#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
ALDH1L2	160428	genome.wustl.edu	37	12	105445872	105445872	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr12:105445872delA	ENST00000258494.9	-	12	1671	c.1531delT	c.(1531-1533)tatfs	p.Y511fs	ALDH1L2_ENST00000424857.2_Frame_Shift_Del_p.Y511fs	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	511	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						AAATACCTATACATCAATCTT	0.383																																						dbGAP											0													95.0	92.0	93.0					12																	105445872		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"""Aldehyde dehydrogenases"""	26777	protein-coding gene	gene with protein product	"""mitochondrial 10-formyltetrahydrofolate dehydrogenase"""	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.1531delT	12.37:g.105445872delA	ENSP00000258494:p.Tyr511fs		Q3SY68|Q68D62|Q6AI55|Q8N922	Frame_Shift_Del	DEL	pfam_Aldehyde_DH_dom,pfam_Formyl_transf_N,pfam_Formyl_trans_C,pfam_Acyl_carrier_prot-like,superfamily_Ald_DH/histidinol_DH,superfamily_Formyl_transf_N,superfamily_Formyl_transferase_C-like,superfamily_Acyl_carrier_prot-like,pirsf_10_FTHF_DH,pfscan_Acyl_carrier_prot-like	p.Y511fs	ENST00000258494.9	37	c.1531	CCDS31891.1	12																																																																																			ALDH1L2	-	pfam_Aldehyde_DH_dom,superfamily_Ald_DH/histidinol_DH,pirsf_10_FTHF_DH	ENSG00000136010		0.383	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALDH1L2	HGNC	protein_coding	OTTHUMT00000406098.1	50	0.00	0	A	XM_090294		105445872	105445872	-1	no_errors	ENST00000258494	ensembl	human	known	69_37n	frame_shift_del	60	37.37	37	DEL	1.000	-
SMIM13	221710	genome.wustl.edu	37	6	11094562	11094562	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr6:11094562delG	ENST00000416247.2	+	1	297	c.16delG	c.(16-18)gggfs	p.G6fs		NM_001135575.1	NP_001129047.1	P0DJ93	SIM13_HUMAN	small integral membrane protein 13	6						integral component of membrane (GO:0016021)											GCACAGCGTCGGGCTGACTCT	0.716																																						dbGAP											0													30.0	30.0	30.0					6																	11094562		692	1591	2283	-	-	-	SO:0001589	frameshift_variant	0				CCDS56396.1	6p24.2	2012-12-03	2012-12-03	2012-12-03	ENSG00000224531	ENSG00000224531			27356	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 228"""	C6orf228			Standard	NM_001135575		Approved		uc011dio.2	P0DJ93	OTTHUMG00000014253	ENST00000416247.2:c.16delG	6.37:g.11094562delG	ENSP00000451866:p.Gly6fs		G3V581	Frame_Shift_Del	DEL	NULL	p.L7fs	ENST00000416247.2	37	c.16	CCDS56396.1	6																																																																																			C6orf228	-	NULL	ENSG00000224531		0.716	SMIM13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	C6orf228	HGNC	protein_coding	OTTHUMT00000039851.3	34	0.00	0	G	NM_001135575		11094562	11094562	+1	no_errors	ENST00000376935	ensembl	human	known	69_37n	frame_shift_del	16	20.00	4	DEL	0.996	-
CDH1	999	genome.wustl.edu	37	16	68849628	68849628	+	Nonsense_Mutation	SNP	C	C	T			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr16:68849628C>T	ENST00000261769.5	+	10	1722	c.1531C>T	c.(1531-1533)Cag>Tag	p.Q511*	RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Nonsense_Mutation_p.Q450*	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	511	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.A510fs*25(1)|p.Q511K(1)|p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CTACACTGCCCAGGAGCCAGA	0.433			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																													dbGAP	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	3	Substitution - Missense(1)|Unknown(1)|Deletion - Frameshift(1)	breast(2)|lung(1)											115.0	104.0	108.0					16																	68849628		2198	4300	6498	-	-	-	SO:0001587	stop_gained	0	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1531C>T	16.37:g.68849628C>T	ENSP00000261769:p.Gln511*		A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Nonsense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,pfam_Cadherin_pro_dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.Q511*	ENST00000261769.5	37	c.1531	CCDS10869.1	16	.	.	.	.	.	.	.	.	.	.	C	20.7	4.038249	0.75617	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	.	.	.	5.5	3.55	0.40652	.	1.950770	0.03146	N	0.167271	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	6.6994	0.23217	0.1287:0.6647:0.1353:0.0713	.	.	.	.	X	511;529;511;450	.	ENSP00000261769:Q511X	Q	+	1	0	CDH1	67407129	0.000000	0.05858	0.048000	0.18961	0.513000	0.34164	0.155000	0.16362	0.692000	0.31613	-0.224000	0.12420	CAG	CDH1	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000039068		0.433	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH1	HGNC	protein_coding	OTTHUMT00000268897.2	190	0.00	0	C	NM_004360		68849628	68849628	+1	no_errors	ENST00000261769	ensembl	human	known	69_37n	nonsense	71	34.26	37	SNP	0.000	T
CRYGA	1418	genome.wustl.edu	37	2	209025576	209025577	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr2:209025576_209025577insC	ENST00000304502.4	-	3	495_496	c.476_477insG	c.(475-477)ggtfs	p.G159fs		NM_014617.3	NP_055432.2	P11844	CRGA_HUMAN	crystallin, gamma A	159	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			endometrium(1)|kidney(3)|large_intestine(1)|lung(7)	12				Epithelial(149;0.067)|LUSC - Lung squamous cell carcinoma(261;0.0708)|Lung(261;0.135)		TGGCATCTGCACCCCCCCAGTC	0.53																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0				CCDS33367.1	2q34	2013-02-14			ENSG00000168582	ENSG00000168582			2408	protein-coding gene	gene with protein product	"""gamma crystallin 5"""	123660		CRYG1			Standard	NM_014617		Approved	CRYG5, CRY-g-A		P11844	OTTHUMG00000154796	ENST00000304502.4:c.477dupG	2.37:g.209025583_209025583dupC	ENSP00000302105:p.Gly159fs		Q53ST5	Frame_Shift_Ins	INS	pfam_Beta/gamma_crystallin,superfamily_G_crystallin-rel,smart_Beta/gamma_crystallin,pfscan_Beta/gamma_crystallin,prints_Beta/gamma_crystallin	p.A160fs	ENST00000304502.4	37	c.477_476	CCDS33367.1	2																																																																																			CRYGA	-	pfam_Beta/gamma_crystallin,superfamily_G_crystallin-rel,smart_Beta/gamma_crystallin,pfscan_Beta/gamma_crystallin	ENSG00000168582		0.530	CRYGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CRYGA	HGNC	protein_coding	OTTHUMT00000337096.1	48	0.00	0	-	NM_014617		209025576	209025577	-1	no_errors	ENST00000304502	ensembl	human	known	69_37n	frame_shift_ins	45	11.76	6	INS	0.408:0.651	C
