#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_ ensembl_gene_id	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_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GMAF	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNP	i_default_gene_name	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_name_source	i_gene_type	i_havana_transcript	i_n_alt_count	i_n_alt_count_full	i_n_alt_count_val	i_n_ref_count	i_n_ref_count_full	i_n_ref_count_val	i_normal_vaf	i_normal_vaf_val	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_t_alt_count_full	i_t_alt_count_val	i_t_ref_count_full	i_t_ref_count_val	i_tier	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_vaf	i_tumor_vaf_val	i_type	i_ucsc_cons	i_variant	t_alt_count	t_ref_count
HRNR	388697	genome.wustl.edu	37	1	152186899	152186899	+	Missense_Mutation	SNP	C	C	G			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr1:152186899C>G	ENST00000368801.2	-	3	7281	c.7206G>C	c.(7204-7206)caG>caC	p.Q2402H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2402					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGCCCAAAGACTGACGGGAGC	0.587													ENSG00000197915																																					0																																										SO:0001583	missense	0			-	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.7206G>C	1.37:g.152186899C>G	ENSP00000357791:p.Gln2402His		Q5DT20|Q5U1F4	Missense_Mutation	SNP	pfam_S100_Ca-bd_sub,pfscan_EF_hand_dom	p.Q2402H	ENST00000368801.2	37	c.7206	CCDS30859.1	1	.	.	.	.	.	.	.	.	.	.	-	6.699	0.497554	0.12762	.	.	ENSG00000197915	ENST00000368801	T	0.02498	4.27	2.76	0.731	0.18277	.	.	.	.	.	T	0.02571	0.0078	L	0.38838	1.175	0.21967	N	0.999446	D	0.76494	0.999	D	0.79784	0.993	T	0.46952	-0.9154	9	0.41790	T	0.15	.	6.5005	0.22166	0.0:0.7311:0.0:0.2689	.	2402	Q86YZ3	HORN_HUMAN	H	2402	ENSP00000357791:Q2402H	ENSP00000357791:Q2402H	Q	-	3	2	HRNR	150453523	0.005000	0.15991	0.026000	0.17262	0.090000	0.18270	-0.029000	0.12329	0.053000	0.16036	0.650000	0.86243	CAG	-	HRNR	-	NULL		0.587	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HRNR	HGNC	protein_coding	OTTHUMT00000034016.1	0	0	0	110	110	22	0.00	0.00	C	XM_373868		152186899	-1	31	5	106	29	tier1	no_errors	ENST00000368801	ensembl	human	known	74_37	missense	22.63	14.71	SNP	0.868	G	31	106
HRNR	388697	genome.wustl.edu	37	1	152187037	152187037	+	Silent	SNP	C	C	T			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr1:152187037C>T	ENST00000368801.2	-	3	7143	c.7068G>A	c.(7066-7068)caG>caA	p.Q2356Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2356					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAGATCCATGCTGAGTGTAAC	0.547													ENSG00000197915																																					0													388.0	608.0	534.0					1																	152187037		2182	4297	6479	SO:0001819	synonymous_variant	0			-	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.7068G>A	1.37:g.152187037C>T			Q5DT20|Q5U1F4	Silent	SNP	pfam_S100_Ca-bd_sub,pfscan_EF_hand_dom	p.Q2356	ENST00000368801.2	37	c.7068	CCDS30859.1	1																																																																																			-	HRNR	-	NULL		0.547	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HRNR	HGNC	protein_coding	OTTHUMT00000034016.1	0	0	0	416	416	102	0.00	0.00	C	XM_373868		152187037	-1	135	22	471	121	tier1	no_errors	ENST00000368801	ensembl	human	known	74_37	silent	22.24	15.38	SNP	0.000	T	135	471
