#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
LRRC48	83450	genome.wustl.edu	37	17	17896105	17896105	+	Silent	SNP	C	C	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr17:17896105C>T	ENST00000399187.1	+	6	689	c.471C>T	c.(469-471)tgC>tgT	p.C157C	LRRC48_ENST00000411504.2_Silent_p.C157C|LRRC48_ENST00000399182.1_Silent_p.C157C|LRRC48_ENST00000584166.1_Silent_p.C157C|LRRC48_ENST00000313838.8_Silent_p.C157C	NM_031294.3	NP_112584.3	Q9H069	LRC48_HUMAN	leucine rich repeat containing 48	157						cytoplasm (GO:0005737)				breast(1)|large_intestine(2)|lung(2)|pancreas(1)|urinary_tract(1)	7	all_neural(463;0.228)					GGTTCAAGTGCCTGCGGACGC	0.532													ENSG00000171962																																					0													58.0	59.0	59.0					17																	17896105		2036	4172	6208	SO:0001819	synonymous_variant	0			-	AK093317	CCDS45622.1, CCDS45623.1	17p11.2	2014-07-18			ENSG00000171962	ENSG00000171962			25384	protein-coding gene	gene with protein product						11997338, 23354437	Standard	NM_001130090		Approved	DKFZP586M1120	uc021trk.1	Q9H069	OTTHUMG00000059355	ENST00000399187.1:c.471C>T	17.37:g.17896105C>T			A8KAE6|Q86SF9|Q86W73|Q8IWG0	Silent	SNP	NULL	p.C157	ENST00000399187.1	37	c.471	CCDS45622.1	17																																																																																			-	LRRC48	-	NULL		0.532	LRRC48-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	LRRC48	HGNC	protein_coding	OTTHUMT00000131945.3	0	0	0	46	46	61	0.00	0.00	C	NM_031294		17896105	+1	5	8	47	29	tier1	no_errors	ENST00000313838	ensembl	human	known	74_37	silent	9.62	21.62	SNP	0.739	T	5	47
COL4A3	1285	genome.wustl.edu	37	2	228104874	228104874	+	Missense_Mutation	SNP	C	C	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr2:228104874C>T	ENST00000396578.3	+	3	322	c.160C>T	c.(160-162)Cct>Tct	p.P54S	AC097662.2_ENST00000606119.1_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000437673.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	54	Triple-helical region.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		GAAGGGCTTTCCTGGACCCCC	0.502													ENSG00000169031																																					0													51.0	53.0	52.0					2																	228104874		1889	4125	6014	SO:0001583	missense	0			-		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"""Collagens"""	2204	protein-coding gene	gene with protein product	"""tumstatin"""	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.160C>T	2.37:g.228104874C>T	ENSP00000379823:p.Pro54Ser		Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	pfam_Collagen,pfam_Collagen_VI_NC,superfamily_C-type_lectin_fold,smart_Collagen_VI_NC	p.P54S	ENST00000396578.3	37	c.160	CCDS42829.1	2	.	.	.	.	.	.	.	.	.	.	C	17.53	3.412277	0.62511	.	.	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.97665	-4.48	5.87	5.87	0.94306	.	0.112285	0.41097	D	0.000960	D	0.98099	0.9373	M	0.79614	2.46	0.36485	D	0.86806	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.91635	0.967;0.982;0.999;0.995	D	0.99271	1.0893	10	0.21014	T	0.42	.	15.7708	0.78167	0.0:1.0:0.0:0.0	.	54;54;54;54	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	S	54	ENSP00000379823:P54S	ENSP00000323334:P54S	P	+	1	0	COL4A3	227813118	0.530000	0.26330	0.447000	0.26932	0.402000	0.30811	1.140000	0.31516	2.792000	0.96026	0.650000	0.86243	CCT	-	COL4A3	-	pfam_Collagen		0.502	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL4A3	HGNC	protein_coding	OTTHUMT00000331409.2	0	0	0	35	35	85	0.00	0.00	C	NM_000091		228104874	+1	4	11	43	61	tier1	no_errors	ENST00000396578	ensembl	human	known	74_37	missense	8.51	15.28	SNP	0.853	T	4	43