CSAD	51380	genome.wustl.edu	37	12	53552385	53552385	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr12:53552385delG	ENST00000444623.1	-	17	1659	c.1392delC	c.(1390-1392)ttcfs	p.F465fs	CSAD_ENST00000379843.3_Frame_Shift_Del_p.F318fs|RP11-1136G11.8_ENST00000550908.1_lincRNA|CSAD_ENST00000453446.2_Frame_Shift_Del_p.F465fs|CSAD_ENST00000267085.4_Frame_Shift_Del_p.F492fs|CSAD_ENST00000379846.1_Frame_Shift_Del_p.F318fs	NM_001244705.1	NP_001231634.1	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	465					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)		pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(4)	14					L-Cysteine(DB00151)	CCACACGGAAGAAGTTGCCCC	0.612																																					Ovarian(109;252 1546 16882 28524 44645)	dbGAP											0													83.0	63.0	70.0					12																	53552385		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			AB044561	CCDS8848.2, CCDS58235.1	12q13.11-q14.3	2008-08-04			ENSG00000139631	ENSG00000139631			18966	protein-coding gene	gene with protein product	"""P-selectin cytoplasmic tail-associated protein"""					15489334	Standard	NM_015989		Approved	PCAP, CSD	uc001sbz.3	Q9Y600	OTTHUMG00000048076	ENST00000444623.1:c.1392delC	12.37:g.53552385delG	ENSP00000415485:p.Phe465fs		A8K0U4|Q4QQH9|Q9UNJ5|Q9Y601	Frame_Shift_Del	DEL	pfam_PyrdxlP-dep_de-COase,pfam_Aminotrans_V/Cys_dSase,pfam_ArAA_b-elim_lyase/Thr_aldolase,superfamily_PyrdxlP-dep_Trfase_major_dom	p.F492fs	ENST00000444623.1	37	c.1473	CCDS58235.1	12																																																																																			CSAD	-	superfamily_PyrdxlP-dep_Trfase_major_dom	ENSG00000139631		0.612	CSAD-017	KNOWN	basic|appris_principal|CCDS	protein_coding	CSAD	HGNC	protein_coding	OTTHUMT00000343697.1	69	0.00	0	G	NM_015989		53552385	53552385	-1	no_errors	ENST00000267085	ensembl	human	known	69_37n	frame_shift_del	32	55.84	43	DEL	1.000	-
CYHR1	50626	genome.wustl.edu	37	8	145689543	145689544	+	Intron	INS	-	-	A			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr8:145689543_145689544insA	ENST00000438911.2	-	2	380				CYHR1_ENST00000530374.1_5'Flank|CYHR1_ENST00000403000.2_Frame_Shift_Ins_p.R182fs|CTD-2517M22.16_ENST00000525461.1_RNA|KIFC2_ENST00000301332.2_5'Flank|CYHR1_ENST00000424149.2_Frame_Shift_Ins_p.R182fs|CYHR1_ENST00000306145.5_Frame_Shift_Ins_p.R182fs	NM_138496.1	NP_612505.1	Q6ZMK1	CYHR1_HUMAN	cysteine/histidine-rich 1							cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)	zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(3)|ovary(2)	7	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			TATGCAGGGCCCGGCAGTAAGC	0.644											OREG0019056	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AB007965	CCDS6426.1, CCDS47943.1	8q24	2004-12-07	2005-07-24		ENSG00000187954	ENSG00000187954			17806	protein-coding gene	gene with protein product			"""cysteine and histidine rich 1"""			10745073	Standard	NM_138496		Approved	CHRP, KIAA0496, MGC13010	uc003zcv.2	Q6ZMK1	OTTHUMG00000165171	ENST00000438911.2:c.246+298->T	8.37:g.145689543_145689544insA		1696	B3KSX0|D3DWM3|Q9BSF6|Q9BSU6	Frame_Shift_Ins	INS	NULL	p.A183fs	ENST00000438911.2	37	c.546_545	CCDS47943.1	8																																																																																			CYHR1	-	NULL	ENSG00000187954		0.644	CYHR1-001	KNOWN	basic|CCDS	protein_coding	CYHR1	HGNC	protein_coding	OTTHUMT00000382438.1	10	0.00	0	-	NM_032687		145689543	145689544	-1	no_errors	ENST00000306145	ensembl	human	known	69_37n	frame_shift_ins	10	33.33	5	INS	0.996:0.993	A
EHMT1	79813	genome.wustl.edu	37	9	140710464	140710464	+	Silent	SNP	G	G	A	rs377320362	byFrequency	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr9:140710464G>A	ENST00000460843.1	+	23	3351	c.3324G>A	c.(3322-3324)gcG>gcA	p.A1108A		NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	1108	Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.				chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		GCAACCACGCGTGCTCCTGCT	0.597													G|||	3	0.000599042	0.0	0.0	5008	,	,		19321	0.0		0.001	False		,,,				2504	0.002					dbGAP											0													65.0	56.0	59.0					9																	140710464		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.3324G>A	9.37:g.140710464G>A			B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	pfam_Ankyrin_rpt,pfam_SET_dom,pfam_Pre-SET_dom,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,smart_Pre-SET_Zn-bd_sub,smart_SET_dom,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_SET_dom,pfscan_Pre-SET_dom,prints_Ankyrin_rpt	p.A1108	ENST00000460843.1	37	c.3324	CCDS7050.2	9																																																																																			EHMT1	-	pfam_Pre-SET_dom,smart_Pre-SET_Zn-bd_sub,pfscan_Pre-SET_dom	ENSG00000181090		0.597	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EHMT1	HGNC	protein_coding	OTTHUMT00000055371.2	59	0.00	0	G	NM_024757		140710464	140710464	+1	no_errors	ENST00000460843	ensembl	human	known	69_37n	silent	21	40.00	14	SNP	0.912	A
EPB41L4A	64097	genome.wustl.edu	37	5	111506043	111506043	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr5:111506043C>T	ENST00000261486.5	-	20	1970	c.1694G>A	c.(1693-1695)gGa>gAa	p.G565E	EPB41L4A_ENST00000507810.1_5'UTR	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	565						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		TTCGGACAATCCGGATGGATC	0.378																																						dbGAP											0													126.0	119.0	121.0					5																	111506043		1835	4084	5919	-	-	-	SO:0001583	missense	0			AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.1694G>A	5.37:g.111506043C>T	ENSP00000261486:p.Gly565Glu		A4FUI6	Missense_Mutation	SNP	pfam_FERM_central,pfam_FERM_N,pfam_FERM_PH-like_C,pfam_FERM-adjacent,superfamily_FERM_central,smart_Band_41_domain,pfscan_FERM_domain,prints_Band_41_fam,prints_Ez/rad/moesin	p.G565E	ENST00000261486.5	37	c.1694	CCDS43350.1	5	.	.	.	.	.	.	.	.	.	.	C	25.5	4.647130	0.87958	.	.	ENSG00000129595	ENST00000261486	D	0.89939	-2.59	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.91327	0.7265	L	0.29908	0.895	0.47441	D	0.999428	D;D	0.89917	0.994;1.0	P;D	0.97110	0.759;1.0	D	0.92656	0.6137	10	0.87932	D	0	.	17.5611	0.87908	0.0:1.0:0.0:0.0	.	565;192	Q9HCS5;Q8N8X1	E41LA_HUMAN;.	E	565	ENSP00000261486:G565E	ENSP00000261486:G565E	G	-	2	0	EPB41L4A	111533942	1.000000	0.71417	0.949000	0.38748	0.890000	0.51754	5.894000	0.69806	2.415000	0.81967	0.563000	0.77884	GGA	EPB41L4A	-	NULL	ENSG00000129595		0.378	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EPB41L4A	HGNC	protein_coding	OTTHUMT00000370969.1	205	0.00	0	C			111506043	111506043	-1	no_errors	ENST00000261486	ensembl	human	known	69_37n	missense	267	10.70	32	SNP	0.993	T
ESPL1	9700	genome.wustl.edu	37	12	53682322	53682323	+	Splice_Site	DEL	GT	GT	-			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	GT	GT					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr12:53682322_53682323delGT	ENST00000257934.4	+	20	4638_4639	c.4547_4548delGT	c.(4546-4548)ggt>g	p.G1517fs	ESPL1_ENST00000552462.1_Splice_Site_p.G1517fs	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1517					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						CTCTCCCCAGGTGGGAAGACTC	0.559											OREG0021863	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Colon(53;1069 1201 2587 5382)	dbGAP											0																																										-	-	-	SO:0001630	splice_region_variant	0			D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.4547-1GT>-	12.37:g.53682322_53682323delGT		994		Frame_Shift_Del	DEL	pfam_Peptidase_C50	p.G1517fs	ENST00000257934.4	37	c.4547_4548	CCDS8852.1	12																																																																																			ESPL1	-	NULL	ENSG00000135476		0.559	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	ESPL1	HGNC	protein_coding	OTTHUMT00000406899.2	33	0.00	0	GT	NM_012291	Frame_Shift_Del	53682322	53682323	+1	no_errors	ENST00000257934	ensembl	human	known	69_37n	frame_shift_del	6	70.00	14	DEL	0.126:0.120	-