HRNR	388697	genome.wustl.edu	37	1	152187081	152187081	+	Missense_Mutation	SNP	C	C	G			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr1:152187081C>G	ENST00000368801.2	-	3	7099	c.7024G>C	c.(7024-7026)Ggt>Cgt	p.G2342R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2342					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCGTGGTGACCAAATCCAGAA	0.577													ENSG00000197915																																					0													362.0	577.0	505.0					1																	152187081		2182	4297	6479	SO:0001583	missense	0			-	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.7024G>C	1.37:g.152187081C>G	ENSP00000357791:p.Gly2342Arg		Q5DT20|Q5U1F4	Missense_Mutation	SNP	pfam_S100_Ca-bd_sub,pfscan_EF_hand_dom	p.G2342R	ENST00000368801.2	37	c.7024	CCDS30859.1	1	.	.	.	.	.	.	.	.	.	.	-	4.933	0.173348	0.09391	.	.	ENSG00000197915	ENST00000368801	T	0.06849	3.25	3.29	0.209	0.15226	.	.	.	.	.	T	0.05456	0.0144	L	0.55481	1.735	0.09310	N	1	D	0.64830	0.994	P	0.56865	0.808	T	0.21042	-1.0257	9	0.52906	T	0.07	.	0.8888	0.01249	0.1855:0.4101:0.1816:0.2229	.	2342	Q86YZ3	HORN_HUMAN	R	2342	ENSP00000357791:G2342R	ENSP00000357791:G2342R	G	-	1	0	HRNR	150453705	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.277000	0.08502	0.055000	0.16094	0.650000	0.86243	GGT	-	HRNR	-	NULL		0.577	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HRNR	HGNC	protein_coding	OTTHUMT00000034016.1	0	0	0	355	355	113	0.00	0.00	C	XM_373868		152187081	-1	109	21	411	121	tier1	no_errors	ENST00000368801	ensembl	human	known	74_37	missense	20.96	14.79	SNP	0.001	G	109	411
LRIG3	121227	genome.wustl.edu	37	12	59281683	59281683	+	Missense_Mutation	SNP	C	C	G			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr12:59281683C>G	ENST00000320743.3	-	8	1265	c.979G>C	c.(979-981)Gat>Cat	p.D327H	LRIG3_ENST00000379141.4_Missense_Mutation_p.D267H	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	327					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			CTTGAATCATCTAACCTTGAT	0.378			T	ROS1	NSCLC								ENSG00000139263																												Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	0													103.0	102.0	103.0					12																	59281683		2203	4300	6503	SO:0001583	missense	0			-	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"""Immunoglobulin superfamily / I-set domain containing"""	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.979G>C	12.37:g.59281683C>G	ENSP00000326759:p.Asp327His		Q6UXL7|Q8NC72	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Leu-rich_rpt,pfam_Immunoglobulin,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like_dom	p.D327H	ENST00000320743.3	37	c.979	CCDS8960.1	12	.	.	.	.	.	.	.	.	.	.	C	19.78	3.890427	0.72524	.	.	ENSG00000139263	ENST00000379141;ENST00000320743	T;T	0.25749	1.78;1.78	5.86	5.86	0.93980	.	0.000000	0.38326	N	0.001725	T	0.40839	0.1133	L	0.29908	0.895	0.58432	D	0.999997	D;D	0.71674	0.985;0.998	P;D	0.69654	0.881;0.965	T	0.02326	-1.1176	9	.	.	.	.	20.5632	0.99335	0.0:1.0:0.0:0.0	.	267;327	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	H	267;327	ENSP00000368436:D267H;ENSP00000326759:D327H	.	D	-	1	0	LRIG3	57567950	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.050000	0.71063	2.937000	0.99478	0.650000	0.86243	GAT	-	LRIG3	-	smart_Leu-rich_rpt_typical-subtyp		0.378	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	LRIG3	HGNC	protein_coding	OTTHUMT00000406623.1	0	0	0	40	40	70	0.00	0.00	C	NM_153377		59281683	-1	10	15	111	132	tier1	no_errors	ENST00000320743	ensembl	human	known	74_37	missense	8.26	10.20	SNP	1.000	G	10	111
