D	0.96190	0.9137	10	0.87932	D	0	-13.0798	16.1198	0.81342	0.0:1.0:0.0:0.0	.	266;266;266;266	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	R	266;266;266;266;266;255;134	ENSP00000352610:G266R;ENSP00000269305:G266R;ENSP00000398846:G266R;ENSP00000391127:G266R;ENSP00000391478:G266R;ENSP00000425104:G134R	ENSP00000269305:G266R	G	-	1	0	TP53	7517867	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	7.587000	0.82613	2.667000	0.90743	0.462000	0.41574	GGA	-	pfam_p53_DNA-bd,superfamily_p53-like_TF_DNA-bd,prints_p53_tumour_suppressor		0.517	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	protein_coding	OTTHUMT00000367397.1	C	NM_000546	-		7577142	-1	no_errors	ENST00000269305	ensembl	human	known	74_37	missense	SNP	1.000	T
STK3	6788	genome.wustl.edu	37	8	99539036	99539036	+	Silent	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr8:99539036G>T	ENST00000419617.2	-	10	1391	c.1251C>A	c.(1249-1251)ccC>ccA	p.P417P	STK3_ENST00000523601.1_Silent_p.P445P	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	417					apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		ACATAGGGAAGGGTTCATGCA	0.358																																																	0								ENSG00000104375						144.0	136.0	139.0					8																	99539036		1866	4106	5972	STK3	SO:0001819	synonymous_variant	0			-	HGNC	BC010640	CCDS47900.1, CCDS59108.1, CCDS75774.1	8q22.2	2011-05-24	2010-06-25		ENSG00000104375	ENSG00000104375			11406	protein-coding gene	gene with protein product		605030	"""serine/threonine kinase 3 (Ste20, yeast homolog)"""			8816758	Standard	NM_006281		Approved	MST2, KRS1	uc003yip.4	Q13188	OTTHUMG00000164651	ENST00000419617.2:c.1251C>A	8.37:g.99539036G>T		Somatic	0	44	0.00		0.4003313805339589	45	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	25	10.34	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Mst1_SARAH_domain,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_SARAH_dom,pfscan_Prot_kinase_dom	p.P417	ENST00000419617.2	37	c.1251	CCDS47900.1	8																																																																																			-	NULL		0.358	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STK3	protein_coding	OTTHUMT00000379635.1	G	NM_006281	-		99539036	-1	no_errors	ENST00000419617	ensembl	human	known	74_37	silent	SNP	0.996	T
TM9SF2	9375	genome.wustl.edu	37	13	100192902	100192902	+	Intron	DEL	T	T	-			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr13:100192902delT	ENST00000376387.4	+	8	1018					NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2						transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					TTGAATGGGATTTTTTTTTGT	0.348																																																	0								ENSG00000125304																																			TM9SF2	SO:0001627	intron_variant	0				HGNC	U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.829-66T>-	13.37:g.100192902delT		Somatic	0	24	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	20	16.67	A8K399|Q2TAY5	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000376387.4	37	NULL	CCDS9493.1	13																																																																																			-	-		0.348	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TM9SF2	protein_coding	OTTHUMT00000045602.3	T				100192902	+1	no_errors	ENST00000466555	ensembl	human	known	74_37	rna	DEL	0.045	-
SCAP	22937	genome.wustl.edu	37	3	47470002	47470002	+	Splice_Site	SNP	C	C	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr3:47470002C>T	ENST00000265565.5	-	4	823		c.e4+1		SCAP_ENST00000545718.1_Intron|SCAP_ENST00000441517.2_Intron	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone						aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		GAGAGGGGTACCTGTCTCTCA	0.552																																					Pancreas(149;978 1908 29304 37806 46700)												0								ENSG00000114650						156.0	147.0	150.0					3																	47470002		2203	4300	6503	SCAP	SO:0001630	splice_region_variant	0			-	HGNC	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"""WD repeat domain containing"""	30634	protein-coding gene	gene with protein product	"""SREBP cleavage activating protein"""	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.410+1G>A	3.37:g.47470002C>T		Somatic	0	75	0.00		0.4003313805339589	0	33.33	1	WXS	Illumina HiSeq 2500	Phase_IV	tier1	10	106	8.55	Q8N2E0|Q8WUA1	Splice_Site	SNP	NA	NA	NA	NA	NA	NA	-	e3+1	ENST00000265565.5	37	c.410+1	CCDS2755.2	3	.	.	.	.	.	.	.	.	.	.	C	21.8	4.199973	0.79015	.	.	ENSG00000114650	ENST00000339815;ENST00000265565	.	.	.	5.68	4.81	0.61882	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2583	0.66067	0.0:0.9277:0.0:0.0723	.	.	.	.	.	-1	.	.	.	-	.	.	SCAP	47445006	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.608000	0.82898	1.401000	0.46761	0.563000	0.77884	.	-	-		0.552	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SCAP	protein_coding	OTTHUMT00000246872.2	C	NM_012235	-	Intron	47470002	-1	no_errors	ENST00000265565	ensembl	human	known	74_37	splice_site	SNP	1.000	T
VANGL2	57216	genome.wustl.edu	37	1	160394931	160394931	+	Silent	SNP	G	G	A	rs146767141		TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr1:160394931G>A	ENST00000368061.2	+	8	1803	c.1329G>A	c.(1327-1329)gcG>gcA	p.A443A		NM_020335.2	NP_065068.1	Q9ULK5	VANG2_HUMAN	VANGL planar cell polarity protein 2	443					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|cell migration involved in kidney development (GO:0035787)|cochlea morphogenesis (GO:0090103)|convergent extension involved in axis elongation (GO:0060028)|convergent extension involved in neural plate elongation (GO:0022007)|digestive tract morphogenesis (GO:0048546)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity involved in neural tube closure (GO:0090177)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|glomerulus development (GO:0032835)|hair follicle development (GO:0001942)|heart looping (GO:0001947)|inner ear receptor stereocilium organization (GO:0060122)|kidney morphogenesis (GO:0060993)|lateral sprouting involved in lung morphogenesis (GO:0060490)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in axis elongation (GO:0003402)|planar cell polarity pathway involved in heart morphogenesis (GO:0061346)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|positive regulation of JUN kinase activity (GO:0043507)|post-anal tail morphogenesis (GO:0036342)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Wnt signaling pathway (GO:0030111)|Rho protein signal transduction (GO:0007266)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell pole (GO:0060187)|cell-cell junction (GO:0005911)|ER to Golgi transport vesicle (GO:0030134)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)		p.A443A(1)		biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	37	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GATACTTGGCGGCTGGACCTA	0.557													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15617	0.0		0.0	False		,,,				2504	0.0																1	Substitution - coding silent(1)	endometrium(1)						ENSG00000162738	G		2,4404	4.2+/-10.8	0,2,2201	81.0	80.0	81.0		1329	-10.1	0.2	1	dbSNP_134	81	0,8600		0,0,4300	no	coding-synonymous	VANGL2	NM_020335.2		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		443/522	160394931	2,13004	2203	4300	6503	VANGL2	SO:0001819	synonymous_variant	0			GMAF=0.0005	HGNC	AB033041	CCDS30915.1	1q22-q23	2013-03-05	2013-03-05		ENSG00000162738	ENSG00000162738			15511	protein-coding gene	gene with protein product	"""vang, van gogh-like 2"", ""loop-tail-associated protein"", ""strabismus"""	600533	"""vang (van gogh, Drosophila)-like 2, vang, van gogh-like 2 (Drosophila)"", ""vang-like 2 (van gogh, Drosophila)"""			11431695	Standard	NM_020335		Approved	KIAA1215, LTAP, LPP1, STBM, STB1, STBM1, MGC119403, MGC119404	uc001fwc.2	Q9ULK5	OTTHUMG00000033122	ENST00000368061.2:c.1329G>A	1.37:g.160394931G>A		Somatic	0	56	0.00		0.4003313805339589	3	40.00	2	WXS	Illumina HiSeq 2500	Phase_IV	tier1	10	58	14.71	D3DVE9|Q5T212	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Strabismus,pirsf_Strabismus	p.A443	ENST00000368061.2	37	c.1329	CCDS30915.1	1																																																																																			-	pfam_Strabismus,pirsf_Strabismus		0.557	VANGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VANGL2	protein_coding	OTTHUMT00000080677.1	G	NM_020335	rs146767141		160394931	+1	no_errors	ENST00000368061	ensembl	human	known	74_37	silent	SNP	0.077	A
C11orf80	79703	genome.wustl.edu	37	11	66512290	66512291	+	In_Frame_Ins	INS	-	-	GGC	rs567536854|rs71045961|rs377555566		TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr11:66512290_66512291insGGC	ENST00000360962.4	+	1	84_85	c.77_78insGGC	c.(76-81)ggggcg>ggGGCggcg	p.34_35insA	C11orf80_ENST00000346672.4_5'UTR|C11orf80_ENST00000532565.2_5'Flank|C11orf80_ENST00000527368.1_3'UTR|C11orf80_ENST00000540737.1_5'UTR|C11orf80_ENST00000527634.1_5'UTR	NM_024650.3	NP_078926.3	Q8N6T0	CK080_HUMAN	chromosome 11 open reading frame 80	34										autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14						GCTGAGGAGGGggcggcggcgg	0.787																																																	0								ENSG00000173715			20,74		9,2,36						-5.0	0.0		dbSNP_130	1	203,337		98,7,165	no	coding	C11orf80	NM_024650.3		107,9,201	A1A1,A1R,RR		37.5926,21.2766,35.1735				223,411				C11orf80	SO:0001652	inframe_insertion	0				HGNC			11q13.2	2012-05-30			ENSG00000173715	ENSG00000173715			26197	protein-coding gene	gene with protein product						18160775	Standard	NM_024650		Approved	FLJ22531	uc021qmd.1	Q8N6T0	OTTHUMG00000167164	ENST00000360962.4:c.99_101dupGGC	11.37:g.66512297_66512299dupGGC	ENSP00000354227:p.Ala34_Ala34dup	Somatic	0	8	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	27	20.59	Q9H677	In_Frame_Ins	INS	NA	NA	NA	NA	NA	NA	NULL	p.30in_frame_insA	ENST00000360962.4	37	c.77_78	CCDS53664.1	11																																																																																			-	NULL		0.787	C11orf80-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	C11orf80	protein_coding		-	NM_024650			66512291	+1	no_errors	ENST00000360962	ensembl	human	known	74_37	in_frame_ins	INS	0.001:0.003	GGC
FSIP2	401024	genome.wustl.edu	37	2	186657269	186657269	+	Silent	SNP	C	C	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr2:186657269C>A	ENST00000424728.1	+	16	5406	c.5406C>A	c.(5404-5406)ctC>ctA	p.L1802L	FSIP2_ENST00000343098.5_Silent_p.L1891L|AC008174.3_ENST00000436557.1_RNA|AC008174.3_ENST00000429929.1_RNA			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	1802										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TCCTTTCTCTCTCCCACTCTA	0.328																																																	0								ENSG00000188738																																			FSIP2	SO:0001819	synonymous_variant	0			-	HGNC	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.5406C>A	2.37:g.186657269C>A		Somatic	0	60	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	29	9.38	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Silent	SNP	NA	NA	NA	NA	NA	NA	NULL	p.L1891	ENST00000424728.1	37	c.5673		2																																																																																			-	NULL		0.328	FSIP2-001	KNOWN	basic	protein_coding	FSIP2	protein_coding	OTTHUMT00000332778.3	C	NM_173651	-		186657269	+1	no_errors	ENST00000343098	ensembl	human	known	74_37	silent	SNP	0.013	A
CX3CL1	6376	genome.wustl.edu	37	16	57416150	57416150	+	Missense_Mutation	SNP	G	G	A	rs558560542		TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr16:57416150G>A	ENST00000006053.6	+	3	511	c.400G>A	c.(400-402)Gaa>Aaa	p.E134K	CX3CL1_ENST00000564948.1_3'UTR|CX3CL1_ENST00000563383.1_Missense_Mutation_p.E140K|CX3CL1_ENST00000565912.1_Missense_Mutation_p.E96K	NM_002996.3	NP_002987.1	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1	134	Mucin-like stalk.				angiogenesis involved in wound healing (GO:0060055)|cell adhesion (GO:0007155)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|immune response (GO:0006955)|leukocyte adhesive activation (GO:0050902)|leukocyte chemotaxis (GO:0030595)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neutrophil chemotaxis (GO:0030593)|positive regulation of angiogenesis (GO:0045766)|positive regulation of calcium-independent cell-cell adhesion (GO:0051041)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transforming growth factor beta1 production (GO:0032914)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chemokine activity (GO:0008009)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)	5						AGCCACAGGCGAAAGCAGTAG	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		16015	0.001		0.0	False		,,,				2504	0.0																0								ENSG00000006210						28.0	31.0	30.0					16																	57416150		2176	4273	6449	CX3CL1	SO:0001583	missense	0			-	HGNC	U84487	CCDS10779.1	16q13	2013-02-25	2002-08-22	2002-08-23	ENSG00000006210	ENSG00000006210		"""Endogenous ligands"""	10647	protein-coding gene	gene with protein product		601880	"""small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin)"""	SCYD1		9177350, 9024663	Standard	NM_002996		Approved	NTN, C3Xkine, ABCD-3, CXC3C, CXC3, fractalkine, neurotactin	uc002eli.3	P78423	OTTHUMG00000133469	ENST00000006053.6:c.400G>A	16.37:g.57416150G>A	ENSP00000006053:p.Glu134Lys	Somatic	0	109	0.00		0.4003313805339589	68	1.45	1	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	118	10.53	O00672	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Chemokine_IL8-like_dom,superfamily_Chemokine_IL8-like_dom,smart_Chemokine_IL8-like_dom,prints_Chemokine_CX3CL1	p.E134K	ENST00000006053.6	37	c.400	CCDS10779.1	16	.	.	.	.	.	.	.	.	.	.	G	13.91	2.377866	0.42105	.	.	ENSG00000006210	ENST00000006053	T	0.04917	3.53	5.52	0.842	0.18927	.	4.963130	0.00357	N	0.000026	T	0.06188	0.0160	L	0.32530	0.975	0.09310	N	1	P	0.39404	0.672	B	0.28553	0.091	T	0.44236	-0.9341	10	0.87932	D	0	-18.0981	9.5259	0.39165	0.0:0.4781:0.3725:0.1494	.	134	P78423	X3CL1_HUMAN	K	134	ENSP00000006053:E134K	ENSP00000006053:E134K	E	+	1	0	CX3CL1	55973651	0.003000	0.15002	0.002000	0.10522	0.027000	0.11550	0.493000	0.22451	0.233000	0.21120	0.650000	0.86243	GAA	-	NULL		0.667	CX3CL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CX3CL1	protein_coding	OTTHUMT00000257345.3	G	NM_002996	-		57416150	+1	no_errors	ENST00000006053	ensembl	human	known	74_37	missense	SNP	0.000	A
FMO5	2330	genome.wustl.edu	37	1	146658796	146658796	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr1:146658796G>T	ENST00000254090.4	-	9	1673	c.1285C>A	c.(1285-1287)Cag>Aag	p.Q429K	RP11-337C18.8_ENST00000607149.1_RNA|FMO5_ENST00000441068.2_Intron|RP11-337C18.8_ENST00000606757.1_RNA|RP11-337C18.10_ENST00000606856.1_RNA|FMO5_ENST00000369272.3_3'UTR	NM_001461.2	NP_001452.2	P49326	FMO5_HUMAN	flavin containing monooxygenase 5	429						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	25	all_hematologic(923;0.0487)					TAGTCTCCCTGAATGGTATGG	0.473																																																	0								ENSG00000131781						62.0	61.0	61.0					1																	146658796		2203	4300	6503	FMO5	SO:0001583	missense	0			-	HGNC	Z47553	CCDS926.1, CCDS44209.1, CCDS44210.1	1q21.1	2011-08-04			ENSG00000131781	ENSG00000131781			3773	protein-coding gene	gene with protein product		603957				8786146, 9119381	Standard	NM_001461		Approved		uc001epi.2	P49326	OTTHUMG00000014607	ENST00000254090.4:c.1285C>A	1.37:g.146658796G>T	ENSP00000254090:p.Gln429Lys	Somatic	0	28	0.00		0.4003313805339589	5	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	21	12.50	B2RBG1|C9JJD1|Q8IV22	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Flavin_mOase-like,pfam_Pyr_nucl-diS_OxRdtase_FAD/NAD,pirsf_DiMe-aniline_mOase,prints_Flavin_mOase,prints_Flavin_mOase_5,prints_Flavin_mOase_2,prints_Flavin_mOase_1	p.Q429K	ENST00000254090.4	37	c.1285	CCDS926.1	1	.	.	.	.	.	.	.	.	.	.	.	27.3	4.819483	0.90873	.	.	ENSG00000131781	ENST00000254090	T	0.53640	0.61	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.48150	0.1484	L	0.59912	1.85	0.80722	D	1	P	0.34815	0.47	P	0.46172	0.506	T	0.45338	-0.9268	10	0.46703	T	0.11	-16.9845	17.5569	0.87894	0.0:0.0:1.0:0.0	.	429	P49326	FMO5_HUMAN	K	429	ENSP00000254090:Q429K	ENSP00000254090:Q429K	Q	-	1	0	FMO5	145125420	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.487000	0.97945	2.735000	0.93741	0.655000	0.94253	CAG	-	pfam_Flavin_mOase-like,pirsf_DiMe-aniline_mOase,prints_Flavin_mOase_5,prints_Flavin_mOase_2		0.473	FMO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FMO5	protein_coding	OTTHUMT00000040373.2	G	NM_001461	-		146658796	-1	no_errors	ENST00000254090	ensembl	human	known	74_37	missense	SNP	1.000	T