AMBRA1	55626	genome.wustl.edu	37	11	46568608	46568609	+	Intron	INS	-	-	A	rs545025314		TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr11:46568608_46568609insA	ENST00000458649.2	-	4	797				AMBRA1_ENST00000534300.1_Intron|AMBRA1_ENST00000533727.1_Intron|AMBRA1_ENST00000314845.3_Intron|AMBRA1_ENST00000426438.1_Intron|AMBRA1_ENST00000528950.1_Intron|AMBRA1_ENST00000298834.3_Intron			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1						autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		gactccgtctcaaaaaaaaaaa	0.465													ENSG00000110497																																					0																																										SO:0001627	intron_variant	0				AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	25990	protein-coding gene	gene with protein product	"""WD repeat domain 94"", ""DDB1 and CUL4 associated factor 3"""	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.378+53->T	11.37:g.46568619_46568619dupA			A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	R	INS	-	NULL	ENST00000458649.2	37	NULL		11																																																																																				AMBRA1	-	-		0.465	AMBRA1-005	KNOWN	basic	protein_coding	AMBRA1	HGNC	protein_coding	OTTHUMT00000390103.1	0	0	0	22	22	27	0.00	0.00	-	NM_017749		46568609	-1	4	2	26	13	tier1	no_errors	ENST00000524783	ensembl	human	known	74_37	rna	13.33	13.33	INS	0.032:0.881	A	4	26
GRIP1	23426	genome.wustl.edu	37	12	67072671	67072671	+	Missense_Mutation	SNP	G	G	C			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr12:67072671G>C	ENST00000398016.3	-	1	82	c.14C>G	c.(13-15)tCt>tGt	p.S5C	GRIP1_ENST00000286445.7_Missense_Mutation_p.S5C|GRIP1_ENST00000359742.4_Missense_Mutation_p.S5C	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	79					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		GCATTTAAAAGAGACAGCTAT	0.463													ENSG00000155974																																					0													109.0	104.0	106.0					12																	67072671		1952	4154	6106	SO:0001583	missense	0			-	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.14C>G	12.37:g.67072671G>C	ENSP00000381098:p.Ser5Cys		B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	pfam_PDZ,superfamily_PDZ,smart_PDZ,pfscan_PDZ	p.S5C	ENST00000398016.3	37	c.14	CCDS41807.1	12	.	.	.	.	.	.	.	.	.	.	G	17.51	3.407165	0.62399	.	.	ENSG00000155974	ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000545666	T;T;T;T;T	0.34472	1.88;1.85;1.87;1.89;1.36	5.61	5.61	0.85477	.	0.287831	0.34555	N	0.003878	T	0.44726	0.1307	N	0.14661	0.345	0.38248	D	0.941512	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.987	T	0.44590	-0.9318	9	.	.	.	-10.9598	19.6209	0.95654	0.0:0.0:1.0:0.0	.	5;5	F5H4N6;Q9Y3R0-3	.;.	C	5	ENSP00000381098:S5C;ENSP00000352780:S5C;ENSP00000286445:S5C;ENSP00000446047:S5C;ENSP00000439124:S5C	.	S	-	2	0	GRIP1	65358938	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.111000	0.77077	2.643000	0.89663	0.462000	0.41574	TCT	-	GRIP1	-	NULL		0.463	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GRIP1	HGNC	protein_coding	OTTHUMT00000401975.2	0	0	0	41	41	88	0.00	0.00	G			67072671	-1	5	5	51	59	tier1	no_errors	ENST00000359742	ensembl	human	known	74_37	missense	8.93	7.58	SNP	1.000	C	5	51