PKD2	5311	genome.wustl.edu	37	4	88929174	88929176	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	GAG	GAG	GAG	-	GAG	GAG	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr4:88929174_88929176delGAG	ENST00000237596.2	+	1	355_357	c.289_291delGAG	c.(289-291)gagdel	p.E102del		NM_000297.3	NP_000288.1	Q9BZL6	KPCD2_HUMAN	polycystic kidney disease 2 (autosomal dominant)	0					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		CTTCGAGGCCgaggaggaggagg	0.739													ENSG00000118762																																					0										18,82,2250		6,0,6,18,46,1099						-3.4	0.9			2	8,117,4707		2,0,4,14,89,2307	no	codingComplex	PKD2	NM_000297.3		8,0,10,32,135,3406	A1A1,A1A2,A1R,A2A2,A2R,RR		2.5869,4.2553,3.1328				26,199,6957				SO:0001651	inframe_deletion	0				U50928	CCDS3627.1	4q22.1	2014-01-28			ENSG00000118762	ENSG00000118762		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""EF-hand domain containing"""	9009	protein-coding gene	gene with protein product	"""transient receptor potential cation channel, subfamily P, member 2"""	173910				8298643	Standard	NM_000297		Approved	PKD4, PC2, Pc-2, TRPP2	uc003hre.3	Q13563	OTTHUMG00000160982	ENST00000237596.2:c.289_291delGAG	4.37:g.88929183_88929185delGAG	ENSP00000237596:p.Glu102del		Q8TB08|Q9P0T6|Q9Y3X8	In_Frame_Del	DEL	pfam_PKD1_2_channel,pfam_Ion_trans_dom,pfscan_EF_hand_dom,prints_PKD_2,prints_PKD_1	p.E100in_frame_del	ENST00000237596.2	37	c.289_291	CCDS3627.1	4																																																																																				PKD2	-	NULL		0.739	PKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PKD2	HGNC	protein_coding	OTTHUMT00000253042.4	0	0	0	32	32	30	0.00	0.00	GAG	NM_000297		88929176	+1	5	2	42	12	tier1	no_errors	ENST00000237596	ensembl	human	known	74_37	in_frame_del	10.64	14.29	DEL	1.000:1.000:1.000	-	5	42
QDPR	5860	genome.wustl.edu	37	4	17510934	17510934	+	Missense_Mutation	SNP	A	A	G			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr4:17510934A>G	ENST00000281243.5	-	2	337	c.158T>C	c.(157-159)aTt>aCt	p.I53T	QDPR_ENST00000513615.1_Missense_Mutation_p.I53T|QDPR_ENST00000428702.2_Intron|QDPR_ENST00000508623.1_Missense_Mutation_p.I53T	NM_000320.2	NP_000311.2	P09417	DHPR_HUMAN	quinoid dihydropteridine reductase	53					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|dihydrobiopterin metabolic process (GO:0051066)|L-phenylalanine catabolic process (GO:0006559)|liver development (GO:0001889)|response to aluminum ion (GO:0010044)|response to glucagon (GO:0033762)|response to lead ion (GO:0010288)|small molecule metabolic process (GO:0044281)|tetrahydrobiopterin biosynthetic process (GO:0006729)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	6,7-dihydropteridine reductase activity (GO:0004155)|electron carrier activity (GO:0009055)|NADH binding (GO:0070404)|NADPH binding (GO:0070402)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	13						CATTTTAACAATGATGCTAGC	0.507													ENSG00000151552																																					0													125.0	107.0	113.0					4																	17510934		2203	4300	6503	SO:0001583	missense	0			-	AB053170	CCDS3421.1	4p15.31	2014-04-01			ENSG00000151552	ENSG00000151552	1.5.1.34	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	9752	protein-coding gene	gene with protein product	"""6,7-dihydropteridine reductase"", ""short chain dehydrogenase/reductase family 33C, member 1"""	612676				19027726	Standard	NM_000320		Approved	DHPR, PKU2, SDR33C1	uc003gpd.3	P09417	OTTHUMG00000128537	ENST00000281243.5:c.158T>C	4.37:g.17510934A>G	ENSP00000281243:p.Ile53Thr		A8K158|B3KW71|Q53F52|Q9H3M5	Missense_Mutation	SNP	pfam_DH_sc/Rdtase_SDR	p.I53T	ENST00000281243.5	37	c.158	CCDS3421.1	4	.	