APPL2	55198	genome.wustl.edu	37	12	105597501	105597501	+	Silent	SNP	G	G	A	rs577280673		TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr12:105597501G>A	ENST00000258530.3	-	9	909	c.684C>T	c.(682-684)tcC>tcT	p.S228S	APPL2_ENST00000539978.2_Silent_p.S185S|APPL2_ENST00000551662.1_Silent_p.S234S|APPL2_ENST00000549573.1_5'UTR	NM_001251904.1|NM_018171.3	NP_001238833.1|NP_060641.2	Q06481	APLP2_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	0	Asp/Glu-rich (highly acidic).|Poly-Glu.				cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						TGTCTGCAACGGAGGATAAAA	0.443																																																	0								ENSG00000136044						178.0	177.0	177.0					12																	105597501		2203	4300	6503	APPL2	SO:0001819	synonymous_variant	0			-	HGNC	AY113704	CCDS9101.1, CCDS58275.1, CCDS58276.1	12q23.3	2014-08-12			ENSG00000136044	ENSG00000136044		"""Pleckstrin homology (PH) domain containing"""	18242	protein-coding gene	gene with protein product		606231				11431708, 17030088	Standard	NM_001251904		Approved	FLJ10659, DIP13B	uc010swu.1	Q8NEU8	OTTHUMG00000169853	ENST00000258530.3:c.684C>T	12.37:g.105597501G>A		Somatic	0	151	0.00		0.4003313805339589	44	15.38	8	WXS	Illumina HiSeq 2500	Phase_IV	tier1	18	198	8.33	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_PTB/PI_dom,pfam_Pleckstrin_homology,pfam_PTB,smart_Pleckstrin_homology,smart_PTB/PI_dom,pfscan_Pleckstrin_homology,pfscan_PTB/PI_dom	p.S234	ENST00000258530.3	37	c.702	CCDS9101.1	12																																																																																			-	NULL		0.443	APPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	APPL2	protein_coding	OTTHUMT00000406238.3	G	NM_018171	-		105597501	-1	no_errors	ENST00000551662	ensembl	human	known	74_37	silent	SNP	0.806	A
ATAD2B	54454	genome.wustl.edu	37	2	24149446	24149446	+	Silent	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr2:24149446G>T	ENST00000238789.5	-	1	538	c.195C>A	c.(193-195)ggC>ggA	p.G65G	UBXN2A_ENST00000404924.1_5'Flank	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	65						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCAGAGTGACGCCGGCGCCAC	0.726																																																	0								ENSG00000119778						2.0	3.0	3.0					2																	24149446		1512	3525	5037	ATAD2B	SO:0001819	synonymous_variant	0			-	HGNC	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"""ATPases / AAA-type"""	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.195C>A	2.37:g.24149446G>T		Somatic	0	10	0.00		0.4003313805339589	9	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	6	36.36	B9ZVQ5|Q6ZNA6|Q8N9E7	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_ATPase_AAA_core,pfam_Bromodomain,pfam_IstB_ATP-bd,superfamily_P-loop_NTPase,superfamily_Bromodomain,smart_AAA+_ATPase,smart_Bromodomain,pfscan_Bromodomain,prints_Bromodomain	p.G65	ENST00000238789.5	37	c.195	CCDS46227.1	2																																																																																			-	NULL		0.726	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	ATAD2B	protein_coding	OTTHUMT00000324333.1	G	NM_017552	-		24149446	-1	no_errors	ENST00000238789	ensembl	human	known	74_37	silent	SNP	0.895	T
XYLB	9942	genome.wustl.edu	37	3	38411731	38411732	+	Intron	INS	-	-	CACA	rs196387|rs71085317|rs150130857	byFrequency	TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr3:38411731_38411732insCACA	ENST00000207870.3	+	9	855				XYLB_ENST00000542835.1_Intron	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)						carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		GCACTGTAGCGcacacacacac	0.5																																																	0								ENSG00000093217																																			XYLB	SO:0001627	intron_variant	0				HGNC	AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"""xylulokinase (H. influenzae) homolog"""			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.765+66->CACA	3.37:g.38411736_38411739dupCACA		Somatic	0	10	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	18	18.18	B2RAW4|B4DDT2|B9EH64	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000207870.3	37	NULL	CCDS2678.1	3																																																																																			-	-		0.500	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	XYLB	protein_coding	OTTHUMT00000254062.2	-	NM_005108			38411732	+1	no_errors	ENST00000487569	ensembl	human	putative	74_37	rna	INS	0.000:0.000	CACA
UCHL3	7347	genome.wustl.edu	37	13	76179970	76179970	+	3'UTR	DEL	A	A	-			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr13:76179970delA	ENST00000377595.3	+	0	745				RP11-29G8.3_ENST00000563635.1_RNA|RP11-173B14.5_ENST00000568302.1_RNA|RP11-173B14.5_ENST00000568735.1_RNA|UCHL3_ENST00000606347.1_3'UTR	NM_001270952.1|NM_006002.4	NP_001257881.1|NP_005993.1	P15374	UCHL3_HUMAN	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)						protein catabolic process (GO:0030163)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(2)|lung(3)|skin(1)	7				GBM - Glioblastoma multiforme(99;0.0125)		TGGAAACACCAAAAACTGTAT	0.323																																																	0								ENSG00000118939						109.0	105.0	106.0					13																	76179970		2203	4300	6503	UCHL3	SO:0001624	3_prime_UTR_variant	0				HGNC	M30496	CCDS9453.1, CCDS73586.1	13q21.33	2008-02-05			ENSG00000118939	ENSG00000118939	3.2.1.15		12515	protein-coding gene	gene with protein product		603090				2530630	Standard	NM_001270952		Approved		uc001vjq.4	P15374	OTTHUMG00000017090	ENST00000377595.3:c.*22A>-	13.37:g.76179970delA		Somatic	0	24	0.00		0.4003313805339589	147	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	21	8.70	B2R970|Q5TBK8|Q6IBE9	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000377595.3	37	NULL	CCDS9453.1	13																																																																																			-	-		0.323	UCHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UCHL3	protein_coding	OTTHUMT00000045292.2	A	NM_006002			76179970	+1	no_errors	ENST00000606347	ensembl	human	known	74_37	rna	DEL	1.000	-
DEAF1	10522	genome.wustl.edu	37	11	680002	680003	+	Intron	INS	-	-	ACCAGGATG	rs71278583|rs398038332|rs67467914	byFrequency	TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr11:680002_680003insACCAGGATG	ENST00000382409.3	-	8	1482				DEAF1_ENST00000525904.1_5'UTR|DEAF1_ENST00000338675.6_Intron|RP11-754B17.1_ENST00000527799.1_RNA	NM_021008.2	NP_066288.2	O75398	DEAF1_HUMAN	DEAF1 transcription factor						anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)		CACAGGAGAAAACCAGGATGGC	0.52														2632	0.525559	0.2927	0.5303	5008	,	,		20992	0.7173		0.5686	False		,,,				2504	0.5951																0								ENSG00000177030																																			DEAF1	SO:0001627	intron_variant	0				HGNC	AF049460	CCDS31327.1	11p15.5	2013-01-10	2013-01-10		ENSG00000177030	ENSG00000177030		"""Zinc fingers, MYND-type"""	14677	protein-coding gene	gene with protein product		602635	"""deformed epidermal autoregulatory factor 1 (Drosophila)"""			9773984	Standard	XR_428838		Approved	NUDR, SPN, ZMYND5	uc001lqq.1	O75398	OTTHUMG00000165363	ENST00000382409.3:c.998-186->CATCCTGGT	11.37:g.680003_680011dupACCAGGATG		Somatic	NA	NA	NA		0.4003313805339589	3	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000382409.3	37	NULL	CCDS31327.1	11																																																																																			-	-		0.520	DEAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DEAF1	protein_coding	OTTHUMT00000383614.3	-	NM_021008			680003	-1	no_errors	ENST00000525904	ensembl	human	known	74_37	rna	INS	0.000:0.000	ACCAGGATG
ALG12	79087	genome.wustl.edu	37	22	50297769	50297769	+	Intron	SNP	C	C	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr22:50297769C>T	ENST00000330817.6	-	10	1512				CITF22-1A6.3_ENST00000610245.1_lincRNA	NM_024105.3	NP_077010.1	Q9BV10	ALG12_HUMAN	ALG12, alpha-1,6-mannosyltransferase						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-1,6-mannosyltransferase activity (GO:0000009)|dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity (GO:0052917)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(3)	12		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		BRCA - Breast invasive adenocarcinoma(115;0.199)|LUAD - Lung adenocarcinoma(64;0.247)		CCCTGTCCCCCGCCCCCAAGG	0.652																																																	0								ENSG00000273192						49.0	49.0	49.0					22																	50297769		692	1591	2283	CITF22-1A6.3	SO:0001627	intron_variant	0			-	Clone_based_vega_gene	AJ303120	CCDS14081.1	22q13.33	2013-02-26	2013-02-26		ENSG00000182858	ENSG00000182858	2.4.1.260	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	19358	protein-coding gene	gene with protein product	"""dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichol alpha-1,6-mannosyltransferase"", ""dol-P-Man dependent alpha-1,6-mannosyltransferase"""	607144	"""asparagine-linked glycosylation 12 homolog (yeast, alpha-1,6-mannosyltransferase)"", ""asparagine-linked glycosylation 12, alpha-1,6-mannosyltransferase homolog (S. cerevisiae)"""			11983712	Standard	NM_024105		Approved	ECM39	uc003biy.3	Q9BV10	OTTHUMG00000150289	ENST00000330817.6:c.1239-55G>A	22.37:g.50297769C>T		Somatic	0	141	0.00		0.4003313805339589	9	43.75	7	WXS	Illumina HiSeq 2500	Phase_IV	tier1	19	185	9.31	A6PWM1|Q4KMH4|Q8NG10|Q96AA4	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000330817.6	37	NULL	CCDS14081.1	22																																																																																			-	-		0.652	ALG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000273192	protein_coding	OTTHUMT00000317405.2	C	NM_024105	-		50297769	+1	no_errors	ENST00000610245	ensembl	human	known	74_37	rna	SNP	0.000	T
AGBL5	60509	genome.wustl.edu	37	2	27282286	27282286	+	Intron	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr2:27282286G>T	ENST00000360131.4	+	11	2248				AGBL5-IT1_ENST00000411862.1_RNA|AGBL5_ENST00000323064.8_Missense_Mutation_p.W701C	NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5						protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGCCAGTCTGGGAGCCCCTGC	0.577																																																	0								ENSG00000084693						54.0	64.0	61.0					2																	27282286		2203	4298	6501	AGBL5	SO:0001627	intron_variant	0			-	HGNC	BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 5"""	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.2089+14G>T	2.37:g.27282286G>T		Somatic	0	73	0.00		0.4003313805339589	28	17.14	6	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	102	12.07	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Peptidase_M14	p.W701C	ENST00000360131.4	37	c.2103	CCDS1732.3	2	.	.	.	.	.	.	.	.	.	.	G	16.76	3.213087	0.58452	.	.	ENSG00000084693	ENST00000323064	T	0.14144	2.53	5.76	4.87	0.63330	.	.	.	.	.	T	0.29028	0.0721	.	.	.	0.80722	D	1	D	0.64830	0.994	P	0.58873	0.847	T	0.00298	-1.1837	7	.	.	.	.	13.8511	0.63496	0.0749:0.0:0.9251:0.0	.	701	Q8NDL9-3	.	C	701	ENSP00000323681:W701C	.	W	+	3	0	AGBL5	27135790	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.913000	0.48790	2.713000	0.92767	0.655000	0.94253	TGG	-	NULL		0.577	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	AGBL5	protein_coding	OTTHUMT00000309033.1	G	NM_021831	-		27282286	+1	no_errors	ENST00000323064	ensembl	human	known	74_37	missense	SNP	1.000	T
LRTM1	57408	genome.wustl.edu	37	3	54952751	54952751	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr3:54952751G>T	ENST00000273286.5	-	3	935	c.773C>A	c.(772-774)cCt>cAt	p.P258H	LRTM1_ENST00000493075.1_Missense_Mutation_p.P182H|CACNA2D3_ENST00000490478.1_Intron|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000288197.5_Intron|CACNA2D3_ENST00000474759.1_Intron	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	258						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(4)	21				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)		GTGGTTCTCAGGAGGCCTCAG	0.627																																																	0								ENSG00000144771						67.0	56.0	60.0					3																	54952751		2203	4300	6503	LRTM1	SO:0001583	missense	0			-	HGNC	AF225421	CCDS2876.1	3p14.3	2006-01-02			ENSG00000144771	ENSG00000144771			25023	protein-coding gene	gene with protein product						12477932	Standard	NM_020678		Approved	HT017	uc003dhl.3	Q9HBL6	OTTHUMG00000158578	ENST00000273286.5:c.773C>A	3.37:g.54952751G>T	ENSP00000273286:p.Pro258His	Somatic	0	41	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	46	8.00	Q8IUU2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Leu-rich_rpt,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C	p.P258H	ENST00000273286.5	37	c.773	CCDS2876.1	3	.	.	.	.	.	.	.	.	.	.	G	2.993	-0.207711	0.06180	.	.	ENSG00000144771	ENST00000273286;ENST00000493075	T;T	0.52057	0.68;1.0	4.19	1.29	0.21616	.	0.648102	0.13792	N	0.362414	T	0.35248	0.0925	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21895	-1.0232	10	0.33141	T	0.24	.	10.1176	0.42601	0.0:0.0:0.4727:0.5273	.	258	Q9HBL6	LRTM1_HUMAN	H	258;182	ENSP00000273286:P258H;ENSP00000419772:P182H	ENSP00000273286:P258H	P	-	2	0	LRTM1	54927791	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	1.191000	0.32138	0.259000	0.21709	-0.428000	0.05917	CCT	-	NULL		0.627	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRTM1	protein_coding	OTTHUMT00000351399.1	G	NM_020678	-		54952751	-1	no_errors	ENST00000273286	ensembl	human	known	74_37	missense	SNP	0.001	T
PEG3	5178	genome.wustl.edu	37	19	57327590	57327590	+	Silent	SNP	A	A	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr19:57327590A>T	ENST00000326441.9	-	10	2583	c.2220T>A	c.(2218-2220)ccT>ccA	p.P740P	PEG3_ENST00000598410.1_Silent_p.P616P|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000423103.2_Silent_p.P740P|PEG3_ENST00000593695.1_Silent_p.P614P|ZIM2_ENST00000593711.1_Intron|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000391708.3_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	740					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		CACTTTCAAGAGGTCTTGTTA	0.408																																																	0								ENSG00000198300						133.0	127.0	129.0					19																	57327590		2203	4300	6503	PEG3	SO:0001819	synonymous_variant	0			-	HGNC	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.2220T>A	19.37:g.57327590A>T		Somatic	0	37	0.00		0.4003313805339589	1	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	53	8.62	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Znf_C2H2,pfam_Tscrpt_reg_SCAN,superfamily_Retrov_capsid_C,smart_Tscrpt_reg_SCAN,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Tscrpt_reg_SCAN	p.P740	ENST00000326441.9	37	c.2220	CCDS12948.1	19																																																																																			-	NULL		0.408	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	PEG3	protein_coding	OTTHUMT00000416099.2	A		-		57327590	-1	no_errors	ENST00000326441	ensembl	human	known	74_37	silent	SNP	0.056	T
