#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
CA8	767	genome.wustl.edu	37	8	61178601	61178601	+	Silent	SNP	C	C	T			TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr8:61178601C>T	ENST00000317995.4	-	3	564	c.300G>A	c.(298-300)tcG>tcA	p.S100S		NM_004056.4	NP_004047.3	P35219	CAH8_HUMAN	carbonic anhydrase VIII	100			S -> P (in CMARQ3; affects protein stability owing to accelerated proteasomal degradation). {ECO:0000269|PubMed:19461874}.		one-carbon metabolic process (GO:0006730)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasm (GO:0005737)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(6)|prostate(2)|skin(1)	16		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)			Zonisamide(DB00909)	ATGGTCCTCCCGAAAGAACTG	0.388													ENSG00000178538																																					0													60.0	58.0	58.0					8																	61178601		2203	4300	6503	SO:0001819	synonymous_variant	0			-	L04656	CCDS6174.1	8q12.1	2012-08-21			ENSG00000178538	ENSG00000178538		"""Carbonic anhydrases"""	1382	protein-coding gene	gene with protein product		114815		CALS		17219437	Standard	NM_004056		Approved	CARP	uc003xtz.1	P35219	OTTHUMG00000165325	ENST00000317995.4:c.300G>A	8.37:g.61178601C>T			A8K0A5|B3KQZ7|Q32MY2	Silent	SNP	pfam_Carbonic_anhydrase_a,superfamily_Carbonic_anhydrase_a,pfscan_Carbonic_anhydrase_a	p.S100	ENST00000317995.4	37	c.300	CCDS6174.1	8																																																																																			-	CA8	-	pfam_Carbonic_anhydrase_a,superfamily_Carbonic_anhydrase_a,pfscan_Carbonic_anhydrase_a		0.388	CA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CA8	HGNC	protein_coding	OTTHUMT00000383445.1	0	0	0	145	145	108	0.00	0.00	C			61178601	-1	13	14	130	96	tier1	no_errors	ENST00000317995	ensembl	human	known	74_37	silent	9.09	12.73	SNP	0.091	T	13	130
CENPF	1063	genome.wustl.edu	37	1	214815232	214815232	+	Missense_Mutation	SNP	A	A	G			TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr1:214815232A>G	ENST00000366955.3	+	12	3719	c.3551A>G	c.(3550-3552)gAg>gGg	p.E1184G		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGAGAGAGTGAGAGAAATCAA	0.338													ENSG00000117724																									Colon(80;575 1284 11000 14801 43496)												0													47.0	53.0	51.0					1																	214815232		2201	4296	6497	SO:0001583	missense	0			-	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.3551A>G	1.37:g.214815232A>G	ENSP00000355922:p.Glu1184Gly		Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	pfam_Centromere_CenpF_N,pfam_Centromere_CenpF_leu-rich_rpt,pfam_CenpF/LEK1_Rb-prot-bd	p.E1184G	ENST00000366955.3	37	c.3551	CCDS31023.1	1	.	.	.	.	.	.	.	.	.	.	A	18.26	3.584359	0.65992	.	.	ENSG00000117724	ENST00000366955	T	0.04156	3.69	5.31	2.89	0.33648	.	0.200392	0.24769	N	0.035750	T	0.17492	0.0420	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.74674	0.984	T	0.02202	-1.1196	9	0.72032	D	0.01	.	11.0085	0.47649	0.701:0.2989:0.0:0.0	.	1184	P49454	CENPF_HUMAN	G	1184	ENSP00000355922:E1184G	ENSP00000355922:E1184G	E	+	2	0	CENPF	212881855	0.954000	0.32549	0.011000	0.14972	0.375000	0.29983	3.113000	0.50376	0.292000	0.22492	0.496000	0.49642	GAG	-	CENPF	-	NULL		0.338	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CENPF	HGNC	protein_coding	OTTHUMT00000089749.1	0	0	0	39	39	52	0.00	0.00	A	NM_016343		214815232	+1	8	24	19	68	tier1	no_errors	ENST00000366955	ensembl	human	known	74_37	missense	29.63	25.81	SNP	0.046	G	8	19
OAS2	4939	genome.wustl.edu	37	12	113425106	113425106	+	Silent	SNP	C	C	T	rs369863340	byFrequency	TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr12:113425106C>T	ENST00000342315.4	+	2	655	c.441C>T	c.(439-441)aaC>aaT	p.N147N	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000449768.2_Silent_p.N147N|OAS2_ENST00000392583.2_Silent_p.N147N	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	147	OAS domain 1.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						CCGCCTTCAACGCTCTGAGTA	0.493													ENSG00000111335	C|||	2	0.000399361	0.0	0.0014	5008	,	,		19067	0.0		0.0	False		,,,				2504	0.001				Pancreas(199;709 2232 18410 33584 35052)												0								C	,,	0,4406		0,0,2203	48.0	51.0	50.0		441,441,441	-6.3	0.1	12		50	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	OAS2	NM_001032731.1,NM_002535.2,NM_016817.2	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	147/173,147/688,147/720	113425106	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	0			-	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"""2'-5'-oligoadenylate synthetase 2 (69-71 kD)"""			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.441C>T	12.37:g.113425106C>T			A8K9T1|Q6PJ33|Q86XX8	Silent	SNP	pfam_2-5-oligoAdlate_synth_1_dom2/C,pfam_Nucleotidyltransferase,pfscan_2-5-oligoadenylate_synth_N	p.N147	ENST00000342315.4	37	c.441	CCDS31906.1	12																																																																																			-	OAS2	-	NULL		0.493	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	OAS2	HGNC	protein_coding	OTTHUMT00000405937.1	0	0	0	45	45	47	0.00	0.00	C			113425106	+1	26	30	36	18	tier1	no_errors	ENST00000342315	ensembl	human	known	74_37	silent	41.94	62.50	SNP	0.389	T	26	36