.	.	.	.	.	.	.	.	.	A	5.272	0.235552	0.10023	.	.	ENSG00000151552	ENST00000513615;ENST00000281243;ENST00000508623	D;D;D	0.94613	-3.47;-3.47;-3.47	5.52	5.52	0.82312	NAD(P)-binding domain (1);	0.556427	0.18452	N	0.140818	D	0.89037	0.6601	N	0.21583	0.68	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.72887	-0.4156	10	0.11485	T	0.65	-17.5901	15.3324	0.74223	1.0:0.0:0.0:0.0	.	53	P09417	DHPR_HUMAN	T	53	ENSP00000422759:I53T;ENSP00000281243:I53T;ENSP00000426377:I53T	ENSP00000281243:I53T	I	-	2	0	QDPR	17120032	0.352000	0.24895	0.003000	0.11579	0.002000	0.02628	5.020000	0.64066	2.091000	0.63221	0.533000	0.62120	ATT	-	QDPR	-	pfam_DH_sc/Rdtase_SDR		0.507	QDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	QDPR	HGNC	protein_coding	OTTHUMT00000250372.1	0	0	0	56	56	75	0.00	0.00	A	NM_000320		17510934	-1	7	7	66	78	tier1	no_errors	ENST00000281243	ensembl	human	known	74_37	missense	9.59	8.24	SNP	0.022	G	7	66
ZNF251	90987	genome.wustl.edu	37	8	145948119	145948119	+	Missense_Mutation	SNP	A	A	G			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr8:145948119A>G	ENST00000292562.7	-	5	1201	c.926T>C	c.(925-927)aTt>aCt	p.I309T	ZNF251_ENST00000524394.1_Intron	NM_138367.1	NP_612376.1	Q9BRH9	ZN251_HUMAN	zinc finger protein 251	309					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|kidney(1)|large_intestine(5)|lung(9)|stomach(1)	17	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;7.54e-38)|all cancers(56;6.19e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.198)		CCGATGTTGAATAAGAGTTGA	0.463													ENSG00000198169																																					0													46.0	51.0	49.0					8																	145948119		2147	4280	6427	SO:0001583	missense	0			-	AK000435	CCDS47944.1	8q24.3	2013-01-08			ENSG00000198169	ENSG00000198169		"""Zinc fingers, C2H2-type"", ""-"""	13045	protein-coding gene	gene with protein product							Standard	NM_138367		Approved		uc003zdv.4	Q9BRH9	OTTHUMG00000165189	ENST00000292562.7:c.926T>C	8.37:g.145948119A>G	ENSP00000292562:p.Ile309Thr		Q2M219	Missense_Mutation	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.I309T	ENST00000292562.7	37	c.926	CCDS47944.1	8	.	.	.	.	.	.	.	.	.	.	A	4.466	0.086369	0.08583	.	.	ENSG00000198169	ENST00000292562	T	0.37584	1.19	3.0	3.0	0.34707	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16257	0.0391	N	0.11927	0.2	0.09310	N	1	B	0.18166	0.026	B	0.17098	0.017	T	0.30327	-0.9982	9	0.06757	T	0.87	-11.5111	5.9532	0.19259	0.8715:0.0:0.1285:0.0	.	309	Q9BRH9	ZN251_HUMAN	T	309	ENSP00000292562:I309T	ENSP00000292562:I309T	I	-	2	0	ZNF251	145918928	0.000000	0.05858	0.607000	0.28956	0.992000	0.81027	0.437000	0.21543	1.362000	0.46000	0.460000	0.39030	ATT	-	ZNF251	-	smart_Znf_C2H2-like,pfscan_Znf_C2H2		0.463	ZNF251-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF251	HGNC	protein_coding	OTTHUMT00000382541.1	0	0	0	59	59	150	0.00	0.00	A	NM_138367		145948119	-1	6	6	45	117	tier1	no_errors	ENST00000292562	ensembl	human	known	74_37	missense	11.76	4.88	SNP	0.000	G	6	45
