#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_CAF	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_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_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_type	i_havana_transcript	i_normal_ref_reads	i_normal_ref_reads_val	i_normal_vaf	i_normal_vaf_val	i_normal_var_reads	i_normal_var_reads_val	i_reference	i_refseq_mrna_id	i_rsID	i_rsID_ref_var_alleles	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_ref_reads	i_tumor_ref_reads_val	i_tumor_vaf	i_tumor_vaf_val	i_tumor_var_reads	i_tumor_var_reads_val	i_type	i_ucsc_cons	i_variant
PPAP2B	8613	genome.wustl.edu	37	1	57044568	57044568	+	Missense_Mutation	SNP	A	A	C			TCGA-XH-A853-01A-11D-A423-09	TCGA-XH-A853-10A-01D-A426-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	baa4c33d-c706-4a74-b55c-b58396e8cebe	cc062673-2f64-4f9d-9e74-818f2ea5a1d6	g.chr1:57044568A>C	ENST00000371250.3	-	1	673	c.122T>G	c.(121-123)cTc>cGc	p.L41R		NM_003713.4	NP_003704.3	O14495	LPP3_HUMAN	phosphatidic acid phosphatase type 2B	41					Bergmann glial cell differentiation (GO:0060020)|blood vessel development (GO:0001568)|canonical Wnt signaling pathway involved in positive regulation of cell-cell adhesion (GO:0044329)|canonical Wnt signaling pathway involved in positive regulation of endothelial cell migration (GO:0044328)|canonical Wnt signaling pathway involved in positive regulation of wound healing (GO:0044330)|dephosphorylation (GO:0016311)|gastrulation with mouth forming second (GO:0001702)|germ cell migration (GO:0008354)|homotypic cell-cell adhesion (GO:0034109)|lipid metabolic process (GO:0006629)|negative regulation of protein phosphorylation (GO:0001933)|phospholipid metabolic process (GO:0006644)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of sphingolipid mediated signaling pathway (GO:1902068)|regulation of Wnt signaling pathway (GO:0030111)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)|sphingosine-1-phosphate phosphatase activity (GO:0042392)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						GAGGCAGAAGAGGTCGAGGCA	0.711																																							0											0													38.0	40.0	40.0					1																	57044568		2203	4300	6503	SO:0001583	missense	0			AB000889	CCDS604.1	1p32.2	2009-05-27			ENSG00000162407	ENSG00000162407	3.1.3.4		9229	protein-coding gene	gene with protein product		607125				9305923	Standard	NM_003713		Approved	PAP-2b, LPP3	uc001cyj.2	O14495	OTTHUMG00000008160	ENST00000371250.3:c.122T>G	1.37:g.57044568A>C	ENSP00000360296:p.Leu41Arg		B2R651|D3DQ52|Q5U0F7|Q96GW0|Q99782	Missense_Mutation	SNP	pfam_P_Acid_Pase_2/haloperoxidase,superfamily_P_Acid_Pase_2/haloperoxidase,smart_P_Acid_Pase_2/haloperoxidase	p.L41R	ENST00000371250.3	37	c.122	CCDS604.1	1	.	.	.	.	.	.	.	.	.	.	A	17.00	3.277934	0.59758	.	.	ENSG00000162407	ENST00000371250	T	0.75938	-0.98	4.74	4.74	0.60224	.	0.171305	0.22476	U	0.059553	T	0.69922	0.3165	L	0.47716	1.5	0.34223	D	0.675694	B	0.22541	0.071	B	0.31337	0.128	T	0.77000	-0.2750	10	0.87932	D	0	.	11.2322	0.48918	0.8474:0.1526:0.0:0.0	.	41	O14495	LPP3_HUMAN	R	41	ENSP00000360296:L41R	ENSP00000360296:L41R	L	-	2	0	PPAP2B	56817156	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.902000	0.63266	2.107000	0.64212	0.456000	0.33151	CTC	0	superfamily_P_Acid_Pase_2/haloperoxidase		0.711	PPAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PPAP2B	protein_coding	OTTHUMT00000022334.2	59	26	0	0.00	0	0	A	NM_003713	0	0		57044568	-1	no_errors	ENST00000371250	ensembl	human	known	74_37	missense	49	31	9.26	11.43	5	4	SNP	1	C
