#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ALDH2	217	genome.wustl.edu	37	12	112229926	112229927	+	Frame_Shift_Ins	INS	-	-	G	rs554937672		TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr12:112229926_112229927insG	ENST00000261733.2	+	8	918_919	c.857_858insG	c.(856-861)ctggggfs	p.LG286fs	ALDH2_ENST00000416293.3_Frame_Shift_Ins_p.LG239fs	NM_000690.3	NP_000681.2	P05091	ALDH2_HUMAN	aldehyde dehydrogenase 2 family (mitochondrial)	286					alcohol metabolic process (GO:0006066)|carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|electron carrier activity (GO:0009055)	p.K289fs*45(2)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	22					Amyl Nitrite(DB01612)|Benzyl alcohol(DB06770)|Disulfiram(DB00822)|Guanidine(DB00536)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)	ACCTTGGAGCTGGGGGGGAAGA	0.574			T	HMGA2	leiomyoma																																	dbGAP		Dom	yes		12	12q24.2	217	aldehyde dehydrogenase 2 family (mitochondrial)		M	2	Insertion - Frameshift(2)	ovary(2)							,	7,4257		0,7,2125					,	5.4	1.0			54	5,8249		0,5,4122	no	frameshift,frameshift	ALDH2	NM_001204889.1,NM_000690.3	,	0,12,6247	A1A1,A1R,RR		0.0606,0.1642,0.0959	,	,		12,12506				-	-	-	SO:0001589	frameshift_variant	0			M26760	CCDS9155.1, CCDS55885.1	12q24.12	2007-12-14				ENSG00000111275	1.2.1.3	"""Aldehyde dehydrogenases"""	404	protein-coding gene	gene with protein product		100650				4015823, 2987944	Standard	NM_000690		Approved		uc001tst.3	P05091	OTTHUMG00000169603	ENST00000261733.2:c.864dupG	12.37:g.112229933_112229933dupG	ENSP00000261733:p.Leu286fs		B4DW54|E7EUE5|Q03639|Q6IB13|Q6IV71	Frame_Shift_Ins	INS	pfam_Aldehyde_DH_dom,superfamily_Ald_DH/histidinol_DH	p.K289fs	ENST00000261733.2	37	c.857_858	CCDS9155.1	12																																																																																			ALDH2	-	pfam_Aldehyde_DH_dom,superfamily_Ald_DH/histidinol_DH	ENSG00000111275		0.574	ALDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALDH2	HGNC	protein_coding	OTTHUMT00000405008.1	34	0.00	0	-	NM_000690		112229926	112229927	+1	no_errors	ENST00000261733	ensembl	human	known	69_37n	frame_shift_ins	35	10.26	4	INS	1.000:0.991	G
AACS	65985	genome.wustl.edu	37	12	125561123	125561123	+	Missense_Mutation	SNP	C	C	G			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr12:125561123C>G	ENST00000316519.6	+	3	530	c.324C>G	c.(322-324)caC>caG	p.H108Q	AACS_ENST00000261686.6_Missense_Mutation_p.H108Q	NM_023928.3	NP_076417.2	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	108					adipose tissue development (GO:0060612)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cellular response to testosterone stimulus (GO:0071394)|fatty acid metabolic process (GO:0006631)|liver development (GO:0001889)|positive regulation of insulin secretion (GO:0032024)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to purine-containing compound (GO:0014074)|response to starvation (GO:0042594)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)	acetoacetate-CoA ligase activity (GO:0030729)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)	p.H108Q(1)		breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|liver(1)|lung(16)|ovary(1)|stomach(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)		TCCTGCGGCACAAAGAGAATG	0.502																																						dbGAP											1	Substitution - Missense(1)	breast(1)											138.0	129.0	132.0					12																	125561123		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK022451	CCDS9263.1	12q24.31	2010-09-29			ENSG00000081760	ENSG00000081760	6.2.1.16	"""Acyl-CoA synthetase family"""	21298	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 1"""	614364				12623130, 17762044	Standard	NM_023928		Approved	FLJ12389, SUR-5, ACSF1	uc001uhc.3	Q86V21	OTTHUMG00000168550	ENST00000316519.6:c.324C>G	12.37:g.125561123C>G	ENSP00000324842:p.His108Gln		Q49AB9|Q49AC3|Q658Q8|Q8IWD2|Q8NEW5|Q9BSJ9|Q9H829|Q9HA19	Missense_Mutation	SNP	pfam_AMP-dep_Synth/Lig,pfam_Acyl-CoA_synth_DUF3448,tigrfam_Acac_CoA_synth	p.H108Q	ENST00000316519.6	37	c.324	CCDS9263.1	12	.	.	.	.	.	.	.	.	.	.	C	9.269	1.045303	0.19748	.	.	ENSG00000081760	ENST00000316519;ENST00000536752;ENST00000261686	T;T;T	0.10192	2.9;2.9;2.9	5.28	3.42	0.39159	Acyl-CoA synthase, domain of unknown function DUF3448 (1);	0.000000	0.85682	D	0.000000	T	0.17916	0.0430	M	0.71296	2.17	0.54753	D	0.999985	P;P	0.49090	0.919;0.833	P;P	0.48677	0.586;0.582	T	0.01386	-1.1368	10	0.41790	T	0.15	.	9.3486	0.38124	0.0:0.7608:0.0:0.2392	.	108;108	Q86V21-2;Q86V21	.;AACS_HUMAN	Q	108	ENSP00000324842:H108Q;ENSP00000442691:H108Q;ENSP00000261686:H108Q	ENSP00000261686:H108Q	H	+	3	2	AACS	124127076	0.594000	0.26849	0.331000	0.25455	0.092000	0.18411	0.394000	0.20834	1.361000	0.45981	0.591000	0.81541	CAC	AACS	-	pfam_Acyl-CoA_synth_DUF3448,tigrfam_Acac_CoA_synth	ENSG00000081760		0.502	AACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AACS	HGNC	protein_coding	OTTHUMT00000400202.1	151	0.00	0	C	NM_023928		125561123	125561123	+1	no_errors	ENST00000316519	ensembl	human	known	69_37n	missense	118	15.71	22	SNP	0.876	G
ARHGEF2	9181	genome.wustl.edu	37	1	155920838	155920838	+	Missense_Mutation	SNP	C	C	G			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr1:155920838C>G	ENST00000361247.4	-	20	2584	c.2485G>C	c.(2485-2487)Gca>Cca	p.A829P	ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.A830P|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.A801P|ARHGEF2_ENST00000313695.7_Missense_Mutation_p.A801P|ARHGEF2_ENST00000462460.2_Missense_Mutation_p.A874P|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.A828P	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	829					actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.A801P(1)		breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					GCTTCGGTTGCCCGTTCTTCA	0.687																																					Melanoma(178;35 2768 6610 28839)	dbGAP											1	Substitution - Missense(1)	breast(1)											9.0	10.0	10.0					1																	155920838		2182	4259	6441	-	-	-	SO:0001583	missense	0			AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	682	protein-coding gene	gene with protein product		607560	"""rho/rac guanine nucleotide exchange factor (GEF) 2"""			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.2485G>C	1.37:g.155920838C>G	ENSP00000354837:p.Ala829Pro		D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	pfam_DH-domain,pfam_Pleckstrin_homology,superfamily_DH-domain,smart_Prot_Kinase_C-like_PE/DAG-bd,smart_DH-domain,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology,pfscan_Prot_Kinase_C-like_PE/DAG-bd,pfscan_DH-domain	p.A830P	ENST00000361247.4	37	c.2488	CCDS53376.1	1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.770030	0.69992	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000313667	T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93	5.12	5.12	0.69794	.	0.000000	0.47852	D	0.000207	T	0.22551	0.0544	N	0.19112	0.55	0.32634	N	0.521588	D;D;D;D	0.67145	0.996;0.989;0.994;0.989	P;P;P;P	0.62382	0.806;0.737;0.865;0.901	T	0.02639	-1.1130	10	0.48119	T	0.1	-22.6821	16.0862	0.81056	0.0:1.0:0.0:0.0	.	873;829;828;830	D3DVA5;Q92974;Q92974-2;Q5VY93	.;ARHG2_HUMAN;.;.	P	801;829;830;801;828	ENSP00000315325:A801P;ENSP00000354837:A829P;ENSP00000357298:A830P;ENSP00000357299:A801P;ENSP00000314787:A828P	ENSP00000314787:A828P	A	-	1	0	ARHGEF2	154187462	0.954000	0.32549	0.988000	0.46212	0.833000	0.47200	3.159000	0.50731	2.660000	0.90430	0.655000	0.94253	GCA	ARHGEF2	-	NULL	ENSG00000116584		0.687	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	ARHGEF2	HGNC	protein_coding	OTTHUMT00000046204.2	8	0.00	0	C	NM_004723		155920838	155920838	-1	no_errors	ENST00000368315	ensembl	human	known	69_37n	missense	18	21.74	5	SNP	0.999	G
ATP10B	23120	genome.wustl.edu	37	5	160047558	160047559	+	Missense_Mutation	DNP	GT	GT	TA			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G|T	G|T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr5:160047558_160047559GT>TA	ENST00000327245.5	-	15	3057_3058	c.2211_2212AC>TA	c.(2209-2214)acACta>acTAta	p.L738I	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	738					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGGGACACTAGTGTGAAGCTGT	0.639																																						dbGAP											0																																										-	-	-	SO:0001583	missense	0			AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"""ATPases / P-type"""	13543	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10B"""			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.2211_2212delinsTA	5.37:g.160047558_160047559delinsTA	ENSP00000313600:p.Leu738Ile		Q9H725	Missense_Mutation|Silent	SNP	pfam_ATPase_P-typ_ATPase-assoc-dom,pfam_Dehalogen-like_hydro,superfamily_HAD-like_dom,superfamily_ATPase_cation_domN,prints_ATPase_P-typ_ion-transptr,tigrfam_ATPase_P-typ_Plipid-transl,tigrfam_ATPase_P-typ_ion-transptr	p.L738I|p.T737	ENST00000327245.5	37	c.2212|c.2211	CCDS43394.1	5																																																																																			ATP10B	-	superfamily_HAD-like_dom,superfamily_ATPase_cation_domN,tigrfam_ATPase_P-typ_Plipid-transl	ENSG00000118322		0.639	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATP10B	HGNC	protein_coding	OTTHUMT00000374127.1	39|40	0.00	0	G|T	NM_025153		160047558|160047559	160047558|160047559	-1	no_errors	ENST00000327245	ensembl	human	known	69_37n	missense|silent	49|50	30.00|29.58	21	SNP	0.910|0.001	T|A
BIRC6	57448	genome.wustl.edu	37	2	32702619	32702619	+	Missense_Mutation	SNP	T	T	A			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr2:32702619T>A	ENST00000421745.2	+	35	7170	c.7036T>A	c.(7036-7038)Tgt>Agt	p.C2346S		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2346					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.C2318S(1)|p.C2346S(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					GGACTTTACATGTCATGCAGA	0.443																																					Pancreas(94;175 1509 16028 18060 45422)	dbGAP											2	Substitution - Missense(2)	breast(2)											137.0	113.0	121.0					2																	32702619		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.7036T>A	2.37:g.32702619T>A	ENSP00000393596:p.Cys2346Ser		Q9ULD1	Missense_Mutation	SNP	pfam_DUF3643,pfam_UBQ-conjugat_E2,pfam_BIR,pfam_UEV_N,superfamily_UBQ-conjugating_enzyme/RWD,superfamily_Galactose-bd-like,superfamily_WD40_repeat_dom,smart_BIR,pfscan_BIR,pfscan_UBQ-conjugat_E2	p.C2346S	ENST00000421745.2	37	c.7036	CCDS33175.2	2	.	.	.	.	.	.	.	.	.	.	T	17.46	3.395612	0.62177	.	.	ENSG00000115760	ENST00000421745	T	0.78126	-1.15	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.81945	0.4930	L	0.34521	1.04	0.80722	D	1	D	0.57899	0.981	D	0.69824	0.966	T	0.80450	-0.1377	10	0.32370	T	0.25	.	16.1611	0.81712	0.0:0.0:0.0:1.0	.	2346	Q9NR09	BIRC6_HUMAN	S	2346	ENSP00000393596:C2346S	ENSP00000393596:C2346S	C	+	1	0	BIRC6	32556123	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.928000	0.87587	2.213000	0.71641	0.477000	0.44152	TGT	BIRC6	-	NULL	ENSG00000115760		0.443	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BIRC6	HGNC	protein_coding	OTTHUMT00000318769.3	179	0.00	0	T	NM_016252		32702619	32702619	+1	no_errors	ENST00000421745	ensembl	human	known	69_37n	missense	135	26.63	49	SNP	1.000	A
C10orf12	26148	genome.wustl.edu	37	10	98744677	98744677	+	Missense_Mutation	SNP	C	C	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr10:98744677C>T	ENST00000286067.2	+	1	3637	c.3530C>T	c.(3529-3531)gCc>gTc	p.A1177V		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	1177								p.A1177V(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		CAGTCTATTGCCTCGGAAACA	0.483																																						dbGAP											1	Substitution - Missense(1)	breast(1)											46.0	54.0	51.0					10																	98744677		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.3530C>T	10.37:g.98744677C>T	ENSP00000286067:p.Ala1177Val		Q9H945|Q9Y457	Missense_Mutation	SNP	NULL	p.A1177V	ENST00000286067.2	37	c.3530	CCDS7452.1	10	.	.	.	.	.	.	.	.	.	.	C	0.823	-0.747839	0.03065	.	.	ENSG00000155640	ENST00000286067	T	0.08458	3.09	5.31	3.42	0.39159	.	0.819155	0.10086	N	0.717857	T	0.06735	0.0172	L	0.27053	0.805	0.09310	N	1	B	0.12630	0.006	B	0.12156	0.007	T	0.37798	-0.9690	10	0.48119	T	0.1	2.3771	6.1094	0.20092	0.0:0.6169:0.1993:0.1838	.	1177	Q8N655	CJ012_HUMAN	V	1177	ENSP00000286067:A1177V	ENSP00000286067:A1177V	A	+	2	0	C10orf12	98734667	0.001000	0.12720	0.216000	0.23742	0.008000	0.06430	0.852000	0.27764	0.598000	0.29829	-0.224000	0.12420	GCC	C10orf12	-	NULL	ENSG00000155640		0.483	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C10orf12	HGNC	protein_coding	OTTHUMT00000049627.1	143	0.00	0	C	NM_015652		98744677	98744677	+1	no_errors	ENST00000286067	ensembl	human	known	69_37n	missense	99	13.04	15	SNP	0.000	T