PCLO	27445	genome.wustl.edu	37	7	82581481	82581481	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr7:82581481C>T	ENST00000333891.9	-	5	9125	c.8788G>A	c.(8788-8790)Gtt>Att	p.V2930I	PCLO_ENST00000437081.1_5'Flank|PCLO_ENST00000423517.2_Missense_Mutation_p.V2930I	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GTTAAATCAACGGGTTTTTCA	0.433													ENSG00000186472																																					0													120.0	120.0	120.0					7																	82581481		1906	4122	6028	SO:0001583	missense	0			-	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.8788G>A	7.37:g.82581481C>T	ENSP00000334319:p.Val2930Ile			Missense_Mutation	SNP	pfam_Znf_piccolo,pfam_C2_dom,pfam_PDZ,superfamily_C2_dom,superfamily_PDZ,superfamily_Znf_FYVE_PHD,smart_PDZ,smart_C2_dom,pfscan_C2_dom,pfscan_PDZ	p.V2930I	ENST00000333891.9	37	c.8788	CCDS47630.1	7	.	.	.	.	.	.	.	.	.	.	C	10.62	1.402034	0.25291	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.20738	2.05;2.08	5.67	5.67	0.87782	.	.	.	.	.	T	0.47525	0.1450	M	0.63843	1.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.40515	-0.9559	9	0.87932	D	0	.	19.7661	0.96342	0.0:1.0:0.0:0.0	.	2930;2930	Q9Y6V0-5;Q9Y6V0-6	.;.	I	2861;2930;2930	ENSP00000334319:V2930I;ENSP00000388393:V2930I	ENSP00000334319:V2930I	V	-	1	0	PCLO	82419417	1.000000	0.71417	1.000000	0.80357	0.267000	0.26476	6.044000	0.71012	2.660000	0.90430	0.557000	0.71058	GTT	-	PCLO	-	NULL		0.433	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	PCLO	HGNC	protein_coding	OTTHUMT00000337368.5	0	0	0	87	87	99	0.00	0.00	C	NM_014510		82581481	-1	7	6	79	72	tier1	no_errors	ENST00000333891	ensembl	human	known	74_37	missense	8.14	7.69	SNP	1.000	T	7	79
LAMB1	3912	genome.wustl.edu	37	7	107577718	107577718	+	Silent	SNP	G	G	A			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr7:107577718G>A	ENST00000222399.6	-	26	3996	c.3766C>T	c.(3766-3768)Ctg>Ttg	p.L1256L	LAMB1_ENST00000474380.1_5'Flank|LAMB1_ENST00000393561.1_Silent_p.L1280L	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1256	Domain II.				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						TCTTTAATCAGTTTCCTGTAA	0.343													ENSG00000091136																																					0													161.0	148.0	152.0					7																	107577718		2203	4300	6503	SO:0001819	synonymous_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.3766C>T	7.37:g.107577718G>A			Q14D91	Silent	SNP	pfam_EGF_laminin,pfam_Laminin_N,superfamily_Prefoldin,superfamily_t-SRE,superfamily_P-loop_NTPase,smart_Laminin_N,smart_EGF_laminin,smart_EG-like_dom,pfscan_Laminin_IV,pfscan_EGF_laminin,pfscan_Laminin_N	p.L1256	ENST00000222399.6	37	c.3766	CCDS5750.1	7																																																																																			-	LAMB1	-	superfamily_t-SRE		0.343	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LAMB1	HGNC	protein_coding	OTTHUMT00000314584.1	0	0	0	60	60	81	0.00	0.00	G	NM_002291		107577718	-1	14	6	72	107	tier1	no_errors	ENST00000222399	ensembl	human	known	74_37	silent	16.28	5.31	SNP	1.000	A	14	72
BTN2A3P	54718	genome.wustl.edu	37	6	26422387	26422388	+	RNA	INS	-	-	CTTCCTCCTCCT	rs141260282	byFrequency	TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr6:26422387_26422388insCTTCCTCCTCCT	ENST00000466808.2	+	0	41_42							Q96KV6	BT2A3_HUMAN	butyrophilin, subfamily 2, member A3, pseudogene							integral component of membrane (GO:0016021)											CGGCCAGCCTCCCTCCTCCTCC	0.589													ENSG00000124549		503	0.100439	0.1188	0.1427	5008	,	,		16333	0.0258		0.1083	False		,,,				2504	0.1145																0																																												0				AL021917		6p22.1	2014-01-14	2011-09-06	2011-09-06	ENSG00000124549	ENSG00000124549		"""Butyrophilins"""	13229	pseudogene	pseudogene		613592	"""butyrophilin, subfamily 2, member A3"""	BTN2A3			Standard	NR_027795		Approved	BTN2.3	uc011dkl.1	Q96KV6	OTTHUMG00000014453		6.37:g.26422387_26422388insCTTCCTCCTCCT			A6NEF4	R	INS	-	NULL	ENST00000466808.2	37	NULL		6																																																																																				BTN2A3P	-	-		0.589	BTN2A3P-001	KNOWN	basic	processed_transcript	BTN2A3P	HGNC	pseudogene	OTTHUMT00000040118.4	0	0	0	14	14	14	0.00	0.00	-	NR_027795		26422388	+1	0	0	8	8	tier1	no_errors	ENST00000465856	ensembl	human	known	74_37	rna	0.00	0.00	INS	0.003:0.002	CTTCCTCCTCCT	0	8