DDX42	11325	genome.wustl.edu	37	17	61898202	61898202	+	IGR	SNP	T	T	C			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr17:61898202T>C	ENST00000578681.1	+	0	4337				FTSJ3_ENST00000427159.2_Missense_Mutation_p.N690S	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42						protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						CCTTTACCGGTTGAAGGAGTT	0.488																																						dbGAP											0													68.0	67.0	67.0					17																	61898202		2203	4300	6503	-	-	-	SO:0001628	intergenic_variant	0			BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"""DEAD-boxes"""	18676	protein-coding gene	gene with protein product	"""splicing factor 3b, subunit 8"""	613369	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"""			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3			17.37:g.61898202T>C			A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	pfam_rRNA_MeTfrase_Spb1_C,pfam_rRNA_MeTrfase_FtsJ_dom,pfam_rRNA_MeTfrase_Spb1_DUF3381	p.N690S	ENST00000578681.1	37	c.2069	CCDS32704.1	17	.	.	.	.	.	.	.	.	.	.	T	11.65	1.703039	0.30232	.	.	ENSG00000108592	ENST00000427159	T	0.46063	0.88	4.76	0.205	0.15204	Ribosomal RNA methyltransferase, Spb1, C-terminal (1);	0.440683	0.24554	N	0.037534	T	0.30479	0.0766	L	0.49571	1.57	0.36895	D	0.890096	B	0.02656	0.0	B	0.06405	0.002	T	0.09314	-1.0680	10	0.52906	T	0.07	.	4.3538	0.11169	0.1818:0.1844:0.0:0.6338	.	690	Q8IY81	RRMJ3_HUMAN	S	690	ENSP00000396673:N690S	ENSP00000396673:N690S	N	-	2	0	FTSJ3	59251934	1.000000	0.71417	0.904000	0.35570	0.677000	0.39632	2.260000	0.43267	-0.140000	0.11394	0.460000	0.39030	AAC	FTSJ3	-	pfam_rRNA_MeTfrase_Spb1_C	ENSG00000108592		0.488	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FTSJ3	HGNC	protein_coding	OTTHUMT00000444368.1	75	0.00	0	T	NM_007372		61898202	61898202	-1	no_errors	ENST00000427159	ensembl	human	known	69_37n	missense	56	26.92	21	SNP	1.000	C
FXYD5	53827	genome.wustl.edu	37	19	35649292	35649292	+	Nonsense_Mutation	SNP	G	G	A			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr19:35649292G>A	ENST00000342879.3	+	3	966	c.188G>A	c.(187-189)tGg>tAg	p.W63*	FXYD5_ENST00000392219.2_Nonsense_Mutation_p.W63*|FXYD5_ENST00000423817.3_Nonsense_Mutation_p.W63*|FXYD5_ENST00000541435.2_Nonsense_Mutation_p.W63*|FXYD5_ENST00000588699.1_Nonsense_Mutation_p.W63*|FXYD5_ENST00000590686.1_Nonsense_Mutation_p.W63*|FXYD5_ENST00000543307.1_Nonsense_Mutation_p.W63*|FXYD5_ENST00000392218.2_Nonsense_Mutation_p.W63*			Q96DB9	FXYD5_HUMAN	FXYD domain containing ion transport regulator 5	63					microvillus assembly (GO:0030033)|negative regulation of calcium-dependent cell-cell adhesion (GO:0046588)	integral component of membrane (GO:0016021)	actin binding (GO:0003779)|cadherin binding (GO:0045296)|ion channel activity (GO:0005216)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9	all_lung(56;9.4e-09)|Lung NSC(56;1.4e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.75e-22)|OV - Ovarian serous cystadenocarcinoma(14;3.17e-20)|all cancers(14;7.07e-19)|LUSC - Lung squamous cell carcinoma(66;0.0221)			ACCCCAACCTGGCCTGCTGAT	0.542																																						dbGAP											0													70.0	66.0	67.0					19																	35649292		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF161462	CCDS12447.1	19q13.12	2008-02-05	2002-01-14		ENSG00000089327	ENSG00000089327			4029	protein-coding gene	gene with protein product	"""dysadherin"""	606669	"""FXYD domain-containing ion transport regulator 5"""				Standard	NM_144779		Approved	OIT2	uc002nyg.2	Q96DB9	OTTHUMG00000048092	ENST00000342879.3:c.188G>A	19.37:g.35649292G>A	ENSP00000344254:p.Trp63*		B7WNZ8|Q6UW44|Q9HC34|Q9P039	Nonsense_Mutation	SNP	pfam_Ion-transport_regulator_FXYD	p.W63*	ENST00000342879.3	37	c.188	CCDS12447.1	19	.	.	.	.	.	.	.	.	.	.	G	13.76	2.334349	0.41297	.	.	ENSG00000089327	ENST00000543307;ENST00000392218;ENST00000392219;ENST00000541435;ENST00000342879;ENST00000423817	.	.	.	3.25	-2.08	0.07254	.	3.482350	0.00649	N	0.000544	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	5.5009	3.4883	0.07627	0.51:0.0:0.2652:0.2248	.	.	.	.	X	63	.	ENSP00000344254:W63X	W	+	2	0	FXYD5	40341132	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.202000	0.09451	-0.402000	0.07633	0.555000	0.69702	TGG	FXYD5	-	NULL	ENSG00000089327		0.542	FXYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FXYD5	HGNC	protein_coding	OTTHUMT00000109443.1	173	0.00	0	G	NM_014164		35649292	35649292	+1	no_errors	ENST00000342879	ensembl	human	known	69_37n	nonsense	144	21.20	39	SNP	0.000	A
GPR56	9289	genome.wustl.edu	37	16	57691314	57691314	+	Missense_Mutation	SNP	C	C	A			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr16:57691314C>A	ENST00000388812.4	+	10	1637	c.1197C>A	c.(1195-1197)caC>caA	p.H399Q	GPR56_ENST00000567835.1_Missense_Mutation_p.H399Q|GPR56_ENST00000562558.1_Missense_Mutation_p.H399Q|GPR56_ENST00000379696.3_Missense_Mutation_p.H399Q|GPR56_ENST00000568909.1_Missense_Mutation_p.H399Q|GPR56_ENST00000456916.1_Missense_Mutation_p.H399Q|GPR56_ENST00000540164.2_Missense_Mutation_p.H399Q|GPR56_ENST00000544297.1_Missense_Mutation_p.H224Q|GPR56_ENST00000538815.1_Missense_Mutation_p.H399Q|GPR56_ENST00000568908.1_Missense_Mutation_p.H399Q|GPR56_ENST00000379694.4_Missense_Mutation_p.H229Q|GPR56_ENST00000388813.5_Missense_Mutation_p.H399Q|GPR56_ENST00000562631.1_Missense_Mutation_p.H399Q			Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56	399					angiogenesis (GO:0001525)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cerebral cortex radial glia guided migration (GO:0021801)|G-protein coupled receptor signaling pathway (GO:0007186)|layer formation in cerebral cortex (GO:0021819)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell adhesion (GO:0045785)|positive regulation of Rho protein signal transduction (GO:0035025)|protein kinase C signaling (GO:0070528)|Rho protein signal transduction (GO:0007266)|vascular endothelial growth factor production (GO:0010573)	extracellular vesicular exosome (GO:0070062)|glial limiting end-foot (GO:0097451)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	15						ACGCCGTGCACAAGCACTACC	0.647																																						dbGAP											0													161.0	136.0	145.0					16																	57691314		2198	4300	6498	-	-	-	SO:0001583	missense	0			AJ011001	CCDS32460.1, CCDS32461.1, CCDS73893.1	16q13	2014-08-08				ENSG00000205336		"""-"", ""GPCR / Class B : Orphans"""	4512	protein-coding gene	gene with protein product		604110				10049584, 10100861	Standard	XM_005256237		Approved	TM7LN4, TM7XN1	uc002emb.2	Q9Y653		ENST00000388812.4:c.1197C>A	16.37:g.57691314C>A	ENSP00000373464:p.His399Gln		A6NIT7|A6NJV9|B0M0K4|B4DR54|O95966|Q6ZMP1|Q8NGB3|Q96HB4	Missense_Mutation	SNP	pfam_GPCR_2_secretin-like,pfam_GPS_dom,smart_GPS_dom,pfscan_GPS_dom,pfscan_GPCR_2-like,prints_GPCR_2_orphan_rcpt_GPR56,prints_GPCR_2_secretin-like	p.H399Q	ENST00000388812.4	37	c.1197	CCDS32460.1	16	.	