CACNA1E	777	genome.wustl.edu	37	1	181688962	181688962	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr1:181688962C>T	ENST00000367573.2	+	13	1714	c.1714C>T	c.(1714-1716)Cga>Tga	p.R572*	CACNA1E_ENST00000357570.5_Nonsense_Mutation_p.R523*|CACNA1E_ENST00000358338.5_Nonsense_Mutation_p.R523*|CACNA1E_ENST00000367570.1_Nonsense_Mutation_p.R572*|CACNA1E_ENST00000526775.1_Nonsense_Mutation_p.R572*|CACNA1E_ENST00000367567.4_Nonsense_Mutation_p.R179*|CACNA1E_ENST00000360108.3_Nonsense_Mutation_p.R572*	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	572					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.R572*(2)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CAGTGTCTTGCGAGCCCTCCG	0.438																																						dbGAP											2	Substitution - Nonsense(2)	breast(2)											99.0	86.0	90.0					1																	181688962		1874	4120	5994	-	-	-	SO:0001587	stop_gained	0			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.1714C>T	1.37:g.181688962C>T	ENSP00000356545:p.Arg572*		B1AM12|B1AM13|B1AM14|Q14580|Q14581	Nonsense_Mutation	SNP	pfam_Ion_trans_dom,pfam_VDCC_a1su_IQ,pfam_PKD1_2_channel,pfscan_EF_HAND_2,prints_VDCCAlpha1,prints_VDCC_R_a1su	p.R572*	ENST00000367573.2	37	c.1714	CCDS55664.1	1	.	.	.	.	.	.	.	.	.	.	C	48	14.690059	0.99806	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	.	.	.	5.46	0.943	0.19531	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4088	0.74902	0.68:0.32:0.0:0.0	.	.	.	.	X	572;572;523;523;179;572;572	.	ENSP00000350183:R523X	R	+	1	2	CACNA1E	179955585	0.439000	0.25610	0.988000	0.46212	0.986000	0.74619	0.276000	0.18716	0.175000	0.19841	-0.274000	0.10170	CGA	CACNA1E	-	pfam_Ion_trans_dom,pfam_PKD1_2_channel	ENSG00000198216		0.438	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	CACNA1E	HGNC	protein_coding	OTTHUMT00000090793.2	229	0.00	0	C	NM_000721		181688962	181688962	+1	no_errors	ENST00000367573	ensembl	human	known	69_37n	nonsense	112	47.91	103	SNP	0.998	T
CLCN4	1183	genome.wustl.edu	37	X	10181872	10181872	+	Silent	SNP	C	C	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chrX:10181872C>T	ENST00000380833.4	+	11	2119	c.1728C>T	c.(1726-1728)atC>atT	p.I576I	AC003666.1_ENST00000410201.1_RNA|CLCN4_ENST00000421085.2_Silent_p.I482I|CLCN4_ENST00000380829.1_Silent_p.I545I	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	576					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.I576I(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						AGGCCCACATCCACTTAAATG	0.607																																					Melanoma(74;1050 1296 1576 30544 38374)	dbGAP											1	Substitution - coding silent(1)	breast(1)											123.0	84.0	97.0					X																	10181872		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"""Ion channels / Chloride channels : Voltage-sensitive"""	2022	protein-coding gene	gene with protein product		302910	"""chloride channel 4"""			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.1728C>T	X.37:g.10181872C>T			A1L3U1|B7Z5Z4|Q9UBU1	Silent	SNP	pfam_Cl-channel_volt-gated,pfam_Cysta_beta_synth_core,superfamily_Cl-channel_core,smart_Cysta_beta_synth_core,prints_Cl-channel_volt-gated,prints_Cl_channel-4	p.I576	ENST00000380833.4	37	c.1728	CCDS14137.1	X																																																																																			CLCN4	-	superfamily_Cl-channel_core,prints_Cl-channel_volt-gated	ENSG00000073464		0.607	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CLCN4	HGNC	protein_coding	OTTHUMT00000055730.1	107	0.00	0	C			10181872	10181872	+1	no_errors	ENST00000380833	ensembl	human	known	69_37n	silent	57	25.97	20	SNP	1.000	T
COX4I2	84701	genome.wustl.edu	37	20	30227901	30227901	+	Splice_Site	SNP	G	G	A			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr20:30227901G>A	ENST00000376075.3	+	3	322		c.e3+1		COX4I2_ENST00000490030.1_Splice_Site	NM_032609.2	NP_115998.2	Q96KJ9	COX42_HUMAN	cytochrome c oxidase subunit IV isoform 2 (lung)						cellular respiration (GO:0045333)|generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)	mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)	p.?(1)		breast(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	11	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.01e-05)|all cancers(5;9.46e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00121)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			AAGGTGGCCTGTAAGTGTCAG	0.602																																						dbGAP											1	Unknown(1)	breast(1)											28.0	20.0	23.0					20																	30227901		2203	4299	6502	-	-	-	SO:0001630	splice_region_variant	0			AF257180	CCDS13187.1	20q11.21	2011-07-04	2004-08-11		ENSG00000131055	ENSG00000131055		"""Mitochondrial respiratory chain complex / Complex IV"""	16232	protein-coding gene	gene with protein product	"""cytochrome c oxidase subunit IV-like 2"""	607976	"""cytochrome c oxidase subunit IV isoform 2"""	COX4L2		11311561, 17937768	Standard	NM_032609		Approved	COXIV-2, COX4B, dJ857M17.2, COX4-2	uc002wwj.1	Q96KJ9	OTTHUMG00000032180	ENST00000376075.3:c.247+1G>A	20.37:g.30227901G>A			Q6GTF4|Q9H0Z4	Splice_Site	SNP	-	e2+1	ENST00000376075.3	37	c.247+1	CCDS13187.1	20	.	.	.	.	.	.	.	.	.	.	G	10.63	1.405456	0.25378	.	.	ENSG00000131055	ENST00000376075	.	.	.	4.74	4.74	0.60224	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1003	0.59216	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COX4I2	29691562	1.000000	0.71417	0.994000	0.49952	0.026000	0.11368	7.004000	0.76317	2.452000	0.82932	0.555000	0.69702	.	COX4I2	-	-	ENSG00000131055		0.602	COX4I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COX4I2	HGNC	protein_coding	OTTHUMT00000078548.1	35	0.00	0	G	NM_032609	Intron	30227901	30227901	+1	no_errors	ENST00000376075	ensembl	human	known	69_37n	splice_site	25	28.57	10	SNP	1.000	A
CSMD2	114784	genome.wustl.edu	37	1	34312489	34312489	+	Nonsense_Mutation	SNP	G	G	C			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr1:34312489G>C	ENST00000373381.4	-	6	1205	c.1029C>G	c.(1027-1029)taC>taG	p.Y343*		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	303	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.Y303*(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GCCTACCTTGGTATTGGGCAC	0.612																																						dbGAP											1	Substitution - Nonsense(1)	breast(1)											64.0	58.0	60.0					1																	34312489		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.1029C>G	1.37:g.34312489G>C	ENSP00000362479:p.Tyr343*		B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Nonsense_Mutation	SNP	pfam_CUB,pfam_Sushi_SCR_CCP,superfamily_CUB,superfamily_Complement_control_module,smart_CUB,smart_Sushi_SCR_CCP,pfscan_CUB,pfscan_Sushi_SCR_CCP	p.Y343*	ENST00000373381.4	37	c.1029		1	.	.	.	.	.	.	.	.	.	.	G	39	7.323588	0.98210	.	.	ENSG00000121904	ENST00000373381	.	.	.	4.82	1.91	0.25777	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.5007	0.33156	0.2562:0.0:0.7438:0.0	.	.	.	.	X	343	.	ENSP00000241312:Y303X	Y	-	3	2	CSMD2	34085076	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	1.108000	0.31123	0.194000	0.20326	0.561000	0.74099	TAC	CSMD2	-	pfam_CUB,superfamily_CUB,smart_CUB,pfscan_CUB	ENSG00000121904		0.612	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	CSMD2	HGNC	protein_coding		79	0.00	0	G	NM_052896		34312489	34312489	-1	no_errors	ENST00000373381	ensembl	human	known	69_37n	nonsense	152	12.14	21	SNP	1.000	C
CXCR3	2833	genome.wustl.edu	37	X	70836243	70836243	+	Missense_Mutation	SNP	G	G	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chrX:70836243G>T	ENST00000373693.3	-	2	1146	c.1079C>A	c.(1078-1080)aCc>aAc	p.T360N	CXCR3_ENST00000373691.4_Missense_Mutation_p.T407N	NM_001504.1	NP_001495.1	P49682	CXCR3_HUMAN	chemokine (C-X-C motif) receptor 3	360					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|calcium-mediated signaling (GO:0019722)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|chemokine (C-C motif) ligand 11 production (GO:0071954)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of execution phase of apoptosis (GO:1900118)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP metabolic process (GO:0030816)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of leukocyte migration (GO:0002685)|T cell chemotaxis (GO:0010818)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|chemokine binding (GO:0019956)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)	p.T360N(1)		breast(1)|central_nervous_system(2)|large_intestine(2)|lung(3)|ovary(2)	10	Renal(35;0.156)					GGCCTCTGAGGTCTCAGACCA	0.652																																						dbGAP											1	Substitution - Missense(1)	breast(1)											23.0	22.0	23.0					X																	70836243		2194	4297	6491	-	-	-	SO:0001583	missense	0			U32674	CCDS14416.1, CCDS48135.1	Xq13	2012-08-08	2002-08-22	2002-08-23	ENSG00000186810	ENSG00000186810		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	4540	protein-coding gene	gene with protein product		300574	"""G protein-coupled receptor 9"""	GPR9		8666380, 9064356	Standard	NM_001142797		Approved	CKR-L2, CMKAR3, IP10-R, MigR, CD183	uc011mpx.2	P49682	OTTHUMG00000033326	ENST00000373693.3:c.1079C>A	X.37:g.70836243G>T	ENSP00000362797:p.Thr360Asn		B2R982|O15185|Q7Z710|Q9P2T4|Q9P2T5	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_Chemokine_CXCR3,prints_7TM_GPCR_Rhodpsn,prints_Chemokine_CXCR4,prints_Chemokine_rcpt,prints_ATII_rcpt	p.T407N	ENST00000373693.3	37	c.1220	CCDS14416.1	X	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.56|16.56	3.157190|3.157190	0.57259|0.57259	.|.	.|.	ENSG00000186810|ENSG00000186810	ENST00000373687|ENST00000373691;ENST00000373693	.|T;T	.|0.70282	.|-0.47;-0.45	5.88|5.88	5.02|5.02	0.67125|0.67125	.|.	.|0.402222	.|0.24200	.|N	.|0.040636	T|T	0.72763|0.72763	0.3501|0.3501	L|L	0.58101|0.58101	1.795|1.795	0.36453|0.36453	D|D	0.866184|0.866184	.|D;P	.|0.57571	.|0.98;0.534	.|P;B	.|0.51229	.|0.663;0.203	T|T	0.76438|0.76438	-0.2959|-0.2959	6|10	0.46703|0.36615	T|T	0.11|0.2	.|.	11.5157|11.5157	0.50520|0.50520	0.0882:0.0:0.9118:0.0|0.0882:0.0:0.9118:0.0	.|.	.|407;360	.|P49682-2;P49682	.|.;CXCR3_HUMAN	T|N	248|407;360	.|ENSP00000362795:T407N;ENSP00000362797:T360N	ENSP00000362791:P248T|ENSP00000362795:T407N	P|T	-|-	1|2	0|0	CXCR3|CXCR3	70752968|70752968	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	2.500000|2.500000	0.45381|0.45381	1.236000|1.236000	0.43740|0.43740	0.544000|0.544000	0.68410|0.68410	CCT|ACC	CXCR3	-	prints_Chemokine_CXCR3	ENSG00000186810		0.652	CXCR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	CXCR3	HGNC	protein_coding	OTTHUMT00000144141.1	49	0.00	0	G			70836243	70836243	-1	no_errors	ENST00000373691	ensembl	human	known	69_37n	missense	54	12.90	8	SNP	1.000	T
DOCK10	55619	genome.wustl.edu	37	2	225727415	225727415	+	Missense_Mutation	SNP	C	C	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr2:225727415C>T	ENST00000258390.7	-	14	1718	c.1651G>A	c.(1651-1653)Gga>Aga	p.G551R	DOCK10_ENST00000409592.3_Missense_Mutation_p.G545R	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	551					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.G551R(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		CGGTATTTTCCCAATTTGCTG	0.338																																						dbGAP											1	Substitution - Missense(1)	breast(1)											97.0	96.0	96.0					2																	225727415		1846	4087	5933	-	-	-	SO:0001583	missense	0			AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.1651G>A	2.37:g.225727415C>T	ENSP00000258390:p.Gly551Arg		B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	pfam_DOCK,pfam_DUF3398,pfam_Pleckstrin_homology,superfamily_ARM-type_fold,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.G551R	ENST00000258390.7	37	c.1651	CCDS46528.1	2	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891199	0.91889	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.52057	0.68;0.68	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.75803	0.3899	M	0.90483	3.12	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.81470	-0.0918	10	0.87932	D	0	.	18.9812	0.92756	0.0:1.0:0.0:0.0	.	551;551;545	Q96BY6;Q96BY6-2;B3FL70	DOC10_HUMAN;.;.	R	545;551	ENSP00000386694:G545R;ENSP00000258390:G551R	ENSP00000258390:G551R	G	-	1	0	DOCK10	225435659	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.443000	0.80521	2.559000	0.86315	0.655000	0.94253	GGA	DOCK10	-	NULL	ENSG00000135905		0.338	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DOCK10	HGNC	protein_coding	OTTHUMT00000331246.1	284	0.00	0	C			225727415	225727415	-1	no_errors	ENST00000258390	ensembl	human	known	69_37n	missense	76	20.83	20	SNP	1.000	T
DOCK5	80005	genome.wustl.edu	37	8	25261154	25261154	+	Missense_Mutation	SNP	G	G	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr8:25261154G>T	ENST00000276440.7	+	48	5051	c.5007G>T	c.(5005-5007)agG>agT	p.R1669S		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1669					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.R1669S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		CTCTGCGGAGGTTGTCCATCA	0.522																																					Pancreas(145;34 1887 3271 10937 30165)	dbGAP											1	Substitution - Missense(1)	breast(1)											253.0	209.0	224.0					8																	25261154		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.5007G>T	8.37:g.25261154G>T	ENSP00000276440:p.Arg1669Ser		B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	pfam_DOCK,pfam_SH3_domain,pfam_SH3_2,superfamily_SH3_domain,superfamily_ARM-type_fold,smart_SH3_domain,pfscan_SH3_domain	p.R1669S	ENST00000276440.7	37	c.5007	CCDS6047.1	8	.	.	.	.	.	.	.	.	.	.	G	15.52	2.856514	0.51376	.	.	ENSG00000147459	ENST00000276440	T	0.04049	3.72	5.81	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.06371	0.0164	L	0.44542	1.39	0.46458	D	0.999058	P	0.39376	0.67	P	0.45071	0.468	T	0.46679	-0.9174	10	0.27785	T	0.31	.	5.3098	0.15823	0.6406:0.0:0.3594:0.0	.	1669	Q9H7D0	DOCK5_HUMAN	S	1669	ENSP00000276440:R1669S	ENSP00000276440:R1669S	R	+	3	2	DOCK5	25317071	0.819000	0.29175	0.989000	0.46669	0.707000	0.40811	1.402000	0.34600	1.238000	0.43771	0.655000	0.94253	AGG	DOCK5	-	NULL	ENSG00000147459		0.522	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DOCK5	HGNC	protein_coding	OTTHUMT00000254955.2	135	0.00	0	G	NM_024940		25261154	25261154	+1	no_errors	ENST00000276440	ensembl	human	known	69_37n	missense	63	44.74	51	SNP	0.960	T