XRN1	54464	genome.wustl.edu	37	3	142037736	142037736	+	Missense_Mutation	SNP	C	C	T			TCGA-XH-A853-01A-11D-A423-09	TCGA-XH-A853-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	baa4c33d-c706-4a74-b55c-b58396e8cebe	cc062673-2f64-4f9d-9e74-818f2ea5a1d6	g.chr3:142037736C>T	ENST00000264951.4	-	38	4528	c.4411G>A	c.(4411-4413)Gtt>Att	p.V1471I	XRN1_ENST00000392981.2_Missense_Mutation_p.V1472I	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	1471					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						ACTTGGCAAACGGTCATTGTC	0.348																																							0											0													78.0	76.0	77.0					3																	142037736		2203	4300	6503	SO:0001583	missense	0			AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.4411G>A	3.37:g.142037736C>T	ENSP00000264951:p.Val1471Ile		Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	pfam_Put_53exo,pirsf_5_3_exoribonuclease_1	p.V1471I	ENST00000264951.4	37	c.4411	CCDS3123.1	3	.	.	.	.	.	.	.	.	.	.	C	10.91	1.485590	0.26686	.	.	ENSG00000114127	ENST00000264951;ENST00000392981	T;T	0.36520	1.25;1.29	4.85	2.04	0.26737	.	0.238496	0.33854	N	0.004489	T	0.15912	0.0383	N	0.12182	0.205	0.80722	D	1	B;B	0.33238	0.403;0.282	B;B	0.19148	0.024;0.011	T	0.08827	-1.0703	10	0.27082	T	0.32	-15.0349	10.3607	0.43991	0.0:0.7871:0.0:0.2129	.	1472;1471	Q8IZH2-2;Q8IZH2	.;XRN1_HUMAN	I	1471;1472	ENSP00000264951:V1471I;ENSP00000376707:V1472I	ENSP00000264951:V1471I	V	-	1	0	XRN1	143520426	0.963000	0.33076	1.000000	0.80357	0.764000	0.43329	0.727000	0.25999	1.021000	0.39600	-0.244000	0.11960	GTT	0	pirsf_5_3_exoribonuclease_1		0.348	XRN1-001	KNOWN	basic|CCDS	protein_coding	XRN1	protein_coding	OTTHUMT00000354087.2	160	208	0	0.48	0	1	C	NM_019001	0	0		142037736	-1	no_errors	ENST00000264951	ensembl	human	known	74_37	missense	116	360	10.77	7.93	14	31	SNP	0.988	T
RIMBP2	23504	genome.wustl.edu	37	12	130890754	130890754	+	Missense_Mutation	SNP	G	G	A			TCGA-XH-A853-01A-11D-A423-09	TCGA-XH-A853-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	baa4c33d-c706-4a74-b55c-b58396e8cebe	cc062673-2f64-4f9d-9e74-818f2ea5a1d6	g.chr12:130890754G>A	ENST00000261655.4	-	17	3123	c.2960C>T	c.(2959-2961)aCa>aTa	p.T987I		NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	987	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		ACCAAAAACTGTAATAATATC	0.259																																							0											0													57.0	60.0	59.0					12																	130890754		2203	4299	6502	SO:0001583	missense	0			AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.2960C>T	12.37:g.130890754G>A	ENSP00000261655:p.Thr987Ile		Q96ID2	Missense_Mutation	SNP	pfam_SH3_2,pfam_SH3_domain,superfamily_SH3_domain,superfamily_Fibronectin_type3,smart_SH3_domain,smart_Fibronectin_type3,pfscan_Fibronectin_type3,pfscan_SH3_domain,prints_SH3_domain	p.T987I	ENST00000261655.4	37	c.2960	CCDS31925.1	12	.	.	.	.	.	.	.	.	.	.	G	22.6	4.316548	0.81469	.	.	ENSG00000060709	ENST00000261655;ENST00000536632	T;T	0.53423	0.62;0.62	5.26	3.36	0.38483	Src homology-3 domain (3);Variant SH3 (1);	0.057942	0.64402	D	0.000002	T	0.36082	0.0954	N	0.25426	0.745	0.80722	D	1	P	0.37207	0.587	B	0.42112	0.376	T	0.04294	-1.0962	10	0.18276	T	0.48	-12.876	10.7588	0.46253	0.0:0.2688:0.5919:0.1393	.	987	O15034	RIMB2_HUMAN	I	987;124	ENSP00000261655:T987I;ENSP00000439030:T124I	ENSP00000261655:T987I	T	-	2	0	RIMBP2	129456707	0.997000	0.39634	0.184000	0.23157	0.941000	0.58515	3.813000	0.55636	0.657000	0.30906	0.563000	0.77884	ACA	0	pfam_SH3_2,pfam_SH3_domain,superfamily_SH3_domain,smart_SH3_domain,pfscan_SH3_domain		0.259	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RIMBP2	protein_coding	OTTHUMT00000399520.1	101	257	0	0.00	0	0	G	NM_015347	0	0		130890754	-1	no_errors	ENST00000261655	ensembl	human	known	74_37	missense	54	430	10	6.93	6	32	SNP	0.801	A