ABCA1	19	genome.wustl.edu	37	9	107576725	107576725	+	Missense_Mutation	SNP	A	A	G			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr9:107576725A>G	ENST00000374736.3	-	26	4164	c.3770T>C	c.(3769-3771)gTg>gCg	p.V1257A		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1257					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CTCAGCATCCACCCCACTCTC	0.478																																																	0								ENSG00000165029						125.0	97.0	106.0					9																	107576725		2203	4300	6503	ABCA1	SO:0001583	missense	0			-	HGNC	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.3770T>C	9.37:g.107576725A>G	ENSP00000363868:p.Val1257Ala	Somatic	0	36	0.00		0.4003313805339589	18	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	64	8.57	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_ABC_transporter-like,superfamily_P-loop_NTPase,smart_AAA+_ATPase,pfscan_ABC_transporter-like	p.V1257A	ENST00000374736.3	37	c.3770	CCDS6762.1	9	.	.	.	.	.	.	.	.	.	.	A	11.69	1.714398	0.30413	.	.	ENSG00000165029	ENST00000374736	D	0.83755	-1.76	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.66674	0.2813	N	0.08118	0	0.80722	D	1	B	0.17038	0.02	B	0.21360	0.034	T	0.63065	-0.6720	10	0.08179	T	0.78	.	15.2403	0.73465	1.0:0.0:0.0:0.0	.	1257	O95477	ABCA1_HUMAN	A	1257	ENSP00000363868:V1257A	ENSP00000363868:V1257A	V	-	2	0	ABCA1	106616546	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.804000	0.91921	2.022000	0.59522	0.454000	0.30748	GTG	-	NULL		0.478	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	ABCA1	protein_coding	OTTHUMT00000053491.1	A	NM_005502	-		107576725	-1	no_errors	ENST00000374736	ensembl	human	known	74_37	missense	SNP	1.000	G
LRRK2	120892	genome.wustl.edu	37	12	40677723	40677723	+	Missense_Mutation	SNP	A	A	G			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr12:40677723A>G	ENST00000298910.7	+	19	2346	c.2288A>G	c.(2287-2289)aAt>aGt	p.N763S	LRRK2_ENST00000343742.2_Missense_Mutation_p.N763S	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	763					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CTCTTACTGAATAGTGGATCT	0.383																																																	0								ENSG00000188906						118.0	111.0	113.0					12																	40677723		2203	4300	6503	LRRK2	SO:0001583	missense	0			-	HGNC	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.2288A>G	12.37:g.40677723A>G	ENSP00000298910:p.Asn763Ser	Somatic	0	34	0.00		0.4003313805339589	10	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	22	12.00	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_MIRO-like,pfam_Small_GTPase,pfam_Leu-rich_rpt,pfam_Small_GTPase_ARF/SAR,superfamily_Kinase-like_dom,superfamily_P-loop_NTPase,superfamily_ARM-type_fold,superfamily_WD40_repeat_dom,smart_Leu-rich_rpt_typical-subtyp,smart_Small_GTPase_Rab_type,smart_Tyr_kinase_cat_dom,smart_Ser/Thr_dual-sp_kinase_dom,prints_Small_GTPase,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom,tigrfam_Small_GTP-bd_dom	p.N763S	ENST00000298910.7	37	c.2288	CCDS31774.1	12	.	.	.	.	.	.	.	.	.	.	A	7.541	0.660709	0.14645	.	.	ENSG00000188906	ENST00000416796;ENST00000343742;ENST00000298910	T;T;T	0.50001	0.76;1.48;1.48	5.03	1.39	0.22231	Ankyrin repeat-containing domain (1);	0.905402	0.09718	N	0.764879	T	0.24198	0.0586	N	0.11560	0.145	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.24905	-1.0147	10	0.16420	T	0.52	.	5.929	0.19128	0.6337:0.1398:0.2264:0.0	.	763;763	E9PC85;Q5S007	.;LRRK2_HUMAN	S	511;763;763	ENSP00000398726:N511S;ENSP00000341930:N763S;ENSP00000298910:N763S	ENSP00000298910:N763S	N	+	2	0	LRRK2	38963990	0.622000	0.27085	0.002000	0.10522	0.831000	0.47069	1.282000	0.33226	0.334000	0.23590	-0.346000	0.07831	AAT	-	superfamily_ARM-type_fold		0.383	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	LRRK2	protein_coding	OTTHUMT00000277179.1	A	XM_058513	-		40677723	+1	no_errors	ENST00000298910	ensembl	human	known	74_37	missense	SNP	0.002	G
PLEKHG1	57480	genome.wustl.edu	37	6	151125824	151125824	+	Missense_Mutation	SNP	G	G	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr6:151125824G>A	ENST00000358517.2	+	7	1070	c.859G>A	c.(859-861)Gcc>Acc	p.A287T	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.A287T			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	287	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A287T(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		GCAGCGAGTCGCCTGGCATAT	0.517																																																	1	Substitution - Missense(1)	central_nervous_system(1)						ENSG00000120278						83.0	76.0	78.0					6																	151125824		2203	4300	6503	PLEKHG1	SO:0001583	missense	0			-	HGNC	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.859G>A	6.37:g.151125824G>A	ENSP00000351318:p.Ala287Thr	Somatic	0	32	0.00		0.4003313805339589	28	16.67	6	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	45	8.16	Q5T1F2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_DH-domain,superfamily_DH-domain,smart_DH-domain,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology,pfscan_DH-domain	p.A287T	ENST00000358517.2	37	c.859	CCDS34552.1	6	.	.	.	.	.	.	.	.	.	.	G	37	6.042648	0.97231	.	.	ENSG00000120278	ENST00000367328;ENST00000535018;ENST00000358517	T;T	0.66638	-0.22;-0.22	6.17	6.17	0.99709	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	D	0.82674	0.5088	M	0.83852	2.665	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.82335	-0.0508	10	0.62326	D	0.03	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	94;287;287	Q5EBL9;Q5JYA6;Q9ULL1	.;.;PKHG1_HUMAN	T	287	ENSP00000356297:A287T;ENSP00000351318:A287T	ENSP00000351318:A287T	A	+	1	0	PLEKHG1	151167517	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	9.731000	0.98807	2.941000	0.99782	0.655000	0.94253	GCC	-	pfam_DH-domain,superfamily_DH-domain,smart_DH-domain,pfscan_DH-domain		0.517	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLEKHG1	protein_coding	OTTHUMT00000042691.1	G		-		151125824	+1	no_errors	ENST00000358517	ensembl	human	known	74_37	missense	SNP	1.000	A
C1orf35	79169	genome.wustl.edu	37	1	228289201	228289201	+	Intron	SNP	C	C	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr1:228289201C>A	ENST00000272139.4	-	7	768				C1orf35_ENST00000472617.1_Intron	NM_024319.2	NP_077295.1	Q9BU76	MMTA2_HUMAN	chromosome 1 open reading frame 35								poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(1)|skin(1)	3		Prostate(94;0.0488)				AGGTGTGCCTCAGACCCTAGT	0.443																																																	0								ENSG00000143793						43.0	46.0	45.0					1																	228289201		2203	4300	6503	C1orf35	SO:0001627	intron_variant	0			-	HGNC	AY137773	CCDS1566.1	1q42.13	2012-06-25			ENSG00000143793	ENSG00000143793			19032	protein-coding gene	gene with protein product	"""multiple myeloma tumor-associated protein 2"""					12545221	Standard	NM_024319		Approved	MGC4174, MMTAG2	uc001hrx.3	Q9BU76	OTTHUMG00000037793	ENST00000272139.4:c.534-27G>T	1.37:g.228289201C>A		Somatic	0	34	0.00		0.4003313805339589	3	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	46	8.00	Q6P5Y0|Q6ZTZ6|Q6ZWA6|Q8IZH3	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000272139.4	37	NULL	CCDS1566.1	1																																																																																			-	-		0.443	C1orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C1orf35	protein_coding	OTTHUMT00000092245.1	C	NM_024319	-		228289201	-1	no_errors	ENST00000469781	ensembl	human	known	74_37	rna	SNP	0.001	A
ALG3	10195	genome.wustl.edu	37	3	183960782	183960782	+	Intron	SNP	T	T	G	rs200645083|rs532747618	byFrequency	TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr3:183960782T>G	ENST00000397676.3	-	8	1040				ALG3_ENST00000455059.1_Intron|MIR1224_ENST00000408193.1_RNA|ALG3_ENST00000445626.2_Intron|EIF2B5_ENST00000444495.1_Intron|ALG3_ENST00000463495.1_5'UTR|ALG3_ENST00000418734.2_Intron	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)|dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity (GO:0052925)			kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GGAGTGTGTGTGGGGGGGACT	0.517														3	0.000599042	0.0	0.0014	5008	,	,		20097	0.0		0.001	False		,,,				2504	0.001																0								ENSG00000214160	T	,	0,4022		0,0,2011	36.0	39.0	38.0		,	-5.4	0.0	3		38	5,8325		0,5,4160	no	intron,intron	ALG3	NM_001006941.2,NM_005787.5	,	0,5,6171	GG,GT,TT		0.06,0.0,0.0405	,	,	183960782	5,12347	2011	4165	6176	ALG3	SO:0001627	intron_variant	0			GMAF=0.0005	HGNC	BC002839	CCDS46967.1, CCDS46968.1	3q27.3	2013-02-26	2013-02-26		ENSG00000214160	ENSG00000214160	2.4.1.258	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	23056	protein-coding gene	gene with protein product	"""carbohydrate deficient glycoprotein syndrome type IV"", ""dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase"", ""dol-P-Man dependent alpha-1,3- mannosyltransferase"""	608750	"""asparagine-linked glycosylation 3 homolog (yeast, alpha-1,3-mannosyltransferase)"", ""asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae)"""			1058125	Standard	NM_005787		Approved	NOT56L, Not56, CDGS4, D16Ertd36e	uc003fne.2	Q92685	OTTHUMG00000156823	ENST00000397676.3:c.1010-37A>C	3.37:g.183960782T>G		Somatic	0	38	0.00		0.4003313805339589	5	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	29	14.71	A8JZZ6|Q9BT71	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000397676.3	37	NULL	CCDS46968.1	3																																																																																			-	-		0.517	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALG3	protein_coding	OTTHUMT00000346033.1	T	NM_005787	rs200645083		183960782	-1	no_errors	ENST00000463495	ensembl	human	known	74_37	rna	SNP	0.000	G
GDPD5	81544	genome.wustl.edu	37	11	75153941	75153941	+	Intron	DEL	C	C	-			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr11:75153941delC	ENST00000336898.3	-	11	1786				GDPD5_ENST00000443276.2_Intron|GDPD5_ENST00000529721.1_Intron|GDPD5_ENST00000533784.1_Intron|GDPD5_ENST00000376282.3_Intron|GDPD5_ENST00000533805.1_Intron|GDPD5_ENST00000526177.1_Intron	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5						cerebral cortex neuron differentiation (GO:0021895)|glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)|negative regulation of Notch signaling pathway (GO:0045746)|neuron projection development (GO:0031175)|positive regulation of neuron differentiation (GO:0045666)|regulation of timing of cell differentiation (GO:0048505)|spinal cord motor neuron differentiation (GO:0021522)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|skin(2)	20						GAATTCTATTCACTGCTCTCA	0.493																																																	0								ENSG00000158555																																			GDPD5	SO:0001627	intron_variant	0				HGNC	AF318377	CCDS8238.1	11q13.4-q13.5	2011-01-25				ENSG00000158555			28804	protein-coding gene	gene with protein product		609632				18667693, 17275818	Standard	NM_030792		Approved	PP1665, GDE2	uc001owp.4	Q8WTR4		ENST00000336898.3:c.948+239G>-	11.37:g.75153941delC		Somatic	0	8	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	11	15.38	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000336898.3	37	NULL	CCDS8238.1	11																																																																																			-	-		0.493	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GDPD5	protein_coding	OTTHUMT00000384409.1	C	NM_030792			75153941	-1	no_errors	ENST00000527322	ensembl	human	known	74_37	rna	DEL	0.000	-
NDUFA9	4704	genome.wustl.edu	37	12	4794302	4794302	+	Intron	DEL	A	A	-	rs374564173|rs546384604	byFrequency	TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr12:4794302delA	ENST00000266544.5	+	10	916				RP11-234B24.6_ENST00000544741.2_Intron|NDUFA9_ENST00000540688.1_Frame_Shift_Del_p.L17fs	NM_005002.4	NP_004993.1	Q16795	NDUA9_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9, 39kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|sodium ion transport (GO:0006814)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21						TTATTTTCTTAAAAAAAAAAA	0.463																																					Colon(75;996 1244 23946 25294 29232)												0								ENSG00000139180																																			NDUFA9	SO:0001627	intron_variant	0				HGNC	AF050641	CCDS8532.1	12p13.3	2011-09-14	2002-08-29		ENSG00000139180	ENSG00000139180		"""Mitochondrial respiratory chain complex / Complex I"", ""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	7693	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 22E, member 1"", ""complex I 39kDa subunit"""	603834	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9 (39kD)"""	NDUFS2L		8486360, 19027726	Standard	NM_005002		Approved	SDR22E1, CI-39k	uc001qnc.3	Q16795		ENST00000266544.5:c.897-123A>-	12.37:g.4794302delA		Somatic	0	15	0.00		0.4003313805339589	1	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	19	13.64	Q14076|Q2NKX0	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	NULL	p.K20fs	ENST00000266544.5	37	c.51	CCDS8532.1	12																																																																																			-	NULL		0.463	NDUFA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NDUFA9	protein_coding	OTTHUMT00000398900.2	A	NM_005002			4794302	+1	no_errors	ENST00000540688	ensembl	human	putative	74_37	frame_shift_del	DEL	0.000	-
GSG1	83445	genome.wustl.edu	37	12	13243611	13243611	+	Nonsense_Mutation	SNP	C	C	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr12:13243611C>A	ENST00000432710.2	-	2	322	c.190G>T	c.(190-192)Gag>Tag	p.E64*	GSG1_ENST00000351606.6_Nonsense_Mutation_p.E64*|GSG1_ENST00000457134.2_Nonsense_Mutation_p.E51*|GSG1_ENST00000396310.2_Nonsense_Mutation_p.E48*|GSG1_ENST00000337630.6_Nonsense_Mutation_p.E51*|GSG1_ENST00000396302.3_Nonsense_Mutation_p.E51*|GSG1_ENST00000537302.1_Nonsense_Mutation_p.E51*|GSG1_ENST00000324458.8_Nonsense_Mutation_p.E64*	NM_001206842.1	NP_001193771.1	Q2KHT4	GSG1_HUMAN	germ cell associated 1	51						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(1)	10		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		AGACCTTTCTCGCACAGGGGC	0.542																																																	0								ENSG00000111305						127.0	110.0	116.0					12																	13243611		2203	4300	6503	GSG1	SO:0001587	stop_gained	0			-	HGNC	BC001796	CCDS8659.2, CCDS44835.1, CCDS44836.1, CCDS55806.1, CCDS55807.1, CCDS55808.1	12p13.31	2007-12-03			ENSG00000111305	ENSG00000111305			19716	protein-coding gene	gene with protein product							Standard	NM_031289		Approved	MGC3146	uc001rbn.3	Q2KHT4	OTTHUMG00000150148	ENST00000432710.2:c.190G>T	12.37:g.13243611C>A	ENSP00000405032:p.Glu64*	Somatic	0	30	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	46	8.00	Q8N4M3|Q8NBR4|Q8NBS0|Q8NBT1|Q96LP9|Q96SI6|Q9BUY4	Nonsense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_GSG-1	p.E64*	ENST00000432710.2	37	c.190	CCDS55808.1	12	.	.	.	.	.	.	.	.	.	.	C	35	5.595618	0.96602	.	.	ENSG00000111305	ENST00000337630;ENST00000324458;ENST00000396310;ENST00000396302;ENST00000457134;ENST00000432710;ENST00000537302;ENST00000351606;ENST00000405543;ENST00000545401;ENST00000542415;ENST00000545699	.	.	.	5.4	3.58	0.41010	.	0.419213	0.26903	N	0.021916	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	12.098	0.53765	0.0:0.8595:0.0:0.1405	.	.	.	.	X	51;64;48;51;51;64;51;64;48;64;64;51	.	ENSP00000320838:E64X	E	-	1	0	GSG1	13134878	0.996000	0.38824	0.987000	0.45799	0.828000	0.46876	0.446000	0.21694	0.659000	0.30945	0.561000	0.74099	GAG	-	pfam_GSG-1		0.542	GSG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	GSG1	protein_coding	OTTHUMT00000316546.1	C	NM_031289	-		13243611	-1	no_errors	ENST00000324458	ensembl	human	known	74_37	nonsense	SNP	1.000	A