SLC13A4	26266	genome.wustl.edu	37	7	135377097	135377097	+	Silent	SNP	G	G	C			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr7:135377097G>C	ENST00000354042.4	-	11	1883	c.1194C>G	c.(1192-1194)gtC>gtG	p.V398V	C7orf73_ENST00000422968.1_3'UTR	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	398					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						CCCAGCCAGGGACAAAGCCAG	0.438													ENSG00000164707																																					0													65.0	75.0	71.0					7																	135377097		2203	4300	6503	SO:0001819	synonymous_variant	0			-	AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"""Solute carriers"""	15827	protein-coding gene	gene with protein product	"""sulphate transporter 1"""	604309	"""solute carrier family 13 (sodium/sulphate symporters), member 4"""			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.1194C>G	7.37:g.135377097G>C			A4D1Q4|Q8N631	Silent	SNP	pfam_Na/sul_symport,pfam_Cit_transptr-like_dom,pfam_DctM	p.V398	ENST00000354042.4	37	c.1194	CCDS5840.1	7																																																																																			-	SLC13A4	-	pfam_Na/sul_symport		0.438	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC13A4	HGNC	protein_coding	OTTHUMT00000340558.1	0	0	0	82	82	109	0.00	0.00	G	NM_012450		135377097	-1	19	7	122	96	tier1	no_errors	ENST00000354042	ensembl	human	known	74_37	silent	13.48	6.80	SNP	0.997	C	19	122
PHF23	79142	genome.wustl.edu	37	17	7140765	7140765	+	Missense_Mutation	SNP	T	T	C			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr17:7140765T>C	ENST00000320316.3	-	3	324	c.98A>G	c.(97-99)gAt>gGt	p.D33G	PHF23_ENST00000571362.1_Missense_Mutation_p.D33G|DVL2_ENST00000005340.5_5'Flank|PHF23_ENST00000454255.2_Missense_Mutation_p.D29G|PHF23_ENST00000576955.1_5'UTR|PHF23_ENST00000570753.1_5'UTR	NM_001284518.1|NM_024297.2	NP_001271447.1|NP_077273.2	Q9BUL5	PHF23_HUMAN	PHD finger protein 23	33							zinc ion binding (GO:0008270)			breast(4)|kidney(2)|large_intestine(6)|lung(3)	15						TTTGTTGAAATCCTCAATTGT	0.453													ENSG00000040633																																					0													135.0	140.0	139.0					17																	7140765		1898	4139	6037	SO:0001583	missense	0			-	AK122791	CCDS42250.1, CCDS67143.1, CCDS67144.1	17p13.1	2014-08-13			ENSG00000040633	ENSG00000040633		"""Zinc fingers, PHD-type"""	28428	protein-coding gene	gene with protein product		612910					Standard	NM_024297		Approved	MGC2941, FLJ16355	uc002gfa.3	Q9BUL5	OTTHUMG00000177972	ENST00000320316.3:c.98A>G	17.37:g.7140765T>C	ENSP00000322579:p.Asp33Gly		A1DZ74|B3KVH8|B4DLK6|D3DTN4|Q8IZK0|Q96HG7|Q9H5X0	Missense_Mutation	SNP	pfam_Znf_PHD-finger,superfamily_Znf_FYVE_PHD,smart_Znf_PHD	p.D33G	ENST00000320316.3	37	c.98	CCDS42250.1	17	.	.	.	.	.	.	.	.	.	.	T	27.1	4.803065	0.90623	.	.	ENSG00000040633	ENST00000320316;ENST00000454255;ENST00000043410	T;T	0.60424	0.19;0.23	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.70404	0.3220	L	0.52905	1.665	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	T	0.73541	-0.3950	10	0.87932	D	0	-9.1676	12.7759	0.57448	0.0:0.0:0.0:1.0	.	33;33	B4DLK6;Q9BUL5	.;PHF23_HUMAN	G	33;29;33	ENSP00000322579:D33G;ENSP00000414607:D29G	ENSP00000043410:D33G	D	-	2	0	PHF23	7081489	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.358000	0.79466	1.898000	0.54952	0.455000	0.32223	GAT	-	PHF23	-	NULL		0.453	PHF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PHF23	HGNC	protein_coding	OTTHUMT00000440047.1	0	0	0	78	78	103	0.00	0.00	T	NM_024297		7140765	-1	8	6	85	88	tier1	no_errors	ENST00000320316	ensembl	human	known	74_37	missense	8.60	6.38	SNP	1.000	C	8	85
