#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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_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
AFF4	27125	genome.wustl.edu	37	5	132232866	132232866	+	Missense_Mutation	SNP	C	C	T			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr5:132232866C>T	ENST00000265343.5	-	11	1835	c.1456G>A	c.(1456-1458)Gtg>Atg	p.V486M	AFF4_ENST00000378595.3_Missense_Mutation_p.V486M	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	486					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCGGGTGACACTTTATGTGGG	0.448																																					Ovarian(126;889 1733 2942 10745 11605)	dbGAP											0													137.0	140.0	139.0					5																	132232866		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"""ALL1 fused gene from 5q31"""	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.1456G>A	5.37:g.132232866C>T	ENSP00000265343:p.Val486Met	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Missense_Mutation	SNP	pfam_TF_AF4/FMR2	p.V486M	ENST00000265343.5	37	c.1456	CCDS4164.1	5	.	.	.	.	.	.	.	.	.	.	C	21.2	4.106577	0.77096	.	.	ENSG00000072364	ENST00000265343;ENST00000378595	T;T	0.64991	-0.13;-0.13	5.8	5.8	0.92144	.	0.302672	0.36519	N	0.002547	T	0.79161	0.4399	M	0.68593	2.085	0.53688	D	0.999978	D;D	0.89917	1.0;0.996	D;D	0.85130	0.997;0.992	T	0.77544	-0.2548	10	0.48119	T	0.1	-7.9212	20.0522	0.97631	0.0:1.0:0.0:0.0	.	486;486	Q9UHB7-2;Q9UHB7	.;AFF4_HUMAN	M	486	ENSP00000265343:V486M;ENSP00000367858:V486M	ENSP00000265343:V486M	V	-	1	0	AFF4	132260765	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.106000	0.50322	2.737000	0.93849	0.563000	0.77884	GTG	AFF4	-	pfam_TF_AF4/FMR2	ENSG00000072364		0.448	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AFF4	HGNC	protein_coding	OTTHUMT00000133049.1	137	0.00	0	C	NM_014423		132232866	132232866	-1	no_errors	ENST00000265343	ensembl	human	known	69_37n	missense	179	40.33	121	SNP	1.000	T
ASXL1	171023	genome.wustl.edu	37	20	31023224	31023224	+	Silent	SNP	G	G	T			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr20:31023224G>T	ENST00000375687.4	+	13	3133	c.2709G>T	c.(2707-2709)tcG>tcT	p.S903S	ASXL1_ENST00000306058.5_Silent_p.S898S	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	903					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						CCATCCCATCGAATGATGAGG	0.483			"""F, N, Mis"""		"""MDS, CMML"""																																	dbGAP		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	0													91.0	87.0	89.0					20																	31023224		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"""additional sex combs like 1 (Drosophila)"""			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.2709G>T	20.37:g.31023224G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	NULL	p.S903	ENST00000375687.4	37	c.2709	CCDS13201.1	20																																																																																			ASXL1	-	NULL	ENSG00000171456		0.483	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ASXL1	HGNC	protein_coding	OTTHUMT00000078624.2	168	0.00	0	G	NM_015338		31023224	31023224	+1	no_errors	ENST00000375687	ensembl	human	known	69_37n	silent	59	44.34	47	SNP	0.000	T
ATG9B	285973	genome.wustl.edu	37	7	150718275	150718276	+	Splice_Site	INS	-	-	G	rs201977926		TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr7:150718275_150718276insG	ENST00000377974.2	-	5	1037_1038	c.962_963insC	c.(961-963)ccg>ccCg	p.P321fs	ATG9B_ENST00000494791.1_5'UTR|ATG9B_ENST00000444312.1_Splice_Site_p.R59fs|ATG9B_ENST00000605952.1_Splice_Site_p.P321fs|ATG9B_ENST00000605938.1_Splice_Site_p.P321fs			Q674R7	ATG9B_HUMAN	autophagy related 9B	321					autophagic vacuole assembly (GO:0000045)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(4)|prostate(1)	14	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCCAGCTCACCGGGGGGATGTG	0.609																																						dbGAP											0																																										-	-	-	SO:0001630	splice_region_variant	0			AK027791		7q36	2014-02-12	2012-06-06	2005-09-11	ENSG00000181652	ENSG00000181652			21899	protein-coding gene	gene with protein product		612205	"""nitric oxide synthase 3 antisense"", ""ATG9 autophagy related 9 homolog B (S. cerevisiae)"""	NOS3AS		15234981, 15755735	Standard	NM_173681		Approved	FLJ14885, APG9L2, SONE	uc011kvc.2	Q674R7	OTTHUMG00000158634	ENST00000377974.2:c.963+1->C	7.37:g.150718281_150718281dupG		Somatic		WXS	Illumina GAIIx	Phase_IV	A1A5D3|Q6JRW5|Q8N8I8	RNA	INS	-	NULL	ENST00000377974.2	37	NULL		7																																																																																			ATG9B	-	-	ENSG00000181652		0.609	ATG9B-201	KNOWN	basic|appris_principal	protein_coding	ATG9B	HGNC	protein_coding		18	0.00	0	-	NM_173681	Frame_Shift_Ins	150718275	150718276	-1	no_errors	ENST00000377974	ensembl	human	known	69_37n	rna	6	25.00	2	INS	1.000:1.000	G
C1orf53	388722	genome.wustl.edu	37	1	197875018	197875018	+	Silent	SNP	G	G	A			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr1:197875018G>A	ENST00000367393.3	+	2	360	c.357G>A	c.(355-357)gcG>gcA	p.A119A	C1orf53_ENST00000542800.1_3'UTR	NM_001024594.2	NP_001019765.1	Q5VUE5	CA053_HUMAN	chromosome 1 open reading frame 53	119										endometrium(1)|lung(1)	2						GTGGCTCTGCGTGCAGACATG	0.443																																						dbGAP											0													170.0	160.0	163.0					1																	197875018		2021	4207	6228	-	-	-	SO:0001819	synonymous_variant	0			BC038214	CCDS44290.1	1q31.3	2011-01-26			ENSG00000203724	ENSG00000203724			30003	protein-coding gene	gene with protein product						15897902	Standard	NM_001024594		Approved		uc001guh.3	Q5VUE5	OTTHUMG00000035659	ENST00000367393.3:c.357G>A	1.37:g.197875018G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A1L4N2|Q5VUE4	Missense_Mutation	SNP	NULL	p.V56M	ENST00000367393.3	37	c.166	CCDS44290.1	1	.	.	.	.	.	.	.	.	.	.	T	13.58	2.278270	0.40294	.	.	ENSG00000203724	ENST00000436652	.	.	.	5.73	3.68	0.42216	.	.	.	.	.	T	0.45716	0.1356	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33523	-0.9865	4	.	.	.	-5.5845	2.1766	0.03864	0.1372:0.4202:0.2675:0.1751	.	.	.	.	M	56	.	.	V	+	1	0	C1orf53	196141641	0.501000	0.26099	0.997000	0.53966	0.800000	0.45204	-0.444000	0.06854	0.245000	0.21373	-1.217000	0.01609	GTG	C1orf53	-	NULL	ENSG00000203724		0.443	C1orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C1orf53	HGNC	protein_coding	OTTHUMT00000086555.1	197	0.00	0	G	NM_001024594		197875018	197875018	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000436652	ensembl	human	putative	69_37n	missense	112	17.04	23	SNP	0.997	A
CARD11	84433	genome.wustl.edu	37	7	2983933	2983933	+	Silent	SNP	G	G	A			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr7:2983933G>A	ENST00000396946.4	-	5	1000	c.597C>T	c.(595-597)gaC>gaT	p.D199D	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	199					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		TGTAGTTGTCGTCCTTCACCT	0.572			Mis		DLBCL																																	dbGAP		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	0													270.0	159.0	196.0					7																	2983933		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.597C>T	7.37:g.2983933G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A4D1Z7|Q2NKN7|Q548H3	Silent	SNP	pfam_CARD,superfamily_DEATH-like,superfamily_PDZ,pfscan_CARD	p.D199	ENST00000396946.4	37	c.597	CCDS5336.2	7																																																																																			CARD11	-	NULL	ENSG00000198286		0.572	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	CARD11	HGNC	protein_coding	OTTHUMT00000059344.4	77	0.00	0	G	NM_032415		2983933	2983933	-1	no_errors	ENST00000396946	ensembl	human	known	69_37n	silent	13	76.36	42	SNP	0.968	A
