#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
ANKRD11	29123	genome.wustl.edu	37	16	89349106	89349106	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr16:89349106C>T	ENST00000301030.4	-	9	4304	c.3844G>A	c.(3844-3846)Gaa>Aaa	p.E1282K	ANKRD11_ENST00000378330.2_Missense_Mutation_p.E1282K	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1282	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.E1282K(1)		breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		TCCAACTTTTCAAGCAGGCTT	0.502																																						dbGAP											1	Substitution - Missense(1)	breast(1)											63.0	63.0	63.0					16																	89349106		2198	4300	6498	-	-	-	SO:0001583	missense	0			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.3844G>A	16.37:g.89349106C>T	ENSP00000301030:p.Glu1282Lys		Q6NTG1|Q6QMF8	Missense_Mutation	SNP	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	p.E1282K	ENST00000301030.4	37	c.3844	CCDS32513.1	16	.	.	.	.	.	.	.	.	.	.	C	19.60	3.857841	0.71834	.	.	ENSG00000167522	ENST00000301030;ENST00000378330	T;T	0.58358	0.34;0.34	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.70124	0.3188	M	0.67953	2.075	0.80722	D	1	D	0.76494	0.999	P	0.62740	0.906	T	0.72194	-0.4364	10	0.62326	D	0.03	.	18.9178	0.92513	0.0:1.0:0.0:0.0	.	1282	Q6UB99	ANR11_HUMAN	K	1282	ENSP00000301030:E1282K;ENSP00000367581:E1282K	ENSP00000301030:E1282K	E	-	1	0	ANKRD11	87876607	1.000000	0.71417	1.000000	0.80357	0.114000	0.19823	7.266000	0.78452	2.633000	0.89246	0.561000	0.74099	GAA	ANKRD11	-	NULL	ENSG00000167522		0.502	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ANKRD11	HGNC	protein_coding	OTTHUMT00000430462.3	86	0.00	0	C	NM_013275		89349106	89349106	-1	no_errors	ENST00000301030	ensembl	human	known	69_37n	missense	46	24.59	15	SNP	1.000	T
ARHGEF2	9181	genome.wustl.edu	37	1	155921009	155921009	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr1:155921009C>T	ENST00000361247.4	-	20	2413	c.2314G>A	c.(2314-2316)Gag>Aag	p.E772K	ARHGEF2_ENST00000462460.2_Missense_Mutation_p.E817K|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.E771K|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.E744K|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.E773K|ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000313695.7_Missense_Mutation_p.E744K	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	772					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.E744K(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)					TCCCGCCGCTCAGGGCCCTCA	0.652																																					Melanoma(178;35 2768 6610 28839)	dbGAP											1	Substitution - Missense(1)	breast(1)											10.0	12.0	11.0					1																	155921009		2117	4193	6310	-	-	-	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.2314G>A	1.37:g.155921009C>T	ENSP00000354837:p.Glu772Lys		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.E773K	ENST00000361247.4	37	c.2317	CCDS53376.1	1	.	.	.	.	.	.	.	.	.	.	C	19.47	3.833628	0.71258	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000313667	T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46	5.3	5.3	0.74995	.	0.000000	0.48767	D	0.000174	T	0.23965	0.0580	N	0.19112	0.55	0.29353	N	0.865234	D;P;D;D	0.62365	0.984;0.779;0.991;0.984	P;B;P;P	0.57101	0.655;0.204;0.813;0.655	T	0.03969	-1.0988	10	0.54805	T	0.06	-29.3362	16.4879	0.84189	0.0:1.0:0.0:0.0	.	816;772;771;773	D3DVA5;Q92974;Q92974-2;Q5VY93	.;ARHG2_HUMAN;.;.	K	744;772;773;744;771	ENSP00000315325:E744K;ENSP00000354837:E772K;ENSP00000357298:E773K;ENSP00000357299:E744K;ENSP00000314787:E771K	ENSP00000314787:E771K	E	-	1	0	ARHGEF2	154187633	0.982000	0.34865	0.967000	0.41034	0.616000	0.37450	3.308000	0.51896	2.762000	0.94881	0.655000	0.94253	GAG	ARHGEF2	-	NULL	ENSG00000116584		0.652	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	ARHGEF2	HGNC	protein_coding	OTTHUMT00000046204.2	11	0.00	0	C	NM_004723		155921009	155921009	-1	no_errors	ENST00000368315	ensembl	human	known	69_37n	missense	17	22.73	5	SNP	0.879	T
ATP9A	10079	genome.wustl.edu	37	20	50273503	50273503	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr20:50273503C>T	ENST00000338821.5	-	14	1744	c.1480G>A	c.(1480-1482)Gta>Ata	p.V494I	ATP9A_ENST00000311637.5_Missense_Mutation_p.V358I|ATP9A_ENST00000402822.1_Missense_Mutation_p.V373I	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	494					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.V494I(1)		breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GCCTGGTATACGCGGCAGGAG	0.577																																						dbGAP											1	Substitution - Missense(1)	breast(1)											91.0	68.0	76.0					20																	50273503		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"""ATPases / P-type"""	13540	protein-coding gene	gene with protein product		609126	"""ATPase, Class II, type 9A"""			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.1480G>A	20.37:g.50273503C>T	ENSP00000342481:p.Val494Ile		E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	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.V494I	ENST00000338821.5	37	c.1480	CCDS33489.1	20	.	.	.	.	.	.	.	.	.	.	C	17.51	3.408286	0.62399	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	T;T;T	0.64438	-0.1;-0.1;-0.1	4.89	4.89	0.63831	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	T	0.34308	0.0893	N	0.03983	-0.305	0.58432	D	0.999992	P;B	0.41313	0.745;0.269	B;B	0.25614	0.062;0.041	T	0.39014	-0.9634	10	0.30078	T	0.28	-19.8218	18.0422	0.89322	0.0:1.0:0.0:0.0	.	373;494	O75110-2;O75110	.;ATP9A_HUMAN	I	358;494;373	ENSP00000309086:V358I;ENSP00000342481:V494I;ENSP00000385875:V373I	ENSP00000309086:V358I	V	-	1	0	ATP9A	49706910	1.000000	0.71417	0.959000	0.39883	0.847000	0.48162	4.926000	0.63433	2.249000	0.74217	0.561000	0.74099	GTA	ATP9A	-	pfam_Dehalogen-like_hydro,superfamily_HAD-like_dom,superfamily_ATPase_cation_domN,tigrfam_ATPase_P-typ_Plipid-transl	ENSG00000054793		0.577	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	ATP9A	HGNC	protein_coding	OTTHUMT00000106494.1	101	0.00	0	C	NM_006045		50273503	50273503	-1	no_errors	ENST00000338821	ensembl	human	known	69_37n	missense	92	25.20	31	SNP	0.992	T