AMZ1	155185	genome.wustl.edu	37	7	2741852	2741906	+	Intron	DEL	TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC	TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC	-	rs798471|rs540419422|rs191436847|rs10624226|rs33915832|rs35358739|rs10694020|rs397762646	byFrequency	TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC	TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr7:2741852_2741906delTGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC	ENST00000312371.4	+	3	672				AMZ1_ENST00000407112.1_Intron	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1								metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		CCTGCACCCTTGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTCTGTGTCCTGC	0.624													ENSG00000174945																																					0																																										SO:0001627	intron_variant	0				AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.305-450TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC>-	7.37:g.2741852_2741906delTGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC			B3KRS0|Q8TF51	R	DEL	-	NULL	ENST00000312371.4	37	NULL	CCDS34589.1	7																																																																																				AMZ1	-	-		0.624	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AMZ1	HGNC	protein_coding	OTTHUMT00000325244.1	0	0	0	2	2	2	0.00	0.00	TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC	NM_133463		2741906	+1	0	0	2	2	tier1	no_errors	ENST00000485540	ensembl	human	known	74_37	rna	0.00	0.00	DEL	0.000:0.000:0.001:0.002:0.002:0.003:0.004:0.003:0.001:0.000:0.000:0.004:0.003:0.003:0.002:0.002:0.002:0.003:0.003:0.001:0.005:0.071:0.077:0.080:0.076:0.071:0.067:0.056:0.014:0.004:0.001:0.002:0.002:0.000:0.001:0.002:0.003:0.004:0.005:0.002:0.002:0.002:0.002:0.002:0.002:0.003:0.000:0.001:0.001:0.000:0.000:0.000:0.001:0.000:0.000	-	0	2
GAPVD1	26130	genome.wustl.edu	37	9	128025963	128025989	+	Intron	DEL	CAGCACTCCATCTGTAGGTATGTCTGT	CAGCACTCCATCTGTAGGTATGTCTGT	-	rs551743640|rs71374244|rs143312600	byFrequency	TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	CAGCACTCCATCTGTAGGTATGTCTGT	CAGCACTCCATCTGTAGGTATGTCTGT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr9:128025963_128025989delCAGCACTCCATCTGTAGGTATGTCTGT	ENST00000495955.1	+	1	92				GAPVD1_ENST00000265956.4_Intron|GAPVD1_ENST00000469528.1_3'UTR|GAPVD1_ENST00000470056.1_Intron|GAPVD1_ENST00000394104.2_Intron|GAPVD1_ENST00000394105.2_Intron|GAPVD1_ENST00000297933.6_Intron|GAPVD1_ENST00000394084.1_Intron|GAPVD1_ENST00000394083.2_Intron			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1						endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CTAAGTGGCACAGCACTCCATCTGTAGGTATGTCTGTCAGCACTCCA	0.564													ENSG00000165219		2105	0.420327	0.4516	0.3818	5008	,	,		19587	0.4454		0.3777	False		,,,				2504	0.4233																0																																										SO:0001627	intron_variant	0					CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.