DYSF	8291	genome.wustl.edu	37	2	71738993	71738993	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr2:71738993delC	ENST00000258104.3	+	5	676	c.399delC	c.(397-399)ttcfs	p.F133fs	DYSF_ENST00000409366.1_Frame_Shift_Del_p.F134fs|DYSF_ENST00000409651.1_Frame_Shift_Del_p.F134fs|DYSF_ENST00000410020.3_Frame_Shift_Del_p.F134fs|DYSF_ENST00000429174.2_Frame_Shift_Del_p.F133fs|DYSF_ENST00000410041.1_Frame_Shift_Del_p.F134fs|DYSF_ENST00000394120.2_Frame_Shift_Del_p.F134fs|DYSF_ENST00000409762.1_Frame_Shift_Del_p.F133fs|DYSF_ENST00000413539.2_Frame_Shift_Del_p.F133fs|DYSF_ENST00000409744.1_Frame_Shift_Del_p.F134fs|DYSF_ENST00000409582.3_Frame_Shift_Del_p.F133fs	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	133					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						TGCCCCTGTTCCCGCCCCCTA	0.667																																						dbGAP											0													56.0	42.0	47.0					2																	71738993		1980	3797	5777	-	-	-	SO:0001589	frameshift_variant	0			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.399delC	2.37:g.71738993delC	ENSP00000258104:p.Phe133fs		A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Frame_Shift_Del	DEL	pfam_C2_Ca-dep,pfam_Ferlin_B-domain,pfam_FerIin-domain,pfam_Ferlin_A-domain,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_MFS_dom_general_subst_transpt,smart_C2_Ca-dep,smart_Peroxin/Ferlin,pfscan_C2_membr_targeting	p.P134fs	ENST00000258104.3	37	c.399	CCDS1918.1	2																																																																																			DYSF	-	superfamily_C2_Ca/lipid-bd_dom_CaLB	ENSG00000135636		0.667	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	DYSF	HGNC	protein_coding	OTTHUMT00000251970.3	52	0.00	0	C	NM_003494		71738993	71738993	+1	no_errors	ENST00000413539	ensembl	human	known	69_37n	frame_shift_del	29	36.96	17	DEL	0.997	-
DYSF	8291	genome.wustl.edu	37	2	71739000	71739001	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr2:71739000_71739001insA	ENST00000258104.3	+	5	683_684	c.406_407insA	c.(406-408)cctfs	p.P136fs	DYSF_ENST00000409366.1_Frame_Shift_Ins_p.P137fs|DYSF_ENST00000409651.1_Frame_Shift_Ins_p.P137fs|DYSF_ENST00000410020.3_Frame_Shift_Ins_p.P137fs|DYSF_ENST00000429174.2_Frame_Shift_Ins_p.P136fs|DYSF_ENST00000410041.1_Frame_Shift_Ins_p.P137fs|DYSF_ENST00000394120.2_Frame_Shift_Ins_p.P137fs|DYSF_ENST00000409762.1_Frame_Shift_Ins_p.P136fs|DYSF_ENST00000413539.2_Frame_Shift_Ins_p.P136fs|DYSF_ENST00000409744.1_Frame_Shift_Ins_p.P137fs|DYSF_ENST00000409582.3_Frame_Shift_Ins_p.P136fs	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	136					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GTTCCCGCCCCCTACTCCTCTG	0.668																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	Exception_encountered	2.37:g.71739000_71739001insA	ENSP00000258104:p.Pro136fs		A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Frame_Shift_Ins	INS	pfam_C2_Ca-dep,pfam_Ferlin_B-domain,pfam_FerIin-domain,pfam_Ferlin_A-domain,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_MFS_dom_general_subst_transpt,smart_C2_Ca-dep,smart_Peroxin/Ferlin,pfscan_C2_membr_targeting	p.P136fs	ENST00000258104.3	37	c.406_407	CCDS1918.1	2																																																																																			DYSF	-	superfamily_C2_Ca/lipid-bd_dom_CaLB	ENSG00000135636		0.668	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	DYSF	HGNC	protein_coding	OTTHUMT00000251970.3	52	0.00	0	-	NM_003494		71739000	71739001	+1	no_errors	ENST00000413539	ensembl	human	known	69_37n	frame_shift_ins	30	34.78	16	INS	0.001:0.019	A
FAM157B	100132403	genome.wustl.edu	37	9	141107536	141107537	+	lincRNA	INS	-	-	GCA	rs367832601|rs554298933|rs370981092		TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr9:141107536_141107537insGCA	ENST00000446912.2	+	0	19_20							P0CG42	F157B_HUMAN	family with sequence similarity 157, member B																		CGgcagcggcggcagcagcagc	0.545																																						dbGAP											0																																										-	-	-			0					9q34	2013-01-24			ENSG00000233013	ENSG00000233013			34080	other	unknown							Standard	NM_001145249		Approved		uc011mfe.1	P0CG42	OTTHUMG00000021000		9.37:g.141107543_141107545dupGCA				RNA	INS	-	NULL	ENST00000446912.2	37	NULL		9																																																																																			FAM157B	-	-	ENSG00000233013		0.545	FAM157B-001	KNOWN	mRNA_end_NF|basic	lincRNA	FAM157B	HGNC	lincRNA	OTTHUMT00000055378.2	30	0.00	0	-	NM_001145249		141107536	141107537	+1	no_errors	ENST00000446912	ensembl	human	known	69_37n	rna	20	25.93	7	INS	0.033:0.036	GCA
BRINP3	339479	genome.wustl.edu	37	1	190067727	190067727	+	Silent	SNP	A	A	G			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr1:190067727A>G	ENST00000367462.3	-	8	1953	c.1722T>C	c.(1720-1722)aaT>aaC	p.N574N	BRINP3_ENST00000534846.1_Silent_p.N472N	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	574					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)		p.N574N(1)									CTCCGAAGGGATTGACATAAA	0.468																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											84.0	90.0	88.0					1																	190067727		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member C"""	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1722T>C	1.37:g.190067727A>G			B3KVP1|B7Z260|O95726|Q2M330	Silent	SNP	pfam_MACPF,smart_MACPF	p.N574	ENST00000367462.3	37	c.1722	CCDS1373.1	1																																																																																			FAM5C	-	NULL	ENSG00000162670		0.468	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM5C	HGNC	protein_coding	OTTHUMT00000086278.1	102	0.97	1	A	NM_199051		190067727	190067727	-1	no_errors	ENST00000367462	ensembl	human	known	69_37n	silent	113	19.86	28	SNP	0.997	G
GLTSCR1	29998	genome.wustl.edu	37	19	48197890	48197891	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr19:48197890_48197891insC	ENST00000396720.3	+	8	2996_2997	c.2802_2803insC	c.(2803-2805)cccfs	p.P935fs	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	935	Poly-Pro.									breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		AGCCGGCAGCACCCCCCCCACC	0.673																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.2810dupC	19.37:g.48197898_48197898dupC	ENSP00000379946:p.Pro935fs		A8MW01	Frame_Shift_Ins	INS	NULL	p.P937fs	ENST00000396720.3	37	c.2802_2803	CCDS46134.1	19																																																																																			GLTSCR1	-	NULL	ENSG00000063169		0.673	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GLTSCR1	HGNC	protein_coding	OTTHUMT00000465846.1	10	0.00	0	-	NM_015711		48197890	48197891	+1	no_errors	ENST00000396720	ensembl	human	known	69_37n	frame_shift_ins	4	33.33	2	INS	0.044:0.226	C
HDAC6	10013	genome.wustl.edu	37	X	48674948	48674948	+	Missense_Mutation	SNP	G	G	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chrX:48674948G>T	ENST00000334136.5	+	19	1877	c.1699G>T	c.(1699-1701)Gac>Tac	p.D567Y	HDAC6_ENST00000376619.2_Missense_Mutation_p.D567Y|HDAC6_ENST00000444343.2_Missense_Mutation_p.D581Y			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	567	Histone deacetylase 2.				aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)	p.D567Y(1)|p.D567H(1)		breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	TTCCAACTTTGACTCCATCTA	0.592																																					Pancreas(112;205 1675 2305 8976 15959)	dbGAP											2	Substitution - Missense(2)	prostate(1)|breast(1)											70.0	53.0	59.0					X																	48674948		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 90"""	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.1699G>T	X.37:g.48674948G>T	ENSP00000334061:p.Asp567Tyr		O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	pfam_His_deacetylse_dom,pfam_Znf_UBP,smart_Znf_UBP,pfscan_Znf_UBP,prints_His_deacetylse	p.D581Y	ENST00000334136.5	37	c.1741	CCDS14306.1	X	.	.	.	.	.	.	.	.	.	.	G	18.55	3.647266	0.67358	.	.	ENSG00000094631	ENST00000444343;ENST00000334136;ENST00000376619;ENST00000436813	T;T;T	0.71934	-0.61;-0.61;-0.61	5.44	4.46	0.54185	Histone deacetylase domain (2);	0.107096	0.64402	D	0.000016	T	0.80706	0.4674	M	0.84773	2.715	0.80722	D	1	D;D;D	0.69078	0.984;0.997;0.984	D;D;D	0.65323	0.914;0.934;0.914	T	0.82114	-0.0617	10	0.72032	D	0.01	-22.9623	4.2051	0.10485	0.3011:0.0:0.6989:0.0	.	557;215;567	B4DZN1;B3KVK5;Q9UBN7	.;.;HDAC6_HUMAN	Y	581;567;567;567	ENSP00000398566:D581Y;ENSP00000334061:D567Y;ENSP00000365804:D567Y	ENSP00000334061:D567Y	D	+	1	0	HDAC6	48559892	1.000000	0.71417	0.943000	0.38184	0.813000	0.45954	3.368000	0.52357	2.265000	0.75225	0.523000	0.50628	GAC	HDAC6	-	pfam_His_deacetylse_dom	ENSG00000094631		0.592	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	HDAC6	HGNC	protein_coding	OTTHUMT00000083394.2	110	0.00	0	G	NM_006044		48674948	48674948	+1	no_errors	ENST00000444343	ensembl	human	known	69_37n	missense	86	13.13	13	SNP	0.998	T
HECTD4	283450	genome.wustl.edu	37	12	112600859	112600860	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr12:112600859_112600860insG	ENST00000430131.2	-	74	12985_12986	c.11840_11841insC	c.(11839-11841)ccafs	p.P3947fs	HECTD4_ENST00000549141.1_5'Flank|HECTD4_ENST00000550722.1_Frame_Shift_Ins_p.P4223fs|HECTD4_ENST00000377560.5_Frame_Shift_Ins_p.P4197fs			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3947	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										CTGTGCCATCTGGGGGGGCGAT	0.629																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.11841dupC	12.37:g.112600866_112600866dupG	ENSP00000404379:p.Pro3947fs		L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Frame_Shift_Ins	INS	pfam_HECT,superfamily_HECT,superfamily_ConA-like_lec_gl,smart_HECT,pfscan_HECT	p.D4198fs	ENST00000430131.2	37	c.12591_12590		12																																																																																			HECTD4	-	pfam_HECT,superfamily_HECT,smart_HECT,pfscan_HECT	ENSG00000173064		0.629	HECTD4-202	KNOWN	basic	protein_coding	HECTD4	HGNC	protein_coding		36	0.00	0	-	NM_173813		112600859	112600860	-1	no_errors	ENST00000377560	ensembl	human	known	69_37n	frame_shift_ins	44	10.20	5	INS	0.555:1.000	G
HIVEP1	3096	genome.wustl.edu	37	6	12125489	12125489	+	Missense_Mutation	SNP	C	C	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr6:12125489C>T	ENST00000379388.2	+	4	5793	c.5461C>T	c.(5461-5463)Cct>Tct	p.P1821S	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1821					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P1821S(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TTTTTCTCAACCTGAAATTAG	0.363																																						dbGAP											1	Substitution - Missense(1)	breast(1)											157.0	144.0	148.0					6																	12125489		1839	4083	5922	-	-	-	SO:0001583	missense	0			J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.5461C>T	6.37:g.12125489C>T	ENSP00000368698:p.Pro1821Ser		B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.P1821S	ENST00000379388.2	37	c.5461	CCDS43426.1	6	.	.	.	.	.	.	.	.	.	.	C	9.101	1.004217	0.19199	.	.	ENSG00000095951	ENST00000379388	T	0.09630	2.96	5.86	4.98	0.66077	.	0.224693	0.23039	N	0.052634	T	0.02455	0.0075	N	0.20845	0.615	0.80722	D	1	B	0.18863	0.031	B	0.12156	0.007	T	0.40794	-0.9544	9	.	.	.	-12.1364	10.4337	0.44421	0.0:0.7919:0.1351:0.073	.	1821	P15822	ZEP1_HUMAN	S	1821	ENSP00000368698:P1821S	.	P	+	1	0	HIVEP1	12233475	0.009000	0.17119	0.270000	0.24601	0.540000	0.34992	1.008000	0.29872	1.458000	0.47871	0.655000	0.94253	CCT	HIVEP1	-	NULL	ENSG00000095951		0.363	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HIVEP1	HGNC	protein_coding	OTTHUMT00000039870.2	179	0.00	0	C	NM_002114		12125489	12125489	+1	no_errors	ENST00000379388	ensembl	human	known	69_37n	missense	75	23.23	23	SNP	0.993	T
IFT140	9742	genome.wustl.edu	37	16	1561044	1561045	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr16:1561044_1561045insC	ENST00000426508.2	-	31	4652_4653	c.4289_4290insG	c.(4288-4290)ccafs	p.P1430fs	IFT140_ENST00000361339.5_Frame_Shift_Ins_p.P624fs|LA16c-385E7.1_ENST00000566922.1_lincRNA	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	1430					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				TGCGTGGCAGTGGGAGACCCAG	0.673																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.4289_4290insG	16.37:g.1561044_1561045insC	ENSP00000406012:p.Pro1430fs		A2A2A8|D3DU75|O60332|Q9UG52	Frame_Shift_Ins	INS	pfam_WD40_repeat,superfamily_WD40_repeat_dom,superfamily_ARM-type_fold,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.L1431fs	ENST00000426508.2	37	c.4290_4289	CCDS10439.1	16																																																																																			IFT140	-	NULL	ENSG00000187535		0.673	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IFT140	HGNC	protein_coding	OTTHUMT00000250438.2	11	0.00	0	-	NM_014714		1561044	1561045	-1	no_errors	ENST00000426508	ensembl	human	known	69_37n	frame_shift_ins	29	34.09	15	INS	0.000:0.968	C