PKHD1	5314	genome.wustl.edu	37	6	51609282	51609282	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr6:51609282G>T	ENST00000371117.3	-	60	10332	c.10057C>A	c.(10057-10059)Ctc>Atc	p.L3353I	PKHD1_ENST00000340994.4_Missense_Mutation_p.L3353I	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3353					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TCCTTGAAGAGATATTTTCTT	0.428																																																	0								ENSG00000170927						95.0	93.0	94.0					6																	51609282		2203	4300	6503	PKHD1	SO:0001583	missense	0			-	HGNC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10057C>A	6.37:g.51609282G>T	ENSP00000360158:p.Leu3353Ile	Somatic	0	33	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	38	9.52	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_IPT,pfam_G8_domain,superfamily_Ig_E-set,superfamily_Pectin_lyase_fold/virulence,smart_IPT,smart_PbH1	p.L3353I	ENST00000371117.3	37	c.10057	CCDS4935.1	6	.	.	.	.	.	.	.	.	.	.	G	22.6	4.310254	0.81358	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.90197	-2.43;-2.63	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000008	D	0.93930	0.8057	M	0.65975	2.015	0.36492	D	0.868468	D;D;D	0.89917	0.999;0.994;1.0	D;D;D	0.80764	0.968;0.945;0.994	D	0.94171	0.7423	10	0.56958	D	0.05	.	18.0999	0.89503	0.0:0.0:1.0:0.0	.	3353;3353;3353	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	I	3353	ENSP00000360158:L3353I;ENSP00000341097:L3353I	ENSP00000341097:L3353I	L	-	1	0	PKHD1	51717241	1.000000	0.71417	0.998000	0.56505	0.934000	0.57294	6.175000	0.71949	2.615000	0.88500	0.650000	0.86243	CTC	-	NULL		0.428	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PKHD1	protein_coding	OTTHUMT00000040893.1	G	NM_138694	-		51609282	-1	no_errors	ENST00000371117	ensembl	human	known	74_37	missense	SNP	1.000	T
ZNF674	641339	genome.wustl.edu	37	X	46360436	46360436	+	Frame_Shift_Del	DEL	A	A	-			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chrX:46360436delA	ENST00000523374.1	-	6	798	c.588delT	c.(586-588)tttfs	p.F196fs	ZNF674_ENST00000518795.1_5'Flank|ZNF674_ENST00000414387.2_Frame_Shift_Del_p.F190fs	NM_001039891.2|NM_001146291.1|NM_001190417.1	NP_001034980.1|NP_001139763.1|NP_001177346.1	Q2M3X9	ZN674_HUMAN	zinc finger protein 674	196					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)	2						GATTAGGGTCAAAAAATCTCT	0.393																																																	0								ENSG00000251192						34.0	29.0	30.0					X																	46360436		1884	4092	5976	ZNF674	SO:0001589	frameshift_variant	0				HGNC	AY971607	CCDS48099.1, CCDS55406.1	Xp11.3	2013-01-08	2010-09-15		ENSG00000251192	ENSG00000251192		"""Zinc fingers, C2H2-type"", ""-"""	17625	protein-coding gene	gene with protein product		300573		MRX92		16385466	Standard	NM_001039891		Approved	ZNF673B	uc004dgr.3	Q2M3X9	OTTHUMG00000021420	ENST00000523374.1:c.588delT	X.37:g.46360436delA	ENSP00000429148:p.Phe196fs	Somatic	0	11	0.00		0.4003313805339589	1	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	18	10.00	B4DHE2|E9PHQ4	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.F196fs	ENST00000523374.1	37	c.588	CCDS48099.1	X																																																																																			-	NULL		0.393	ZNF674-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ZNF674	protein_coding	OTTHUMT00000056357.2	A	NM_001039891			46360436	-1	no_errors	ENST00000523374	ensembl	human	known	74_37	frame_shift_del	DEL	0.054	-
WDR55	54853	genome.wustl.edu	37	5	140048683	140048683	+	Missense_Mutation	SNP	G	G	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr5:140048683G>A	ENST00000358337.5	+	6	917	c.680G>A	c.(679-681)tGt>tAt	p.C227Y	WDR55_ENST00000520764.1_3'UTR	NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	227					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)				NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGGTAGCCTGTGGCTCCAGT	0.527																																																	0								ENSG00000120314						77.0	80.0	79.0					5																	140048683		2203	4300	6503	WDR55	SO:0001583	missense	0			-	HGNC	AK000202	CCDS4235.1	5q31.3	2013-01-09			ENSG00000120314	ENSG00000120314		"""WD repeat domain containing"""	25971	protein-coding gene	gene with protein product						12477932	Standard	NM_017706		Approved	FLJ20195, FLJ21702	uc003lgr.4	Q9H6Y2	OTTHUMG00000129506	ENST00000358337.5:c.680G>A	5.37:g.140048683G>A	ENSP00000351100:p.Cys227Tyr	Somatic	0	65	0.00		0.4003313805339589	47	9.62	5	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	76	9.52	Q9NXK4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pirsf_WD_repeat_p55,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.C227Y	ENST00000358337.5	37	c.680	CCDS4235.1	5	.	.	.	.	.	.	.	.	.	.	G	20.2	3.942498	0.73672	.	.	ENSG00000120314	ENST00000358337	T	0.40476	1.03	4.97	4.97	0.65823	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.68550	0.3013	M	0.85630	2.765	0.80722	D	1	D;P	0.71674	0.998;0.947	D;P	0.74023	0.982;0.527	T	0.75274	-0.3375	10	0.87932	D	0	-7.876	17.0088	0.86400	0.0:0.0:1.0:0.0	.	66;227	G3V1J0;Q9H6Y2	.;WDR55_HUMAN	Y	227	ENSP00000351100:C227Y	ENSP00000351100:C227Y	C	+	2	0	WDR55	140028867	1.000000	0.71417	0.999000	0.59377	0.930000	0.56654	9.539000	0.98076	2.286000	0.76751	0.467000	0.42956	TGT	-	superfamily_WD40_repeat_dom,smart_WD40_repeat,pirsf_WD_repeat_p55,pfscan_WD40_repeat_dom		0.527	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WDR55	protein_coding	OTTHUMT00000251680.3	G	NM_017706	-		140048683	+1	no_errors	ENST00000358337	ensembl	human	known	74_37	missense	SNP	1.000	A
WRB	7485	genome.wustl.edu	37	21	40768975	40768975	+	3'UTR	DEL	T	T	-			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr21:40768975delT	ENST00000333781.5	+	0	776				WRB_ENST00000541890.1_Intron|WRB_ENST00000380708.1_3'UTR|WRB_ENST00000398753.1_3'UTR|WRB_ENST00000466787.1_3'UTR	NM_004627.4	NP_004618.2	O00258	WRB_HUMAN	tryptophan rich basic protein						tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(3)	3		Prostate(19;1.2e-06)				ATAGTTTAGATTTTTTTTTTG	0.333																																																	0								ENSG00000182093																																			WRB	SO:0001624	3_prime_UTR_variant	0				HGNC		CCDS13664.1, CCDS54485.1	21q22.3	2007-10-04			ENSG00000182093	ENSG00000182093			12790	protein-coding gene	gene with protein product		602915				9544840	Standard	NM_004627		Approved	CHD5	uc002yxs.3	O00258	OTTHUMG00000066250	ENST00000333781.5:c.*110T>-	21.37:g.40768975delT		Somatic	0	29	0.00		0.4003313805339589	56	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	23	17.86	A8KAP8|A8MQ44|D3DSH9|O60740	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000333781.5	37	NULL	CCDS13664.1	21																																																																																			-	-		0.333	WRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WRB	protein_coding	OTTHUMT00000141745.3	T				40768975	+1	no_errors	ENST00000466787	ensembl	human	known	74_37	rna	DEL	0.000	-
DNAJC13	23317	genome.wustl.edu	37	3	132165329	132165329	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr3:132165329G>T	ENST00000260818.6	+	3	327	c.79G>T	c.(79-81)Gtc>Ttc	p.V27F	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	27					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						GTATAAGCGTGTCTTTTCAGT	0.289																																																	0								ENSG00000138246						86.0	82.0	83.0					3																	132165329		2203	4300	6503	DNAJC13	SO:0001583	missense	0			-	HGNC	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.79G>T	3.37:g.132165329G>T	ENSP00000260818:p.Val27Phe	Somatic	0	67	0.00		0.4003313805339589	15	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	45	8.16	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_DnaJ_domain,superfamily_ARM-type_fold,superfamily_GYF,smart_DnaJ_domain,pfscan_DnaJ_domain	p.V27F	ENST00000260818.6	37	c.79	CCDS33857.1	3	.	.	.	.	.	.	.	.	.	.	G	26.0	4.693764	0.88735	.	.	ENSG00000138246	ENST00000260818	T	0.22134	1.97	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.20577	0.0495	L	0.27053	0.805	0.80722	D	1	B;P	0.50943	0.126;0.94	B;B	0.43680	0.085;0.427	T	0.00964	-1.1498	10	0.37606	T	0.19	.	19.4758	0.94987	0.0:0.0:1.0:0.0	.	27;27	A7E2Y5;O75165	.;DJC13_HUMAN	F	27	ENSP00000260818:V27F	ENSP00000260818:V27F	V	+	1	0	DNAJC13	133648019	1.000000	0.71417	1.000000	0.80357	0.769000	0.43574	9.869000	0.99810	2.607000	0.88179	0.563000	0.77884	GTC	-	NULL		0.289	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DNAJC13	protein_coding	OTTHUMT00000356807.2	G	NM_015268	-		132165329	+1	no_errors	ENST00000260818	ensembl	human	known	74_37	missense	SNP	1.000	T
ALDH9A1	223	genome.wustl.edu	37	1	165638239	165638239	+	Silent	SNP	C	C	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr1:165638239C>A	ENST00000354775.4	-	8	1435	c.1131G>T	c.(1129-1131)gtG>gtT	p.V377V	ALDH9A1_ENST00000538148.1_Silent_p.V283V	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	353					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					CACCACATAACACTTTAGCAC	0.333																																					Ovarian(179;1583 2014 18106 33801 42447)												0								ENSG00000143149						107.0	111.0	110.0					1																	165638239		2203	4299	6502	ALDH9A1	SO:0001819	synonymous_variant	0			-	HGNC	U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"""Aldehyde dehydrogenases"""	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.1131G>T	1.37:g.165638239C>A		Somatic	0	42	0.00		0.4003313805339589	421	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	37	9.76	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Aldehyde_DH_dom,superfamily_Ald_DH/histidinol_DH	p.V377	ENST00000354775.4	37	c.1131	CCDS1250.2	1																																																																																			-	pfam_Aldehyde_DH_dom,superfamily_Ald_DH/histidinol_DH		0.333	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALDH9A1	protein_coding	OTTHUMT00000083899.1	C		-		165638239	-1	no_errors	ENST00000354775	ensembl	human	known	74_37	silent	SNP	0.795	A
SLC18A2	6571	genome.wustl.edu	37	10	119001250	119001250	+	Missense_Mutation	SNP	C	C	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr10:119001250C>A	ENST00000298472.5	+	2	189	c.46C>A	c.(46-48)Cgc>Agc	p.R16S	RP11-501J20.5_ENST00000425264.1_RNA|SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	16					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	GCAGGAGAGCCGCCGCTCGCG	0.706																																																	0								ENSG00000165646						25.0	24.0	24.0					10																	119001250		2203	4300	6503	SLC18A2	SO:0001583	missense	0			-	HGNC	L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"""Solute carriers"""	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.46C>A	10.37:g.119001250C>A	ENSP00000298472:p.Arg16Ser	Somatic	0	17	0.00		0.4003313805339589	1	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	17	19.05	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_MFS,pfam_Sub_transporter,superfamily_MFS_dom_general_subst_transpt,pfscan_MFS_dom	p.R16S	ENST00000298472.5	37	c.46	CCDS7599.1	10	.	.	.	.	.	.	.	.	.	.	C	24.6	4.552699	0.86127	.	.	ENSG00000165646	ENST00000298472	T	0.04502	3.61	5.19	4.28	0.50868	Major facilitator superfamily domain, general substrate transporter (1);	0.058865	0.64402	D	0.000004	T	0.12092	0.0294	M	0.80746	2.51	0.58432	D	0.999998	P	0.38863	0.65	B	0.43413	0.419	T	0.00891	-1.1525	10	0.56958	D	0.05	-15.5374	12.191	0.54270	0.0:0.9208:0.0:0.0792	.	16	Q05940	VMAT2_HUMAN	S	16	ENSP00000298472:R16S	ENSP00000298472:R16S	R	+	1	0	SLC18A2	118991240	1.000000	0.71417	0.982000	0.44146	0.992000	0.81027	1.594000	0.36697	1.181000	0.42912	0.563000	0.77884	CGC	-	superfamily_MFS_dom_general_subst_transpt		0.706	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC18A2	protein_coding	OTTHUMT00000050563.1	C	NM_003054	-		119001250	+1	no_errors	ENST00000298472	ensembl	human	known	74_37	missense	SNP	1.000	A
LUZP1	7798	genome.wustl.edu	37	1	23420544	23420544	+	Silent	SNP	G	G	T	rs536365038		TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr1:23420544G>T	ENST00000302291.4	-	4	1012	c.211C>A	c.(211-213)Cgg>Agg	p.R71R	LUZP1_ENST00000418342.1_Silent_p.R71R|LUZP1_ENST00000314174.5_Silent_p.R71R|LUZP1_ENST00000374623.3_Silent_p.R71R			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	71					artery development (GO:0060840)|neural fold bending (GO:0021503)|ventricular septum development (GO:0003281)	membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(2)	31		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		CTCAGCACCCGCTGGCGCAGC	0.507																																																	0								ENSG00000169641						142.0	150.0	147.0					1																	23420544		2203	4300	6503	LUZP1	SO:0001819	synonymous_variant	0			-	HGNC	BC051733	CCDS30628.1	1p36	2008-02-05			ENSG00000169641	ENSG00000169641			14985	protein-coding gene	gene with protein product		601422				8812416	Standard	NM_033631		Approved	LUZP	uc010odv.1	Q86V48	OTTHUMG00000003227	ENST00000302291.4:c.211C>A	1.37:g.23420544G>T		Somatic	0	30	0.00		0.4003313805339589	16	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	43	8.51	Q5TH93|Q8N4X3|Q8TEH1	Silent	SNP	NA	NA	NA	NA	NA	NA	NULL	p.R71	ENST00000302291.4	37	c.211	CCDS30628.1	1																																																																																			-	NULL		0.507	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	LUZP1	protein_coding	OTTHUMT00000008900.3	G	NM_033631	-		23420544	-1	no_errors	ENST00000302291	ensembl	human	known	74_37	silent	SNP	1.000	T
AC026781.1	0	genome.wustl.edu	37	5	92053196	92053197	+	RNA	INS	-	-	ATAC	rs2021049|rs373902040	byFrequency	TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr5:92053196_92053197insATAC	ENST00000408883.1	-	0	23_24																											tatatatatatacacagacaca	0.317																																																	0								ENSG00000221810																																			AC026781.1			0				Clone_based_ensembl_gene																													5.37:g.92053196_92053197insATAC		Somatic	0	19	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	15	16.67		RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000408883.1	37	NULL		5																																																																																			-	-		0.317	AC026781.1-201	NOVEL	basic	miRNA	ENSG00000221810	miRNA		-				92053197	-1	no_errors	ENST00000408883	ensembl	human	novel	74_37	rna	INS	0.000:0.001	ATAC