CBX4	8535	genome.wustl.edu	37	17	77808750	77808751	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr17:77808750_77808751insG	ENST00000269397.4	-	5	867_868	c.690_691insC	c.(688-693)cccaacfs	p.N231fs		NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	231	Interaction with BMI1.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			ATCATTCCGTTGGGGGGGCCCT	0.639											OREG0024799	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"""NS5ATP1-binding protein 16"", ""Pc class 2 homolog (Drosophila)"""	603079	"""chromobox homolog 4 (Drosophila Pc class)"""			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.691dupC	17.37:g.77808757_77808757dupG	ENSP00000269397:p.Asn231fs	Somatic	1178	WXS	Illumina GAIIx	Phase_IV	B1PJR7|Q6TPI8|Q96C04	Frame_Shift_Ins	INS	pfam_Chromo_domain,superfamily_Chromodomain-like,smart_Chromo_domain/shadow,prints_Chromo_dom_subgr,pfscan_Chromo_domain/shadow	p.N230fs	ENST00000269397.4	37	c.691_690	CCDS32758.1	17																																																																																			CBX4	-	NULL	ENSG00000141582		0.639	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CBX4	HGNC	protein_coding	OTTHUMT00000318007.1	21	0.00	0	-	NM_003655		77808750	77808751	-1	no_errors	ENST00000269397	ensembl	human	known	69_37n	frame_shift_ins	14	12.50	2	INS	1.000:1.000	G
CD200R1	131450	genome.wustl.edu	37	3	112648015	112648015	+	Missense_Mutation	SNP	C	C	G			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr3:112648015C>G	ENST00000440122.2	-	4	596	c.542G>C	c.(541-543)aGg>aCg	p.R181T	CD200R1_ENST00000295863.4_Intron|CD200R1_ENST00000308611.3_Intron|CD200R1_ENST00000490004.1_Missense_Mutation_p.R158T|CD200R1_ENST00000471858.1_Intron	NM_138939.2	NP_620385.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	0	Ig-like C2-type.				regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						TGTGAAATACCTCAATATATG	0.398																																						dbGAP											0													86.0	80.0	82.0					3																	112648015		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000440122.2:c.542G>C	3.37:g.112648015C>G	ENSP00000405733:p.Arg181Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	NULL	p.R181T	ENST00000440122.2	37	c.542	CCDS46889.1	3	.	.	.	.	.	.	.	.	.	.	C	9.574	1.121790	0.20877	.	.	ENSG00000163606	ENST00000440122;ENST00000490004	T;T	0.22134	1.97;1.99	4.97	3.18	0.36537	.	.	.	.	.	T	0.16557	0.0398	.	.	.	0.09310	N	1	B;B	0.25105	0.118;0.031	B;B	0.19946	0.027;0.027	T	0.20773	-1.0265	8	0.87932	D	0	.	7.5648	0.27872	0.0:0.8014:0.0:0.1986	.	158;181	Q8TD46-3;Q8TD46-2	.;.	T	181;158	ENSP00000405733:R181T;ENSP00000418801:R158T	ENSP00000405733:R181T	R	-	2	0	CD200R1	114130705	.	.	0.001000	0.08648	0.032000	0.12392	.	.	0.509000	0.28195	0.455000	0.32223	AGG	CD200R1	-	NULL	ENSG00000163606		0.398	CD200R1-003	KNOWN	basic|CCDS	protein_coding	CD200R1	HGNC	protein_coding	OTTHUMT00000354468.1	561	0.00	0	C	NM_138806		112648015	112648015	-1	no_errors	ENST00000440122	ensembl	human	known	69_37n	missense	337	43.27	257	SNP	0.001	G
CERS3	204219	genome.wustl.edu	37	15	101009639	101009639	+	Silent	SNP	C	C	T			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr15:101009639C>T	ENST00000394113.1	-	12	1479	c.789G>A	c.(787-789)ctG>ctA	p.L263L	CERS3_ENST00000560944.1_Intron|CERS3_ENST00000538112.2_Silent_p.L263L|CERS3_ENST00000284382.4_Silent_p.L263L			Q8IU89	CERS3_HUMAN	ceramide synthase 3	263	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|keratinocyte differentiation (GO:0030216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AGATGAAAAACAGGGTGTTAC	0.428																																						dbGAP											0													111.0	109.0	110.0					15																	101009639		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS10384.1	15q26.3	2012-11-19	2011-07-08	2011-07-08	ENSG00000154227	ENSG00000154227		"""Homeoboxes / CERS class"""	23752	protein-coding gene	gene with protein product		615276	"""LAG1 longevity assurance homolog 3 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 3"""	LASS3			Standard	NM_178842		Approved	MGC27091	uc002bwb.3	Q8IU89	OTTHUMG00000172568	ENST00000394113.1:c.789G>A	15.37:g.101009639C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q8NE64|Q8NEN6	Silent	SNP	pirsf_Longevity_assurance_LAG1_LAC1,pfam_TLC-dom,pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,smart_TLC-dom,pfscan_TLC-dom,pfscan_Homeodomain	p.L263	ENST00000394113.1	37	c.789	CCDS10384.1	15																																																																																			CERS3	-	pirsf_Longevity_assurance_LAG1_LAC1,pfam_TLC-dom,smart_TLC-dom,pfscan_TLC-dom	ENSG00000154227		0.428	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	CERS3	HGNC	protein_coding	OTTHUMT00000313594.4	155	0.00	0	C	NM_178842		101009639	101009639	-1	no_errors	ENST00000284382	ensembl	human	known	69_37n	silent	98	44.00	77	SNP	0.999	T
CHD6	84181	genome.wustl.edu	37	20	40050464	40050464	+	Missense_Mutation	SNP	G	G	C			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr20:40050464G>C	ENST00000373233.3	-	31	4988	c.4811C>G	c.(4810-4812)cCc>cGc	p.P1604R		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1604					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GGACAGCTGGGGGTCGTTCAT	0.537																																						dbGAP											0													97.0	75.0	83.0					20																	40050464		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.4811C>G	20.37:g.40050464G>C	ENSP00000362330:p.Pro1604Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	pfam_SNF2_N,pfam_Chromo_domain,pfam_Helicase_C,pfam_Helicase/UvrB_dom,pfam_BRK_domain,pfam_DNA/RNA_helicase_DEAD/DEAH_N,superfamily_Chromodomain-like,smart_Chromo_domain/shadow,smart_Helicase_ATP-bd,smart_Helicase_C,smart_BRK_domain,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_Chromo_domain/shadow	p.P1604R	ENST00000373233.3	37	c.4811	CCDS13317.1	20	.	.	.	.	.	.	.	.	.	.	G	24.3	4.516056	0.85495	.	.	ENSG00000124177	ENST00000373233	T	0.78707	-1.2	5.89	5.89	0.94794	.	0.000000	0.64402	D	0.000009	D	0.89966	0.6868	M	0.85777	2.775	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.90460	0.4445	10	0.87932	D	0	-15.7519	20.305	0.98623	0.0:0.0:1.0:0.0	.	1604	Q8TD26	CHD6_HUMAN	R	1604	ENSP00000362330:P1604R	ENSP00000362330:P1604R	P	-	2	0	CHD6	39483878	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.814000	0.96858	0.650000	0.86243	CCC	CHD6	-	NULL	ENSG00000124177		0.537	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHD6	HGNC	protein_coding	OTTHUMT00000079270.1	88	0.00	0	G			40050464	40050464	-1	no_errors	ENST00000373233	ensembl	human	known	69_37n	missense	73	42.06	53	SNP	1.000	C
COG1	9382	genome.wustl.edu	37	17	71199175	71199175	+	Missense_Mutation	SNP	G	G	A			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr17:71199175G>A	ENST00000299886.4	+	8	2190	c.2110G>A	c.(2110-2112)Gat>Aat	p.D704N		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	704					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			ATTACTTCTAGATGATGCTGG	0.463																																						dbGAP											0													98.0	92.0	94.0					17																	71199175		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"""Components of oligomeric golgi complex"""	6545	protein-coding gene	gene with protein product		606973	"""low density lipoprotein receptor defect B complementing"""	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.2110G>A	17.37:g.71199175G>A	ENSP00000299886:p.Asp704Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	pfam_Vps51	p.D704N	ENST00000299886.4	37	c.2110	CCDS11692.1	17	.	.	.	.	.	.	.	.	.	.	G	15.89	2.967666	0.53507	.	.	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.26223	1.75;1.76	6.17	5.2	0.72013	.	0.497073	0.24345	N	0.039323	T	0.21718	0.0523	L	0.42245	1.32	0.35340	D	0.786379	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.12156	0.007;0.007;0.007	T	0.18398	-1.0338	10	0.23891	T	0.37	-6.4743	10.819	0.46593	0.1442:0.0:0.8558:0.0	.	704;704;704	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	N	704	ENSP00000400111:D704N;ENSP00000299886:D704N	ENSP00000299886:D704N	D	+	1	0	COG1	68710770	0.597000	0.26874	0.361000	0.25849	0.978000	0.69477	2.864000	0.48404	1.598000	0.50083	0.655000	0.94253	GAT	COG1	-	NULL	ENSG00000166685		0.463	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COG1	HGNC	protein_coding	OTTHUMT00000441638.1	49	0.00	0	G			71199175	71199175	+1	no_errors	ENST00000299886	ensembl	human	known	69_37n	missense	46	56.60	60	SNP	0.796	A