IFT88	8100	genome.wustl.edu	37	13	21170288	21170289	+	Splice_Site	INS	-	-	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr13:21170288_21170289insT	ENST00000319980.6	+	10	752_753		c.e10-1		IFT88_ENST00000382778.4_Splice_Site|IFT88_ENST00000351808.5_Splice_Site|IFT88_ENST00000537103.1_Splice_Site	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88						anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		GTCTTTAATAGCCCAGAGGAAA	0.262																																						dbGAP											0																																										-	-	-	SO:0001630	splice_region_variant	0			AK058172	CCDS31944.1, CCDS31945.1	13q12.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000032742	ENSG00000032742		"""Intraflagellar transport homologs"", ""Tetratricopeptide (TTC) repeat domain containing"""	20606	protein-coding gene	gene with protein product	"""polaris homolog"""	600595	"""tetratricopeptide repeat domain 10"", ""intraflagellar transport 88 homolog (Chlamydomonas)"""	TTC10		7633404	Standard	XM_005266546		Approved	hTg737, Tg737, D13S1056E, MGC26259	uc001uni.3	Q13099	OTTHUMG00000016517	ENST00000319980.6:c.426-1->T	13.37:g.21170288_21170289insT			A2A491|B4DUS2|Q5SZJ6|Q8N719	Frame_Shift_Ins	INS	pfam_TPR-1,pfam_TPR_2,pfam_OMP_IML2_mit/TPR_39,smart_TPR_repeat,smart_Sel1-like,pfscan_TPR_repeat,pfscan_TPR-contain_dom	p.E145fs	ENST00000319980.6	37	c.427_426	CCDS31944.1	13																																																																																			IFT88	-	NULL	ENSG00000032742		0.262	IFT88-002	KNOWN	basic|CCDS	protein_coding	IFT88	HGNC	protein_coding	OTTHUMT00000044075.3	140	0.00	0	-	NM_006531	Intron	21170288	21170289	+1	no_errors	ENST00000319980	ensembl	human	known	69_37n	frame_shift_ins	17	10.53	2	INS	1.000:0.996	T
ITGA4	3676	genome.wustl.edu	37	2	182339924	182339924	+	Silent	SNP	G	G	A			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr2:182339924G>A	ENST00000397033.2	+	4	895	c.465G>A	c.(463-465)aaG>aaA	p.K155K	ITGA4_ENST00000478440.1_Intron|ITGA4_ENST00000339307.4_Silent_p.K155K	NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	155					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)	p.K155K(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	TTTACATAAAGAATGAAAATA	0.393																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											87.0	86.0	86.0					2																	182339924		1824	4080	5904	-	-	-	SO:0001819	synonymous_variant	0				CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"""CD molecules"", ""Integrins"""	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.465G>A	2.37:g.182339924G>A			D3DPG4|Q7Z4L6	Silent	SNP	pfam_Integrin_alpha-2,pfam_FG-GAP,smart_Int_alpha_beta-p,prints_Integrin_alpha	p.K155	ENST00000397033.2	37	c.465	CCDS42788.1	2																																																																																			ITGA4	-	NULL	ENSG00000115232		0.393	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ITGA4	HGNC	protein_coding	OTTHUMT00000334427.1	228	0.00	0	G			182339924	182339924	+1	no_errors	ENST00000397033	ensembl	human	known	69_37n	silent	64	22.89	19	SNP	0.984	A
KCNN3	3782	genome.wustl.edu	37	1	154842243	154842244	+	Missense_Mutation	DNP	AA	AA	CT			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr1:154842243_154842244AA>CT	ENST00000271915.4	-	1	512_513	c.197_198TT>AG	c.(196-198)cTT>cAG	p.L66Q	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	66	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	gctgctgctgaagctgcggagg	0.703																																						dbGAP											0																																										-	-	-	SO:0001583	missense	0			AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.197_198delinsCT	1.37:g.154842243_154842244delinsCT	ENSP00000271915:p.Leu66Gln		B1ANX0|O43517|Q86VF9|Q8WXG7	Silent|Missense_Mutation	SNP	pfam_K_chnl_Ca-activ_SK,pfam_CaM-bd_dom,pfam_Ion_trans_2,superfamily_CaM-bd_dom,prints_K_chnl_Ca-activ_SK	p.L66|p.L66H	ENST00000271915.4	37	c.198|c.197	CCDS30880.1	1																																																																																			KCNN3	-	NULL	ENSG00000143603		0.703	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	KCNN3	HGNC	protein_coding	OTTHUMT00000090688.3	12	0.00	0	A	NM_002249		154842243|154842244	154842243|154842244	-1	no_errors	ENST00000271915	ensembl	human	known	69_37n	silent|missense	55|54	19.12|17.91	13|12	SNP	0.000|0.166	C|T
LRRC37A3	374819	genome.wustl.edu	37	17	62892271	62892271	+	Missense_Mutation	SNP	A	A	T	rs62071406		TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr17:62892271A>T	ENST00000584306.1	-	3	1635	c.1105T>A	c.(1105-1107)Tct>Act	p.S369T	LRRC37A3_ENST00000577487.1_5'Flank|LRRC37A3_ENST00000400877.3_Intron|RP11-927P21.1_ENST00000584131.1_RNA|LRRC37A3_ENST00000319651.5_Missense_Mutation_p.S369T|LRRC37A3_ENST00000339474.5_Intron|RP11-927P21.1_ENST00000584959.1_RNA|RP11-927P21.1_ENST00000577938.1_RNA	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	369						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						TCCCTAGAAGACTCAGAAGGC	0.537																																						dbGAP											0													25.0	32.0	30.0					17																	62892271		1973	4078	6051	-	-	-	SO:0001583	missense	0			AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.1105T>A	17.37:g.62892271A>T	ENSP00000464535:p.Ser369Thr		Q49A01|Q49A80|Q8NB33	Missense_Mutation	SNP	pfam_Leu-rich_rpt,smart_Leu-rich_rpt_typical-subtyp	p.S369T	ENST00000584306.1	37	c.1105	CCDS32708.1	17	.	.	.	.	.	.	.	.	.	.	.	3.342	-0.134342	0.06711	.	.	ENSG00000176809	ENST00000319651	T	0.58506	0.33	2.69	-3.39	0.04868	.	.	.	.	.	T	0.43010	0.1228	L	0.31294	0.92	0.09310	N	1	P	0.52061	0.95	P	0.46718	0.525	T	0.36890	-0.9729	9	0.56958	D	0.05	.	3.9507	0.09368	0.5048:0.1903:0.3049:0.0	.	369	O60309	L37A3_HUMAN	T	369	ENSP00000325713:S369T	ENSP00000325713:S369T	S	-	1	0	LRRC37A3	60322733	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-1.093000	0.03362	-0.631000	0.05560	0.234000	0.17832	TCT	LRRC37A3	-	NULL	ENSG00000176809		0.537	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	LRRC37A3	HGNC	protein_coding	OTTHUMT00000445377.1	15	0.00	0	A	NM_199340		62892271	62892271	-1	no_errors	ENST00000319651	ensembl	human	known	69_37n	missense	12	33.33	6	SNP	0.000	T
LRRC7	57554	genome.wustl.edu	37	1	70291446	70291446	+	Missense_Mutation	SNP	C	C	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr1:70291446C>T	ENST00000035383.5	+	3	353	c.323C>T	c.(322-324)cCa>cTa	p.P108L	LRRC7_ENST00000415775.2_5'UTR|LRRC7_ENST00000370958.1_Missense_Mutation_p.P146L|LRRC7_ENST00000310961.5_Missense_Mutation_p.P113L	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	108						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.P146L(1)|p.P108L(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CAAGAATTTCCAGAAAACATA	0.244																																						dbGAP											2	Substitution - Missense(2)	breast(2)											69.0	68.0	69.0					1																	70291446		2203	4277	6480	-	-	-	SO:0001583	missense	0				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.323C>T	1.37:g.70291446C>T	ENSP00000035383:p.Pro108Leu		Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	pfam_Leu-rich_rpt,pfam_PDZ,superfamily_PDZ,smart_Leu-rich_rpt_typical-subtyp,smart_PDZ,pfscan_PDZ	p.P108L	ENST00000035383.5	37	c.323	CCDS645.1	1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.545823	0.86022	.	.	ENSG00000033122	ENST00000310961;ENST00000370958;ENST00000035383;ENST00000335298	T;T;T	0.61040	1.26;0.14;1.43	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.83972	0.5370	H	0.98178	4.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.89543	0.3794	10	0.72032	D	0.01	.	18.1861	0.89793	0.0:1.0:0.0:0.0	.	108;146	Q96NW7;B1AKT2	LRRC7_HUMAN;.	L	113;146;108;108	ENSP00000309245:P113L;ENSP00000359997:P146L;ENSP00000035383:P108L	ENSP00000035383:P108L	P	+	2	0	LRRC7	70064034	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.046000	0.76592	2.616000	0.88540	0.655000	0.94253	CCA	LRRC7	-	pfam_Leu-rich_rpt,smart_Leu-rich_rpt_typical-subtyp	ENSG00000033122		0.244	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRRC7	HGNC	protein_coding	OTTHUMT00000131261.1	209	0.00	0	C	NM_020794		70291446	70291446	+1	no_errors	ENST00000035383	ensembl	human	known	69_37n	missense	37	15.91	7	SNP	1.000	T
LRRC7	57554	genome.wustl.edu	37	1	70504659	70504659	+	Missense_Mutation	SNP	G	G	C			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr1:70504659G>C	ENST00000035383.5	+	19	3068	c.3038G>C	c.(3037-3039)aGt>aCt	p.S1013T	LRRC7_ENST00000415775.2_Missense_Mutation_p.S297T|LRRC7_ENST00000310961.5_Missense_Mutation_p.S1018T	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1013						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.S1013T(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						TACGGAAGTAGTAAGGGGCCA	0.463																																						dbGAP											1	Substitution - Missense(1)	breast(1)											40.0	40.0	40.0					1																	70504659		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.3038G>C	1.37:g.70504659G>C	ENSP00000035383:p.Ser1013Thr		Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	pfam_Leu-rich_rpt,pfam_PDZ,superfamily_PDZ,smart_Leu-rich_rpt_typical-subtyp,smart_PDZ,pfscan_PDZ	p.S1013T	ENST00000035383.5	37	c.3038	CCDS645.1	1	.	.	.	.	.	.	.	.	.	.	G	3.198	-0.164256	0.06502	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.40476	1.03;1.1;2.22	5.84	5.84	0.93424	.	0.142496	0.64402	D	0.000006	T	0.23965	0.0580	L	0.54323	1.7	0.30164	N	0.801954	B;B;B	0.30634	0.288;0.152;0.094	B;B;B	0.28011	0.079;0.085;0.039	T	0.08680	-1.0710	10	0.33940	T	0.23	.	14.5986	0.68424	0.0:0.0:0.8451:0.1549	.	297;1013;1013	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	T	1018;1013;297;836	ENSP00000309245:S1018T;ENSP00000035383:S1013T;ENSP00000394867:S297T	ENSP00000035383:S1013T	S	+	2	0	LRRC7	70277247	1.000000	0.71417	0.844000	0.33320	0.013000	0.08279	2.962000	0.49176	2.769000	0.95229	0.563000	0.77884	AGT	LRRC7	-	NULL	ENSG00000033122		0.463	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRRC7	HGNC	protein_coding	OTTHUMT00000131261.1	61	0.00	0	G	NM_020794		70504659	70504659	+1	no_errors	ENST00000035383	ensembl	human	known	69_37n	missense	56	11.11	7	SNP	0.833	C
MAGEL2	54551	genome.wustl.edu	37	15	23890432	23890432	+	Missense_Mutation	SNP	C	C	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr15:23890432C>T	ENST00000532292.1	-	1	743	c.649G>A	c.(649-651)Gct>Act	p.A217T		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	100					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)	p.A217T(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		TCCTGCAGAGCATATGGCAGT	0.567																																						dbGAP											1	Substitution - Missense(1)	breast(1)											63.0	67.0	65.0					15																	23890432		1996	4174	6170	-	-	-	SO:0001583	missense	0			AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.649G>A	15.37:g.23890432C>T	ENSP00000433433:p.Ala217Thr			Missense_Mutation	SNP	pfam_MAGE,pfscan_MAGE	p.A217T	ENST00000532292.1	37	c.649		15	.	.	.	.	.	.	.	.	.	.	C	10.92	1.486570	0.26686	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.21	0.0951	0.14484	.	.	.	.	.	T	0.19208	0.0461	N	0.24115	0.695	0.09310	N	1	.	.	.	.	.	.	T	0.22312	-1.0220	5	.	.	.	.	0.7455	0.00981	0.1632:0.3688:0.1823:0.2857	.	.	.	.	I	248	.	.	M	-	3	0	MAGEL2	21441525	0.011000	0.17503	0.006000	0.13384	0.919000	0.55068	0.191000	0.17076	0.030000	0.15379	-0.219000	0.12488	ATG	MAGEL2	-	NULL	ENSG00000254585		0.567	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	MAGEL2	HGNC	protein_coding	OTTHUMT00000395182.2	71	0.00	0	C	NM_019066		23890432	23890432	-1	no_errors	ENST00000532292	ensembl	human	known	69_37n	missense	15	31.82	7	SNP	0.005	T
MAML2	84441	genome.wustl.edu	37	11	95825407	95825407	+	Silent	SNP	C	C	T	rs61901862		TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr11:95825407C>T	ENST00000524717.1	-	2	3072	c.1788G>A	c.(1786-1788)caG>caA	p.Q596Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	596					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.Q596Q(1)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgctgctgtt	0.532			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																	dbGAP		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	1	Substitution - coding silent(1)	kidney(1)											28.0	35.0	33.0					11																	95825407		2119	4148	6267	-	-	-	SO:0001819	synonymous_variant	0			AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1788G>A	11.37:g.95825407C>T			A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	pfam_Neuroggenic_mastermind-like_N	p.Q596	ENST00000524717.1	37	c.1788	CCDS44714.1	11																																																																																			MAML2	-	NULL	ENSG00000184384		0.532	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MAML2	HGNC	protein_coding	OTTHUMT00000395540.1	169	0.59	1	C			95825407	95825407	-1	no_errors	ENST00000440572	ensembl	human	known	69_37n	silent	148	19.89	37	SNP	0.003	T