PNLIPRP2	5408	genome.wustl.edu	37	10	118401628	118401628	+	RNA	SNP	G	G	A			TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr10:118401628G>A	ENST00000298771.7	+	0	1206				PNLIPRP2_ENST00000537242.1_RNA|PNLIPRP2_ENST00000433618.4_RNA	NR_103727.1		P54317	LIPR2_HUMAN	pancreatic lipase-related protein 2						galactolipid catabolic process (GO:0019376)|lipid digestion (GO:0044241)|phospholipid catabolic process (GO:0009395)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	acylglycerol lipase activity (GO:0047372)|calcium ion binding (GO:0005509)|galactolipase activity (GO:0047714)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			endometrium(1)|large_intestine(1)|lung(11)|prostate(3)	16				all cancers(201;0.015)		ATTTTCAGAGGATCCCTCAAA	0.348													ENSG00000165862																																					0													43.0	42.0	43.0					10																	118401628		1868	4088	5956			0			-	M93284		10q26.12	2014-03-14				ENSG00000266200	3.1.1.3		9157	protein-coding gene	gene with protein product		604423				1379598	Standard	NM_005396		Approved	PLRP2	uc001lcq.3	P54317			10.37:g.118401628G>A			A8K627|Q6IB55	Missense_Mutation	SNP	pirsf_Lipoprotein_lipase_LIPH,pfam_Lipase_N,pfam_PLAT/LH2_dom,superfamily_Lipase_LipOase,smart_PLAT/LH2_dom,prints_Lipase_panc,prints_Lipase,pfscan_PLAT/LH2_dom	p.G393E	ENST00000298771.7	37	c.1178		10	.	.	.	.	.	.	.	.	.	.	G	18.48	3.632132	0.67015	.	.	ENSG00000165862	ENST00000537242	T	0.49432	0.78	5.7	5.7	0.88788	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.000000	0.56097	D	0.000038	T	0.50103	0.1596	.	.	.	0.33503	D	0.590124	D	0.53745	0.962	P	0.54856	0.762	T	0.48151	-0.9060	9	0.09084	T	0.74	.	17.6068	0.88040	0.0:0.0:1.0:0.0	.	394	P54317	LIPR2_HUMAN	E	393	ENSP00000446346:G393E	ENSP00000446346:G393E	G	+	2	0	PNLIPRP2	118391618	0.998000	0.40836	1.000000	0.80357	0.986000	0.74619	3.190000	0.50973	2.706000	0.92434	0.557000	0.71058	GGA	-	PNLIPRP2	-	pirsf_Lipoprotein_lipase_LIPH,pfam_PLAT/LH2_dom,superfamily_Lipase_LipOase,smart_PLAT/LH2_dom,pfscan_PLAT/LH2_dom		0.348	PNLIPRP2-004	KNOWN	basic	processed_transcript	PNLIPRP2	HGNC	polymorphic_pseudogene	OTTHUMT00000050546.6	0	0	0	93	93	63	0.00	0.00	G	NM_005396		118401628	+1	29	11	48	61	tier1	no_errors	ENST00000537242	ensembl	human	known	74_37	missense	37.66	15.28	SNP	1.000	A	29	48
PTPRK	5796	genome.wustl.edu	37	6	128505867	128505867	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr6:128505867G>A	ENST00000368215.3	-	7	871	c.872C>T	c.(871-873)cCg>cTg	p.P291L	PTPRK_ENST00000368226.4_Missense_Mutation_p.P291L|PTPRK_ENST00000368213.5_Missense_Mutation_p.P291L|PTPRK_ENST00000368227.3_Missense_Mutation_p.P291L|PTPRK_ENST00000368207.3_Missense_Mutation_p.P291L|PTPRK_ENST00000532331.1_Missense_Mutation_p.P291L|PTPRK_ENST00000368210.3_Missense_Mutation_p.P291L|PTPRK_ENST00000524481.1_5'UTR			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	291					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		GGGTCTTGGCGGTTCTAGGAG	0.393													ENSG00000152894																																					0													57.0	54.0	55.0					6																	128505867		2203	4299	6502	SO:0001583	missense	0			-	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.872C>T	6.37:g.128505867G>A	ENSP00000357198:p.Pro291Leu		B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	pfam_Tyr_Pase_rcpt/non-rcpt,pfam_MAM_dom,pfam_Fibronectin_type3,pfam_Ig_I-set,superfamily_ConA-like_lec_gl_sf,superfamily_Fibronectin_type3,smart_MAM_dom,smart_Ig_sub,smart_Fibronectin_type3,smart_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_cat,pfscan_Fibronectin_type3,pfscan_MAM_dom,pfscan_Tyr/Dual-sp_Pase,pfscan_Tyr_Pase_rcpt/non-rcpt,pfscan_Ig-like_dom,prints_Tyr_Pase_rcpt/non-rcpt,prints_MAM_dom	p.P291L	ENST00000368215.3	37	c.872		6	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.0|21.0	4.084153|4.084153	0.76642|0.76642	.|.	.|.	ENSG00000152894|ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000427676|ENST00000490332	T;T;T;T;T;T;T|.	0.32023|.	1.47;1.47;1.47;1.47;1.47;1.47;1.47|.	5.51|5.51	5.51|5.51	0.81932|0.81932	Fibronectin, type III (3);Immunoglobulin-like fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73830|0.73830	0.3637|0.3637	M|M	0.78049|0.78049	2.395|2.395	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D|.	0.97110|.	0.999;1.0;1.0;1.0;0.999;0.999|.	T|T	0.73534|0.73534	-0.3952|-0.3952	10|5	0.52906|.	T|.	0.07|.	.|.	19.4299|19.4299	0.94759|0.94759	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	291;291;291;148;291;291|.	B4DHC3;B7ZMG0;Q15262-3;F5GWP2;Q15262;Q15262-2|.	.;.;.;.;PTPRK_HUMAN;.|.	L|C	291;291;291;291;291;291;291;148|108	ENSP00000357209:P291L;ENSP00000357210:P291L;ENSP00000432973:P291L;ENSP00000357196:P291L;ENSP00000357193:P291L;ENSP00000357198:P291L;ENSP00000357190:P291L|.	ENSP00000357190:P291L|.	P|R	-|-	2|1	0|0	PTPRK|PTPRK	128547560|128547560	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.881000|0.881000	0.50899|0.50899	9.869000|9.869000	0.99810|0.99810	2.585000|2.585000	0.87301|0.87301	0.563000|0.563000	0.77884|0.77884	CCG|CGC	-	PTPRK	-	superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_Fibronectin_type3		0.393	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	PTPRK	HGNC	protein_coding	OTTHUMT00000042163.1	0	0	1	73	73	146	0.00	0.68	G			128505867	-1	7	23	78	128	tier1	no_errors	ENST00000368227	ensembl	human	known	74_37	missense	8.24	15.23	SNP	1.000	A	7	78