BMP15	9210	genome.wustl.edu	37	X	50659301	50659301	+	Silent	SNP	T	T	C			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chrX:50659301T>C	ENST00000252677.3	+	2	873	c.873T>C	c.(871-873)tgT>tgC	p.C291C		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	291					female gamete generation (GO:0007292)|granulosa cell development (GO:0060016)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)		p.C291C(1)		NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(1)	26	Ovarian(276;0.236)					ATAACCAGTGTTCCCTCCACC	0.502																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											107.0	91.0	96.0					X																	50659301		2203	4299	6502	-	-	-	SO:0001819	synonymous_variant	0			AF082349	CCDS14334.1	Xp11.2	2013-02-06			ENSG00000130385	ENSG00000130385		"""Bone morphogenetic proteins"""	1068	protein-coding gene	gene with protein product		300247				9849956	Standard	NM_005448		Approved	GDF9B	uc011mnw.2	O95972	OTTHUMG00000021525	ENST00000252677.3:c.873T>C	X.37:g.50659301T>C			Q17RM6|Q5JST1|Q9UMS1	Silent	SNP	pfam_TGF-b_C,smart_TGF-b_C,prints_Inhibin_asu	p.C291	ENST00000252677.3	37	c.873	CCDS14334.1	X																																																																																			BMP15	-	pfam_TGF-b_C,smart_TGF-b_C,prints_Inhibin_asu	ENSG00000130385		0.502	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BMP15	HGNC	protein_coding	OTTHUMT00000056572.1	127	0.78	1	T	NM_005448		50659301	50659301	+1	no_errors	ENST00000252677	ensembl	human	known	69_37n	silent	80	27.27	30	SNP	0.931	C
CACNB1	782	genome.wustl.edu	37	17	37347809	37347809	+	Missense_Mutation	SNP	G	G	T			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr17:37347809G>T	ENST00000394303.3	-	3	416	c.209C>A	c.(208-210)tCt>tAt	p.S70Y	CACNB1_ENST00000582877.1_5'UTR|CACNB1_ENST00000394310.3_Missense_Mutation_p.S70Y|CACNB1_ENST00000344140.5_Missense_Mutation_p.S70Y	NM_000723.4	NP_000714.3	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1 subunit	70					axon guidance (GO:0007411)|protein targeting to membrane (GO:0006612)|transport (GO:0006810)	sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.S70C(2)|p.S70Y(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	16					Dronedarone(DB04855)|Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	AGATACATCAGAGTCTGATGG	0.587																																					Esophageal Squamous(5;100 366 38393 41452 45827)	dbGAP											4	Substitution - Missense(4)	lung(2)|breast(2)											89.0	73.0	79.0					17																	37347809		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS11334.1, CCDS42311.1, CCDS45665.1	17q21-q22	2013-03-20			ENSG00000067191	ENSG00000067191		"""Calcium channel subunits"""	1401	protein-coding gene	gene with protein product		114207		CACNLB1		8381767, 8395940	Standard	NM_000723		Approved		uc002hrm.2	Q02641	OTTHUMG00000133217	ENST00000394303.3:c.209C>A	17.37:g.37347809G>T	ENSP00000377840:p.Ser70Tyr		A8K114|O15331|Q02639|Q02640|Q8N3X9|Q9C085|Q9UD79	Missense_Mutation	SNP	pfam_Guanylate_kin,pfam_VDCC_L_bsu,superfamily_SH3_domain,smart_Guanylate_kin/L-typ_Ca_channel,pfscan_SH3_domain,prints_VDCC_L_bsu,prints_VDCC_L_b1su	p.S70Y	ENST00000394303.3	37	c.209	CCDS42311.1	17	.	.	.	.	.	.	.	.	.	.	G	29.0	4.971655	0.92919	.	.	ENSG00000067191	ENST00000539338;ENST00000394303;ENST00000344140;ENST00000394310;ENST00000536613	T;T;T	0.80304	-1.31;-1.36;-1.32	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.90452	0.7010	M	0.83953	2.67	0.80722	D	1	D;D;D;D;D	0.76494	0.994;0.999;0.999;0.994;0.999	D;D;D;D;D	0.91635	0.989;0.998;0.999;0.983;0.998	D	0.91817	0.5464	10	0.87932	D	0	-9.8133	17.5951	0.88009	0.0:0.0:1.0:0.0	.	23;70;70;70;70	F5H6X1;Q6TME4;Q02641-2;Q02641-3;Q02641	.;.;.;.;CACB1_HUMAN	Y	20;70;70;70;23	ENSP00000377840:S70Y;ENSP00000345461:S70Y;ENSP00000377847:S70Y	ENSP00000345461:S70Y	S	-	2	0	CACNB1	34601335	1.000000	0.71417	0.998000	0.56505	0.943000	0.58893	9.592000	0.98245	2.503000	0.84419	0.585000	0.79938	TCT	CACNB1	-	pfam_VDCC_L_bsu	ENSG00000067191		0.587	CACNB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CACNB1	HGNC	protein_coding	OTTHUMT00000256945.3	124	0.00	0	G			37347809	37347809	-1	no_errors	ENST00000394303	ensembl	human	known	69_37n	missense	61	12.86	9	SNP	1.000	T
CHST9	83539	genome.wustl.edu	37	18	24497058	24497058	+	Missense_Mutation	SNP	T	T	G			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr18:24497058T>G	ENST00000284224.8	-	6	774	c.497A>C	c.(496-498)aAt>aCt	p.N166T	AQP4-AS1_ENST00000582605.1_RNA|AQP4-AS1_ENST00000578701.1_RNA|AQP4-AS1_ENST00000579964.1_RNA|CHST9_ENST00000580774.1_3'UTR|CHST9_ENST00000581714.1_Missense_Mutation_p.N166T|AQP4-AS1_ENST00000568797.1_RNA	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	166					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)	p.N166T(1)|p.N81T(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|skin(3)	28	all_lung(6;0.0145)|Ovarian(20;0.124)					CTTCCATTTATTATCTTTGAC	0.388																																						dbGAP											2	Substitution - Missense(2)	breast(2)											135.0	127.0	129.0					18																	24497058		1826	4071	5897	-	-	-	SO:0001583	missense	0			AF239821	CCDS42422.1, CCDS58618.1	18q11.2	2011-04-28			ENSG00000154080	ENSG00000154080		"""Sulfotransferases, membrane-bound"""	19898	protein-coding gene	gene with protein product		610191				11139592, 11445554	Standard	NM_031422		Approved	GALNAC4ST-2, GALNAC-4-ST2	uc002kwe.4	Q7L1S5		ENST00000284224.8:c.497A>C	18.37:g.24497058T>G	ENSP00000284224:p.Asn166Thr		Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Missense_Mutation	SNP	pfam_Sulfotransferase	p.N166T	ENST00000284224.8	37	c.497	CCDS42422.1	18	.	.	.	.	.	.	.	.	.	.	T	2.624	-0.287852	0.05605	.	.	ENSG00000154080	ENST00000284224	T	0.64991	-0.13	6.16	1.17	0.20885	.	1.605430	0.02707	N	0.112341	T	0.44767	0.1309	N	0.19112	0.55	0.09310	N	1	B	0.22800	0.075	B	0.21360	0.034	T	0.18178	-1.0345	10	0.12103	T	0.63	-2.1638	5.6782	0.17761	0.1207:0.3417:0.0:0.5376	.	166	Q7L1S5	CHST9_HUMAN	T	166	ENSP00000284224:N166T	ENSP00000284224:N166T	N	-	2	0	CHST9	22751056	0.001000	0.12720	0.042000	0.18584	0.268000	0.26511	0.341000	0.19909	-0.023000	0.13963	0.528000	0.53228	AAT	CHST9	-	NULL	ENSG00000154080		0.388	CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHST9	HGNC	protein_coding	OTTHUMT00000446549.1	226	0.00	0	T	NM_031422		24497058	24497058	-1	no_errors	ENST00000284224	ensembl	human	known	69_37n	missense	78	48.03	73	SNP	0.030	G
CTNNA2	1496	genome.wustl.edu	37	2	80136851	80136851	+	Silent	SNP	C	C	T			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr2:80136851C>T	ENST00000402739.4	+	6	989	c.984C>T	c.(982-984)cgC>cgT	p.R328R	CTNNA2_ENST00000466387.1_Silent_p.R328R|CTNNA2_ENST00000540488.1_Silent_p.R328R|CTNNA2_ENST00000541047.1_Silent_p.R328R|CTNNA2_ENST00000496558.1_Silent_p.R328R|CTNNA2_ENST00000361291.4_Silent_p.R362R	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	328					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)	p.R328R(2)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						ACGACCGGCGCGAGAGGATCG	0.637																																						dbGAP											2	Substitution - coding silent(2)	breast(2)											50.0	56.0	54.0					2																	80136851		2082	4220	6302	-	-	-	SO:0001819	synonymous_variant	0				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.984C>T	2.37:g.80136851C>T			B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Silent	SNP	pfam_Vinculin/catenin,superfamily_Vinculin/catenin,prints_Alpha_catenin,prints_Vinculin	p.R362	ENST00000402739.4	37	c.1086		2																																																																																			CTNNA2	-	pfam_Vinculin/catenin	ENSG00000066032		0.637	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	CTNNA2	HGNC	protein_coding	OTTHUMT00000328511.4	35	0.00	0	C	NM_004389		80136851	80136851	+1	no_errors	ENST00000361291	ensembl	human	known	69_37n	silent	22	18.52	5	SNP	0.309	T