-199+1725CAGCACTCCATCTGTAGGTATGTCTGT>-	9.37:g.128025963_128025989delCAGCACTCCATCTGTAGGTATGTCTGT			A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Splice_Site	DEL	-	NULL	ENST00000495955.1	37	c.NULL		9																																																																																				GAPVD1	-	-		0.564	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	GAPVD1	HGNC	protein_coding	OTTHUMT00000355644.1	0	0	0	0	0	0	0.00	0.00	CAGCACTCCATCTGTAGGTATGTCTGT			128025989	+1	1	1	1	1	tier1	no_errors	ENST00000469528	ensembl	human	known	74_37	splice_site_del	50.00	50.00	DEL	1.000:1.000:1.000:1.000:1.000:0.999:0.996:0.980:0.970:0.963:0.961:0.959:0.952:0.948:0.947:0.950:0.961:0.966:0.966:0.969:0.974:0.982:0.984:0.985:0.984:0.985:0.993	-	1	1
PLXNB3	5365	genome.wustl.edu	37	X	153033837	153033837	+	Missense_Mutation	SNP	G	G	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chrX:153033837G>T	ENST00000361971.5	+	4	1334	c.1220G>T	c.(1219-1221)gGg>gTg	p.G407V	PLXNB3_ENST00000538966.1_Missense_Mutation_p.G430V|U52111.14_ENST00000434284.1_RNA|PLXNB3_ENST00000538282.1_Missense_Mutation_p.G60V|PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538776.1_Missense_Mutation_p.G60V|U52111.14_ENST00000416854.1_RNA	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	407	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGCAGATGGGCACATGATA	0.697													ENSG00000198753																																					0													39.0	37.0	38.0					X																	153033837		2202	4297	6499	SO:0001583	missense	0			-	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.1220G>T	X.37:g.153033837G>T	ENSP00000355378:p.Gly407Val		B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	pfam_Plexin_cytoplasmic_RasGAP_dom,pfam_IPT,pfam_Plexin_repeat,pfam_Semap_dom,superfamily_Semap_dom,superfamily_Rho_GTPase_activation_prot,superfamily_Ig_E-set,superfamily_Plexin-like_fold,smart_Semap_dom,smart_Plexin-like_fold,smart_IPT,pfscan_Semap_dom	p.G430V	ENST00000361971.5	37	c.1289	CCDS14729.1	X	.	.	.	.	.	.	.	.	.	.	G	16.11	3.030184	0.54790	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538282	T;T;T;T	0.11495	2.77;2.77;3.46;3.46	4.83	4.83	0.62350	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.283230	0.32987	N	0.005408	T	0.34366	0.0895	M	0.83118	2.625	0.58432	D	0.999992	D;D;D;D	0.89917	0.999;1.0;0.999;0.999	D;D;D;D	0.85130	0.973;0.997;0.984;0.991	T	0.12091	-1.0561	10	0.59425	D	0.04	.	11.9485	0.52942	0.0:0.1716:0.8284:0.0	.	60;89;430;407	B7Z3H9;B7Z9A5;F5H773;Q9ULL4	.;.;.;PLXB3_HUMAN	V	430;407;60;60	ENSP00000442736:G430V;ENSP00000355378:G407V;ENSP00000445569:G60V;ENSP00000441919:G60V	ENSP00000355378:G407V	G	+	2	0	PLXNB3	152687031	1.000000	0.71417	0.849000	0.33467	0.471000	0.32888	3.242000	0.51384	2.113000	0.64589	0.513000	0.50165	GGG	-	PLXNB3	-	pfam_Semap_dom,superfamily_Semap_dom,smart_Semap_dom,pfscan_Semap_dom		0.697	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	PLXNB3	HGNC	protein_coding	OTTHUMT00000061063.1	0	0	0	17	17	4	0.00	0.00	G			153033837	+1	4	0	14	8	tier1	no_errors	ENST00000538966	ensembl	human	known	74_37	missense	22.22	0.00	SNP	0.996	T	4	14