.	.	.	.	.	.	.	.	.	C	14.60	2.583534	0.46006	.	.	ENSG00000205336	ENST00000388813;ENST00000388812;ENST00000538815;ENST00000456916;ENST00000540164;ENST00000544297;ENST00000379694;ENST00000379696	T;T;T;T;T;T;T;T	0.46063	1.27;0.88;1.27;0.88;1.27;1.76;1.17;0.88	5.11	4.16	0.48862	.	0.000000	0.64402	D	0.000006	T	0.54581	0.1867	L	0.54863	1.705	0.52501	D	0.999958	D;D;P;D;D	0.89917	1.0;0.998;0.73;0.998;0.999	D;P;P;P;D	0.68353	0.956;0.905;0.492;0.905;0.957	T	0.50874	-0.8776	10	0.35671	T	0.21	.	10.7395	0.46145	0.0:0.9107:0.0:0.0893	.	224;404;399;399;229	F5H144;B4DR54;Q9Y653-2;Q9Y653;E7ENB2	.;.;.;GPR56_HUMAN;.	Q	399;399;399;399;399;224;229;399	ENSP00000373465:H399Q;ENSP00000373464:H399Q;ENSP00000444415:H399Q;ENSP00000398034:H399Q;ENSP00000444911:H399Q;ENSP00000438006:H224Q;ENSP00000369016:H229Q;ENSP00000369018:H399Q	ENSP00000369016:H229Q	H	+	3	2	GPR56	56248815	1.000000	0.71417	0.978000	0.43139	0.114000	0.19823	2.288000	0.43514	1.146000	0.42352	0.491000	0.48974	CAC	GPR56	-	NULL	ENSG00000205336		0.647	GPR56-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GPR56	HGNC	protein_coding	OTTHUMT00000433436.3	60	0.00	0	C			57691314	57691314	+1	no_errors	ENST00000379696	ensembl	human	known	69_37n	missense	11	26.67	4	SNP	1.000	A
GRM1	2911	genome.wustl.edu	37	6	146720226	146720226	+	Missense_Mutation	SNP	G	G	A			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr6:146720226G>A	ENST00000282753.1	+	7	2286	c.2051G>A	c.(2050-2052)cGc>cAc	p.R684H	GRM1_ENST00000392299.2_Missense_Mutation_p.R684H|GRM1_ENST00000361719.2_Missense_Mutation_p.R684H|GRM1_ENST00000492807.2_Missense_Mutation_p.R684H|GRM1_ENST00000507907.1_Missense_Mutation_p.R684H|GRM1_ENST00000355289.4_Missense_Mutation_p.R684H			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	684					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		CGTATTGCACGCATCCTGGCT	0.522																																						dbGAP											0													203.0	196.0	198.0					6																	146720226		2203	4300	6503	-	-	-	SO:0001583	missense	0			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.2051G>A	6.37:g.146720226G>A	ENSP00000282753:p.Arg684His		B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	pfam_ANF_lig-bd_rcpt,pfam_GPCR_3_C,pfam_Metabotropic_Glu_rcpt_Homer-bd,pfam_GPCR_3_9-Cys_dom,prints_GPCR_3_mtglu_rcpt_1,prints_GPCR_3,prints_GPCR_3_mtglu_rcpt,prints_GPCR_3_mtglu_rcpt_5,pfscan_GPCR_3_C	p.R684H	ENST00000282753.1	37	c.2051	CCDS5209.1	6	.	.	.	.	.	.	.	.	.	.	G	28.2	4.900562	0.92035	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	D;D;D;D;D;D	0.89746	-2.56;-2.56;-2.56;-2.56;-2.56;-2.56	5.51	5.51	0.81932	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.95262	0.8463	M	0.88775	2.98	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.95597	0.8659	10	0.87932	D	0	.	19.4081	0.94656	0.0:0.0:1.0:0.0	.	684;684;684	F8W805;Q13255;Q13255-2	.;GRM1_HUMAN;.	H	684	ENSP00000354896:R684H;ENSP00000376119:R684H;ENSP00000424095:R684H;ENSP00000282753:R684H;ENSP00000347437:R684H;ENSP00000425599:R684H	ENSP00000282753:R684H	R	+	2	0	GRM1	146761919	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.604000	0.88044	0.585000	0.79938	CGC	GRM1	-	pfam_GPCR_3_C,prints_GPCR_3,pfscan_GPCR_3_C	ENSG00000152822		0.522	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GRM1	HGNC	protein_coding	OTTHUMT00000042574.1	173	0.00	0	G	NM_000838		146720226	146720226	+1	no_errors	ENST00000282753	ensembl	human	known	69_37n	missense	183	27.09	68	SNP	1.000	A
HK1	3098	genome.wustl.edu	37	10	71154851	71154851	+	Nonsense_Mutation	SNP	C	C	T	rs113021525		TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr10:71154851C>T	ENST00000359426.6	+	16	2469	c.2365C>T	c.(2365-2367)Cag>Tag	p.Q789*	HK1_ENST00000404387.2_Nonsense_Mutation_p.Q793*|HK1_ENST00000298649.3_Nonsense_Mutation_p.Q788*|HK1_ENST00000360289.2_Nonsense_Mutation_p.Q777*|HK1_ENST00000448642.2_Nonsense_Mutation_p.Q824*	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	789	Catalytic.|Hexokinase type-2 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						GTTTCTCTCTCAGATCGAGAG	0.572																																						dbGAP											0													49.0	43.0	45.0					10																	71154851		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.2365C>T	10.37:g.71154851C>T	ENSP00000352398:p.Gln789*		E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Nonsense_Mutation	SNP	pfam_Hexokinase_C,pfam_Hexokinase_N,prints_Hexokinase	p.Q824*	ENST00000359426.6	37	c.2470	CCDS7292.1	10	.	.	.	.	.	.	.	.	.	.	C	41	9.077622	0.99059	.	.	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-26.8645	18.9396	0.92600	0.0:1.0:0.0:0.0	.	.	.	.	X	777;824;793;788;789;789	.	ENSP00000298649:Q788X	Q	+	1	0	HK1	70824857	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.720000	0.84759	2.456000	0.83038	0.557000	0.71058	CAG	HK1	-	pfam_Hexokinase_C	ENSG00000156515		0.572	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HK1	HGNC	protein_coding	OTTHUMT00000048429.2	76	0.00	0	C	NM_000188		71154851	71154851	+1	no_errors	ENST00000448642	ensembl	human	known	69_37n	nonsense	87	20.91	23	SNP	1.000	T
HSPA12B	116835	genome.wustl.edu	37	20	3721533	3721534	+	Frame_Shift_Ins	INS	-	-	C	rs200790194		TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr20:3721533_3721534insC	ENST00000254963.2	+	3	260_261	c.115_116insC	c.(115-117)gccfs	p.A39fs	HSPA12B_ENST00000542646.1_Intron	NM_001197327.1|NM_052970.4	NP_001184256.1|NP_443202.3	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B	39							ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	14						CTGCGGCATTGCCCCCCTCACA	0.658																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AK056712	CCDS13061.1	20p13	2011-09-02	2003-04-10	2003-04-10	ENSG00000132622	ENSG00000132622		"""Heat shock proteins / HSP70"""	16193	protein-coding gene	gene with protein product		610702	"""chromosome 20 open reading frame 60"""	C20orf60		12552099	Standard	NM_052970		Approved	dJ1009E24.2	uc002wjd.3	Q96MM6	OTTHUMG00000031755	ENST00000254963.2:c.121dupC	20.37:g.3721539_3721539dupC	ENSP00000254963:p.Ala39fs		D3DVX7|Q2TAK3|Q9BR52	Frame_Shift_Ins	INS	NULL	p.L41fs	ENST00000254963.2	37	c.115_116	CCDS13061.1	20																																																																																			HSPA12B	-	NULL	ENSG00000132622		0.658	HSPA12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HSPA12B	HGNC	protein_coding	OTTHUMT00000077756.2	76	0.00	0	-	NM_052970		3721533	3721534	+1	no_errors	ENST00000254963	ensembl	human	known	69_37n	frame_shift_ins	23	11.54	3	INS	1.000:1.000	C