DROSHA	29102	genome.wustl.edu	37	5	31526807	31526807	+	Missense_Mutation	SNP	A	A	C			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr5:31526807A>C	ENST00000511367.2	-	4	477	c.233T>G	c.(232-234)tTt>tGt	p.F78C	DROSHA_ENST00000504361.1_5'Flank|DROSHA_ENST00000513349.1_Missense_Mutation_p.F78C|DROSHA_ENST00000442743.1_Missense_Mutation_p.F78C|DROSHA_ENST00000344624.3_Missense_Mutation_p.F78C	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	78	Pro-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)	p.F78C(1)		breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						GAAGGGTACAAAGTCTGGTCG	0.587																																						dbGAP											1	Substitution - Missense(1)	breast(1)											33.0	38.0	37.0					5																	31526807		1961	4137	6098	-	-	-	SO:0001583	missense	0			AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.233T>G	5.37:g.31526807A>C	ENSP00000425979:p.Phe78Cys		E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	pfam_RNase_III_dom,pfam_Ds-RNA-bd,superfamily_RNase_III_dom,smart_RNase_III_dom,smart_Ds-RNA-bd,pfscan_Ds-RNA-bd,pfscan_RNase_III_dom	p.F78C	ENST00000511367.2	37	c.233	CCDS47195.1	5	.	.	.	.	.	.	.	.	.	.	A	14.97	2.695003	0.48202	.	.	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188;ENST00000507438	T;T;T;T;T	0.59502	1.07;1.07;0.5;0.5;0.26	5.04	5.04	0.67666	.	0.061105	0.64402	D	0.000003	T	0.56031	0.1958	N	0.24115	0.695	0.50039	D	0.999848	D;D;D	0.65815	0.995;0.983;0.983	P;P;P	0.57468	0.821;0.615;0.615	T	0.60367	-0.7277	10	0.66056	D	0.02	-12.9574	10.1043	0.42524	0.8506:0.0:0.0:0.1494	.	78;78;78	Q9NRR4-2;E7EMP9;Q9NRR4	.;.;RNC_HUMAN	C	78;78;78;78;71;71;78	ENSP00000425979:F78C;ENSP00000339845:F78C;ENSP00000409335:F78C;ENSP00000424161:F78C;ENSP00000430921:F78C	ENSP00000265075:F71C	F	-	2	0	DROSHA	31562564	1.000000	0.71417	0.986000	0.45419	0.987000	0.75469	4.668000	0.61568	1.905000	0.55150	0.460000	0.39030	TTT	DROSHA	-	NULL	ENSG00000113360		0.587	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	DROSHA	HGNC	protein_coding	OTTHUMT00000366561.3	61	0.00	0	A	NM_013235		31526807	31526807	-1	no_errors	ENST00000344624	ensembl	human	known	69_37n	missense	42	26.32	15	SNP	1.000	C
FARP2	9855	genome.wustl.edu	37	2	242312707	242312707	+	Splice_Site	SNP	T	T	A			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr2:242312707T>A	ENST00000264042.3	+	2	353		c.e2+2		FARP2_ENST00000373287.4_Splice_Site|FARP2_ENST00000545004.1_Splice_Site|FARP2_ENST00000479427.1_Splice_Site	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2						actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.?(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		GACATTGAGGTAAGAAGCATG	0.403																																						dbGAP											1	Unknown(1)	breast(1)											71.0	74.0	73.0					2																	242312707		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.183+2T>A	2.37:g.242312707T>A			B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Splice_Site	SNP	-	e1+2	ENST00000264042.3	37	c.183+2	CCDS33424.1	2	.	.	.	.	.	.	.	.	.	.	T	13.11	2.138521	0.37728	.	.	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287;ENST00000418082;ENST00000445489	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4463	0.67352	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	FARP2	241961380	1.000000	0.71417	0.990000	0.47175	0.325000	0.28411	6.224000	0.72265	2.143000	0.66587	0.460000	0.39030	.	FARP2	-	-	ENSG00000006607		0.403	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FARP2	HGNC	protein_coding	OTTHUMT00000323153.1	93	0.00	0	T		Intron	242312707	242312707	+1	no_errors	ENST00000264042	ensembl	human	known	69_37n	splice_site	76	29.09	32	SNP	1.000	A
HIST1H3B	8358	genome.wustl.edu	37	6	26031937	26031937	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr6:26031937C>T	ENST00000244661.2	-	1	351	c.352G>A	c.(352-354)Gtg>Atg	p.V118M		NM_003537.3	NP_003528.1	P68431	H31_HUMAN	histone cluster 1, H3b	118					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)	p.V118M(1)		breast(3)|central_nervous_system(10)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	25						ATAATAGTCACTCGCTTAGCA	0.512																																						dbGAP											1	Substitution - Missense(1)	breast(1)											77.0	78.0	77.0					6																	26031937		2203	4300	6503	-	-	-	SO:0001583	missense	0			X00090	CCDS4573.1	6p22.1	2011-01-27	2006-10-11	2003-03-14	ENSG00000124693	ENSG00000274267		"""Histones / Replication-dependent"""	4776	protein-coding gene	gene with protein product		602819	"""H3 histone family, member L"", ""histone 1, H3b"""	H3FL		6647026, 9119399, 12408966	Standard	NM_003537		Approved	H3/l	uc003nfs.1	P68431	OTTHUMG00000014415	ENST00000244661.2:c.352G>A	6.37:g.26031937C>T	ENSP00000244661:p.Val118Met		A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	pfam_Histone_core_D,superfamily_Histone-fold,smart_Histone_H3,prints_Histone_H3	p.V118M	ENST00000244661.2	37	c.352	CCDS4573.1	6	.	.	.	.	.	.	.	.	.	.	c	14.88	2.668045	0.47677	.	.	ENSG00000124693	ENST00000244661	T	0.50001	0.76	5.17	5.17	0.71159	.	.	.	.	.	T	0.61048	0.2316	.	.	.	0.45621	D	0.998557	.	.	.	.	.	.	T	0.65742	-0.6094	6	0.87932	D	0	.	18.0207	0.89253	0.0:1.0:0.0:0.0	.	.	.	.	M	118	ENSP00000244661:V118M	ENSP00000244661:V118M	V	-	1	0	HIST1H3B	26139916	1.000000	0.71417	0.970000	0.41538	0.008000	0.06430	7.492000	0.81482	2.545000	0.85829	0.561000	0.74099	GTG	HIST1H3B	-	pfam_Histone_core_D,superfamily_Histone-fold,smart_Histone_H3,prints_Histone_H3	ENSG00000124693		0.512	HIST1H3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HIST1H3B	HGNC	protein_coding	OTTHUMT00000040077.1	68	0.00	0	C	NM_003537		26031937	26031937	-1	no_errors	ENST00000244661	ensembl	human	known	69_37n	missense	63	19.23	15	SNP	1.000	T