MAP3K6	9064	genome.wustl.edu	37	1	27685238	27685239	+	Frame_Shift_Ins	INS	-	-	G	rs551271693|rs34008139		TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr1:27685238_27685239insG	ENST00000493901.1	-	20	2783_2784	c.2544_2545insC	c.(2542-2547)cccttcfs	p.F849fs	MAP3K6_ENST00000357582.2_Frame_Shift_Ins_p.F849fs|MAP3K6_ENST00000374040.3_Frame_Shift_Ins_p.F841fs	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	849	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)	p.F709fs*40(1)		breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		AGCTCGTGGAAGGGGGGGCGAC	0.624																																						dbGAP											1	Insertion - Frameshift(1)	lung(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6858	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 2"""	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.2545dupC	1.37:g.27685245_27685245dupG	ENSP00000419591:p.Phe849fs		A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Frame_Shift_Ins	INS	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_SAM/pointed,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.F848fs	ENST00000493901.1	37	c.2545_2544	CCDS299.1	1																																																																																			MAP3K6	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000142733		0.624	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	MAP3K6	HGNC	protein_coding	OTTHUMT00000013469.2	58	0.00	0	-	NM_004672		27685238	27685239	-1	no_errors	ENST00000357582	ensembl	human	known	69_37n	frame_shift_ins	40	11.11	5	INS	1.000:0.991	G
MBNL1	4154	genome.wustl.edu	37	3	152177106	152177106	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr3:152177106delC	ENST00000463374.1	+	8	1668	c.1157delC	c.(1156-1158)accfs	p.T386fs	MBNL1_ENST00000485910.1_Frame_Shift_Del_p.T300fs|MBNL1_ENST00000355460.2_Frame_Shift_Del_p.T368fs|MBNL1_ENST00000545754.1_Frame_Shift_Del_p.T312fs|MBNL1_ENST00000493459.1_Frame_Shift_Del_p.T341fs|MBNL1_ENST00000324210.5_Frame_Shift_Del_p.T380fs|MBNL1_ENST00000324196.5_Frame_Shift_Del_p.T338fs|MBNL1_ENST00000498502.1_3'UTR|MBNL1_ENST00000485509.1_Frame_Shift_Del_p.T338fs|MBNL1_ENST00000282486.6_Frame_Shift_Del_p.T386fs|MBNL1_ENST00000492948.1_3'UTR|MBNL1_ENST00000282488.7_Frame_Shift_Del_p.T300fs|RP11-362A9.3_ENST00000463255.1_RNA|MBNL1_ENST00000357472.3_3'UTR	NM_207293.1	NP_997176.1	Q9NR56	MBNL1_HUMAN	muscleblind-like splicing regulator 1	386					alternative mRNA splicing, via spliceosome (GO:0000380)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|mRNA splice site selection (GO:0006376)|myoblast differentiation (GO:0045445)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|skeletal muscle tissue development (GO:0007519)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			AAGTATGTTACCCAGATGTAG	0.313																																						dbGAP											0													44.0	44.0	44.0					3																	152177106		2203	4295	6498	-	-	-	SO:0001589	frameshift_variant	0			Y13829	CCDS3163.1, CCDS3164.1, CCDS3165.1, CCDS3166.1, CCDS3167.1, CCDS3168.1, CCDS54656.1	3q25	2013-01-18	2012-02-23	2003-03-14	ENSG00000152601	ENSG00000152601		"""Zinc fingers, CCCH-type domain containing"""	6923	protein-coding gene	gene with protein product		606516	"""muscleblind (Drosophila)-like"", ""muscleblind-like (Drosophila)"""	MBNL			Standard	NM_021038		Approved	KIAA0428, EXP42, EXP40, EXP35, EXP	uc003ezm.3	Q9NR56	OTTHUMG00000159163	ENST00000463374.1:c.1157delC	3.37:g.152177106delC	ENSP00000418108:p.Thr386fs		E9PBW7|O43311|O43797|Q86UV8|Q86UV9|Q96P92|Q96RE3	Frame_Shift_Del	DEL	smart_Znf_CCCH	p.Q387fs	ENST00000463374.1	37	c.1157	CCDS3165.1	3																																																																																			MBNL1	-	NULL	ENSG00000152601		0.313	MBNL1-006	KNOWN	basic|CCDS	protein_coding	MBNL1	HGNC	protein_coding	OTTHUMT00000353604.1	91	0.00	0	C	NM_021038		152177106	152177106	+1	no_errors	ENST00000282486	ensembl	human	known	69_37n	frame_shift_del	15	11.76	2	DEL	1.000	-
MIR518C	574477	genome.wustl.edu	37	19	54214334	54214334	+	RNA	SNP	G	G	A			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr19:54214334G>A	ENST00000384822.1	+	0	101				MIR517A_ENST00000385001.1_RNA|MIR519D_ENST00000385246.1_RNA|MIR524_ENST00000385242.1_RNA	NR_030199.1				microRNA 518c																		GGAGTGTTACGGTTTGAGAAA	0.463																																						dbGAP											0													102.0	94.0	97.0					19																	54214334		1568	3582	5150	-	-	-			0					19q13.42	2011-09-12		2008-12-18	ENSG00000207553	ENSG00000207553		"""ncRNAs / Micro RNAs"""	32109	non-coding RNA	RNA, micro				MIRN518C			Standard	NR_030199		Approved	hsa-mir-518c	uc021vac.1				19.37:g.54214334G>A				RNA	SNP	-	NULL	ENST00000384822.1	37	NULL		19																																																																																			MIR524	-	-	ENSG00000207977		0.463	MIR518C-201	KNOWN	basic	miRNA	MIR524	HGNC	miRNA		247	0.00	0	G	NR_030199		54214334	54214334	+1	no_errors	ENST00000385242	ensembl	human	known	69_37n	rna	152	15.56	28	SNP	0.006	A
MLPH	79083	genome.wustl.edu	37	2	238449564	238449564	+	Silent	SNP	A	A	G			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr2:238449564A>G	ENST00000264605.3	+	11	1704	c.1410A>G	c.(1408-1410)gcA>gcG	p.A470A	MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000409373.1_Intron|MLPH_ENST00000410032.1_Silent_p.A327A|MLPH_ENST00000445024.2_Silent_p.A470A|MLPH_ENST00000338530.4_Silent_p.A442A	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	470					melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)	p.A470A(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		ACAGAGTGGCAGTGACGGCCT	0.592																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											58.0	50.0	53.0					2																	238449564		2199	4298	6497	-	-	-	SO:0001819	synonymous_variant	0			AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.1410A>G	2.37:g.238449564A>G			B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	pfam_Myelin-assoc_OBP	p.S69G	ENST00000264605.3	37	c.205	CCDS2518.1	2	.	.	.	.	.	.	.	.	.	.	A	0.855	-0.737176	0.03111	.	.	ENSG00000115648	ENST00000436965	.	.	.	5.13	-4.33	0.03677	.	.	.	.	.	T	0.36853	0.0982	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34104	-0.9842	4	.	.	.	-19.0003	0.817	0.01104	0.4198:0.17:0.1974:0.2127	.	.	.	.	R	191	.	.	Q	+	2	0	MLPH	238114303	0.000000	0.05858	0.002000	0.10522	0.093000	0.18481	-2.571000	0.00913	-1.124000	0.02936	-1.510000	0.00946	CAG	MLPH	-	pfam_Myelin-assoc_OBP	ENSG00000115648		0.592	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MLPH	HGNC	protein_coding	OTTHUMT00000257083.2	12	0.00	0	A	NM_024101		238449564	238449564	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000432475	ensembl	human	known	69_37n	missense	19	17.39	4	SNP	0.000	G
MSN	4478	genome.wustl.edu	37	X	64958834	64958834	+	Silent	SNP	C	C	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chrX:64958834C>T	ENST00000360270.5	+	12	1519	c.1347C>T	c.(1345-1347)gcC>gcT	p.A449A		NM_002444.2	NP_002435.1	P26038	MOES_HUMAN	moesin	449					cellular component movement (GO:0006928)|establishment of endothelial barrier (GO:0061028)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|regulation of lymphocyte migration (GO:2000401)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|uropod (GO:0001931)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|structural constituent of cytoskeleton (GO:0005200)	p.A449A(1)	MSN/ALK(6)	breast(4)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	43						CTGGACAGGCCCAGATGGTAC	0.532			T	ALK	ALCL																																	dbGAP		Dom	yes		X	Xq11.2-q12	4478	moesin		L	1	Substitution - coding silent(1)	breast(1)											65.0	53.0	57.0					X																	64958834		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			M69066	CCDS14382.1	Xq11.1	2010-10-20			ENSG00000147065	ENSG00000147065			7373	protein-coding gene	gene with protein product		309845				1924289, 7628534	Standard	XM_005262269		Approved		uc004dwf.3	P26038	OTTHUMG00000021723	ENST00000360270.5:c.1347C>T	X.37:g.64958834C>T				Silent	SNP	pirsf_ERM,pfam_ERM_C,pfam_FERM_PH-like_C,pfam_FERM_central,pfam_FERM_N,superfamily_FERM_central,superfamily_Moesin,smart_Band_41_domain,prints_Ez/rad/moesin,prints_Band_41_fam,pfscan_FERM_domain	p.A449	ENST00000360270.5	37	c.1347	CCDS14382.1	X																																																																																			MSN	-	pirsf_ERM,pfam_ERM_C	ENSG00000147065		0.532	MSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MSN	HGNC	protein_coding	OTTHUMT00000056981.1	499	0.00	0	C	NM_002444		64958834	64958834	+1	no_errors	ENST00000360270	ensembl	human	known	69_37n	silent	594	15.24	107	SNP	0.987	T
MUC4	4585	genome.wustl.edu	37	3	195513420	195513420	+	Silent	SNP	G	G	A	rs71321842	byFrequency	TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr3:195513420G>A	ENST00000463781.3	-	2	5490	c.5031C>T	c.(5029-5031)caC>caT	p.H1677H	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.H1677H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCGTGACCGGTGG	0.612																																						dbGAP											0													36.0	34.0	34.0					3																	195513420		690	1583	2273	-	-	-	SO:0001819	synonymous_variant	0			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.5031C>T	3.37:g.195513420G>A			O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	pfam_Nidogen_extracell_dom,pfam_AMOP,pfam_VWF_type-D,smart_Nidogen_extracell_dom,smart_AMOP,smart_VWF_type-D,smart_EGF-like,pfscan_AMOP,pfscan_EG-like_dom	p.H1677	ENST00000463781.3	37	c.5031	CCDS54700.1	3																																																																																			MUC4	-	NULL	ENSG00000145113		0.612	MUC4-001	KNOWN	basic|CCDS	protein_coding	MUC4	HGNC	protein_coding	OTTHUMT00000324081.6	31	0.00	0	G	NM_018406		195513420	195513420	-1	no_errors	ENST00000463781	ensembl	human	known	69_37n	silent	71	14.46	12	SNP	0.010	A
NTRK3	4916	genome.wustl.edu	37	15	88576185	88576185	+	Silent	SNP	G	G	A	rs2229910	byFrequency	TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr15:88576185G>A	ENST00000360948.2	-	13	1649	c.1488C>T	c.(1486-1488)gcC>gcT	p.A496A	NTRK3_ENST00000317501.3_Silent_p.A496A|NTRK3_ENST00000357724.2_Silent_p.A488A|NTRK3_ENST00000558676.1_Silent_p.A488A|NTRK3_ENST00000542733.2_Silent_p.A398A|NTRK3_ENST00000394480.2_Silent_p.A496A|NTRK3_ENST00000557856.1_Silent_p.A488A|NTRK3_ENST00000540489.2_Silent_p.A496A|NTRK3_ENST00000355254.2_Silent_p.A496A|NTRK3_ENST00000558306.1_5'UTR	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	496					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.A496A(1)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			TGTCGGGCCCGGCATCCAGTG	0.602			T	ETV6	"""congenital fibrosarcoma, Secretory breast """					TSP Lung(13;0.10)																												dbGAP		Dom	yes		15	15q25	4916	"""neurotrophic tyrosine kinase, receptor, type 3"""		"""E, M"""	1	Substitution - coding silent(1)	stomach(1)											96.0	63.0	74.0					15																	88576185		2201	4299	6500	-	-	-	SO:0001819	synonymous_variant	0			U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"""	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1488C>T	15.37:g.88576185G>A			B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Silent	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_Ig_I-set,pfam_Immunoglobulin,pfam_LRR-contain_N,superfamily_Kinase-like_dom,smart_LRR-contain_N,smart_Cys-rich_flank_reg_C,smart_Ig_sub,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom,pfscan_Ig-like,prints_Tyr_kinase_NGF_rcpt,prints_Tyr_kin_neurotrophic_rcpt_3,prints_Ser-Thr/Tyr_kinase_cat_dom	p.A496	ENST00000360948.2	37	c.1488	CCDS32322.1	15																																																																																			NTRK3	-	NULL	ENSG00000140538		0.602	NTRK3-204	KNOWN	basic|CCDS	protein_coding	NTRK3	HGNC	protein_coding		108	0.00	0	G			88576185	88576185	-1	no_errors	ENST00000360948	ensembl	human	known	69_37n	silent	152	16.48	30	SNP	0.054	A
NUP205	23165	genome.wustl.edu	37	7	135333164	135333164	+	Missense_Mutation	SNP	G	G	A	rs566054477		TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr7:135333164G>A	ENST00000285968.6	+	43	5925	c.5899G>A	c.(5899-5901)Gca>Aca	p.A1967T		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1967					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)	p.A1967T(1)		breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						TCAGGCTGATGCAATCAACGC	0.328													G|||	0	0.0	0.0	0.0	5008	,	,		16832	0.0		0.0	False		,,,				2504	0.0					dbGAP											1	Substitution - Missense(1)	breast(1)											83.0	81.0	82.0					7																	135333164		2203	4300	6503	-	-	-	SO:0001583	missense	0			D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.5899G>A	7.37:g.135333164G>A	ENSP00000285968:p.Ala1967Thr		A6H8X3|Q86YC1	Missense_Mutation	SNP	pfam_DUF3414	p.A1967T	ENST00000285968.6	37	c.5899	CCDS34759.1	7	.	.	.	.	.	.	.	.	.	.	g	12.50	1.956731	0.34565	.	.	ENSG00000155561	ENST00000285968	T	0.33654	1.4	4.97	4.06	0.47325	.	0.305989	0.40385	N	0.001118	T	0.26376	0.0644	L	0.34521	1.04	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.05053	-1.0909	10	0.38643	T	0.18	-7.7965	9.7463	0.40448	0.0768:0.0:0.7712:0.152	.	1967	Q92621	NU205_HUMAN	T	1967	ENSP00000285968:A1967T	ENSP00000285968:A1967T	A	+	1	0	NUP205	134983704	0.999000	0.42202	0.396000	0.26296	0.914000	0.54420	2.087000	0.41653	1.162000	0.42619	0.561000	0.74099	GCA	NUP205	-	NULL	ENSG00000155561		0.328	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NUP205	HGNC	protein_coding	OTTHUMT00000340358.1	197	0.00	0	G			135333164	135333164	+1	no_errors	ENST00000285968	ensembl	human	known	69_37n	missense	71	14.46	12	SNP	0.959	A