TES	26136	genome.wustl.edu	37	7	115897455	115897455	+	Missense_Mutation	SNP	C	C	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr7:115897455C>A	ENST00000358204.4	+	7	1400	c.1185C>A	c.(1183-1185)agC>agA	p.S395R	AC002066.1_ENST00000446355.2_RNA|TES_ENST00000393481.2_Missense_Mutation_p.S386R|TES_ENST00000537767.1_Missense_Mutation_p.S153R|AC073130.3_ENST00000444244.1_RNA	NM_015641.3	NP_056456.1	Q9UGI8	TES_HUMAN	testis derived transcript (3 LIM domains)	395	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|protein complex (GO:0043234)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(4)|lung(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	12	Lung NSC(10;0.0137)|all_lung(10;0.0148)	Breast(660;0.0602)	STAD - Stomach adenocarcinoma(10;0.00878)			CTTGCTGCAGCAAATGCCTCA	0.498																																																	0								ENSG00000135269						114.0	97.0	103.0					7																	115897455		2203	4300	6503	TES	SO:0001583	missense	0			-	HGNC	AJ250865	CCDS5763.1, CCDS5764.1	7q31.2	2004-04-20			ENSG00000135269	ENSG00000135269			14620	protein-coding gene	gene with protein product		606085				10950921	Standard	NM_015641		Approved	DKFZP586B2022, TESS-2, TESTIN	uc003vho.3	Q9UGI8	OTTHUMG00000023092	ENST00000358204.4:c.1185C>A	7.37:g.115897455C>A	ENSP00000350937:p.Ser395Arg	Somatic	0	32	0.00		0.4003313805339589	265	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	19	13.64	A4D0U6|Q9GZQ1|Q9HAJ9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_PET_domain,pfam_Znf_LIM,smart_Znf_LIM,pfscan_Znf_LIM	p.S395R	ENST00000358204.4	37	c.1185	CCDS5763.1	7	.	.	.	.	.	.	.	.	.	.	C	19.74	3.883712	0.72410	.	.	ENSG00000135269	ENST00000358204;ENST00000537767;ENST00000257721;ENST00000393481	T;D;D	0.87334	0.19;-2.24;-2.24	5.64	5.64	0.86602	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	T	0.80053	0.4553	N	0.20530	0.585	0.80722	D	1	B	0.27679	0.185	B	0.23150	0.044	T	0.74297	-0.3711	10	0.25751	T	0.34	-17.831	20.0769	0.97748	0.0:1.0:0.0:0.0	.	395	Q9UGI8	TES_HUMAN	R	395;153;395;386	ENSP00000350937:S395R;ENSP00000441607:S153R;ENSP00000377121:S386R	ENSP00000257721:S395R	S	+	3	2	TES	115684691	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.030000	0.70903	2.820000	0.97059	0.650000	0.86243	AGC	-	pfam_Znf_LIM,smart_Znf_LIM		0.498	TES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TES	protein_coding	OTTHUMT00000059413.2	C	NM_015641	-		115897455	+1	no_errors	ENST00000358204	ensembl	human	known	74_37	missense	SNP	1.000	A
PTPRU	10076	genome.wustl.edu	37	1	29644393	29644393	+	Missense_Mutation	SNP	A	A	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr1:29644393A>T	ENST00000345512.3	+	26	3806	c.3677A>T	c.(3676-3678)gAt>gTt	p.D1226V	PTPRU_ENST00000428026.2_Missense_Mutation_p.D1213V|PTPRU_ENST00000356870.3_Missense_Mutation_p.D1222V|PTPRU_ENST00000460170.2_Missense_Mutation_p.D1222V|PTPRU_ENST00000323874.8_Missense_Mutation_p.D1222V|PTPRU_ENST00000373779.3_Missense_Mutation_p.D1216V	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	1226	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		ATCTCCACTGATGGGGACTCC	0.627																																																	0								ENSG00000060656						79.0	69.0	72.0					1																	29644393		2203	4300	6503	PTPRU	SO:0001583	missense	0			-	HGNC	U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9683	protein-coding gene	gene with protein product	"""pi R-PTP-Psi"""	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.3677A>T	1.37:g.29644393A>T	ENSP00000334941:p.Asp1226Val	Somatic	0	50	0.00		0.4003313805339589	26	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	73	9.88	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Tyr_Pase_rcpt/non-rcpt,pfam_MAM_dom,pfam_Fibronectin_type3,superfamily_ConA-like_lec_gl_sf,superfamily_Fibronectin_type3,smart_MAM_dom,smart_Fibronectin_type3,smart_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_cat,pfscan_Fibronectin_type3,pfscan_MAM_dom,pfscan_Tyr/Dual-sp_Pase,pfscan_Tyr_Pase_rcpt/non-rcpt,prints_Tyr_Pase_rcpt/non-rcpt,prints_MAM_dom	p.D1226V	ENST00000345512.3	37	c.3677	CCDS334.1	1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.569925	0.86542	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	D;D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75;-1.75	4.89	4.89	0.63831	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.060491	0.64402	D	0.000004	D	0.90435	0.7005	M	0.88031	2.925	0.80722	D	1	D;D;D;D;D	0.64830	0.993;0.993;0.993;0.994;0.994	P;P;P;P;P	0.58077	0.742;0.742;0.742;0.832;0.832	D	0.91872	0.5508	9	.	.	.	.	14.1517	0.65389	1.0:0.0:0.0:0.0	.	1213;1222;1216;1222;1226	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	V	1226;1216;1222;1222;1213;1222	ENSP00000334941:D1226V;ENSP00000362884:D1216V;ENSP00000349333:D1222V;ENSP00000314987:D1222V;ENSP00000392332:D1213V;ENSP00000432906:D1222V	.	D	+	2	0	PTPRU	29516980	1.000000	0.71417	0.720000	0.30636	0.901000	0.52897	9.131000	0.94446	2.177000	0.69029	0.533000	0.62120	GAT	-	pfam_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_rcpt/non-rcpt,pfscan_Tyr_Pase_rcpt/non-rcpt		0.627	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	PTPRU	protein_coding	OTTHUMT00000010447.1	A		-		29644393	+1	no_errors	ENST00000345512	ensembl	human	known	74_37	missense	SNP	0.972	T
UBN2	254048	genome.wustl.edu	37	7	138968377	138968377	+	Missense_Mutation	SNP	C	C	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr7:138968377C>A	ENST00000473989.3	+	15	2726	c.2726C>A	c.(2725-2727)tCt>tAt	p.S909Y	UBN2_ENST00000288561.8_Missense_Mutation_p.S826Y	NM_173569.3	NP_775840.3	Q6ZU65	UBN2_HUMAN	ubinuclein 2	909	Ser-rich.					extracellular space (GO:0005615)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	42						GCTGCCTCTTCTCATGCTCTG	0.488																																																	0								ENSG00000157741						79.0	78.0	78.0					7																	138968377		2000	4177	6177	UBN2	SO:0001583	missense	0			-	HGNC	AK098644	CCDS43655.1, CCDS43655.2	7q34	2008-12-08			ENSG00000157741	ENSG00000157741			21931	protein-coding gene	gene with protein product		613841				19029251	Standard	NM_173569		Approved	FLJ25778, KIAA2030	uc011kqr.2	Q6ZU65	OTTHUMG00000157623	ENST00000473989.3:c.2726C>A	7.37:g.138968377C>A	ENSP00000418648:p.Ser909Tyr	Somatic	0	45	0.00		0.4003313805339589	6	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	37	9.76	A4D1S2|Q2YDY4|Q6P1K0|Q86XN9|Q8N7D1	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.S909Y	ENST00000473989.3	37	c.2726	CCDS43655.2	7	.	.	.	.	.	.	.	.	.	.	C	17.03	3.284339	0.59867	.	.	ENSG00000157741	ENST00000473989;ENST00000288561	T;T	0.35236	1.32;1.39	5.62	4.74	0.60224	.	0.200144	0.38381	N	0.001711	T	0.47284	0.1437	L	0.34521	1.04	0.44447	D	0.997376	D	0.67145	0.996	D	0.74023	0.982	T	0.33752	-0.9856	10	0.27785	T	0.31	-12.1646	15.1234	0.72463	0.0:0.9317:0.0:0.0683	.	909	Q6ZU65	UBN2_HUMAN	Y	909;826	ENSP00000418648:S909Y;ENSP00000288561:S826Y	ENSP00000288561:S826Y	S	+	2	0	UBN2	138618917	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.495000	0.66912	1.517000	0.48917	0.467000	0.42956	TCT	-	NULL		0.488	UBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UBN2	protein_coding	OTTHUMT00000349272.3	C	NM_173569	-		138968377	+1	no_errors	ENST00000473989	ensembl	human	known	74_37	missense	SNP	1.000	A
NDST4	64579	genome.wustl.edu	37	4	115749050	115749050	+	Silent	SNP	C	C	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr4:115749050C>A	ENST00000264363.2	-	14	3219	c.2541G>T	c.(2539-2541)gtG>gtT	p.V847V		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	847	Heparan sulfate N-sulfotransferase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		TGGATAGTTCCACATTATGAT	0.428																																																	0								ENSG00000138653						113.0	108.0	110.0					4																	115749050		2203	4300	6503	NDST4	SO:0001819	synonymous_variant	0			-	HGNC	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"""Sulfotransferases, membrane-bound"""	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.2541G>T	4.37:g.115749050C>A		Somatic	0	44	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	31	11.43	Q2KHM8	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Heparan_SO4_deacetylase,pfam_Sulfotransferase_dom,superfamily_P-loop_NTPase	p.V847	ENST00000264363.2	37	c.2541	CCDS3706.1	4																																																																																			-	superfamily_P-loop_NTPase		0.428	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NDST4	protein_coding	OTTHUMT00000256427.1	C	NM_022569	-		115749050	-1	no_errors	ENST00000264363	ensembl	human	known	74_37	silent	SNP	1.000	A
USP36	57602	genome.wustl.edu	37	17	76798549	76798554	+	In_Frame_Del	DEL	TTTTTC	TTTTTC	-	rs200324254|rs71964596		TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	TTTTTC	TTTTTC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr17:76798549_76798554delTTTTTC	ENST00000542802.3	-	17	3317_3322	c.2874_2879delGAAAAA	c.(2872-2880)aagaaaaaa>aaa	p.958_960KKK>K	USP36_ENST00000312010.6_In_Frame_Del_p.958_960KKK>K|USP36_ENST00000449938.2_In_Frame_Del_p.563_565KKK>K			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	956					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)	p.K959_K960delKK(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			CTGCTTTCTTTTTTTCTTTTTCTTTT	0.534														1638	0.327077	0.0454	0.4092	5008	,	,		13018	0.4107		0.5129	False		,,,				2504	0.3722																1	Deletion - In frame(1)	ovary(1)						ENSG00000055483			526,3738		42,442,1648						-4.5	0.0		dbSNP_130	46	4276,3978		1111,2054,962	no	coding	USP36	NM_025090.3		1153,2496,2610	A1A1,A1R,RR		48.1948,12.3358,38.3608				4802,7716				USP36	SO:0001651	inframe_deletion	0				HGNC	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"""Ubiquitin-specific peptidases"""	20062	protein-coding gene	gene with protein product		612543	"""ubiquitin specific protease 36"""			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.2874_2879delGAAAAA	17.37:g.76798555_76798560delTTTTTC	ENSP00000441214:p.Lys958_Lys959del	Somatic	NA	NA	NA		0.4003313805339589	34	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Peptidase_C19/C67,pfscan_Peptidase_C19/C67	p.KK959in_frame_del	ENST00000542802.3	37	c.2879_2874	CCDS32755.1	17																																																																																			-	NULL		0.534	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	USP36	protein_coding	OTTHUMT00000437472.3	TTTTTC	NM_025090			76798554	-1	no_errors	ENST00000312010	ensembl	human	known	74_37	in_frame_del	DEL	0.178:0.173:0.043:0.038:0.100:0.107	-
TTN	7273	genome.wustl.edu	37	2	179539093	179539093	+	Silent	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr2:179539093G>T	ENST00000591111.1	-	147	33758	c.33534C>A	c.(33532-33534)atC>atA	p.I11178I	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.I11552I|TTN_ENST00000342992.6_Silent_p.I10251I|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	11178	Glu-rich.|Pro-rich.				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)			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)			GTTCTTCTGGGATTTCTTCTT	0.338																																																	0								ENSG00000155657						99.0	87.0	91.0					2																	179539093		1814	4080	5894	TTN	SO:0001819	synonymous_variant	0			-	HGNC	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.33534C>A	2.37:g.179539093G>T		Somatic	0	77	0.00		0.4003313805339589	42	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	53	8.62	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	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Ig_I-set,pfam_Fibronectin_type3,pfam_Immunoglobulin,pfam_Ig_V-set,pfam_Titin_Z,pfam_PPAK_motif,pfam_Prot_kinase_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_dom,pfscan_Ig-like_dom	p.I10251	ENST00000591111.1	37	c.30753		2																																																																																			-	superfamily_Calpain_domain_III,superfamily_RNaseH-like_dom		0.338	TTN-019	PUTATIVE	basic	protein_coding	TTN	protein_coding	OTTHUMT00000460310.1	G	NM_133378	-		179539093	-1	no_errors	ENST00000342992	ensembl	human	known	74_37	silent	SNP	0.999	T
PRPF3	9129	genome.wustl.edu	37	1	150315720	150315728	+	Intron	DEL	AAAAAATAT	AAAAAATAT	-	rs374394798|rs587654594|rs200239014|rs56047090|rs140732761|rs149908445|rs58514816|rs56860451|rs66790680	byFrequency	TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	AAAAAATAT	AAAAAATAT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr1:150315720_150315728delAAAAAATAT	ENST00000324862.6	+	10	1447				PRPF3_ENST00000543398.1_Intron|PRPF3_ENST00000467329.1_Intron|PRPF3_ENST00000414970.2_Intron	NM_004698.2	NP_004689.1	O43395	PRPF3_HUMAN	pre-mRNA processing factor 3						mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 x U5 tri-snRNP complex (GO:0046540)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)		agagaaaaaaaaaaaaTATATATATATAT	0.407																																					Ovarian(168;1070 2670 5178 20729)												0								ENSG00000117360																																			PRPF3	SO:0001627	intron_variant	0				HGNC	AF001947	CCDS951.1	1q21.1	2013-07-16	2013-06-10		ENSG00000117360	ENSG00000117360			17348	protein-coding gene	gene with protein product		607301	"""retinitis pigmentosa 18 (autosomal dominant)"", ""PRP3 pre-mRNA processing factor 3 homolog (yeast)"", ""PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae)"""	RP18			Standard	NM_004698		Approved	Prp3, hPrp3, SNRNP90	uc001eum.4	O43395	OTTHUMG00000012807	ENST00000324862.6:c.1283-57AAAAAATAT>-	1.37:g.150315720_150315728delAAAAAATAT		Somatic	NA	NA	NA		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	B4DSY9|O43446|Q5VT54	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000324862.6	37	NULL	CCDS951.1	1																																																																																			-	-		0.407	PRPF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRPF3	protein_coding	OTTHUMT00000035836.1	AAAAAATAT	NM_004698			150315728	+1	no_errors	ENST00000493553	ensembl	human	known	74_37	rna	DEL	0.001:0.001:0.000:0.001:0.000:0.001:0.001:0.002:0.004	-
RNF220	55182	genome.wustl.edu	37	1	45097823	45097823	+	Intron	SNP	G	G	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr1:45097823G>A	ENST00000355387.2	+	6	1356				RNF220_ENST00000443020.2_Intron|RNF220_ENST00000361799.2_Intron|RNF220_ENST00000372247.2_Intron			Q5VTB9	RN220_HUMAN	ring finger protein 220						protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(1)|large_intestine(3)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	29						AGCGCCCGGCGGCTATGCCGA	0.756																																																	0								ENSG00000187147																																			RNF220	SO:0001627	intron_variant	0			-	HGNC	AK056424	CCDS510.1	1p34.1	2008-06-13	2008-06-13	2008-06-13	ENSG00000187147	ENSG00000187147		"""RING-type (C3HC4) zinc fingers"""	25552	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 164"""	C1orf164		11042152	Standard	NM_018150		Approved	FLJ10597	uc001clv.1	Q5VTB9	OTTHUMG00000007697	ENST00000355387.2:c.907-192G>A	1.37:g.45097823G>A		Somatic	0	127	0.00		0.4003313805339589	97	17.09	20	WXS	Illumina HiSeq 2500	Phase_IV	tier1	21	217	8.79	B3KPJ3|B4DLZ9|E9PCS1|Q4KMX2|Q9NVP6	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000355387.2	37	NULL	CCDS510.1	1																																																																																			-	-		0.756	RNF220-001	KNOWN	basic|CCDS	protein_coding	RNF220	protein_coding	OTTHUMT00000020683.4	G	NM_018150	-		45097823	+1	no_errors	ENST00000471494	ensembl	human	known	74_37	rna	SNP	1.000	A
DGKH	160851	genome.wustl.edu	37	13	42793907	42793907	+	Missense_Mutation	SNP	A	A	C			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr13:42793907A>C	ENST00000337343.4	+	28	3440	c.3419A>C	c.(3418-3420)aAg>aCg	p.K1140T	DGKH_ENST00000261491.5_Missense_Mutation_p.K1140T|DGKH_ENST00000538674.1_Missense_Mutation_p.K895T|DGKH_ENST00000379274.2_Missense_Mutation_p.K1004T|DGKH_ENST00000536612.1_Missense_Mutation_p.K1004T|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000540693.1_Missense_Mutation_p.K1140T	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	1140					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		AAGGTTCAGAAGCAGAAGACA	0.413																																																	0								ENSG00000102780						62.0	53.0	56.0					13																	42793907		2203	4300	6503	DGKH	SO:0001583	missense	0			-	HGNC	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.3419A>C	13.37:g.42793907A>C	ENSP00000337572:p.Lys1140Thr	Somatic	0	37	0.00		0.4003313805339589	3	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	40	11.11	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Diacylglycerol_kin_accessory,pfam_Diacylglycerol_kinase_cat_dom,pfam_Pleckstrin_homology,pfam_SAM_2,pfam_Prot_Kinase_C-like_PE/DAG-bd,pfam_SAM_type1,superfamily_SAM/pointed,smart_Pleckstrin_homology,smart_Prot_Kinase_C-like_PE/DAG-bd,smart_Diacylglycerol_kinase_cat_dom,smart_Diacylglycerol_kin_accessory,smart_SAM,pfscan_Pleckstrin_homology,pfscan_SAM,pfscan_Prot_Kinase_C-like_PE/DAG-bd	p.K1140T	ENST00000337343.4	37	c.3419	CCDS9381.1	13	.	.	.	.	.	.	.	.	.	.	A	22.8	4.331860	0.81801	.	.	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612;ENST00000538674	D;T;D;T;T;T	0.83837	-1.77;-1.31;-1.77;-1.46;-1.47;1.46	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.90075	0.6900	M	0.71581	2.175	0.58432	D	0.999992	D;P;D;B	0.76494	0.998;0.57;0.999;0.255	D;B;D;B	0.71414	0.957;0.295;0.973;0.067	D	0.91144	0.4948	10	0.72032	D	0.01	.	15.8028	0.78468	1.0:0.0:0.0:0.0	.	895;1004;1140;1140	F5GYP2;Q86XP1-3;Q86XP1-2;Q86XP1	.;.;.;DGKH_HUMAN	T	1140;1140;1140;1004;1004;895	ENSP00000440823:K1140T;ENSP00000337572:K1140T;ENSP00000261491:K1140T;ENSP00000368576:K1004T;ENSP00000445114:K1004T;ENSP00000441308:K895T	ENSP00000261491:K1140T	K	+	2	0	DGKH	41691907	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.549000	0.73900	2.183000	0.69458	0.533000	0.62120	AAG	-	NULL		0.413	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	DGKH	protein_coding	OTTHUMT00000044699.2	A	NM_178009	-		42793907	+1	no_errors	ENST00000337343	ensembl	human	known	74_37	missense	SNP	1.000	C