KCNJ6	3763	genome.wustl.edu	37	21	39087178	39087178	+	Missense_Mutation	SNP	C	C	A			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr21:39087178C>A	ENST00000609713.1	-	3	871	c.282G>T	c.(280-282)ttG>ttT	p.L94F	KCNJ6_ENST00000288309.6_Missense_Mutation_p.L94F|KCNJ6-IT1_ENST00000435001.1_RNA	NM_002240.3	NP_002231.1	P48051	KCNJ6_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 6	94					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)|inward rectifier potassium channel activity (GO:0005242)	p.L94F(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22					Halothane(DB01159)	TGACAAAAATCAATAGGTTGA	0.468																																					Pancreas(48;379 1118 2936 19024 28214)	dbGAP											1	Substitution - Missense(1)	breast(1)											176.0	167.0	170.0					21																	39087178		1943	4148	6091	-	-	-	SO:0001583	missense	0			U24660	CCDS42927.1	21q22.1	2011-07-05			ENSG00000157542	ENSG00000157542		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6267	protein-coding gene	gene with protein product		600877		KCNJ7		7796919, 16382105	Standard	NM_002240		Approved	Kir3.2, GIRK2, KATP2, BIR1, hiGIRK2	uc002ywo.3	P48051	OTTHUMG00000086667	ENST00000609713.1:c.282G>T	21.37:g.39087178C>A	ENSP00000477437:p.Leu94Phe		Q3MJ74|Q53WW6	Missense_Mutation	SNP	pfam_K_chnl_inward-rec_Kir_Cr2,superfamily_Ig_E-set,pirsf_K_chnl_inward-rec_Kir,prints_K_chnl_inward-rec_Kir_Cr2,prints_K_chnl_inward-rec_Kir3.2	p.L94F	ENST00000609713.1	37	c.282	CCDS42927.1	21	.	.	.	.	.	.	.	.	.	.	C	10.72	1.429028	0.25726	.	.	ENSG00000157542	ENST00000400482;ENST00000288309	D;D	0.94793	-3.52;-3.52	6.17	-3.32	0.04973	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.110846	0.64402	N	0.000018	D	0.86343	0.5910	N	0.21583	0.68	0.38429	D	0.946398	B	0.06786	0.001	B	0.15052	0.012	T	0.67673	-0.5610	10	0.35671	T	0.21	.	9.3385	0.38065	0.0901:0.2355:0.5627:0.1117	.	94	P48051	IRK6_HUMAN	F	94	ENSP00000383330:L94F;ENSP00000288309:L94F	ENSP00000288309:L94F	L	-	3	2	KCNJ6	38009048	0.999000	0.42202	0.562000	0.28370	0.986000	0.74619	0.567000	0.23608	-0.679000	0.05217	0.655000	0.94253	TTG	KCNJ6	-	pfam_K_chnl_inward-rec_Kir_Cr2,pirsf_K_chnl_inward-rec_Kir,prints_K_chnl_inward-rec_Kir_Cr2	ENSG00000157542		0.468	KCNJ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNJ6	HGNC	protein_coding	OTTHUMT00000194828.2	160	0.00	0	C	NM_002240		39087178	39087178	-1	no_errors	ENST00000288309	ensembl	human	known	69_37n	missense	148	11.38	19	SNP	0.977	A
KIAA2026	158358	genome.wustl.edu	37	9	5921255	5921255	+	Missense_Mutation	SNP	G	G	T			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr9:5921255G>T	ENST00000399933.3	-	8	4740	c.4741C>A	c.(4741-4743)Caa>Aaa	p.Q1581K	KIAA2026_ENST00000381461.2_Missense_Mutation_p.Q1551K	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1581								p.Q756K(1)|p.Q1581K(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		ACAATTGCTTGACCTATGTTT	0.373																																						dbGAP											2	Substitution - Missense(2)	breast(2)											178.0	161.0	167.0					9																	5921255		1881	4121	6002	-	-	-	SO:0001583	missense	0			AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.4741C>A	9.37:g.5921255G>T	ENSP00000382815:p.Gln1581Lys		A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	superfamily_Bromodomain	p.Q1581K	ENST00000399933.3	37	c.4741		9	.	.	.	.	.	.	.	.	.	.	G	14.72	2.621142	0.46736	.	.	ENSG00000183354	ENST00000399933;ENST00000381461	.	.	.	5.0	4.08	0.47627	.	0.093857	0.45361	D	0.000372	T	0.41282	0.1152	L	0.34521	1.04	0.29639	N	0.844899	B	0.33612	0.419	B	0.38500	0.275	T	0.37079	-0.9721	9	0.27082	T	0.32	-6.2142	15.365	0.74513	0.0:0.1401:0.8599:0.0	.	1581	Q5HYC2	K2026_HUMAN	K	1581;1551	.	ENSP00000370870:Q1551K	Q	-	1	0	KIAA2026	5911255	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.944000	0.75940	1.306000	0.44926	0.484000	0.47621	CAA	KIAA2026	-	NULL	ENSG00000183354		0.373	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	KIAA2026	HGNC	protein_coding	OTTHUMT00000051652.2	317	0.31	1	G	NM_001017969		5921255	5921255	-1	no_errors	ENST00000399933	ensembl	human	novel	69_37n	missense	194	31.45	89	SNP	1.000	T
KIR3DL1	3811	genome.wustl.edu	37	19	55284926	55284926	+	Intron	SNP	G	G	A			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr19:55284926G>A	ENST00000538269.1	+	2	61				KIR2DL3_ENST00000434419.2_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR2DL1_ENST00000336077.6_Missense_Mutation_p.R71H|KIR2DL1_ENST00000291633.7_Missense_Mutation_p.R71H|KIR3DL1_ENST00000541392.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)	p.R71H(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		GACACTTTGCGCCTCATTGGA	0.502																																						dbGAP											1	Substitution - Missense(1)	breast(1)											105.0	94.0	98.0					19																	55284926		2174	4195	6369	-	-	-	SO:0001627	intron_variant	0			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000538269.1:c.35-44063G>A	19.37:g.55284926G>A			O43473|Q14946|Q16541	Missense_Mutation	SNP	pfam_Immunoglobulin,smart_Ig_sub	p.R71H	ENST00000538269.1	37	c.212		19	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.211317	0.00289	.	.	ENSG00000125498	ENST00000336077;ENST00000291633	T;T	0.21734	1.99;1.99	1.24	0.0778	0.14409	.	.	.	.	.	T	0.07954	0.0199	N	0.16066	0.365	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.001;0.004	T	0.38802	-0.9644	9	0.02654	T	1	.	3.1268	0.06409	0.7092:0.0:0.2908:0.0	.	71;71	Q6IST4;Q6H2H3	.;.	H	71	ENSP00000336769:R71H;ENSP00000291633:R71H	ENSP00000291633:R71H	R	+	2	0	KIR2DL1	59976738	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.668000	0.05268	-0.007000	0.14345	-0.507000	0.04495	CGC	KIR2DL1	-	pfam_Immunoglobulin,smart_Ig_sub	ENSG00000125498		0.502	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	KIR2DL1	HGNC	protein_coding		479	0.00	0	G	NM_013289		55284926	55284926	+1	no_errors	ENST00000336077	ensembl	human	known	69_37n	missense	258	27.53	98	SNP	0.000	A
LGR4	55366	genome.wustl.edu	37	11	27393924	27393924	+	Silent	SNP	A	A	C			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr11:27393924A>C	ENST00000379214.4	-	16	1844	c.1401T>G	c.(1399-1401)gcT>gcG	p.A467A	LGR4_ENST00000389858.4_Silent_p.A443A	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	467					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)	p.A467A(1)		NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						AGCACTGATAAGCATATGGTA	0.383																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											114.0	112.0	112.0					11																	27393924		2202	4299	6501	-	-	-	SO:0001819	synonymous_variant	0			AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"""GPCR / Class A : Orphans"""	13299	protein-coding gene	gene with protein product		606666	"""G protein-coupled receptor 48"", ""leucine-rich repeat-containing G protein-coupled receptor 4"""	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.1401T>G	11.37:g.27393924A>C			A6NCH3|G5E9B3|Q8N537|Q9NYD1	Silent	SNP	pfam_Leu-rich_rpt,pfam_7TM_GPCR_Rhodpsn,pfam_LRR-contain_N,smart_LRR-contain_N,smart_Leu-rich_rpt_typical-subtyp,pfscan_GPCR_Rhodpsn_supfam,prints_Gphrmn_rcpt,prints_7TM_GPCR_Rhodpsn	p.A467	ENST00000379214.4	37	c.1401	CCDS31449.1	11																																																																																			LGR4	-	NULL	ENSG00000205213		0.383	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LGR4	HGNC	protein_coding	OTTHUMT00000257467.1	191	0.52	1	A	NM_018490		27393924	27393924	-1	no_errors	ENST00000379214	ensembl	human	known	69_37n	silent	75	18.48	17	SNP	1.000	C