TCHH	7062	genome.wustl.edu	37	1	152084230	152084235	+	In_Frame_Del	DEL	CAACGT	CAACGT	-	rs72477385	byFrequency	TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	CAACGT	CAACGT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr1:152084230_152084235delCAACGT	ENST00000368804.1	-	2	1457_1462	c.1458_1463delACGTTG	c.(1456-1464)gaacgttgg>gag	p.RW487del		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	487	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.R487S(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAGCTTCAGCCAACGTTCGCGCCTct	0.67													ENSG00000159450																																					1	Substitution - Missense(1)	endometrium(1)																																								SO:0001651	inframe_deletion	0				L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1458_1463delACGTTG	1.37:g.152084230_152084235delCAACGT	ENSP00000357794:p.Arg487_Trp488del		Q5VUI3	In_Frame_Del	DEL	pfam_S100_Ca-bd_sub,pfscan_EF_hand_dom	p.RW487in_frame_del	ENST00000368804.1	37	c.1463_1458	CCDS41396.1	1																																																																																				TCHH	-	NULL		0.670	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TCHH	HGNC	protein_coding	OTTHUMT00000036671.2	0	0	0	7	7	7	0.00	0.00	CAACGT	NM_007113		152084235	-1	0	0	3	3	tier1	no_errors	ENST00000368804	ensembl	human	known	74_37	in_frame_del	0.00	0.00	DEL	0.000:0.000:0.000:0.000:0.000:0.000	-	0	3
TRIO	7204	genome.wustl.edu	37	5	14487871	14487871	+	Silent	SNP	C	C	T			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr5:14487871C>T	ENST00000344204.4	+	48	7158	c.7134C>T	c.(7132-7134)ccC>ccT	p.P2378P	TRIO_ENST00000537187.1_Intron|TRIO_ENST00000344135.5_5'Flank	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	2378					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CCCTGCCTCCCCCTggcgcgg	0.756													ENSG00000038382																																					0													4.0	5.0	5.0					5																	14487871		1980	3966	5946	SO:0001819	synonymous_variant	0			-	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"""	12303	protein-coding gene	gene with protein product		601893	"""triple functional domain (PTPRF interacting)"""			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.7134C>T	5.37:g.14487871C>T			D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	pfam_DH-domain,pfam_Prot_kinase_dom,pfam_Spectrin_repeat,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Ig_I-set,pfam_SH3_domain,superfamily_Kinase-like_dom,superfamily_DH-domain,superfamily_SH3_domain,superfamily_CRAL-TRIO_dom,superfamily_Capsid/spike_ssD_virus,smart_CRAL-TRIO_dom,smart_Spectrin/alpha-actinin,smart_DH-domain,smart_Pleckstrin_homology,smart_SH3_domain,smart_Ig_sub,smart_Ig_sub2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_CRAL-TRIO_dom,pfscan_Pleckstrin_homology,pfscan_SH3_domain,pfscan_Prot_kinase_dom,pfscan_Ig-like_dom,pfscan_DH-domain	p.P2378	ENST00000344204.4	37	c.7134	CCDS3883.1	5																																																																																			-	TRIO	-	NULL		0.756	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRIO	HGNC	protein_coding	OTTHUMT00000253711.2	0	0	0	9	9	6	0.00	0.00	C	NM_007118		14487871	+1	4	0	8	3	tier1	no_errors	ENST00000344204	ensembl	human	known	74_37	silent	33.33	0.00	SNP	0.171	T	4	8