CEP250	11190	genome.wustl.edu	37	20	34067816	34067816	+	Missense_Mutation	SNP	T	T	C			TCGA-XH-A853-01A-11D-A423-09	TCGA-XH-A853-10A-01D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	baa4c33d-c706-4a74-b55c-b58396e8cebe	cc062673-2f64-4f9d-9e74-818f2ea5a1d6	g.chr20:34067816T>C	ENST00000397527.1	+	20	3152	c.2432T>C	c.(2431-2433)cTg>cCg	p.L811P	RP3-477O4.14_ENST00000453914.1_RNA|RP3-477O4.14_ENST00000416260.1_RNA|CEP250_ENST00000342580.4_Missense_Mutation_p.L811P|RP3-477O4.14_ENST00000444933.1_RNA	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	811	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			GTGAGGTGCCTGAAGCTGGAA	0.577																																							0											0													78.0	79.0	78.0					20																	34067816		2203	4300	6503	SO:0001583	missense	0			AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.2432T>C	20.37:g.34067816T>C	ENSP00000380661:p.Leu811Pro		E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	superfamily_Prefoldin	p.L811P	ENST00000397527.1	37	c.2432	CCDS13255.1	20	.	.	.	.	.	.	.	.	.	.	T	19.84	3.902062	0.72754	.	.	ENSG00000126001	ENST00000397527;ENST00000342580	T;T	0.16196	2.36;2.44	4.59	4.59	0.56863	.	0.179093	0.26812	N	0.022377	T	0.43100	0.1232	M	0.79805	2.47	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.44221	-0.9342	10	0.66056	D	0.02	.	12.6931	0.56988	0.0:0.0:0.0:1.0	.	811	Q9BV73	CP250_HUMAN	P	811	ENSP00000380661:L811P;ENSP00000341541:L811P	ENSP00000341541:L811P	L	+	2	0	CEP250	33531230	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.644000	0.61397	1.943000	0.56356	0.459000	0.35465	CTG	0	NULL		0.577	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CEP250	protein_coding	OTTHUMT00000078877.7	87	82	0	0.00	0	0	T	NM_007186	0	0		34067816	1	no_errors	ENST00000397527	ensembl	human	known	74_37	missense	71	122	8.97	6.87	7	9	SNP	1	C
TTC28	23331	genome.wustl.edu	37	22	28501660	28501660	+	Missense_Mutation	SNP	T	T	A			TCGA-XH-A853-01A-11D-A423-09	TCGA-XH-A853-10A-01D-A426-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	baa4c33d-c706-4a74-b55c-b58396e8cebe	cc062673-2f64-4f9d-9e74-818f2ea5a1d6	g.chr22:28501660T>A	ENST00000397906.2	-	8	3055	c.2914A>T	c.(2914-2916)Aat>Tat	p.N972Y		NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	972					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						TGTTCGTAATTCCCTAATTGG	0.532																																							0											0													80.0	69.0	72.0					22																	28501660		692	1591	2283	SO:0001583	missense	0			AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.2914A>T	22.37:g.28501660T>A	ENSP00000381003:p.Asn972Tyr		K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Missense_Mutation	SNP	pfam_TPR_1,pfam_TPR_2,smart_TPR_repeat,pfscan_TPR_repeat,pfscan_TPR-contain_dom	p.N972Y	ENST00000397906.2	37	c.2914	CCDS46678.1	22	.	.	.	.	.	.	.	.	.	.	T	18.32	3.598620	0.66332	.	.	ENSG00000100154	ENST00000397906	D	0.94687	-3.49	5.81	5.81	0.92471	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.97676	0.9238	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98548	1.0635	10	0.87932	D	0	-22.767	15.3511	0.74389	0.0:0.0:0.0:1.0	.	972	Q96AY4	TTC28_HUMAN	Y	972	ENSP00000381003:N972Y	ENSP00000381003:N972Y	N	-	1	0	TTC28	26831660	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.288000	0.78691	2.217000	0.71921	0.533000	0.62120	AAT	0	smart_TPR_repeat,pfscan_TPR_repeat,pfscan_TPR-contain_dom		0.532	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	TTC28	protein_coding	OTTHUMT00000320930.2	64	157	0	0.63	0	1	T	XM_929318	0	0		28501660	-1	no_errors	ENST00000397906	ensembl	human	novel	74_37	missense	42	262	8.7	5.73	4	16	SNP	1	A