KIAA2013	90231	genome.wustl.edu	37	1	11985345	11985345	+	Frame_Shift_Del	DEL	T	T	-			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr1:11985345delT	ENST00000376572.3	-	1	1135	c.950delA	c.(949-951)aagfs	p.K317fs	KIAA2013_ENST00000376576.3_Frame_Shift_Del_p.K317fs	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN	KIAA2013	317						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CAGCATTTCCTTCCGTGCCAA	0.617																																						dbGAP											0													52.0	52.0	52.0					1																	11985345		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			AB095933	CCDS141.1	1p36.22	2011-02-09			ENSG00000116685	ENSG00000116685			28513	protein-coding gene	gene with protein product						12477932	Standard	NM_138346		Approved	MGC33867, RP5-1077B9.1	uc001atk.3	Q8IYS2	OTTHUMG00000002391	ENST00000376572.3:c.950delA	1.37:g.11985345delT	ENSP00000365756:p.Lys317fs		Q5JXC1|Q8IVF8|Q8NDI7|Q9BSY1	Frame_Shift_Del	DEL	pfam_DUF2152	p.K317fs	ENST00000376572.3	37	c.950	CCDS141.1	1																																																																																			KIAA2013	-	pfam_DUF2152	ENSG00000116685		0.617	KIAA2013-002	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA2013	HGNC	protein_coding	OTTHUMT00000006858.1	54	0.00	0	T	NM_138346		11985345	11985345	-1	no_errors	ENST00000376576	ensembl	human	known	69_37n	frame_shift_del	30	11.76	4	DEL	1.000	-
KRTAP3-2	83897	genome.wustl.edu	37	17	39155871	39155871	+	Missense_Mutation	SNP	T	T	A			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr17:39155871T>A	ENST00000391587.1	-	1	267	c.235A>T	c.(235-237)Acc>Tcc	p.T79S		NM_031959.2	NP_114165.1	Q9BYR7	KRA32_HUMAN	keratin associated protein 3-2	79						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(1)|lung(1)	3		Breast(137;0.00043)				AGGTTGAGGGTCTCCAGGCCC	0.607																																						dbGAP											0													63.0	79.0	74.0					17																	39155871		2203	4296	6499	-	-	-	SO:0001583	missense	0			AJ406932	CCDS32644.1	17q21.2	2013-06-25			ENSG00000212900	ENSG00000212900		"""Keratin associated proteins"""	16779	protein-coding gene	gene with protein product						11279113	Standard	NM_031959		Approved	KAP3.2	uc002hvs.3	Q9BYR7	OTTHUMG00000133581	ENST00000391587.1:c.235A>T	17.37:g.39155871T>A	ENSP00000375429:p.Thr79Ser			Missense_Mutation	SNP	pfam_Keratin_matx	p.T79S	ENST00000391587.1	37	c.235	CCDS32644.1	17	.	.	.	.	.	.	.	.	.	.	T	11.70	1.715877	0.30413	.	.	ENSG00000212900	ENST00000391587	T	0.20738	2.05	5.76	4.68	0.58851	.	0.451840	0.20825	N	0.084983	T	0.14356	0.0347	.	.	.	0.29462	N	0.857679	B	0.06786	0.001	B	0.12837	0.008	T	0.13737	-1.0498	9	0.27785	T	0.31	.	9.2525	0.37564	0.1605:0.0:0.0:0.8395	.	79	Q9BYR7	KRA32_HUMAN	S	79	ENSP00000375429:T79S	ENSP00000375429:T79S	T	-	1	0	KRTAP3-2	36409397	0.979000	0.34478	0.943000	0.38184	0.796000	0.44982	2.249000	0.43169	0.996000	0.38943	0.456000	0.33151	ACC	KRTAP3-2	-	pfam_Keratin_matx	ENSG00000212900		0.607	KRTAP3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRTAP3-2	HGNC	protein_coding	OTTHUMT00000257685.1	201	0.00	0	T			39155871	39155871	-1	no_errors	ENST00000391587	ensembl	human	known	69_37n	missense	184	33.33	92	SNP	0.942	A
NAV2	89797	genome.wustl.edu	37	11	20136311	20136312	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr11:20136311_20136312insC	ENST00000396087.3	+	40	7410_7411	c.7311_7312insC	c.(7312-7314)cccfs	p.P2438fs	NAV2_ENST00000360655.4_Frame_Shift_Ins_p.P2315fs|NAV2_ENST00000311043.8_Frame_Shift_Ins_p.P1443fs|NAV2_ENST00000533917.1_Frame_Shift_Ins_p.P1443fs|NAV2_ENST00000349880.4_Frame_Shift_Ins_p.P2379fs|NAV2_ENST00000540292.1_Frame_Shift_Ins_p.P2369fs|NAV2_ENST00000527559.2_Frame_Shift_Ins_p.P2367fs|NAV2_ENST00000396085.1_Frame_Shift_Ins_p.P2382fs	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	2438					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						GCAAGCAGATGCCCCCCAGTGA	0.589																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.7317dupC	11.37:g.20136317_20136317dupC	ENSP00000379396:p.Pro2438fs		A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Frame_Shift_Ins	INS	pfam_CH-domain,superfamily_CH-domain,smart_CH-domain,smart_AAA+_ATPase,pfscan_CH-domain	p.S2439fs	ENST00000396087.3	37	c.7311_7312	CCDS58126.1	11																																																																																			NAV2	-	NULL	ENSG00000166833		0.589	NAV2-001	KNOWN	basic|CCDS	protein_coding	NAV2	HGNC	protein_coding	OTTHUMT00000324112.1	108	0.92	1	-	NM_145117		20136311	20136312	+1	no_errors	ENST00000396087	ensembl	human	known	69_37n	frame_shift_ins	62	10.14	7	INS	0.998:1.000	C
ONECUT2	9480	genome.wustl.edu	37	18	55103477	55103479	+	In_Frame_Del	DEL	CAC	CAC	-			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	CAC	CAC					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr18:55103477_55103479delCAC	ENST00000491143.2	+	1	561_563	c.529_531delCAC	c.(529-531)cacdel	p.H184del	AC090340.1_ENST00000581316.1_RNA	NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	184	Poly-His.				cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|epithelial cell development (GO:0002064)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ morphogenesis (GO:0009887)|peripheral nervous system neuron development (GO:0048935)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|lung(4)|ovary(2)|skin(1)	15		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		ccaccatccgcaccaccaccacc	0.655																																						dbGAP											0										142,294,3708		10,1,121,12,269,1659						-3.2	0.9			40	19,703,7402		1,0,17,11,681,3352	no	codingComplex	ONECUT2	NM_004852.2		11,1,138,23,950,5011	A1A1,A1A2,A1R,A2A2,A2R,RR		8.8872,10.5212,9.4392				161,997,11110				-	-	-	SO:0001651	inframe_deletion	0			Y18198	CCDS42440.1	18q21.31	2012-03-09	2007-07-16		ENSG00000119547	ENSG00000119547		"""Homeoboxes / CUT class"""	8139	protein-coding gene	gene with protein product		604894	"""one cut domain, family member 2"""			9915796	Standard	NM_004852		Approved	OC-2	uc002lgo.3	O95948	OTTHUMG00000159776	ENST00000491143.2:c.529_531delCAC	18.37:g.55103486_55103488delCAC	ENSP00000419185:p.His184del			In_Frame_Del	DEL	pfam_Hmoeo_CUT,pfam_Homeodomain,superfamily_Lambda_DNA-bd_dom,superfamily_Homeodomain-like,smart_Homeodomain,pfscan_Homeodomain,pfscan_Hmoeo_CUT	p.H180in_frame_del	ENST00000491143.2	37	c.529_531	CCDS42440.1	18																																																																																			ONECUT2	-	NULL	ENSG00000119547		0.655	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ONECUT2	HGNC	protein_coding	OTTHUMT00000357264.3	47	0.00	0	CAC			55103477	55103479	+1	no_errors	ENST00000262095	ensembl	human	known	69_37n	in_frame_del	20	16.67	4	DEL	1.000:1.000:1.000	-