TUBB8P12	260334	genome.wustl.edu	37	18	49507	49507	+	Silent	SNP	G	G	C			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr18:49507G>C	ENST00000308911.6	-	1	50	c.51C>G	c.(49-51)ggC>ggG	p.G17G	RP11-683L23.1_ENST00000594555.1_5'Flank|RP11-683L23.1_ENST00000573909.1_Intron																							CAACCTTGGCGCCGATCTGGT	0.682													ENSG00000173213																																					0																																										SO:0001819	synonymous_variant	0			-																												ENST00000308911.6:c.51C>G	18.37:g.49507G>C				Silent	SNP	pfam_Tubulin_FtsZ_GTPase,pfam_Tubulin/FtsZ_2-layer-sand-dom,superfamily_Tubulin_FtsZ_GTPase,superfamily_Tub_FtsZ_C,smart_Tubulin_FtsZ_GTPase,smart_Tubulin/FtsZ_2-layer-sand-dom,prints_Beta_tubulin,prints_Tubulin,prints_Epsilon_tubulin,prints_Gamma_tubulin,prints_Delta_tubulin,prints_Alpha_tubulin	p.G17	ENST00000308911.6	37	c.51		18																																																																																			-	RP11-683L23.1	-	pfam_Tubulin_FtsZ_GTPase,superfamily_Tubulin_FtsZ_GTPase,prints_Tubulin		0.682	RP11-683L23.1-201	KNOWN	basic|appris_principal	protein_coding	ENSG00000173213	Clone_based_vega_gene	protein_coding		0	0	0	41	41	0	0.00	0.00	G			49507	-1	5	0	44	1	tier1	no_errors	ENST00000308911	ensembl	human	known	74_37	silent	10.20	0.00	SNP	0.875	C	5	44
MSH3	4437	genome.wustl.edu	37	5	79950700	79950717	+	In_Frame_Del	DEL	GCAGCGGCTGCAGCGGCC	GCAGCGGCTGCAGCGGCC	-	rs530525176|rs2431220|rs2405875|rs144776112|rs201874762|rs201906899	byFrequency	TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	GCAGCGGCTGCAGCGGCC	GCAGCGGCTGCAGCGGCC					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr5:79950700_79950717delGCAGCGGCTGCAGCGGCC	ENST00000265081.6	+	1	234_251	c.154_171delGCAGCGGCTGCAGCGGCC	c.(154-171)gcagcggctgcagcggccdel	p.AAAAAA52del	DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000505337.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	52	Poly-Ala.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		CCCTGGCGCTgcagcggctgcagcggccgcagcggccg	0.693								Mismatch excision repair (MMR)					ENSG00000113318																									Melanoma(88;1010 1399 13793 26548 36275)												0									,	1153,2933		197,759,1087					,		0.2		dbSNP_100	12	2199,5723		382,1435,2144	no	coding,utr-5	DHFR,MSH3	NM_002439.3,NM_000791.3	,	579,2194,3231	A1A1,A1R,RR		27.7581,28.2183,27.9147	,	,		3352,8656				SO:0001651	inframe_deletion	0				U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.154_171delGCAGCGGCTGCAGCGGCC	5.37:g.79950700_79950717delGCAGCGGCTGCAGCGGCC	ENSP00000265081:p.Ala52_Ala57del		A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	In_Frame_Del	DEL	pfam_D_mismatch_repair_MutS_C,pfam_D_mismatch_repair_MutS_core,pfam_D_mmatch_repair_MutS_con_dom,pfam_D_mismatch_repair_MutS-lik_N,pfam_D_mismatch_repair_MutS_clamp,superfamily_D_mismatch_repair_MutS_core,superfamily_P-loop_NTPase,superfamily_D_mismatch_repair_MutS_N,superfamily_D_mmatch_repair_MutS_con_dom,smart_D_mismatch_repair_MutS_core,smart_D_mismatch_repair_MutS_C	p.AAAAAA55in_frame_del	ENST00000265081.6	37	c.154_171	CCDS34195.1	5																																																																																				MSH3	-	NULL		0.693	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	MSH3	HGNC	protein_coding	OTTHUMT00000369471.1	0	0	0	0	0	0	0.00	0.00	GCAGCGGCTGCAGCGGCC	NM_002439		79950717	+1	0	0	0	0	tier1	no_errors	ENST00000265081	ensembl	human	known	74_37	in_frame_del	0.00	0.00	DEL	0.640:0.607:0.574:0.541:0.508:0.474:0.440:0.406:0.372:0.338:0.304:0.271:0.238:0.205:0.172:0.140:0.107:0.075	-	0	0