OXR1	55074	genome.wustl.edu	37	8	107726212	107726212	+	Splice_Site	SNP	A	A	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr8:107726212A>T	ENST00000442977.2	+	10	2057	c.1958A>T	c.(1957-1959)gAg>gTg	p.E653V	OXR1_ENST00000531443.1_Splice_Site_p.E652V|OXR1_ENST00000452423.2_Splice_Site_p.E142V|OXR1_ENST00000445937.1_Splice_Site_p.E652V|OXR1_ENST00000517566.2_Splice_Site_p.E652V|OXR1_ENST00000312046.6_Splice_Site_p.E645V	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	653					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)	p.E564V(1)|p.E653V(1)		NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			AGAGAATGGGAGGTAAGGAGA	0.338																																						dbGAP											2	Substitution - Missense(2)	breast(2)											58.0	61.0	60.0					8																	107726212		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 3"""	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.1959+1A>T	8.37:g.107726212A>T			A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Missense_Mutation	SNP	pfam_TLDc,pfam_Peptidoglycan-bd_lysin,pfam_GRAM,smart_Peptidoglycan-bd_Lysin_subgr,smart_TLDc	p.E653V	ENST00000442977.2	37	c.1958	CCDS56548.1	8	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.482021|4.482021	0.84747|0.84747	.|.	.|.	ENSG00000164830|ENSG00000164830	ENST00000445937;ENST00000531443;ENST00000517566;ENST00000452423;ENST00000442977;ENST00000312046|ENST00000519415	T;T;T;T;T;T|.	0.25912|.	1.77;1.77;2.0;1.97;2.0;1.78|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77336|0.77336	0.4115|0.4115	M|M	0.81802|0.81802	2.56|2.56	0.45704|0.45704	D|D	0.998615|0.998615	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.91635|.	0.999;0.999;0.999;0.999|.	T|T	0.79019|0.79019	-0.1974|-0.1974	10|5	0.62326|.	D|.	0.03|.	-9.0436|-9.0436	15.8351|15.8351	0.78791|0.78791	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	645;653;652;652|.	Q8N573-2;Q8N573;D3HIS6;Q8N573-5|.	.;OXR1_HUMAN;.;.|.	V|C	652;652;652;142;653;645|366	ENSP00000402918:E652V;ENSP00000431966:E652V;ENSP00000429205:E652V;ENSP00000395032:E142V;ENSP00000405424:E653V;ENSP00000311026:E645V|.	ENSP00000311026:E645V|.	E|S	+|+	2|1	0|0	OXR1|OXR1	107795388|107795388	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.908000|0.908000	0.53690|0.53690	9.339000|9.339000	0.96797|0.96797	2.152000|2.152000	0.67230|0.67230	0.260000|0.260000	0.18958|0.18958	GAG|AGC	OXR1	-	NULL	ENSG00000164830		0.338	OXR1-201	KNOWN	basic|CCDS	protein_coding	OXR1	HGNC	protein_coding		108	0.00	0	A	NM_181354	Missense_Mutation	107726212	107726212	+1	no_errors	ENST00000442977	ensembl	human	known	69_37n	missense	28	28.21	11	SNP	1.000	T
PDE3A	5139	genome.wustl.edu	37	12	20799761	20799761	+	Silent	SNP	C	C	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr12:20799761C>T	ENST00000359062.3	+	12	2482	c.2442C>T	c.(2440-2442)taC>taT	p.Y814Y	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	814	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)	p.Y814Y(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	ATGATAAATACGGATGTCTGT	0.423																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											179.0	169.0	172.0					12																	20799761		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"""Phosphodiesterases"""	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.2442C>T	12.37:g.20799761C>T			O60865|Q13348|Q17RD1	Silent	SNP	pfam_PDEase_catalytic_dom,smart_HD/PDEase_dom	p.Y814	ENST00000359062.3	37	c.2442	CCDS31754.1	12																																																																																			PDE3A	-	smart_HD/PDEase_dom	ENSG00000172572		0.423	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PDE3A	HGNC	protein_coding	OTTHUMT00000401756.2	246	0.00	0	C			20799761	20799761	+1	no_errors	ENST00000359062	ensembl	human	known	69_37n	silent	110	19.12	26	SNP	0.203	T
PER3	8863	genome.wustl.edu	37	1	7844971	7844972	+	Frame_Shift_Ins	INS	-	-	G	rs547192999		TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr1:7844971_7844972insG	ENST00000361923.2	+	1	209_210	c.34_35insG	c.(34-36)cggfs	p.R12fs	PER3_ENST00000377541.1_Frame_Shift_Ins_p.R12fs|PER3_ENST00000377532.3_Frame_Shift_Ins_p.R12fs	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	12					circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		CCCCGGGAGACGGGGGGCTAAG	0.693																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.40dupG	1.37:g.7844977_7844977dupG	ENSP00000355031:p.Arg12fs		Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Frame_Shift_Ins	INS	pfam_Period_circadian-like_C,pfam_PAS_fold_3,pfam_PAS_fold,smart_PAS,pfscan_PAS	p.A14fs	ENST00000361923.2	37	c.34_35	CCDS89.1	1																																																																																			PER3	-	NULL	ENSG00000049246		0.693	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	PER3	HGNC	protein_coding	OTTHUMT00000003607.1	12	0.00	0	-	NM_016831		7844971	7844972	+1	no_errors	ENST00000361923	ensembl	human	known	69_37n	frame_shift_ins	11	15.38	2	INS	0.000:0.000	G
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|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)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)											99.0	89.0	92.0					3																	178952085		1912	4130	6042	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg		Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.H1047R	ENST00000263967.3	37	c.3140	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	PIK3CA	-	superfamily_Kinase-like_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	ENSG00000121879		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	92	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	79	27.93	31	SNP	1.000	G
PIWIL1	9271	genome.wustl.edu	37	12	130831527	130831527	+	Silent	SNP	G	G	A			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr12:130831527G>A	ENST00000245255.3	+	6	845	c.573G>A	c.(571-573)gtG>gtA	p.V191V		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	191					gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)	p.V191V(1)		breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		GAGAGGATGTGAGGATAACGA	0.368																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											119.0	115.0	116.0					12																	130831527		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"""Argonaute/PIWI family"""	9007	protein-coding gene	gene with protein product		605571	"""piwi (Drosophila)-like 1"", ""piwi-like 1 (Drosophila)"""			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.573G>A	12.37:g.130831527G>A			A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Silent	SNP	pfam_Piwi,pfam_PAZ,pfam_GAGE,superfamily_RNaseH-like_dom,superfamily_PAZ,smart_PAZ,smart_Piwi,pfscan_PAZ,pfscan_Piwi	p.V191	ENST00000245255.3	37	c.573	CCDS9268.1	12																																																																																			PIWIL1	-	superfamily_PAZ	ENSG00000125207		0.368	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PIWIL1	HGNC	protein_coding	OTTHUMT00000399510.1	343	0.00	0	G			130831527	130831527	+1	no_errors	ENST00000245255	ensembl	human	known	69_37n	silent	86	24.56	28	SNP	1.000	A
PPM1B	5495	genome.wustl.edu	37	2	44457659	44457659	+	Missense_Mutation	SNP	G	G	A			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr2:44457659G>A	ENST00000282412.4	+	6	1654	c.1242G>A	c.(1240-1242)atG>atA	p.M414I	PPM1B_ENST00000378540.4_Intron|PPM1B_ENST00000345249.4_Missense_Mutation_p.M127I|PPM1B_ENST00000409432.3_3'UTR|PPM1B_ENST00000378551.2_Intron	NM_002706.4	NP_002697.1	O75688	PPM1B_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1B	414					cytokine-mediated signaling pathway (GO:0019221)|N-terminal protein myristoylation (GO:0006499)|negative regulation of defense response to virus (GO:0050687)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)	cytosol (GO:0005829)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)	p.M414I(1)		kidney(4)|large_intestine(3)|lung(7)|skin(2)	16		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				TGGAGGAGATGCTGACTAGTT	0.473																																						dbGAP											1	Substitution - Missense(1)	breast(1)											81.0	82.0	81.0					2																	44457659		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ005801	CCDS1816.1, CCDS1817.1, CCDS1818.1, CCDS46271.1	2p22.1	2012-04-17	2010-03-05		ENSG00000138032	ENSG00000138032	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9276	protein-coding gene	gene with protein product	"""protein phosphatase 2C, beta isoform"""	603770	"""protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform"""			9684878	Standard	NM_002706		Approved	PPC2BETAX, PP2CB, PP2CBETA	uc002rtt.3	O75688	OTTHUMG00000128757	ENST00000282412.4:c.1242G>A	2.37:g.44457659G>A	ENSP00000282412:p.Met414Ile		Q461Q2|Q4J6C1|Q4J6C2|Q658R4|Q96ER6|Q9HAY8	Missense_Mutation	SNP	pfam_PP2C-like,pfam_PP2C_C,superfamily_PP2C-like,superfamily_PP2C_C,smart_PP2C-like	p.M414I	ENST00000282412.4	37	c.1242	CCDS1817.1	2	.	.	.	.	.	.	.	.	.	.	G	15.12	2.737753	0.49045	.	.	ENSG00000138032	ENST00000282412;ENST00000345249	T	0.22134	1.97	5.19	5.19	0.71726	.	0.153604	0.64402	D	0.000017	T	0.18257	0.0438	N	0.24115	0.695	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.03240	-1.1057	10	0.51188	T	0.08	-16.8406	19.0653	0.93108	0.0:0.0:1.0:0.0	.	414	O75688	PPM1B_HUMAN	I	414;127	ENSP00000282412:M414I	ENSP00000282412:M414I	M	+	3	0	PPM1B	44311163	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.103000	0.77014	2.572000	0.86782	0.591000	0.81541	ATG	PPM1B	-	NULL	ENSG00000138032		0.473	PPM1B-001	KNOWN	basic|CCDS	protein_coding	PPM1B	HGNC	protein_coding	OTTHUMT00000250672.1	145	0.00	0	G	NM_002706		44457659	44457659	+1	no_errors	ENST00000282412	ensembl	human	known	69_37n	missense	63	28.41	25	SNP	1.000	A
PSIP1	11168	genome.wustl.edu	37	9	15490113	15490114	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr9:15490113_15490114insA	ENST00000380733.4	-	4	501_502	c.158_159insT	c.(157-159)ttafs	p.L53fs	PSIP1_ENST00000380715.1_Frame_Shift_Ins_p.L53fs|PSIP1_ENST00000380738.4_Frame_Shift_Ins_p.L53fs|PSIP1_ENST00000397519.2_Frame_Shift_Ins_p.L53fs|PSIP1_ENST00000380716.4_Frame_Shift_Ins_p.L53fs			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1	53	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)			breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		CCTTTGGTCCTAAAAAAGCACT	0.302																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"""PC4 and SFRS1 interacting protein 2"""	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.159dupT	9.37:g.15490119_15490119dupA	ENSP00000370109:p.Leu53fs		D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	Frame_Shift_Ins	INS	pfam_LEDGF,pfam_PWWP,smart_PWWP,prints_Treacle-like_TCS,pfscan_PWWP	p.L53fs	ENST00000380733.4	37	c.159_158	CCDS6479.1	9																																																																																			PSIP1	-	pfam_PWWP,smart_PWWP,pfscan_PWWP	ENSG00000164985		0.302	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	PSIP1	HGNC	protein_coding	OTTHUMT00000055445.1	267	0.00	0	-	NM_033222		15490113	15490114	-1	no_errors	ENST00000380733	ensembl	human	known	69_37n	frame_shift_ins	44	38.03	27	INS	1.000:1.000	A
RNF222	643904	genome.wustl.edu	37	17	8296596	8296596	+	Missense_Mutation	SNP	G	G	A	rs554178516		TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr17:8296596G>A	ENST00000399398.2	-	3	492	c.184C>T	c.(184-186)Ccc>Tcc	p.P62S	RNF222_ENST00000344001.3_Missense_Mutation_p.P62S	NM_001146684.2	NP_001140156.1	A6NCQ9	RN222_HUMAN	ring finger protein 222	62						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.P62S(1)		breast(1)	1						CGGCAGATGGGGCAGACCAGG	0.647													G|||	1	0.000199681	0.0	0.0	5008	,	,		17607	0.0		0.001	False		,,,				2504	0.0					dbGAP											1	Substitution - Missense(1)	breast(1)											24.0	27.0	26.0					17																	8296596		692	1591	2283	-	-	-	SO:0001583	missense	0				CCDS45608.1	17p13.1	2013-01-09			ENSG00000189051	ENSG00000189051		"""RING-type (C3HC4) zinc fingers"""	34517	protein-coding gene	gene with protein product							Standard	NM_001146684		Approved		uc010vuy.1	A6NCQ9	OTTHUMG00000132049	ENST00000399398.2:c.184C>T	17.37:g.8296596G>A	ENSP00000382330:p.Pro62Ser			Missense_Mutation	SNP	pfam_Znf_C3HC4_RING-type,smart_Znf_RING,pfscan_Znf_RING	p.P62S	ENST00000399398.2	37	c.184	CCDS45608.1	17	.	.	.	.	.	.	.	.	.	.	G	24.4	4.527848	0.85706	.	.	ENSG00000189051	ENST00000344001;ENST00000399398	D;D	0.94576	-3.46;-3.46	4.42	4.42	0.53409	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.97334	0.9128	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97983	1.0350	10	0.72032	D	0.01	0.1371	16.5357	0.84372	0.0:0.0:1.0:0.0	.	62	A6NCQ9	RN222_HUMAN	S	62	ENSP00000343799:P62S;ENSP00000382330:P62S	ENSP00000343799:P62S	P	-	1	0	RNF222	8237321	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.212000	0.77941	2.445000	0.82738	0.643000	0.83706	CCC	RNF222	-	pfam_Znf_C3HC4_RING-type,smart_Znf_RING,pfscan_Znf_RING	ENSG00000189051		0.647	RNF222-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	RNF222	HGNC	protein_coding	OTTHUMT00000255072.2	15	0.00	0	G	NM_001146684.2		8296596	8296596	-1	no_errors	ENST00000344001	ensembl	human	known	69_37n	missense	17	32.00	8	SNP	1.000	A