CSMD2	114784	genome.wustl.edu	37	1	34191064	34191064	+	Missense_Mutation	SNP	C	C	T	rs200072338		TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr1:34191064C>T	ENST00000373381.4	-	17	2757	c.2581G>A	c.(2581-2583)Gtt>Att	p.V861I		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	821						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CCGTGGTAAACCCCGATCAAG	0.537													ENSG00000121904																																					0													114.0	114.0	114.0					1																	34191064		2203	4300	6503	SO:0001583	missense	0			-	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.2581G>A	1.37:g.34191064C>T	ENSP00000362479:p.Val861Ile		B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	pfam_CUB_dom,pfam_Sushi_SCR_CCP,superfamily_CUB_dom,superfamily_Sushi_SCR_CCP,smart_CUB_dom,smart_Sushi_SCR_CCP,pfscan_CUB_dom,pfscan_Sushi_SCR_CCP	p.V861I	ENST00000373381.4	37	c.2581		1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.431673	0.25813	.	.	ENSG00000121904	ENST00000373381	T	0.59906	0.23	5.89	4.97	0.65823	CUB (5);	0.119417	0.56097	D	0.000026	T	0.47691	0.1459	N	0.17379	0.485	0.80722	D	1	P;B	0.40083	0.702;0.084	B;B	0.43623	0.425;0.232	T	0.47355	-0.9124	10	0.36615	T	0.2	.	15.5007	0.75698	0.1395:0.8605:0.0:0.0	.	821;861	Q7Z408;E7EUA6	CSMD2_HUMAN;.	I	861	ENSP00000362479:V861I	ENSP00000241312:V821I	V	-	1	0	CSMD2	33963651	1.000000	0.71417	1.000000	0.80357	0.003000	0.03518	4.467000	0.60155	1.480000	0.48289	-0.181000	0.13052	GTT	-	CSMD2	-	pfam_CUB_dom,superfamily_CUB_dom,smart_CUB_dom,pfscan_CUB_dom		0.537	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	CSMD2	HGNC	protein_coding		0	0	0	61	61	148	0.00	0.00	C	NM_052896		34191064	-1	36	56	57	78	tier1	no_errors	ENST00000373381	ensembl	human	known	74_37	missense	38.71	41.79	SNP	0.994	T	36	57
DENND4C	55667	genome.wustl.edu	37	9	19296118	19296118	+	Missense_Mutation	SNP	A	A	G			TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr9:19296118A>G	ENST00000380432.2	+	2	239	c.206A>G	c.(205-207)aAa>aGa	p.K69R	DENND4C_ENST00000602925.1_Missense_Mutation_p.K305R|DENND4C_ENST00000434457.2_Missense_Mutation_p.K305R			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	69					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						ATGGTCTCCAAATCCATCAAT	0.383													ENSG00000137145																																					0													157.0	147.0	150.0					9																	19296118		1857	4097	5954	SO:0001583	missense	0			-	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.206A>G	9.37:g.19296118A>G	ENSP00000369797:p.Lys69Arg		A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	pfam_DENN_dom,pfam_dDENN_dom,pfam_uDENN_dom,smart_uDENN_dom,smart_DENN_dom,smart_dDENN_dom,pfscan_DENN_dom,pfscan_uDENN_dom,pfscan_dDENN_dom	p.K305R	ENST00000380432.2	37	c.914		9	.	.	.	.	.	.	.	.	.	.	A	12.04	1.818868	0.32145	.	.	ENSG00000137145	ENST00000380437	.	.	.	4.88	3.74	0.42951	.	0.106321	0.64402	N	0.000006	T	0.38506	0.1043	N	0.21282	0.65	0.80722	D	1	B	0.10296	0.003	B	0.11329	0.006	T	0.11641	-1.0579	9	0.10377	T	0.69	-15.5586	10.5893	0.45300	0.924:0.0:0.076:0.0	.	69	Q5VZ89	DEN4C_HUMAN	R	69	.	ENSP00000369802:K69R	K	+	2	0	DENND4C	19286118	1.000000	0.71417	0.886000	0.34754	0.640000	0.38277	2.155000	0.42301	0.880000	0.35969	0.482000	0.46254	AAA	-	DENND4C	-	NULL		0.383	DENND4C-201	KNOWN	basic	protein_coding	DENND4C	HGNC	protein_coding		0	0	1	83	83	109	0.00	0.91	A	NM_017925		19296118	+1	18	48	66	74	tier1	no_errors	ENST00000602925	ensembl	human	known	74_37	missense	21.43	39.34	SNP	1.000	G	18	66
NXT2	55916	genome.wustl.edu	37	X	108781279	108781279	+	Missense_Mutation	SNP	T	T	A	rs34213752		TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chrX:108781279T>A	ENST00000372106.1	+	2	152	c.21T>A	c.(19-21)ttT>ttA	p.F7L	NXT2_ENST00000218004.1_Missense_Mutation_p.F62L|NXT2_ENST00000372107.1_5'UTR|NXT2_ENST00000372103.1_5'UTR	NM_001242617.1	NP_001229546.1	Q9NPJ8	NXT2_HUMAN	nuclear transport factor 2-like export factor 2	7					mRNA transport (GO:0051028)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(1)|lung(1)|ovary(1)	6						TGTAGGATTTTAAAACTTATG	0.363													ENSG00000101888																																					0													111.0	110.0	110.0					X																	108781279		2203	4300	6503	SO:0001583	missense	0			-	AF246127	CCDS14546.1, CCDS56605.1, CCDS56606.1	Xq22.3	2008-02-05			ENSG00000101888	ENSG00000101888			18151	protein-coding gene	gene with protein product		300320				11073998	Standard	NM_018698		Approved	P15-2	uc004eoe.2	Q9NPJ8	OTTHUMG00000022185	ENST00000372106.1:c.21T>A	X.37:g.108781279T>A	ENSP00000361178:p.Phe7Leu		D3DUY1|Q0VAN8|Q5JYV5|Q5JYV6|Q5JYV7|Q9H8U0|Q9NQ64|Q9NRL7|Q9Y3M4|Q9Y3M5	Missense_Mutation	SNP	pfam_NTF2,pfscan_Nuclear_transport_factor_2_euk	p.F62L	ENST00000372106.1	37	c.186	CCDS56605.1	X	.	