PIK3CA	5290	genome.wustl.edu	37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003		TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr3:178936091G>A	ENST00000263967.3	+	10	1790	c.1633G>A	c.(1633-1635)Gag>Aag	p.E545K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545K(881)|p.E545Q(18)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGAAATCACTGAGCAGGAGAA	0.353	E545K(BC3C_URINARY_TRACT)|E545K(BFTC909_KIDNEY)|E545K(DLD1_LARGE_INTESTINE)|E545K(ESS1_ENDOMETRIUM)|E545K(HCC202_BREAST)|E545K(HCT15_LARGE_INTESTINE)|E545K(HSC4_UPPER_AERODIGESTIVE_TRACT)|E545K(HT1197_URINARY_TRACT)|E545K(HUH28_BILIARY_TRACT)|E545K(KYSE510_OESOPHAGUS)|E545K(L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|E545K(MCF7_BREAST)|E545K(MDAMB361_BREAST)|E545K(MKN1_STOMACH)|E545K(NCIH460_LUNG)|E545K(NCIH508_LARGE_INTESTINE)|E545K(NCIH596_LUNG)|E545K(RERFLCSQ1_LUNG)|E545K(TCCSUP_URINARY_TRACT)|E545K(TE5_OESOPHAGUS)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	899	Substitution - Missense(899)	breast(308)|large_intestine(286)|urinary_tract(97)|lung(44)|endometrium(37)|ovary(25)|stomach(17)|upper_aerodigestive_tract(16)|skin(14)|central_nervous_system(13)|cervix(13)|thyroid(7)|oesophagus(7)|penis(4)|kidney(3)|soft_tissue(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|NS(1)|pituitary(1)											61.0	60.0	60.0					3																	178936091		1813	4072	5885	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1633G>A	3.37:g.178936091G>A	ENSP00000263967:p.Glu545Lys		Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.E545K	ENST00000263967.3	37	c.1633	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	G	36	5.703347	0.96812	.	.	ENSG00000121879	ENST00000263967	T	0.63255	-0.03	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73822	0.3636	L	0.51914	1.62	0.80722	D	1	D	0.62365	0.991	D	0.62955	0.909	T	0.68872	-0.5294	10	0.32370	T	0.25	-25.7963	20.0024	0.97423	0.0:0.0:1.0:0.0	.	545	P42336	PK3CA_HUMAN	K	545	ENSP00000263967:E545K	ENSP00000263967:E545K	E	+	1	0	PIK3CA	180418785	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAG	PIK3CA	-	pfam_PInositide-3_kin_accessory_dom,superfamily_ARM-type_fold,smart_PInositide-3_kin_accessory_dom	ENSG00000121879		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	48	0.00	0	G			178936091	178936091	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	58	26.58	21	SNP	1.000	A
PIKFYVE	200576	genome.wustl.edu	37	2	209212650	209212650	+	Silent	SNP	C	C	T			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr2:209212650C>T	ENST00000264380.4	+	35	5435	c.5277C>T	c.(5275-5277)tcC>tcT	p.S1759S		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1759	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						ATCTCTCTTCCCAGAAGAGAG	0.478																																						dbGAP											0													70.0	72.0	71.0					2																	209212650		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.5277C>T	2.37:g.209212650C>T			Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	pfam_PInositol-4-P-5-kinase_core,pfam_Cpn60/TCP-1,pfam_DEP_dom,pfam_Znf_FYVE,superfamily_Znf_FYVE_PHD,smart_Znf_FYVE,smart_DEP_dom,smart_PInositol-4P-5-kinase_core_sub,pfscan_DEP_dom,pfscan_Znf_FYVE-rel	p.S1759	ENST00000264380.4	37	c.5277	CCDS2382.1	2																																																																																			PIKFYVE	-	NULL	ENSG00000115020		0.478	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PIKFYVE	HGNC	protein_coding	OTTHUMT00000256477.2	57	0.00	0	C	NM_015040		209212650	209212650	+1	no_errors	ENST00000264380	ensembl	human	known	69_37n	silent	56	13.85	9	SNP	1.000	T
PLEKHA4	57664	genome.wustl.edu	37	19	49363612	49363612	+	Silent	SNP	G	G	A			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr19:49363612G>A	ENST00000263265.6	-	6	1026	c.471C>T	c.(469-471)gaC>gaT	p.D157D	PLEKHA4_ENST00000355496.5_Silent_p.D157D|PLEKHA4_ENST00000596713.1_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	157						cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)	p.D157D(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		CTCACTAGTCGTCCCCCTCCG	0.652																																						dbGAP											1	Substitution - coding silent(1)	large_intestine(1)											48.0	51.0	50.0					19																	49363612		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"""Pleckstrin homology (PH) domain containing"""	14339	protein-coding gene	gene with protein product		607769	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"""			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.471C>T	19.37:g.49363612G>A			Q8N4M8|Q8N658	Silent	SNP	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.D157	ENST00000263265.6	37	c.471	CCDS12737.1	19																																																																																			PLEKHA4	-	NULL	ENSG00000105559		0.652	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLEKHA4	HGNC	protein_coding	OTTHUMT00000466216.1	105	0.00	0	G			49363612	49363612	-1	no_errors	ENST00000263265	ensembl	human	known	69_37n	silent	36	25.00	12	SNP	0.157	A
PRDM16	63976	genome.wustl.edu	37	1	3301795	3301795	+	Missense_Mutation	SNP	G	G	A			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr1:3301795G>A	ENST00000270722.5	+	4	567	c.518G>A	c.(517-519)cGt>cAt	p.R173H	PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000511072.1_Missense_Mutation_p.R174H|PRDM16_ENST00000378391.2_Missense_Mutation_p.R173H|PRDM16_ENST00000442529.2_Missense_Mutation_p.R173H|PRDM16_ENST00000514189.1_Missense_Mutation_p.R174H|PRDM16_ENST00000441472.2_Missense_Mutation_p.R173H|PRDM16_ENST00000378398.3_Missense_Mutation_p.R173H			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	173	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|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)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)	p.R173H(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		AAGTACATCCGTGTGGCGTGC	0.577			T	EVI1	"""MDS, AML"""																																	dbGAP		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	1	Substitution - Missense(1)	kidney(1)											99.0	111.0	107.0					1																	3301795		2174	4268	6442	-	-	-	SO:0001583	missense	0			AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.518G>A	1.37:g.3301795G>A	ENSP00000270722:p.Arg173His		A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	pfam_Znf_C2H2,pfam_Znf_BED_prd,smart_SET_dom,smart_Znf_C2H2-like,pfscan_SET_dom,pfscan_Znf_C2H2	p.R173H	ENST00000270722.5	37	c.518	CCDS41236.2	1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.143291	0.77888	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722	D;D;T;T;T;D;T	0.88664	-2.41;-2.41;-0.67;-0.67;-0.67;-2.41;-0.67	4.67	4.67	0.58626	SET domain (2);	0.125508	0.35067	N	0.003472	D	0.93536	0.7937	M	0.69248	2.105	0.58432	D	0.999995	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.87578	0.987;0.998;0.977;0.987	D	0.93748	0.7056	10	0.52906	T	0.07	.	16.893	0.86092	0.0:0.0:1.0:0.0	.	173;173;173;173	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	H	174;173;173;173;173;174;173	ENSP00000426975:R174H;ENSP00000367651:R173H;ENSP00000407968:R173H;ENSP00000405253:R173H;ENSP00000367643:R173H;ENSP00000421400:R174H;ENSP00000270722:R173H	ENSP00000270722:R173H	R	+	2	0	PRDM16	3291655	1.000000	0.71417	0.940000	0.37924	0.674000	0.39518	4.713000	0.61895	2.297000	0.77311	0.561000	0.74099	CGT	PRDM16	-	smart_SET_dom,pfscan_SET_dom	ENSG00000142611		0.577	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PRDM16	HGNC	protein_coding	OTTHUMT00000001382.3	24	0.00	0	G	NM_022114		3301795	3301795	+1	no_errors	ENST00000270722	ensembl	human	known	69_37n	missense	8	38.46	5	SNP	0.991	A