MTR	4548	genome.wustl.edu	37	1	237015858	237015858	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr1:237015858C>T	ENST00000366577.5	+	17	2127	c.1733C>T	c.(1732-1734)tCc>tTc	p.S578F	MTR_ENST00000535889.1_Missense_Mutation_p.S578F	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	578	Pterin-binding. {ECO:0000255|PROSITE- ProRule:PRU00334}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)	p.S578F(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	GGAGGTCTTTCCAACTTGTCC	0.408																																						dbGAP											1	Substitution - Missense(1)	breast(1)											75.0	77.0	76.0					1																	237015858		2203	4300	6503	-	-	-	SO:0001583	missense	0			U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.1733C>T	1.37:g.237015858C>T	ENSP00000355536:p.Ser578Phe		A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Missense_Mutation	SNP	pfam_S_MeTrfase,pfam_VitB12-dep_Met_synth_activ_dom,pfam_Pterin-binding,pfam_Cbl-bd_cap,pfam_Cobalamin-bd,superfamily_VitB12-dep_Met_synth_activ_dom,superfamily_S_MeTrfase,superfamily_Dihydropteroate_synth-like,superfamily_Cobalamin-bd,superfamily_Cbl-bd_cap,pirsf_MetH,pfscan_VitB12-dep_Met_synth_activ_dom,pfscan_S_MeTrfase,pfscan_Pterin-binding,tigrfam_MetH	p.S578F	ENST00000366577.5	37	c.1733	CCDS1614.1	1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.002886	0.93287	.	.	ENSG00000116984	ENST00000366577;ENST00000535889;ENST00000366576	D;D;D	0.93133	-3.17;-3.17;-3.17	5.45	5.45	0.79879	Dihydropteroate synthase-like (1);Pterin-binding (3);	0.000000	0.85682	D	0.000000	D	0.98147	0.9388	H	0.97465	4.01	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98953	1.0795	10	0.87932	D	0	-18.8818	19.4782	0.94998	0.0:1.0:0.0:0.0	.	578;578	B7ZLW7;Q99707	.;METH_HUMAN	F	578;578;132	ENSP00000355536:S578F;ENSP00000441845:S578F;ENSP00000355535:S132F	ENSP00000355535:S132F	S	+	2	0	MTR	235082481	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.431000	0.80335	2.838000	0.97847	0.655000	0.94253	TCC	MTR	-	pfam_Pterin-binding,superfamily_Dihydropteroate_synth-like,pirsf_MetH,pfscan_Pterin-binding,tigrfam_MetH	ENSG00000116984		0.408	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MTR	HGNC	protein_coding	OTTHUMT00000096632.2	69	0.00	0	C	NM_000254		237015858	237015858	+1	no_errors	ENST00000366577	ensembl	human	known	69_37n	missense	98	14.04	16	SNP	1.000	T
MTR	4548	genome.wustl.edu	37	1	237023136	237023136	+	Missense_Mutation	SNP	C	C	A			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr1:237023136C>A	ENST00000366577.5	+	19	2351	c.1957C>A	c.(1957-1959)Caa>Aaa	p.Q653K	MTR_ENST00000535889.1_Missense_Mutation_p.Q653K	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	653					cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)	p.Q653K(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	AATTCAGACTCAAGGCACAGG	0.413																																						dbGAP											1	Substitution - Missense(1)	breast(1)											118.0	112.0	114.0					1																	237023136		2203	4300	6503	-	-	-	SO:0001583	missense	0			U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.1957C>A	1.37:g.237023136C>A	ENSP00000355536:p.Gln653Lys		A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Missense_Mutation	SNP	pfam_S_MeTrfase,pfam_VitB12-dep_Met_synth_activ_dom,pfam_Pterin-binding,pfam_Cbl-bd_cap,pfam_Cobalamin-bd,superfamily_VitB12-dep_Met_synth_activ_dom,superfamily_S_MeTrfase,superfamily_Dihydropteroate_synth-like,superfamily_Cobalamin-bd,superfamily_Cbl-bd_cap,pirsf_MetH,pfscan_VitB12-dep_Met_synth_activ_dom,pfscan_S_MeTrfase,pfscan_Pterin-binding,tigrfam_MetH	p.Q653K	ENST00000366577.5	37	c.1957	CCDS1614.1	1	.	.	.	.	.	.	.	.	.	.	C	0.339	-0.951550	0.02285	.	.	ENSG00000116984	ENST00000417743;ENST00000366577;ENST00000535889;ENST00000366576	T;T;T	0.81415	-0.14;-0.16;-1.49	5.24	3.31	0.37934	.	0.756865	0.12931	N	0.427357	T	0.59459	0.2195	N	0.03608	-0.345	0.23449	N	0.997659	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.53556	-0.8422	10	0.59425	D	0.04	-1.2476	8.2162	0.31514	0.2744:0.6524:0.0:0.0733	.	653;653;653	B7ZLW8;B7ZLW7;Q99707	.;.;METH_HUMAN	K	507;653;653;207	ENSP00000355536:Q653K;ENSP00000441845:Q653K;ENSP00000355535:Q207K	ENSP00000355535:Q207K	Q	+	1	0	MTR	235089759	0.278000	0.24230	0.960000	0.40013	0.038000	0.13279	0.423000	0.21313	1.423000	0.47198	0.655000	0.94253	CAA	MTR	-	pirsf_MetH,tigrfam_MetH	ENSG00000116984		0.413	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MTR	HGNC	protein_coding	OTTHUMT00000096632.2	127	0.00	0	C	NM_000254		237023136	237023136	+1	no_errors	ENST00000366577	ensembl	human	known	69_37n	missense	113	13.74	18	SNP	0.644	A
MYH13	8735	genome.wustl.edu	37	17	10248682	10248682	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr17:10248682C>T	ENST00000418404.3	-	14	1584	c.1421G>A	c.(1420-1422)aGc>aAc	p.S474N	MYH13_ENST00000252172.4_Missense_Mutation_p.S474N			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	474	Myosin motor.				cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.S474N(2)		breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CTGCTCCAGGCTGTTGAACTG	0.438																																						dbGAP											2	Substitution - Missense(2)	breast(2)											135.0	127.0	130.0					17																	10248682		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.1421G>A	17.37:g.10248682C>T	ENSP00000404570:p.Ser474Asn		O95252|Q9P0U8	Missense_Mutation	SNP	pfam_Myosin_tail,pfam_Myosin_head_motor_dom,pfam_Myosin_N,superfamily_Prefoldin,smart_Myosin_head_motor_dom,prints_Myosin_head_motor_dom,pfscan_IQ_motif_EF-hand-BS	p.S474N	ENST00000418404.3	37	c.1421	CCDS45613.1	17	.	.	.	.	.	.	.	.	.	.	C	15.02	2.709575	0.48517	.	.	ENSG00000006788	ENST00000252172;ENST00000418404	D	0.91464	-2.85	4.46	4.46	0.54185	Myosin head, motor domain (3);	.	.	.	.	D	0.96062	0.8717	M	0.93375	3.41	0.34705	D	0.727196	P	0.36065	0.535	P	0.52646	0.705	D	0.99964	1.1814	9	0.72032	D	0.01	.	17.6701	0.88214	0.0:1.0:0.0:0.0	.	474	Q9UKX3	MYH13_HUMAN	N	474;149	ENSP00000252172:S474N	ENSP00000252172:S474N	S	-	2	0	MYH13	10189407	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.070000	0.30653	2.471000	0.83476	0.655000	0.94253	AGC	MYH13	-	pfam_Myosin_head_motor_dom,smart_Myosin_head_motor_dom,prints_Myosin_head_motor_dom	ENSG00000006788		0.438	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	MYH13	HGNC	protein_coding	OTTHUMT00000442255.1	270	0.00	0	C	NM_003802		10248682	10248682	-1	no_errors	ENST00000252172	ensembl	human	known	69_37n	missense	128	51.49	138	SNP	1.000	T