.	.	.	.	.	.	.	.	.	T	11.43	1.637768	0.29157	.	.	ENSG00000101888	ENST00000218004;ENST00000372106	.	.	.	4.75	3.58	0.41010	.	0.098140	0.64402	D	0.000001	T	0.48021	0.1477	L	0.28458	0.855	0.80722	D	1	D;P	0.55800	0.973;0.767	P;B	0.56278	0.795;0.398	T	0.36089	-0.9762	9	0.25106	T	0.35	.	5.9762	0.19379	0.0:0.2182:0.0:0.7818	.	7;62	Q9NPJ8;Q9NPJ8-3	NXT2_HUMAN;.	L	62;7	.	ENSP00000218004:F62L	F	+	3	2	NXT2	108667935	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.815000	0.55651	0.719000	0.32188	0.486000	0.48141	TTT	-	NXT2	-	NULL		0.363	NXT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NXT2	HGNC	protein_coding	OTTHUMT00000057886.1	0	0	0	86	86	78	0.00	0.00	T	NM_018698		108781279	+1	63	60	64	51	tier1	no_errors	ENST00000218004	ensembl	human	known	74_37	missense	49.61	54.05	SNP	1.000	A	63	64
TM4SF1	4071	genome.wustl.edu	37	3	149093481	149093482	+	Frame_Shift_Del	DEL	CA	CA	-	rs145699705		TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	CA	CA	CA	-	CA	CA	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr3:149093481_149093482delCA	ENST00000305366.3	-	2	569_570	c.252_253delTG	c.(250-255)tgtggcfs	p.CG84fs	TM4SF1-AS1_ENST00000484046.1_RNA|TM4SF1-AS1_ENST00000496491.1_RNA|TM4SF1_ENST00000472441.1_5'UTR	NM_014220.2	NP_055035.1	P30408	T4S1_HUMAN	transmembrane 4 L six family member 1	84						integral component of plasma membrane (GO:0005887)				endometrium(3)|large_intestine(1)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			CATCGTTTGCCACAGTTTTCAT	0.515													ENSG00000169908																																					0																																										SO:0001589	frameshift_variant	0				M90657	CCDS3143.1	3q21-q25	2005-03-21	2005-03-21		ENSG00000169908	ENSG00000169908			11853	protein-coding gene	gene with protein product		191155	"""transmembrane 4 superfamily member 1"""	M3S1		1565644	Standard	NM_014220		Approved	L6	uc003exb.1	P30408	OTTHUMG00000159597	ENST00000305366.3:c.252_253delTG	3.37:g.149093483_149093484delCA	ENSP00000304277:p.Cys84fs		Q6IB51	Frame_Shift_Del	DEL	pfam_L6_membrane	p.C84fs	ENST00000305366.3	37	c.253_252	CCDS3143.1	3																																																																																				TM4SF1	-	pfam_L6_membrane		0.515	TM4SF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TM4SF1	HGNC	protein_coding	OTTHUMT00000356368.1	0	0	0	32	32	99	0.00	0.00	CA			149093482	-1	18	36	10	11	tier1	no_errors	ENST00000305366	ensembl	human	known	74_37	frame_shift_del	64.29	76.60	DEL	1.000:0.919	-	18	10
FAN1	22909	genome.wustl.edu	37	15	31217365	31217365	+	Silent	SNP	G	G	A	rs141117593		TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr15:31217365G>A	ENST00000362065.4	+	9	2499	c.2208G>A	c.(2206-2208)ccG>ccA	p.P736P	RP11-540B6.6_ENST00000602886.1_RNA|FAN1_ENST00000568145.1_3'UTR	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	736					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						TGGCGGATCCGGAAGTCAGAA	0.552								Direct reversal of damage					ENSG00000198690																																					0								A		1,4403	2.1+/-5.4	0,1,2201	46.0	48.0	47.0		2208	-11.4	0.0	15	dbSNP_134	47	0,8600		0,0,4300	no	coding-synonymous	FAN1	NM_014967.4		0,1,6501	AA,AG,GG		0.0,0.0227,0.0077		736/1018	31217365	1,13003	2202	4300	6502	SO:0001819	synonymous_variant	0			-		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"""KIAA1018"", ""myotubularin related protein 15"""	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.2208G>A	15.37:g.31217365G>A			A8K4M2|Q86WU8	Silent	SNP	pfam_VRR_NUC,smart_Znf_Rad18_put	p.P736	ENST00000362065.4	37	c.2208	CCDS32186.1	15																																																																																			rs141117593	FAN1	-	NULL		0.552	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAN1	HGNC	protein_coding	OTTHUMT00000430740.1	0	0	0	67	67	65	0.00	0.00	G	NM_014967		31217365	+1	7	5	75	51	tier1	no_errors	ENST00000362065	ensembl	human	known	74_37	silent	8.43	8.93	SNP	0.000	A	7	75