LAMA2	3908	genome.wustl.edu	37	6	129637283	129637283	+	Missense_Mutation	SNP	A	A	G			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr6:129637283A>G	ENST00000421865.2	+	27	4074	c.4025A>G	c.(4024-4026)aAa>aGa	p.K1342R		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1342	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		ATTCTTATCAAAGCTACTTAT	0.343																																																	0								ENSG00000196569						63.0	70.0	68.0					6																	129637283		2203	4298	6501	LAMA2	SO:0001583	missense	0			-	HGNC	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.4025A>G	6.37:g.129637283A>G	ENSP00000400365:p.Lys1342Arg	Somatic	0	54	0.00		0.4003313805339589	15	16.67	3	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	65	9.72	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Laminin_G,pfam_EGF_laminin,pfam_Laminin_N,pfam_Laminin_I,pfam_Laminin_B_type_IV,pfam_Laminin_II,superfamily_ConA-like_lec_gl_sf,superfamily_Galactose-bd-like,superfamily_t-SNARE,smart_Laminin_N,smart_EGF_laminin,smart_EG-like_dom,smart_Laminin_B_subgr,smart_Laminin_G,pfscan_Laminin_B_type_IV,pfscan_EGF_laminin,pfscan_Laminin_G,pfscan_Laminin_N	p.K1342R	ENST00000421865.2	37	c.4025	CCDS5138.1	6	.	.	.	.	.	.	.	.	.	.	A	21.0	4.084463	0.76642	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.32023	1.47	5.54	5.54	0.83059	Laminin B type IV (2);Laminin B, subgroup (1);	0.051277	0.85682	D	0.000000	T	0.22627	0.0546	L	0.28608	0.87	0.49213	D	0.999763	P;P	0.52692	0.955;0.955	P;P	0.53224	0.721;0.721	T	0.01945	-1.1242	10	0.22706	T	0.39	.	15.9796	0.80097	1.0:0.0:0.0:0.0	.	1342;1342	A6NF00;P24043	.;LAMA2_HUMAN	R	1342	ENSP00000400365:K1342R	ENSP00000346769:K1342R	K	+	2	0	LAMA2	129678976	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.629000	0.67798	2.225000	0.72522	0.528000	0.53228	AAA	-	pfam_Laminin_B_type_IV,smart_Laminin_B_subgr,pfscan_Laminin_B_type_IV		0.343	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LAMA2	protein_coding	OTTHUMT00000042180.1	A		-		129637283	+1	no_errors	ENST00000421865	ensembl	human	known	74_37	missense	SNP	1.000	G
CYP19A1	1588	genome.wustl.edu	37	15	51503060	51503060	+	Frame_Shift_Del	DEL	T	T	-			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr15:51503060delT	ENST00000396402.1	-	10	1610	c.1457delA	c.(1456-1458)aacfs	p.N486fs	CYP19A1_ENST00000260433.2_Frame_Shift_Del_p.N486fs|CYP19A1_ENST00000559878.1_Frame_Shift_Del_p.N486fs|RP11-108K3.1_ENST00000559909.1_lincRNA|CYP19A1_ENST00000396404.4_Frame_Shift_Del_p.N486fs	NM_000103.3	NP_000094.2	P11511	CP19A_HUMAN	cytochrome P450, family 19, subfamily A, polypeptide 1	486					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|prostate gland growth (GO:0060736)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)	aromatase activity (GO:0070330)|electron carrier activity (GO:0009055)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			endometrium(1)|kidney(4)|large_intestine(9)|lung(11)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	33				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Betamethasone(DB00443)|Bifonazole(DB04794)|Buserelin(DB06719)|Carbimazole(DB00389)|Chlorphenesin(DB00856)|Clomifene(DB00882)|Clotrimazole(DB00257)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Dinoprostone(DB00917)|Drostanolone(DB00858)|Econazole(DB01127)|Edetic Acid(DB00974)|Etomidate(DB00292)|Exemestane(DB00990)|Ketoconazole(DB01026)|Letrozole(DB01006)|Levomethadyl Acetate(DB01227)|Levonorgestrel(DB00367)|Mefloquine(DB00358)|Melatonin(DB01065)|Methadone(DB00333)|Methyltestosterone(DB06710)|Miconazole(DB01110)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nicotine(DB00184)|Paclitaxel(DB01229)|Raloxifene(DB00481)|Sulfathiazole(DB06147)|Tamoxifen(DB00675)|Terbinafine(DB00857)|Testolactone(DB00894)|Testosterone(DB00624)|Tioconazole(DB01007)|Trastuzumab(DB00072)	TTCCAGCATGTTTTTAGTCTC	0.458																																					Melanoma(142;1016 1807 39614 48966 51721)												0								ENSG00000137869						251.0	224.0	233.0					15																	51503060		2196	4293	6489	CYP19A1	SO:0001589	frameshift_variant	0				HGNC	D14473	CCDS10139.1	15q21	2009-01-26	2003-02-14	2003-02-28	ENSG00000137869	ENSG00000137869		"""Cytochrome P450s"""	2594	protein-coding gene	gene with protein product		107910	"""cytochrome P450, subfamily XIX (aromatization of androgens)"""	CYP19		8477708	Standard	NM_031226		Approved	ARO, P-450AROM, CPV1, ARO1, CYAR, aromatase	uc001zza.4	P11511	OTTHUMG00000131747	ENST00000396402.1:c.1457delA	15.37:g.51503060delT	ENSP00000379683:p.Asn486fs	Somatic	0	32	0.00		0.4003313805339589	1	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	28	9.68	Q16731|Q3B764|Q58FA0|Q8IYJ7	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Cyt_P450,superfamily_Cyt_P450,prints_Cyt_P450_E_grp-I,prints_Cyt_P450,prints_Cyt_P450_E_grp-IV,prints_Cyt_P450_B	p.N486fs	ENST00000396402.1	37	c.1457	CCDS10139.1	15																																																																																			-	superfamily_Cyt_P450		0.458	CYP19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYP19A1	protein_coding	OTTHUMT00000254669.1	T				51503060	-1	no_errors	ENST00000260433	ensembl	human	known	74_37	frame_shift_del	DEL	0.000	-
CIDEA	1149	genome.wustl.edu	37	18	12254562	12254563	+	Intron	INS	-	-	CCGCGCACACACCCAT	rs71369912	byFrequency	TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr18:12254562_12254563insCCGCGCACACACCCAT	ENST00000320477.9	+	1	103					NM_001279.3	NP_001270.1	O60543	CIDEA_HUMAN	cell death-inducing DFFA-like effector a						apoptotic process (GO:0006915)|cell death (GO:0008219)|lipid metabolic process (GO:0006629)|lipid storage (GO:0019915)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of execution phase of apoptosis (GO:1900118)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of sequestering of triglyceride (GO:0010890)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|response to stilbenoid (GO:0035634)|temperature homeostasis (GO:0001659)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|mitochondrial envelope (GO:0005740)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)	13						GCTCCGCGACCCCGCGCACACA	0.703														1926	0.384585	0.1082	0.3228	5008	,	,		14723	0.6359		0.4672	False		,,,				2504	0.4581																0								ENSG00000176194																																			CIDEA	SO:0001627	intron_variant	0				HGNC	AF041378	CCDS11856.1	18p11.21	2008-08-01			ENSG00000176194	ENSG00000176194			1976	protein-coding gene	gene with protein product		604440				9564035, 18509062	Standard	NM_001279		Approved	CIDE-A	uc002kqt.4	O60543	OTTHUMG00000131691	ENST00000320477.9:c.38+142->CCGCGCACACACCCAT	18.37:g.12254562_12254563insCCGCGCACACACCCAT		Somatic	NA	NA	NA		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	B0YIY7|Q6UPR7	Frame_Shift_Ins	INS	NA	NA	NA	NA	NA	NA	NULL	p.H64fs	ENST00000320477.9	37	c.180_181	CCDS11856.1	18																																																																																			-	NULL		0.703	CIDEA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	CIDEA	protein_coding	OTTHUMT00000254599.2	-	NM_001279			12254563	+1	no_errors	ENST00000522713	ensembl	human	known	74_37	frame_shift_ins	INS	0.077:0.122	CCGCGCACACACCCAT
ZDHHC11	79844	genome.wustl.edu	37	5	711614	711614	+	Intron	SNP	C	C	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr5:711614C>A	ENST00000424784.2	-	14	1931				ZDHHC11B_ENST00000522356.1_5'UTR			Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11							endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			TTCCATTTCCCAGTACTGTGC	0.502																																																	0								ENSG00000206077																																			ZDHHC11B	SO:0001627	intron_variant	0			-	HGNC	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000424784.2:c.1237-615G>T	5.37:g.711614C>A		Somatic	0	20	0.00		0.4003313805339589	2	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	15	16.67	Q6UWR9	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000424784.2	37	NULL	CCDS3857.1	5																																																																																			-	-		0.502	ZDHHC11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	ZDHHC11B	protein_coding		C	NM_024786	-		711614	-1	no_errors	ENST00000522356	ensembl	human	known	74_37	rna	SNP	0.001	A
STAM	8027	genome.wustl.edu	37	10	17738849	17738849	+	Silent	SNP	C	C	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr10:17738849C>A	ENST00000377524.3	+	8	1019	c.804C>A	c.(802-804)ctC>ctA	p.L268L	RP11-390B4.3_ENST00000445235.1_RNA|STAM_ENST00000540523.1_Silent_p.L157L	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	268	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						CTGCAGATCTCACTGCTGAAC	0.358																																																	0								ENSG00000136738						122.0	107.0	112.0					10																	17738849		2203	4300	6503	STAM	SO:0001819	synonymous_variant	0			-	HGNC	U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"""HSE1 homolog (S. cerevisiae)"""	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	ENST00000377524.3:c.804C>A	10.37:g.17738849C>A		Somatic	0	30	0.00		0.4003313805339589	63	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	30	11.43	B0YJ99|D3DRU5|Q8N6D9	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_VHS,pfam_SH3_domain,pfam_SH3_2,pfam_Ubiquitin-int_motif,superfamily_ENTH_VHS,superfamily_SH3_domain,smart_VHS_subgr,smart_SH3_domain,pfscan_SH3_domain,pfscan_Ubiquitin-int_motif,pfscan_VHS,prints_SH3_domain,prints_p67phox	p.L268	ENST00000377524.3	37	c.804	CCDS7122.1	10																																																																																			-	superfamily_SH3_domain,smart_SH3_domain,pfscan_SH3_domain		0.358	STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STAM	protein_coding	OTTHUMT00000047039.1	C	NM_003473	-		17738849	+1	no_errors	ENST00000377524	ensembl	human	known	74_37	silent	SNP	0.971	A
SGTA	6449	genome.wustl.edu	37	19	2757763	2757763	+	Missense_Mutation	SNP	G	G	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr19:2757763G>A	ENST00000221566.2	-	10	916	c.755C>T	c.(754-756)tCg>tTg	p.S252L		NM_003021.3	NP_003012.1	O43765	SGTA_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	252					viral process (GO:0016032)	cytoplasm (GO:0005737)				endometrium(2)|large_intestine(2)|lung(2)|ovary(1)	7		Hepatocellular(1079;0.137)		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)		GTTGCCACCCGAAATCATGCC	0.667																																																	0								ENSG00000104969						84.0	67.0	73.0					19																	2757763		2202	4300	6502	SGTA	SO:0001583	missense	0			-	HGNC	AJ223828	CCDS12094.1	19p13	2013-01-10	2003-11-24	2003-11-26		ENSG00000104969		"""Tetratricopeptide (TTC) repeat domain containing"""	10819	protein-coding gene	gene with protein product		603419	"""small glutamine-rich tetratricopeptide repeat (TPR)-containing"""	SGT		9740675, 12735788	Standard	NM_003021		Approved		uc002lwi.1	O43765		ENST00000221566.2:c.755C>T	19.37:g.2757763G>A	ENSP00000221566:p.Ser252Leu	Somatic	0	113	0.00		0.4003313805339589	329	7.32	26	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	151	8.43	D6W610|Q6FIA9|Q9BTZ9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_TPR_1,pfam_TPR_2,smart_TPR_repeat,pfscan_TPR_repeat,pfscan_TPR-contain_dom	p.S252L	ENST00000221566.2	37	c.755	CCDS12094.1	19	.	.	.	.	.	.	.	.	.	.	G	10.49	1.365421	0.24684	.	.	ENSG00000104969	ENST00000221566	T	0.37235	1.21	4.68	3.63	0.41609	.	0.439728	0.26055	N	0.026613	T	0.32645	0.0836	M	0.72118	2.19	0.58432	D	0.999995	P	0.46512	0.879	B	0.34180	0.177	T	0.26395	-1.0104	10	0.52906	T	0.07	-13.5307	11.172	0.48577	0.0:0.0:0.8153:0.1847	.	252	O43765	SGTA_HUMAN	L	252	ENSP00000221566:S252L	ENSP00000221566:S252L	S	-	2	0	SGTA	2708763	1.000000	0.71417	0.121000	0.21740	0.002000	0.02628	7.190000	0.77755	0.951000	0.37770	-0.181000	0.13052	TCG	-	NULL		0.667	SGTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SGTA	protein_coding	OTTHUMT00000451448.2	G	NM_003021	-		2757763	-1	no_errors	ENST00000221566	ensembl	human	known	74_37	missense	SNP	0.964	A
BPIFB3	359710	genome.wustl.edu	37	20	31652609	31652609	+	Silent	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr20:31652609G>T	ENST00000375494.3	+	8	882	c.882G>T	c.(880-882)ctG>ctT	p.L294L		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	294					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TTGGACTCCTGCAGACCAACG	0.637																																																	0								ENSG00000186190						71.0	60.0	64.0					20																	31652609		2203	4300	6503	BPIFB3	SO:0001819	synonymous_variant	0			-	HGNC	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.882G>T	20.37:g.31652609G>T		Somatic	0	28	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	57	8.06	Q5TDX7	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Lipid-bd_serum_glycop_N,pfam_Lipid-bd_serum_glycop_C,superfamily_Bactericidal_perm-incr_a/b_dom,smart_Lipid-bd_serum_glycop_N,smart_Lipid-bd_serum_glycop_C	p.L294	ENST00000375494.3	37	c.882	CCDS13212.1	20																																																																																			-	pfam_Lipid-bd_serum_glycop_C,superfamily_Bactericidal_perm-incr_a/b_dom,smart_Lipid-bd_serum_glycop_C		0.637	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BPIFB3	protein_coding	OTTHUMT00000078654.2	G	NM_182658	-		31652609	+1	no_errors	ENST00000375494	ensembl	human	known	74_37	silent	SNP	1.000	T