LARGE	9215	genome.wustl.edu	37	22	33700401	33700401	+	Missense_Mutation	SNP	C	C	T	rs368030516		TCGA-XH-A853-01A-11D-A423-09	TCGA-XH-A853-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	baa4c33d-c706-4a74-b55c-b58396e8cebe	cc062673-2f64-4f9d-9e74-818f2ea5a1d6	g.chr22:33700401C>T	ENST00000354992.2	-	13	2115	c.1544G>A	c.(1543-1545)cGc>cAc	p.R515H	LARGE_ENST00000397394.2_Missense_Mutation_p.R515H|LARGE_ENST00000402320.1_Missense_Mutation_p.R463H|LARGE_ENST00000452586.2_Missense_Mutation_p.R314H|LARGE_ENST00000437602.2_Missense_Mutation_p.R515H|LARGE_ENST00000337431.2_Missense_Mutation_p.R463H	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	515					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				CTGTGCGTAGCGGAGGAACTG	0.627																																					Colon(70;397 1175 4573 19089 45288)		0											0								C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	80.0	66.0	70.0		1544,1544	4.2	1.0	22		70	0,8600		0,0,4300	no	missense,missense	LARGE	NM_004737.4,NM_133642.3	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	515/757,515/757	33700401	1,13005	2203	4300	6503	SO:0001583	missense	0			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"""Glycosyltransferase family 8 domain containing"""	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.1544G>A	22.37:g.33700401C>T	ENSP00000347088:p.Arg515His		B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Missense_Mutation	SNP	pfam_Glyco_trans_8	p.R515H	ENST00000354992.2	37	c.1544	CCDS13912.1	22	.	.	.	.	.	.	.	.	.	.	C	13.88	2.368647	0.42003	2.27E-4	0.0	ENSG00000133424	ENST00000443693;ENST00000429788;ENST00000354992;ENST00000337431;ENST00000397394;ENST00000402320;ENST00000452586;ENST00000437602	T;T;T;T;T;T	0.55052	0.98;1.03;0.98;1.03;0.54;1.95	5.27	4.24	0.50183	.	0.046988	0.85682	D	0.000000	T	0.45895	0.1365	L	0.45581	1.43	0.80722	D	1	B;B;B;B	0.33857	0.429;0.023;0.211;0.126	B;B;B;B	0.31191	0.125;0.008;0.052;0.059	T	0.39313	-0.9620	10	0.33940	T	0.23	-1.2646	15.8902	0.79291	0.0:0.8643:0.1357:0.0	.	515;314;463;515	B7Z2I9;E9PH73;O95461-2;O95461	.;.;.;LARGE_HUMAN	H	192;192;515;463;515;463;314;515	ENSP00000347088:R515H;ENSP00000336636:R463H;ENSP00000380549:R515H;ENSP00000385223:R463H;ENSP00000407917:R314H;ENSP00000388544:R515H	ENSP00000336636:R463H	R	-	2	0	LARGE	32030401	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	7.257000	0.78362	1.204000	0.43247	-0.176000	0.13171	CGC	0	NULL		0.627	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LARGE	protein_coding	OTTHUMT00000320515.2	98	75	0	0.00	0	0	C	NM_133642	rs368030516	C->T		33700401	-1	no_errors	ENST00000354992	ensembl	human	known	74_37	missense	58	127	7.94	7.97	5	11	SNP	1	T
RIMS2	9699	genome.wustl.edu	37	8	104863873	104863880	+	Intron	DEL	ACACACAC	ACACACAC	-	rs56306101|rs10529078|rs369439768|rs59712615	byFrequency	TCGA-XH-A853-01A-11D-A423-09	TCGA-XH-A853-10A-01D-A426-09	ACACACAC	ACACACAC					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	baa4c33d-c706-4a74-b55c-b58396e8cebe	cc062673-2f64-4f9d-9e74-818f2ea5a1d6	g.chr8:104863873_104863880delACACACAC	ENST00000507740.1	+	1	358				RIMS2_ENST00000522174.1_Intron|RIMS2_ENST00000262231.10_Intron|RIMS2_ENST00000406091.3_Intron|AP001572.1_ENST00000401294.1_RNA	NM_014677.4	NP_055492.3	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			AATGCTATGTacacacacacacacacac	0.365										HNSCC(12;0.0054)																													0											0																																										SO:0001627	intron_variant	0			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000507740.1:c.122+32016ACACACAC>-	8.37:g.104863881_104863888delACACACAC			B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	RNA	DEL	0	NULL	ENST00000507740.1	37	NULL	CCDS43761.1	8																																																																																			0	0		0.365	RIMS2-005	NOVEL	basic|CCDS	protein_coding	ENSG00000216113	protein_coding	OTTHUMT00000367215.1	11	0	0	0.00	0	0	ACACACAC	NM_001100117	0	0		104863880	1	no_errors	ENST00000401294	ensembl	human	novel	74_37	rna	27	0	15.62	0.00	5	0	DEL	0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000	0