PRND	23627	genome.wustl.edu	37	20	4705447	4705447	+	Missense_Mutation	SNP	C	C	A			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr20:4705447C>A	ENST00000305817.2	+	2	321	c.250C>A	c.(250-252)Cag>Aag	p.Q84K		NM_012409.2	NP_036541.2	Q9UKY0	PRND_HUMAN	prion protein 2 (dublet)	84	Globular.				protein homooligomerization (GO:0051260)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	13						CAACTACTGGCAGTTCCCCGA	0.597																																						dbGAP											0													73.0	57.0	62.0					20																	4705447		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF106918	CCDS13081.1	20p13	2013-09-19			ENSG00000171864	ENSG00000171864			15748	protein-coding gene	gene with protein product	"""prion-like protein doppel"""	604263				10525406, 10577243	Standard	NM_012409		Approved	DPL, dJ1068H6.4, DOPPEL, PrPLP	uc002wkz.3	Q9UKY0	OTTHUMG00000031789	ENST00000305817.2:c.250C>A	20.37:g.4705447C>A	ENSP00000306900:p.Gln84Lys		A7U7M5|Q9H311|Q9H312|Q9NTM4	Missense_Mutation	SNP	pfam_Prion/Doppel_prot_b-ribbon_dom,pfam_Doppel,superfamily_Prion/Doppel_prot_b-ribbon_dom	p.Q84K	ENST00000305817.2	37	c.250	CCDS13081.1	20	.	.	.	.	.	.	.	.	.	.	C	17.38	3.375337	0.61735	.	.	ENSG00000171864	ENST00000305817	D	0.88509	-2.39	5.37	5.37	0.77165	Prion/Doppel protein, beta-ribbon domain (3);	0.181066	0.27100	N	0.020921	D	0.87665	0.6234	M	0.64404	1.975	0.36229	D	0.852493	P	0.35908	0.527	B	0.38106	0.265	D	0.88585	0.3139	10	0.28530	T	0.3	-26.0588	14.5898	0.68356	0.0:1.0:0.0:0.0	.	84	Q9UKY0	PRND_HUMAN	K	84	ENSP00000306900:Q84K	ENSP00000306900:Q84K	Q	+	1	0	PRND	4653447	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.545000	0.53648	2.502000	0.84385	0.557000	0.71058	CAG	PRND	-	pfam_Prion/Doppel_prot_b-ribbon_dom,superfamily_Prion/Doppel_prot_b-ribbon_dom	ENSG00000171864		0.597	PRND-002	KNOWN	basic|appris_principal|CCDS	protein_coding	PRND	HGNC	protein_coding	OTTHUMT00000077827.2	56	0.00	0	C	NM_012409		4705447	4705447	+1	no_errors	ENST00000305817	ensembl	human	known	69_37n	missense	37	26.00	13	SNP	1.000	A
PWP2	5822	genome.wustl.edu	37	21	45528869	45528869	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr21:45528869C>T	ENST00000291576.7	+	2	150	c.23C>T	c.(22-24)tCa>tTa	p.S8L		NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	8					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		TCACAGTTTTCAAATTTGCTG	0.433																																						dbGAP											0													102.0	90.0	94.0					21																	45528869		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"""WD repeat domain containing"""	9711	protein-coding gene	gene with protein product		601475	"""PWP2 (periodic tryptophan protein, yeast) homolog"""	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.23C>T	21.37:g.45528869C>T	ENSP00000291576:p.Ser8Leu		B2RAG8|Q96A77	Missense_Mutation	SNP	pfam_WD40_repeat,pfam_SSU_processome_Utp12,superfamily_Quinonprotein_ADH-like,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom,prints_G-protein_beta_WD-40_rep	p.S8L	ENST00000291576.7	37	c.23	CCDS33579.1	21	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972087	0.74246	.	.	ENSG00000241945	ENST00000291576;ENST00000456705	T;T	0.62364	0.03;0.73	4.75	4.75	0.60458	.	0.000000	0.64402	D	0.000004	T	0.81697	0.4877	M	0.90019	3.08	0.52501	D	0.999954	D	0.76494	0.999	D	0.80764	0.994	D	0.85531	0.1209	10	0.87932	D	0	-1.1311	13.4955	0.61424	0.0:0.8428:0.1572:0.0	.	8	Q15269	PWP2_HUMAN	L	8	ENSP00000291576:S8L;ENSP00000411749:S8L	ENSP00000291576:S8L	S	+	2	0	PWP2	44353297	1.000000	0.71417	0.876000	0.34364	0.622000	0.37654	5.416000	0.66417	2.358000	0.79984	0.563000	0.77884	TCA	PWP2	-	NULL	ENSG00000241945		0.433	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PWP2	HGNC	protein_coding	OTTHUMT00000195736.3	85	0.00	0	C	NM_005049		45528869	45528869	+1	no_errors	ENST00000291576	ensembl	human	known	69_37n	missense	106	40.11	71	SNP	0.995	T
RNF19A	25897	genome.wustl.edu	37	8	101300149	101300149	+	Missense_Mutation	SNP	T	T	G			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr8:101300149T>G	ENST00000519449.1	-	3	570	c.254A>C	c.(253-255)aAt>aCt	p.N85T	RNF19A_ENST00000341084.2_Missense_Mutation_p.N85T	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	85					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			CACCCCGCCATTTAGCTCCCT	0.383																																						dbGAP											0													145.0	139.0	141.0					8																	101300149		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"""RING-type (C3HC4) zinc fingers"""	13432	protein-coding gene	gene with protein product		607119	"""ring finger protein 19"", ""ring finger protein 19A"", ""ring finger protein 19A, E3 ubiquitin protein ligase"""	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.254A>C	8.37:g.101300149T>G	ENSP00000428968:p.Asn85Thr		A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	pfam_Znf_C6HC,smart_Znf_RING,smart_Znf_C6HC,pfscan_Znf_RING	p.N85T	ENST00000519449.1	37	c.254	CCDS6286.1	8	.	.	.	.	.	.	.	.	.	.	T	12.38	1.920730	0.33908	.	.	ENSG00000034677	ENST00000519449;ENST00000341084;ENST00000519527;ENST00000523167;ENST00000522369;ENST00000432381;ENST00000517584	D;D	0.83673	-1.75;-1.75	5.57	3.0	0.34707	.	0.224693	0.46442	N	0.000288	T	0.63414	0.2509	N	0.12182	0.205	0.38913	D	0.957578	B	0.02656	0.0	B	0.01281	0.0	T	0.52845	-0.8521	10	0.15499	T	0.54	.	7.0481	0.25056	0.0:0.0716:0.2844:0.644	.	85	Q9NV58	RN19A_HUMAN	T	85;85;85;85;85;85;54	ENSP00000428968:N85T;ENSP00000342667:N85T	ENSP00000342667:N85T	N	-	2	0	RNF19A	101369325	1.000000	0.71417	0.997000	0.53966	0.956000	0.61745	2.531000	0.45650	0.903000	0.36546	0.528000	0.53228	AAT	RNF19A	-	NULL	ENSG00000034677		0.383	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	RNF19A	HGNC	protein_coding	OTTHUMT00000380004.1	47	0.00	0	T	NM_015435		101300149	101300149	-1	no_errors	ENST00000341084	ensembl	human	known	69_37n	missense	84	20.00	21	SNP	1.000	G
SHE	126669	genome.wustl.edu	37	1	154461722	154461722	+	Missense_Mutation	SNP	G	G	A			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr1:154461722G>A	ENST00000304760.2	-	3	915	c.829C>T	c.(829-831)Cgg>Tgg	p.R277W		NM_001010846.2	NP_001010846.1	Q5VZ18	SHE_HUMAN	Src homology 2 domain containing E	277										breast(4)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	14	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TTGGAACTCCGTCTTTTGGCC	0.632																																						dbGAP											0													50.0	56.0	54.0					1																	154461722		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK074067	CCDS30877.1	1q21.3	2013-02-14			ENSG00000169291	ENSG00000169291		"""SH2 domain containing"""	27004	protein-coding gene	gene with protein product		610482				9315092	Standard	NM_001010846		Approved		uc001ffb.3	Q5VZ18	OTTHUMG00000036072	ENST00000304760.2:c.829C>T	1.37:g.154461722G>A	ENSP00000307369:p.Arg277Trp		Q8TEQ5	Missense_Mutation	SNP	pfam_SH2,smart_SH2,pfscan_SH2,prints_SH2	p.R277W	ENST00000304760.2	37	c.829	CCDS30877.1	1	.	.	.	.	.	.	.	.	.	.	G	12.81	2.050329	0.36181	.	.	ENSG00000169291	ENST00000304760	T	0.37584	1.19	5.61	1.18	0.20946	.	0.663946	0.14874	N	0.293343	T	0.19327	0.0464	L	0.59436	1.845	0.09310	N	1	D	0.56968	0.978	B	0.43623	0.425	T	0.04386	-1.0955	10	0.66056	D	0.02	-16.8692	10.4036	0.44243	0.0:0.1233:0.4947:0.382	.	277	Q5VZ18	SHE_HUMAN	W	277	ENSP00000307369:R277W	ENSP00000307369:R277W	R	-	1	2	SHE	152728346	0.000000	0.05858	0.001000	0.08648	0.141000	0.21300	0.508000	0.22692	0.392000	0.25172	0.650000	0.86243	CGG	SHE	-	NULL	ENSG00000169291		0.632	SHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SHE	HGNC	protein_coding	OTTHUMT00000087910.2	36	0.00	0	G	NM_001010846		154461722	154461722	-1	no_errors	ENST00000304760	ensembl	human	known	69_37n	missense	25	19.35	6	SNP	0.000	A