NOTCH3	4854	genome.wustl.edu	37	19	15281551	15281551	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr19:15281551C>T	ENST00000263388.2	-	26	4897	c.4822G>A	c.(4822-4824)Gct>Act	p.A1608T		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1608					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.A1608T(2)		breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			AGGTAGTCAGCGGCGCTCTGG	0.662																																						dbGAP											2	Substitution - Missense(2)	breast(2)											24.0	23.0	24.0					19																	15281551		2203	4300	6503	-	-	-	SO:0001583	missense	0			U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.4822G>A	19.37:g.15281551C>T	ENSP00000263388:p.Ala1608Thr		Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	pfam_EGF-like_dom,pfam_EGF-like_Ca-bd,pfam_Ankyrin_rpt,pfam_Notch_dom,pfam_Notch_NODP_dom,pfam_Notch_NOD_dom,pfam_EGF_extracell,pfam_DUF3454_notch,superfamily_Ankyrin_rpt-contain_dom,superfamily_Notch_dom,smart_EGF-like,smart_EGF-like_Ca-bd,smart_Notch_dom,smart_Ankyrin_rpt,pirsf_Notch,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_EG-like_dom,pfscan_Notch_dom,prints_Notch_3,prints_Notch_dom	p.A1608T	ENST00000263388.2	37	c.4822	CCDS12326.1	19	.	.	.	.	.	.	.	.	.	.	C	23.9	4.474301	0.84640	.	.	ENSG00000074181	ENST00000263388	T	0.52754	0.65	3.8	3.8	0.43715	Notch, NODP domain (1);	.	.	.	.	T	0.72415	0.3457	M	0.89095	3.005	0.54753	D	0.999988	D	0.89917	1.0	D	0.97110	1.0	T	0.79818	-0.1643	9	0.87932	D	0	.	14.6492	0.68784	0.0:1.0:0.0:0.0	.	1608	Q9UM47	NOTC3_HUMAN	T	1608	ENSP00000263388:A1608T	ENSP00000263388:A1608T	A	-	1	0	NOTCH3	15142551	1.000000	0.71417	0.063000	0.19743	0.522000	0.34438	7.139000	0.77314	1.984000	0.57885	0.485000	0.47835	GCT	NOTCH3	-	pfam_Notch_NODP_dom,pirsf_Notch	ENSG00000074181		0.662	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NOTCH3	HGNC	protein_coding	OTTHUMT00000465714.1	17	0.00	0	C	NM_000435		15281551	15281551	-1	no_errors	ENST00000263388	ensembl	human	known	69_37n	missense	10	47.62	10	SNP	0.999	T
PHRF1	57661	genome.wustl.edu	37	11	608503	608514	+	In_Frame_Del	DEL	GGACGCGCTCTG	GGACGCGCTCTG	-	rs553793466|rs144630030|rs370880150|rs376527396	byFrequency	TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	GGACGCGCTCTG	GGACGCGCTCTG					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr11:608503_608514delGGACGCGCTCTG	ENST00000264555.5	+	14	3175_3186	c.3047_3058delGGACGCGCTCTG	c.(3046-3060)cggacgcgctctggg>cgg	p.TRSG1017del	PHRF1_ENST00000413872.2_In_Frame_Del_p.TRSG1015del|PHRF1_ENST00000416188.2_In_Frame_Del_p.TRSG1016del|PHRF1_ENST00000533464.1_In_Frame_Del_p.TRSG1013del	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1017	Arg-rich.				mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)	p.G1020_S1023delGTRS(2)|p.R1023L(1)|p.R1018L(1)|p.G1025_S1028delGTRS(1)		breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GAGCACGGACGGACGCGCTCTGGGACGCGCTC	0.675														425	0.0848642	0.2368	0.0519	5008	,	,		20295	0.001		0.0527	False		,,,				2504	0.0225					dbGAP											5	Deletion - In frame(3)|Substitution - Missense(2)	lung(2)|breast(2)|ovary(1)								711,3413		97,517,1448						-2.3	0.0		dbSNP_132	33	442,7712		38,366,3673	no	coding	PHRF1	NM_020901.2		135,883,5121	A1A1,A1R,RR		5.4207,17.2405,9.3908				1153,11125				-	-	-	SO:0001651	inframe_deletion	0			BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.3047_3058delGGACGCGCTCTG	11.37:g.608503_608514delGGACGCGCTCTG	ENSP00000264555:p.Thr1017_Gly1020del		A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	In_Frame_Del	DEL	pfam_Znf_PHD-finger,pfam_Znf_C3HC4_RING-type,superfamily_Znf_FYVE_PHD,smart_Znf_RING,smart_Znf_PHD,pfscan_Znf_PHD-finger,pfscan_Znf_RING	p.GTRS1020in_frame_del	ENST00000264555.5	37	c.3047_3058		11																																																																																			PHRF1	-	NULL	ENSG00000070047		0.675	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	PHRF1	HGNC	protein_coding	OTTHUMT00000382133.1	12	0.00	0	GGACGCGCTCTG	NM_020901		608503	608514	+1	no_errors	ENST00000264555	ensembl	human	known	69_37n	in_frame_del	12	33.33	6	DEL	0.000:0.000:0.000:0.003:0.000:0.010:0.008:0.000:0.404:0.408:0.000:0.000	-
PPEF1	5475	genome.wustl.edu	37	X	18800500	18800500	+	Nonsense_Mutation	SNP	G	G	T			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chrX:18800500G>T	ENST00000361511.4	+	11	1236	c.742G>T	c.(742-744)Gaa>Taa	p.E248*	PPEF1_ENST00000349874.5_Nonsense_Mutation_p.E248*|PPEF1_ENST00000359763.6_Nonsense_Mutation_p.E195*|PPEF1_ENST00000544635.1_Nonsense_Mutation_p.E183*|PPEF1_ENST00000543630.1_Nonsense_Mutation_p.E248*	NM_006240.2|NM_152224.1	NP_006231.2|NP_689410.1	O14829	PPE1_HUMAN	protein phosphatase, EF-hand calcium binding domain 1	248	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|phototransduction, visible light (GO:0007603)|protein dephosphorylation (GO:0006470)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)	p.E248*(1)		breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	43	Hepatocellular(33;0.183)					CTTCACGAAAGAAATTTTGCA	0.318																																						dbGAP											1	Substitution - Nonsense(1)	breast(1)											83.0	77.0	79.0					X																	18800500		2201	4298	6499	-	-	-	SO:0001587	stop_gained	0			BC036026	CCDS14188.1, CCDS43920.1	Xp22	2013-01-10			ENSG00000086717	ENSG00000086717		"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"", ""EF-hand domain containing"""	9243	protein-coding gene	gene with protein product	"""protein phosphatase 7, catalytic subunit, alpha isozyme"""	300109		PPEF		9215685, 9326663	Standard	NM_152224		Approved	PPP7CA	uc004cyq.3	O14829	OTTHUMG00000021219	ENST00000361511.4:c.742G>T	X.37:g.18800500G>T	ENSP00000354871:p.Glu248*		A6NHP4|A8K348|O15253|Q9NU21|Q9UJH0	Nonsense_Mutation	SNP	pfam_Metallo_PEstase_dom,pfam_EF-hand,pfam_PPP_dom,pfam_IQ_motif_EF-hand-BS,smart_IQ_motif_EF-hand-BS,smart_Ser/Thr-sp_prot-phosphatase,smart_EF_hand_Ca-bd,pirsf_Ser/Thr-Pase_EF-hand_contain,pfscan_EF_HAND_2,pfscan_IQ_motif_EF-hand-BS,prints_Ser/Thr-sp_prot-phosphatase	p.E248*	ENST00000361511.4	37	c.742	CCDS14188.1	X	.	.	.	.	.	.	.	.	.	.	G	37	6.562826	0.97667	.	.	ENSG00000086717	ENST00000361511;ENST00000359763;ENST00000349874;ENST00000543630;ENST00000544635	.	.	.	4.93	4.93	0.64822	.	0.000000	0.56097	D	0.000031	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-26.3907	16.4211	0.83759	0.0:0.0:1.0:0.0	.	.	.	.	X	248;195;248;248;183	.	ENSP00000341892:E248X	E	+	1	0	PPEF1	18710421	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	8.868000	0.92320	2.163000	0.67991	0.600000	0.82982	GAA	PPEF1	-	pfam_Metallo_PEstase_dom,smart_Ser/Thr-sp_prot-phosphatase,pirsf_Ser/Thr-Pase_EF-hand_contain,prints_Ser/Thr-sp_prot-phosphatase	ENSG00000086717		0.318	PPEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PPEF1	HGNC	protein_coding	OTTHUMT00000055953.3	278	0.00	0	G	NM_006240		18800500	18800500	+1	no_errors	ENST00000361511	ensembl	human	known	69_37n	nonsense	123	23.98	41	SNP	1.000	T