HMCN1	83872	genome.wustl.edu	37	1	185834938	185834938	+	Missense_Mutation	SNP	A	A	C			TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr1:185834938A>C	ENST00000271588.4	+	4	793	c.564A>C	c.(562-564)gaA>gaC	p.E188D	HMCN1_ENST00000367492.2_Missense_Mutation_p.E188D	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	188	VWFA.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TCTATGAAGAAATTGCCTCTA	0.348													ENSG00000143341																																					0													86.0	91.0	89.0					1																	185834938		2203	4300	6503	SO:0001583	missense	0			-	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.564A>C	1.37:g.185834938A>C	ENSP00000271588:p.Glu188Asp		A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Ig_V-set,pfam_G2_nidogen/fibulin_G2F,pfam_EGF-like_Ca-bd_dom,pfam_Thrombospondin_1_rpt,superfamily_GFP,superfamily_Thrombospondin_1_rpt,superfamily_Growth_fac_rcpt_N_dom,superfamily_Cadherin-like,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Thrombospondin_1_rpt,smart_G2_nidogen/fibulin_G2F,smart_EGF-like_Ca-bd_dom,smart_EG-like_dom,pfscan_EG-like_dom,pfscan_G2_nidogen/fibulin_G2F,pfscan_Thrombospondin_1_rpt,pfscan_Ig-like_dom	p.E188D	ENST00000271588.4	37	c.564	CCDS30956.1	1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.243643	0.79912	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	D;D	0.97752	-4.52;-4.52	5.65	4.51	0.55191	von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	D	0.96595	0.8889	N	0.17631	0.505	0.50467	D	0.999877	D	0.89917	1.0	D	0.87578	0.998	D	0.95376	0.8469	10	0.42905	T	0.14	.	9.0609	0.36433	0.858:0.0:0.142:0.0	.	188	Q96RW7	HMCN1_HUMAN	D	188	ENSP00000271588:E188D;ENSP00000356462:E188D	ENSP00000271588:E188D	E	+	3	2	HMCN1	184101561	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.274000	0.51631	2.135000	0.66039	0.533000	0.62120	GAA	-	HMCN1	-	NULL		0.348	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HMCN1	HGNC	protein_coding	OTTHUMT00000131848.1	0	0	1	129	129	109	0.00	0.91	A	NM_031935		185834938	+1	21	6	168	113	tier1	no_errors	ENST00000271588	ensembl	human	known	74_37	missense	11.11	5.04	SNP	1.000	C	21	168
DPP3	10072	genome.wustl.edu	37	11	66249827	66249862	+	In_Frame_Del	DEL	CTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG	CTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG	-	rs114567543|rs34243583|rs375779987	byFrequency	TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	CTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG	CTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr11:66249827_66249862delCTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG	ENST00000360510.2	+	2	221_256	c.156_191delCTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG	c.(154-192)acctcccctgaggccccctacatctatgctctgctcagc>acc	p.SPEAPYIYALLS53del	DPP3_ENST00000541961.1_In_Frame_Del_p.SPEAPYIYALLS53del|DPP3_ENST00000530165.1_In_Frame_Del_p.SPEAPYIYALLS53del|DPP3_ENST00000531863.1_In_Frame_Del_p.SPEAPYIYALLS73del|DPP3_ENST00000453114.1_In_Frame_Del_p.SPEAPYIYALLS53del|CTD-3074O7.5_ENST00000533502.1_RNA|CTD-3074O7.5_ENST00000527274.2_RNA|DPP3_ENST00000532677.1_In_Frame_Del_p.SPEAPYIYALLS72del|CTD-3074O7.5_ENST00000527092.1_RNA|CTD-3074O7.5_ENST00000525142.1_RNA			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	53					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						TGCTTCAGACCTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAGCCGCCTCTTC	0.653													ENSG00000254986																																					0																																										SO:0001651	inframe_deletion	0				AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"""dipeptidylpeptidase III"", ""dipeptidylpeptidase 3"""			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.156_191delCTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG	11.37:g.66249827_66249862delCTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG	ENSP00000353701:p.Ser53_Ser64del		B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	In_Frame_Del	DEL	pirsf_Dipeptidyl-peptase3	p.SPEAPYIYALLS53in_frame_del	ENST00000360510.2	37	c.156_191	CCDS8141.1	11																																																																																				DPP3	-	pirsf_Dipeptidyl-peptase3		0.653	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	DPP3	HGNC	protein_coding	OTTHUMT00000393424.2	0	0	0	14	14	14	0.00	0.00	CTCCCCTGAGGCCCCCTACATCTATGCTCTGCTCAG			66249862	+1	0	0	7	7	tier1	no_errors	ENST00000360510	ensembl	human	known	74_37	in_frame_del	0.00	0.00	DEL	0.253:0.995:0.998:0.972:0.992:0.976:0.006:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.854:0.865:0.996:1.000:1.000:1.000:1.000:1.000:0.999:0.962:0.999:1.000:0.997:0.998:1.000:1.000:1.000:1.000:1.000:1.000:1.000	-	0	7
DPP3	10072	genome.wustl.edu	37	11	66249858	66249859	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr11:66249858_66249859insT	ENST00000360510.2	+	2	252_253	c.187_188insT	c.(187-189)ctcfs	p.L63fs	DPP3_ENST00000541961.1_Frame_Shift_Ins_p.L63fs|DPP3_ENST00000530165.1_Frame_Shift_Ins_p.L63fs|DPP3_ENST00000531863.1_Frame_Shift_Ins_p.L83fs|DPP3_ENST00000453114.1_Frame_Shift_Ins_p.L63fs|CTD-3074O7.5_ENST00000533502.1_RNA|CTD-3074O7.5_ENST00000527274.2_RNA|DPP3_ENST00000532677.1_Frame_Shift_Ins_p.L82fs|CTD-3074O7.5_ENST00000527092.1_RNA|CTD-3074O7.5_ENST00000525142.1_RNA			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	63					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						CTATGCTCTGCTCAGCCGCCTC	0.644													ENSG00000254986																																					0																																										SO:0001589	frameshift_variant	0				AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"""dipeptidylpeptidase III"", ""dipeptidylpeptidase 3"""			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.188dupT	11.37:g.66249859_66249859dupT	ENSP00000353701:p.Leu63fs		B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Frame_Shift_Ins	INS	pirsf_Dipeptidyl-peptase3	p.S64fs	ENST00000360510.2	37	c.187_188	CCDS8141.1	11																																																																																				DPP3	-	pirsf_Dipeptidyl-peptase3		0.644	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	DPP3	HGNC	protein_coding	OTTHUMT00000393424.2	0	0	0	39	39	11	0.00	0.00	-			66249859	+1	2	0	14	9	tier1	no_errors	ENST00000360510	ensembl	human	known	74_37	frame_shift_ins	12.50	0.00	INS	1.000:1.000	T	2	14