CPSF4	10898	genome.wustl.edu	37	7	99054076	99054076	+	Missense_Mutation	SNP	G	G	A			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr7:99054076G>A	ENST00000292476.5	+	8	773	c.763G>A	c.(763-765)Gcc>Acc	p.A255T	CPSF4_ENST00000441580.1_Missense_Mutation_p.A177T|CPSF4_ENST00000436336.2_Missense_Mutation_p.A230T|PTCD1_ENST00000555673.1_Intron|ATP5J2_ENST00000466753.1_Intron|CPSF4_ENST00000451876.1_Missense_Mutation_p.A197T|ATP5J2-PTCD1_ENST00000413834.1_Intron|ATP5J2-PTCD1_ENST00000437572.1_Intron			O95639	CPSF4_HUMAN	cleavage and polyadenylation specific factor 4, 30kDa	255					modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA processing (GO:0006397)|viral life cycle (GO:0019058)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(5)	14	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					AGGACACTACGCCAACAGATG	0.572																																						dbGAP											0													88.0	75.0	79.0					7																	99054076		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS5664.1, CCDS47652.1	7q22	2007-10-18	2002-08-29		ENSG00000160917	ENSG00000160917			2327	protein-coding gene	gene with protein product		603052	"""cleavage and polyadenylation specific factor 4, 30kD subunit"""			9651582, 9224719	Standard	NM_006693		Approved	NAR, CPSF30	uc003uqj.3	O95639	OTTHUMG00000154599	ENST00000292476.5:c.763G>A	7.37:g.99054076G>A	ENSP00000292476:p.Ala255Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	D6W5S8|Q6FGE6|Q86TF8|Q9BTW6	Missense_Mutation	SNP	pfam_Znf_CCCH,pfam_Znf_CCHC,superfamily_Znf_CCHC,smart_Znf_CCCH,smart_Znf_CCHC,pfscan_Znf_CCHC	p.A255T	ENST00000292476.5	37	c.763	CCDS5664.1	7	.	.	.	.	.	.	.	.	.	.	G	18.34	3.602452	0.66445	.	.	ENSG00000160917	ENST00000436336;ENST00000451876;ENST00000292476;ENST00000441580	T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38	6.01	6.01	0.97437	Zinc finger, CCHC retroviral-type (1);Zinc finger, CCHC-type (3);	0.000000	0.85682	D	0.000000	D	0.91164	0.7217	M	0.83118	2.625	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.943;0.998;0.982	D	0.91243	0.5023	10	0.87932	D	0	-10.5643	20.5109	0.99210	0.0:0.0:1.0:0.0	.	177;229;255;230	B7Z7B0;O95639-3;O95639;O95639-2	.;.;CPSF4_HUMAN;.	T	230;197;255;177	ENSP00000395311:A230T;ENSP00000396060:A197T;ENSP00000292476:A255T;ENSP00000402224:A177T	ENSP00000292476:A255T	A	+	1	0	CPSF4	98892012	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.458000	0.97634	2.851000	0.98039	0.609000	0.83330	GCC	CPSF4	-	pfam_Znf_CCHC,superfamily_Znf_CCHC,smart_Znf_CCHC,pfscan_Znf_CCHC	ENSG00000160917		0.572	CPSF4-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CPSF4	HGNC	protein_coding	OTTHUMT00000336254.1	34	0.00	0	G			99054076	99054076	+1	no_errors	ENST00000292476	ensembl	human	known	69_37n	missense	5	80.00	20	SNP	1.000	A
DYSF	8291	genome.wustl.edu	37	2	71839796	71839797	+	Frame_Shift_Ins	INS	-	-	C	rs398123786		TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr2:71839796_71839797insC	ENST00000258104.3	+	39	4470_4471	c.4193_4194insC	c.(4192-4197)tgccccfs	p.CP1398fs	DYSF_ENST00000413539.2_Frame_Shift_Ins_p.CP1429fs|DYSF_ENST00000409744.1_Frame_Shift_Ins_p.CP1385fs|DYSF_ENST00000409582.3_Frame_Shift_Ins_p.CP1415fs|DYSF_ENST00000409762.1_Frame_Shift_Ins_p.CP1415fs|DYSF_ENST00000410020.3_Frame_Shift_Ins_p.CP1416fs|DYSF_ENST00000429174.2_Frame_Shift_Ins_p.CP1398fs|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409366.1_Frame_Shift_Ins_p.CP1399fs|DYSF_ENST00000394120.2_Frame_Shift_Ins_p.CP1399fs|DYSF_ENST00000409651.1_Frame_Shift_Ins_p.CP1430fs|DYSF_ENST00000410041.1_Frame_Shift_Ins_p.CP1416fs	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1398	C2 5. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GAGCTCTACTGCCCCCCCATCA	0.619																																						dbGAP											0			GRCh37	CM053841	DYSF	M																																				-	-	-	SO:0001589	frameshift_variant	0			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.4200dupC	2.37:g.71839803_71839803dupC	ENSP00000258104:p.Cys1398fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Frame_Shift_Ins	INS	pfam_C2_Ca-dep,pfam_Ferlin_B-domain,pfam_FerIin-domain,pfam_Ferlin_A-domain,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_MFS_dom_general_subst_transpt,smart_C2_Ca-dep,smart_Peroxin/Ferlin,pfscan_C2_membr_targeting	p.I1432fs	ENST00000258104.3	37	c.4286_4287	CCDS1918.1	2																																																																																			DYSF	-	pfam_C2_Ca-dep,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep	ENSG00000135636		0.619	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	DYSF	HGNC	protein_coding	OTTHUMT00000251970.3	43	0.00	0	-	NM_003494		71839796	71839797	+1	no_errors	ENST00000413539	ensembl	human	known	69_37n	frame_shift_ins	45	11.76	6	INS	1.000:0.989	C
FGF18	8817	genome.wustl.edu	37	5	170883698	170883698	+	Silent	SNP	C	C	T			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr5:170883698C>T	ENST00000274625.5	+	5	1057	c.513C>T	c.(511-513)gaC>gaT	p.D171D		NM_003862.2	NP_003853.1	O76093	FGF18_HUMAN	fibroblast growth factor 18	171					anatomical structure morphogenesis (GO:0009653)|angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|chondrocyte development (GO:0002063)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intramembranous ossification (GO:0001957)|lung development (GO:0030324)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleolus (GO:0005730)	growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)	p.D171D(1)		endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	9	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ACCAGCAGGACGTGCATTTCA	0.637																																						dbGAP											1	Substitution - coding silent(1)	endometrium(1)											57.0	67.0	63.0					5																	170883698		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB007422	CCDS4378.1	5q34	2008-02-05			ENSG00000156427	ENSG00000156427			3674	protein-coding gene	gene with protein product		603726				9660775, 9742123	Standard	NM_003862		Approved	FGF-18, ZFGF5	uc003mbk.3	O76093	OTTHUMG00000130464	ENST00000274625.5:c.513C>T	5.37:g.170883698C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	D3DQL7|Q6UWF1	Silent	SNP	pfam_IL1_HBGF,superfamily_Cytokine_IL1-like,smart_IL1_HBGF,prints_IL1_HBGF	p.D171	ENST00000274625.5	37	c.513	CCDS4378.1	5																																																																																			FGF18	-	pfam_IL1_HBGF,superfamily_Cytokine_IL1-like,smart_IL1_HBGF	ENSG00000156427		0.637	FGF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FGF18	HGNC	protein_coding	OTTHUMT00000252857.2	47	0.00	0	C	NM_033649, NM_003862		170883698	170883698	+1	no_errors	ENST00000274625	ensembl	human	known	69_37n	silent	19	50.00	19	SNP	0.882	T