POTEE	445582	genome.wustl.edu	37	2	132022031	132022031	+	Silent	SNP	C	C	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr2:132022031C>T	ENST00000356920.5	+	15	3097	c.3003C>T	c.(3001-3003)ggC>ggT	p.G1001G	PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000303908.3_Intron|POTEE_ENST00000358087.5_3'UTR	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	1001	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											TGCTGTCTGGCGGCACCACCA	0.537													ENSG00000188219																																					0													1.0	1.0	1.0					2																	132022031		335	417	752	SO:0001819	synonymous_variant	0			-	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33895	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 2"""	608914	"""ANKRD26-like family C, member 1A"""	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.3003C>T	2.37:g.132022031C>T			Q6S8J4|Q6S8J5|Q6S8J8	Silent	SNP	pfam_Actin-related,pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,smart_Actin-related,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,prints_Actin-related	p.G1001	ENST00000356920.5	37	c.3003	CCDS46414.1	2																																																																																			-	POTEE	-	pfam_Actin-related,smart_Actin-related		0.537	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	POTEE	HGNC	protein_coding		0	0	0	19	19	0	0.00	0.00	C	NM_001083538		132022031	+1	5	1	11	0	tier1	no_errors	ENST00000356920	ensembl	human	known	74_37	silent	29.41	100.00	SNP	1.000	T	5	11
RCVRN	5957	genome.wustl.edu	37	17	9801316	9801317	+	3'UTR	INS	-	-	GTGTGTGCGC	rs531533066|rs376748693	byFrequency	TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr17:9801316_9801317insGTGTGTGCGC	ENST00000226193.5	-	0	1138_1139				RCVRN_ENST00000570909.3_5'UTR	NM_002903.2	NP_002894.1	P35243	RECO_HUMAN	recoverin						phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of calcium ion transport (GO:0051924)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	dendrite (GO:0030425)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	12						tgtgtgtgtgtgcgcgcgcgtg	0.589													ENSG00000109047																																					0																																										SO:0001624	3_prime_UTR_variant	0				BC001720	CCDS11151.1	17p13.1	2013-01-10		2006-09-26	ENSG00000109047	ENSG00000109047		"""EF-hand domain containing"""	9937	protein-coding gene	gene with protein product		179618		RCV1		1387789, 12507501, 1467959, 12789533	Standard	NM_002903		Approved		uc002gme.1	P35243	OTTHUMG00000130268	ENST00000226193.5:c.*96->GCGCACACAC	17.37:g.9801316_9801317insGTGTGTGCGC			Q53XL0	R	INS	-	NULL	ENST00000226193.5	37	NULL	CCDS11151.1	17																																																																																				RCVRN	-	-		0.589	RCVRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RCVRN	HGNC	protein_coding	OTTHUMT00000252600.2	0	0	0	0	0	0	0.00	0.00	-	NM_002903		9801317	-1	0	0	0	0	tier1	no_errors	ENST00000570909	ensembl	human	putative	74_37	rna	0.00	0.00	INS	0.000:0.000	GTGTGTGCGC	0	0
APBA2	321	genome.wustl.edu	37	15	29393906	29393906	+	Missense_Mutation	SNP	G	G	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr15:29393906G>T	ENST00000558402.1	+	11	2042	c.1443G>T	c.