OR2AG1	144125	genome.wustl.edu	37	11	6806992	6806992	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr11:6806992T>C	ENST00000307401.4	+	1	745	c.724T>C	c.(724-726)Tct>Cct	p.S242P		NM_001004489.2	NP_001004489.1	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG, member 1	242						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TGTCACCTGCTCTTCCCACCT	0.493													ENSG00000170803																																					0													185.0	162.0	169.0					11																	6806992		2201	4296	6497	SO:0001583	missense	0			-	AB065823	CCDS31414.1	11p15.4	2012-08-09			ENSG00000170803	ENSG00000170803		"""GPCR / Class A : Olfactory receptors"""	15142	protein-coding gene	gene with protein product				OR2AG3			Standard	NM_001004489		Approved		uc001mer.2	Q9H205	OTTHUMG00000165735	ENST00000307401.4:c.724T>C	11.37:g.6806992T>C	ENSP00000307447:p.Ser242Pro		B9EKV7|Q6IFG7|Q96R26	Missense_Mutation	SNP	pfam_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,prints_Olfact_rcpt,prints_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM	p.S242P	ENST00000307401.4	37	c.724	CCDS31414.1	11	.	.	.	.	.	.	.	.	.	.	T	16.43	3.119959	0.56613	.	.	ENSG00000170803	ENST00000307401	T	0.38722	1.12	4.23	3.06	0.35304	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000156	T	0.66528	0.2798	M	0.93328	3.405	0.30419	N	0.778329	D	0.76494	0.999	D	0.74674	0.984	T	0.66814	-0.5828	10	0.87932	D	0	.	4.9213	0.13871	0.1871:0.0:0.1943:0.6186	.	242	Q9H205	O2AG1_HUMAN	P	242	ENSP00000307447:S242P	ENSP00000307447:S242P	S	+	1	0	OR2AG1	6763568	0.000000	0.05858	0.994000	0.49952	0.991000	0.79684	0.014000	0.13333	0.746000	0.32786	0.528000	0.53228	TCT	-	OR2AG1	-	pfam_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,prints_Olfact_rcpt,pfscan_GPCR_Rhodpsn_7TM		0.493	OR2AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR2AG1	HGNC	protein_coding	OTTHUMT00000385980.1	0	0	0	82	82	111	0.00	0.00	T	NM_001004489		6806992	+1	8	2	70	63	tier1	no_errors	ENST00000307401	ensembl	human	known	74_37	missense	10.26	3.08	SNP	0.963	C	8	70
ADAMTSL4	54507	genome.wustl.edu	37	1	150524368	150524368	+	Intron	DEL	A	A	-	rs199813152		TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	g.chr1:150524368delA	ENST00000271643.4	+	3	152				ADAMTSL4_ENST00000483335.1_3'UTR|MIR4257_ENST00000581735.1_RNA|ADAMTSL4_ENST00000369041.5_Intron|ADAMTSL4_ENST00000369039.5_Intron|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000369038.2_5'Flank	NM_019032.4	NP_061905.2	Q6UY14	ATL4_HUMAN	ADAMTS-like 4						apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			tctccatctcaaaaaaaaaaa	0.527													ENSG00000143382																																					0																																										SO:0001627	intron_variant	0				BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"""thrombospondin repeat containing 1"""	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000271643.4:c.-84-313A>-	1.37:g.150524368delA			B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	R	DEL	-	NULL	ENST00000271643.4	37	NULL	CCDS955.1	1																																																																																				ADAMTSL4	-	-		0.527	ADAMTSL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	ADAMTSL4	HGNC	protein_coding		0	0	0	16	16	18	0.00	0.00	A	NM_019032		150524368	+1	7	2	63	44	tier1	no_errors	ENST00000483335	ensembl	human	known	74_37	rna	10.00	4.35	DEL	0.000	-	7	63