FOXM1	2305	genome.wustl.edu	37	12	2977870	2977870	+	Silent	SNP	C	C	T	rs143382475		TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr12:2977870C>T	ENST00000359843.3	-	4	773	c.705G>A	c.(703-705)gaG>gaA	p.E235E	FOXM1_ENST00000342628.2_Silent_p.E235E|FOXM1_ENST00000361953.3_Silent_p.E235E|FOXM1_ENST00000537018.1_5'UTR	NM_021953.3	NP_068772.2	Q08050	FOXM1_HUMAN	forkhead box M1	235					cell cycle (GO:0007049)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|liver development (GO:0001889)|mitotic cell cycle (GO:0000278)|negative regulation of cell aging (GO:0090344)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of cell cycle arrest (GO:0071156)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of Ras protein signal transduction (GO:0046578)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3)	24			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			AGGGTGGCCGCTCAGACACAG	0.502																																						dbGAP											0													166.0	144.0	151.0					12																	2977870		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			Y12773	CCDS8515.1, CCDS8516.1, CCDS8517.1	12p13	2007-09-18			ENSG00000111206	ENSG00000111206		"""Forkhead boxes"""	3818	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 2"""	602341		FKHL16		9032290, 9441747	Standard	NM_202002		Approved	HFH-11, trident, HNF-3, INS-1, MPP2, MPHOSPH2, TGT3	uc001qlf.3	Q08050	OTTHUMG00000168118	ENST00000359843.3:c.705G>A	12.37:g.2977870C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	O43258|O43259|O43260|Q4ZGG7|Q9BRL2	Silent	SNP	pfam_TF_fork_head,smart_TF_fork_head,pfscan_TF_fork_head,prints_TF_fork_head	p.E235	ENST00000359843.3	37	c.705	CCDS8515.1	12																																																																																			FOXM1	-	smart_TF_fork_head	ENSG00000111206		0.502	FOXM1-002	KNOWN	basic|CCDS	protein_coding	FOXM1	HGNC	protein_coding	OTTHUMT00000398272.1	106	0.00	0	C	NM_021953		2977870	2977870	-1	no_errors	ENST00000342628	ensembl	human	known	69_37n	silent	90	45.78	76	SNP	0.613	T
GYG2	8908	genome.wustl.edu	37	X	2779579	2779580	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chrX:2779579_2779580insG	ENST00000381163.3	+	9	1229_1230	c.947_948insG	c.(946-951)gtggggfs	p.VG316fs	GYG2_ENST00000398806.3_Frame_Shift_Ins_p.VG285fs|GYG2_ENST00000338623.5_Frame_Shift_Ins_p.VG316fs|GYG2_ENST00000542787.1_Frame_Shift_Ins_p.VG316fs|GYG2_ENST00000381161.1_3'UTR	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	316					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	glycogenin glucosyltransferase activity (GO:0008466)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CACAGTGATGTGGGGGGGCCGT	0.579																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	2.4.1.186	"""Glycosyltransferase family 8 domain containing"""	4700	protein-coding gene	gene with protein product	"""glycogenin glucosyltransferase"""	300198				9857012	Standard	NM_001079855		Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.954dupG	X.37:g.2779586_2779586dupG	ENSP00000370555:p.Val316fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B7WNN6|O15485|O15486|O15487|O15489|O15490	Frame_Shift_Ins	INS	pfam_Glyco_trans_8	p.P319fs	ENST00000381163.3	37	c.947_948	CCDS14121.1	X																																																																																			GYG2	-	NULL	ENSG00000056998		0.579	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GYG2	HGNC	protein_coding	OTTHUMT00000055645.1	27	0.00	0	-	NM_003918		2779579	2779580	+1	no_errors	ENST00000381163	ensembl	human	known	69_37n	frame_shift_ins	19	17.39	4	INS	0.000:0.000	G
HSD11B2	3291	genome.wustl.edu	37	16	67470244	67470245	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr16:67470244_67470245insG	ENST00000326152.5	+	4	889_890	c.757_758insG	c.(757-759)tggfs	p.W253fs	ATP6V0D1_ENST00000567694.1_5'Flank	NM_000196.3	NP_000187.3	P80365	DHI2_HUMAN	hydroxysteroid (11-beta) dehydrogenase 2	253					female pregnancy (GO:0007565)|glucocorticoid biosynthetic process (GO:0006704)|regulation of blood volume by renal aldosterone (GO:0002017)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)	11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity (GO:0003845)|NAD binding (GO:0051287)|steroid binding (GO:0005496)			breast(1)|endometrium(1)|liver(2)|lung(3)|upper_aerodigestive_tract(1)	8		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0401)|Epithelial(162;0.0891)		ACTCCTTCCCTGGGGGGTCAAG	0.614																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U14631	CCDS10837.1	16q22	2011-09-14			ENSG00000176387	ENSG00000176387	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	5209	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 9C, member 3"""	614232				7859916, 8611140, 19027726	Standard	NM_000196		Approved	SDR9C3	uc002etd.3	P80365	OTTHUMG00000137507	ENST00000326152.5:c.763dupG	16.37:g.67470250_67470250dupG	ENSP00000316786:p.Trp253fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A7LB28|C5HTY7|Q13194|Q6P2G9|Q8N439|Q96QN8|Q9UC50|Q9UC51|Q9UCW5|Q9UCW6|Q9UCW7|Q9UCW8	Frame_Shift_Ins	INS	pfam_DH_sc/Rdtase_SDR,prints_Glc/ribitol_DH	p.V255fs	ENST00000326152.5	37	c.757_758	CCDS10837.1	16																																																																																			HSD11B2	-	prints_Glc/ribitol_DH	ENSG00000176387		0.614	HSD11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HSD11B2	HGNC	protein_coding	OTTHUMT00000268826.3	43	0.00	0	-	NM_000196		67470244	67470245	+1	no_errors	ENST00000326152	ensembl	human	known	69_37n	frame_shift_ins	18	10.00	2	INS	1.000:1.000	G
LAMB1	3912	genome.wustl.edu	37	7	107638937	107638937	+	Splice_Site	SNP	C	C	T			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr7:107638937C>T	ENST00000222399.6	-	4	444	c.214G>A	c.(214-216)Gag>Aag	p.E72K	LAMB1_ENST00000393561.1_Splice_Site_p.E96K|LAMB1_ENST00000393560.1_Splice_Site_p.E72K|U3_ENST00000458938.1_RNA	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	72	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						TTTTTGTCCTCCTACAAACAA	0.353																																						dbGAP											0													107.0	100.0	102.0					7																	107638937		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"""Laminins"""	6486	protein-coding gene	gene with protein product		150240	"""cutis laxa with marfanoid phenotype"""	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.214-1G>A	7.37:g.107638937C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q14D91	Missense_Mutation	SNP	pfam_EGF_laminin,pfam_Laminin_N,superfamily_Prefoldin,superfamily_t-SNARE,smart_Laminin_N,smart_EGF_laminin,smart_EGF-like,pfscan_Laminin_IV,pfscan_EGF_laminin,pfscan_Laminin_N	p.E72K	ENST00000222399.6	37	c.214	CCDS5750.1	7	.	.	.	.	.	.	.	.	.	.	C	35	5.507768	0.96386	.	.	ENSG00000091136	ENST00000393561;ENST00000222399;ENST00000393560;ENST00000439976;ENST00000393559	T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98	6.08	6.08	0.98989	Laminin, N-terminal (3);	.	.	.	.	D	0.86748	0.6007	M	0.71581	2.175	0.80722	D	1	D;P;P;D	0.89917	0.992;0.679;0.85;1.0	P;B;P;D	0.91635	0.887;0.271;0.733;0.999	D	0.86173	0.1601	9	0.66056	D	0.02	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	158;72;72;96	C9J296;E7EPA6;P07942;G3XAI2	.;.;LAMB1_HUMAN;.	K	96;72;72;158;72	ENSP00000377191:E96K;ENSP00000222399:E72K;ENSP00000377190:E72K;ENSP00000412686:E158K;ENSP00000377189:E72K	ENSP00000222399:E72K	E	-	1	0	LAMB1	107426173	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	7.487000	0.81328	2.894000	0.99253	0.655000	0.94253	GAG	LAMB1	-	pfam_Laminin_N,smart_Laminin_N,pfscan_Laminin_N	ENSG00000091136		0.353	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LAMB1	HGNC	protein_coding	OTTHUMT00000314584.1	126	0.00	0	C	NM_002291	Missense_Mutation	107638937	107638937	-1	no_errors	ENST00000222399	ensembl	human	known	69_37n	missense	22	38.89	14	SNP	1.000	T