ANKRD42	338699	genome.wustl.edu	37	11	82921150	82921151	+	Intron	INS	-	-	A			TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr11:82921150_82921151insA	ENST00000393392.2	+	4	408				ANKRD42_ENST00000260047.6_Intron|ANKRD42_ENST00000526731.1_Intron|ANKRD42_ENST00000528722.1_Intron|ANKRD42_ENST00000531895.1_Intron|ANKRD42_ENST00000533342.1_Intron|ANKRD42_ENST00000393389.3_Intron|RP11-727A23.7_ENST00000531869.1_RNA	NM_182603.2	NP_872409.2	Q8N9B4	ANR42_HUMAN	ankyrin repeat domain 42						positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18						TTTTGTAATCTAAAAAAAAAAA	0.277													ENSG00000254551																																					0																																										SO:0001627	intron_variant	0				AK095193	CCDS8265.1, CCDS73355.1, CCDS73356.1	11q14.1	2014-06-12			ENSG00000137494	ENSG00000137494		"""Ankyrin repeat domain containing"""	26752	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 79"""						Standard	XM_005273971		Approved	FLJ37874, SARP, PPP1R79	uc001ozz.1	Q8N9B4	OTTHUMG00000167075	ENST00000393392.2:c.247-191->A	11.37:g.82921161_82921161dupA			Q49A49	Splice_Site	INS	-	NULL	ENST00000393392.2	37	c.NULL	CCDS8265.1	11																																																																																				RP11-727A23.7	-	-		0.277	ANKRD42-001	KNOWN	basic|CCDS	protein_coding	ENSG00000254551	Clone_based_vega_gene	protein_coding	OTTHUMT00000392934.1	0	0	0	33	33	8	0.00	0.00	-	NM_182603		82921151	-1	6	0	40	9	tier1	no_errors	ENST00000531869	ensembl	human	known	74_37	splice_site_ins	13.04	0.00	INS	0.001:0.000	A	6	40
CTAGE4	100128553	genome.wustl.edu	37	7	143882454	143882454	+	Missense_Mutation	SNP	A	A	G	rs199890465		TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr7:143882454A>G	ENST00000486333.1	+	1	1896	c.1858A>G	c.(1858-1860)Act>Gct	p.T620A		NM_198495.2	NP_940897.2	Q8IX94	CTGE4_HUMAN	CTAGE family, member 4	620						integral component of membrane (GO:0016021)				endometrium(1)|ovary(2)	3						TCCTGATTCAACTCTTCCTCC	0.453													ENSG00000225932																																					0													0.0	1.0	1.0					7																	143882454		0	5	5	SO:0001583	missense	0			-	AF338232	CCDS55176.1	7q35	2009-10-15			ENSG00000225932	ENSG00000225932			24772	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma-associated antigen 4"""	608910				12839582, 11149944	Standard	NM_198495		Approved	FLJ43692, cTAGE-4	uc010lpc.3	Q8IX94	OTTHUMG00000157997	ENST00000486333.1:c.1858A>G	7.37:g.143882454A>G	ENSP00000419539:p.Thr620Ala		A8K871|O95046	Missense_Mutation	SNP	superfamily_tR-bd_arm	p.T620A	ENST00000486333.1	37	c.1858	CCDS55176.1	7	.	.	.	.	.	.	.	.	.	.	.	1.759	-0.487290	0.04352	.	.	ENSG00000225932	ENST00000486333	T	0.59638	0.25	.	.	.	.	.	.	.	.	T	0.11965	0.0291	N	0.00162	-1.95	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16394	-1.0404	7	0.02654	T	1	.	.	.	.	.	620	Q8IX94	CTGE4_HUMAN	A	620	ENSP00000419539:T620A	ENSP00000419539:T620A	T	+	1	0	CTAGE4	143513387	0.869000	0.29996	0.052000	0.19188	0.053000	0.15095	-0.081000	0.11321	-1.345000	0.02214	-1.352000	0.01234	ACT	rs199890465	CTAGE4	-	NULL		0.453	CTAGE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CTAGE4	HGNC	protein_coding	OTTHUMT00000349970.1	0	0	0	11	11	0	0.00	0.00	A	NM_198495		143882454	+1	11	0	23	0	tier1	no_errors	ENST00000486333	ensembl	human	known	74_37	missense	32.35	0.00	SNP	0.063	G	11	23
CTB-25J19.1	0	genome.wustl.edu	37	19	7019354	7019354	+	lincRNA	SNP	G	G	A			TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr19:7019354G>A	ENST00000358469.4	-	0	466																											GCTGGAAACCGCCCAGGGGTG	0.637													ENSG00000196589																																					0																																												0			-																													19.37:g.7019354G>A				R	SNP	-	NULL	ENST00000358469.4	37	NULL		19	.	.	.	.	.	.	.	.	.	.	.	8.613	0.889658	0.17540	.	.	ENSG00000196589	ENST00000358469	.	.	.	2.25	1.14	0.20703	.	1.300580	0.05899	N	0.629589	T	0.40743	0.1129	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.44802	-0.9304	6	0.87932	D	0	-6.5201	5.9507	0.19245	0.0:0.0:0.6904:0.3095	.	.	.	.	W	145	.	ENSP00000351254:R145W	R	-	1	2	AC010606.1	6970354	0.001000	0.12720	0.000000	0.03702	0.011000	0.07611	0.994000	0.29693	0.510000	0.28216	0.313000	0.20887	CGG	-	CTB-25J19.1	-	-		0.637	CTB-25J19.1-001	KNOWN	basic	lincRNA	ENSG00000196589	Clone_based_vega_gene	lincRNA	OTTHUMT00000458496.1	0	0	0	31	31	3	0.00	0.00	G			7019354	-1	13	0	19	2	tier1	no_errors	ENST00000358469	ensembl	human	known	74_37	rna	40.62	0.00	SNP	0.000	A	13	19