RHOQ	23433	genome.wustl.edu	37	2	46803351	46803351	+	Silent	SNP	A	A	G			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr2:46803351A>G	ENST00000238738.4	+	3	646	c.327A>G	c.(325-327)gaA>gaG	p.E109E	RHOQ_ENST00000465198.1_3'UTR|RP11-417F21.1_ENST00000506009.2_RNA	NM_012249.3	NP_036381.2	P17081	RHOQ_HUMAN	ras homolog family member Q	109					cellular response to insulin stimulus (GO:0032869)|cortical actin cytoskeleton organization (GO:0030866)|GTP catabolic process (GO:0006184)|insulin receptor signaling pathway (GO:0008286)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin filament (GO:0005884)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	GBD domain binding (GO:0032427)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|profilin binding (GO:0005522)	p.E109E(1)		skin(2)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			AACTTAAGGAATACGCACCAA	0.408																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											83.0	78.0	80.0					2																	46803351		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			M31470	CCDS33191.1	2p21	2012-02-27	2012-02-27	2004-03-24	ENSG00000119729	ENSG00000119729			17736	protein-coding gene	gene with protein product		605857	"""RAS-like, family 7, member A"", ""ras homolog gene family, member Q"""	RASL7A, ARHQ		2108320	Standard	NM_012249		Approved	TC10	uc002rva.3	P17081	OTTHUMG00000150653	ENST00000238738.4:c.327A>G	2.37:g.46803351A>G			D6W5A6|Q0VGN1|Q52LS8|Q53SJ1|Q6NS39|Q6P146|Q7Z480	Silent	SNP	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom	p.E109	ENST00000238738.4	37	c.327	CCDS33191.1	2																																																																																			RHOQ	-	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,tigrfam_Small_GTP-bd_dom	ENSG00000119729		0.408	RHOQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RHOQ	HGNC	protein_coding	OTTHUMT00000319409.1	152	0.65	1	A	NM_012249		46803351	46803351	+1	no_errors	ENST00000238738	ensembl	human	known	69_37n	silent	89	32.06	42	SNP	1.000	G
RNA5-8SP6	100873336	genome.wustl.edu	37	Y	10037842	10037842	+	RNA	SNP	A	A	G			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chrY:10037842A>G	ENST00000515896.1	+	0	79									RNA, 5.8S ribosomal pseudogene 6																		GAATTGCAGGACACATTGATC	0.512																																						dbGAP											0																																										-	-	-			0					Yp11.2	2012-08-07	2012-08-07	2012-08-07	ENSG00000251705	ENSG00000251705			41960	pseudogene	RNA, pseudogene			"""RNA, 5.8S ribosomal 6"""	RN5-8S6			Standard	NG_033474		Approved						Y.37:g.10037842A>G				RNA	SNP	-	NULL	ENST00000515896.1	37	NULL		Y																																																																																			RNA5-8SP6	-	-	ENSG00000251705		0.512	RNA5-8SP6-201	KNOWN	basic	rRNA	RNA5-8SP6	HGNC	rRNA		18	0.00	0	A			10037842	10037842	+1	no_errors	ENST00000515896	ensembl	human	known	69_37n	rna	14	22.22	4	SNP	1.000	G
SMYD2	56950	genome.wustl.edu	37	1	214491454	214491454	+	Silent	SNP	A	A	G			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr1:214491454A>G	ENST00000366957.5	+	4	403	c.381A>G	c.(379-381)aaA>aaG	p.K127K	SMYD2_ENST00000491455.1_3'UTR|SMYD2_ENST00000415093.2_Silent_p.K127K	NM_020197.2	NP_064582.2	Q9NRG4	SMYD2_HUMAN	SET and MYND domain containing 2	127	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|RNA polymerase II core binding (GO:0000993)	p.K127K(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0122)|all cancers(67;0.0209)|GBM - Glioblastoma multiforme(131;0.106)|Epithelial(68;0.144)		CTTCGGAAAAATTGTTAGCTG	0.433																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											104.0	110.0	108.0					1																	214491454		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF226053	CCDS31022.1	1q32.3	2011-07-01			ENSG00000143499	ENSG00000143499		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20982	protein-coding gene	gene with protein product		610663					Standard	NM_020197		Approved	HSKM-B, ZMYND14, KMT3C	uc021pix.1	Q9NRG4	OTTHUMG00000037066	ENST00000366957.5:c.381A>G	1.37:g.214491454A>G			B2R9P9|I6L9H7|Q4V765|Q5VSH9|Q96AI4	Silent	SNP	pfam_SET_dom,pfam_Znf_MYND,smart_SET_dom,pfscan_SET_dom,pfscan_Znf_MYND	p.K127	ENST00000366957.5	37	c.381	CCDS31022.1	1																																																																																			SMYD2	-	pfam_SET_dom,smart_SET_dom	ENSG00000143499		0.433	SMYD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SMYD2	HGNC	protein_coding	OTTHUMT00000089998.1	180	0.00	0	A	NM_020197		214491454	214491454	+1	no_errors	ENST00000366957	ensembl	human	known	69_37n	silent	69	53.06	78	SNP	0.043	G
SOS1	6654	genome.wustl.edu	37	2	39281877	39281877	+	Missense_Mutation	SNP	T	T	C			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr2:39281877T>C	ENST00000426016.1	-	6	684	c.598A>G	c.(598-600)Act>Gct	p.T200A	SOS1_ENST00000395038.2_Missense_Mutation_p.T200A|SOS1_ENST00000402219.2_Missense_Mutation_p.T200A|SOS1_ENST00000428721.2_Missense_Mutation_p.T143A			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	200	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.T200A(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				TCATAGTAAGTTTGTTCTCCT	0.318									Noonan syndrome																													dbGAP											1	Substitution - Missense(1)	breast(1)											91.0	103.0	99.0					2																	39281877		2203	4297	6500	-	-	-	SO:0001583	missense	0	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11187	protein-coding gene	gene with protein product		182530	"""gingival fibromatosis, hereditary, 1"""	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.598A>G	2.37:g.39281877T>C	ENSP00000387784:p.Thr200Ala		A8K2G3|B4DXG2	Missense_Mutation	SNP	pfam_RasGRF_CDC25,pfam_Ras-like_Gua-exchang_fac_N,pfam_DH-domain,pfam_Pleckstrin_homology,pfam_Histone_core_D,superfamily_Ras_GEF_dom,superfamily_Histone-fold,superfamily_DH-domain,smart_DH-domain,smart_Pleckstrin_homology,smart_Ras-like_Gua-exchang_fac_N,smart_RasGRF_CDC25,pfscan_Pleckstrin_homology,pfscan_DH-domain,pfscan_RasGRF_CDC25,pfscan_Ras-like_Gua-exchang_fac_N	p.T200A	ENST00000426016.1	37	c.598	CCDS1802.1	2	.	.	.	.	.	.	.	.	.	.	T	17.71	3.456990	0.63401	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000395038;ENST00000263879;ENST00000428721	D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02	5.88	5.88	0.94601	Dbl homology (DH) domain (3);	0.207897	0.49916	D	0.000121	D	0.88009	0.6322	L	0.29908	0.895	0.58432	D	0.999995	B	0.02656	0.0	B	0.06405	0.002	D	0.83837	0.0255	10	0.59425	D	0.04	.	16.2792	0.82664	0.0:0.0:0.0:1.0	.	200	Q07889	SOS1_HUMAN	A	200;200;200;200;143	ENSP00000387784:T200A;ENSP00000384675:T200A;ENSP00000378479:T200A;ENSP00000399992:T143A	ENSP00000263879:T200A	T	-	1	0	SOS1	39135381	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	4.452000	0.60054	2.243000	0.73865	0.533000	0.62120	ACT	SOS1	-	superfamily_DH-domain,pfscan_DH-domain	ENSG00000115904		0.318	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	SOS1	HGNC	protein_coding	OTTHUMT00000219948.3	188	0.00	0	T	NM_005633		39281877	39281877	-1	no_errors	ENST00000402219	ensembl	human	known	69_37n	missense	116	24.03	37	SNP	1.000	C