LPHN2	23266	genome.wustl.edu	37	1	82456779	82456779	+	Missense_Mutation	SNP	C	C	A			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr1:82456779C>A	ENST00000370728.1	+	25	4975	c.4330C>A	c.(4330-4332)Cca>Aca	p.P1444T	LPHN2_ENST00000271029.4_Missense_Mutation_p.P1416T|LPHN2_ENST00000370730.1_Missense_Mutation_p.P1401T|LPHN2_ENST00000319517.6_Missense_Mutation_p.P1388T|LPHN2_ENST00000370715.1_3'UTR|LPHN2_ENST00000359929.3_Missense_Mutation_p.P1388T|LPHN2_ENST00000370713.1_3'UTR|LPHN2_ENST00000370717.2_Missense_Mutation_p.P1459T|LPHN2_ENST00000394879.1_Missense_Mutation_p.P1446T|LPHN2_ENST00000335786.5_Missense_Mutation_p.P1401T|LPHN2_ENST00000370727.1_Missense_Mutation_p.P1416T|LPHN2_ENST00000370723.1_Missense_Mutation_p.P1446T|LPHN2_ENST00000469377.2_3'UTR|LPHN2_ENST00000370721.1_Missense_Mutation_p.P1369T|LPHN2_ENST00000370725.1_Missense_Mutation_p.P1459T			O95490	LPHN2_HUMAN	latrophilin 2	1444					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		agggtgtattccagAAGGAGA	0.418																																						dbGAP											0													32.0	34.0	33.0					1																	82456779		2201	4296	6497	-	-	-	SO:0001583	missense	0			AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"""-"", ""GPCR / Class B : Orphans"""	18582	protein-coding gene	gene with protein product		607018	"""latrophilin 1"""	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.4330C>A	1.37:g.82456779C>A	ENSP00000359763:p.Pro1444Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Missense_Mutation	SNP	pfam_GPCR_2_latrophilin_rcpt_C,pfam_Olfac-like,pfam_DUF3497,pfam_GPCR_2_secretin-like,pfam_Lectin_gal-bd_dom,pfam_GPS_dom,pfam_GPCR_2_extracellular_dom,smart_Olfac-like,smart_GPCR_2_extracellular_dom,smart_GPS_dom,prints_GPCR_2_latrophilin,prints_GPCR_2_secretin-like,pfscan_GPS_dom,pfscan_Lectin_gal-bd_dom,pfscan_Olfac-like,pfscan_GPCR_2_extracellular_dom,pfscan_GPCR_2-like	p.P1459T	ENST00000370728.1	37	c.4375		1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	12.55|12.55|12.55	1.972300|1.972300|1.972300	0.34754|0.34754|0.34754	.|.|.	.|.|.	ENSG00000117114|ENSG00000117114|ENSG00000117114	ENST00000449420|ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786|ENST00000402328	.|T;T;T;T;T;T;T;T;T;T;T;T|.	.|0.71222|.	.|-0.46;-0.49;-0.55;-0.49;-0.43;-0.39;-0.5;-0.5;-0.43;-0.39;-0.49;-0.55|.	5.67|5.67|5.67	5.67|5.67|5.67	0.87782|0.87782|0.87782	.|.|.	.|0.059135|.	.|0.64402|.	.|D|.	.|0.000002|.	T|T|T	0.69851|0.69851|0.69851	0.3157|0.3157|0.3157	M|M|M	0.66939|0.66939|0.66939	2.045|2.045|2.045	0.58432|0.58432|0.58432	D|D|D	0.999997|0.999997|0.999997	.|P;B|.	.|0.36048|.	.|0.534;0.043|.	.|B;B|.	.|0.42030|.	.|0.373;0.017|.	T|T|T	0.67082|0.67082|0.67082	-0.5760|-0.5760|-0.5760	5|10|5	.|0.87932|.	.|D|.	.|0|.	.|.|.	19.7629|19.7629|19.7629	0.96329|0.96329|0.96329	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|1388;368|.	.|O95490-2;B3KVU1|.	.|.;.|.	L|T|Y	1335|1369;1444;1401;1416;1459;1446;1388;1388;1459;1446;1416;1401|455	.|ENSP00000359756:P1369T;ENSP00000359763:P1444T;ENSP00000359765:P1401T;ENSP00000359762:P1416T;ENSP00000359760:P1459T;ENSP00000359758:P1446T;ENSP00000353006:P1388T;ENSP00000322270:P1388T;ENSP00000359752:P1459T;ENSP00000378344:P1446T;ENSP00000271029:P1416T;ENSP00000337306:P1401T|.	.|ENSP00000271029:P1416T|.	F|P|S	+|+|+	3|1|2	2|0|0	LPHN2|LPHN2|LPHN2	82229367|82229367|82229367	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.714000|0.714000|0.714000	0.30535|0.30535|0.30535	0.944000|0.944000|0.944000	0.59088|0.59088|0.59088	5.508000|5.508000|5.508000	0.67006|0.67006|0.67006	2.666000|2.666000|2.666000	0.90696|0.90696|0.90696	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	TTC|CCA|TCC	LPHN2	-	pfam_GPCR_2_latrophilin_rcpt_C	ENSG00000117114		0.418	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	LPHN2	HGNC	protein_coding	OTTHUMT00000027188.1	84	0.00	0	C	NM_012302		82456779	82456779	+1	no_errors	ENST00000370717	ensembl	human	known	69_37n	missense	65	26.97	24	SNP	1.000	A
LTBP2	4053	genome.wustl.edu	37	14	74967606	74967607	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr14:74967606_74967607insG	ENST00000261978.4	-	36	5832_5833	c.5446_5447insC	c.(5446-5448)cacfs	p.H1816fs	LTBP2_ENST00000556690.1_Frame_Shift_Ins_p.H1772fs	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	1816	EGF-like 20; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.H1816fs*>7(2)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		GGCAGTGCAGTGGGGGGGCCCT	0.619																																						dbGAP											2	Insertion - Frameshift(2)	haematopoietic_and_lymphoid_tissue(2)																																								-	-	-	SO:0001589	frameshift_variant	0				CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"""Latent transforming growth factor, beta binding proteins"""	6715	protein-coding gene	gene with protein product		602091	"""chromosome 14 open reading frame 141"""	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.5447dupC	14.37:g.74967613_74967613dupG	ENSP00000261978:p.His1816fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q99907|Q9NS51	Frame_Shift_Ins	INS	pfam_EGF-like_Ca-bd,pfam_TB_dom,pfam_EGF-like_dom,superfamily_TB_dom,superfamily_Growth_fac_rcpt,smart_EGF-like,smart_EGF-like_Ca-bd,pfscan_EG-like_dom	p.H1816fs	ENST00000261978.4	37	c.5447_5446	CCDS9831.1	14																																																																																			LTBP2	-	pfam_EGF-like_Ca-bd,smart_EGF-like_Ca-bd,smart_EGF-like,pfscan_EG-like_dom	ENSG00000119681		0.619	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LTBP2	HGNC	protein_coding	OTTHUMT00000413595.1	26	0.00	0	-	NM_000428		74967606	74967607	-1	no_errors	ENST00000261978	ensembl	human	known	69_37n	frame_shift_ins	22	15.38	4	INS	0.813:0.817	G
NEURL4	84461	genome.wustl.edu	37	17	7227492	7227492	+	Missense_Mutation	SNP	G	G	A			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr17:7227492G>A	ENST00000399464.2	-	11	2012	c.1997C>T	c.(1996-1998)cCg>cTg	p.P666L	NEURL4_ENST00000570460.1_Missense_Mutation_p.P644L|NEURL4_ENST00000315614.7_Missense_Mutation_p.P666L	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	666	NHR 3. {ECO:0000255|PROSITE- ProRule:PRU00400}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						ATAGACGCCCGGGGGCACGTT	0.672											OREG0024134	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0													66.0	78.0	74.0					17																	7227492		2090	4234	6324	-	-	-	SO:0001583	missense	0				CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"""neuralized homolog 4 (Drosophila)"""			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.1997C>T	17.37:g.7227492G>A	ENSP00000382390:p.Pro666Leu	Somatic	640	WXS	Illumina GAIIx	Phase_IV	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	pfam_Neu_Z,superfamily_ConA-like_lec_gl,smart_Neu_Z,pfscan_Neu_Z	p.P666L	ENST00000399464.2	37	c.1997	CCDS42251.1	17	.	.	.	.	.	.	.	.	.	.	G	18.51	3.639330	0.67244	.	.	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.73897	-0.79;-0.79	5.56	5.56	0.83823	Concanavalin A-like lectin/glucanase (1);NEUZ (1);	0.000000	0.85682	D	0.000000	T	0.80281	0.4594	L	0.43923	1.385	0.80722	D	1	D;D	0.71674	0.998;0.993	P;P	0.59595	0.86;0.543	T	0.79804	-0.1649	10	0.46703	T	0.11	-21.6325	18.296	0.90146	0.0:0.0:1.0:0.0	.	666;666	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	L	666	ENSP00000319826:P666L;ENSP00000382390:P666L	ENSP00000319826:P666L	P	-	2	0	NEURL4	7168216	1.000000	0.71417	0.847000	0.33407	0.117000	0.20001	9.100000	0.94213	2.608000	0.88229	0.655000	0.94253	CCG	NEURL4	-	superfamily_ConA-like_lec_gl,pfscan_Neu_Z	ENSG00000215041		0.672	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NEURL4	HGNC	protein_coding	OTTHUMT00000255434.2	22	0.00	0	G	NM_032442		7227492	7227492	-1	no_errors	ENST00000399464	ensembl	human	known	69_37n	missense	7	41.67	5	SNP	0.998	A
MYH3	4621	genome.wustl.edu	37	17	10543517	10543517	+	Silent	SNP	C	C	T			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr17:10543517C>T	ENST00000583535.1	-	22	2565	c.2478G>A	c.(2476-2478)aaG>aaA	p.K826K	MYH3_ENST00000226209.7_Silent_p.K826K	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	826					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						AGGGCCAGTGCTTGACGTTCA	0.458																																						dbGAP											0													131.0	121.0	124.0					17																	10543517		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.2478G>A	17.37:g.10543517C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q15492	Silent	SNP	pfam_Myosin_tail,pfam_Myosin_head_motor_dom,pfam_Myosin_N,superfamily_Prefoldin,smart_Myosin_head_motor_dom,prints_Myosin_head_motor_dom,pfscan_IQ_motif_EF-hand-BS	p.K826	ENST00000583535.1	37	c.2478	CCDS11157.1	17																																																																																			MYH3	-	NULL	ENSG00000109063		0.458	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MYH3	HGNC	protein_coding	OTTHUMT00000252734.2	231	0.00	0	C	NM_002470		10543517	10543517	-1	no_errors	ENST00000226209	ensembl	human	known	69_37n	silent	33	73.81	93	SNP	0.999	T