(1441-1443)caG>caT	p.Q481H	APBA2_ENST00000411764.1_Missense_Mutation_p.Q469H|APBA2_ENST00000558330.1_Missense_Mutation_p.Q469H|APBA2_ENST00000561069.1_Missense_Mutation_p.Q481H|APBA2_ENST00000558259.1_Missense_Mutation_p.Q481H			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	481	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CAGCCTCTCAGGACTGCATCG	0.577													ENSG00000034053																																					0													86.0	62.0	71.0					15																	29393906		2203	4300	6503	SO:0001583	missense	0			-	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1443G>T	15.37:g.29393906G>T	ENSP00000453293:p.Gln481His		E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	pfam_PTB/PI_dom,pfam_PDZ,superfamily_PDZ,smart_PTB/PI_dom,smart_PDZ,pfscan_PDZ,pfscan_PTB/PI_dom	p.Q481H	ENST00000558402.1	37	c.1443	CCDS10022.1	15	.	.	.	.	.	.	.	.	.	.	G	17.98	3.519651	0.64634	.	.	ENSG00000034053	ENST00000411764;ENST00000219865;ENST00000382938	T	0.55760	0.5	4.47	-0.63	0.11530	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.133176	0.50627	D	0.000118	T	0.62429	0.2427	L	0.55481	1.735	0.58432	D	0.999997	D;D;D;D	0.76494	0.997;0.998;0.999;0.999	D;D;D;D	0.91635	0.972;0.986;0.999;0.979	T	0.62267	-0.6890	10	0.87932	D	0	.	10.3879	0.44152	0.4494:0.0:0.5506:0.0	.	469;173;469;481	Q5XKC0;Q6ZVB1;E9PGI4;Q99767	.;.;.;APBA2_HUMAN	H	469;481;173	ENSP00000409312:Q469H	ENSP00000219865:Q481H	Q	+	3	2	APBA2	27181198	1.000000	0.71417	0.971000	0.41717	0.976000	0.68499	0.729000	0.26028	0.002000	0.14630	-0.150000	0.13652	CAG	-	APBA2	-	pfam_PTB/PI_dom,smart_PTB/PI_dom,pfscan_PTB/PI_dom		0.577	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	APBA2	HGNC	protein_coding	OTTHUMT00000251362.3	0	0	0	26	26	52	0.00	0.00	G	NM_005503		29393906	+1	4	3	37	36	tier1	no_errors	ENST00000558259	ensembl	human	known	74_37	missense	9.76	7.69	SNP	0.998	T	4	37
VRTN	55237	genome.wustl.edu	37	14	74824312	74824312	+	Missense_Mutation	SNP	C	C	T	rs377542755		TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr14:74824312C>T	ENST00000256362.4	+	2	1067	c.826C>T	c.(826-828)Cgt>Tgt	p.R276C		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	276					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						GCTGCTCAACCGTGAACCTGG	0.652													ENSG00000133980																																					0								C	CYS/ARG	0,4406		0,0,2203	44.0	42.0	42.0		826	3.4	0.1	14		42	1,8599	1.2+/-3.3	0,1,4299	no	missense	VRTN	NM_018228.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	276/703	74824312	1,13005	2203	4300	6503	SO:0001583	missense	0			-	AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 115"", ""vertebrae development homolog (pig)"""	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.826C>T	14.37:g.74824312C>T	ENSP00000256362:p.Arg276Cys		Q9NVC7	Missense_Mutation	SNP	pfam_Transposase_8	p.R276C	ENST00000256362.4	37	c.826	CCDS9830.1	14	.	.	.	.	.	.	.	.	.	.	C	12.22	1.873727	0.33069	0.0	1.16E-4	ENSG00000133980	ENST00000256362	T	0.46819	0.86	5.2	3.39	0.38822	.	0.791785	0.11486	N	0.559193	T	0.42607	0.1210	N	0.14661	0.345	0.45554	D	0.998508	D	0.76494	0.999	P	0.57846	0.828	T	0.33979	-0.9847	10	0.87932	D	0	-6.7824	4.9155	0.13844	0.2107:0.6157:0.0:0.1736	.	276	Q9H8Y1	VRTN_HUMAN	C	276	ENSP00000256362:R276C	ENSP00000256362:R276C	R	+	1	0	VRTN	73894065	1.000000	0.71417	0.050000	0.19076	0.047000	0.14425	5.128000	0.64733	0.780000	0.33566	0.561000	0.74099	CGT	-	VRTN	-	pfam_Transposase_8		0.652	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VRTN	HGNC	protein_coding	OTTHUMT00000412339.1	0	0	0	43	43	29	0.00	0.00	C	NM_018228		74824312	+1	6	3	59	31	tier1	no_errors	ENST00000256362	ensembl	human	known	74_37	missense	9.23	8.57	SNP	0.846	T	6	59