SCRIB	23513	genome.wustl.edu	37	8	144891156	144891156	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr8:144891156delC	ENST00000320476.3	-	15	1744	c.1738delG	c.(1738-1740)gatfs	p.D581fs	SCRIB_ENST00000356994.2_Frame_Shift_Del_p.D581fs|SCRIB_ENST00000377533.3_Frame_Shift_Del_p.D500fs	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	581	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			TCCCTGTCATCCCCGGGCAGC	0.647																																					Pancreas(51;966 1133 10533 14576 29674)	dbGAP											0													52.0	53.0	52.0					8																	144891156		2203	4299	6502	-	-	-	SO:0001589	frameshift_variant	0			AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.1738delG	8.37:g.144891156delC	ENSP00000322938:p.Asp581fs		Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Frame_Shift_Del	DEL	pfam_PDZ,pfam_Leu-rich_rpt,superfamily_PDZ,smart_Leu-rich_rpt_typical-subtyp,smart_PDZ,pfscan_PDZ	p.D580fs	ENST00000320476.3	37	c.1738	CCDS6411.1	8																																																																																			SCRIB	-	NULL	ENSG00000180900		0.647	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	SCRIB	HGNC	protein_coding	OTTHUMT00000382215.1	43	0.00	0	C	NM_015356		144891156	144891156	-1	no_errors	ENST00000320476	ensembl	human	known	69_37n	frame_shift_del	24	59.68	37	DEL	0.044	-
SEC31B	25956	genome.wustl.edu	37	10	102247412	102247412	+	Silent	SNP	C	C	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr10:102247412C>T	ENST00000370345.3	-	26	3598	c.3501G>A	c.(3499-3501)ctG>ctA	p.L1167L		NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	1167					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)		p.L1167L(1)		NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		GGACAGCCTTCAGGATAGGCA	0.557																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											49.0	41.0	44.0					10																	102247412		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.3501G>A	10.37:g.102247412C>T			B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Silent	SNP	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.L1167	ENST00000370345.3	37	c.3501	CCDS7495.1	10																																																																																			SEC31B	-	NULL	ENSG00000075826		0.557	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	SEC31B	HGNC	protein_coding	OTTHUMT00000051198.1	31	0.00	0	C	NM_015490		102247412	102247412	-1	no_errors	ENST00000370345	ensembl	human	known	69_37n	silent	114	11.63	15	SNP	1.000	T
SEMA4C	54910	genome.wustl.edu	37	2	97526846	97526847	+	In_Frame_Ins	INS	-	-	GAG			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr2:97526846_97526847insGAG	ENST00000305476.5	-	15	2150_2151	c.2018_2019insCTC	c.(2017-2019)ggg>ggCTCg	p.673_674insS		NM_017789.4	NP_060259.4	Q9C0C4	SEM4C_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	673					cell migration in hindbrain (GO:0021535)|cerebellum development (GO:0021549)|muscle cell differentiation (GO:0042692)|neural tube closure (GO:0001843)|positive regulation of stress-activated MAPK cascade (GO:0032874)|semaphorin-plexin signaling pathway (GO:0071526)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle membrane (GO:0030672)	receptor activity (GO:0004872)			NS(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	17						GGCACACAGCCCCCAGGGCCAC	0.683																																						dbGAP											0																																										-	-	-	SO:0001652	inframe_insertion	0			AB051526	CCDS2029.1	2q11.2	2013-01-11			ENSG00000168758	ENSG00000168758		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10731	protein-coding gene	gene with protein product	"""M-Sema F"""	604462		SEMAI		7656991	Standard	NM_017789		Approved	Semacl1, Semaf	uc002sxh.4	Q9C0C4	OTTHUMG00000130535	ENST00000305476.5:c.2018_2019insCTC	2.37:g.97526846_97526847insGAG	ENSP00000306844:p.Gly673_Ala674insSer		Q32MJ3|Q7Z5X0	In_Frame_Ins	INS	pfam_Semaphorin/CD100_Ag,pfam_Plexin_repeat,superfamily_Semaphorin/CD100_Ag,superfamily_Plexin-like_fold,smart_Semaphorin/CD100_Ag,smart_Plexin-like,smart_Ig_sub,pfscan_Semaphorin/CD100_Ag,pfscan_Ig-like	p.674in_frame_insS	ENST00000305476.5	37	c.2019_2018	CCDS2029.1	2																																																																																			SEMA4C	-	NULL	ENSG00000168758		0.683	SEMA4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SEMA4C	HGNC	protein_coding	OTTHUMT00000252957.1	9	0.00	0	-	NM_017789		97526846	97526847	-1	no_errors	ENST00000305476	ensembl	human	known	69_37n	in_frame_ins	5	37.50	3	INS	0.625:0.993	GAG
SETD5	55209	genome.wustl.edu	37	3	9484993	9484993	+	Splice_Site	SNP	T	T	A			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr3:9484993T>A	ENST00000406341.1	+	10	1269	c.1079T>A	c.(1078-1080)gTg>gAg	p.V360E	SETD5_ENST00000407969.1_Splice_Site_p.V379E|SETD5_ENST00000402198.1_Splice_Site_p.V360E|SETD5_ENST00000402466.1_Splice_Site_p.V262E|SETD5_ENST00000302463.6_Splice_Site_p.V262E			Q9C0A6	SETD5_HUMAN	SET domain containing 5	360	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.							p.V262E(1)|p.V360E(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		TTCACACAGGTGCGACACATG	0.413																																						dbGAP											2	Substitution - Missense(2)	breast(2)											52.0	50.0	50.0					3																	9484993		1929	4102	6031	-	-	-	SO:0001630	splice_region_variant	0			BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.1078-1T>A	3.37:g.9484993T>A			Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Missense_Mutation	SNP	pfam_SET_dom,smart_SET_dom,pfscan_SET_dom	p.V360E	ENST00000406341.1	37	c.1079	CCDS46741.1	3	.	.	.	.	.	.	.	.	.	.	T	29.2	4.981882	0.93044	.	.	ENSG00000168137	ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000302463	D;D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81;-1.81	6.03	6.03	0.97812	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.93154	0.7820	M	0.85630	2.765	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.994	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.998;0.989	D	0.94005	0.7279	10	0.87932	D	0	-4.4771	16.5582	0.84512	0.0:0.0:0.0:1.0	.	29;262;262;360;379	B3KXG4;B3KRD6;Q9C0A6-3;Q9C0A6;E7EWN3	.;.;.;SETD5_HUMAN;.	E	360;262;360;379;262	ENSP00000385852:V360E;ENSP00000384429:V262E;ENSP00000383939:V360E;ENSP00000384114:V379E;ENSP00000302028:V262E	ENSP00000302028:V262E	V	+	2	0	SETD5	9459993	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	8.013000	0.88655	2.308000	0.77769	0.533000	0.62120	GTG	SETD5	-	pfam_SET_dom,smart_SET_dom,pfscan_SET_dom	ENSG00000168137		0.413	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	SETD5	HGNC	protein_coding	OTTHUMT00000318425.1	95	0.00	0	T	XM_371614	Missense_Mutation	9484993	9484993	+1	no_errors	ENST00000402198	ensembl	human	known	69_37n	missense	44	26.67	16	SNP	1.000	A
SLC1A2	6506	genome.wustl.edu	37	11	35327749	35327749	+	Missense_Mutation	SNP	G	G	A			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr11:35327749G>A	ENST00000278379.3	-	5	884	c.602C>T	c.(601-603)cCg>cTg	p.P201L	SLC1A2_ENST00000606205.1_Missense_Mutation_p.P201L|SLC1A2_ENST00000395753.1_Missense_Mutation_p.P192L|SLC1A2_ENST00000395750.1_Missense_Mutation_p.P192L	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 2	201					adult behavior (GO:0030534)|cellular response to extracellular stimulus (GO:0031668)|D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|positive regulation of glucose import (GO:0046326)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|visual behavior (GO:0007632)	axolemma (GO:0030673)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.P201L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)			CTCCTCGTCCGGCGGTGGTGC	0.498											OREG0020883	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									NSCLC(100;1273 1575 12993 16869 47409)|Ovarian(164;45 1946 8965 30452 48454)	dbGAP											1	Substitution - Missense(1)	breast(1)											88.0	83.0	85.0					11																	35327749		2202	4298	6500	-	-	-	SO:0001583	missense	0			AB209444	CCDS31459.1, CCDS55756.1	11p13-p12	2013-05-22			ENSG00000110436	ENSG00000110436		"""Solute carriers"""	10940	protein-coding gene	gene with protein product		600300				1448170	Standard	NM_004171		Approved	GLT-1, EAAT2	uc001mwd.3	P43004	OTTHUMG00000044391	ENST00000278379.3:c.602C>T	11.37:g.35327749G>A	ENSP00000278379:p.Pro201Leu	854	B4DQE9|Q14417|Q541G6|U3KQQ4	Missense_Mutation	SNP	pfam_Na-dicarboxylate_symporter,prints_Na-dicarboxylate_symporter	p.P201L	ENST00000278379.3	37	c.602	CCDS31459.1	11	.	.	.	.	.	.	.	.	.	.	G	7.765	0.706126	0.15239	.	.	ENSG00000110436	ENST00000278379;ENST00000395750;ENST00000395753;ENST00000449068	T;T;T;T	0.55052	0.54;0.54;0.54;0.99	5.3	5.3	0.74995	.	1.710630	0.02633	N	0.104553	T	0.37812	0.1017	N	0.08118	0	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.10450	0.005;0.004	T	0.16041	-1.0416	10	0.25106	T	0.35	-0.1527	10.5503	0.45083	0.1199:0.0:0.8801:0.0	.	201;201	B4DQE9;P43004	.;EAA2_HUMAN	L	201;192;192;197	ENSP00000278379:P201L;ENSP00000379099:P192L;ENSP00000379102:P192L;ENSP00000406133:P197L	ENSP00000278379:P201L	P	-	2	0	SLC1A2	35284325	0.039000	0.19947	0.015000	0.15790	0.013000	0.08279	2.375000	0.44283	2.651000	0.90000	0.561000	0.74099	CCG	SLC1A2	-	pfam_Na-dicarboxylate_symporter	ENSG00000110436		0.498	SLC1A2-001	KNOWN	basic|CCDS	protein_coding	SLC1A2	HGNC	protein_coding	OTTHUMT00000258181.1	140	0.71	1	G	NM_004171		35327749	35327749	-1	no_errors	ENST00000278379	ensembl	human	known	69_37n	missense	156	35.27	85	SNP	0.020	A
SLC27A1	376497	genome.wustl.edu	37	19	17608208	17608208	+	Missense_Mutation	SNP	C	C	T	rs144747772		TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr19:17608208C>T	ENST00000252595.7	+	7	1238	c.1141C>T	c.(1141-1143)Cgc>Tgc	p.R381C	SLC27A1_ENST00000598424.1_Missense_Mutation_p.R202C|CTD-3131K8.2_ENST00000596643.1_lincRNA|SLC27A1_ENST00000442725.1_Missense_Mutation_p.R381C	NM_198580.1	NP_940982.1	Q6PCB7	S27A1_HUMAN	solute carrier family 27 (fatty acid transporter), member 1	381	Sufficient for oligomerization. {ECO:0000250}.				adiponectin-activated signaling pathway (GO:0033211)|cardiolipin biosynthetic process (GO:0032049)|cellular lipid metabolic process (GO:0044255)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid transport (GO:0015909)|medium-chain fatty acid transport (GO:0001579)|negative regulation of phospholipid biosynthetic process (GO:0071072)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phosphatidylglycerol biosynthetic process (GO:0006655)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylserine biosynthetic process (GO:0006659)|positive regulation of heat generation (GO:0031652)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to cold (GO:0009409)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fatty acid transporter activity (GO:0015245)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.R381C(2)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						CTTCGGCGTACGCCAAATCGG	0.697																																						dbGAP											2	Substitution - Missense(2)	breast(2)											50.0	43.0	45.0					19																	17608208		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC059399	CCDS32953.1	19p13.11	2013-07-15			ENSG00000130304	ENSG00000130304		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10995	protein-coding gene	gene with protein product		600691				10873384	Standard	NM_198580		Approved	FATP1, FATP, MGC71751, FLJ00336, ACSVL5	uc002ngu.1	Q6PCB7	OTTHUMG00000182878	ENST00000252595.7:c.1141C>T	19.37:g.17608208C>T	ENSP00000252595:p.Arg381Cys		A6NIH2|B7Z662	Missense_Mutation	SNP	pfam_AMP-dep_Synth/Lig	p.R381C	ENST00000252595.7	37	c.1141	CCDS32953.1	19	.	.	.	.	.	.	.	.	.	.	C	18.37	3.610214	0.66558	.	.	ENSG00000130304	ENST00000442725;ENST00000252595	T;T	0.47177	0.85;0.85	4.37	3.32	0.38043	AMP-dependent synthetase/ligase (1);	1.038110	0.07574	N	0.919123	T	0.51483	0.1677	L	0.38175	1.15	0.21604	N	0.999621	P;D;D	0.54601	0.919;0.967;0.967	P;P;P	0.53062	0.717;0.717;0.717	T	0.41142	-0.9525	10	0.56958	D	0.05	-9.6887	10.5761	0.45227	0.0:0.9019:0.0:0.0981	.	202;381;381	B7Z662;Q6PCB7;B7Z3U1	.;S27A1_HUMAN;.	C	381	ENSP00000413424:R381C;ENSP00000252595:R381C	ENSP00000252595:R381C	R	+	1	0	SLC27A1	17469208	0.000000	0.05858	0.766000	0.31476	0.937000	0.57800	-0.083000	0.11286	0.950000	0.37743	0.456000	0.33151	CGC	SLC27A1	-	pfam_AMP-dep_Synth/Lig	ENSG00000130304		0.697	SLC27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC27A1	HGNC	protein_coding	OTTHUMT00000464145.1	36	0.00	0	C	NM_198580		17608208	17608208	+1	no_errors	ENST00000252595	ensembl	human	known	69_37n	missense	29	34.09	15	SNP	0.284	T
TMEM132D	121256	genome.wustl.edu	37	12	129559224	129559224	+	Missense_Mutation	SNP	C	C	A			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr12:129559224C>A	ENST00000422113.2	-	9	2822	c.2496G>T	c.(2494-2496)caG>caT	p.Q832H	TMEM132D_ENST00000389441.4_Missense_Mutation_p.Q370H	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	832					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.Q832H(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TCCCCCATTCCTGCGAGGGTT	0.532																																						dbGAP											1	Substitution - Missense(1)	breast(1)											130.0	117.0	122.0					12																	129559224		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.2496G>T	12.37:g.129559224C>A	ENSP00000408581:p.Gln832His		Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	NULL	p.Q832H	ENST00000422113.2	37	c.2496	CCDS9266.1	12	.	.	.	.	.	.	.	.	.	.	C	3.791	-0.043679	0.07452	.	.	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.10477	2.87;3.65	4.2	-8.4	0.00965	.	0.600559	0.15764	N	0.245765	T	0.05640	0.0148	L	0.38953	1.18	0.09310	N	0.999994	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.002	T	0.27839	-1.0062	9	.	.	.	-4.0182	7.6501	0.28344	0.0996:0.6748:0.0998:0.1258	.	832;370	Q14C87;Q14C87-2	T132D_HUMAN;.	H	370;832	ENSP00000374092:Q370H;ENSP00000408581:Q832H	.	Q	-	3	2	TMEM132D	128125177	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-1.701000	0.01903	-1.462000	0.01907	0.462000	0.41574	CAG	TMEM132D	-	NULL	ENSG00000151952		0.532	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMEM132D	HGNC	protein_coding	OTTHUMT00000399592.1	346	0.57	2	C	NM_133448		129559224	129559224	-1	no_errors	ENST00000422113	ensembl	human	known	69_37n	missense	209	18.99	49	SNP	0.001	A