NIPBL	25836	genome.wustl.edu	37	5	37006526	37006526	+	Missense_Mutation	SNP	C	C	T			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr5:37006526C>T	ENST00000282516.8	+	17	4422	c.3923C>T	c.(3922-3924)gCg>gTg	p.A1308V	NIPBL_ENST00000448238.2_Missense_Mutation_p.A1308V	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1308					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			ACAAAATCAGCGGATGCTTGT	0.338																																						dbGAP											0													117.0	109.0	112.0					5																	37006526		2203	4299	6502	-	-	-	SO:0001583	missense	0			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.3923C>T	5.37:g.37006526C>T	ENSP00000282516:p.Ala1308Val	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.A1308V	ENST00000282516.8	37	c.3923	CCDS3920.1	5	.	.	.	.	.	.	.	.	.	.	C	21.5	4.158810	0.78226	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	T;T	0.57907	0.37;0.37	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.44201	0.1282	L	0.43152	1.355	0.80722	D	1	P;P	0.40794	0.609;0.729	B;B	0.38327	0.14;0.271	T	0.43360	-0.9396	10	0.02654	T	1	.	19.6236	0.95670	0.0:1.0:0.0:0.0	.	1308;1308	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	V	1308	ENSP00000282516:A1308V;ENSP00000406266:A1308V	ENSP00000282516:A1308V	A	+	2	0	NIPBL	37042283	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.460000	0.80816	2.643000	0.89663	0.555000	0.69702	GCG	NIPBL	-	NULL	ENSG00000164190		0.338	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NIPBL	HGNC	protein_coding	OTTHUMT00000207582.1	102	0.00	0	C	NM_015384		37006526	37006526	+1	no_errors	ENST00000282516	ensembl	human	known	69_37n	missense	60	34.07	31	SNP	1.000	T
NLRP10	338322	genome.wustl.edu	37	11	7982638	7982638	+	Missense_Mutation	SNP	G	G	A			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr11:7982638G>A	ENST00000328600.2	-	2	682	c.521C>T	c.(520-522)tCg>tTg	p.S174L		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	174	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				defense response to fungus (GO:0050832)|defense response to Gram-negative bacterium (GO:0050829)|dendritic cell migration (GO:0036336)|helper T cell enhancement of adaptive immune response (GO:0035397)|innate immune response (GO:0045087)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 type immune response (GO:2000318)	cytoplasm (GO:0005737)|extrinsic component of plasma membrane (GO:0019897)	ATP binding (GO:0005524)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGTGCCAGCCGACCCCTGTAG	0.547																																						dbGAP											0													53.0	54.0	54.0					11																	7982638		2201	4296	6497	-	-	-	SO:0001583	missense	0			AY154465	CCDS7784.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000182261		"""Nucleotide-binding domain and leucine rich repeat containing"""	21464	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 10"""	609662	"""NACHT, leucine rich repeat and PYD containing 10"""	NALP10		12563287	Standard	NM_176821		Approved	NOD8, PAN5, Pynod, CLR11.1	uc001mfv.1	Q86W26		ENST00000328600.2:c.521C>T	11.37:g.7982638G>A	ENSP00000327763:p.Ser174Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2M3C4|Q6JGT0	Missense_Mutation	SNP	pfam_DAPIN,superfamily_DEATH-like,pfscan_NACHT_NTPase,pfscan_DAPIN	p.S174L	ENST00000328600.2	37	c.521	CCDS7784.1	11	.	.	.	.	.	.	.	.	.	.	G	11.60	1.686998	0.29962	.	.	ENSG00000182261	ENST00000328600	T	0.80304	-1.36	5.25	-0.519	0.11939	NACHT nucleoside triphosphatase (1);	1.130040	0.06837	N	0.794968	T	0.67878	0.2940	N	0.24115	0.695	0.09310	N	1	P	0.42039	0.769	B	0.43386	0.418	T	0.57825	-0.7744	10	0.36615	T	0.2	.	3.1186	0.06383	0.0879:0.1455:0.3204:0.4462	.	174	Q86W26	NAL10_HUMAN	L	174	ENSP00000327763:S174L	ENSP00000327763:S174L	S	-	2	0	NLRP10	7939214	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.126000	0.15769	0.017000	0.15025	0.655000	0.94253	TCG	NLRP10	-	pfscan_NACHT_NTPase	ENSG00000182261		0.547	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NLRP10	HGNC	protein_coding	OTTHUMT00000385705.1	106	0.00	0	G	NM_176821		7982638	7982638	-1	no_errors	ENST00000328600	ensembl	human	known	69_37n	missense	110	41.18	77	SNP	0.000	A
ORMDL3	94103	genome.wustl.edu	37	17	38079470	38079470	+	Missense_Mutation	SNP	G	G	A			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr17:38079470G>A	ENST00000394169.1	-	5	1715	c.221C>T	c.(220-222)aCc>aTc	p.T74I	ORMDL3_ENST00000584220.1_Missense_Mutation_p.T58I|ORMDL3_ENST00000582052.1_5'Flank|ORMDL3_ENST00000579695.1_Missense_Mutation_p.T74I|ORMDL3_ENST00000304046.2_Missense_Mutation_p.T74I			Q8N138	ORML3_HUMAN	ORMDL sphingolipid biosynthesis regulator 3	74					ceramide metabolic process (GO:0006672)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|SPOTS complex (GO:0035339)				endometrium(3)|kidney(1)|lung(1)	5	Colorectal(19;0.000442)		Lung(15;0.0234)			CTGGTCCGGGGTCTCAAAGGG	0.562																																						dbGAP											0													169.0	161.0	163.0					17																	38079470		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS11355.1	17q12	2014-06-16	2014-06-16		ENSG00000172057	ENSG00000172057			16038	protein-coding gene	gene with protein product		610075	"""ORM1 (S. cerevisiae)-like 3"", ""ORM1-like 3 (S. cerevisiae)"""			23066021	Standard	NM_139280		Approved		uc002htj.2	Q8N138	OTTHUMG00000133249	ENST00000394169.1:c.221C>T	17.37:g.38079470G>A	ENSP00000377724:p.Thr74Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KS83|Q6UY83	Missense_Mutation	SNP	pfam_ORMDL,pirsf_ORMDL	p.T74I	ENST00000394169.1	37	c.221	CCDS11355.1	17	.	.	.	.	.	.	.	.	.	.	G	29.5	5.013532	0.93346	.	.	ENSG00000172057	ENST00000304046;ENST00000394169	.	.	.	5.39	5.39	0.77823	.	0.055149	0.64402	N	0.000001	D	0.82788	0.5113	M	0.77313	2.365	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.83414	0.0029	9	0.51188	T	0.08	-21.3462	19.1554	0.93507	0.0:0.0:1.0:0.0	.	74	Q8N138	ORML3_HUMAN	I	74	.	ENSP00000304858:T74I	T	-	2	0	ORMDL3	35332996	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.869000	0.99810	2.528000	0.85240	0.655000	0.94253	ACC	ORMDL3	-	pfam_ORMDL,pirsf_ORMDL	ENSG00000172057		0.562	ORMDL3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	ORMDL3	HGNC	protein_coding	OTTHUMT00000257003.1	93	0.00	0	G	NM_139280		38079470	38079470	-1	no_errors	ENST00000304046	ensembl	human	known	69_37n	missense	74	20.43	19	SNP	1.000	A
PHKA2	5256	genome.wustl.edu	37	X	18954268	18954268	+	Splice_Site	SNP	C	C	A			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chrX:18954268C>A	ENST00000379942.4	-	11	1707	c.1042G>T	c.(1042-1044)Gtc>Ttc	p.V348F		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	348					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					TATTCTTGGACCTGGAAAACA	0.512																																						dbGAP											0													64.0	45.0	52.0					X																	18954268		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0				CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.1042-1G>T	X.37:g.18954268C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	pfam_Glyco_hydro_15,superfamily_6-hairpin_glycosidase-like	p.V348F	ENST00000379942.4	37	c.1042	CCDS14190.1	X	.	.	.	.	.	.	.	.	.	.	C	21.0	4.083162	0.76642	.	.	ENSG00000044446	ENST00000379942	D	0.90620	-2.7	5.41	5.41	0.78517	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.054776	0.64402	D	0.000001	D	0.93897	0.8047	M	0.88842	2.985	0.80722	D	1	B	0.27559	0.181	B	0.42851	0.4	D	0.93546	0.6882	10	0.87932	D	0	-26.9122	11.994	0.53191	0.0:0.9187:0.0:0.0813	.	348	P46019	KPB2_HUMAN	F	348	ENSP00000369274:V348F	ENSP00000369274:V348F	V	-	1	0	PHKA2	18864189	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.029000	0.57253	2.402000	0.81655	0.600000	0.82982	GTC	PHKA2	-	pfam_Glyco_hydro_15,superfamily_6-hairpin_glycosidase-like	ENSG00000044446		0.512	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PHKA2	HGNC	protein_coding	OTTHUMT00000055960.1	26	0.00	0	C	NM_000292	Missense_Mutation	18954268	18954268	-1	no_errors	ENST00000379942	ensembl	human	known	69_37n	missense	25	24.24	8	SNP	1.000	A