LRBA	987	genome.wustl.edu	37	4	151560934	151560943	+	Intron	DEL	TGTGTGTGTG	TGTGTGTGTG	-	rs13148325|rs57540184|rs57210930|rs72005085		TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	TGTGTGTGTG	TGTGTGTGTG					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr4:151560934_151560943delTGTGTGTGTG	ENST00000357115.3	-	38	6165				LRBA_ENST00000507224.1_Intron|AC110813.1_ENST00000408308.1_RNA|LRBA_ENST00000535741.1_Intron|LRBA_ENST00000510413.1_Intron	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing							cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					tatatatatatgtgtgtgtgtatatatata	0.195													ENSG00000221235																																					0																																										SO:0001627	intron_variant	0				AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"""WD repeat domain containing"""	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.5922-40651CACACACACA>-	4.37:g.151560934_151560943delTGTGTGTGTG			Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	R	DEL	-	NULL	ENST00000357115.3	37	NULL	CCDS3773.1	4																																																																																				AC110813.1	-	-		0.195	LRBA-002	KNOWN	basic|CCDS	protein_coding	ENSG00000221235	Clone_based_ensembl_gene	protein_coding	OTTHUMT00000364939.1	0	0	0	0	0	0	0.00	0.00	TGTGTGTGTG			151560943	-1	0	0	0	0	tier1	no_errors	ENST00000408308	ensembl	human	novel	74_37	rna	0.00	0.00	DEL	0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000	-	0	0
SPDYC	387778	genome.wustl.edu	37	11	64943049	64943050	+	IGR	INS	-	-	T	rs529153118|rs185303412		TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr11:64943049_64943050insT	ENST00000377185.2	+	0	991				AP003068.18_ENST00000534819.1_RNA	NM_001008778.1	NP_001008778.1			speedy/RINGO cell cycle regulator family member C											breast(1)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)	16						cgcccggctaattttttttttg	0.525													ENSG00000255200																																					0																																										SO:0001628	intergenic_variant	0				AY820305	CCDS31606.1	11q13.1	2013-05-08	2013-05-08		ENSG00000204710	ENSG00000204710		"""Speedy homologs"""	32681	protein-coding gene	gene with protein product		614030	"""speedy homolog C (Xenopus laevis)"""			15611625	Standard	NM_001008778		Approved	Ringo2	uc010rnz.2	Q5MJ68	OTTHUMG00000165611		11.37:g.64943059_64943059dupT				R	INS	-	NULL	ENST00000377185.2	37	NULL	CCDS31606.1	11																																																																																				AP003068.18	-	-		0.525	SPDYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000255200	Clone_based_vega_gene	protein_coding	OTTHUMT00000385299.1	0	0	0	9	9	0	0.00	0.00	-	NM_001008778		64943050	-1	2	0	7	0	tier1	no_errors	ENST00000534819	ensembl	human	known	74_37	rna	22.22	0.00	INS	0.991:0.969	T	2	7
RP11-435B5.5	0	genome.wustl.edu	37	1	143378564	143378564	+	lincRNA	SNP	G	G	A	rs138693387		TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr1:143378564G>A	ENST00000428624.1	+	0	1284				RP11-435B5.3_ENST00000430699.1_lincRNA|RP11-435B5.4_ENST00000423249.1_lincRNA																							AAAGTCATTGGCTTTAGAAAC	0.328													ENSG00000238261																																					0																																												0			-																													1.37:g.143378564G>A				R	SNP	-	NULL	ENST00000428624.1	37	NULL		1																																																																																			rs138693387	RP11-435B5.5	-	-		0.328	RP11-435B5.5-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	LOC101927345	Clone_based_vega_gene	lincRNA	OTTHUMT00000037971.1	0	0	0	9	9	0	0.00	0.00	G			143378564	+1	4	0	6	0	tier1	no_errors	ENST00000428624	ensembl	human	known	74_37	rna	40.00	0.00	SNP	0.013	A	4	6
SORCS3	22986	genome.wustl.edu	37	10	106927044	106927044	+	Missense_Mutation	SNP	T	T	A			TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr10:106927044T>A	ENST00000369701.3	+	13	2065	c.1838T>A	c.(1837-1839)tTc>tAc	p.F613Y		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	613					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		AATGTCTGGTTCCTAGACTGG	0.443													ENSG00000156395																									NSCLC(116;1497 1690 7108 13108 14106)												0													133.0	116.0	122.0					10																	106927044		2203	4300	6503	SO:0001583	missense	0			-	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1838T>A	10.37:g.106927044T>A	ENSP00000358715:p.Phe613Tyr		Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	pfam_PKD_dom,superfamily_PKD_dom,smart_VPS10,pfscan_PKD_dom	p.F613Y	ENST00000369701.3	37	c.1838	CCDS7558.1	10	.	.	.	.	.	.	.	.	.	.	T	7.815	0.716459	0.15306	.	.	