POLE	5426	genome.wustl.edu	37	12	133208932	133208932	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr12:133208932G>T	ENST00000320574.5	-	45	6342	c.6299C>A	c.(6298-6300)cCt>cAt	p.P2100H	POLE_ENST00000434528.3_5'Flank|POLE_ENST00000535270.1_Missense_Mutation_p.P2073H	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	2100					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	CTCCAGGGCAGGGTTATTGAG	0.512								DNA polymerases (catalytic subunits)																																									0								ENSG00000177084						100.0	90.0	93.0					12																	133208932		2203	4300	6503	POLE	SO:0001583	missense	0			-	HGNC		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.6299C>A	12.37:g.133208932G>T	ENSP00000322570:p.Pro2100His	Somatic	0	30	0.00		0.4003313805339589	50	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	39	9.30	Q13533|Q86VH9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_DNA_pol_e_suA_C,pfam_DNA-dir_DNA_pol_B_exonuc,pfam_DNA-dir_DNA_pol_B_multi_dom,pfam_3'-5'_exonuclease_PolB-like,superfamily_RNaseH-like_dom,smart_DNA-dir_DNA_pol_B	p.P2100H	ENST00000320574.5	37	c.6299	CCDS9278.1	12	.	.	.	.	.	.	.	.	.	.	G	31	5.068271	0.93950	.	.	ENSG00000177084	ENST00000434528;ENST00000320574;ENST00000455752;ENST00000320557;ENST00000535270	T;T;T	0.28255	1.62;1.62;1.62	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.64972	0.2647	M	0.89968	3.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.985;0.993	T	0.73490	-0.3966	10	0.87932	D	0	.	18.8911	0.92403	0.0:0.0:1.0:0.0	.	2100;310	Q07864;B3KS74	DPOE1_HUMAN;.	H	310;2100;2111;15;2073	ENSP00000322570:P2100H;ENSP00000406383:P2111H;ENSP00000445753:P2073H	ENSP00000322473:P15H	P	-	2	0	POLE	131719005	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.762000	0.98944	2.453000	0.82957	0.484000	0.47621	CCT	-	NULL		0.512	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POLE	protein_coding	OTTHUMT00000397689.2	G	NM_006231	-		133208932	-1	no_errors	ENST00000320574	ensembl	human	known	74_37	missense	SNP	1.000	T
ITPR1	3708	genome.wustl.edu	37	3	4836803	4836803	+	Missense_Mutation	SNP	C	C	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr3:4836803C>T	ENST00000443694.2	+	50	6818	c.6818C>T	c.(6817-6819)tCg>tTg	p.S2273L	ITPR1_ENST00000456211.2_Missense_Mutation_p.S2225L|ITPR1_ENST00000423119.2_Missense_Mutation_p.S2240L|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.S2273L|ITPR1_ENST00000302640.8_Missense_Mutation_p.S2273L|ITPR1_ENST00000357086.4_Missense_Mutation_p.S2240L			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2288					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	AGCAGCATTTCGTTTAACCTG	0.527																																																	0								ENSG00000150995						126.0	124.0	125.0					3																	4836803		2056	4202	6258	ITPR1	SO:0001583	missense	0			-	HGNC	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.6818C>T	3.37:g.4836803C>T	ENSP00000401671:p.Ser2273Leu	Somatic	0	101	0.00		0.4003313805339589	32	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	11	125	8.09	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ca-rel_channel,pfam_Ins145_P3_rcpt,pfam_MIR_motif,pfam_RIH_assoc-dom,pfam_Ion_trans_dom,superfamily_MIR_motif,smart_MIR_motif,prints_InsP3_rcpt-bd,pfscan_MIR_motif	p.S2273L	ENST00000443694.2	37	c.6818	CCDS54551.1	3	.	.	.	.	.	.	.	.	.	.	C	14.02	2.409777	0.42715	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.91124	-2.79;-2.79;-2.78;-2.78;-2.78;-2.79	5.42	4.55	0.56014	.	0.174700	0.52532	N	0.000074	D	0.85570	0.5727	L	0.35288	1.05	0.80722	D	1	B;P	0.37330	0.006;0.59	B;B	0.39185	0.002;0.293	T	0.82149	-0.0600	10	0.20519	T	0.43	.	13.9817	0.64308	0.0:0.9271:0.0:0.0729	.	2288;2240	Q14643;G5E9P1	ITPR1_HUMAN;.	L	2288;2273;2273;2240;734;2240;2225;2273	ENSP00000306253:S2273L;ENSP00000346595:S2273L;ENSP00000405934:S2240L;ENSP00000349597:S2240L;ENSP00000397885:S2225L;ENSP00000401671:S2273L	ENSP00000306253:S2273L	S	+	2	0	ITPR1	4811803	1.000000	0.71417	0.034000	0.17996	0.706000	0.40770	5.981000	0.70524	1.274000	0.44362	0.561000	0.74099	TCG	-	NULL		0.527	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	ITPR1	protein_coding	OTTHUMT00000337982.3	C	NM_002222	-		4836803	+1	no_errors	ENST00000302640	ensembl	human	known	74_37	missense	SNP	1.000	T
ZC3H18	124245	genome.wustl.edu	37	16	88643648	88643648	+	Silent	SNP	C	C	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr16:88643648C>T	ENST00000301011.5	+	2	317	c.117C>T	c.(115-117)gaC>gaT	p.D39D	ZC3H18_ENST00000452588.2_Silent_p.D39D	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	39						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		AGGATTTGGACGGGGCGGGGG	0.617																																					Ovarian(121;375 2276 20373 38669)												0								ENSG00000158545						28.0	30.0	29.0					16																	88643648		2198	4300	6498	ZC3H18	SO:0001819	synonymous_variant	0			-	HGNC	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"""Zinc fingers, CCCH-type domain containing"""	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.117C>T	16.37:g.88643648C>T		Somatic	0	84	0.00		0.4003313805339589	42	10.42	5	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	113	10.94	Q96DG4|Q96MP7	Silent	SNP	NA	NA	NA	NA	NA	NA	smart_Znf_CCCH	p.D39	ENST00000301011.5	37	c.117	CCDS10967.1	16																																																																																			-	NULL		0.617	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	ZC3H18	protein_coding	OTTHUMT00000269168.1	C	NM_144604	-		88643648	+1	no_errors	ENST00000301011	ensembl	human	known	74_37	silent	SNP	0.063	T
KIAA1731	85459	genome.wustl.edu	37	11	93432279	93432279	+	Frame_Shift_Del	DEL	C	C	-			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr11:93432279delC	ENST00000325212.6	+	15	4363	c.4201delC	c.(4201-4203)ccafs	p.P1401fs	KIAA1731_ENST00000411936.1_Frame_Shift_Del_p.P1401fs|KIAA1731_ENST00000531700.1_Intron|KIAA1731_ENST00000344196.4_5'UTR			Q9C0D2	K1731_HUMAN	KIAA1731	1401						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ACCCCTAGTACCACAGCATTC	0.418																																																	0								ENSG00000166004						30.0	24.0	26.0					11																	93432279		692	1591	2283	KIAA1731	SO:0001589	frameshift_variant	0				HGNC	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.4201delC	11.37:g.93432279delC	ENSP00000316681:p.Pro1401fs	Somatic	0	13	0.00		0.4003313805339589	13	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	17	10.53	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	NULL	p.P1401fs	ENST00000325212.6	37	c.4201	CCDS44708.1	11																																																																																			-	NULL		0.418	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	KIAA1731	protein_coding	OTTHUMT00000394640.1	C	NM_033395			93432279	+1	no_errors	ENST00000411936	ensembl	human	known	74_37	frame_shift_del	DEL	0.000	-
LCN8	138307	genome.wustl.edu	37	9	139649957	139649957	+	Missense_Mutation	SNP	T	T	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr9:139649957T>A	ENST00000371688.3	-	4	533	c.238A>T	c.(238-240)Atc>Ttc	p.I80F	LCN8_ENST00000482893.1_5'UTR	NM_178469.3	NP_848564.2	Q6JVE9	LCN8_HUMAN	lipocalin 8	103					response to hormone (GO:0009725)|transport (GO:0006810)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)	10	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;5.56e-06)|Epithelial(140;8.32e-05)		AGCACGTGGATCTCTCTGTGG	0.617																																																	0								ENSG00000204001						56.0	40.0	45.0					9																	139649957		2202	4299	6501	LCN8	SO:0001583	missense	0			-	HGNC	AK124003	CCDS35183.1	9q34.3	2011-10-24	2005-01-11		ENSG00000204001	ENSG00000204001		"""Lipocalins"""	27038	protein-coding gene	gene with protein product		612902	"""chromosome 9 open reading frame 137"", ""lipocalin 5"""	LCN5			Standard	XM_005266058		Approved		uc004cjb.1	Q6JVE9	OTTHUMG00000020942	ENST00000371688.3:c.238A>T	9.37:g.139649957T>A	ENSP00000360753:p.Ile80Phe	Somatic	0	112	0.00		0.4003313805339589	8	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	18	175	9.33	A1L4A8|A6NMN9|Q5T5R4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Lipocln_cytosolic_FA-bd_dom,superfamily_Calycin-like	p.I80F	ENST00000371688.3	37	c.238	CCDS35183.1	9	.	.	.	.	.	.	.	.	.	.	T	15.89	2.967014	0.53507	.	.	ENSG00000204001	ENST00000371688	T	0.07908	3.15	3.62	2.42	0.29668	.	.	.	.	.	T	0.07954	0.0199	L	0.60455	1.87	0.33944	D	0.643614	P	0.43701	0.815	B	0.37304	0.246	T	0.30966	-0.9960	9	0.27082	T	0.32	.	6.8845	0.24191	0.0:0.0:0.2375:0.7625	.	80	Q6JVE9-2	.	F	80	ENSP00000360753:I80F	ENSP00000360753:I80F	I	-	1	0	LCN8	138769778	0.187000	0.23238	0.989000	0.46669	0.901000	0.52897	0.205000	0.17356	0.715000	0.32103	0.402000	0.26972	ATC	-	pfam_Lipocln_cytosolic_FA-bd_dom,superfamily_Calycin-like		0.617	LCN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LCN8	protein_coding	OTTHUMT00000055109.1	T	NM_178469	-		139649957	-1	no_errors	ENST00000371688	ensembl	human	known	74_37	missense	SNP	0.991	A
THADA	63892	genome.wustl.edu	37	2	43458367	43458367	+	Missense_Mutation	SNP	C	C	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr2:43458367C>T	ENST00000405006.4	-	38	5933	c.5582G>A	c.(5581-5583)cGt>cAt	p.R1861H	THADA_ENST00000415080.2_Missense_Mutation_p.R1542H|THADA_ENST00000405975.2_Missense_Mutation_p.R1861H|THADA_ENST00000330266.7_Intron|AC010883.5_ENST00000423354.1_RNA	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1861										breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				GCTTGGGGGACGCCAGCCGGA	0.527																																																	0								ENSG00000115970						38.0	40.0	40.0					2																	43458367		1949	4143	6092	THADA	SO:0001583	missense	0			-	HGNC	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.5582G>A	2.37:g.43458367C>T	ENSP00000385995:p.Arg1861His	Somatic	0	56	0.00		0.4003313805339589	117	18.06	26	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	69	10.26	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_DUF2428_death-receptor-like,superfamily_ARM-type_fold	p.R1861H	ENST00000405006.4	37	c.5582	CCDS46268.1	2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.636|6.636	0.485869|0.485869	0.12641|0.12641	.|.	.|.	ENSG00000115970|ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006|ENST00000407351	T;T;T|.	0.11821|.	2.93;2.74;2.93|.	5.08|5.08	-6.53|-6.53	0.01866|0.01866	.|.	1.482320|.	0.03977|.	N|.	0.292682|.	T|T	0.16471|0.16471	0.0396|0.0396	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B;B|.	0.15473|.	0.013;0.001|.	B;B|.	0.08055|.	0.003;0.001|.	T|T	0.27020|0.27020	-1.0086|-1.0086	10|5	0.36615|.	T|.	0.2|.	-37.2225|-37.2225	2.4389|2.4389	0.04490|0.04490	0.1029:0.2513:0.2044:0.4414|0.1029:0.2513:0.2044:0.4414	.|.	1788;1861|.	B6ZDQ0;Q6YHU6|.	.;THADA_HUMAN|.	H|I	1861;1788;1542;1861|1101	ENSP00000386088:R1861H;ENSP00000416048:R1542H;ENSP00000385995:R1861H|.	ENSP00000349464:R1788H|.	R|V	-|-	2|1	0|0	THADA|THADA	43311871|43311871	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	-1.943000|-1.943000	0.01539|0.01539	-0.955000|-0.955000	0.03636|0.03636	-0.150000|-0.150000	0.13652|0.13652	CGT|GTC	-	NULL		0.527	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	THADA	protein_coding	OTTHUMT00000326070.3	C	NM_022065	-		43458367	-1	no_errors	ENST00000405006	ensembl	human	known	74_37	missense	SNP	0.000	T
FGD6	55785	genome.wustl.edu	37	12	95603287	95603287	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr12:95603287G>T	ENST00000343958.4	-	2	1996	c.1773C>A	c.(1771-1773)aaC>aaA	p.N591K	FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000546711.1_Missense_Mutation_p.N591K|FGD6_ENST00000549499.1_Missense_Mutation_p.N591K	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	591					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						AAGGCTCACTGTTTGACGATA	0.438																																																	0								ENSG00000180263						118.0	119.0	119.0					12																	95603287		2203	4300	6503	FGD6	SO:0001583	missense	0			-	HGNC	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.1773C>A	12.37:g.95603287G>T	ENSP00000344446:p.Asn591Lys	Somatic	0	30	0.00		0.4003313805339589	7	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	44	8.33	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_DH-domain,pfam_Pleckstrin_homology,pfam_Znf_FYVE,superfamily_DH-domain,smart_DH-domain,smart_Pleckstrin_homology,smart_Znf_FYVE,pfscan_Pleckstrin_homology,pfscan_Znf_FYVE-rel,pfscan_DH-domain	p.N591K	ENST00000343958.4	37	c.1773	CCDS31878.1	12	.	.	.	.	.	.	.	.	.	.	G	6.130	0.392284	0.11638	.	.	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000549499	T;T;T	0.68181	-0.21;-0.31;-0.23	6.04	2.5	0.30297	.	0.122297	0.36972	N	0.002306	T	0.52158	0.1717	L	0.41236	1.265	0.09310	N	1	B	0.18863	0.031	B	0.13407	0.009	T	0.36601	-0.9741	10	0.28530	T	0.3	-6.8269	8.447	0.32847	0.5855:0.0:0.4145:0.0	.	591	Q6ZV73	FGD6_HUMAN	K	591	ENSP00000344446:N591K;ENSP00000450342:N591K;ENSP00000449005:N591K	ENSP00000344446:N591K	N	-	3	2	FGD6	94127418	0.775000	0.28604	0.073000	0.20177	0.413000	0.31143	1.427000	0.34881	0.558000	0.29135	-0.367000	0.07326	AAC	-	NULL		0.438	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FGD6	protein_coding	OTTHUMT00000407600.1	G	NM_018351	-		95603287	-1	no_errors	ENST00000343958	ensembl	human	known	74_37	missense	SNP	0.001	T
LGALS9C	654346	genome.wustl.edu	37	17	18380164	18380165	+	5'UTR	DEL	GA	GA	-	rs376412531|rs549220784	byFrequency	TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	GA	GA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr17:18380164_18380165delGA	ENST00000328114.6	+	0	77_78				LGALS9C_ENST00000412421.2_5'UTR|LGALS9C_ENST00000578983.1_3'UTR|LGALS9C_ENST00000583322.1_5'UTR|KRT16P4_ENST00000580052.2_RNA|LGALS9C_ENST00000584941.1_5'UTR|LGALS9C_ENST00000581545.1_5'UTR	NM_001040078.2	NP_001035167.2	Q6DKI2	LEG9C_HUMAN	lectin, galactoside-binding, soluble, 9C								carbohydrate binding (GO:0030246)			NS(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)	7						AGAGGCGGTGGAGAGATGGCCT	0.584														221	0.0441294	0.0204	0.0692	5008	,	,		29591	0.0		0.1223	False		,,,				2504	0.0235																0								ENSG00000171916			333,3927		7,319,1804						2.2	0.0		dbSNP_130	55	1892,6306		176,1540,2383	no	utr-5	LGALS9C	NM_001040078.2		183,1859,4187	A1A1,A1R,RR		23.0788,7.8169,17.86				2225,10233				LGALS9C	SO:0001623	5_prime_UTR_variant	0				HGNC		CCDS32587.1	17p11.2	2011-08-04			ENSG00000171916	ENSG00000171916		"""Lectins, galactoside-binding"""	33874	protein-coding gene	gene with protein product							Standard	NM_001040078		Approved		uc002gtw.3	Q6DKI2	OTTHUMG00000059251	ENST00000328114.6:c.-4GA>-	17.37:g.18380168_18380169delGA		Somatic	0	110	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	19	123	13.38	B0AZM7	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000328114.6	37	NULL	CCDS32587.1	17																																																																																			-	-		0.584	LGALS9C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	LGALS9C	protein_coding	OTTHUMT00000131456.2	GA	NM_001040078			18380165	+1	no_errors	ENST00000578983	ensembl	human	known	74_37	rna	DEL	0.000:0.001	-
TMEFF1	8577	genome.wustl.edu	37	9	103271362	103271362	+	Missense_Mutation	SNP	G	G	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr9:103271362G>A	ENST00000374879.4	+	3	814	c.382G>A	c.(382-384)Gct>Act	p.A128T	TMEFF1_ENST00000334943.6_Missense_Mutation_p.A89T|MSANTD3-TMEFF1_ENST00000502978.1_Missense_Mutation_p.C91Y	NM_003692.4	NP_003683.2	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 1	128	Kazal-like 1. {ECO:0000255|PROSITE- ProRule:PRU00798}.				multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(7)|lung(9)|stomach(1)	19		Acute lymphoblastic leukemia(62;0.0452)				CAGAAGGGCTGCTTGTAAGCA	0.358																																																	0								ENSG00000241697						107.0	107.0	107.0					9																	103271362		2203	4300	6503	TMEFF1	SO:0001583	missense	0			-	HGNC	U19878	CCDS6750.1	9q31	2010-05-04			ENSG00000241697	ENSG00000241697			11866	protein-coding gene	gene with protein product	"""tomoregulin-1"", ""cancer/testis antigen family 120, member 1"""	603421		C9orf2		9730596	Standard	NM_003692		Approved	H7365, CT120.1		Q8IYR6	OTTHUMG00000020367	ENST00000374879.4:c.382G>A	9.37:g.103271362G>A	ENSP00000364013:p.Ala128Thr	Somatic	0	41	0.00		0.4003313805339589	7	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	39	9.30	Q13086|Q8N3T8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Kazal_dom,smart_Kazal_dom,pfscan_EG-like_dom	p.A128T	ENST00000374879.4	37	c.382	CCDS6750.1	9	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.4|20.4	3.989218|3.989218	0.74589|0.74589	.|.	.|.	ENSG00000241697|ENSG00000251349	ENST00000334943;ENST00000374879|ENST00000502978	T;T|.	0.04454|.	3.62;3.62|.	5.58|5.58	3.53|3.53	0.40419|0.40419	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);|.	0.210998|.	0.42053|.	D|.	0.000770|.	T|T	0.74906|0.74906	0.3778|0.3778	M|M	0.83223|0.83223	2.63|2.63	0.52501|0.52501	D|D	0.999957|0.999957	D;B|.	0.59357|.	0.985;0.419|.	D;B|.	0.65773|.	0.938;0.201|.	T|T	0.77040|0.77040	-0.2735|-0.2735	10|5	0.72032|.	D|.	0.01|.	-23.6415|-23.6415	12.1429|12.1429	0.54008|0.54008	0.0:0.0:0.6452:0.3548|0.0:0.0:0.6452:0.3548	.|.	128;89|.	Q8IYR6;Q8IYR6-2|.	TEFF1_HUMAN;.|.	T|Y	89;128|91	ENSP00000334447:A89T;ENSP00000364013:A128T|.	ENSP00000334447:A89T|.	A|C	+|+	1|2	0|0	TMEFF1|C9orf30-TMEFF1	102311183|102311183	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	5.310000|5.310000	0.65780|0.65780	1.305000|1.305000	0.44909|0.44909	0.650000|0.650000	0.86243|0.86243	GCT|TGC	-	pfam_Kazal_dom,smart_Kazal_dom		0.358	TMEFF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMEFF1	protein_coding	OTTHUMT00000053418.1	G	NM_003692	-		103271362	+1	no_errors	ENST00000374879	ensembl	human	known	74_37	missense	SNP	1.000	A