SNX3	8724	genome.wustl.edu	37	6	108581992	108581992	+	Missense_Mutation	SNP	C	C	A			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr6:108581992C>A	ENST00000230085.8	-	1	472	c.134G>T	c.(133-135)cGc>cTc	p.R45L	SNX3_ENST00000368982.4_Missense_Mutation_p.R45L|SNX3_ENST00000349379.5_Intron|SNX3_ENST00000426155.2_Missense_Mutation_p.R45L	NM_003795.4	NP_003786.1	O60493	SNX3_HUMAN	sorting nexin 3	45	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				hemoglobin biosynthetic process (GO:0042541)|intracellular protein transport (GO:0006886)|intralumenal vesicle formation (GO:0070676)|membrane invagination (GO:0010324)|negative regulation of early endosome to late endosome transport (GO:2000642)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein transport (GO:0051224)|negative regulation of viral entry into host cell (GO:0046597)|regulation of cellular protein metabolic process (GO:0032268)|regulation of intracellular protein transport (GO:0033157)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein phosphatase binding (GO:0019903)			large_intestine(1)	1		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0136)|Epithelial(106;0.0564)|OV - Ovarian serous cystadenocarcinoma(136;0.0717)|all cancers(137;0.0743)		AGTGGTGAAGCGGCCCCGGCC	0.632																																						dbGAP											0													52.0	58.0	56.0					6																	108581992		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF034546	CCDS5064.1, CCDS5065.1, CCDS75501.1	6q21	2010-08-05			ENSG00000112335	ENSG00000112335		"""Sorting nexins"""	11174	protein-coding gene	gene with protein product		605930				9819414	Standard	XM_005267192		Approved	Grd19	uc003psh.3	O60493	OTTHUMG00000015323	ENST00000230085.8:c.134G>T	6.37:g.108581992C>A	ENSP00000230085:p.Arg45Leu		A8K0B1|E1P5E4|E1P5E5|O60718|Q4TT29|Q4TT31|Q5JXJ7|Q5JXJ8|Q96AP9|Q9C0J5|Q9NU45	Missense_Mutation	SNP	pfam_Phox,superfamily_Phox,smart_Phox,pfscan_Phox	p.R45L	ENST00000230085.8	37	c.134	CCDS5064.1	6	.	.	.	.	.	.	.	.	.	.	C	20.4	3.990572	0.74589	.	.	ENSG00000112335	ENST00000230085;ENST00000426155;ENST00000368982	T;T;T	0.39056	1.1;1.24;1.1	5.37	3.57	0.40892	Phox homologous domain (5);	0.047827	0.85682	D	0.000000	T	0.53158	0.1779	M	0.84219	2.685	0.80722	D	1	D;D	0.64830	0.966;0.994	P;D	0.68192	0.88;0.956	T	0.59716	-0.7402	10	0.66056	D	0.02	-16.7305	10.3969	0.44207	0.1345:0.7952:0.0:0.0702	.	45;45	O60493-2;O60493	.;SNX3_HUMAN	L	45	ENSP00000230085:R45L;ENSP00000401779:R45L;ENSP00000357978:R45L	ENSP00000230085:R45L	R	-	2	0	SNX3	108688685	1.000000	0.71417	1.000000	0.80357	0.596000	0.36781	5.197000	0.65141	0.631000	0.30412	-0.314000	0.08810	CGC	SNX3	-	pfam_Phox,superfamily_Phox,smart_Phox,pfscan_Phox	ENSG00000112335		0.632	SNX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SNX3	HGNC	protein_coding	OTTHUMT00000041717.1	61	0.00	0	C			108581992	108581992	-1	no_errors	ENST00000230085	ensembl	human	known	69_37n	missense	26	18.75	6	SNP	1.000	A
UBR4	23352	genome.wustl.edu	37	1	19439358	19439359	+	In_Frame_Ins	INS	-	-	CAA			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr1:19439358_19439359insCAA	ENST00000375254.3	-	78	11487_11488	c.11460_11461insTTG	c.(11458-11463)aaagtc>aaaTTGgtc	p.3820_3821KV>KLV	UBR4_ENST00000375267.2_In_Frame_Ins_p.3820_3821KV>KLV|UBR4_ENST00000375226.2_In_Frame_Ins_p.3796_3797KV>KLV|UBR4_ENST00000375218.3_3'UTR|UBR4_ENST00000375217.2_In_Frame_Ins_p.3813_3814KV>KLV	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	3820					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GAAGCAAAGACTTTCTAAGAAC	0.391																																						dbGAP											0																																										-	-	-	SO:0001652	inframe_insertion	0			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.11460_11461insTTG	1.37:g.19439358_19439359insCAA	ENSP00000364403:p.Lys3820_Val3821insLeu		A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	In_Frame_Ins	INS	superfamily_WD40_repeat_dom,superfamily_ARM-type_fold,smart_Znf_N-recognin_met,pfscan_Znf_N-recognin	p.3820in_frame_insL	ENST00000375254.3	37	c.11461_11460	CCDS189.1	1																																																																																			UBR4	-	NULL	ENSG00000127481		0.391	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UBR4	HGNC	protein_coding	OTTHUMT00000007085.1	133	0.00	0	-	NM_020765		19439358	19439359	-1	no_errors	ENST00000375267	ensembl	human	known	69_37n	in_frame_ins	112	16.42	22	INS	1.000:1.000	CAA
WHSC1	7468	genome.wustl.edu	37	4	1954980	1954981	+	Intron	INS	-	-	G			TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9308f50c-1320-4c45-acc7-38f43b6f9a36	add72fe8-59ed-4a39-a37c-4f463a978acf	g.chr4:1954980_1954981insG	ENST00000382895.3	+	14	2568				WHSC1_ENST00000508803.1_Intron|WHSC1_ENST00000382892.2_Intron|WHSC1_ENST00000382891.5_Intron|WHSC1_ENST00000482415.2_Intron|WHSC1_ENST00000382888.3_Frame_Shift_Ins_p.G38fs	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1						anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		TTGATTTTAGTGGCTCAGAACT	0.446			T	IGH@	MM																																	dbGAP		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	0																																										-	-	-	SO:0001627	intron_variant	0			AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"""Zinc fingers, PHD-type"""	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.2138-70->G	4.37:g.1954982_1954982dupG			A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Frame_Shift_Ins	INS	pfam_SET_dom,pfam_PWWP,pfam_Znf_PHD-finger,superfamily_Znf_FYVE_PHD,smart_Znf_PHD,smart_PWWP,smart_AWS,smart_SET_dom,smart_Post-SET_dom,pfscan_AWS,pfscan_PWWP,pfscan_SET_dom,pfscan_Post-SET_dom,pfscan_Znf_PHD-finger,pfscan_Znf_RING	p.S38fs	ENST00000382895.3	37	c.111_112	CCDS33940.1	4																																																																																			WHSC1	-	NULL	ENSG00000109685		0.446	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	WHSC1	HGNC	protein_coding	OTTHUMT00000366269.2	22	0.00	0	-	NM_133330		1954980	1954981	+1	no_errors	ENST00000382888	ensembl	human	known	69_37n	frame_shift_ins	12	29.41	5	INS	0.000:0.001	G