ENSG00000156395	ENST00000369701;ENST00000393176	T;T	0.31247	1.5;1.5	5.76	5.76	0.90799	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.23806	0.0576	L	0.28400	0.85	0.44395	D	0.997305	B	0.20052	0.041	B	0.28011	0.085	T	0.09122	-1.0689	9	.	.	.	.	11.188	0.48669	0.1371:0.0:0.0:0.8629	.	613	Q9UPU3	SORC3_HUMAN	Y	613;58	ENSP00000358715:F613Y;ENSP00000376876:F58Y	.	F	+	2	0	SORCS3	106917034	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.037000	0.41174	2.197000	0.70478	0.533000	0.62120	TTC	-	SORCS3	-	smart_VPS10		0.443	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SORCS3	HGNC	protein_coding	OTTHUMT00000050221.1	0	0	0	42	42	95	0.00	0.00	T	NM_014978		106927044	+1	6	2	43	53	tier1	no_errors	ENST00000369701	ensembl	human	known	74_37	missense	12.24	3.64	SNP	1.000	A	6	43
IL27	246778	genome.wustl.edu	37	16	28515297	28515297	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr16:28515297G>A	ENST00000356897.1	-	2	128	c.106C>T	c.(106-108)Ccc>Tcc	p.P36S		NM_145659.3	NP_663634.2	Q8TAD2	IL17D_HUMAN	interleukin 27	0					inflammatory response (GO:0006954)	extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	10						CTCAGCTGGGGCCTCCCTGGG	0.642													ENSG00000197272																																					0													33.0	37.0	35.0					16																	28515297		2197	4300	6497	SO:0001583	missense	0			-	AY099296	CCDS10633.1	16p11	2011-07-21	2003-12-17	2003-12-19	ENSG00000197272	ENSG00000197272		"""Interleukins and interleukin receptors"""	19157	protein-coding gene	gene with protein product		608273	"""interleukin 30"""	IL30		12121660	Standard	NM_145659		Approved	IL-27, p28, IL27p28, IL-27A, IL27A, MGC71873	uc002dqc.3	Q8NEV9	OTTHUMG00000097023	ENST00000356897.1:c.106C>T	16.37:g.28515297G>A	ENSP00000349365:p.Pro36Ser		B1AM69	Missense_Mutation	SNP	superfamily_4_helix_cytokine-like_core	p.P36S	ENST00000356897.1	37	c.106	CCDS10633.1	16	.	.	.	.	.	.	.	.	.	.	G	8.600	0.886568	0.17540	.	.	ENSG00000197272	ENST00000356897	T	0.33654	1.4	3.31	-0.043	0.13861	.	0.424701	0.17329	N	0.178218	T	0.15565	0.0375	N	0.16903	0.455	0.22330	N	0.999197	B	0.25563	0.129	B	0.18263	0.021	T	0.18053	-1.0349	10	0.19590	T	0.45	.	3.3114	0.07017	0.2273:0.0:0.5697:0.203	.	36	Q8NEV9	IL27A_HUMAN	S	36	ENSP00000349365:P36S	ENSP00000349365:P36S	P	-	1	0	IL27	28422798	0.001000	0.12720	0.965000	0.40720	0.938000	0.57974	0.160000	0.16462	-0.371000	0.08004	0.306000	0.20318	CCC	-	IL27	-	NULL		0.642	IL27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IL27	HGNC	protein_coding	OTTHUMT00000214114.1	0	0	0	98	98	18	0.00	0.00	G	NM_145659		28515297	-1	12	2	72	23	tier1	no_errors	ENST00000356897	ensembl	human	known	74_37	missense	14.29	8.00	SNP	0.951	A	12	72
CHD3	1107	genome.wustl.edu	37	17	7802799	7802799	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DX-A7EO-01A-11D-A36J-09	TCGA-DX-A7EO-10A-01D-A36M-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	47ab4d85-5769-476e-ac23-1784e08c7f9a	2ffcc5f0-8943-482f-ac54-c8491c0d4a0f	g.chr17:7802799G>T	ENST00000330494.7	+	15	2632	c.2482G>T	c.(2482-2484)Gag>Tag	p.E828*	CHD3_ENST00000380358.4_Nonsense_Mutation_p.E887*|CHD3_ENST00000358181.4_Nonsense_Mutation_p.E828*	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	828	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				CATCATTCGTGAGAATGAATT	0.483													ENSG00000170004																																					0													131.0	128.0	129.0					17																	7802799		2203	4300	6503	SO:0001587	stop_gained	0			-	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"""Zinc fingers, PHD-type"""	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.2482G>T	17.37:g.7802799G>T	ENSP00000332628:p.Glu828*		D3DTQ9|E9PG89|Q9Y4I0	Nonsense_Mutation	SNP	pfam_CHD_C2,pfam_SNF2_N,pfam_DUF1086,pfam_CHD_N,pfam_DUF1087,pfam_Znf_PHD-finger,pfam_Chromo_domain,pfam_Helicase_C,pfam_HDA_complex_subunit-2/3,pfam_Helicase/UvrB_dom,superfamily_P-loop_NTPase,superfamily_Chromodomain-like,superfamily_Znf_FYVE_PHD,superfamily_HMG_box_dom,smart_Znf_PHD,smart_Chromo_domain/shadow,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Znf_PHD-finger,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_Chromo_domain/shadow	p.E828*	ENST00000330494.7	37	c.2482	CCDS32554.1	17	.	.	.	.	.	.	.	.	.	.	G	40	7.919312	0.98560	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	.	.	.	5.1	5.1	0.69264	.	0.000000	0.46758	D	0.000279	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-35.2494	19.0554	0.93062	0.0:0.0:1.0:0.0	.	.	.	.	X	887;828;828	.	ENSP00000332628:E828X	E	+	1	0	CHD3	7743524	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.657000	0.98554	2.813000	0.96785	0.561000	0.74099	GAG	-	CHD3	-	pfam_SNF2_N,pfam_Helicase/UvrB_dom,superfamily_P-loop_NTPase,smart_Helicase_ATP-bd,pfscan_Helicase_ATP-bd		0.483	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CHD3	HGNC	protein_coding	OTTHUMT00000318050.1	0	0	0	42	42	84	0.00	0.00	G	NM_001005273		7802799	+1	3	2	26	43	tier1	no_errors	ENST00000330494	ensembl	human	known	74_37	nonsense	10.34	4.44	SNP	1.000	T	3	26