PLXNA1	5361	genome.wustl.edu	37	3	126724942	126724943	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	CT	CT					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr3:126724942_126724943delCT	ENST00000393409.2	+	7	1918_1919	c.1918_1919delCT	c.(1918-1920)ctcfs	p.L640fs	PLXNA1_ENST00000251772.4_Frame_Shift_Del_p.L617fs	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	640					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		GGTGGTGAAACTCTACCTAAAG	0.574																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.1918_1919delCT	3.37:g.126724944_126724945delCT	ENSP00000377061:p.Leu640fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Del	DEL	pfam_Plexin_cytoplasmic_RasGAP_dom,pfam_Semaphorin/CD100_Ag,pfam_IPT_TIG_rcpt,pfam_Plexin_repeat,superfamily_Semaphorin/CD100_Ag,superfamily_Rho_GTPase_activation_prot,superfamily_Ig_E-set,superfamily_Plexin-like_fold,smart_Semaphorin/CD100_Ag,smart_Plexin-like,smart_IPT_TIG_rcpt,pfscan_Semaphorin/CD100_Ag	p.Y641fs	ENST00000393409.2	37	c.1918_1919	CCDS33847.2	3																																																																																			PLXNA1	-	NULL	ENSG00000114554		0.574	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLXNA1	HGNC	protein_coding	OTTHUMT00000356451.1	9	0.00	0	CT	NM_032242		126724942	126724943	+1	no_errors	ENST00000393409	ensembl	human	known	69_37n	frame_shift_del	1	75.00	3	DEL	1.000:1.000	-
POLA1	5422	genome.wustl.edu	37	X	24859809	24859809	+	Missense_Mutation	SNP	A	A	T			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chrX:24859809A>T	ENST00000379059.3	+	33	3774	c.3759A>T	c.(3757-3759)aaA>aaT	p.K1253N	POLA1_ENST00000379068.3_Missense_Mutation_p.K1259N	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	1253	DNA-binding region. {ECO:0000255}.				cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	ATTATCATAAAGATGAAGAGA	0.378																																						dbGAP											0													89.0	76.0	80.0					X																	24859809		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"""DNA polymerases"""	9173	protein-coding gene	gene with protein product		312040	"""polymerase (DNA directed), alpha"", ""polymerase (DNA directed), alpha 1"", ""N syndrome (mental retardation, malformations, chromosome breakage)"""	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.3759A>T	X.37:g.24859809A>T	ENSP00000368349:p.Lys1253Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	Q86UQ7	Missense_Mutation	SNP	pfam_DNA-dir_DNA_pol_B_multi_dom,pfam_DNA-dir_DNA_pol_B_exonuc,pfam_Znf_DNA-dir_DNA_pol_B_alpha,pfam_DNA_pol_a_cat_su_N,superfamily_RNaseH-like_dom,smart_DNA-dir_DNA_pol_B,prints_DNA-dir_DNA_pol_B,tigrfam_DNA-dir_DNA_pol_B_pol2	p.K1259N	ENST00000379059.3	37	c.3777	CCDS14214.1	X	.	.	.	.	.	.	.	.	.	.	A	10.91	1.483884	0.26598	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.17370	2.28;2.28	5.31	4.14	0.48551	.	0.163970	0.51477	D	0.000099	T	0.14056	0.0340	L	0.47716	1.5	0.44652	D	0.997635	B	0.20780	0.048	B	0.17433	0.018	T	0.08513	-1.0718	10	0.22706	T	0.39	-9.531	8.056	0.30606	0.8393:0.0:0.1607:0.0	.	1253	P09884	DPOLA_HUMAN	N	1259;1253	ENSP00000368358:K1259N;ENSP00000368349:K1253N	ENSP00000368349:K1253N	K	+	3	2	POLA1	24769730	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.409000	0.44583	0.755000	0.32990	0.437000	0.28790	AAA	POLA1	-	NULL	ENSG00000101868		0.378	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	POLA1	HGNC	protein_coding	OTTHUMT00000056111.1	193	0.00	0	A	NM_016937		24859809	24859809	+1	no_errors	ENST00000379068	ensembl	human	known	69_37n	missense	53	56.91	70	SNP	1.000	T
POLR2A	5430	genome.wustl.edu	37	17	7412461	7412461	+	Missense_Mutation	SNP	A	A	G			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr17:7412461A>G	ENST00000322644.6	+	21	4063	c.3664A>G	c.(3664-3666)Act>Gct	p.T1222A		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1222					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				GAAGCACATGACTGACCGGAA	0.562																																						dbGAP											0													83.0	56.0	65.0					17																	7412461		2203	4300	6503	-	-	-	SO:0001583	missense	0					17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.3664A>G	17.37:g.7412461A>G	ENSP00000314949:p.Thr1222Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	pfam_RNA_pol_Rpb1_1,pfam_RNA_pol_Rpb1_5,pfam_RNA_pol_Rpb1_6,pfam_RNA_pol_asu,pfam_RNA_pol_Rpb1_7,pfam_RNA_pol_Rpb1_3,pfam_RNA_pol_Rpb1_4,pfam_RNA_pol_II_repeat_euk,smart_RNA_pol_N	p.T1222A	ENST00000322644.6	37	c.3664	CCDS32548.1	17	.	.	.	.	.	.	.	.	.	.	A	17.54	3.415599	0.62511	.	.	ENSG00000181222	ENST00000535204;ENST00000545644;ENST00000322644	T	0.67171	-0.25	5.51	5.51	0.81932	RNA polymerase Rpb1, domain 5 (1);RNA polymerase Rpb1, domain 7 (1);	0.000000	0.85682	D	0.000000	T	0.75221	0.3820	M	0.88906	2.99	0.80722	D	1	B	0.32968	0.392	B	0.37943	0.261	T	0.79029	-0.1970	10	0.87932	D	0	-9.6201	14.6568	0.68838	1.0:0.0:0.0:0.0	.	1222	P24928	RPB1_HUMAN	A	1178;121;1222	ENSP00000314949:T1222A	ENSP00000314949:T1222A	T	+	1	0	SLC35G6	7353185	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.561000	0.90715	2.109000	0.64355	0.369000	0.22263	ACT	POLR2A	-	pfam_RNA_pol_Rpb1_5,pfam_RNA_pol_Rpb1_7	ENSG00000181222		0.562	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POLR2A	HGNC	protein_coding	OTTHUMT00000437967.1	86	0.00	0	A	NM_000937		7412461	7412461	+1	no_errors	ENST00000322644	ensembl	human	known	69_37n	missense	3	92.50	37	SNP	1.000	G
PRKRIR	5612	genome.wustl.edu	37	11	76062581	76062581	+	Missense_Mutation	SNP	T	T	A			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr11:76062581T>A	ENST00000260045.3	-	5	1718	c.1613A>T	c.(1612-1614)gAa>gTa	p.E538V	PRKRIR_ENST00000531878.1_5'Flank	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	538					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						ATTTGTGGCTTCCTCAAACCA	0.428																																						dbGAP											0													14.0	15.0	15.0					11																	76062581		1957	3843	5800	-	-	-	SO:0001583	missense	0			AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"""THAP (C2CH-type zinc finger) domain containing"""	9440	protein-coding gene	gene with protein product	"""THAP domain containing 12"""	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.1613A>T	11.37:g.76062581T>A	ENSP00000260045:p.Glu538Val	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Missense_Mutation	SNP	pfam_Znf_C2CH,pfam_HATC,superfamily_RNaseH-like_dom,smart_Znf_C2CH,pfscan_Znf_C2CH	p.E538V	ENST00000260045.3	37	c.1613	CCDS8243.1	11	.	.	.	.	.	.	.	.	.	.	T	21.2	4.118160	0.77323	.	.	ENSG00000137492	ENST00000529901;ENST00000260045	.	.	.	5.13	5.13	0.70059	Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.77651	0.4162	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.79347	-0.1841	9	0.52906	T	0.07	.	15.3812	0.74658	0.0:0.0:0.0:1.0	.	538	O43422	P52K_HUMAN	V	363;538	.	ENSP00000260045:E538V	E	-	2	0	PRKRIR	75740229	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.313000	0.78978	2.107000	0.64212	0.524000	0.50904	GAA	PRKRIR	-	superfamily_RNaseH-like_dom	ENSG00000137492		0.428	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRKRIR	HGNC	protein_coding	OTTHUMT00000383188.1	221	0.00	0	T	NM_004705		76062581	76062581	-1	no_errors	ENST00000260045	ensembl	human	known	69_37n	missense	199	40.24	134	SNP	1.000	A