CHD9	80205	genome.wustl.edu	37	16	53190179	53190179	+	Missense_Mutation	SNP	C	C	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr16:53190179C>A	ENST00000398510.3	+	1	265	c.178C>A	c.(178-180)Cca>Aca	p.P60T	CHD9_ENST00000564845.1_Missense_Mutation_p.P60T|CHD9_ENST00000566029.1_Missense_Mutation_p.P60T|CHD9_ENST00000447540.1_Missense_Mutation_p.P60T			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	60					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				TCAAGGTACTCCAACACATCA	0.358																																																	0								ENSG00000177200						102.0	95.0	97.0					16																	53190179		1871	4094	5965	CHD9	SO:0001583	missense	0			-	HGNC	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.178C>A	16.37:g.53190179C>A	ENSP00000381522:p.Pro60Thr	Somatic	0	51	0.00		0.4003313805339589	3	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	35	10.26	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_SNF2_N,pfam_BRK_domain,pfam_Chromo_domain,pfam_Helicase_C,pfam_DNA/RNA_helicase_DEAD/DEAH_N,superfamily_P-loop_NTPase,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.P60T	ENST00000398510.3	37	c.178		16	.	.	.	.	.	.	.	.	.	.	C	7.889	0.731897	0.15507	.	.	ENSG00000177200	ENST00000447540;ENST00000398510	T;T	0.62364	0.03;0.03	5.84	2.75	0.32379	.	0.101212	0.43919	D	0.000502	T	0.49983	0.1589	L	0.43152	1.355	0.29478	N	0.856592	B;B;B;B	0.26845	0.013;0.008;0.161;0.013	B;B;B;B	0.23852	0.037;0.016;0.049;0.037	T	0.48375	-0.9041	10	0.52906	T	0.07	-4.0561	8.2478	0.31700	0.0:0.7253:0.1283:0.1465	.	60;60;60;60	Q3L8U1-3;Q3L8U1;Q8NAR9;Q3L8U1-2	.;CHD9_HUMAN;.;.	T	60	ENSP00000396345:P60T;ENSP00000381522:P60T	ENSP00000381522:P60T	P	+	1	0	CHD9	51747680	0.996000	0.38824	0.998000	0.56505	0.863000	0.49368	0.964000	0.29306	0.330000	0.23485	0.650000	0.86243	CCA	-	NULL		0.358	CHD9-020	KNOWN	basic	protein_coding	CHD9	protein_coding	OTTHUMT00000422345.1	C	NM_025134	-		53190179	+1	no_errors	ENST00000398510	ensembl	human	known	74_37	missense	SNP	0.960	A
ELMO2	63916	genome.wustl.edu	37	20	45017815	45017815	+	Silent	SNP	G	G	A			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr20:45017815G>A	ENST00000290246.6	-	7	482	c.288C>T	c.(286-288)aaC>aaT	p.N96N	ELMO2_ENST00000488853.1_5'UTR|ELMO2_ENST00000445496.2_5'UTR|ELMO2_ENST00000439931.2_Silent_p.N96N|ELMO2_ENST00000372176.1_Silent_p.N8N|ELMO2_ENST00000352077.2_Silent_p.N96N|ELMO2_ENST00000396391.1_Silent_p.N96N	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	96					apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				GGGTCTCCATGTTGGATGACT	0.562																																																	0								ENSG00000062598						111.0	96.0	101.0					20																	45017815		2203	4300	6503	ELMO2	SO:0001819	synonymous_variant	0			-	HGNC	AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"""Engulfment and cell motility proteins"""	17233	protein-coding gene	gene with protein product		606421	"""engulfment and cell motility 2 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.288C>T	20.37:g.45017815G>A		Somatic	0	32	0.00		0.4003313805339589	65	1.49	1	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	37	9.76	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_DUF3361,pfam_Engulfment_cell_motility_ELMO,superfamily_ARM-type_fold	p.N96	ENST00000290246.6	37	c.288	CCDS13398.1	20																																																																																			-	superfamily_ARM-type_fold		0.562	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ELMO2	protein_coding	OTTHUMT00000080466.1	G	NM_022086	-		45017815	-1	no_errors	ENST00000439931	ensembl	human	known	74_37	silent	SNP	0.998	A
STOML2	30968	genome.wustl.edu	37	9	35101135	35101135	+	Missense_Mutation	SNP	C	C	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr9:35101135C>T	ENST00000356493.5	-	7	783	c.721G>A	c.(721-723)Gca>Aca	p.A241T	STOML2_ENST00000452248.2_Missense_Mutation_p.A196T|STOML2_ENST00000487490.1_5'Flank|RP11-182N22.8_ENST00000431804.1_RNA	NM_013442.1	NP_038470.1	Q9UJZ1	STML2_HUMAN	stomatin (EPB72)-like 2	241					CD4-positive, alpha-beta T cell activation (GO:0035710)|cellular calcium ion homeostasis (GO:0006874)|interleukin-2 production (GO:0032623)|lipid localization (GO:0010876)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|mitochondrial calcium ion transport (GO:0006851)|mitochondrial protein processing (GO:0034982)|mitochondrion organization (GO:0007005)|positive regulation of cardiolipin metabolic process (GO:1900210)|positive regulation of mitochondrial DNA replication (GO:0090297)|positive regulation of mitochondrial membrane potential (GO:0010918)|protein oligomerization (GO:0051259)|stress-induced mitochondrial fusion (GO:1990046)|T cell receptor signaling pathway (GO:0050852)	cytoskeleton (GO:0005856)|extrinsic component of plasma membrane (GO:0019897)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	cardiolipin binding (GO:1901612)|receptor binding (GO:0005102)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	16			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TCCTGACCTGCTGCCTGATTT	0.557																																																	0								ENSG00000165283						103.0	103.0	103.0					9																	35101135		2203	4300	6503	STOML2	SO:0001583	missense	0			-	HGNC	AF190167	CCDS6577.1, CCDS69588.1, CCDS75830.1	9p13.1	2008-02-05			ENSG00000165283	ENSG00000165283			14559	protein-coding gene	gene with protein product		608292				10713127, 17121834	Standard	NM_001287031		Approved	SLP-2, HSPC108	uc003zwi.3	Q9UJZ1	OTTHUMG00000019851	ENST00000356493.5:c.721G>A	9.37:g.35101135C>T	ENSP00000348886:p.Ala241Thr	Somatic	0	46	0.00		0.4003313805339589	360	8.63	34	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	58	9.38	B4E1K7|D3DRN3|O60376|Q53G29|Q96FY2|Q9P042	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Band_7,smart_Band_7,prints_Stomatin	p.A241T	ENST00000356493.5	37	c.721	CCDS6577.1	9	.	.	.	.	.	.	.	.	.	.	C	11.80	1.747165	0.30955	.	.	ENSG00000165283	ENST00000356493;ENST00000452248	D;D	0.98135	-3.47;-4.74	5.02	5.02	0.67125	.	0.170779	0.52532	D	0.000076	D	0.93396	0.7894	N	0.05487	-0.04	0.50632	D	0.999886	B;B	0.14012	0.005;0.009	B;B	0.22152	0.038;0.038	D	0.89456	0.3733	10	0.23891	T	0.37	.	18.5271	0.90976	0.0:1.0:0.0:0.0	.	196;241	B4E1K7;Q9UJZ1	.;STML2_HUMAN	T	241;196	ENSP00000348886:A241T;ENSP00000395743:A196T	ENSP00000348886:A241T	A	-	1	0	STOML2	35091135	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	3.840000	0.55843	2.623000	0.88846	0.563000	0.77884	GCA	-	NULL		0.557	STOML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STOML2	protein_coding	OTTHUMT00000052273.1	C	NM_013442	-		35101135	-1	no_errors	ENST00000356493	ensembl	human	known	74_37	missense	SNP	0.999	T
LRIG2	9860	genome.wustl.edu	37	1	113667283	113667283	+	3'UTR	DEL	T	T	-			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr1:113667283delT	ENST00000361127.5	+	0	3956				LRIG2_ENST00000492207.1_3'UTR	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2						innervation (GO:0060384)|regulation of platelet-derived growth factor receptor signaling pathway (GO:0010640)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(10)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	31	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		TTCTTGTGAATTTTTTTTTTT	0.363																																																	0								ENSG00000198799																																			LRIG2	SO:0001624	3_prime_UTR_variant	0				HGNC	AB018349	CCDS30808.1	1p13.1	2013-01-11			ENSG00000198799	ENSG00000198799		"""Immunoglobulin superfamily / I-set domain containing"""	20889	protein-coding gene	gene with protein product		608869					Standard	XM_005271369		Approved	KIAA0806	uc001edf.1	O94898	OTTHUMG00000012133	ENST00000361127.5:c.*560T>-	1.37:g.113667283delT		Somatic	0	12	0.00		0.4003313805339589	21	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	20	20.00	Q9NSN2	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000361127.5	37	NULL	CCDS30808.1	1																																																																																			-	-		0.363	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRIG2	protein_coding	OTTHUMT00000033549.2	T	NM_014813			113667283	+1	no_errors	ENST00000466161	ensembl	human	known	74_37	rna	DEL	0.014	-
TRPC3	7222	genome.wustl.edu	37	4	122824166	122824166	+	Silent	SNP	G	G	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chr4:122824166G>T	ENST00000379645.3	-	9	2377	c.2304C>A	c.(2302-2304)tcC>tcA	p.S768S	TRPC3_ENST00000513531.1_Silent_p.S640S|TRPC3_ENST00000264811.5_Silent_p.S695S	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	683	Binds to IP3R3.				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						CATCAAAATAGGATAACCAAA	0.308																																																	0								ENSG00000138741						80.0	80.0	80.0					4																	122824166		2203	4300	6503	TRPC3	SO:0001819	synonymous_variant	0			-	HGNC	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.2304C>A	4.37:g.122824166G>T		Somatic	0	54	0.00		0.4003313805339589	1	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	41	8.89	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Silent	SNP	NA	NA	NA	NA	NA	NA	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.S768	ENST00000379645.3	37	c.2304	CCDS47130.1	4																																																																																			-	tigrfam_TRP_channel		0.308	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TRPC3	protein_coding	OTTHUMT00000364252.1	G	NM_003305	-		122824166	-1	no_errors	ENST00000379645	ensembl	human	known	74_37	silent	SNP	0.819	T
GPR143	4935	genome.wustl.edu	37	X	9728813	9728813	+	Missense_Mutation	SNP	C	C	T			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chrX:9728813C>T	ENST00000467482.1	-	2	450	c.304G>A	c.(304-306)Gtc>Atc	p.V102I	GPR143_ENST00000380929.2_Missense_Mutation_p.V122I			P51810	GP143_HUMAN	G protein-coupled receptor 143	102					calcium-mediated signaling using intracellular calcium source (GO:0035584)|eye pigment biosynthetic process (GO:0006726)|G-protein coupled receptor signaling pathway (GO:0007186)|melanosome localization (GO:0032400)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|neuropeptide signaling pathway (GO:0007218)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of calcium-mediated signaling (GO:0050848)|signal transduction (GO:0007165)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|G-protein coupled receptor activity (GO:0004930)|L-DOPA binding (GO:0072544)|L-DOPA receptor activity (GO:0035643)|tyrosine binding (GO:0072545)			endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Hepatocellular(5;0.000888)				ATATCCGAGACGCTGTCAACA	0.483																																																	0								ENSG00000101850						92.0	67.0	75.0					X																	9728813		2203	4298	6501	GPR143	SO:0001583	missense	0			-	HGNC	Z48804	CCDS14134.1, CCDS14134.2	Xp22.3	2013-09-27	2003-12-01		ENSG00000101850	ENSG00000101850		"""GPCR / Unclassified : 7TM orphan receptors"""	20145	protein-coding gene	gene with protein product	"""ocular albinism 1"""	300808	"""ocular albinism 1 (Nettleship-Falls)"""	OA1		7647783, 10471510	Standard	NM_000273		Approved		uc004cst.2	P51810	OTTHUMG00000021118	ENST00000467482.1:c.304G>A	X.37:g.9728813C>T	ENSP00000417161:p.Val102Ile	Somatic	0	50	0.00		0.4003313805339589	0	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	56	11.11	Q6NTI7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ocular_alb1,pfam_GPCR_2_secretin-like,prints_Ocular_alb1	p.V122I	ENST00000467482.1	37	c.364	CCDS14134.2	X	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.006|0.006	-2.058442|-2.058442	0.00390|0.00390	.|.	.|.	ENSG00000101850|ENSG00000101850	ENST00000447366|ENST00000467482;ENST00000380929;ENST00000431126	.|D;D;D	.|0.99042	.|-5.36;-5.36;-5.36	4.47|4.47	-1.27|-1.27	0.09347|0.09347	.|.	.|0.295033	.|0.36519	.|N	.|0.002557	D|D	0.88647|0.88647	0.6493|0.6493	N|N	0.00436|0.00436	-1.5|-1.5	0.09310|0.09310	N|N	0.999996|0.999996	.|B	.|0.06786	.|0.001	.|B	.|0.01281	.|0.0	D|D	0.87118|0.87118	0.2189|0.2189	5|10	.|0.02654	.|T	.|1	-7.6441|-7.6441	4.8129|4.8129	0.13353|0.13353	0.0:0.2704:0.1495:0.5801|0.0:0.2704:0.1495:0.5801	.|.	.|102	.|P51810	.|GP143_HUMAN	H|I	37|102;122;18	.|ENSP00000417161:V102I;ENSP00000370316:V122I;ENSP00000406138:V18I	.|ENSP00000370316:V122I	R|V	-|-	2|1	0|0	GPR143|GPR143	9688813|9688813	1.000000|1.000000	0.71417|0.71417	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	1.998000|1.998000	0.40796|0.40796	-0.664000|-0.664000	0.05324|0.05324	-1.514000|-1.514000	0.00941|0.00941	CGT|GTC	-	pfam_Ocular_alb1,pfam_GPCR_2_secretin-like		0.483	GPR143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR143	protein_coding	OTTHUMT00000055714.2	C	NM_000273	-		9728813	-1	no_errors	ENST00000380929	ensembl	human	known	74_37	missense	SNP	0.612	T
VMA21	203547	genome.wustl.edu	37	X	150565816	150565816	+	Frame_Shift_Del	DEL	G	G	-			TCGA-K1-A6RT-01A-32D-A33E-09	TCGA-K1-A6RT-10A-01D-A33H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7d8c3144-ea5e-4383-9875-36d81b7fec6f	1fa603b9-e9b3-4f9d-b3fc-688e7b46617d	g.chrX:150565816delG	ENST00000330374.6	+	1	141	c.36delG	c.(34-36)ctgfs	p.L12fs	VMA21_ENST00000477649.1_Intron|VMA21_ENST00000370361.1_Intron	NM_001017980.3	NP_001017980.1			VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	7						TGAACGCACTGCAGCCTCCTG	0.711																																																	0								ENSG00000160131						5.0	4.0	4.0					X																	150565816		1889	3592	5481	VMA21	SO:0001589	frameshift_variant	0				HGNC	AK096835	CCDS35430.1	Xq28	2014-09-17			ENSG00000160131	ENSG00000160131			22082	protein-coding gene	gene with protein product		300913	"""myopathy with excessive autophagy"""	MEAX		2892402, 10757644, 19379691	Standard	NM_001017980		Approved	XMEA	uc004feu.3	Q3ZAQ7	OTTHUMG00000024168	ENST00000330374.6:c.36delG	X.37:g.150565816delG	ENSP00000333255:p.Leu12fs	Somatic	0	11	0.00		0.4003313805339589	80	0.00	0	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	17	10.53		Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_VMA21-like_domain	p.Q13fs	ENST00000330374.6	37	c.36	CCDS35430.1	X																																																																																			-	NULL		0.711	VMA21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VMA21	protein_coding	OTTHUMT00000060876.1	G	NM_001017980			150565816	+1	no_errors	ENST00000330374	ensembl	human	known	74_37	frame_shift_del	DEL	0.999	-