TOM1	10043	genome.wustl.edu	37	22	35695926	35695926	+	Missense_Mutation	SNP	A	A	G			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr22:35695926A>G	ENST00000449058.2	+	1	130	c.5A>G	c.(4-6)gAc>gGc	p.D2G	TOM1_ENST00000447733.1_Intron|RP3-510H16.3_ENST00000609073.1_RNA|TOM1_ENST00000436462.2_5'UTR|TOM1_ENST00000425375.1_Missense_Mutation_p.D2G|TOM1_ENST00000411850.1_Missense_Mutation_p.D2G|TOM1_ENST00000382034.5_5'UTR	NM_005488.2	NP_005479.1	O60784	TOM1_HUMAN	target of myb1 (chicken)	2					endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	clathrin binding (GO:0030276)	p.D2G(1)		NS(1)|breast(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)	19						GCAGCAATGGACTTTCTCCTG	0.687																																						dbGAP											1	Substitution - Missense(1)	breast(1)											56.0	44.0	48.0					22																	35695926		2199	4293	6492	-	-	-	SO:0001583	missense	0			AJ006973	CCDS13913.1, CCDS46696.1, CCDS46697.1, CCDS46698.1	22q13.1	2011-01-31	2001-11-28		ENSG00000100284	ENSG00000100284			11982	protein-coding gene	gene with protein product		604700	"""target of myb1 (chicken) homolog"""			10329004, 15047686	Standard	NM_005488		Approved		uc003anp.3	O60784	OTTHUMG00000150958	ENST00000449058.2:c.5A>G	22.37:g.35695926A>G	ENSP00000394466:p.Asp2Gly		B4DEL9|B4DNA1|Q5TIJ6|Q86X74	Missense_Mutation	SNP	pfam_VHS,pfam_GAT,superfamily_ENTH_VHS,smart_VHS_subgr,pirsf_TOM1,pfscan_GAT,pfscan_VHS	p.D2G	ENST00000449058.2	37	c.5	CCDS13913.1	22	.	.	.	.	.	.	.	.	.	.	A	19.02	3.745981	0.69418	.	.	ENSG00000100284	ENST00000456128;ENST00000449058;ENST00000411850;ENST00000425375;ENST00000450839;ENST00000451197	T;T;T;T	0.20738	2.05;2.05;2.05;2.05	5.16	5.16	0.70880	ENTH/VHS (2);	0.118506	0.56097	D	0.000030	T	0.39963	0.1098	L	0.46157	1.445	0.80722	D	1	D;B;P;P	0.67145	0.996;0.354;0.933;0.913	D;B;P;B	0.79784	0.993;0.101;0.461;0.276	T	0.17289	-1.0374	10	0.62326	D	0.03	-28.0313	15.1604	0.72778	1.0:0.0:0.0:0.0	.	2;2;2;2	O60784-3;B4DKQ5;O60784-2;O60784	.;.;.;TOM1_HUMAN	G	2	ENSP00000393714:D2G;ENSP00000394466:D2G;ENSP00000413697:D2G;ENSP00000394924:D2G	ENSP00000338422:D2G	D	+	2	0	TOM1	34025926	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	5.464000	0.66719	2.172000	0.68678	0.408000	0.27601	GAC	TOM1	-	superfamily_ENTH_VHS,pirsf_TOM1	ENSG00000100284		0.687	TOM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	TOM1	HGNC	protein_coding	OTTHUMT00000320641.1	25	0.00	0	A	NM_005488		35695926	35695926	+1	no_errors	ENST00000411850	ensembl	human	known	69_37n	missense	32	27.27	12	SNP	1.000	G
TSC22D1	8848	genome.wustl.edu	37	13	45148362	45148362	+	Missense_Mutation	SNP	G	G	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr13:45148362G>T	ENST00000458659.2	-	1	2339	c.1849C>A	c.(1849-1851)Ccc>Acc	p.P617T	TSC22D1_ENST00000501704.2_Intron|TSC22D1_ENST00000460842.1_5'Flank	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	617	Gln-rich.				negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P617T(1)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		CCTGGAAGGGGAGTTTGCACT	0.522																																						dbGAP											1	Substitution - Missense(1)	breast(1)											83.0	83.0	83.0					13																	45148362		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"""transforming growth factor beta 1 induced transcript 4"""	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.1849C>A	13.37:g.45148362G>T	ENSP00000397435:p.Pro617Thr		B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	pfam_TSC-22_Dip_Bun	p.P617T	ENST00000458659.2	37	c.1849	CCDS31966.1	13	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471692	0.43942	.	.	ENSG00000102804	ENST00000458659	T	0.32023	1.47	4.74	4.74	0.60224	.	0.000000	0.51477	D	0.000088	T	0.35480	0.0933	L	0.27053	0.805	0.80722	D	1	D	0.56968	0.978	P	0.55508	0.777	T	0.03840	-1.0999	10	0.30854	T	0.27	.	16.4617	0.84056	0.0:0.0:1.0:0.0	.	617	Q15714	T22D1_HUMAN	T	617	ENSP00000397435:P617T	ENSP00000397435:P617T	P	-	1	0	TSC22D1	44046362	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.436000	0.44819	2.466000	0.83321	0.491000	0.48974	CCC	TSC22D1	-	NULL	ENSG00000102804		0.522	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	TSC22D1	HGNC	protein_coding	OTTHUMT00000044743.2	66	0.00	0	G	NM_006022		45148362	45148362	-1	no_errors	ENST00000458659	ensembl	human	known	69_37n	missense	35	20.45	9	SNP	1.000	T
TSC22D1	8848	genome.wustl.edu	37	13	45150041	45150042	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr13:45150041_45150042insG	ENST00000458659.2	-	1	659_660	c.169_170insC	c.(169-171)gatfs	p.D57fs	TSC22D1_ENST00000501704.2_Frame_Shift_Ins_p.D57fs|TSC22D1_ENST00000460842.1_5'Flank	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	57					negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		AGGCGGAAAATCCTCGGAAGAT	0.629																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"""transforming growth factor beta 1 induced transcript 4"""	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.169_170insC	13.37:g.45150041_45150042insG	ENSP00000397435:p.Asp57fs		B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Frame_Shift_Ins	INS	pfam_TSC-22_Dip_Bun	p.D57fs	ENST00000458659.2	37	c.170_169	CCDS31966.1	13																																																																																			TSC22D1	-	NULL	ENSG00000102804		0.629	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	TSC22D1	HGNC	protein_coding	OTTHUMT00000044743.2	34	0.00	0	-	NM_006022		45150041	45150042	-1	no_errors	ENST00000458659	ensembl	human	known	69_37n	frame_shift_ins	22	46.34	19	INS	1.000:1.000	G
TYK2	7297	genome.wustl.edu	37	19	10463112	10463113	+	Frame_Shift_Ins	INS	-	-	G	rs373614901		TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr19:10463112_10463113insG	ENST00000525621.1	-	23	3796_3797	c.3315_3316insC	c.(3313-3318)cccacgfs	p.T1106fs	TYK2_ENST00000524462.1_Frame_Shift_Ins_p.T921fs|TYK2_ENST00000529422.1_Intron|TYK2_ENST00000264818.6_Frame_Shift_Ins_p.T1106fs	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	1106	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			GCTCTCACCGTGGGGGGGCTCT	0.599																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0				CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.3316dupC	19.37:g.10463119_10463119dupG	ENSP00000431885:p.Thr1106fs		Q6QB10|Q96CH0	Frame_Shift_Ins	INS	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_FERM_central,smart_Band_41_domain,smart_SH2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Tyr_kinase_non-rcpt_Jak/Tyk2,pfscan_FERM_domain,pfscan_Prot_kinase_cat_dom,prints_Tyr_kinase_non-rcpt_Jak/Tyk2,prints_Ser-Thr/Tyr_kinase_cat_dom,prints_Tyr_kinase_non-rcpt_TYK2_N	p.T1105fs	ENST00000525621.1	37	c.3316_3315	CCDS12236.1	19																																																																																			TYK2	-	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Tyr_kinase_non-rcpt_Jak/Tyk2,pfscan_Prot_kinase_cat_dom	ENSG00000105397		0.599	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TYK2	HGNC	protein_coding	OTTHUMT00000389443.1	14	0.00	0	-			10463112	10463113	-1	no_errors	ENST00000264818	ensembl	human	known	69_37n	frame_shift_ins	16	15.79	3	INS	0.001:0.001	G
WNT9A	7483	genome.wustl.edu	37	1	228111953	228111954	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr1:228111953_228111954insC	ENST00000272164.5	-	3	510_511	c.500_501insG	c.(499-501)ggcfs	p.G167fs		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	167					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal system morphogenesis (GO:0048704)|iris morphogenesis (GO:0061072)|mitotic cell cycle checkpoint (GO:0007093)|multicellular organismal development (GO:0007275)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of smoothened signaling pathway (GO:0045880)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)	p.G167fs*38(1)|p.C168fs*6(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Prostate(94;0.0405)				TGTCTCCGCAGCCCCCCCACTG	0.629																																						dbGAP											2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(1)|pancreas(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AB060283	CCDS31045.1	1q42	2008-02-05	2003-03-11	2003-03-14	ENSG00000143816	ENSG00000143816		"""Wingless-type MMTV integration sites"""	12778	protein-coding gene	gene with protein product		602863	"""wingless-type MMTV integration site family, member 14"""	WNT14		9441749	Standard	NM_003395		Approved		uc001hri.2	O14904	OTTHUMG00000037592	ENST00000272164.5:c.501dupG	1.37:g.228111960_228111960dupC	ENSP00000272164:p.Gly167fs		A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Frame_Shift_Ins	INS	pfam_Wnt,smart_Wnt,prints_Wnt,prints_Wnt14	p.C168fs	ENST00000272164.5	37	c.501_500	CCDS31045.1	1																																																																																			WNT9A	-	pfam_Wnt,smart_Wnt,prints_Wnt	ENSG00000143816		0.629	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WNT9A	HGNC	protein_coding	OTTHUMT00000091646.1	23	0.00	0	-	NM_003395		228111953	228111954	-1	no_errors	ENST00000272164	ensembl	human	known	69_37n	frame_shift_ins	23	11.54	3	INS	1.000:1.000	C
ZNF69	7620	genome.wustl.edu	37	19	12016540	12016540	+	Missense_Mutation	SNP	C	C	T			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr19:12016540C>T	ENST00000429654.2	+	4	1468	c.1328C>T	c.(1327-1329)cCc>cTc	p.P443L	ZNF69_ENST00000340180.5_Intron			Q9UC07	ZNF69_HUMAN	zinc finger protein 69	443					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|skin(2)	4				Lung(535;0.011)		GGAGAGAAGCCCTATGAATGT	0.448																																						dbGAP											0																																										-	-	-	SO:0001583	missense	0			X60076	CCDS32914.1	19p13.2	2013-01-08	2006-05-12		ENSG00000198429	ENSG00000198429		"""Zinc fingers, C2H2-type"", ""-"""	13138	protein-coding gene	gene with protein product		194543	"""zinc finger protein 69 (Cos5)"""			1639391	Standard	NM_021915		Approved	Cos5	uc002mst.4	Q9UC07	OTTHUMG00000156526	ENST00000429654.2:c.1328C>T	19.37:g.12016540C>T	ENSP00000402985:p.Pro443Leu		Q86VA7	Missense_Mutation	SNP	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.P443L	ENST00000429654.2	37	c.1328		19	.	.	.	.	.	.	.	.	.	.	c	14.43	2.532067	0.45073	.	.	ENSG00000198429	ENST00000429654	T	0.17054	2.3	1.22	0.131	0.14755	.	.	.	.	.	T	0.23451	0.0567	.	.	.	0.48341	D	0.999633	.	.	.	.	.	.	T	0.05599	-1.0875	6	0.66056	D	0.02	.	6.5769	0.22571	0.0:0.8187:0.0:0.1813	.	.	.	.	L	443	ENSP00000402985:P443L	ENSP00000402985:P443L	P	+	2	0	ZNF69	11877540	0.001000	0.12720	0.004000	0.12327	0.012000	0.07955	0.546000	0.23284	0.093000	0.17368	0.405000	0.27470	CCC	ZNF69	-	pfscan_Znf_C2H2	ENSG00000198429		0.448	ZNF69-002	KNOWN	basic|appris_principal	protein_coding	ZNF69	HGNC	protein_coding	OTTHUMT00000344082.1	108	0.00	0	C	NM_021915		12016540	12016540	+1	no_errors	ENST00000429654	ensembl	human	known	69_37n	missense	101	12.93	15	SNP	0.993	T
ZNF831	128611	genome.wustl.edu	37	20	57768868	57768868	+	Missense_Mutation	SNP	C	C	A			TCGA-AO-A0J5-01A-11W-A050-09	TCGA-AO-A0J5-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	93ae73f6-c355-47be-a355-faa78c0632d4	7a28e38f-8fc4-4ac7-974c-03925fab2da6	g.chr20:57768868C>A	ENST00000371030.2	+	1	2794	c.2794C>A	c.(2794-2796)Ctg>Atg	p.L932M		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	932							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.L932M(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GCTCTCTGCCCTGGCAGATAA	0.637																																						dbGAP											1	Substitution - Missense(1)	breast(1)											57.0	57.0	57.0					20																	57768868		1956	4156	6112	-	-	-	SO:0001583	missense	0			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.2794C>A	20.37:g.57768868C>A	ENSP00000360069:p.Leu932Met		Q5TDR4|Q8TCP0	Missense_Mutation	SNP	smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.L932M	ENST00000371030.2	37	c.2794	CCDS42894.1	20	.	.	.	.	.	.	.	.	.	.	C	8.853	0.945010	0.18356	.	.	ENSG00000124203	ENST00000371030	T	0.04360	3.64	3.85	-0.903	0.10534	.	2.889780	0.01145	N	0.006299	T	0.04003	0.0112	N	0.19112	0.55	0.09310	N	1	P	0.39964	0.697	B	0.38500	0.275	T	0.24584	-1.0156	10	0.46703	T	0.11	1.7693	3.709	0.08413	0.1473:0.3899:0.3686:0.0942	.	932	Q5JPB2	ZN831_HUMAN	M	932	ENSP00000360069:L932M	ENSP00000360069:L932M	L	+	1	2	ZNF831	57202263	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.203000	0.09438	-0.229000	0.09854	-0.211000	0.12701	CTG	ZNF831	-	NULL	ENSG00000124203		0.637	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	ZNF831	HGNC	protein_coding	OTTHUMT00000079916.2	30	0.00	0	C	NM_178457		57768868	57768868	+1	no_errors	ENST00000371030	ensembl	human	novel	69_37n	missense	15	31.82	7	SNP	0.000	A