RGPD3	653489	genome.wustl.edu	37	2	107051114	107051116	+	In_Frame_Del	DEL	AAC	AAC	-			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	AAC	AAC					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr2:107051114_107051116delAAC	ENST00000409886.3	-	14	2122_2124	c.2035_2037delGTT	c.(2035-2037)gttdel	p.V679del	RGPD3_ENST00000304514.7_In_Frame_Del_p.V679del	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	679					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TCCAATAAGAAACAACACTTTTT	0.31																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0				CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.2035_2037delGTT	2.37:g.107051117_107051119delAAC	ENSP00000386588:p.Val679del	Somatic		WXS	Illumina GAIIx	Phase_IV	B8ZZM4	In_Frame_Del	DEL	pfam_Ran_bind_dom,pfam_GRIP,pfam_TPR-1,pfam_TPR_2,smart_TPR_repeat,smart_Ran_bind_dom,smart_GRIP,pfscan_GRIP,pfscan_TPR_repeat,pfscan_TPR-contain_dom,pfscan_Ran_bind_dom	p.V679in_frame_del	ENST00000409886.3	37	c.2037_2035	CCDS46379.1	2																																																																																			RGPD3	-	NULL	ENSG00000153165		0.310	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	RGPD3	HGNC	protein_coding	OTTHUMT00000329975.1	8	0.00	0	AAC	XM_929931		107051114	107051116	-1	no_errors	ENST00000304514	ensembl	human	known	69_37n	in_frame_del	5	37.50	3	DEL	1.000:1.000:1.000	-
SCN4A	6329	genome.wustl.edu	37	17	62034875	62034875	+	Missense_Mutation	SNP	G	G	A	rs121908556		TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr17:62034875G>A	ENST00000435607.1	-	13	2099	c.2023C>T	c.(2023-2025)Cgg>Tgg	p.R675W	SCN4A_ENST00000578147.1_Missense_Mutation_p.R675W	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	675			R -> G (in NKPP). {ECO:0000269|PubMed:15596759}.|R -> Q (in NKPP). {ECO:0000269|PubMed:15596759, ECO:0000269|PubMed:18046642}.|R -> W (in NKPP). {ECO:0000269|PubMed:15596759}.		membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.R675W(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTGAAGACCCGCAGCTGCCAA	0.587																																						dbGAP											1	Substitution - Missense(1)	endometrium(1)	GRCh37	CM043573|CM043574	SCN4A	M	rs121908556						46.0	51.0	49.0					17																	62034875		2089	4215	6304	-	-	-	SO:0001583	missense	0			U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.2023C>T	17.37:g.62034875G>A	ENSP00000396320:p.Arg675Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	pfam_Ion_trans_dom,pfam_Na_trans_assoc,pfam_PKD1_2_channel,prints_Na_channel_a4su,prints_Na_channel_asu,prints_PKD_2,pfscan_IQ_motif_EF-hand-BS	p.R675W	ENST00000435607.1	37	c.2023	CCDS45761.1	17	.	.	.	.	.	.	.	.	.	.	G	16.69	3.194491	0.58017	.	.	ENSG00000007314	ENST00000435607	D	0.99652	-6.3	3.66	1.41	0.22369	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99704	0.9887	H	0.97940	4.11	0.51482	A	0.999928	D	0.89917	1.0	D	0.79784	0.993	D	0.97690	1.0178	9	0.87932	D	0	.	9.6497	0.39890	0.0:0.0:0.4044:0.5956	.	675	P35499	SCN4A_HUMAN	W	675	ENSP00000396320:R675W	ENSP00000396320:R675W	R	-	1	2	SCN4A	59388607	0.972000	0.33761	0.999000	0.59377	0.928000	0.56348	1.286000	0.33273	0.875000	0.35847	0.561000	0.74099	CGG	SCN4A	-	pfam_Ion_trans_dom	ENSG00000007314		0.587	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SCN4A	HGNC	protein_coding		26	0.00	0	G	NM_000334		62034875	62034875	-1	no_errors	ENST00000435607	ensembl	human	known	69_37n	missense	12	62.50	20	SNP	0.998	A
TRBV7-3	28595	genome.wustl.edu	37	7	142247224	142247224	+	RNA	SNP	C	C	T			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr7:142247224C>T	ENST00000390361.3	-	0	281									T cell receptor beta variable 7-3																		TTGGGCAGCCCTGAGTCATCT	0.557																																						dbGAP											0													69.0	69.0	69.0					7																	142247224		1928	4125	6053	-	-	-			0			X61440		7q34	2012-02-07			ENSG00000211714	ENSG00000211714		"""T cell receptors / TRB locus"""	12237	other	T cell receptor gene						8650574	Standard	NG_001333		Approved	TRBV73, TCRBV6S1A1N1, TCRBV7S3			OTTHUMG00000158528		7.37:g.142247224C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Ig_V-set,pfscan_Ig-like	p.G78R	ENST00000390361.3	37	c.232		7																																																																																			TRBV7-3	-	pfam_Ig_V-set,pfscan_Ig-like	ENSG00000211714		0.557	TRBV7-3-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TRBV7-3	HGNC	TR_V_gene	OTTHUMT00000351234.2	159	0.00	0	C	NG_001333		142247224	142247224	-1	no_stop_codon:bad_bp_length_for_coding_region	ENST00000390361	ensembl	human	known	69_37n	missense	90	39.74	60	SNP	0.085	T
TRBV7-3	28595	genome.wustl.edu	37	7	142247229	142247229	+	RNA	SNP	T	T	A			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr7:142247229T>A	ENST00000390361.3	-	0	276									T cell receptor beta variable 7-3																		CAGCCCTGAGTCATCTGCCGC	0.557																																						dbGAP											0													67.0	68.0	67.0					7																	142247229		1928	4119	6047	-	-	-			0			X61440		7q34	2012-02-07			ENSG00000211714	ENSG00000211714		"""T cell receptors / TRB locus"""	12237	other	T cell receptor gene						8650574	Standard	NG_001333		Approved	TRBV73, TCRBV6S1A1N1, TCRBV7S3			OTTHUMG00000158528		7.37:g.142247229T>A		Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Ig_V-set,pfscan_Ig-like	p.D76V	ENST00000390361.3	37	c.227		7																																																																																			TRBV7-3	-	pfam_Ig_V-set,pfscan_Ig-like	ENSG00000211714		0.557	TRBV7-3-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TRBV7-3	HGNC	TR_V_gene	OTTHUMT00000351234.2	164	0.00	0	T	NG_001333		142247229	142247229	-1	no_stop_codon:bad_bp_length_for_coding_region	ENST00000390361	ensembl	human	known	69_37n	missense	89	39.19	58	SNP	0.000	A
ZC3H12A	80149	genome.wustl.edu	37	1	37941282	37941282	+	Frame_Shift_Del	DEL	C	C	-			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr1:37941282delC	ENST00000373087.6	+	2	301	c.185delC	c.(184-186)tccfs	p.S62fs	RP11-422J8.1_ENST00000424989.1_RNA	NM_025079.2	NP_079355.2			zinc finger CCCH-type containing 12A											NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GGCTATTCATCCACGGAGATC	0.642																																						dbGAP											0													59.0	56.0	57.0					1																	37941282		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0				CCDS417.1	1p34.3	2012-07-05			ENSG00000163874	ENSG00000163874		"""Zinc fingers, CCCH-type domain containing"""	26259	protein-coding gene	gene with protein product	"""MCP induced protein 1"""	610562				18178554, 22055188	Standard	NM_025079		Approved	FLJ23231, MCPIP1	uc001cbb.4	Q5D1E8	OTTHUMG00000004221	ENST00000373087.6:c.185delC	1.37:g.37941282delC	ENSP00000362179:p.Ser62fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Del	DEL	pfam_RNase_Zc3h12	p.T63fs	ENST00000373087.6	37	c.185	CCDS417.1	1																																																																																			ZC3H12A	-	NULL	ENSG00000163874		0.642	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZC3H12A	HGNC	protein_coding	OTTHUMT00000012154.2	37	0.00	0	C	NM_025079		37941282	37941282	+1	no_errors	ENST00000373082	ensembl	human	known	69_37n	frame_shift_del	10	16.67	2	DEL	0.013	-
ZNF208	7757	genome.wustl.edu	37	19	22157191	22157191	+	Silent	SNP	G	G	T			TCGA-A7-A0CD-01A-11W-A019-09	TCGA-A7-A0CD-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	d29ba065-28ca-4dfb-9588-06be857f67b2	1f53f23c-bb31-4247-ba6a-fa2b4d7d9fbf	g.chr19:22157191G>T	ENST00000397126.4	-	4	793	c.645C>A	c.(643-645)acC>acA	p.T215T	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	215					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				AATAAGTAAGGGTTGAGGACC	0.363																																						dbGAP											0													61.0	66.0	64.0					19																	22157191		2058	4214	6272	-	-	-	SO:0001819	synonymous_variant	0			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.645C>A	19.37:g.22157191G>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.T215	ENST00000397126.4	37	c.645	CCDS54240.1	19																																																																																			ZNF208	-	pfscan_Znf_C2H2	ENSG00000160321		0.363	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	ZNF208	HGNC	protein_coding	OTTHUMT00000464302.1	501	0.20	1	G	NM_007153		22157191	22157191	-1	no_errors	ENST00000397126	ensembl	human	known	69_37n	silent	308	39.25	199	SNP	0.000	T