STAG2	10735	genome.wustl.edu	37	X	123195704	123195704	+	Nonsense_Mutation	SNP	G	G	T			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chrX:123195704G>T	ENST00000371160.1	+	17	1908	c.1618G>T	c.(1618-1620)Gga>Tga	p.G540*	STAG2_ENST00000218089.9_Nonsense_Mutation_p.G540*|STAG2_ENST00000371145.3_Nonsense_Mutation_p.G540*|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000354548.5_Nonsense_Mutation_p.G471*|STAG2_ENST00000371144.3_Nonsense_Mutation_p.G540*|STAG2_ENST00000371157.3_Nonsense_Mutation_p.G540*	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	540					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.G540*(2)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TCCTCCCGTGGGAAGAGGGAC	0.358																																						dbGAP											2	Substitution - Nonsense(2)	breast(2)											67.0	64.0	65.0					X																	123195704		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1618G>T	X.37:g.123195704G>T	ENSP00000360202:p.Gly540*		B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Nonsense_Mutation	SNP	pfam_STAG,superfamily_ARM-type_fold	p.G540*	ENST00000371160.1	37	c.1618	CCDS14607.1	X	.	.	.	.	.	.	.	.	.	.	G	41	8.674455	0.98910	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	.	.	.	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-8.884	17.2439	0.87021	0.0:0.0:1.0:0.0	.	.	.	.	X	540;540;471;540;540;540;540	.	ENSP00000218089:G540X	G	+	1	0	STAG2	123023385	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.809000	0.99208	2.083000	0.62718	0.600000	0.82982	GGA	STAG2	-	superfamily_ARM-type_fold	ENSG00000101972		0.358	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	STAG2	HGNC	protein_coding	OTTHUMT00000156159.2	154	0.00	0	G	NM_006603		123195704	123195704	+1	no_errors	ENST00000218089	ensembl	human	known	69_37n	nonsense	81	29.57	34	SNP	1.000	T
TCOF1	6949	genome.wustl.edu	37	5	149776147	149776149	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	AAG	AAG					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr5:149776147_149776149delAAG	ENST00000504761.2	+	24	4084_4086	c.4084_4086delAAG	c.(4084-4086)aagdel	p.K1366del	TCOF1_ENST00000451292.1_In_Frame_Del_p.K1403del|TCOF1_ENST00000323668.7_In_Frame_Del_p.K1289del|TCOF1_ENST00000513346.1_In_Frame_Del_p.K1366del|TCOF1_ENST00000377797.3_In_Frame_Del_p.K1367del|TCOF1_ENST00000445265.2_In_Frame_Del_p.K1290del|TCOF1_ENST00000439160.2_In_Frame_Del_p.K1329del			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1366	Poly-Lys.				skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)	p.K1362delK(1)|p.K1285delK(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCCCAGGAGCAAGAAGAAGAAGA	0.601																																						dbGAP											2	Deletion - In frame(2)	breast(2)							,,,,	142,4018		6,130,1944					,,,,	3.8	1.0			10	321,7729		16,289,3720	no	coding,coding,coding,coding,coding	TCOF1	NM_001195141.1,NM_001135245.1,NM_001135244.1,NM_001135243.1,NM_000356.3	,,,,	22,419,5664	A1A1,A1R,RR		3.9876,3.4135,3.792	,,,,	,,,,		463,11747				-	-	-	SO:0001651	inframe_deletion	0				CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.4084_4086delAAG	5.37:g.149776156_149776158delAAG	ENSP00000421655:p.Lys1366del		A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	In_Frame_Del	DEL	pfam_TCS_treacle,smart_LisH_dimerisation,pfscan_LisH_dimerisation,prints_Treacle-like_TCS	p.K1402in_frame_del	ENST00000504761.2	37	c.4195_4197	CCDS54936.1	5																																																																																			TCOF1	-	NULL	ENSG00000070814		0.601	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	TCOF1	HGNC	protein_coding	OTTHUMT00000380552.1	35	0.00	0	AAG	NM_001008656		149776147	149776149	+1	no_errors	ENST00000451292	ensembl	human	known	69_37n	in_frame_del	42	10.64	5	DEL	1.000:1.000:1.000	-
TP53	7157	genome.wustl.edu	37	17	7578253	7578253	+	Missense_Mutation	SNP	C	C	A			TCGA-A2-A0SX-01A-12D-A099-09	TCGA-A2-A0SX-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	b54bc31e-bdcc-4ad5-998e-5a9c542f83bb	ee7f21d0-efa1-4d19-9b82-03e1a90432b4	g.chr17:7578253C>A	ENST00000269305.4	-	6	785	c.596G>T	c.(595-597)gGa>gTa	p.G199V	TP53_ENST00000420246.2_Missense_Mutation_p.G199V|TP53_ENST00000445888.2_Missense_Mutation_p.G199V|TP53_ENST00000455263.2_Missense_Mutation_p.G199V|TP53_ENST00000413465.2_Missense_Mutation_p.G199V|TP53_ENST00000359597.4_Missense_Mutation_p.G199V|TP53_ENST00000574684.1_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	199	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		G -> A (in a sporadic cancer; somatic mutation).|G -> E (in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G199E(11)|p.G199V(11)|p.0?(8)|p.?(5)|p.G106V(2)|p.G67V(2)|p.E198_L201>V(1)|p.N200fs*4(1)|p.E198fs*7(1)|p.G199A(1)|p.P191fs*6(1)|p.I195_G199delIRVEG(1)|p.G199fs*48(1)|p.G199fs*42(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACGCAAATTTCCTTCCACTCG	0.542		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	dbGAP	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	47	Substitution - Missense(27)|Whole gene deletion(8)|Unknown(6)|Deletion - Frameshift(4)|Deletion - In frame(1)|Complex - frameshift(1)	central_nervous_system(8)|biliary_tract(6)|large_intestine(5)|breast(5)|peritoneum(4)|bone(4)|stomach(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(2)|oesophagus(2)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|pancreas(1)											118.0	106.0	110.0					17																	7578253		2203	4300	6503	-	-	-	SO:0001583	missense	0	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.596G>T	17.37:g.7578253C>A	ENSP00000269305:p.Gly199Val		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	pfam_p53_DNA-bd,pfam_p53_tetrameristn,pfam_p53_transactivation_domain,superfamily_p53-like_TF_DNA-bd,superfamily_p53_tetrameristn,prints_p53_tumour_suppressor	p.G199V	ENST00000269305.4	37	c.596	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	C	17.16	3.317964	0.60524	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99814	-6.89;-6.89;-6.89;-6.89;-6.89;-6.89;-6.89;-6.89	5.28	5.28	0.74379	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.052866	0.85682	D	0.000000	D	0.99792	0.9912	M	0.89095	3.005	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.987;1.0;1.0;1.0;1.0	D;D;P;D;D;D;D	0.97110	0.999;0.999;0.883;0.999;0.999;0.999;1.0	D	0.97102	0.9798	10	0.87932	D	0	-10.2871	16.7921	0.85592	0.0:1.0:0.0:0.0	.	160;199;199;106;199;199;199	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	V	199;199;199;199;199;199;188;106;67;106;67	ENSP00000410739:G199V;ENSP00000352610:G199V;ENSP00000269305:G199V;ENSP00000398846:G199V;ENSP00000391127:G199V;ENSP00000391478:G199V;ENSP00000425104:G67V;ENSP00000423862:G106V	ENSP00000269305:G199V	G	-	2	0	TP53	7518978	1.000000	0.71417	0.976000	0.42696	0.024000	0.10985	7.775000	0.85489	2.634000	0.89283	0.563000	0.77884	GGA	TP53	-	pfam_p53_DNA-bd,superfamily_p53-like_TF_DNA-bd	ENSG00000141510		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	HGNC	protein_coding	OTTHUMT00000367397.1	212	0.00	0	C	NM_000546		7578253	7578253	-1	no_errors	ENST00000269305	ensembl	human	known	69_37n	missense	74	47.59	69	SNP	1.000	A
